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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 …

Forest Resources For Bioenergy, Gerry Solano Avila

Doctoral Dissertations

The overall objective of this dissertation is to evaluate forest resources biomass availability for the production of bioenergy. Chapter II provides measures of the impact that the road sustainability criteria have on the supply of feedstock for forest products and bioenergy. A linear cost minimization programming is used in estimating forest biomass supply curves. Chapter III provides estimates on the changes in US timberland acreages overtime and the ability of timberland to meet conventional timber products and woody biomass demand within the conterminous United States. Chapter IV utilizes the Biofuels Facility Location Analysis Modeling Endeavor (BioFLAME), a Geographic Information System …

Non-Canonical Signaling From The Etr1 And Etr2 Ethylene Receptors In Arabidopsis Thaliana, Arkadipta Bakshi

Doctoral Dissertations

The gaseous phytohormone ethylene regulates several physiological and developmental processes in higher plants. There are five ethylene receptor isoforms that mediate the responses to ethylene in the model plant Arabidopsis thaliana. Prior research has shown that these five ethylene receptor isoforms in Arabidopsis have both overlapping and non-overlapping roles in regulating diverse responses such as growth in air, growth recovery after removal of ethylene, and ethylene stimulated nutational bending. Functional divergence of ETR1 has been determined in controlling some of these traits and in some of these cases, ETR1 subfunctionalization requires the receiver domain. Using homology modeling and sequence …

Morphological And Gene Expression Plasticity In Neotropical Cichlid Fishes, Sharon Fern Clemmensen

Doctoral Dissertations

Trophic divergence in cichlid fish is linked to morphological shifts in the pharyngeal jaw apparatus. For instance, in the Heroine cichlids of Central America, the ability to crush hard-shelled mollusks is a convergent phenotype with multiple evolutionary origins. These durophagous species often have very similar pharyngeal jaw morphologies associated with the pharyngeal jaw apparatus and some of these similarities could be due to phenotypically plastic responses to mechanical stress. I examined the durophagous cichlid Vieja maculicauda for differences in pharyngeal osteology, dentition, and soft tissues when exposed to different diet regimes. Here I discuss the effect on the morphology and …

Design And Synthesis Of Analogs Of Myo-Inositol, Serine, And Cysteine To Enable Chemical Biology Studies, Tanei J. Ricks

Doctoral Dissertations

Phosphorylated myo-inositol compounds including inositol phosphates (InsPs) as well as the phosphatidylinositol polyphosphate lipids (PIP_ns) are critical biomolecules that regulate many of the most important biological processes and pathways. They are aberrant in many disease states due to their regulatory function. The same is true of the phospholipid phosphatidylserine (PS) which can serve as a marker to begin apoptosis. However, the full scope of activities of these structures is not clear, particularly since techniques that enable global detection and analysis of the production of these compounds spatially and temporally are lacking. With all of these obstacles 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 …

Development Of Ms-Based Proteomics Approaches To Examine Metabolic Pathways And Protein:Protein Interactions In Microbial Systems, Chen Qian

Doctoral Dissertations

The proteome is perhaps the most functional operating machinery for almost all biological processes, serving as the bridge to link the genome and phenotypes. The proteome undergoes dynamic changes in terms of the abundance or interactions, responding to the environmental stimuli. Understanding this dynamic of protein alterations is the key to delineate critical biological mechanisms. Mass-spectrometry-based proteomics is a powerful tool to systematically monitor the heterogeneous alterations of the proteome, including the changes of abundance, modifications and interactions. In this dissertation, a research project was built upon current proteomics approaches to solve the issues regarding to the sample preparation and …

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 …

A Transcriptomic Analysis Of Salmonella Enterica Newport In Planta And After Postharvest Sanitization, Laurel Lynn Dunn

Doctoral Dissertations

The consumption of fresh produce is increasingly linked to incidence of foodborne illness. Pathogens including Salmonella enterica, Shiga toxigenic Escherichia coli, and Listeria monocytogenes are exposed to produce crops through direct human or animal contact, contaminated agricultural water, bioaerosols, run-off, and improperly treated compost. S. enterica has demonstrated exceptional tolerance to the stresses encountered in the environment, on plant tissue, and from postharvest antimicrobial mitigation strategies. Understanding the transcriptomic mechanisms S. enterica employs to survive these hazards is integral for the development of more effective preventive controls and post-harvest steps to prevent the pathogen from infecting consumers.

Effect Modification Of The Association Between Aerobic Physical Activity And Diabetes-Related Mortality By Race-Ethnicity: A Population-Based Prospective Study Using Nhanes Iii And 1999-2006 Nhanes, William Robert Boyer Ii

Doctoral Dissertations

Purpose: To examine potential effect modification by race-ethnicity of the relationship between physical activity (PA) and diabetes-related mortality risk using a sample of U.S. adults from the Third National Health and Nutrition Examination Survey (NHANES III). Methods: The sample (n=10,717) included adults (≥20 years) who attended the Mobile Examination Center (MEC). An age-standardized PA score (PAS) was calculated from the self-reported frequency and intensity of 12 leisure-time aerobic activities. The PA scores were then grouped into three categories: inactive (PAS = 0), insufficiently active (PAS >0 - Results: There was no interaction between PA and race-ethnicity (p=0.83). Compared to inactive …

Complete Denitrification By The Non-Denitrifier Anaeromyxobacter Dehalogenans: The Role Of Coupled Biotic-Abiotic Reactions, Jenny Rae Onley

Doctoral Dissertations

Nitrous oxide (N₂O) is a potent greenhouse gas and ozone-depleting substance produced by many different pathways in the nitrogen cycle, including nitrification, denitrification, and chemodenitrification. Abiotic sources of N₂O such as the chemical reaction between nitrite (NO₂^-) and ferrous ion (Fe[II]) are generally neglected in studies of N turnover in soils. Abiotic controls containing nitrate (NO₃^-) and ferric iron (Fe[III]) fail to capture potential reactions between intermediates of N cycle pathways (e.g., NO₂^- as an intermediate in NO₃ - reduction to ammonium [NH₄⁺] or …

Conservation Decisions: Designing, Financing And Fundraising For Protected Areas, Rachel Elizabeth Fovargue

Doctoral Dissertations

Establishing protection for conservation is a complicated process that involves many critical decisions, from spatial prioritization to garnering the necessary financial support to complete a project. In my research, I address questions that inform various components of this process. First, I ask questions about protected area design using a case study of a large reef system in Australia. I find that simple design rules can facilitate the pursuit of conservation and extractive management goals. Second, I address questions about costs incurred by the financing of new protection. I establish a unique dataset of projects financed by a conservation non-profit through …

Response Of Glyphosate Resistant Palmer Amaranth (Amaranthus Palmeri) To Protoporphyrinogen Oxidase Inhibiting Herbicides In Tennessee, Alinna Marie Umphres

Doctoral Dissertations

In many agronomic cropping systems across the United States, Palmer amaranth (Amaranthus palmeri) is the most economic and troublesome weed for producers. The introduction of glyphosate resistant (GR) crops gave producers the benefit of controlling Palmer amaranth as well as other weeds, a broad window of application, and reduced tillage practices. With the confirmation of GR Palmer amaranth, producers implemented protoporphyrinogen oxidase (PPO or Protox)-inhibiting herbicides to control these populations in crops such as soybean [Glycine max (L.) Merr.] and cotton [Gossypium hirsutum (L.)]. However the continuous use of PPO herbicides has caused a shift in …

Identification Of Molecular Mechanisms Of Resistance To Transgenic Maize Producing The Cry1fa Protein In Different Spodoptera Frugiperda Populations, Rahul Banerjee

Doctoral Dissertations

The use of transgenic maize event TC1507 producing the Cry1Fa insecticidal protein from the bacterium Bacillus thuringiensis has been very useful to control the target lepidopteran insect pest Spodoptera frugiperda. The extensive use of this transgenic maize event resulted in high selection pressure for development of Cry1Fa resistance in field insects in multiple locations, including Brazil, Puerto Rico and the southeastern USA. Resistance developed in Puerto Rico was characterized in the 456LS3 strain originated from that island as monogenic, autosomal recessive and associated with reduced expression of a membrane bound alkaline phosphatase (SfmALP2). Currently, we focused on identifying the …

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. …

Managing Exoelectrogenic Microbial Community Development Through Bioprocess Control For Conversion Of Biomass-Derived Streams, Alex James Lewis

Doctoral Dissertations

Bioelectrochemical systems are an emerging technology capable of utilizing aqueous waste streams generated during biomass conversion of lignocellulosic feedstocks to produce valuable co-products and thus, have potential to be integrated into biorefineries. In a microbial electrolysis cell, organic compounds are converted to electrons, protons, and CO₂ by fermentative and exoelectrogenic bacteria in the anode compartment. By having the ability to extract electrons from waste streams, these systems can treat water while also producing hydrogen, and thus can improve the efficiency of biomass to fuel production by minimizing external hydrogen requirement and enabling water recycle. The overall goal of this …

Using The Suprachiasmatic Nucleus As A Model System To Assess Tolerance And Withdrawal To Alcohol, Jonathan Houghton Lindsay

Doctoral Dissertations

Alcohol abuse induces many disorders including depression, metabolic syndrome, and sleep disturbances. The strong link between alcohol abuse and sleep problems, along with the close connection between sleep and circadian rhythms, led us to investigate ethanol’s effects on the circadian clock. Previous work has shown that acute ethanol blocks photic phase shifts in vivo and glutamatergic phase shifts in vitro. However, neural systems become tolerant to ethanol across different timeframes. Despite both ethanol tolerance and ethanol withdrawal syndrome being listed as criteria for developing alcohol use disorders, little is known about how ethanol tolerance and withdrawal induced hyperexcitability develop and …

Transmission Pattern Of Major Clonal Lineages Of Toxoplasma Gondii, Pooja Saraf

Doctoral Dissertations

Toxoplasma gondii is the most successful zoonotic pathogen known today. One-third of people are chronically infected worldwide. Different strains of T. gondii shows variability in mouse virulence which may potentially correlate with disease manifestation in humans. As a result, mouse is used as the model organism to study the virulence of T. gondii strains. To study the virulence on a global scale, it is necessary to establish a standardized approach for mice virulence assays. Thus, we review the methodologies used in different labs and put forth standardized approaches to study the T. gondii virulence in mice (Chapter 1). Recent …

Genetic Analysis Of Field Populations Of The Plant Pathogens Cercospora Sojina, Corynespora Cassiicola And Phytophthora Colocasiae, Sandesh Kumar Shrestha

Doctoral Dissertations

Genetic markers and whole genome sequencing (WGS) were used to study the disease dynamics and population structure for three important plant pathogens; Cercospora sojina (frogeye leaf spot of soybean), Corynespora cassiicola (target spot of soybean, cotton and many other crops) and Phytophthora colocasiae (taro leaf blight). For each pathogen, genome sequencing was used to guide the development of single nucleotide polymorphism (SNP) markers and both were used to investigate diversity in field populations. Investigation of C. sojina in Tennessee included comparisons of extant populations and historical isolates, revealing a dominant, potentially long-lived, clonal lineage. Characterization of QoI fungicide resistance indicates …

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 …

Identifying Extinction Risk Patterns In Pollination Networks And Conservation Planning To Reduce The Cost Of Management-Necessitated Travel, Christine Elise Dumoulin

Doctoral Dissertations

Extinction rates are currently far above background levels, as a result of human activity. Although conservation spending is substantial, there is a shortfall between the cost of meeting biodiversity targets and the resources available to do so. Consequently, decision-makers are faced with the task of identifying which taxonomic groups and geographical regions are of greatest concern, and prioritizing approaches with the greatest conservation benefit. In this dissertation, I develop novel approaches in both of these areas.

First, I take a stochastic, community dynamic approach to modeling extinction risk patterns in pollination networks. Despite the ecological and agricultural importance of pollination …

Butyrate, A Major Bacterial-Derived Metabolite: Understanding Of Butyrate Metabolism In Cancerous Colonocytes, Anna Han

Doctoral Dissertations

The prohibitory effects of dietary fiber in colorectal cancer have been identified, although the detailed mechanism of this beneficial effect remain unclear. Butyrate, a fermentation metabolite of fiber, has anti-cancer properties by inhibiting cell proliferation and increasing cell apoptosis in cancer cells. A major mechanism, whereby butyrate exerts anti-cancer effects in colorectal cancer, is its role as an HDAC inhibitor. Moreover, it has been suggested that the metabolic fate of butyrate is significantly related to its role as an HDAC inhibitor. Therefore, understanding butyrate metabolism in cancerous colonocytes sheds important light on how butyrate has its selective and inhibitory effects …

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. …

Biotic And Abiotic Drivers Of Plant Symbionts Determine Plant Performance, The Maintenance Of Diversity, And Response To Global Change, Jeremiah A. Henning

Doctoral Dissertations

Interactions among organisms regulate the structure and function of ecosystems and the response of ecosystems to global change. The outcome of species interactions is shaped by the partners involved in the interaction and the climate contexts of the systems in which they reside. Global change is altering the distributions of organisms as well as the climate contexts of the systems they reside within, shifting the biotic and abiotic factors shaping species interactions. Thus, predicting the response of ecosystem structure and function to global change remains unresolved. For my dissertation, I explored how the interactions among plants and their mutualistic communities …

Evaluating The Effects Of Wearable Technologies To Improve Physical Activity Levels For College Students With Intellectual And Developmental Disabilities, Kelly Nicole Kraiss

Doctoral Dissertations

Regular physical activity can decrease the likelihood of being overweight or obese as well as other negative health outcomes. Adults with intellectual and developmental disabilities (I/DD) are more likely to be obese, less likely to be physically active, and at greater risk for health conditions and disease. Thus, there is a need for interventions that aim to increase the physical activity levels of adults with I/DD. However, interventions and related research in this field are limited. The purpose of this dissertation was to examine two independent single-subject design interventions that incorporated the use of wearable technology, a Fitbit, in order …

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 …