Life Sciences Commons^™

Assessing The Functional Similarity Of Native And Invasive Anolis Lizards In The Food Webs Of Structurally-Simple Habitats In Florida, Nathan W. Turnbough

Doctoral Dissertations

Invasive species often displace ecologically-similar native species, but the extent to which invading and displaced species function similarly in the food web processes of invaded communities is largely unknown. I investigated whether populations and individuals of an invasive Anolis lizard (the brown anole, Anolis sagrei) and the native congener it displaces in Florida (the green anole, Anolis carolinensis) are functionally equivalent in the food webs of open and structurally-simple habitats. In a system of invaded and uninvaded dredge-spoils islands, I found that both arthropod communities and winter bird communities covaried with brown anole abundance (and therefore the identity …

Ecology Of Organohalide-Respiring Dehalococcoides Mccartyi: Corrinoid Cofactor-Related Community Interactions And Controls Over Strain Selection, Burcu Şimşir

Doctoral Dissertations

Organohalides such as tetrachloroethene (PCE) and trichloroethene (TCE) are among the most prevalent toxic groundwater contaminants. Remediation of organohalide-contaminated sites has high priority, and efficient and cost-effective remedies are needed to prevent environment and human exposure through contaminated water. Bacterial organohalide-respiration plays a major role in organohalide detoxification. Dehalococcoides mccartyi (Dhc) are key mediators in bioremediation, since only Dhc strains have been documented in complete detoxification of chlorinated ethenes to benign ethene. Dhc depends on other microorganisms in the environment for essential growth requirements (e.g., hydrogen and vitamins). For successful implementation of the reductive dechlorination to remediate contaminated …

Antibacterial Activity And Chemical Characterization Of Resin From Sciadopitys Verticillata (Thunb.) Siebold And Zuccarini, David Ira Yates

Doctoral Dissertations

Sciadopitys verticillata produces white viscous resin that is unique among the conifers. This research investigated effects of resin on bacteria from different ecological niches and the chemical composition of the resin. Each bacterial species was evaluated separately for response to winter- and summer-collected resins. Exposure to winter-collected resin reduced numbers of colonies of Bacillus cereus, Erwinia amylovora, Agrobacterium tumefaciens, and Escherichia coli and increased numbers of Xanthomonascampestris, Pseudomonas fluorescens, and Pseudomonas syringae. Summer-collected resin affectedpopulation growth of two bacterial species; population counts of E. amylovora decreased and those of P. fluorescens increased. Selected strains of …

Bioremediation Of Chlorinated Ethenes: Ph Effects, Novel Dechlorinators And Decision-Making Tools, Yi Yang

Doctoral Dissertations

Chlorinated solvents have been widely used in different areas of modern society. Usage of these chlorinated solvents was not necessarily accompanied with proper handling and disposal of these hazardous compounds, which caused a variety of environmental problems and continues to affect human health. Remediation of chlorinated ethenes contaminated sites has high priority for state regulators and site owners. Among the available treatment technologies, bioremediation shows great promise as a cost-effective corrective strategy for a variety of environmental pollutants. Prerequisites are that the microbiology involved in contaminant degradation and geochemical factors, such as pH, are understood, so that bioremediation technologies can …

Towards Understanding Osmolyte Effects On Folate(S) And Dihydrofolate Reductase Proteins, Purva Prashant Bhojane

Doctoral Dissertations

Osmolytes are small molecules that alter water activity and probe role of water in biological processes. Osmotic stress approach explored the role of water in ligand binding to dihydrofolate reductase (DHFR). DHFR catalyzes NADPH dependent reduction of dihydrofolate (DHF) to tetrahydrofolate (THF), which is essential for the synthesis of DNA, amino acids and other metabolic intermediates. R67 DHFR is a plasmid-encoded DHFR that confers resistance against trimethoprim, which is a potent inhibitor of E.coli chromosomal DHFR.

Osmolytes addition decreases the affinity of the substrate towards both the DHFRs. Weak preferential interactions between the osmolytes and DHF impede substrate binding to …

Utilizing Cover Crops To Improve Sustainability Of Conventional Weed Management Programs, Garret Brown Montgomery

Doctoral Dissertations

Research was conducted from the fall of 2014 to the fall of 2016 to evaluate the optimal utilization of cover crops for weed control in no-till environments. Studies included a corn (Zea mays L.) termination timing study to evaluation different termination intervals of cereal rye (Cereal rye L.), hairy vetch (Vicia villosa Roth.), and a combination of cereal rye and hairy vetch cover crops on corn growth and development, an evaluation of a roller crimper for cover crop termination prior to corn study, an evaluation of a roller crimper for cover crop termination prior to soybeans [ …

Molecular And Ecological Aspects Of The Interactions Between Aureococcus Anophagefferens And Its Giant Virus, Mohammad Moniruzzaman

Doctoral Dissertations

Viruses are increasingly being recognized as an important biotic component of all ecosystems including agents that control the rapid ecological events that are harmful algal blooms (HABS). Aureococcus anophagefferens is a pelagophyte which causes recurrent ecosystem devastating brown tide blooms along the east coast of the USA and has recently spread to China and South Africa. It has been suggested that a large virus (AaV) is possibly an important agent for demise of brown tide blooms. This observation is consistent with the recognition of a number of other giant viruses modulating algal blooms in marine systems. In this dissertation, we …

Spatial Crowding And Confinement Effects On Bursty Gene Expression, Charles Wei-Shing Chin

Doctoral Dissertations

Synthetic biology and genetic engineering are valuable tools in the development of new, sustainable energy generation technologies. The characterization of stochastic gene expression is vital to the efficient application of genetic engineering techniques. Transcriptional bursting, in which periods of high expression are punctuated by periods of no expression, is extensively observed in gene expression. While various molecular mechanisms have been hypothesized to be responsible for transcriptional bursting, spatial considerations have largely been neglected. This work uses computational modeling to examine in detail the influence of spatial factors such as macromolecular crowding and confinement on gene expression.

In the first part …

The Impact Of Stability Ball Seating On Behavior And Academic Achievement Among Elementary School Students In Grades 1 Through 4., Sheila R. Borders

Doctoral Dissertations

This study was designed to answer three questions: 1) What is the impact of stability ball seating on the behavior of students in grades 1 through 4? 2) What is the impact of stability ball seating on the mathematics scores of students in grades 1 through 4? and 3) What is the impact of stability ball seating on the reading scores of students in grades 1 through 4? Research has shown that stability ball seating is linked to behavior and academic achievement among students diagnosed with attention deficit hyperactivity disorder (ADHD) and/or autism spectrum disorder (ASD). This study examines the …

Cohesion Without Cohesins In Drosophila Meiosis, Avik Mukherjee

Doctoral Dissertations

Meiosis is essential for sexual reproduction. The proper segregation of chromosomes in meiosis requires multiple functions of a multi-subunit protein complex known as cohesin. Cohesin forms a ring around duplicated sister chromatids and prevents them from separating prematurely. In Drosophila, mitotic cohesin is composed of four subunits: SMC1 and SMC3 and SCC1/RAD21 and SCC3/SA and are required for mitotic cohesion. However, RAD21 is dispensable for meiotic cohesion and although SMC1 and SMC3 are present on meiotic centromeres and on synapsed chromosome arms, as expected, their functions in meiosis remain poorly characterized. Moreover, unlike in other eukaryotes in which screens for …

Whole Genome Sequencing As A Tool For Identifying Phenotypic Properties And Underlying Genetic Mechanisms In Staphylococcus Pseudintermedius, Matthew C. Riley

Doctoral Dissertations

Staphylococcus pseudintermedius is a Gram-positive bacterial opportunistic pathogen commonly associated with dermal infections in canines, but capable of causing serious disease in other species. Reports of human infections caused by S. pseudintermedius along with an increase in resistance to multiple antibiotics highlights the importance of this organism. Whole genome sequencing can allow large scale investigation of genetic mechanisms underlying phenotypic properties that contribute to the expansion of successful S. pseudintermedius clonal lineages.

The increase in multidrug and methicillin-resistant S. pseudintermedius (MRSP) may result from horizontal transfer of genetic material between bacterial isolates, yet is thought to be rare in Staphylococci …

Tetrameric Photosystem I: From Initial Discovery And Characterization In Chroococcidiopsis Sp. Ts-821 To Exploration Of Its Distribution And Understanding Of Its Significance In Cyanobacteria, Meng Li

Doctoral Dissertations

Photosystem I (PSI) forms trimeric complexes in most characterized cyanobacteria. We had reported the tetrameric form of PSI in the unicellular cyanobacterium, Chroococcidiopsis sp. TS-821 (TS-821). Using Cryo-EM, a 3D model of the PSI tetramer structure at 11.5 [Angstrom] resolution was obtained and a 2D map within the membrane plane of at 6.1 [Angstrom]. In contrast to the three-fold symmetry in trimeric PSI crystal structure from T. elongatus, two different inter-monomer interactions involving PsaLs are found in the PSI tetramer. Phylogenetic analysis based on PsaL protein sequences shows that TS-821 is closely related to heterocyst-forming cyanobacteria. Additionally, this tetrameric …

Microbial Respiration And Community Response To Crude Oil In Deep Eastern Mediterranean And The Great Australian Bight, Jiang Liu

Doctoral Dissertations

The Deep Water Horizon (DWH) oil spill in 2010 was the largest deep ocean oil spill in world history. Very limited information about oil biodegradation is available in deep oceans other than GOM since DWH. In this study, we investigate the microbial communities’ response to crude oil contamination in the deep Eastern Mediterranean sea (E.Med) and Great Australian Bight (GAB). In addition, we will assess feasible methods for oil bioremediation in those locations.

First, we discovered the fast adaption of the E.Med deep water microbial community to oil contamination in terms of phylogeny and functional genes. Based on the 16S …

On The Quantification Of Complexity And Diversity From Phenotypes To Ecosystems, Zachary Harrison Marion

Doctoral Dissertations

A cornerstone of ecology and evolution is comparing and explaining the complexity of natural systems, be they genomes, phenotypes, communities, or entire ecosystems. These comparisons and explanations then beget questions about how complexity should be quantified in theory and estimated in practice. Here I embrace diversity partitioning using Hill or effective numbers to move the empirical side of the field regarding the quantification of biological complexity.

First, at the level of phenotypes, I show that traditional multivariate analyses ignore individual complexity and provide relatively abstract representations of variation among individuals. I then suggest using well-known diversity indices from community ecology …

Improved Fungicidal Control Of Large Patch Through Optimal Use Of Surfactants And Spray Rate Volume, Jesse J. Benelli

Doctoral Dissertations

Large patch (Rhizoctonia solani AG 2-2LP) epidemics cause significant damage to Japanese lawngrass (JLG; Zoysia japonica) in the transition zone. Large patch primarily affects the stems and sheaths of JLG and is difficult to control using traditional fungicide sprays. Field and growth chamber experiments were conducted during 2015-2016 in TN and GA to evaluate methods to enhance fungicidal control of large patch in JLG landscapes. The 1^st experiment evaluated the most critical application target site that resulted in the greatest amount large patch control. In this experiment, four fungicides (azoxystrobin, flutolanil, tebuconazole, and chlorothalonil) were dispensed as …

Alternative Approaches To Improving The Welfare Of Transition Dairy Cows And Their Calves: Use Of Exercise, Randi Alyson Black

Doctoral Dissertations

Transition cows are the cows most susceptible to disease and prevalence has not changed over the past decade. However, increased physical activity during late gestation may represent a management option to improve transition. Therefore, the objectives of this study were to determine the effect of exercise, pasture turnout, or total confinement on 1.) physical fitness and cortisol concentrations during the dry period, 2.) neutrophil function and behavior during the dry period, 3.) horn growth and wear and sole thickness during the dry period 4.) calving behavior and cortisol concentrations at parturition, and 5.) calf performance, behavior, and cortisol concentrations at …

Development, Implementation And Evaluation Of A Pilot Intervention: Promoting Breast Milk Expression In A Neonatal Intensive Care Unit, Katherine Marie Bower

Doctoral Dissertations

Background: Very preterm infants receiving breast milk experience better health outcomes compared to formula fed infants. However, these infants often lack the ability to coordinate sucking and swallowing and are unable to breastfeed at delivery. Consequently, mothers of very preterm infants must initiate milk expression. While these mothers demonstrate high milk expression initiation rates, continuation of this behavior until infant discharge from the Neonatal Intensive Care Unit (NICU) is a significant challenge.Therefore, the primary aim of this study was to gain an understanding of mothers’ experiences expressing milk for their very preterm infants in a Level III NICU and to …

Molecular Dynamics Simulations Of Enzymes With Quantum Mechanical/Molecular Mechanical Potentials, Yufei Yue

Doctoral Dissertations

S-adenosyl methionine (SAM) dependent methylation process is universally found in all branches of life. It has important implications in mammalian pathogenesis and plant metabolism. The methyl transfer is normally catalyzed by SAM-dependent methyltransferases(MTases). Two MTases are studied in this dissertation: the 1,7-dimethylxanthine methyltransferase (DXMT) which involve in plant caffeine biosynthesis, and the protein arginine methyltransferase 5(PRMT5) that participates in eukaryotic posttranslational modification. The late phase of caffeine biosynthesis starts from the substrate xanthosine and ends with the product caffeine, with theobromine as an intermediate product. DXMT is a key enzyme in this process and catalyzes two methylation steps: 1)methylation of …

Computational Analyses Of Mrna Ribosome Loading In Arabidopsis Thaliana, Joseph Benjamin Ernest

Doctoral Dissertations

Translation of mRNA into protein is a critical step in gene expression, but the principles guiding its regulation at the genome level are not completely understood. Translation can be quantified at a genome scale by measuring the ribosome loading of mRNA—the extent to which mRNA is associated with ribosomes. In this dissertation, I present investigations into how genome-wide ribosome loading is controlled in Arabidopsis thaliana. In chapter 1, I give an overview of regulation of ribosome loading and translation. In chapter 2, I present research demonstrating for the first time that genome-wide ribosome loading in plants is partially controlled by …

Electron Transport To Photosystem I By Soluble Carriers: Evolution Of The Interacting Pair, Khoa Dang Nguyen

Doctoral Dissertations

Oxygenic photosynthesis is driven via sequential action of Photosystem II (PSII) and (PSI) reaction centers via the Z-­‐scheme. Both of these pigment– membrane protein complexes are found in cyanobacteria, algae, and plants. PSI, unlike PSII, is remarkably stable and does not undergo limiting photo-­‐damage. This stability, as well as other fundamental structural differences, makes PSI the most attractive reaction centers for applied photosynthetic applications. These applied applications exploit the efficient light harvesting and high quantum yield of PSI where the isolated PSI particles are redeployed providing electrons directly as a photocurrent or, via a coupled catalyst to yield H2. Here, …

Improving Metabolic Engineering And Characterization Of Clostridium Thermocellum For Improved Cellulosic Ethanol Production, Beth Alexandra Papanek

Doctoral Dissertations

Biofules are an important option for humanity to move away from its dependence on fossil fuels. Transitioning from food crops to lignocellulosic alternatives for the production of biofuels is equally important. Most commonly, biofuels are produced using a crop such as corn or soybeans to feed sugars to the yeast, Saccharomyces cerevisiae for the fermentation of ethanol. Lignocellulosic biofuel production would eliminate the need for food crops and transition to biomass such as switchgrass, poplar, or corn stover. Currently, lignocellulosic biofuel production is limited primarily because of the cost of converting the biomass to fermentable sugars than can then be …

Effects Of Television Viewing On Psycho-Physiological And Behavioral Outcomes, Brittany Star Overstreet

Doctoral Dissertations

Purpose: To determine the effects of television viewing during exercise on 1) preference for exercise and 2) treadmill walking time. Methods: Twenty-five insufficiently active adults (mean±standard deviation; age: 46±12 years; Body mass index: 31±5 kilogram/squared meter (kg/m²) were recruited for this study. In part 1, participants performed three randomized 1/3-mile walking bouts at an intensity equivalent to 70% of their oxygen consumption at ventilatory threshold (VO₂-at-VT). During these exercise bouts, individuals viewed 1) their favorite television program (FavTV), 2) a standardized nature program (NatTV) or 3) no-TV program (NoTV). A behavioral choice paradigm was used to …

Modification Of Carbohydrate Active Enzymes In Switchgrass (Panicum Virgatum L.) To Improve Saccharification And Biomass Yields For Biofuels, Jonathan Duran Willis

Doctoral Dissertations

The natural recalcitrance of plant cell walls is a major commercial hurdle for plant biomass to be converted into a viable energy source as alternative to fossil fuels. To circumvent this hurdle manipulation of carbohydrate enzymes active in the cellulose and hemicellulose portions of the plant cell wall can be utilized to improve feedstocks. Production of cellulolytic enzymes by plants have been evaluated for reducing the cost associated with lignocellulosic biofuels. Plants have successfully served as bioreactors producing bacterial and fungal glycosyl hydrolases, which have altered plant growth to improve saccharification. A bioprospecting opportunity lies with the utilization of insect …

The Effects Of Exogenous Fatty Acids On Enterococcus Faecalis Og1rf, Holly Elizabeth Johnson Saito

Doctoral Dissertations

Enterococcus faecalis is a commensal of the mammalian intestine and an opportunistic pathogen that infects various locations in the human host. Specifically, the organism can infect surgical wounds, the urinary tract, and is an agent of endocarditis. Regardless of niche, this organism has access to fatty acid sources in the host, which may influence its ability to survive and cause infection; yet, the effects of exogenous fatty acids were unknown in E. faecalis. We have shown that complex sources of fatty acids such as bile or serum can significantly alter the membrane content and protect E. faecalis from acute …

Long-Term Treatment With Insulin And Retinoic Acid Increased Glucose Usage In L6 Muscle Cells Via Glycogenesis, Matthew Ray Goff

Doctoral Dissertations

Skeletal muscle glucose metabolism can affect whole body glucose homeostasis significantly. Vitamin A (VA) plays a role in a number of physiological functions including glucose metabolism. However, its role in skeletal muscle glucose metabolism has not been well established. Insulin controls glucose metabolism in the skeletal muscle via the regulations of glucose uptake, glycogenesis, and glycolysis. We hypothesize that insulin and VA signaling pathways may converge to regulate glucose metabolism in skeletal muscle. Here, the effects of retinoic acid (RA) alone and in combination with insulin on glucose utilization in rat L6 muscle cells were studied. L6 cells were treated …

Decoding The Cellular Zipcode: Functional Analysis Of Transit Peptide Motifs And Mechanistic Implications In Plastid Targeting And Import, Kristen N. Holbrook

Doctoral Dissertations

Eukaryotic organisms are defined by their compartmentalization and various organelles. The membranes that define these organelles require complex nanomachines (known as translocons) to selectively mediate the import of proteins from the cytosol where they are synthesized into the organelle. The plastid, (specifically the chloroplast) which is characteristic of plant cells, possibly represents the most complex system of protein sorting, requiring many different translocons located in the three membranes found in this organelle. Despite having a small genome, the vast majority of plastid-localized proteins are nuclear-encoded and must be post-translationally imported from the cytosol. These proteins are encoded as a larger …

Anaerobic Soil Disinfestation: Meta-Analysis And Optimization Of Amendment Carbon Rate And C:N Ratio To Control Key Plant Pathogens And Weeds, Utsala Shrestha

Doctoral Dissertations

Anaerobic soil disinfestation (ASD) is an environmentally friendly and cost effective pre-plant soil treatment technique that allows effective control of soilborne pests by creating anaerobic conditions, particularly for specialty and organic crop production under diverse environmental conditions. In spite of being a proven technique, ASD has to be optimized to fit into local production systems with specific pathogen pressure using locally available amendments for successful implementation on a commercial scale. Our meta-analysis study on soilborne pathogens, plant parasitic nematodes, and weeds validated that ASD is an effective approach to control various soilborne pathogens. This study aims to optimize the carbon …

Characterization Of An Ethylene Receptor In Synechocystis Sp. Pcc 6803, Randy Francis Lacey

Doctoral Dissertations

In plants, ethylene functions as a hormone regulating many growth and developmental processes. Ethylene receptors in plants resemble bacterial two-component signaling systems. Because of this it, ethylene receptors are thought to have been acquired by gene transfer from the cyanobacterial endosymbiont that lead to the development of the chloroplast. However, prior to this work, functional ethylene receptors were thought to only be found in green plants. Here, we show that the cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis) contains a functional ethylene receptor, SynEtr1. SynEtr1 contains a predicted ethylene binding domain, a photosensory cyanobacteriochrome (CBCR) domain, and a histidine …

Pigment Dispersing Factor: Transcriptional Regulation And Its Role In Metabolism In Drosophila Melanogaster, Sudershana Nair

Doctoral Dissertations

Almost all living organisms have circadian clocks coordinating physiology and behavior, and an innate molecular clock drives rhythmic changes by integrating environmental and metabolic stimuli to generate 24 hour timing. Drosophila melanogaster has proved to be an excellent model organism with a well-characterized circadian clock and the neural circuits underlying clock have been intensely investigated. The neuropeptide pigment-dispersing factor (PDF) plays an essential role in maintaining circadian rhythmicity and synchronizes circadian clock neurons. However, the regulation of Pdf has been a black box with no known protein identified that directly regulates it, and its role in metabolism hasn’t been looked …

Nanocomposite Adhesive Of English Ivy (Hedera Helix): Bioproduction, Nanoparticle Isolation, And Molecular Analysis, Jason Neil Burris

Doctoral Dissertations

English ivy naturally produces organic nanoparticles from its adventitious root hairs, and possesses characteristics that may allow them to replace metal-based nanoparticles in common applications, such as sunscreen. At the onset of the research, it was hypothesized that a physical mechanism of attachment, similar to the gecko footpad, was used to generate the adhesive force for attachment; however, through the results obtained from recent work, it is clear that a biochemical mechanism is involved in the generation of the strength of adhesion. Therefore, the goal of this research was to provide a better understanding of the genetic basis of nanoparticle …