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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 [ …

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 …

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 …

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 …

Improving Conservation Efforts Through A Better Understanding Of Forest Elephant Ecology, The Impacts Of Threats On Elephants And Freshwater Fisheries In Northern Congo, Roger Patrick Boundja

Doctoral Dissertations

IMPROVING CONSERVATION EFFORTS THROUGH A BETTER UNDERSTANDING OF FOREST ELEPHANT ECOLOGY, THE IMPACTS OF THREATS ON ELEPHANTS AND FRESHWATER FISHERIES IN NORTHERN SEPTEMBER 2016 ROGER PATRICK BOUNDJA, B.Sc. FORESTRY, MARIEN NGOUABI UNIVERSITY, BRAZZAVILLE MSc. UNIVERSITY OF CAPE TOWN PhD. UNIVERSITY OF MASSACHUSETTS AMHERST Directed by: Professor Curtice R. Griffin Catch data, including fish numbers, length-weight were collected during a multi-mesh Gillnet fisheries-independent survey in 2007-2008, and fisheries-dependent mixed gear surveys in 2009-2010 and 2015 across 400km stretch of the Sangha River located in the Sangha Tri-National. Overall, very high species richness (Chao 2 mean=250, SD=16.15) and diversity index (Simpson Inverse …

Chemopreventive Effects Of Cranberry In Association With The Alteration Of Gut Microbiota, Xiaokun Cai

Doctoral Dissertations

Accumulating evidence showed that microbiota play important roles in colonic inflammation and inflammation-associated colon carcinogenesis. Fruits and vegetable are known to have protective effects against colon carcinogenesis. Cranberry fruit contains large amount of flavonoids, phenolic acids and dietary fiber, which has been studied for their potential chemopreventive effect from in vitro model. To better understand the effect, we studied the protective effects of whole cranberry powder against colitis in mice treated with dextran sulfate sodium (DSS) and inflammation-associated colon carcinogenesis in mic treated with azoxymethane (AOM) and DSS, and its impact on gut microbiota. In DSS-induced colitis mice model, 1.5% …

Expansion Of And Reclassification Within The Family Lachnospiraceae, Kelly N. Haas

Doctoral Dissertations

Many of the taxa in the family Lachnospiraceae are currently misclassified as Clostridium spp. Here attempt to rectify many of these issues, beginning with an in-depth genomic and physiologic analysis of Clostridium methoxybenzovorans, culminating in the assertion that is a heterotype of Clostridium indolis, followed by reclassification of the broader group in which this organism resides. We propose two novel genera, Lacriformis and Enterocloster, to reclassify this clade, this includes reclassification of Clostridium sphenoides, Clostridium indolis, Clostridium saccharolyticum, Clostridium celerecrescens, Clostridium xylanolyticum, Clostridium algidixylanolyticum, Clostridium aerotolerans, Clostridium amygdalinum, and …

The Consequences Of Speed: Studies Of Cavitation During The Mantis Shrimp Strike And The Control Of Rapid Deceleration During Toad Landing, Suzanne M. Cox

Doctoral Dissertations

There are consequences of moving quickly in this world. Here we investigate how two very different species, mantis shrimp (Odontodactylus scyllarus) and cane toads (Bufo marinus), negotiate forces that result from moving rapidly in different environments. To study the mechanical principles and fluid dynamics of ultrafast power-amplified systems, we built Ninjabot, a physical model of the extremely fast mantis shrimp. While mantis shrimp produce damaging cavitation upon impact with their prey, they do not cavitate during the forward portion of their strike despite extreme speeds. In order to study cavitation onset in non-linear flows common during …

Distribution And Population Dynamics Of Ungulates In The Mongolian Gobi, Buuveibaatar Bayarbaatar

Doctoral Dissertations

The Mongolian Gobi is one of the most spectacular and important regions in Central Asia, comprising the largest area of intact grassland in the world. In recent years, a growing human population, expanding exploitation of natural resources, and the development of infrastructure in the region place increasing pressure on these species and their habitats. This dissertation has focused on three species of ungulates such as Mongolian saiga (Saiga tatarica mongolica) in western Mongolia, and Asiatic wild ass (Equus hemionus), and goitered gazelle (Gazella subgutturosa) in Southern Gobi. The study on endangered saiga antelope in …

The Neural Correlates Of Emotion Reactivity And Regulation In Young Children With Adhd, Claudia I. Lugo-Candelas

Doctoral Dissertations

Attention-deficit hyperactivity disorder (ADHD) is the most frequently occurring pediatric neurobehavioral disorder. Although emotion reactivity and regulation are frequently impaired in ADHD, few studies have examined these factors in preschool aged children with ADHD, and none have explored the neural correlates of emotion reactivity and regulation in this group though event-related potentials (ERPs). Children aged 4 to 7 with (n = 24) and without (n = 30) ADHD symptoms completed an attention task composed of four blocks: baseline, frustration, suppression, and recovery. In the frustration and suppression blocks, negative affect was induced by false negative feedback. During the …

Evaluating Resistance Surfaces For Modeling Wildlife Movement And Connectivity, Katherine Zeller

Doctoral Dissertations

The continued growth of human populations and associated development in many areas of the world is causing persistent fragmentation of natural habitats. In response, wildlife corridors are often promoted as essential for the conservation of wildlife species. Wildlife corridors allow for the movement of individuals between habitat patches and confer many benefits including the maintenance of metapopulations and metapopulation dynamics, the maintenance of seasonal migratory routes, genetic exchange, and the potential for individuals and populations to shift their ranges in response to climate change. Wildlife corridors are modeled across a resistance-to-movement surface where resistance represents the willingness of an organism …

X-Ray Characterization Of Mesophases And Phase Transitions Of Dna Analogues In Solutions, Mustafa Selcuk Yasar

Doctoral Dissertations

We think of DNA as double-stranded helices (duplex), but the polymer exists in many conformations. Several triplex and quadruplex DNA structures can be formed in laboratory settings and exist in nature. This thesis first provides a brief description of the nature of the order in arrays of duplex DNA under biologically relevant molecular crowding conditions. Then we compare the duplex DNA mesophases with the corresponding liquid crystalline phase behavior of the triplex and quadruplex DNA analogues. In particular, we focus on G-quadruplexes. Observed in the folds of guanine-rich oligonucleotides, G-quadruplex structures are based on G-quartets formed by hydrogen bonding and …

Development Of Bacteriophage Based Detection Technique For Food Safety And Environment Monitoring, Ziyuan Wang

Doctoral Dissertations

Foodborne or waterborne pathogens which are responsible for numerous worldwide outbreaks of disease have caused serious health problems and enormous economic cost. Development of new bacterial detection technologies with high sensitivity and specificity is of great importance for food safety and public health. This has highlighted the significance of developing rapid and effective techniques for pathogen screening. Thus we aim to explore a bacteriophage mediated detection system for foodborne or waterborne bacteria monitoring. Bacteriophage as a novel recognition probe has been applied in various biosensor by immobilizing phage particles on solid sensor surface. They possess high specificity for targeted microorganism …

Regional Recruitment Dynamics And Seasonal Ecology Of Juvenile Bluefish (Pomatomus Saltatrix), David G. Stormer

Doctoral Dissertations

Recruitment in fishes, defined as the survival of a cohort through the first year of life, can be highly variable and affected by small changes in biological and physical factors. Much of the historical focus into the sources of recruitment variability has concentrated on the larval stage, but recent attention has shifted to the relatively longer juvenile period. Spawning behavior that results in the production of multiple cohorts over time and space within a year-class may dampen recruitment variability by decreasing natural mortality risk. The bluefish (Pomatomus saltatrix) is a migratory marine species that produces multiple cohorts of …

Biopolymer Electrospun Nanofiber Mats To Inactivate And Remove Bacteria, Katrina Ann Rieger

Doctoral Dissertations

The persistence of antibiotic resistance in bacterial pathogens remains a primary concern for immunocompromised and critically-ill hospital patients. Hospital associated infections can be deadly and reduce the successes of medical advancements, such as, cancer therapies and medical implants. Thus, it is imperative to develop materials that can (i) deliver new antibiotics with accuracy, as well as (ii) uptake pathogenic microbes. In this work, we will demonstrate that electrospun nanofiber mats offer a promising platform for both of these objectives because of their high surface-to-volume ratio, interconnected high porosity, gas permeability, and ability to contour to virtually any surface. To provide …

Label-Free And Aptamer-Based Surface Enhanced Raman Spectroscopy For Detection Of Food Contaminants, Shintaro Pang

Doctoral Dissertations

The development of analytical methods to detect food contaminants is a critical step for improving food safety. Surface enhanced Raman spectroscopy (SERS) is an emerging detection technology that has the potential to rapidly, accurately and sensitively detect a wide variety of food contaminants. However, SERS detection becomes a challenge in real complex matrix, such as food, since non-specific matrix signals have the potential to drown out target associated Raman peaks. In this dissertation, we focused on the development and application of label-free, aptamer-based SERS in order to improve the accuracy and specificity of target contaminant detection in food. To accomplish …

Bacteriophage-Based Colorimetric Detection Of Escherichia Coli In Drinking Water, Juhong Chen

Doctoral Dissertations

One of the major safety causes in drinking water is from the bacteria contamination, especially in developing countries and resource-limited settings. Although many of these Escherichia coli (E. coli) strains in drinking water are nonpathogenic, they sever as the indicator for bacterial contamination. And, the more widely used method to detect E. coli in drinking water is to determine the activity of β-galactosidase (β-gal), which is released by E. coli. Rapid, sensitive and inexpensive detection of E. coli in drinking water can reduce the risk of food-borne bacteria infection and stop the disease widely spreading. In this …

Characterizing Colorectal Cancer Cells And Their Interactions With Polymethoxyflavones By Raman Microscopy, Hua Zhang

Doctoral Dissertations

Polymethoxyflavones (PMFs), especially Nobiletin (NBT) and 5-demethylnobiletin (5DN), have been widely studied and proved to have anti-cancer effects. However, their exact modes of action against cancer cells are not fully understood. Raman spectroscopy is a molecular vibrational spectroscopy can be used to measure overall biochemical function of single cells noninvasively and without adding any chemical labels. Herein, we characterized the cellular responses of human colorectal cancer HT29 and HCT116 cells, that grow on the gold coated slides, to the treatments of NBT and 5DN using Raman microscopy. Raman microscopic images obtained indicated the different modes of action of these two …