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Biological Simulations And Biologically Inspired Adaptive Systems, Edgar Alfredo Duenez-Guzman

Doctoral Dissertations

Many of the most challenging problems in modern science lie at the interface of several fields. To study these problems, there is a pressing need for trans-disciplinary research incorporating computational and mathematical models. This dissertation presents a selection of new computational and mathematical techniques applied to biological simulations and problem solving: (i) The dynamics of alliance formation in primates are studied using a continuous time individual-based model. It is observed that increasing the cognitive abilities of individuals stabilizes alliances in a phase transition-like manner. Moreover, with strong cultural transmission an egalitarian regime is established in a few generations. (ii) A …

Morphological And Molecular Systematics Of Psychodidae (Diptera), Gregory Russel Curler

Doctoral Dissertations

A general overview of family Psychodidae is given. Genus Eurygarka Quate is revised to include three species. Genus Gondwanoscurus Jezek is revised to include seven species. The status of genus Stupkaiella Vaillant is revised. Eight new Nearctic species: Eurygarka cyphostylus sp. nov., E. nelderi sp. nov., Stupkaiella lasiostyla sp. nov., S. robinsoni sp. nov., S. capricorna sp. nov., Trichomyia rostrata sp. nov., Australopericoma delta sp. nov., and Threticus thelyceratus sp. nov., and two new Oriental species: Gondwanoscurus cruciferus sp. nov. and G. ornithostylus sp. nov. are described. Two Nearctic species: Eurygarka helicis (Dyar) and Stupkaiella bipunctata (Kincaid), and four Oriental …

Formation Of Multiple Dimer Interfaces In The Active And Inactive States Of A Model G Protein-Coupled Receptor, Hee Jung Kim

Doctoral Dissertations

G protein-coupled receptors (GPCRs) are a class of integral membrane receptor proteins that are characterized by seven-transmembrane (7TM) domains connected by intracellular and extracellular loops, an extracellular N-terminus, and an intracellular Cterminus. GPCRs recognize neurotransmitters, sensory molecules and chemotactic agents and are involved in the control of many aspects of metabolism. Since GPCRs play important roles in diverse processes such as pain perception, growth and blood pressure regulation, and viral pathogenesis, GPCRs became important target for therapeutic agents. The tridecapeptide α-factor pheromone (W₁H₂W₃L₄Q₅L₆K₇P₈G_{9 …}

Laboratory Models Of Infection And Transmission Of Mycobacterium Ulcerans; Causative Agent Of Buruli Ulcer Disease, Lydia Mosi

Doctoral Dissertations

Identification of the environmental reservoir of Mycobacterium ulcerans, the etiological agent of Buruli ulcer, within the aquatic ecosystem has been a salient research area within the last five years. Based on extensive environmental sampling and elegant laboratory models, associations have been made between the bacterial DNA and aquatic invertebrates, biofilms, plants, fish and detritus material captured on 0.2μm pore filters. These studies have suggested that M. ulcerans is widely distributed within many functional feeding groups and may be concentrated through different trophic links; however, the specific route of transmission to humans remains a mystery. In this study we have …

“Saccharomyces Cerevisiae G Protein Coupled Receptor, Ste2p Interactions With Its Ligand, Α-Factor And Cognate Gα Protein, Gpa1p, George Kwabena Essien Umanah

Doctoral Dissertations

The Saccharomyces cerevisiae alpha-factor receptor, Ste2p, belongs to the G proteincoupled receptors (GPCRs), a class of integral membrane proteins that are characterized by seven-transmembrane (TM) domains. Ste2p-alpha-factor pair has been used extensively as a paradigm for investigating GPCRs structure and function. Upon binding of alpha-factor to Ste2p, a signal is transduced via an associated guanine-nucleotide binding protein, Gpa1p, initiating a cascade of events similar to those for mammalian GPCRs signal transduction. GPCRs are essential in many physiological processes associated with human diseases. Many aspects of structure and function are highly conserved across GPCRs, irrespective of primary amino acid sequence. This …

Nontarget Host Utilization Of Thistle Species By Introduced Biological Control Agents And Spatial Prediction Of Non-Target Feeding Habitats, Gregory J. Wiggins

Doctoral Dissertations

Rhinocyllus conicus Fröelich and Trichosirocalus horridus (Panzer) were introduced from Europe into North America as biological control agents of the exotic weed species Carduus nutans L. Concern exists over the feeding of these weevils on at least 25 species of native Cirsium thistles. Research was conducted to 1) estimate phenological synchrony of the eight thistle species in Tennessee with R. conicus and T. horridus, 2) investigate naturally-occurring populations of the five native Cirsium thistle species for non-target activity by R. conicus and T. horridus, 3) quantify the impacts to plants of each thistle species to feeding of R. …

Environmental Implications Of Francisella Tularensis Biofilms, Jeffrey J. Margolis '00

Doctoral Dissertations

Francisella tularensis survives in one of the widest environmental ranges of any pathogen. Numerous mammals and arthropod vectors are infected by this highly virulent organism. How this zoonotic pathogen persists outside of its many hosts remains unexplored. We aimed to examine how F. tularensis interacts with environmental surfaces, and hypothesized that biofilm formation may enable survival of this organism in nature. By understanding the role these surface-attached bacterial communities play in F. tularensis ecology, we hope to gain insight into the mechanisms of environmental persistence and transmission of this pathogen.

We identify chitin as a potential non-host niche for F. …

The Casein Micelle As An Encapsulation System For Triclosan: Methods Of Micelle Dissociation, Encapsulation, Release, And In Vitro Delivery, Adrienne L. Roach

Doctoral Dissertations

This dissertation reports on the use of the casein micelle as an encapsulation and potential delivery system for a low molecular weight hydrophobic compound, triclosan. The ability of the casein micelle to serve in this capacity was tested in a series of experiments investigating: 1) micelle dissociation to expose hydrophobic binding sites of interaction, 2) encapsulation of triclosan, 3) the release of triclosan under various conditions, and 4) the intercellular delivery of triclosan to human liver cells in vitro for the inactivation of a malaria-causing parasite. Casein micelle dissociation and reassociaiton was achieved through high pressure homogenization and solvent-mediated pressure-induced …

Direct Effects Of Heat Stress During Meiotic Maturation On Bovine Oocyte And Cumulus Rna, Rebecca R. Payton

Doctoral Dissertations

Heat-induced reductions in developmental competence after direct exposure of oocytes to 41ºC have been coincident with reduced protein synthesis. Since heat stress perturbs RNA integrity and polyadenylation in somatic cells, it was hypothesized that heat stress during meiotic maturation may alter RNA within oocytes and/or their surrounding cumulus to account for some of the reductions in development. Initial efforts utilized microcapillary electrophoresis to examine oocyte and cumulus RNA without heat stress as a first step toward transcriptome profile analysis. Size distribution of RNA, rRNA ratio, and other related endpoints differed for oocyte RNA compared to cumulus, and were conserved across …

Role Of Dietary Calcium And Dairy In Modulating Oxidative Stress, Inflammatory Stress And Lifespan, Antje Eerenstein Bruckbauer

Doctoral Dissertations

Oxidative stress and inflammatory stress have been implicated as a cause of tissue damage in multiple organ systems, leading to the development of chronic diseases such as obesity, diabetes, hypertony and atherosclerosis. They are also recognized as major factors contributing to the physiological process of aging. Previous studies have demonstrated that dietary calcium regulates reactive oxygen species production (ROS) production in adipocytes in vitro and in vivo, and inhibits adipocyte-derived inflammatory cytokine expression by suppression of calcitriol. In addition, high calcium diets modulate energy metabolism and partitioning between adipose tissue and muscle resulting in a decrease in fat storage and …

Foraging Behavior Of Nerodia Clarkii Compressicauda, With Special Reference To Lingual Luring, Kerry Andrew Hansknecht

Doctoral Dissertations

Predators use a variety of tactics with which to obtain prey. Here, I describe lingual luring by the mangrove saltmarsh snake (Nerodia clarkii compressicauda), a somewhat unique behavior that involves the use of the tongue to attract fish prey close enough to permit their capture. The lure is characterized by considerable upward curling of the distal portion of the tongue as it protrudes from the mouth. In addition, luring tongue flicks are significantly greater in duration than chemosensory tongue flicks. Both visual and chemical cues are sufficient to stimulate lingual luring, the latter more so than the former. …

Climate-Driven Impacts Of Groundfish On Food Webs In The Northern Bering Sea, Xuehua Cui

Doctoral Dissertations

Groundfish distributions were examined in spring 2006 and 2007 in the northern Bering Sea around St. Lawrence Island (SLI). Arctic cod (Boreogadus saida), Bering flounder (Hippoglossoides robustus), and snailfish (Liparidae) were the dominant species south of SLI, whereas Arctic alligatorfish (Ulcina olrikii) and Arctic staghorn sculpin (Gymnocanthus tricuspis), or shorthorn sculpin (Myoxocephalus scorpius) were dominant north of SLI. The results indicate that bottom water (or water column) chlorophyll a and sediment parameters had greater influence on fish distribution in 2006 (cold, pre-bloom conditions), whereas bottom water temperature and sediment grain …

Structure-Function Studies Of The Large Subunit Of Ribonucleotide Reductase From Homo Sapiens And Saccharomyces Cerevisiae, James Wesley Fairman

Doctoral Dissertations

Sufficient pools of deoxyribonucleotide triphophates (dNTPs) are essential for the high fidelity replication and repair of DNA, the hereditary material for a majority of living organisms. Ribonucleotide reductase (Rnr) catalyzes the rate-limiting step of de-novo DNA synthesis, the reduction of ribonucleosides to deoxyribonucleosides. Since the cell relies primarily upon ribonucleotide reductase for its dNTPs, both the cellular levels and activity of Rnr are heavily regulated, especially when DNA damage occurs or during replication blocks in the cell cycle. If dNTP pools become too high, too low, or imbalanced, genomic instability results, leading to either the formation of cancerous cells or …

Ecological And Evolutionary Factors Affecting Rabies Virus Infection In Colonial Insectivorous Bats, Amy S. Turmelle

Doctoral Dissertations

An introductory section provides a review for the role of bats as reservoirs of infectious diseases, and highlights the rationale for investigations of host life history, ecology, and evolution in regard to bat epizootiology. Chapter 1 presents field investigations of life history, ecology, body condition, and rabies virus neutralizing antibody seroprevalence in six natural colonies of Brazilian free-tailed bats from caves and bridge roosts in Texas. Chapter 2 presents a replicate field investigation of life history, ecology, body condition, and rabies virus neutralizing antibody seroprevalence in six natural colonies of Brazilian free tailed bats from bridges and bat house roosts …

Geographic Variation And Phenotypic Plasticity Of Body Size And Cell Size In The Lizard, Anolis Carolinensis, Rachael Goodman

Doctoral Dissertations

Patterns of geographic variation in body size and cell size have long fascinated biologists, and climatic variables have often been considered to explain such patterns. Environmental temperature can profoundly influence the phenotype, including body size. of ectotherms, and reptiles in particular. This dissertation presents four studies that examine how temperature shapes morphology on developmental and evolutionary timescales in the green anole lizard, Anolis carolinensis. The first three studies examined variation in and phenotypic plasticity of cell size and body size through laboratory experiments using eggs and juveniles from wild-caught females in five populations of A. carolinensis. The fourth …

Nodulin 26-Like Intrinsic Protein Nip2;1 And Nip7;1: Characterization Of Transport Functions And Roles In Developmental And Stress Responses In Arabidopsis, Won-Gyu Choi

Doctoral Dissertations

Nodulin-intrinsic proteins (NIPs) are plant-specific, water and solute transporters with homology to soybean nodulin 26. In this study, it is shown that Arabidopsis NIP2;1 (AtNIP2;1) expression is acutely stimulated upon waterlogging (70-fold in whole seedlings within 1 hr) and hypoxia (> 1000-fold in roots within 2 hr). Subcellular localization of a AtNIP2;1::YFP fusion protein shows localization to the plasma membrane. Analysis of AtNIP2;1 protein in Xenopus oocytes shows that it is a transporter of lactic acid, a fermentation end product.

Experiments with T-DNA insertional mutants in the AtNIP2;1 promoter showed that reduced AtNIP2;1 expression induced higher lactic acid …

Micro, Nano Encapsulation Methods For Sustained Release Drug Formulations And Biomimetic Applications, Shantanu Balkundi

Doctoral Dissertations

The Layer-by-Layer (LbL) assembly technique was used to obtain a new type of protein/polyphenol microcapsule based on naturally occurring polyphenol (-)-epigallocatechin gallate (EGCG) and gelatin, type A. The dependence of permeability on the molecular weight of permeating substances was studied and compared with commonly used polyallylamine/polystyrene sulfonate capsules. A quartz crystal microbalance was used to monitor the regularities of EGCG adsorption in alternation with type A and B Gelatins and electrophoretic mobility measurements were used that indicated that the nature of assembly was dependent on Gelatin properties. It was shown that EGCG retains its antioxidant activity in the LbL assemblies. …

Discrete Nondeterministic Modeling Of Biochemical Networks, John R. Jack

Doctoral Dissertations

The ideas expressed in this work pertain to biochemical modeling. We explore our technique, the Nondeterministic Waiting Time algorithm, for modeling molecular signaling cascades. The algorithm is presented with pseudocode along with an explanation of its implementation. The entire source code can be found in the Appendices. This algorithm builds on earlier work from the lab of Dr. Andrei Nun, the advisor for this dissertation. We discuss several important extensions including: (i) a heap with special maintenance functions for sorting reaction waiting times, (ii) a nondeterministic component for handling reaction competition, and (iii) a memory enhancement allowing slower reactions to …

An Examination Of Factors Affecting Weight And Health In Exercising Adults, Cynthia West Dupuis

Doctoral Dissertations

Obesity is a significant problem in American society with approximately 65% of the population classified as overweight and the obesity rate exceeding 30% of all American adults. Obesity is associated with widespread physical and mental health problems which lead to increased healthcare costs, increased work absenteeism, and decreased work productivity. The factors of genetics and diet have been studied extensively by researchers in relation to weight gain and health. Physical exercise also has been established as a factor that affects weight and health, but exercise programs of all types suffer from an average attrition rate of approximately 50%. The additional …