Genetics and Genomics Commons^™

Genetic Underpinnings Of Novel Trait Development In A Euwallacea-Fusarium Mutualism, Elaina J. Spahr

Graduate Theses, Dissertations, and Problem Reports (ETD)

Evolutionary Developmental Biology seeks to answer fundamental questions about the mechanisms underlying the evolution and innovation towards increasing structural complexity within the body plan. The ambrosia symbiosis, a polyphyletic group of xylem-feeding beetles, provides a wealth of diversity in novel pouch-like structures called mycangia. This diversity could serve as a rich model for understanding how mutualisms may prompt structural innovation and diversification in a host organism. The ambrosia symbiosis has become a fast-growing research subject in entomology and forest pathology but has yet to experience the same attention under the lens of evolutionary developmental genetics.

Development of mycangia was examined …

A Tool For Biometric Interpretation Of Forensic Str Dna Profiles, Ahmad Jamal Baroudi

Graduate Theses, Dissertations, and Problem Reports (ETD)

Rapid DNA biometric identification applications are becoming more essential and widely used in human identity validation processes. Despite their powerful identification capabilities, processing a sample to generate a forensic DNA profile still takes longer compared with other rapid biometric technologies. Methods used to speed up the analysis could lead to signal artifacts similar to those arising from low copy or degraded DNA samples, making the electropherogram unsuitable for forensic interpretation and analysis. The goal of this research effort is to apply biometrics and mathematical approaches to forensic STR (Short Tandem Repeat) profiles. To accomplish this goal, a multi-function software tool …

Tree Species Influence On Microbial Functional Gene Abundance And N Cycling In Riparian Soil, Elizabeth Matejczyk

Graduate Theses, Dissertations, and Problem Reports (ETD)

Little is known about how above-ground vegetation may differentially influence the below-ground microbial community structure, abundance, and function. Abundance of soil microbial N cycling genes responsible for nitrification (amoA), denitrification (nirK and nirS), and nitrous oxide reduction (nosZ) may vary with tree species and increasing N availability, and these variables may be used to predict production of NO₃^- and N₂O from soil. Variability of nitrification and denitrification rates have also been linked to tree mycorrhizal associations, with soil beneath tree species associated with arbuscular mycorrhizal (AM) exhibiting greater denitrification rates …

Effects Of 4-Methylcyclohexanemethanol On Stress Response Pathway Regulators, In Saccharomyces Cerevisiae, Suk Lan Ser

Graduate Theses, Dissertations, and Problem Reports (ETD)

Hydrotropes are small molecules capable of inducing liquid-liquid phase separation by altering the solubility and conformation states of organic compounds that are increasingly becoming important in organizing chemical reactions and regulating complexes. They prevent protein aggregation causing these proteins to form condensates. Mediator, a highly conserved multi-subunit complex, plays an important role in transcription. Med15, a subunit found within the tail domain of the Mediator complex, works with stress-induced transcription factors and is regulated by many kinases, including CDKs and the AMP kinase, Snf1. Living cells respond by changing molecular and cellular pathways when they are exposed to stressful conditions. …

Maternal Engineered Nanomaterial Inhalation Exposure: Cardiac Molecular Reprogramming In Progeny Through Epigenetic And Epitranscriptomic Mechanisms, Amina Kunovac

Graduate Theses, Dissertations, and Problem Reports (ETD)

Introduction: Nano-titanium dioxide (TiO₂), a prominently utilized engineered nanomaterial (ENM), is being employed for its physiochemical properties in several fields including the food industry, manufacturing, and biomedicine. As the prevalence of this ENM, and other particulate matter grows, so does the concern for antagonistic consequences on long-term heart function in vulnerable populations, which until now have not been investigated. Due to the reliance of the heart on the ATP generating capacity of mitochondria for contraction, understanding the role of mitochondrial bioenergetics and structure is pivotal in understanding the repercussions of particulate matter exposure during gestation. As the mass …

Initial And Advanced Stages Of Microbiota Establishment Within The Tsetse Fly, Miguel Eduardo Medina Munoz

Graduate Theses, Dissertations, and Problem Reports (ETD)

Symbiosis is a long-term physical association between two or more species, although little is known regarding its evolutionary origins, particularly at the genetic level. Tsetse flies are the vector of African trypanosomes, causative agents of Human and Animal African Trypanosomiases. Tsetse provide an ideal model for studying initial and advanced stages of symbiosis. Tsetse have a simple digestive tract microbiota primarily consisting of two bacteria; the ancient mutualist Wigglesworthia glossinidia and the recently acquired Sodalis glossinidius. This work presents a chronological study in evolutionary terms of the history of a microbial-insect association. First, I present concepts on symbiosis and …

The Receptor Basis Of Serotonergic Modulation In An Olfactory Network, Tyler Ryan Sizemore

Graduate Theses, Dissertations, and Problem Reports (ETD)

Neuromodulation is a nearly ubiquitous process that endows the nervous system with the capacity to alter neural function at every level (synaptic, circuit, network, etc.) without necessarily adding new neurons. Through the actions of neuromodulators, the existing neural circuitry can be adaptively tuned to achieve flexible network output and similarly dynamic behavioral output. However, despite their near ubiquity in all sensory modalities, the mechanisms underlying neuromodulation of sensory processing remain poorly understood. In this dissertation, I address three main questions regarding the mechanisms of one modulator (serotonin) within one sensory modality (olfaction). I begin by establishing a "functional atlas" of …

The Origin Of Novel Trait Inferred From Transcriptomic Analysis And A Targeted Gene Approach In The Beetle Horns., Naureen Fatima

Graduate Theses, Dissertations, and Problem Reports (ETD)

The origin of the evolutionary new trait (evolutionary novelty) and its subsequent evolution is of great interest for biologists in various fields, and beetle horns have been used to address this fundamental biological question. Previous studies on one of the horned beetle species, Onthophagus taurus, that utilized comparative gene expression analyses, suggested legs to be a strong candidate of the origin of horns. At the same time, their horns are secondary sexual traits whose development is regulated by the same gene (doublesex) as genitalia, which also originates from paired appendages such as legs. However, little is known …

Population Genetics Of A Reintroduced Fisher (Pekania Pennanti) Population In West Virginia, Caroline E. Harms

Graduate Theses, Dissertations, and Problem Reports (ETD)

Fishers (Pekania pennanti) were reintroduced in West Virginia in 1969 with no population wide genetic analysis ever having been conducted. Genetic analysis of reintroduced populations is vital to assess genetic diversity as an indicative of population viability. My objective was to collect fisher samples throughout West Virginia, nearby states where fisher may be migrating (PA and NY), and the New Hampshire source population to provide a full genetic interpretation of the reintroduced West Virginia population. Genetic analysis was used to measure genetic diversity, admixture or delineation of subpopulations, and effective population size. Sample location and genetic data were …

Evaluation Of The Performance Of Probabilistic Genotyping Software On Complex Mixture Samples, Kristen Newland

Graduate Theses, Dissertations, and Problem Reports (ETD)

Probabilistic genotyping systems use sophisticated algorithms to aid DNA analysts with complex mixture interpretation. These systems are used to generate a likelihood ration (LR) which is used to provide the analyst with the statistical weight of the match between an evidence profile and a known contributor. Complex mixtures occur from samples consisting of more than two contributors and samples that have experienced degradation or consist of low template quantity.

This study was performed to compare the performance of three mixture analysis software tools on the same set of samples to determine the capabilities of each software, false inclusions, and false …

Trees, Fungi, Insects: How Host Plant Genetics Builds A Community, Sandra Jeanne Simon

Graduate Theses, Dissertations, and Problem Reports (ETD)

Organisms, such as fungi and insects, can cause millions of acres of agricultural and forest damage, while others provide billions of dollars in ecological services such as education, aesthetic enjoyment, pollination, and gardening. Plant breeding and biotechnology can potentially help establish a balance between the proliferation of detrimental pests and attraction of beneficial insects. Variation in plant physiological and morphological characteristics are extremely important in the ability of host tissues to support many different types of organisms. When that variation is genetically heritable in a plant population, shifts in the underlying genes can have predictable consequences in structuring entire ecosystems. …

The Role Of Genotype In Saccharomyces Cerevisiae Resistance To 4-Methylcyclohexanemethanol, Michael C. Ayers

Graduate Theses, Dissertations, and Problem Reports (ETD)

The chemical 4-methylcyclohexanemethanol (MCHM) spilled in the Elk River near Charleston, WV in January 2014, impacting the drinking water of 300,000 residents. Initial studies on MCHM following the spill attempted to characterize its toxicological effects in animals, but largely ignored characterization of its effects on cellular pathways and metabolism. In this study, I used this chemical as a novel stressor for the model eukaryote S. cerevisiae to explore the relationship of genotype and stress phenotypes. Initial exploration characterized the stress phenotype of MCHM in yeast through growth assays, cell cycle analysis, and transcriptomic data. MCHM exposure caused cells to arrest …

Evolutionary Genomics Of Dynamic Sex Chromosomes In The Salicaceae, Ran Zhou

Graduate Theses, Dissertations, and Problem Reports (ETD)

Identifying the sex-determination region (SDR) and other genomic features of sex chromosomes are of great importance in the studies of the evolution of sex. However, the process of accurately identifying the size and location of the SDR is often difficult, even when a genomic sequence is available. This usually is hindered by large repetitive elements and a lack of recombination in the SDR. In this thesis, I assemble sex chromosomes with whole genomic sequencing data, identify SDRs and explore their genomic features in two sister species from the Salicaceae family. I also develop an interpretation of the lability of the …

The Exploration Of Nanotoxicological Copper And Interspecific Saccharomyces Hybrids, Matthew Joseph Winans Phd

Graduate Theses, Dissertations, and Problem Reports (ETD)

Nanotechnology takes advantage of cellular biology’s natural nanoscale operations by interacting with biomolecules differently than soluble or bulk materials, often altering normal cellular processes such as metabolism or growth. To gain a better understanding of how copper nanoparticles hybridized on cellulose fibers called carboxymethyl cellulose (CMC) affected growth of Saccharomyces cerevisiae, the mechanisms of toxicity were explored. Multiple methodologies covering genetics, proteomics, metallomics, and metabolomics were used during this investigation. The work that lead to this dissertation discovered that these cellulosic copper nanoparticles had a unique toxicity compared to copper. Further investigation suggested a possible ionic or molecular mimicry …

The Morphological, Physiological, And Genetic Underpinnings Of Intraspecific Salinity Tolerance In Sorghum Bicolor, Ashley N. Henderson

Graduate Theses, Dissertations, and Problem Reports (ETD)

Decreases in land quality and quantity threaten the efficient production of agriculturally and economically pivotal crops. Such reductions in arable lands are a consequence of population growth and urbanization, and often result in the introduction of various abiotic stresses. The most common abiotic stressors include water limitation (drought), water logging (over watering), poor water quality (salinity), and extreme temperatures (cold, frost, heat). Each of these stressors negatively impact plant growth, development, and yield. Soil salinity, specifically, is a considerable constraint affecting lands used in agriculture. Salts in the soil rise both naturally and through anthropogenic factors making the abundance a …

The Host Gatekeeper: Using The Flagellar Pathway To Understand Symbiont Host Adaptation, Adam R. Pollio

Graduate Theses, Dissertations, and Problem Reports (ETD)

The acquisition of microbial partners is a strategy used by a diverse group of arthropods to overcome ecological barriers that might normally make certain niches uninhabitable. The unique phylogenetic opportunities attainable from the natural experiment of the Sodalis-allied clade allow for better understanding of how molecular structures evolve through time. Here, we focus on the evolution of the flagellar synthesis pathway, due to its complexity and ability to diverge in response to ecological pressures. We used this molecular pathway and natural experiment to show that normal evolutionary outcomes associated with symbiosis (i.e., genome reduction) do not explain the predicted conservation …

Evidence Of Y Chromosome Long Non-Coding Rnas Involved In The Radiation Response Of Male Non-Small Cell Lung Cancer Cells, Tayvia Brownmiller

Graduate Theses, Dissertations, and Problem Reports (ETD)

Non-small cell lung cancer (NSCLC) is the number one cause of cancer related mortality in the United States and worldwide. Advanced and therapeutically resistant lung tumors contribute to the high rate of mortality from NSCLC, therefore there is a need for new methods of diagnosing and treating this disease. Long non-coding RNAs (lncRNAs) have been shown to be a crucial component of human molecular biology, regulating nearly every cellular pathway from chromatin condensation to transcription and translation. Furthermore, many lncRNAs have been classified as oncogenes or tumor suppressors, highlighting the various molecular mechanisms they are involved in regarding the formation …

Genetic And Biochemical Characterization Of Ergot Alkaloid Synthesizing Fungi And Their Symbionts, Matthew Duane Maust

Graduate Theses, Dissertations, and Problem Reports (ETD)

Ergot alkaloids are fungal tryptophan derived toxins which affect mammalian circulation and neurotransmission. These compounds are biosynthesized by a conserved genetic pathway, known as the ergot alkaloid synthesis (EAS) pathway by fungi belonging to the ascomycete families Trichocomaceae and Clavicipitaceae. Several Ipomoea species and related plants in the morning glory family harbor vertically transmitted symbiotic fungi in the genus Periglandula, also members of Clavicipitaceae, that produce ergot alkaloids. Metabolomic analysis of seeds identified a previously uncharacterized glycoside form of the pharmaceutically important ergot alkaloid, ergonovine. Several species belonging to the fungal genus Metarhizium have recently been shown to have the …

The Effects Of Internal Physiology On Polyphenic Horn Development In The Dung Beetle Onthophagus Taurus, Naomi Garrett Williamson

Graduate Theses, Dissertations, and Problem Reports (ETD)

An organism’s phenotype can be affected in development by alterations to gene expression based on environmental inputs. Nutrition is one such environmental input and the central regulator of development of large horn or small horn phenotypes in the dung beetle species, Onthophagus taurus. However, little is known about the nature of chemical compounds that are critical to this plastic horn development. To better understand these compounds, we are utilizing an untargeted metabolomic approach as well as a targeted gene approach. Through the metabolomic approach, it was uncovered that environmental conditions tend to have a greater impact on metabolomic composition …

Developmental Mechanisms For The Diversification Of Polyphenic Morphs In The Head Horn Of Onthophagine Beetles (Coleoptera: Scarabaeidae Onthophagus Taurus): Plasticity Through Nutrition, Logan Paul Zeigler

Graduate Theses, Dissertations, and Problem Reports (ETD)

Developmental plasticity is the phenotypic variation between organisms that is caused by environmental interactions affecting the developmental systems of organisms. The research focused primarily on nutrition-responsive developmental plasticity. In this research we used the nutritionally determined head horn development of Onthophagus taurus to better understand the developmental mechanisms and genetic underpinnings of nutrition-responsive trait development. We focused specifically on altering the availability of specific nutrition-related primary metabolites, cholesterol and palmitic acid, identified in the activity of The Hedgehog pathway, a critical pathway in head horn development. By altering diet composition using cholesterol, reducing transcript expression of an acyltransferase gene, rasp …

American Population Study Of Pigmentation Based Genotype Interpretation For Phenotypic Determination Of Hair And Eye Color Using Hirisplex, Emma Leigh Combs

Graduate Theses, Dissertations, and Problem Reports (ETD)

Currently the largest limitation with DNA evidence is that a comparison to a known source sample is required for any interpretation with the current methods. Simply put, if an unknown sample from a crime scene is collected and results in a profile, but there is no suspect or match from CODIS to compare it to, the profile is essentially useless and no information can be gained from it. Research has been performed within the area of forensic DNA phenotyping as a potential tool to aid in taking steps forward to use genotypic information as an investigative tool. Populations studies have …

The Effect Of Bovine Galectin-1, A Conceptus Secretory Protein, On The Endometrial Transcriptome, Lindsay Faye Grose

Graduate Theses, Dissertations, and Problem Reports (ETD)

Early embryonic loss in cattle is detrimental to reproduction thus, the profitability of both the beef and dairy industries. Therefore, an important aspect of study is to find techniques that beef or dairy producers could use to decrease early embryonic loss Galectin-1, the protein that was investigated in this research is important in modulating the maternal immune system in rodent and human early pregnancies by promoting fetomaternal immune tolerance. The role of galectin-1 within the reproductive tissues has not been thoroughly investigated in cattle. Galectin-1 is located in the caruncular and intercaruncular regions of the bovine endometrium, specifically the maternal …

Genetic Regulation Of The Elicitation Of Glyceollin Biosynthesis In Soybean, Md. Asraful Jahan

Graduate Theses, Dissertations, and Problem Reports (ETD)

Glyceollin phytoalexins are the pathogen-elicited defense metabolites that belong to the isoflavonoid family of molecules of soybean (Glycine max L. Merr). Phytophthora root and stem rot of soybean caused by Phytophthora sojae is a destructive disease throughout the soybean-growing regions worldwide causing devastating economic damages (globally $1-2 billion and over $250 million in the USA) every year. Engineering soybean plants that produce higher levels of glyceollins could confer resistance against this pathogen. Glyceollins also show anticancer and neuroprotective activities in mammals, therefore they are important for agriculture and medical research. Firstly, we were interested in understanding how biotic and …

Effects Of Commercial Formulations Of Glyphosate On Saccharomyces Cerevisiae, Apoorva Ravi Shankar

Graduate Theses, Dissertations, and Problem Reports (ETD)

Commercial formulations of glyphosate are among the most extensively used herbicides around the world. The active ingredient, glyphosate, targets the aromatic amino acid pathway. This pathway is absent in mammals, resulting in low toxicity. Different formulations contain varying adjuvants and surfactants, whose synergistic effects are yet to be extensively studied at the cellular level. In this study, I tested multiple commercial formulations that showed a variation in growth phenotype among different yeast strains. To gain a better understanding of response and resistance mechanisms at the genome and transcriptome level, I carried out an in-lab evolution study, along with a transcriptome …

Characterization Of Nodule-Specific, Slac And Mate Membrane Transporters In Medicago Truncatula, Lina Yang

Graduate Theses, Dissertations, and Problem Reports (ETD)

Legumes play a crucial role in sustainable agriculture because of their intrinsic ability to reduce atmospheric N₂ into NH₃ via symbiotic nitrogen fixation (SNF). SNF is carried out in the symbiosome, a quasi-organelle containing endosymbiotic rhizobial bacteria in the cytoplasm of infected cells of the nodule. Therefore, the bacteria are surrounded by a symbiosome membrane (SM), which is derived from the plant plasma membrane during infection. SNF requires constant nutritional exchanges between symbionts, including reduced carbon (dicarboxylates) from the plant for reduced nitrogen (NH₄⁺) from the bacteroids. This exchange of nutrients and signals is fundamental …

Enhancing Water Stress Tolerance In Floriculture Crops, Suejin Park

Graduate Theses, Dissertations, and Problem Reports (ETD)

Water deficit is one of the major constraints on plant growth and development, causing reduction of crop productivity. To minimize water loss, among many adaptation strategies, plants close their stomata to reduce transpiration. The stomatal closure is regulated by light, internal CO2 concentration, and plant hormones, mainly abscisic acid. Plants’ response mechanisms to water deficit are complex processes involving numerous genes and various signaling pathways. Floriculture crops are often exposed to water deficit during shipping and retailing, and these periods often result in damaged crops and profit loss. Understanding of plant responses to water deficit stress will provide us an …

Population Health Of Spotted Salamanders (Ambystoma Maculatum) In Created Vernal Pools: An Integrative Approach, Alice R. Millikin

Graduate Theses, Dissertations, and Problem Reports (ETD)

Habitat creation is an important tool for conservation to counteract habitat loss and degradation. Vernal pools are susceptible to destruction due to limited detection, protection, and regulation. These wetlands provide fishless breeding habitat for many amphibian species including spotted salamanders (Ambystoma maculatum) in eastern North America. Determining whether created vernal pool habitat is successful is often determined by demographic data of colonizing populations. I suggest that hormone levels, population genetics, and disease prevalence can improve our understanding of population health in created habitat. The goal of this dissertation was to assess the health of spotted salamander larvae in …

Association Genetics And Local Adaptation Of Populus Trichocarpa Torr. & Gray, Hari Bahadur Chhetri

Graduate Theses, Dissertations, and Problem Reports (ETD)

A major goal in plant science is overcoming the recalcitrance of plant biomass to cellulose extraction, to enable efficient production of cellulosic biofuel. We have started to understand the genetic basis of some important traits such as cell wall chemistry, but we do not know anything about the key structural and functional traits such as wood anatomy that greatly affect plant biomass recalcitrance. Furthermore, biofuel feedstocks have to be adapted to varied environmental conditions to ensure high productivity in plantations, but little is known about the molecular mechanisms underlying local adaptation. With the advancement in sequencing and genotyping technologies, association …

Glial Cell Expansion And Intercellular Signaling In The Developing Medial Nucleus Of The Trapezoid Body (Mntb), Ashley N. Brandebura

Graduate Theses, Dissertations, and Problem Reports (ETD)

Neural circuit formation is a complex process involving coordinated communication between neurons, glia and vascular-associated cells (VACs). Each cell type is responsible for a unique transcriptional and translational contribution to tissue maturation. Deciphering the intercellular signaling patterns which guide neural circuit formation during normal development is thus an essential step in understanding which components of neural circuit formation go awry in neurodevelopmental disorders. The medial nucleus of the trapezoid body (MNTB), located in the auditory brainstem, was used as a model system to study the dynamics of neural circuit formation because it contains a mostly homogeneous population of postsynaptic neurons …