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The Transcriptome Response Of The White-Rot Fungus Phanerochaete Chrysosporium To Maple And Miscanthus, Mashael Rashed Alaradi

Masters Theses

Lignocellulosic biomass is a valuable feedstock for the production of liquid biofuels. However, liquid biofuel production from lignocellulose is economically challenging due to the difficulties associated with separating the cellulosic sugars from lignin. In addition, the current thermochemical methods to deconstruct lignocellulose typically involve hazardous chemicals that can negatively impact the environment. Recent studies have demonstrated the efficacy of white-rot fungi as alternative pretreatment agents that can lower the costs of lignocellulose deconstruction and reduce negative impacts on the environment. However, understanding of the biochemical mechanisms of lignocellulose breakdown used by these fungi is limited, particularly with respect to the …

A Population Genetics Study Of Discula Destructiva, The Causal Agent Of Dogwood Anthracnose, Kristie Lynn Mantooth

Masters Theses

Flowering dogwood (Cornus florida L.) is prized as an ornamental and contributes millions of dollars to the economy through tourism and sales each year. Dogwood anthracnose, caused by Discula destructiva Redlin, was observed in the late 1970s on the east and west coasts of the United States and by 1991 had quickly spread throughout much of the native ranges of C. florida and C. nuttalli. The objectives of this study were to investigate the genetic diversity and population structure of D. destructiva using simple sequence repeats (SSRs), and to test the cross-transferability of these markers to other Discula …

Association Of Genotype At Drd2 With Growth And Reproductive Performance Traits In Bulls Grazing Toxic Endophyte-Infected Tall Fescue, Kaysie Jennings

Masters Theses

Fescue toxicosis can negatively impact growth and fertility of beef cattle grazing tall fescue infected with an endophytic fungus. The fungus produces ergot alkaloids that contribute to the hardiness of the plant, but can be detrimental to the animal if consumed. A single nucleotide polymorphism (SNP) in the dopamine receptor D2 gene (DRD2) has been associated with serum prolactin concentrations and hair coat scores in cattle grazing toxic endophyte-infected (TE) tall fescue; cattle with the GG genotype had decreased serum prolactin concentrations and increased hair coat scores. Separately, heifers with the AA genotype calved sooner than AG or GG heifers. …

Population Genetics And Genomics Within The Genus Pityopsis, Elizabeth Anne Hatmaker

Masters Theses

Pityopsis (Asteraceae) includes seven species; one species, P. ruthii, is federally endangered. The genus exhibits a range of ploidy levels, widespread hybridization among species with overlapping ranges, and interesting adaptive traits such as fire-stimulated flowering. However, taxonomy of Pityopsis has remained unresolved. Resolving interspecific relationships can lead to a deeper understanding of the inheritance and hybridization patterns, as well as the evolution of adaptable traits. Our first objective was to examine population structure and gene flow within Pityopsis ruthii. Polymorphic microsatellite markers (7 chloroplast and 12 nuclear) were developed and used to examine genetic diversity of 814 P. …

Scalable Parallelization Of A Markov Coalescent Genealogy Sampler, Philip E. Davis

Masters Theses

Coalescent genealogy samplers are effective tools for the study of population genetics. They are used to estimate the historical parameters of a population based upon the sampling of present-day genetic information. A popular approach employs Markov chain Monte Carlo (MCMC) methods. While effective, these methods are very computationally intensive, often taking weeks to run. Although attempts have been made to leverage parallelism in an effort to reduce runtimes, they have not resulted in scalable solutions. Due to the inherently sequential nature of MCMC methods, their performance has suffered diminishing returns when applied to large-scale computing clusters. In the interests of …

Characterization Of Insertion Sequence Is605 In Halanaerobium Hydrogeniformans, Michael C. Sadler

Masters Theses

"Insertion sequences are the smallest prokaryotic transposable elements. These genes play a significant evolutionary role by promoting genome plasticity. Insertion sequences are highly diverse elements that have largely been uncharacterized. As such, the ability to accurately identify, annotate, and infer genomic impact of insertion sequences is lacking. The study of new insertion sequences contributes knowledge to their annotation and evolution. Halanaerobium hydrogeniformans is a unique organism with an abnormally high number of insertion sequences. A family of insertion sequences, IS200/605, showed several interesting distinctions from other elements in the genome, including severe open reading frame degradation, and was characterized in …

Impact Of Transcription Factors On Fibroblast Specific Gene Silencing In Somatic Cell Hybrids, Tania Ray

Masters Theses

As totipotent cells differentiate to specific cell types in multicellular organisms, certain sets of genes are turned off (gene silencing/gene extinction) while others are turned on (gene activation). Cell type specific gene silencing and gene activation is the basis of cell differentiation. Somatic cell hybrids which are produced by fusing different types of somatic cells from two different tissues have been used as a valuable resource to discern the phenomenon of lineage- specific gene extinction. Identification of regulatory factors that mediate gene extinction in hybrids are key to understanding regulatory mechanisms that govern cell differentiation in a multicellular organism. Transcription …

Low-Head Dams On Habitat, Fish Functional Guilds And Genetic Structuring In A Midwestern River System, Shannon Cassandra Frary Smith

Masters Theses

The natural flow regime of the majority of rivers in the United States has been altered by anthropogenic structures. This loss of connectivity plays a strong role in shaping river ecosystems by altering physical habitat characteristics and shaping fish community assemblages. Although the impacts of large dams on river systems are well documented and often easy to observe, there are fewer studies on the effects of smaller low-head dams. Additionally, the influences of low-head dams on the genetic structuring of small-bodied riverine fishes have yet to be fully explored. I assessed the effects of two low-head dams on the Vermilion …

Genetic Structure And Diversity Of Channel Catfish (Ictalurus Punctatus) In Three Large Midwestern Rivers, Vaclav Alexei Sotola

Masters Theses

Little information is available regarding the genetic structure and diversity of sportfishes in large rivers, which can be vital to continuing the sustainable exploitation of these fisheries. Additionally, impoundments often have vast impacts on riverine systems. These impacts include altering the flow regime, changing the nutrient load, and preventing migratory fish from reaching their spawning grounds. If fishes are prevented from reaching their spawning grounds, their genetic diversity and structuring could begin to change relative to historic measures, potentially decreasing their fitness and ability to survive. I screened microsatellite loci to assess the genetic population structure and diversity of channel …

Expression Of Insulin Responsive Genes In Insulin Resistant Conditions, And The Effect Of Selenium On Gene Expression, David L. Ruff

Masters Theses

Chronically high blood glucose levels lead to many problems, such as insulin resistance, the hallmark of Type II diabetes. Increased flux through the hexosamine biosynthesis pathway is one mechanism by which high glucose as well as glucosamine has been shown to induce insulin resistance. This study tests the effects of glucosamine induced insulin resistance on insulin regulation of the metabolic genes glucose-6-phosphate dehydrogenase (G6PDH) and fatty acid synthase (FAS) as well as insulin responsive proteins tribbles homolog (TRIB3) and sterol regulatory element binding protein (SERBP-1c) 1c.

Selenium, a micronutrient has been shown to be an effective insulin mimetic in Type …

Rare Occurrences Of Free-Living Bacteria Belonging To Sedimenticola From Subtidal Seagrass Beds Associated With The Lucinid Clam, Stewartia Floridana, Aaron M. Goemann

Masters Theses

Lucinid clams and their sulfur-oxidizing endosymbionts comprise two compartments of a three-stage, biogeochemical relationship among the clams, seagrasses, and microbial communities in marine sediments. A population of the lucinid clam, Stewartia floridana, was sampled from a subtidal seagrass bed at Bokeelia Island Seaport in Florida to test the hypotheses: (1) S. floridana, like other lucinids, are more abundant in seagrass beds than bare sediments; (2) S. floridana gill microbiomes are dominated by one bacterial operational taxonomic unit (OTU) at a sequence similarity threshold level of 97% (a common cutoff for species level taxonomy) from 16S rRNA genes; …

Population Structure Of Late Blight (Phytophthora Infestans) In Colombia And Ecuador And Downy Mildew (Peronospora Farinosa F. Sp. Spinaciae) On Spinach In Arizona And California, Rebecca Marie Lyon

Masters Theses

In this study, Phytophthora infestans and Peronospora farinosa f. sp. spinaciae populations were analyzed using single nucleotide polymorphisms (SNPs). In Ecuador and Colombia, Phytophthora infestans causes significant damage to potato and tomato and the epidemiology is known to be highly clonal. Our objective was to measure population structure within the context of this clonal epidemiology using both synonymous and nonsynonymous markers. Candidate SNP sites were selected by comparing the draft genomes of the Ecuadorian isolates EC1-3527 and EC1-3626. Genotypes were assessed directly from infected tissue using a targeted sequencing approach. A total of 54 polymorphic sites were assessed in 93 …

Distribution Of Abc Transporter Genes Across The Plant Kingdom, Thomas Scott Lane

Masters Theses

The ATP-binding cassette (ABC) transporter gene superfamily is ubiquitous among extant organisms. ABC transporters act to transport compounds across cellular membranes and are involved in a diverse range of biological processes and functions including cancer resistance in humans, drug resistance among vertebrates, and herbicide resistance in weeds. This superfamily of genes appears to be larger and more diverse in the plant kingdom—yet, we know relatively less about ABC transporter function in plants compared with mammals and bacteria. Therefore, we undertook a plant kingdom-wide transcriptomic survey of ABC transporters to better understand their diversity.

We utilized sequence similarity-based informatics techniques to …

Genetic Structure Of Yellow Perch Populations In Coastal Areas Of Eastern Lake Michigan, Jessica N. Wesolek

Masters Theses

Genetic population substructure is often overlooked because of discontinuities between management and actual population structure as in the case of yellow perch, an ecologically and economically important indigenous fish species in the Laurentian Great Lakes. A knowledge gaps pertaining to the natural history of yellow perch relates to the biological connectivity between nearshore Lake Michigan and drowned river mouth (DRM) lakes, where it remains unclear whether resident yellow perch from Lake Michigan use DRM lakes for spawning or whether DRM lakes contribute to nearshore yellow perch populations in Lake Michigan. I used DNA fingerprinting (genotyping) to explore biological connectivity between …

Molecular Marker Assisted Backcross Development And Evaluation Of An Environmentally Friendly, Commercially Acceptable Low Seed Phytate Soybean, Jeffrey David Boehm Jr.

Masters Theses

Soybean [Glycine max (L). Merrill] is the world’s top oilseed crop. High protein soymeal is a primary soybean use and staple food of livestock and fish. The storage form of phosphorus (P) in the seed is phytic acid, or phytate [myo-inositol 1,2,3,4,5,6 hexakisphosphate] which binds and chelates key nutritional cations forming stable salts that are non-digestible. Livestock waste laden with phytate P is an environmental concern, and a source of nonpoint P pollution causing eutrophication and surface water quality deterioration. The primary objective of this research was the development of a commercially acceptable low phytate (LP) soybean …

R-Fap: Rapid Functional Annotation Of Prokaryotes Using Taxon-Specific Pan-Genomes And 10-Mer Peptides, Jordan Matthew Utley

Masters Theses

The growing implementation of next-generation sequencing technologies presents numerous fields with the opportunity to identify bacteria in near real-time. Fields such as counter-terrorism, forensics, medicine, and even microbial ecology are positioned to benefit from such advances and implementation. However, with the ability to rapidly produce high-quality sequence data comes the need to interpret this data as quickly as it is produced. While gene prediction algorithms have kept pace, functional prediction methods have not.

To bypass the need for large-scale queries to multiple databases for each newly-sequenced genome, the project detailed herein seeks to identify the genes shared within a taxonomic …

Population Demographics And Genetic Structure Of Black Bears In Coastal Louisiana, Jesse Charles Troxler

Masters Theses

The range and abundance of the Louisiana black bear (Ursus americanus luteolus) were greatly diminished during the 20th century. This subspecies was reduced to 3 small, isolated subpopulations in Louisiana as bottomland hardwood habitat was converted to agriculture. These bears were listed as threatened by the U.S. Fish and Wildlife Service in 1992 and a recovery plan was published in 1995. Recovery requires estimates of population parameters to evaluate current population status and future viability. I conducted a mark-recapture study from 2010 to 2012 to estimate demographic parameters of the coastal population of Louisiana black bears. Because inbreeding …

Single-Nucleotide Polymorphisms Associated With Performance Traits In Beef Cattle Grazing Endophyte-Infected Tall Fescue, Bryan Christopher Bastin

Masters Theses

Tall fescue (Lolium arundinaceum Schreb.) is the most prevalent forage in the Midsouth United States due in part to the presence of the endophytic fungus Neotyphodium coenophialum. The fungus, while conferring hardiness to tall fescue, contributes to decreased production efficiency in cow-calf operations. A previous genome-wide association study was performed using the Illumina 50k bovine SNP chip. Twenty-four SNP were found to be associated (P < 0.05) with adjusted birth weight and adjusted 205-day weights of calves from 48 beef cows at Ames Plantation. The first objective was to validate each SNP by testing associations with several additional phenotypes. Custom Taqman genotyping assays (Applied Biosystems, Foster City, CA) were subsequently designed to genotype each SNP in beef cattle located at Tennessee Tech University (n = 654), to validate associations in a large, independent herd. The results yielded 15 associations that were significant (P < 0.05) with 6 phenotypes linked to those affected by fescue toxicosis. The second objective investigated the link between fescue toxicosis and the XK, Kell blood group complex subunit-related, member 4 …

Trends In Borrelia Spp. Prevalence In Ixodes Spp. Ticks From The Southeastern Coastal United States, Lauren Paul Maestas

Masters Theses

The Lyme borreliosis (LB) cycle, involving Ixodes scapularis and Borrelia burgdorferi sensu stricto (Bbss), is well documented in the northeastern US, where LB is becoming increasingly prevalent. In coastal North Carolina, I. affinis has been shown to have a higher incidence of Bbss than I. scapularis. My objectives were, to assess changes in prevalence of Bbss in Ixodes spp. along a transect from Virginia to Florida, and to assess the value of dogs and mesomammals as sentinels for spread of Borrelia burgdorferi sensu lato.

Ixodes spp. were collected at sites from 37.4^o N to 30.0^{o …}

Molecular Systematics Of The Subfamily Phasiinae (Diptera: Tachinidae), Jeremy Daniel Blaschke

Masters Theses

The subfamily Phasiinae (Diptera: Tachinidae) is composed of obligate endoparasitoid flies that attack heteropteran insects, many of which are important agricultural pests. To lay a foundation for future studies in phasiine life history and their potential for use as biological control agents, the phylogenetic relationships within Phasiinae were explored using nucleotide sequences of two genes, CAD and LGL. A total of 63 taxa for CAD and 73 taxa for LGL were included in the analyses, representing 58 genera. Maximum likelihood inference methods were employed to reconstruct phylogenetic relationships in separate analyses of each gene and in a combined dataset. Phylogenetic …

Microarray Analysis Of Mrna Translation State In Arabidopsis Thaliana, Bayu Sisay Tiruneh

Masters Theses

The synthesis of proteins – translation – is one of the cellular processes that consume a great deal of energy. Genome-wide assays performed in Arabidopsis and other organisms have revealed that the translation status of mRNAs responds dramatically to different stresses and environmental and growth signals. Similar assays have revealed how translation of specific mRNAs is perturbed by genetic mutations in eukaryotic translation initiation factors (eIFs). I performed genome-wide analyses of translation state in A. thaliana seedlings with mutant genotypes for a specific eIF (subunit h of eIF3) and the large ribosomal protein, L24 (RPL24B). Using data from prior microarray …

Genomic Analysis And Functional Characterization Of The Terpene Synthase Gene Family In Brachypodium Distachyon, Ayla Marie Norris

Masters Theses

Brachypodium distachyon is a small, temperate grass native to the Mediterranean region. While not agriculturally important, it possesses many characteristics such as rapid generation time, self-pollination, a small genome size, and ease of genetic transformation, that make it an attractive model organism for genetic studies. Brachypodium is closely related to other grasses of economical importance such as rice, sorghum, and especially wheat, and in fact it is the first member of the Pooideae grass sub-family to have its genome fully sequenced. Cereal grasses such as rice, sorghum, and maize have been reported to produce a class of secondary metabolites called …

Diffuse Interactions Between Symbiotic Bacteria And Salamanders, Amanda Lee Allison

Masters Theses

A growing body of evidence indicates that all animals and plants have intimate associations (symbioses) with microbes. Scientific opinion has shifted from viewing microbes primarily as pathogens to the idea that healthy animals and plants carry specialized communities of coevolving microorganisms. However, the generality of this proposition is unknown because surveys rarely compare host-associated microbial assemblages with those of similar host species or free-living assemblages in relevant microhabitats. To evaluate the specificity and consistency of microbial associations in salamanders, I analyzed just over 3.6 million 16S ribosomal RNA gene sequences from paired samples from host-associated bacteria on the skin of …

Molecular Marker Assisted Development And Stability Analysis Of Low Phytate, High Inorganic Phosphorus Soybean [Glycine Max (L.) Merrill], Suzannah Joy Wiggins

Masters Theses

Phytate [myo-inositol 1,2,3,4,5,6-hexakisphosphate] is a mixed cation salt of phytic acid which binds to other minerals, in many field crops including soybean [Glycine max (L.) Merr.]. Livestock with monogastric digestive systems lack the ability to break bonds between phytate and these minerals, causing phytate phosphorus (P) to be excreted in the waste and contributing to possible P and other mineral deficiencies. Discovery of single sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers associated with low phytate QTL (cqPha-001 and cqPha-002) have aided in development of low phytate soybean lines. The objectives of this study were …

Studies On Enzyme Functional Evolution In The Sabath Multigene Family Using Phylogenetic And Biochemical Approaches, Ruiqi Huang

Masters Theses

Gene duplication is believed to be the major source for providing genetic materials for the innovation and diversification of protein functions; natural selection and/or neutral drift then works on these genetic materials to guide their evolutionary directions. Here, I used the salicylic acid/benzoic acid/theobromine (SABATH) multigene family to study how natural selection acted on duplicated genes to prompt functional diversification. Members in this family methylate plant secondary metabolites by transferring the methyl group from S-adenosyl-L-methionine (SAM) to the carboxyl group or ring nitrogen of the substrates. In the Apocynaceae and Solanaceae lineage of this family, I documented three putative gene …

Consequences Of Gene Flow And Transgene Introgression In Hybrids Between Transgenic Brassica Napus And Its Weedy Wild Relative Brassica Rapa, Reginald Jason Millwood

Masters Theses

The adventitious presence of transgenes and their potential impact on the environment has been a topic of concern for many years. To address these concerns the following chapters discuss past and current research of gene flow and introgression, methods for transgene detection and monitoring, and the results from field-level experiments using artificially introgressed advanced generation hybrids. The field studies were designed to be a worst-case scenario where hybrids were produced by hand-crossing transgenic Brassica napus (AACC, 2n = 38) and its weedy wild relative Brassica rapa (AA, 2n = 20). B. napus was transgenic for the green fluorescent protein [m-GFP-5 …

Capture-Recapture Of White-Tailed Deer Using Dna Sampling From Fecal Pellet-Groups, Matthew James Goode

Masters Theses

Reliable density estimates of game and keystone species such as white-tailed deer (Odocoileus virginianus) are desirable to set proper management strategies and for evaluating those strategies over time. However, traditional methods for estimating white-tailed deer density have been inhibited by behavior, densely forested areas that can hamper observation (detection), and invalid techniques of estimating effective trapping area. We wanted to evaluate a noninvasive method of mark-recapture estimation using DNA extracted from fecal pellets as the individual marker and for gender determination, coupled with a spatial detection function to estimate density (Spatially Explicit Capture-Recapture, SECR). We collected pellet groups …

Functional Analysis Of The Cyp6a8 Gene Promoter Of Drosophila Melanogaster For Caffeine- And Phenobarbital-Inducibility By Site-Directed Mutagenesis, Olivia Nichole Hill

Masters Theses

Cytochrome P450 enzymes (CYPs), found in almost all organisms, are involved in endobiotic metabolism and detoxification of xenobiotic compounds, such as drugs, pollutants, and insecticides. In insects, CYPs play a major role in conferring resistance to various insecticides including DDT. In Drosophila and other insects, DDT-resistant strains exhibit increased expression of multiple P450 genes; however, the mechanism of overexpression is unknown. Since many CYP genes including Cyp6a8 of Drosophila are induced by caffeine and other xenobiotics, these chemicals are used as tools to understand the regulation of these genes. Previously it was shown that the 0.8-kb (-1/-732) and 0.2-kb (-1/-170) …

Nuclear Receptors In Ecdysone-Mediated Programmed Cell Death In Drosophila Melanogaster, Ritika Sehgal

Masters Theses

The steroid hormone ecdysone plays vital roles during Drosophila development. Pulses of 20E during Drosophila life cycle function as temporal cues, signaling the onset of metamorphic processes, including the stage specific programmed cell death of larval tissues. Ecdysone is the critical developmental cue orchestrating the metamorphic reformation of CNS, resulting in the formation of adult-specific neural circuitry. Ecdysone signaling is transduced by a heterodimeric receptor complex formed between two nuclear receptors: EcR and Ultraspiracle (USP). There are 18 nuclear receptors known in Drosophila and EcR is the only receptor whose functions in neuronal PCD have been well recognized. Therefore, the …

Functional Cloning And Characterization Of Antibiotic Resistance Genes From The Chicken Gut Microflora, Wei Zhou

Masters Theses

A recent study using human fecal samples in conjunction with a culture-independent approach revealed immense diversity of antibiotic resistance (AR) genes in the human gut microflora. We hypothesize that food animal gut microflora also contain diverse and novel AR genes which could contribute to the emergence and transmission of AR in pathogens important in animal and human health. To test this, we examined AR reservoir in chicken gut microflora using a metagenomic, functional cloning method. Total genomic DNA was extracted from individual cecal contents of two free range chickens and two conventionally raised chickens. The DNAs were physically sheered into …