Genetics Commons^™

Overview And Methods Of Molecular Paleontology: A Review, Shelby Touchstone

Williams Honors College, Honors Research Projects

Molecular paleontology—the study of ancient biomolecules preserved in fossils and sediments, including ancient DNA, lipids, and proteins—has motivated researchers since the 1950s, inspiring both scientific inquiry and broader cultural imagination. Think Jurassic Park. This honors thesis presents a comprehensive review of the history, current state, and methods of the field of molecular paleontology. Drawing on peer-reviewed literature and scholarly resources accessed through databases such as EBSCO and Bierce library, this review examines key techniques such as Next Generation Sequencing and amino acid racemization and will go over limitations and controversies in the field. It will also explore potential new …

Microarray Analysis Of Human Abdominal Aortic Aneurysm With Emphasis On Cardiovascular Genes Revealed Differentially Expressed Genes, Song Lu, Li Ping Li, John V. White, Xiaoying Zhang, Ifeyinwa Nwaneshiudu, Adaobi Nwaneshiudu, Nectaria Ntaoula, John Gaughan, Dimitri S. Monos, Wan-Lu Lin, Charalambos C. Solomides, Emilia L. Oleszak, Chris D. Platsoucas

Biological Sciences Faculty Publications

Background/Aim: We examined gene expression profiles in abdominal aortic aneurysm (AAA) lesions vs. normal aortas by cDNA microarray and real-time quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR).

Materials and Methods: Phosphorus (32P)-labeled cDNA from AAA specimens (mean AAA size 6.65 cm) and normal aortas were hybridized with a 588-gene microarray primarily of the cardiovascular system. The results were validated by qRT-PCR.

Results: A total of 35 out of the 588 genes were differentially expressed, with either log2 ratio of AAAs/controls ≥1 (upregulated; 20 genes) or ≤−1 (downregulated; 15 genes) in AAA lesions vs. normal aorta, and 25 of these were significantly …

Recurrence And Co-Occurrence Of Enhancer-Promoter Interactions Across Human Samples, Satvik Gunjala

Honors Undergraduate Theses

Experimental mapping of enhancer-promoter interactions (EPIs) is resource-intensive, and current computational prediction methods struggle with intrinsic genomic complexity and reliance on limited training data. To address this bottleneck and provide insights for improved computational methods, this study systematically analyzed chromatin contact datasets to investigate the recurrence and co-occurrence of enhancer-promoter interactions across human samples. Putative interactions were evaluated across two HiChIP datasets comprising 218 total samples and one Hi-C dataset comprising 266 samples to assess recurrence across samples and assess sequencing depth related to unique EPIs. Additionally, a preliminary item-based collaborative filtering recommender model was developed to assess co-occurrence patterns …

Regulation And Localization Of Urease In Sporosarcina Pasteurii: Implications For Coastal Protection, Amar Kosovac

UNF Graduate Theses and Dissertations

Coastal erosion is a persistent problem exacerbated by global warming. As the climate changes, the southeastern coast is likely to experience an increased frequency and intensity of storms, which can significantly damage the coastline. The coast is crucial as it serves as a habitat for numerous animals, supports tourism, and underpins infrastructure. Microbially induced calcite precipitation (MICP) is a novel method to enhance erosion resistance in sandy soils using the non-pathogenic bacterium Sporosarcina pasteurii. S. pasteurii produces urease to catalyze urea into bicarbonate, which drives the precipitation of calcium carbonate. Maximal expression of urease is a limiting factor for …

The Forensic Implications Of Hydrochloric Acid (Hcl) Exposure On Dna Preservation In Human Teeth, Shaelyn Lee Zimmerman

Graduate Student Theses, Dissertations, & Professional Papers

Identity is a human right, and forensic anthropological methods are often aimed at returning identity to decedents. Three main pathways are used for the identification of human remains: fingerprints, dental records, and DNA analysis. Identification efforts may be hindered when perpetrators attempt to obscure the victim’s identity. In cases where corrosive substances, such as hydrochloric acid (HCl) are used, dental comparison and fingerprinting often fail and genetic analysis becomes the best chance of achieving personal identification.

Previous studies have shown teeth are an excellent source of DNA. Large, multi-rooted teeth, such as molars, are often preferred because they contain the …

The Disruption Of Gastrointestinal Hormonal Control Of Digestion In Nile Tilapia By Omeprazole, Rema Abutaha

Theses and Dissertations (Comprehensive)

Stomach acidity is a critical feature of the digestive system, facilitating the breakdown of protein through the activation of the protease pepsin. Gastric acid is secreted by H⁺/K⁺ ATPase, the gastric proton pump. A previous study on Nile tilapia (Oreochromis niloticus) showed that inhibiting the production of stomach acid using the proton pump inhibitor omeprazole (omz), reduced growth that correlated with an acceleration of the rate of gastric emptying. This contrasts with omz exposure studies in mammals in which there is a delay in gastric emptying and no impact on growth. To understand the mechanism …

Acute Fatty Liver Of Pregnancy And Fetal Fatty Acid Oxidation Disorders: A Systematic Review, Dante Varotsis, Sarah Araji, Rebecca Horgan, Jennifer E. Powel, Rodney Mclaren Jr., Brian Kirmse, Mona Makhamreh, Huda B. Al-Kouatly

Department of Obstetrics & Gynecology Faculty Publications

OBJECTIVE:

To evaluate the association between maternal acute fatty liver of pregnancy (AFLP) and fetal fatty acid oxidation (FAO) disorders and to define the clinical and genetic characteristics of mothers with AFLP and their fetuses affected by FAO disorders, we performed a systematic literature review of all reported cases of AFLP that underwent genetic testing for FAO disorders.

DATA SOURCES:

We searched PubMed, Ovid MEDLINE, Cochrane Library, CINAHL (EBSCO), Scopus, and ClinicalTrials.gov. Terms included were related to AFLP and FAO testing.

METHODS OF STUDY SELECTION:

We conducted a systematic literature review from inception through May 18, 2025, to evaluate the …

Comparative Analysis Of Six New Chloroplast Genomes In Platanthera (Orchidaceae) Enhances Understanding Of Its Diversification, Lisa E. Wallace, Martin I. Batalla, Matthew Maisonave

Biological Sciences Faculty Publications

Platanthera is among the most diverse genera of orchids in north temperate regions, with high species diversity in Asia and North America. Despite many ecological studies in this group, little is known about its genomic diversity. Here, we report the newly annotated chloroplast genomes from six species in subgenus Limnorchis from North America and compare them with plastomes published for Platanthera species from Asia and Europe. We found that the plastomes of species in subg. Limnorchis are among the smallest reported for Platanthera thus far. While major structural differences were not detected in the newly sequenced species, ndh genes were …

Larval Genomics As A Viable, Fisheries-Independent Tool For Investigating Population Structure In Tropical Pacific Tunas, Jacob E. Jaskiel, Hannah E. Aichelman, Giulia Anderson, Louw Claassens, James E. Fifer, Christina M. Hernandez, Alexa K. Huzar, Joel K. Llopiz, Jan W. Witting, Sean P. Mullen, Randi D. Rotjan

Biological Sciences Faculty Publications

Understanding how dispersal, life history, and environmental variability shape genetic connectivity in the open ocean remains a central challenge in evolutionary biology. Highly migratory marine predators like tunas have traditionally been considered genetically homogeneous across ocean basins, yet emerging genomic evidence suggests that cryptic population structure can persist even in species with high gene flow and large effective population sizes. We used 2bRAD sequencing of 348 larval and subadult skipjack (Katsuwonus pelamis), yellowfin (Thunnus albacares), and bigeye tuna (T. obesus) collected from the central Pacific across 7 years of sampling to examine species boundaries, …

Computational And Ai Frameworks For Identifying Key Regulatory Genes And Their Target Genes In Plants And Humans, Md Khairul Islam

Dissertations, Master's Theses and Master's Reports

This dissertation presents computational and AI-driven frameworks for identifying key regulatory genes and their downstream targets across plant and human biological systems. Three studies address distinct challenges in genomic regulation using advanced machine learning and bioinformatics approaches.

The first study introduces DyGAF (Dynamic Gene Attention Focus), a dual-attention transformer framework that identifies and ranks disease-relevant biomarker genes by simultaneously modeling independent molecular responses and interdependent regulatory network behavior. Two attention models provide complementary perspectives on gene importance and are fused through a novel combination metric. Applied to COVID-19 nasopharyngeal swab profiles, the attention-weighted representations achieved 94.23% classification accuracy, high sensitivity, …

Physiologic Markers Of Mortality In Acute Valve Syndrome: An Ischemic Physiology Score Stratifies Patient Risk, Omar Saleh, Nicholas J. Valle, Israa Saleh, Raymond Benza, Deepak R. Talreja, Matthew R. Summers

Department of Medicine Faculty Publications

Background: Acute valve syndrome (AVS) represents a high-risk phenotype of advanced valvular disease with largely uncharacterized risk heterogeneity. We aimed to validate an expanded AVS definition and develop a physiology-dependent risk stratification tool using available clinical markers.

Methods: This retrospective study analyzed 2380 patients undergoing aortic valve replacement for severe aortic stenosis and classified them as AVS (n = 1556) or progressive valvular disease (n = 824). The primary outcome was 1-year all-cause mortality. An L2-regularized logistic regression model was developed to predict 1-year mortality using admission laboratory markers and comorbidity burden. Model performance was assessed using nested cross-validation with …

Capillary Electrophoresis Vs Massively Parallel Sequencing: A Cost-Benefit Analysis, Samia Williams

Honors Projects

Massively Parallel Sequencing (MPS) is a new Forensic Science field allowing multiple samples to be sequenced simultaneously. In contrast to CE, multiple types of genetic markers including those from different nucleic acids can be used in the same assay. Additionally, MPS has opened the doors to certain fields of Forensic DNA Analysis like Forensic Investigative Genetic Genealogy and Forensic Phenotyping assays containing upwards of 100 SNPs. While quite expensive and requiring a high cost for initiating, MPS has the potential to save time and greatly increase the throughput of Forensic DNA Analysis in crime labs.

Neural Rrp6 Depletion Drives Circrna Accumulation And Motor Impairment In Drosophila Melanogaster Neurons, Joseph Serio

Honors Theses

Circular RNAs (circRNAs) are a class of ubiquitous eukaryotic RNAs created by back splicing. These noncoding RNAs can modulate gene expression and are implicated in aging and neurodegenerative diseases. To limit the contribution of circRNAs to aging and pathobiology, it is essential to understand how turnover of these molecules is regulated, as it is not clear which enzymes are chiefly responsible for degrading circRNAs in neurons. This study evaluates the roles of ribonucleases potentially involved in neural circRNA turnover using the model fly Drosophila melanogaster. A mifepristone-activated GAL4/UAS GeneSwitch expressed RNAi transgenes and inactivated the ribonucleases. Flies were evaluated on …

The Genetic And Environmental Determinants Of Stress Resilience Across Model Systems, Carson Len Stacy

Graduate Theses and Dissertations

Survival in fluctuating environments demands that organisms effectively anticipate and respond to future challenges. This capacity is shaped by both genetic background and environmental context. In this dissertation, I apply a population aware lens to explore how genetic diversity and environmental conditions intersect to shape stress survival. Integrating functional genomics and transcriptomics in Saccharomyces cerevisiae (brewer’s yeast) and a vertebrate (common canary) system, I dissect gene-by-environment (GE) interactions that underpin resilience. First, I move beyond a single reference genome by using a pan-genomic CRISPR knockout screen to assess osmotic stress survival across diverse S. cerevisiae isolates. This analysis reveals a …

Characterization Of Mitochondrial Dna Repair Components And Repair Choices At Targeted Double-Strand Breaks In Arabidopsis Thaliana, Moira Rodriguez

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Plant mitochondrial genomes are complex when compared to most other eukaryotic mitochondrial genomes. They are large and variable in size, expand and rearrange frequently, abundant in non-tandem repeats, but maintain a very low synonymous substitution rate in the remaining coding regions. Many of these complexities can be explained by the increased use of double-strand break repair for DNA damage. To advance the understanding of mitochondrial genome dynamics as it relates to double-strand break repair, we performed a forward genetics screen to identify proteins involved in DNA repair in plant mitochondrial genomes. Through this screen, we identified an RNA/DNA helicase, Suv3, …

Context Dependent Regulation Of Dicer Function During Oocyte-To-Embryo Transition, Nick A. Newkirk

Dissertations and Theses (Open Access)

Over two decades ago, Dicer was discovered as the primary enzyme responsible for the generation of small RNAs known as the microRNAs (miRNAs) and short interfering RNAs (siRNAs). Spatiotemporal regulation of Dicer-dependent small-RNA biogenesis affects many aspects of biology, including aging, disease progression, fertility, and cancer. Interestingly, a distinct population of Dicer-dependent small RNAs, known as the endogenous siRNAs (endo-siRNAs), are uniquely abundant in the germ cells and gametes, and are critical for normal fertility. Despite their function regulating new life, the mechanisms controlling their biogenesis and subsequent germ cell functions remain poorly defined. Work to parse these mechanisms in …

Cooperative Genomic Events Driving Mutant Tp53-Driven Dcis Progression, Rhiannon L. Morrissey

Dissertations and Theses (Open Access)

Ductal carcinoma in situ (DCIS) is a mammary lesion characterized by abnormal epithelial cells occurring in mammary ducts while still being confined to the luminal space. Not all DCIS becomes invasive, and no strategy currently exists in patients to stratify indolent DCIS from DCIS at risk of progression. The standard of care includes surgical resection and radiation therapy, which constitutes overtreatment for most women whose DCIS would not progress forward. Several studies of human DCIS and breast cancer suggest that TP53 mutations occur early in DCIS, suggesting a critical role for mutant TP53 in driving disease progression. Using a somatic …

Population Genomics Of Pacific Herring Spawning Aggregations In The Eastern Bering Sea, Sydney A. Almgren

Fisheries

Pacific herring (Clupea pallasii) is a critical forage fish to the marine environment, economy, and culture of Alaska. However, despite the importance of Pacific herring in Alaska and throughout the North Pacific, knowledge gaps exist for foundational genomic characteristics of the species, including genetic population structure and the basis of genetic sex determination. In this thesis, I addressed these knowledge gaps using low coverage, whole genome sequencing. I assessed population structure and genetic diversity across seven sampling sites and found three genetic populations: Unalaska, the farthest south sampling location, Kotzebue, the farthest north, and a third group unassociated with geographic …

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 …

From Morphology To Machine Learning And Genomics: Understanding Phenotypic Variation In Wild Ducks, Sara Gonzalez

Open Access Theses & Dissertations

Understanding the genetic underpinning and distribution of phenotypic variation within and between divergent groups is core towards shedding light into how populations diverge and adapt, as well as how hybridization breaks or builds on these scenarios; and thus, central to evolutionary biology. In wild organisms, however, quantifying and linking phenotypic traits to underlying genetic processes, like mutation, gene expression, epigenetics and allele interactions, remains challenging. This difficulty arises from the complex interplay between morphology, environment, and gene regulation, as well as the logistical barriers of collecting and standardizing large-scale data across individuals and populations. As a result, researchers are increasingly …