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The Tangled Web Of Community Ecology: Making Sense Of Complex Data, Monica Lynn Beals

Doctoral Dissertations

Ecological communities are governed by complicated processes that give rise to observable patterns. Making sense of these patterns, much less inferring the underlying processes, has proved challenging for several reasons. Manipulative experiments in natural communities may not be feasible due to large numbers of variables, lack of adequate replication, or the risk of undesirable consequences (e.g., introducing an invasive species). The multivariate nature of ecological datasets presents analytical problems as well; many statistical techniques familiar to ecologists have difficulty handling large numbers of potentially collinear variables. I present results from three studies of spider communities in which I employ a …

Avian Community Ecology: Patterns Of Co-Occurrence, Nestedness, And Morphology, Michael David Collins

Doctoral Dissertations

A central tenet of the competition paradigm is that community structure is governed by deterministic rules. The competition paradigm pervades nearly all subdisciplines and extends to the broadest, deepest questions in ecology. To determine whether patterns of co-occurrence, nestedness, and morphology in avian communities are consistent with a competition hypothesis, I use null models to compare observed patterns to patterns expected in the absence of competition.

I use presence-absence matrices of birds in three archipelagoes to test whether species exhibit exclusive distributions. Congeneric birds co-occur significantly less frequently than predicted in two archipelagoes, consistent with a competition hypothesis. However, when …

Studies On Cytochrome P450 Genes In Drosophila Melanogaster: Relationship Between Over Expression And Ddt Resistance, And Xenobiotic Induction, Srilalitha Kuruganti

Doctoral Dissertations

Cytochrome P450 monooxygenases (CYPs), are involved in the metabolism of a diverse group of endogenous and xenobiotic compounds. In insects, CYPs are involved in conferring resistance against insecticides. In Drosophila, the expression of Cyp6a2, Cyp6a8, Cyp6g1, Cyp6w1 and Cyp12d1 is higher in the resistant compared to susceptible strains. Recent study by Daborn et al (2002, Science, 297, 2253-2256) showed that Cyp6g1 alone can confer resistance phenotype. The aim of my first objective was to re- examine this claim and second to examine the effect of common xenobiotic compounds on the transcriptome of Drosophila.

In first objective, six strains …

An Integrated Experimental And Computational Approach To Proteomics: Scaling From High Resolution Qualitative Analysis To Quantitative Measurements With Confidence Evaluation, Chongle Pan

Doctoral Dissertations

As a component of systems biology, proteomics aims to characterize the entire protein complement of an organism, including qualitative identification of protein types and quantitative measurement of protein abundance changes as a function of different cellular states. This dissertation presents an integrated experimental and computational approach to improve proteomic measurements, including qualitative measurements using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and quantitative measurements with statistically derived confidence evaluation.

Although FT-ICR-MS provides high-performance mass measurements, its potential has not yet been fully explored for proteomics applications. A novel tandem mass spectrometry method was developed for FT-ICR-MS to obtain sequence …

Cross-Species Comparison Of Spermatocyte Responses To Induced Dna Damage: The Laboratory Mouse And Drosophila Melanogaster, Shannon Marie Matulis

Doctoral Dissertations

Maintenance of genomic stability is of crucial importance for all organisms. Cells are continually exposed to exogenous and endogenous agents that can damage DNA. Of special interest is the manner in which male germ cells respond to and repair induced DNA double strand breaks (DSBs), as the propagation of cells carrying damaged DNA can lead to the production of heritable mutations, genetic diseases, and sterility. In addition, treatment of male germ cells with DNA damaging agents, such as many chemotherapeutic drugs, can ultimately result in infertility. This research focused on investigating the mechanisms by which male germ cells, specifically those …

Physicochemical Characterization And Antibacterial Potential Of Naturally-Occurring Antimicrobial Polypeptide-Bearing Phospholipid Liposomes Against The Foodborne Pathogens Listeria Monocytogenes And Escherichia Coli O157:H7, Thomas Matthew Taylor

Doctoral Dissertations

Liposomes are spherical bilayer vesicles formed from dispersion of polar lipids in aqueous solvents and have been studied for their ability to act as drug delivery vehicles by shielding reactive or sensitive compounds prior to release. In the food industry, liposomes have been used to deliver food flavors and nutrients; more recently they have been investigated for their ability to incorporate food antimicrobials.

Thermal stability of liposomes, in the presence and absence of nisin, was evaluated using differential scanning calorimetry (DSC) and low-intensity ultrasonic spectroscopy (US). Observed phase transition temperatures for liposomes measured via DSC and US were in close …

Supplementation Of Purified Fiber To Tall Fescue Grass Hay Diets, Howard Martin Blalock

Doctoral Dissertations

Experiments were conducted to define the degradation kinetics of purified fiber products compared to conventional feedstuffs. In situ analysis was conducted on soybean hulls, dried distillers grains, dried corn gluten feed, rice mill, wheat middlings, solka floc, oat fiber (200 and 300 series), corn bran, red and white wheat bran using nylon bags. In situ results determined oat fiber (300) and solka floc were most similar to soybean hulls and secondly to corn gluten feed. An oat fiber: solka floc mixture was formulated for subsequent experiments. The in vitro experiment consisted of alfalfa hay, soybean hulls, corn gluten feed, oat …

Inhibition Of Direct Prostaglandin F2Α Effects On Pre-Attachment Embryos Improves Reproductive Efficiency In Cattle, Fernando Nestor Scenna

Doctoral Dissertations

Prostaglandin F_2α (PGF_2α) has been shown to have detrimental effects on embryonic development, quality and hatching ability of embryos and pregnancy rates in cows. However, information about PGF_2α receptor (FPr) mRNA and protein in the preattachment bovine embryo is absent in the literature. The first experiment was design to identify the period of time during in vitro embryo development that is most susceptible to PGF_2α and to determine FPr mRNA and protein in bovine embryos. Prostaglandin F_2α decreased development of embryos to compact morula, but had no effect on development to blastocyst. In addition, …

Differential Expression Of Skin Cancer And Hair-Follicle Cycle Regulated Genes In Tumor Susceptible K14-Agouti Mice, Yesim Aydin Son

Doctoral Dissertations

The mouse agouti protein is transiently expressed in the skin and signals through the melanocortin 1 receptor to switch pigment production of hair-follicle melanocytes from black to yellow. Ubiquitous over-expression of agouti protein in mice carrying the spontaneous dominant mutations Ay and Avy causes a pleiotropic syndrome characterized by solid yellow hair color, obesity, diabetes, and increased susceptibility to carcinogenesis in a wide variety of tissues, including the skin. Over-expression of agouti in the skin of keratin 14 (K14)- Agouti transgenic mice promotes skin carcinogenesis, even in the absence of obesity and diabetes. In this study cDNA microarray …

Integrated Computational And Experimental Platform For Characterizing Protein Isoforms And Ptms In Microbial Systems By Top-Down Ft-Icr Mass Spectrometry, Heather Marie Connelly

Doctoral Dissertations

The goals of this dissertation research were to develop an integrated computational and experimental platform for characterizing protein isoforms and post translational modifications (PTMs) in microbial systems by top-down FT-ICR mass spectrometry. To accomplish this goal, we employed methodologies of microbial growth, intact protein and protein complex extractions, followed by sample preparation and then progressed to identification of the instrumentation needed to integrate the top-down and bottom-up proteomics methodologies used in these studies. Emphasis is placed on the development of integrated top-down and bottom-up informatics and the challenges faced in the integration of these two large mass spectrometry data sets …

Vertical Export Of Biogenic Matter In The Chukchi And Barents Seas, Catherine Lalande

Doctoral Dissertations

Drifting sediment traps were deployed in 2004 in the ChukchiSeato investigate the variability in the vertical flux of biogenic matter in the presence and absence of sea ice. Measurements of chlorophyll-a, particulate organic carbon (POC), particulate organic nitrogen, phytoplankton, zooplankton fecal pellets, and the stable carbon isotope composition of the sinking material were accomplished along two shelf-to-basin transects. POC fluxes obtained in ice-covered and ice-free conditions were of different composition but of similar magnitude, indicating that the export fluxes in the presence of ice cover contributed significantly to the annual export of biogenic matter in the Chukchi Sea. …

Spatial Processes And Ecotoxicological Risk Assessment Modeling, Steven Thomas Purucker

Doctoral Dissertations

This dissertation considers the importance of spatial processes in the application of models for environmental risk assessment. The appropriate incorporation of space as an ecological variable to construct spatially delineated risk estimates can improve estimates of the risk outcomes and improve resulting risk management decisions. Three environmental problems are considered, corresponding to three different case studies measuring an ecotoxicological effect at progressively broader spatial scales. The first application addresses how the presence of spatial auto­correlation can affect the exposure of ecological receptors in the environment. The presence of significant spatial correlation can impact methods for adequately determining summary concentrations, hypothesis …

Historical Processes, Evolutionary Change, And Phenotypic Plasticity: Geographic Variation In Behavior, Morphology, And Life-History Traits Of Common Gartersnake, Thamnophis Sirtalis, Populations, John S. Playk Jr.

Doctoral Dissertations

Islands have long been of interest to biologists, as they are often home to unusual species or populations of species that are characterized by unique behavior, morphology, and gene pools. My research explores the mechanisms driving and maintaining phenotypic variation in the common gartersnake, Thamnophis sirtalis, populations of the Beaver Archipelago. Specifically, I focused on antipredator-related traits, foraging/feeding-related traits, and reproductive life-history traits, as all are known to vary with differences in predator composition and resource availability, which vary among the islands of the Beaver Archipelago and between the islands and the surrounding mainland. Since the exact origin of …

Explaining Species Diversity By Linking Local And Large Scale Processes, Marc William Cadotte

Doctoral Dissertations

Large-scale processes are known to be important for patterns of species richness, yet the ways in which local and larger scale processes interact is not clear. I first examined published experiments that manipulated dispersal among local communities using meta- analyses. I show that local communities often readily increase diversity, but that there may be declines at larger spatial scales. I then used metacommunities consisting of microbial aquatic communities to examine how processes at different scales affect local and metacommunity richness. Specifically, I manipulated the potential dispersal rate, whether dispersal was localized or global, and variation in initial community composition. I …

Differential Neutrophil Function And Intracellular Signaling In Dairy Cows With Specific Cxcr1 Genotypes, Magdalena Rambeaud

Doctoral Dissertations

Mastitis continues to be the most economically devastating disease affecting dairy cows worldwide. Neutrophil recruitment to the mammary gland and neutrophil functional ability once there often determine whether a bacterial infection is eliminated or becomes chronic. A slow or ineffective neutrophil attack allows bacteria to continue their assault and generate a longer lasting and potentially more damaging infection. Since neutrophils are key players in the resolution of mastitis, and a polymorphism in CXCR1 +777 (G→C) has been associated with susceptibility to mastitis, the hypothesis of this research was that different CXCR1 +777 genotypes were associated with efficiency of in vitro …

Potential Development Of Resistance To Food Antimicrobials By Foodborne Pathogens, Lilia Milagros Santiago Santiago

Doctoral Dissertations

The potential for development of resistance of four strains of Listeria monocytogenes (101, 108, 310 and Scott A) and Salmonella Typhimurium DT 104 (2380, 2576, 2582, 2486) to food antimicrobials sodium benzoate (SB), potassium sorbate (PS), sodium diacetate (SD) and sodium lactate (SL) at pH 6.0 was studied. Cells were not subjected to any pre-stress condition. An agar dilution assay was performed to determine susceptibility and adaptation to different and increasing antimicrobial concentrations. A microbroth dilution assay was used to determine tolerance development after two consecutives exposures to same antimicrobial concentrations, and one further exposure to a step higher concentration. …

Linking Work Stress, Parental Self-Efficacy, Ineffective Parenting, And Youth Problem Behavior, Owen Arthur Anderson

Doctoral Dissertations

The purpose of this study was to examine the relationships among work stress, parental self-efficacy, ineffective parenting behavior, and youth problem behaviors. Questionnaires were collected from 297 families assessing parent perceptions of work stress and parental self-efficacy; youth perceptions of ineffective parenting behavior; and parent, youth, and teacher perceptions of youth internalizing and externalizing problem behavior. There was evidence of work to family spillover, in that work stress (mothers’ work-family conflict and fathers’ job dissatisfaction) was linked to diminished parental self-efficacy and increased ineffective parenting behaviors, which in turn, were associated with higher levels of youth internalizing and externalizing problem …

Unveiling The Regulatory Network For Di/Tri-Peptide Utilization In Saccharomyces Cerevisiae, Houjian Cai

Doctoral Dissertations

Dipeptides and tripeptides serve as important sources of amino acids, nitrogen and carbon for the growth of all organisms. To identify genes involved in the regulation of small peptide utilization, I performed a systematic, functional examination of this process in a haploid, non-essential, single-gene deletion mutant library of Saccharomyces cerevisiae. In addition, we used high-throughput phenotyping in which we grew yeast cells on 284 different dipeptides or 11 tripeptides as the sole nitrogen source to dissect different mechanisms of di/tri-peptide utilization in seven genetically diverse strains. I have identified 103 candidate genes involved in regulating peptide utilization: 57 genes …

Environmental Manipulation To Increase The Nutritional Content In Leafy Vegetables, Mark Gregory Lefsrud

Doctoral Dissertations

In plants, carotenoids play critical roles in both light harvesting and energy dissipation for photosynthetic mechanism. In humans, carotenoids have been associated with reduced risk of lung cancer and chronic eye diseases, such as cataracts and age-related macular degeneration. Increasing carotenoid levels in plants, that are commonly consumed in the diet would impart health benefits without changing the dietary habits of individuals.

Kale (Brassica oleracea L. var. acephala D.C.) ranks highest and spinach (Spinacia oleracea L.) ranks second among vegetable crops for the accumulation of the carotenoids, lutein and b-carotene. However, kale has low consumption rates, while spinach …

Molecular And Physiological Basis For Hair Loss In Near Naked Hairless And Oak Ridge Rhino-Like Mouse Models: Tracking The Role Of The Hairless Gene, Yutao Liu

Doctoral Dissertations

Hairless mice have been widely used in basic research and clinical trials. Two new mouse mutants with hair loss arose spontaneously in the breeding colony of Oak Ridge National Laboratory. The first homozygotes mutant, called near naked hairless (Hrⁿ), never develops a normal coat, while heterozygotes display a sparse coat and become completely nude as they age. The Hrⁿ/Hrⁿ mutant mice are significantly smaller in body size and have very short, curly, and few vibrissae. Histological analysis revealed premature keratinization in the precortical region of hair follicles, formation of mineralized dermal cysts, and loss …

Vitronectin And Plasminogen Activator Inhibitor-1 Form Higher-Order Complexes That Localize To The Extracellular Matrix And Adopt Adhesive Properties, Kenneth H. Minor

Doctoral Dissertations

Vitronectin is a human circulatory protein that is recruited to the extracellular matrix (ECM) during tissue remodeling pathways linked to injury, inflammation, and tumor metastasis. Whereas circulating vitronectin is monomeric, the tissue-associated form is multimeric and contains multivalent binding sites for both cell-surface receptors and components of the extracellular matrix. In addition, matrix-associated vitronectin directly regulates plasmin-regulated matrix proteolysis through the localization and stabilization of the serine protease inhibitor, plasminogen activator inhibitor type-1 (PAI-1). As a component of the ECM, vitronectin adopts a pro-adhesive role, providing a unique regulatory link between cell adhesion and pericellular proteolysis. The mechanism by which …

Computational Analysis Of Mass Spectrometric Data For Whole Organism Proteomic Studies, Evgenia Razumovskaya

Doctoral Dissertations

In the last decades great breakthroughs have been achieved in the study of the genomes, supplying us with the vast knowledge of the genes and a large number of sequenced organisms. With the availability of genome information, the new systematic studies have arisen. One of the most prominent areas is proteomics. Proteomics is a discipline devoted to the study of the organism’s expressed protein content. Proteomics studies are concerned with a wide range of problems. Some of the major proteomics focuses upon the studies of protein expression patterns, the detection of protein-protein interactions, protein quantitation, protein localization analysis, and characterization …

Characterizing The Fate And Transport Of Solutes In Soil, Youngho Seo

Doctoral Dissertations

Increasing concerns about contamination of soil and aquatic environments have emphasized the importance of information about the fate and transport of agricultural chemicals in soil. The objective of this research was to provide an improved understanding of the behavior of reactive chemicals including nitrate, phosphate, and antibiotics in soil through leaching and surface runoff in order to develop appropriate technologies that can prevent or minimize contamination of soil and water by agricultural activity. In a first experiment, a time domain reflectometry (TDR) method was tested for its ability to measure preferential flow of nitrate and phosphate in soil. Saturated miscible …

Management Of Hybrid Bluegrass (Poa Arachnifera Torr. X Poa Pratensis L.) In The Transition Zone, Travis Charles Teuton

Doctoral Dissertations

Dura Blue™ and Thermal Blue™ hybrid bluegrass (Poa arachnifera Torr. x Poa pratensis L.) have been selected for increased heat and drought tolerance and offer an alternative to traditional Kentucky bluegrass and tall fescue in the transition zone. Dura Blue and Thermal Blue were compared to Apollo™ Kentucky bluegrass, Dynasty™ tall fescue, and Kentucky 31 tall fescue. All turfgrass species tested were acceptable for use in the transition zone. Thermal Blue should be seeded from 50 to 150 kg seed/ha. Thermal Blue should be seeded in September for highest quality and most rapid turf cover. However, January and April …

Applying Landscape-Scale Modeling To Everglades Restoration, Scott M. Duke-Sylvester

Doctoral Dissertations

In this dissertation I describe the implementation and application of three spatially-explicit, landscape-scale models designed to address specific aspects of Everglades restoration. The first is a model of vegetation succession for the Everglades. The second is a fire model for the Everglades. The third is a model of the spread and optimal spatial control of an invasive, non-native plant.

I developed the succession and fire models as part of the Across Trophic Level System Simulation (ATLSS). These models are used to assess the relative effects of alternative hydrology scenarios on the distribution of vegetation and fires. In addition to the …

Developmental And Neurogenetic Studies On The Peptidergic Nerve System In Drosophila, Youn-Jeong Choi

Doctoral Dissertations

Neuropeptides in insects act as neurotransmitters and neuromodulators in the central nervous system (CNS) and as regulatory hormones released to the circulation. To gain insight into the mechanisms of tissue-specific Corazonin (Crz) regulation and functions in Drosophila, I cloned Crz-encoding genes from different species, and performed the phylogenetic analysis of Crz-encoding genes as well as Crz primary structures. To compare Crz expression patterns among different species, I performed in situ hybridization and immunohistochemistry to detect Crz expression in the CNS. Although Crz gene sequences reveal a great deal of diversity, Crz expression patterns are conserved among different …