Genetics and Genomics Commons^™

A Genetic Analysis Of The Rare Endemic Astragalus Ripleyi Barneby, Juan Antonio Jaramillo-Chico

Master's Theses

Astragalus ripleyi Barneby is a rare endemic species found in the San Luis Valley of the southern portions of the Rocky Mountains in Colorado and New Mexico. Though not federally listed as endangered, the species is on the Bureau of Land Management’s Sensitive Species List, warranting protection and continued management. This study aims to provide information about the genetic health of the species to inform conservation efforts and provide updated management recommendations. A genetic health analysis was conducted investigating the levels of diversity present in the species, how genetic diversity is structured across the known range of the species and …

Marine Heatwaves And Fish Reproduction: Endocrine Responses In The Eurythermal Sheepshead Minnow (Cyprinodon Variegatus), Isabel Villafuerte

Master's Theses

Marine heatwaves associated with climate change are increasing in frequency and severity, posing significant threats to fish populations in shallow habitats such as estuaries and salt marshes. Because temperature is a primary regulator of fish reproduction, understanding how heatwaves affect reproductive physiology is critical for anticipating the biological consequences of ongoing climate change for coastal fishes. Here we examined how simulated heatwave conditions affect the reproductive hypothalamic-pituitary-gonadal (HPG) endocrine axis in the estuarine sheepshead minnow (Cyprinodon variegatus), a eurythermal fish well suited to studying thermal stress responses in estuarine environments. Adult sheepshead minnows acclimated to a daily oscillating …

Large Scale Kmer-Based Proteomic Analysis: An Application Towards Evolutionary Constraint Discovery, Matthew Chak

Master's Theses

Large protein databases now make it possible to study short peptides across natural protein sequence space at unprecedented scale, but exhaustively counting k-mers across billions of protein sequences remains computationally difficult. This thesis develops an exact amino-acid k-mer counting method based on direct addressing, in which fixed-length amino-acid strings are encoded as base-20 integers and updated with a sliding-window recurrence. By avoiding key storage and collision resolution, this approach removes overhead inherent to hash-map-based methods when the k-mer space is sufficiently dense. A memory analysis shows when direct addressing is preferable to open-addressing hash tables, and expected-saturation calculations motivate its …

Investigating Cryptic Diversity In The Hawaiian Endemic Plant, Psychotria Mariniana (Rubiaceae), Uyen Thi Hoang Nguyen

Master's Theses

Islands, with their isolation and steep environmental gradients, serve as natural laboratories for studying speciation. Molecular phylogenetic and population genetic methods utilizing Next-Generation Sequencing (NGS) have revolutionized our ability to document patterns of genetic divergence and diversity. Cryptic diversity, genetically distinct populations that were previously unrecognized as unique, and cryptic speciation, where divergent genetic populations may be deserving of status as unique species, have been observed in many taxa. The Hawaiian Islands provide an ideal setting for studying divergence and speciation due to their extreme isolation, known ages, and volcanic origin. Previous work has investigated the evolutionary relationships of the …

Investigating The Taxonomic Uncertainties Of Potentilla Rupincola, Natalie Elizabeth Hieber

Master's Theses

Landscape stewardship is an integral role for land managers that becomes more important when rare or endangered species occur within managed areas. Conservation across the landscape is a primary concern for land managers, but resources allocated for conservation can be limited due to many competing goals. Taxonomic uncertainty surrounding rare and endangered taxa, particularly plant taxa, that have historically been classified solely using morphological features further complicates conservation planning. One such taxon is Potentilla rupincola, a rare plant endemic to the eastern Rocky Mountains in Colorado. For over a century, botanists have debated whether P. rupincola is a distinct species …

Effects Of Urbanization On The Population Genetics And Morphology Of The White-Footed Mouse (Peromyscus Leucopus) Across An Urban–Rural Gradient, Sydney A. Morton

Master's Theses

Urbanization alters landscapes in ways that can reshape wildlife populations by changing habitat connectivity, resource availability, and selective pressures. To investigate how urbanization influences both genetic differentiation and morphology in small mammals, I examined Peromyscus leucopus (PELE) across an urban–rural gradient in northern Georgia. Using RADseq SNP data from PELE individuals across 13 sites, I quantified pairwise genetic differentiation (F_ST) and tested how various environmental variables, including impervious surface cover, human population density, and tree canopy cover, predict genetic differentiation after accounting for geographic distance. Genetic differentiation increased with geographic distance and, after controlling for isolation by …

Gene Expression Of Anthocyanin Pigments In The California Native Plant Leptosiphon Parviflorus: Interactions Between Flower Color Morphology And Abiotic Stressors, Weston Gonor

Master's Theses

For plants to survive in harsh conditions imposed by abiotic stressors, they must develop mechanisms of adaptation. One of the common types of adaptation seen in plants is the production of anthocyanin pigments, which have been shown to protect plants from UV radiation, metabolic stress, and drought. In this study, we used the flower color polymorphic species Leptosiphon parviflorus to investigate the role of anthocyanin pigments in protecting plants from abiotic stress. To accomplish this, RNA samples were taken from flower, leaf and root tissue of different flower color morphs of Leptosiphon parviflorus (Polemoniaceae) grown in high magnesium and water …

Enhancing Preparedness: A Genetic Study Of Sar-Cov-2 And Other Microbial Public Health Threats In Wastewater From A College Town, Christian N. Hutchinson

Master's Theses

Problem

The SARS-CoV-2 (COVID-19) pandemic revealed both the systemic vulnerabilities of our healthcare system as well as the importance of timely, localized data for informing public health responses. Traditional testing approaches were essential but often failed to capture the full extent of viral spread, especially in those with mild or asymptomatic conditions that relied on at home testing. This underreporting hindered effective allocation of resources and made developing effective intervention strategies difficult. We also realized the potential for wastewater surveillance to be applied to tracking antimicrobial resistance gene markers. Taken together, this approach should have important implications for improving public …

Topodino: Self-Supervised Topological Representation Learning For Neuronal Morphologies, Yasser Binbisher

Master's Theses

Neuronal cell types are categorized by transcriptomic identity, yet their morphological heterogeneity defies this classification. In response, researchers have adopted unsupervised graph representation learning as a tool to reveal morphological variation within single-class transcriptomic types. However, the complex geometry of neuronal morphology—especially long axons and dense dendrites—challenges graph neural networks, which struggle with message propagation across extended structures. To mitigate this, current approaches enforce sub-sampling on neuronal graphs and omit axons entirely, sacrificing critical biological features for computational efficiency. To overcome this trade-off, this thesis introduces TopoDINO, a self-supervised, topology-aware representation learning model designed to preserve the full hierarchical organization …

Identification Of Methylation Patterns, Associated Dna Methylating Proteins, And Methyltransferase Inhibitors On The Promoter Regions Of Dax-1, Brandon Tyler Toy

Master's Theses

The DAX-1 gene (Dosage-Sensitive Sex Reversal, Adrenal Hypoplasia Congenita, Critical Region on the X chromosome, gene 1) encodes for an orphan nuclear hormone receptor and its mutation is implicated in multiple diseases including congenital adrenal hypoplasia, adrenal cancer, and breast cancer. Previous research has linked DAX-1 downregulation to tumor initiation in breast tissue, suggesting the gene acts as a tumor suppressor with respect to breast cancer. Additional studies completed by the Tzagarakis-Foster laboratory have shown that methylation of the DAX-1 promoter region is heavily influential in breast cancer development, with release of epigenetic repression resulting in slowing of cellular proliferation …

Tricolored Bat (Perimyotis Subflavus) Population Genetic Structure In The Southeastern United States, Laura Henderson

Master's Theses

Tricolored bats (Perimyotis subflavus) have experienced substantial population losses from white-nose syndrome (WNS), a disease caused by the pathogenic fungus Pseudogymnoascus destructans (Pd) which infects hibernating bats. Determining population genetic structure helps assess genetic diversity and the impacts of wildlife threats to populations. Pre-WNS data shows weak-to-negligible structure and panmictic P. subflavus populations at core portions of their range. However, current genetic data from their southeastern U.S. range is lacking. I sought to determine whether recent genetic data help resolve genetic structure among southeastern populations and assess genetic differences at two stages of impact: post-WNS and …

Reports Of Autosomal Recessive Disease And Consanguineous Mating Within The Human Population, Johnathon L. Schluter

Master's Theses

It is anecdotally evident when investigating published reports of autosomal recessive disease that a substantial number of cases are the result of related (consanguineous) mating. This research seeks to quantify the percent of manuscripts describing autosomal recessive diseases published between 2000 and 2020 in which consanguineous mating is indicated. We analyzed 602 peer-reviewed manuscripts to identify the percentage of cases presented in which consanguineous mating was indicated, the underlying genes (novel gene or new mutation) and geographical region. These papers were accessed through a specific set of parameters on the free access PubMed Central (PMC) database. A total of 552 …

Regulation Of Intracellular Sorting Of The Bruno Protein In Drosophila Flight Muscles, Travis Main

Master's Theses

Understanding mechanisms of intracellular sorting is a fundamental inquiry of cell biology. We used the B-body and protein Bruno (Bru) as a model to study the formation of nuclear domains that are membraneless organelles inside the cell nucleus. Specifically, we sought to identify protein sequences that regulate Bru's affinity to B-bodies and protein aggregation. We generated various Bru mutants and subsequently tested them in vivo using fluorescence microscopy. We found that the protein solubility of Bru is determined through an interplay of RNA recognition motifs (RRMs) and intrinsically disordered regions (IDRs). Using truncation analysis, we identified a 31-amino acid region …

The Role Of B Cell Activation State And Sex In Aryl Hydrocarbon Receptor Mediated Induction Of Chemokine Receptor 9 And Alpha4beta7 Expression In Vitro, Logan Bauerle

Master's Theses

Defense of mucosal tissues from microbial infection and allergy is reliant on continual production of antibodies. The aryl hydrocarbon receptor (AhR) is known to regulate B cell development and is associated with suppression of systemic humoral immunity. Recent attention has been paid to the role of the AhR in altering expression of cell adhesion molecules (CAMs). B cells express CAMs and chemokine receptors to migrate around the body for localized secretion of antibodies. AhR agonists promote B cell migration to the small intestine through upregulation of chemokine receptor 9 (CCR9) and integrin α₄β₇. Both the AhR …

Species Delimitation Of Slimy Salamanders, Plethodon Kisatchie And Plethodon Mississippi, Across The Lower Mississippi River, Brock Hunter Stevenson

Master's Theses

Species are fundamental units of biodiversity yet delimiting species can be challenging. Slimy Salamanders of the Plethodon glutinosus species complex are a classic example of cryptic species for which species boundaries and relationships have proved difficult to determine. Once thought to be a single species ranging across the eastern United States, protein analysis revealed high genetic divergences among geographically distinct groups of populations, leading to 16 species being recognized within the group. Two of these species, the Louisiana Slimy Salamander (Plethodon kisatchie) and the Mississippi Slimy Salamander (Plethodon mississippi), are closely related but occur on opposite sides of the Mississippi …

Genetic Parameters For Heat And Salinity Stress Tolerance In Northern Gulf Of Mexico Eastern Oyster, Crassostrea Virginica, Paul Mcdonald

Master's Theses

Summer mortalities in Gulf of Mexico eastern oysters have been linked to excessively high temperatures, and chronic exposure to low salinity. In this study, the feasibility of improving tolerance to these two stresses by selection was evaluated in common garden experiments employing a pool of 160 families. Heat stress tolerance was evaluated in seed (3.5 months) and adults (14 months) by applying a sustained temperature of 38-39 °C until all oysters expired. Low salinity challenges on juveniles (9 months) and adults (15 months) applied a salinity of 2.5 psu. Survival duration of individual oysters during challenges was recorded and tissue …

Annotation Of Non-Model Species’ Genomes, Taiya Jarva

Master's Theses

The innovations in high throughput sequencing technologies in recent decades has allowed unprecedented examination and characterization of the genetic make-up of both model and non-model species, which has led to a surge in the use of genomics in fields which were previously considered unfeasible. These advances have greatly expanded the realm of possibilities in the fields of ecology and conservation. It is now possible to the identification of large cohorts of genetic markers, including single nucleotide polymorphisms (SNPs) and larger structural variants, as well as signatures of selection and local adaptation. Markers can be used to identify species, define population …

Integrative Analyses Of Genomic And Metabolomic Data Reveal Molecular Mechanisms Associated With Uterine Disease Traits In Transitioning Dairy Cattle, Leanna C. Sanchez, Mohammed Abo-Ismail, Daniel Peterson, Fernando Campos-Chillon

Master's Theses

The metritis complex (MC), characterizing post-partum uterine diseases in dairy cattle has negative implications on animal welfare, production efficiency, and the economic stability of the dairy industry. The studies in this thesis aimed to investigate the genetic architecture of the metritis complex and identify genomic regions and metabolites associated with the development of MC. Thereby enhancing our understanding of the biological pathways and molecular mechanisms involved in the pathophysiology of MC during the transition period in Jersey and Holstein dairy cattle.

Chapter 2 sheds light on the previous work done on MC. The goals of this review were to (1) …

Comparative Analysis Of Rhizosphere And Endosphere Microbiome Of Different Blueberry Species (Vaccinium Sp.), Niladri Bhowmik

Master's Theses

Blueberries are an important agricultural commodity in all over the United States. Due to its health benefits, there is a huge demand globally, thus expanding the industry. Breeding programs are essential to maintain such industries. Challenges that play a role in contemporary breeding programs are various biotic and abiotic stress factors. Studies have shown that microorganisms are recruited by plants to alleviate them during stressful conditions. Though blueberries have been cultivated for about 100 years, how the microbiome has been affected due to this is poorly understood. We hypothesized that interspecific crosses and artificial selection have significantly changed the microbiome …

Population Genetics Of Cownose Rays, Rhinoptera Spp. In The Western Atlantic, Helen Weber

Master's Theses

Using molecular tools (e.g., the NADH subunit II mitochondrial gene), this study was the first to document the Brazilian cownose ray, Rhinoptera brasiliensis, within the northwestern Atlantic (NWA), and was the first study to examine population structure in R. brasiliensis within the NWA or northern Gulf of Mexico (GMX), revealing novel insights into the population biology of the animal and extending its range by nearly 1,500 km. This study also examined the sympatrically occurring American cownose ray, R. bonasus, and found population structure between the NWA and the GMX and the NWA and the southwestern Atlantic (SWA). High …

Distribution And Ecological Function Of Pacific Lamprey In The San Luis Obispo Creek Watershed, Parker Kalan

Master's Theses

Pacific lamprey (Entosphenus tridentatus) is an endemic species to coastal watersheds along the Pacific Rim in North America and Asia. The species' geographic distribution is retracting and has not been mapped precisely, and the ability for the species to provide ecosystem services, such as water filtration, for supporting watershed management has not been tested. The San Luis Obispo Creek watershed, California, USA is at the southern end of Pacific lamprey’s retracting distribution, and the San Luis Obispo watershed is impacted by degraded water quality, making investigation of Pacific lamprey in the San Luis Obispo Creek watershed of direct …

Investigation Of Dna Variability And Phylogenetic Relationships Of Perlesta (Plecoptera: Perlidae) In Mississippi, James C. Valentine, Mac H. Alford

Master's Theses

The genus Perlesta Banks, 1906 (Plecoptera: Perlidae) consists of 35 species, 33 native to the United States and Canada and two native to China. For over a century these small, brown stonefly adults and freckled yellow nymphs have gone by the name of the type species of the genus, Perlesta placida, but taxonomic work in the genus since 1989 has resulted in the recognition of additional species. These species were mostly recognized and described using morphological characteristics, but two areas that are lacking include (1) linking nymphs to adults and (2) phylogenetic analysis of all species occurring in Mississippi …

Reassessment Of Species Boundaries And Phylogenetic Relationships In The Desmodium Ciliare Complex (Fabaceae) Using Morphological And Dna Data, Joshua Wilkinson

Master's Theses

Desmodium (Beggar's ticks) is a generally weedy genus of approximately 280 species in the angiosperm family Fabaceae (Subfamily Papilionoideae, Tribe Desmodieae) characterized by indehiscent loments constricted into segments. Within the Southeastern U.S., the Desmodium ciliare group is one of two Desmodium species complexes that have been historically difficult, with much argument about the limits of species and the role of hybridization. There are three commonly recognized species within the D. ciliare group, D. ciliare (Muhl. ex Willd.) DC., Desmodium marilandicum (L.) DC., and D. obtusum (Muhl. ex Willd.) DC., with two supposed hybrids in addition to the …

Dna Methylation Patterns Of Line-1 Elements Specific To Hc21p In Cancer Cells, Dametria Jetters

Master's Theses

Long Interspersed Nuclear Elements (LINEs) are retrotransposons. They function by making a cDNA copy, reverse-transcribing it into DNA and reinserting itself back into the genome; thereby, increasing its copy number. Sequencing of the human genome revealed that LINEs (L1) are underrepresented on the short arm of human chromosome 21 (HC21), but it is enriched in full-length copies. A number of previous studies have investigated the DNA methylation patterns of L1s in cancer cells, but these studies are typically done in euchromatic regions. The heterochromatic short arm of HC21 is primarily composed of heterochromatin. However these regions can be targeted for …

Lotus: A Web-Based Computational Tool For The Preliminary Investigation Of A Novel Mst Method Utilizing A Library Of 16s Rrna Bacteroides Otus, Ginger Dewitte

Master's Theses

Microbial Source Tracking (MST) is a field of study that attempts to identify the source of fecal contamination in waterways in order to assist with development of remediation strategies. Biologists at Cal Poly Center for Applications in Biotechnology (CAB) are developing a new MST method using microbes from the genus Bacteroides. Bacteroides species are host-specific microorganisms that can theoretically be used to trace back to a single host species. After fecal samples are collected, biologists use Next-Generation Sequencing (NGS) techniques to obtain only the genetic sequences of microorganisms belonging to the phylum Bacteroidetes. Investigators hypothesize that similar sequences belong …

Assessment Of Genetic Diversity In Largetooth Sawfish, Pristis Pristis, Populations Over The 20th Century, Ann Fearing

Master's Theses

The Critically Endangered Largetooth Sawfish, Pristis pristis, experienced global declines in range and abundance over the past century and Australia is now their last stronghold. This research aimed to understand whether these declines have been accompanied by a reduction in levels of genetic diversity. Using P. pristis tissue samples sourced from natural history specimens, three fragments (616-bp, 386-bp, 141-bp) in the mitochondrial DNA (mtDNA) control region were PCR-amplified. At each fragment, significant genetic structure was found in P. pristis overall (Φ_ST=0.946, N=9; 0.813, N=54; 0.771, N=99). The Indo-West Pacific and Atlantic/Eastern Pacific each harbor genetically distinct lineages of …

Development And Use Of An Environmental Dna Tool To Monitor Recovery Of The Critically Endangered Smalltooth Sawfish, Pristis Pectinata, In The Northwest Atlantic, Ryan N. Lehman

Master's Theses

The Critically Endangered Smalltooth Sawfish, Pristis pectinata, was once common in the tropical and subtropical waters of the Atlantic Ocean; however, following global declines in range and abundance over the past century, individuals were restricted to the waters of south and southwest Florida (SWFL) by about the 1980’s. Recently, public encounter reports have emerged in historically occupied habitats in United States waters, suggesting individuals are present in, or re-occupying, these areas, although the status of P. pectinata outside of SWFL is not currently well understood. Targeted environmental DNA (eDNA) surveys were chosen to assess the occurrence of P …

Interrelationships Among Monorchiid Trematodes With Special Emphasis On Some Northwestern Atlantic Genera, Apryle Panyi

Master's Theses

The Monorchiidae Odhner, 1911 is a cosmopolitan family of flukes (Trematoda: Digenea) comprising species that parasitize the digestive tract of estuarine and marine fishes as adults. Compared with other oceans, recent morphological or molecular taxonomic work conducted on monorchiid species from the northwestern Atlantic Ocean has been sparse (Manter, 1931; Overstreet, 1969; Andres et al., 2018; Wee et al., 2018, 2019, 2020). Therefore, the present work investigated the interrelationships of some monorchiids from the northwestern Atlantic Ocean with emphasis on several genera and investigated if Lasiotocus minutus (Manter, 1931) Thomas, 1959 constitutes a complex of cryptic species. New morphological and …

Using Crispr-Cas9 As A Restriction Enzyme, Zack Crawley

Master's Theses

Restriction digests are a commonly utilized process for cleaving DNA at specific, but relatively common sites. Restriction enzymes have widespread use in DNA manipulation. CRISPR/Cas9 is a recently identified endonuclease which utilizes a customizable guide sequence to recognize and cut specific ~20 bp sites located in a DNA sequence. This preliminary research aimed to exploit the potential benefit of DNA restriction using the CRISPR/Cas9 procedure through alterations of different components involved in that system. We sought to refine existing CRISPR/Cas9 protocols and make a budget friendly, user-selectable CRISPR/Cas9 restriction digest protocol. The motivation for this research was to simplify and …

Dna Methylation Patterns Of Repetitive Elements On Hc21, Navy Neang

Master's Theses

Cancer is one of the most prominent diseases resulting in death, thus the need for early detection remains essential to its treatments. It is usually associated with DNA methylation changes during tumorigenesis. While many studies focus on euchromatin, some studies have looked at the methylation changes in heterochromatin, since the methylation changes of repetitive elements is common and they contribute to karyotypic instability leading to enhanced chances for more mutations in tumor progression. Using bisulfite PCR and HC21 as a model, this study examines the DNA methylation changes of three repetitive elements in prostate cancer, NBL2, satellite I subfamilies, and …