Genetics Commons^™

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.

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, …

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 …

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 …

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 …

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 …

Population Structure Analysis Of Four Basal Higher-Attines Using Bioinformatic Approaches, Gabriel Mcdanield

Biology Theses

Metapopulations within the family Formicidae are unique among other animals due to the large colonies they build, and the mating strategies required to fertilize a specialized reproductive caste that will often produce young for the life of the colony. One group of ants, the fungus-gardeners (tribe Attini). The population structure of North American non-leafcutting, fungus-gardening ants has been understudied, especially in the southwest of the United States. Additionally, not much is known about their dispersal biology, so the dynamics of dispersal of these species and how they affect population structure is likewise not well known. To shed light on the …

Leveraging Dna Methylation Profiling And Microrna Sequencing To Characterize The Epigenomic Landscape Of Major Depressive Disorder Disease Trajectory, Jan Dahrendorff

USF Tampa Graduate Theses and Dissertations

Major depressive disorder (MDD) is a common and debilitating mental disorder associated with a significant disease burden and economic cost. Despite ample evidence documenting the efficacy of a diverse array of established MDD therapies, a large proportion of patients are inadequately responsive to initial treatment attempts, with first-line treatments leading to remission in only ~30% of the patients. Importantly, about a third of patients even fail to achieve symptom improvement after two or more antidepressant trials, resulting in what is commonly defined as treatment-resistant depression (TRD). The ability to identify which treatments are most likely to elicit a positive response …

Bioaccumulation Pattern Of Per- And Polyfluoroalkyl Substances (Pfas) In Fish Tissues From Two Freshwater Systems, Margaret D. Taiwo, Husam Kafeenah, David D. Duvernell, Michael O. Eze

Biological Sciences Faculty Research & Creative Works

Per- and polyfluoroalkyl substances (PFAS) are known for their persistence, ubiquity, bioaccumulation in different matrices of the environment and their detrimental effect on human health. In this study, we used EPA 1633 to examine the prevalence of ten PFAS compounds in two freshwater systems and investigated their bioaccumulation pattern across different tissues of grass carp fish (Ctenopharyngodon idella), common carp (Cyprinus carpio), and flathead catfish (Pylodictis olivaris). Among the PFAS compounds analyzed, PFBS exhibited the highest concentration in the freshwater sample, exceeding the U.S. EPA regulatory limit of 4 ng/L for drinking water. The total PFAS concentrations in the muscle, …

Using Rattlesnake Venom To Model Complex Trait Evolution Across Ecological And Evolutionary Scales, Samuel R. Hirst

USF Tampa Graduate Theses and Dissertations

A central challenge in evolutionary biology is understanding how genetic variation leads to phenotypicdiversity, particularly for complex traits that strongly influence fitness. Traits form the substrate of natural selection, but it is genes, that are inherited across generations. To fully understand the evolutionary process, we must therefore connect the molecular basis of trait variation with the evolutionary outcomes of such traits.

For relatively simple traits, the genotype–phenotype relationship is well understood. Classic systems, such as coat color in beach mice or toxin resistance in garter snakes, have provided effective examples of how relatively few loci underlie conspicuous adaptive differences across …

Purple Tomatoes Boost Nutrition Crop Value And Create New Opportunities For United States (U.S) Agriculture, Tariq Alam

Agronomic Crops

The agricultural landscape in the United States is continually evolving, with growers and the tomato industry seeking innovative ways to meet consumer demands while enhancing profitability. The introduction of both bioengineered and classically bred anthocyanins-enriched purple tomatoes presents a unique opportunity for U.S. growers to cultivate a high-value crop that appeals to niche markets and commands premium pricing. Bioengineered purple tomatoes achieve high anthocyanin levels through the introduction of snapdragon transcription factors, while classically bred 'Indigo Rose' purple tomatoes are developed via classical breeding methods, providing an alternative for consumers who prefer traditionally bred products. Specifically, the purple tomato holds …

Bioinformatic Analysis Of Pogz Variants In Relation To White Sutton Syndrome, Hannah Rollins

Theses

White-Sutton syndrome (WHSUS) is a rare neurodevelopmental disorder caused by mutations in the Pogo Transposable Element with ZNF Domain (POGZ) gene, which encodes pogo-transposable element with ZNF domain, a chromatin regulator essential for proper mitotic progression and DNA repair. This study uses a bioinformatic framework to evaluate the structural and functional impact of missense mutations in the conserved amino acid region (positions 500–800) of the POGZ protein. Protein modeling, variant effect prediction, conservation analysis, and molecular dynamics simulations were employed to gain an understanding of the effects of POGZ missense mutations on protein structure and movement with specific emphasis on …

Uncovering The Pml::Rara Fusion In Cytogenetically Cryptic And Fish-Negative Acute Promyelocytic Leukemia-A Case Report And Comprehensive Literature Review, Busra Delikkaya, Jaime Eberle-Singh, Arianna Morton, Jerald Gong, Jinglan Liu

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

The PML::RARA fusion resulting from t(15;17) is the genetic hallmark of acute promyelocytic leukemia (APL), typically detected by cytogenetics and/or fluorescence in situ hybridization (FISH) studies. Rarely, APL patients present with normal cytogenetics and FISH findings, complicating diagnosis and delaying life-saving therapy. We report a 23-year-old male with clinical, morphologic and immunophenotypic features consistent with APL but negative for FISH studies. Despite prompt initiation of all-trans retinoic acid (ATRA) based on clinical suspicion, the patient succumbed to intracranial hemorrhage. Quantitative reverse transcriptase PCR (qRT-PCR) confirmed a long isoform PML::RARA fusion. A review of 34 published cytogenetics- and FISH-negative cases since …

The Evaluation Of Variants Within Eight Collagen Genes Col1a1, Col1a2, Col3a1, Col5a1, Col11a1, Col15a1, Col22a1, And Col27a1 And A Risk Of Non-Contact Knee Ligament Rupture In Elite Handball Players: A Case-Control Study, Katarzyna Krawczak-Wójcik, Andrzej Mastalerz, Aleksandra Bojarczuk, Monika Johne, Alison V. September, Aleksandra Garbacz, Katarzyna Komar, Ewelina Maculewicz

Baltic Journal of Health and Physical Activity

Introduction: Knee ligament ruptures are common injuries among athletes. While most previous studies examined single collagen gene polymorphisms, few have investigated haplotype-level associations across multiple genes, particularly in elite handball players. Materials and methods: This case-control study analyzed variants in eight collagen genes (COL1A1, COL1A2, COL3A1, COL5A1, COL11A1, COL15A1, COL22A1, and COL27A1) in 103 elite Polish handball players with non-contact knee ligament rupture and 226 matched controls. Results: The COL22A1 rs11784270 CC genotype was associated with an increased risk (OR = 2.88, p = 0.01), with the strongest effect in the …

Teaching Molecular Genetics Using Paramecium And Rna Interference: Research-Based Learning And Project Ownership, M. S. Valentine, K. Johnson, M. B. Veramendi, C. James, J. Kozak, A. Patwardhan, R. Quartey

Montclair State University Scholarship & Creative Works

Research-based course design is beneficial to both the instructor and the students by providing project ownership, independence, increased engagement, and publishable results. Paramecium, a single-celled eukaryote, is a common organism observed in many high school and college classrooms that can be easily cultured and manipulated to navigate through guided student-driven research projects. Presented here are research-centered student projects that include designing and creating an RNA interference (RNAi) plasmid to deplete a gene product in Paramecium. Because RNAi can be used in a large number of model organisms, the techniques presented can be applied in a variety of ways. …

The Chromosome Complement Of Male Chrysoperla Rufilabris (Burmeister, 1839), With Evidence Of Distance Segregation In Meiosis I, Valoria G. Maslin, Allison M. Eisenhauer, Leocadia V. Paliulis

Faculty Journal Articles

Neuropteran insects display a phenomenon called distance segregation during male meiosis I, where the X and Y chromosomes are unconnected from prometaphase I through anaphase I. Here we investigate chromosome number and patterns of chromosome segregation of a previously unstudied Neuropteran: the green lacewing, Chrysoperla rufilabris (Burmeister, 1839). Testes of male C. rufilabris were isolated and prepared following a chromosome squash method. Living meiosis I spermatocytes were also imaged. The data revealed a chromosome number of 2n=12 in males (2n=10+XY) and evidence of distance segregation of X and Y chromosomes in meiosis I spermatocytes.

A Complicated History Of Mitogenome Introgression Among Luxilus Species (Teleostei, Family Leuciscidae) In The Ozark Highlands, David D. Duvernell, Carson Arnold, Shila Koju, Abby J. Wicks, Thomas E. Dowling

Biological Sciences Faculty Research & Creative Works

Hybridization is common among minnows and shiners in the family Leuciscidae, and mitonuclear discordance can reveal evidence of historical hybridization and introgression events that have shaped extant species and populations. We have identified a notable case of serial mitogenome replacement in populations of two shiner species, Luxilus zonatus and L. chrysocephalus, which are syntopic in drainages throughout the northern and eastern Ozark Interior Highlands of North America. These mitogenome replacement events involved L. zonatus acquiring the mitogenome of L. chrysocephalus, and populations of L. chrysocephalus acquiring the mitogenome of an allopatric congeneric species, L. cornutus. The latter species has a …

Genetic And Geographic Profiling Of Fragrance-Associated Badh2 Mutations In Rice From China, Laos, And Vietnam, Lenie A. Quiatchon-Baeza, Venea Dara Daygon, Mariafe N. Calingacion, Melissa A. Fitzgerald

The Philippine Agricultural Scientist

Fragrance in rice is a culturally and economically significant trait in Asia and around the world. This study aimed to develop a genetic and geographic profile of the fragrance-associated BADH2 mutations (badh2.1 and badh2.11) in 1,067 rice varieties from China, Laos, and Vietnam, which are part of the International Rice Genebank Collection. Seventy-three varieties were found to carry the common eight-base pair (bp) deletion in exon 7 of the genes (badh2.1, also known as badh2.7), primarily from indica varieties, with some belonging to japonica, javanica, and intermediate varieties. Conversely, 59 varieties possess the recently identified badh2 allele, badh2.11 (also known …

Impact Of Sowing Time And Plant Density On Selected Traits And Yield Of Cotton Genotypes In Pakistan, Muhammad Rizwan Jamil, Kalim Ullah, Muhammad Mohibullah, Saeed Muhammad, Hafiz Abdul Haq, Sundas Batool, Rashida Aslam, Wasif Rasool

The Philippine Agricultural Scientist

Extremely diversified cropping environments prevail in most cotton-growing areas of Pakistan due to prevailing rainfed conditions, prolonging the crop’s cultivation period. To contribute to the development of desired breeding traits for effective breeding programs, this study examined the production and growth pattern of 8 cotton genotypes. Four experiments were conducted in 2018 and 2019 at 2 locations in Dera Ismail Khan, Pakistan, to evaluate the performance of the studied genotypes at 3 plant densities and 2 sowing dates. Traits such as days to first flower opening, flowering duration, monopodial branches per plant, plant height at harvest, height-to-node ratio, fruiting branch …

Bmp Signaling Co-Regulation Of Immune Response And Lipid Metabolism, Katerina K. Yamamoto

Dissertations, Theses, and Capstone Projects

The Bone Morphogenetic Proteins (BMPs) are secreted peptide ligands of the Transforming Growth Factor beta (TGF-β) family, initially identified for their roles in development and differentiation across animal species. They are now increasingly recognized for their roles in physiology and infectious disease. In the nematode Caenorhabditis elegans, the BMP ligand DBL-1 controls fat metabolism and immune response, in addition to its roles in body size regulation and development. DBL-1 regulates classical aspects of innate immunity, including the induction of anti-microbial peptides. We theorized that BMP-dependent regulation of fat metabolism could also promote resilience against microbial pathogens. We found that …

Retinal Precursor Cell Enriched Multiomic And Pseudo-Time Analysis Of Developing And Reprogrammed Photoreceptors, Brendon M. Patierno

Dissertations, Theses, and Capstone Projects

The vertebrate retina is a complex tissue made up of seven major cell subtypes which during development must differentiate and localize into a highly organized structure. These neuronal cells do not regenerate if damaged or diseased, and the progressive deterioration of cone photoreceptor cells is the leading cause of age related blindness. Currently there are no cures for this disease, but one promising therapeutic avenue is cell transplantation research. If we can further elucidate the gene regulatory networks that define cone cell development, this knowledge could be applied to the generation of healthy cone cells in clinically relevant models.

The …

Exploring The Role Of Ecological Traits In Shaping Spatial Patterns Of Genetic Diversity, Rilquer Mascarenhas Da Silva

Dissertations, Theses, and Capstone Projects

The field of comparative phylogeography aims at uncovering common underlying causes for shared patterns of diversity and diversification at the population level. However, it is now widely accepted that intraspecific genetic diversity patterns can differ considerably across co-occurring taxa due to ecological processes acting at the population level (and influencing individual movement and abundance). To model the processes underlying lineage diversification and demographic shifts in response to environmental changes, phylogeographers and population geneticists are now faced with the challenge of incorporating measurements of species ecological traits into their molecular studies. This dissertation aimed at investigating how different types of ecological …

Crossroads Of Covid-19 And Alzheimer’S: Investigating Sars-Cov-2 Nsp6 And Orf7a In Amyloid-Β42 Toxicity, Jeffrey William Huettemann, Amit Singh

Research from the Berry Summer Thesis Institute, 2025

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resulted in several hundred million contracted cases of coronavirus disease 2019 (COVID-19) and a global pandemic. In some of these cases, previous neurological diseases, such as Alzheimer’s disease (AD), seemed to progress much more rapidly after the COVID-19 infection. Thus, we became interested in studying the effects of SARS-CoV-2 infection on prior neurological disease progressions.

To modulate this condition, we used Drosophila melanogaster as a genetic model system. We had previously developed the Alzheimer’s Disease Fly Model with expression of human amyloid beta 42 (Aβ42) peptide, which is responsible for extracellular Aβ-42 …

Performance Analysis Of Computational Methods For Predicting Protein Function In Rare Diseases, Aichetou Mohamed Sidiya, Hanin Alzaher, Razan Almahdi, Tayeb Brahimi

Effat Undergraduate Research Journal

Protein function prediction is crucial for understanding the underlying mechanisms of rare diseases. With the increasing availability of computational methods including machine learning-based approaches, network-based methods, and sequence-based methods, predicting protein functions has become more accessible. However, it is not clear which of these methods performs better or how they compare to each other in terms of accuracy, efficiency, and scalability. In this study, we evaluate several computational methods for predicting protein functions in rare diseases using key performance indicators (KPIs). We analyze the strengths and weaknesses of each method and provide recommendations for researchers and clinicians interested in using …

Enhancing Cataract Surgery Outcomes: Optimal Use Of Pre- And Post-Operative Eye Drops, Keith Skolnick M.D., Anu Valiaveedu

Mako: NSU Undergraduate Student Journal

Many preoperative and postoperative cataract patients struggle with comprehending the use of prescription medication as directed. Language barriers and low health literacy levels are major factors contributing to improper use of prescriptions. To increase patients comprehension, the Fort Lauderdale Eye Institute employed an educational intervention consisting of a live presentation and an instructional video. Results found that 44% of patients were hesitant to ask questions to clinical staff, 32% felt overwhelmed, and nearly 70% lacked confidence in using their prescribed eye drops. Following the intervention, 91% of patients reported increased confidence in their medications, and most indicated that the video …

Global Erk/Mapk Activation Determines Oncogenic Fitness In Kras-Mutant Pancreatic Ductal Adenocarcinoma, Rachel A. Burge

MUSC Theses and Dissertations

In pancreatic ductal adenocarcinoma (PDAC), ~95% of cases harbor an activating KRAS mutation. The most common KRAS mutations in PDAC are KRAS^G12D (42%), KRAS^G12V (31%), and KRAS^G12R (15%). Patients harboring KRAS^G12R mutations have increased overall survival compared to those with KRAS^G12D/V-mutations. While KRAS^G12D/Vare common in all KRAS-mutant cancers, KRAS^G12Ris only common in PDAC.

KRAS^G12R is unable to activate the lipid kinase PIK3CA, a KRAS effector that is important for tumorigenesis in murine models. To investigate the tumorigenic potential of KRAS^G12R and the mechanisms that enable this mutation …

Analysis Of An Ethanol Sensitive Bmp-Nkx2.3-Fgf Signaling Pathway In Pouch Morphogenesis., Hieu Dai Le Vo

Electronic Theses and Dissertations

Craniofacial malformations lie at the heart of Fetal Alcohol Spectrum Disorders (FASD). While there is growing evidence for a genetic component to FASD, little is known of the cellular mechanisms underlying these ethanol-sensitive loci in facial development. Bone Morphogenetic Protein (Bmp) signaling pathway dependent pouch formation is a key mechanism in facial development. We have previously shown that multiple Bmp mutants are sensitized to ethanol-induced facial defects. However, ethanol does not directly impact Bmp signaling. This suggests that downstream effectors, like nkx2.3 and Fibroblast Growth Factor (Fgf) signaling, may mediate the impact of ethanol on Bmp mutants. Here, I …

The Role Of Cleavage And Polyadenylation Spcific Factor 6 (Cpsf6) In Hematopoiesis, Fengxi Ye

Dissertations and Theses (Open Access)

Cleavage and polyadenylation specific factor 6 (Cpsf6) translocation is frequently reported in APLL, which is Acute Promyelocytic Leukemia (APL)-like acute myeloid leukemia (AML) and other types of blood diseases associated with abnormal hematopoiesis. CPSF6 is a subunit of the Cleavage Factor I mammalian (CFIm) complex, which regulates post-transcriptional alternative polyadenylation (APA) of pre-mRNAs. Previous research indicated that Cpsf6 plays an essential role in alternative polyadenylation, development, and tumorigenesis. However, the role of Cpsf6 in hematopoiesis is unknown. Given its roles in APA, development and cancer, we hypothesize that Cpsf6 plays a critical role in hematopoiesis and that its …

Exploring Variability Of The Cg18562578 Methylquant Assay For The Forensic Discrimination Of Monozygotic Twins, Sydney E. Arnold

Student Theses

Monozygotic (MZ) twins possess identical DNA sequences, posing a problem for forensic scientists, as they are incapable of distinguishing MZ twins from each other using traditional DNA identification methods. However, the epigenomes of MZ twins will differ and might be used for their forensic discrimination. Here, we explored the variability of an assay previously developed by our laboratory that showed high discrimination potential for MZ twins using buccal swab DNA, cg18562578 MethylQuant. We measured precision at each step: bisulfite conversion, nested PCR, and qPCR, reproducibility, and repeatability. DNA methylation ratios were compared between two analysts carrying each step using the …