Genetics Commons^™

Examining Loss Of Imprint In F1 Hybrid Female Mice Due To X Chromosome Epimutation And The Implications For Autism, Arianna H. Roach

Honors Scholar Theses

Sex biases are prevalent among various neurodevelopmental disorders, with males experiencing them at higher frequencies or severities than females. This male bias is poorly understood, and our lab aims to elucidate this mechanism using our model of transgenerational epigenetic inheritance. Our lab identified the cluster of genes Xlr3b/4b/4c on the X chromosome that are imprinted in the female brain. Preliminary studies suggest that Xlr3 acts as a mediator molecule in our model. Xlr3 knockdown male mice exhibited significant meiocyte loss that can be attributed to Meiotic Sex Chromosome Inactivation. Their female offspring also displayed loss of imprinting of Xlr3 and …

The Role Of Elongin B In Drosophila Melanogaster Muscle Development, Madelyne Dayan

Student Theses and Dissertations

Muscle atrophy is a result of a number of muscle diseases, as well as aging, disuse, and infections. Muscles weakened in these ways exhibit a characteristic decrease in size, strength, and mobility. The similarities between muscle in humans and Drosophila allow for direct comparisons to be made in vertebrates from studying muscle in Drosophila. Differential gene expression has been shown to play an important role in embryonic muscle development in Drosophila melanogaster. A previous study identified Elongin B (EloB) to be involved in somatic muscle morphogenesis in Drosophila, with mutant embryos displaying severe muscle defects, including thin, mis-attached, and missing …

Rnai Pathway Homeostasis Is Essential For Longevity In C. Elegans., Sejal Dulal

2025 Spring Honors Capstone Projects - Archive

RNA interference (RNAi) is a gene regulatory mechanism that is conserved across all animal species, including humans and the microscopic nematode, Caenorhabditis elegans. Many studies have identified the RNAi pathway factors and dissected the regulatory mechanisms of RNAi pathways, but there is little understanding of how the RNAi pathways themselves are regulated. Previously, Rogers and Phillips identified a feedback loop mediated by a pair of small RNA sensors, Sensor of siRNAs-1 (sosi-1) and eri-6[e-f], embedded within the genomic locus of a small RNA biogenesis factor, ERI-6/7. In this feedback motif, loss of small RNA-mediated silencing of …

A Review On Treatment, Prevention, And Research Of Worldwide Parasitic Disease: Toxoplasmosis, Hannah Skinner

All Theses

Toxoplasmosis is a worldwide, yet often overlooked, parasitic disease caused by the protozoan parasite, Toxoplasma gondii. The parasite is capable of infecting humans and almost all warm-blooded vertebrates. Over a million people are infected in the United States with toxoplasmosis each year. Most infections are asymptomatic but severe cases can lead to vision impairment, neurological disorders, and congenital birth defects. T. gondii is transmitted through undercooked meat, infected feline feces, or contaminated water and soil. The burden of T. gondii infection is most notable in livestock, felines, and immunocompromised humans. Despite being a widespread disease, toxoplasmosis is neglected in …

Life History Inhibits Deleterious Effects Of Dams On Genetic Health And Structure Of A Headwater Stream Fish, Riley Phelps

Electronic Theses and Dissertations

Habitat loss, fragmentation, and land use changes in river networks are common globally. The resulting fragmentation of landscapes and riverscapes threatens biodiversity and can affect dispersal and subsequently, gene flow and genetic health of species. Headwater streams are an integral part of river networks and contribute to biodiversity by providing habitat for temporary and permanent residents, yet they are easily altered and fragmented. The sandhills chub (Semotilus lumbee) is an endemic headwater leuciscid that lives in highly fragmented streams of the sandhills ecoregion in North and South Carolina, USA. New knowledge on the population genetics of the sandhills chub is …

A Genetic And Spatial Analysis Of The Last Megafaunal Species (Tapirus Terrestris) In The Paraguayan Dry Chaco Forest, Emily Bowers

LSU New Orleans Theses and Dissertations

No abstract provided.

Investigating The Effects Of Sod1 Knockout On Oxidative Stress And Stress Coping Styles In Zebrafish Using Crispr Technology, Tai Prauner, Ryan Wong

Theses/Capstones/Creative Projects

Reactive oxygen species are byproducts of cellular metabolism that, when not efficiently neutralized, can damage DNA, proteins, and lipids. Superoxide dismutase 1 (SOD1) is an antioxidant enzyme that converts superoxide radicals into less harmful molecules. While its molecular function is well documented, the role of SOD1 in shaping stress-related behavior remains underexplored. This project aimed to establish foundational tools for studying the behavioral impact of SOD1 knockout across proactive and reactive stress-coping styles in zebrafish.

To support future gene-editing experiments, microinjection and breeding protocols were refined across wildtype AB, proactive, and reactive zebrafish lines. No embryos were injected with CRISPR-Cas9 …

Sibship Analysis Of Fall And Spring Spawn Gulf Sturgeon Eggs In The Choctawhatchee River, Florida, Lyric Mccullouch

Honors Theses

The Gulf sturgeon (Acipenser oxyrinchus desotoi) is an anadromous species that inhabits rivers along the northern Gulf of Mexico. Facing challenges from overfishing and habitat alteration, the Gulf sturgeon is listed as threatened under the Endangered Species Act. This study investigated the genetic distinctiveness of fall and spring spawning groups of Gulf sturgeon in the Choctawhatchee River, a critical habitat for the species. In this study, I used microsatellite loci to analyze Gulf sturgeon eggs previously collected in the fall and spring of 2019 and 2020. The goals of this study were to verify the genetic identity of …

Developing A Small Molecule To Inhibit Hsf1 Expression In Cancer And Evaluating Natural Genetic Variation In Small Molecule Toxicity., Michaela Kendal Foley

Theses and Dissertations

Each year cancer affects nearly 20 million people worldwide and genetic differences across populations can impact cancer onset and progression. Specifically, tumors with high levels of HSF1, the master regulator of the cytoprotective heat shock response (HSR), are correlated with poor patient outcomes in multiple cancers such as prostate, breast, and melanoma. Subsequently, the development of pharmacological inhibitors of HSF1 represents a promising strategy for anticancer therapeutics. Using a luciferase-based transcriptional reporter, two small molecule libraries were screened for inhibitors of HSF1 expression in human embryonic kidney cells, yielding ten compounds that decrease HSF1 expression. To identify if cancer lines …

Therapeutic Applications Of A Novel Humanized Monoclonal Antibody Targeting Chemokine Receptor Ccr9 In Pancreatic Cancer, Hannah G. Mcdonald, Anna M. Reagan, Charles J. Bailey, Mei Gao, Muqiang Gao, Angelica L. Solomon, Michael J. Cavnar, Prakash Pandalai, Mautin Barry-Hundeyin, Megan Harper, Justin A. Rueckert, Ángela Turrero, Araceli Tobio, Anxo Vidal, Daniel Roca-Lema, Elia Álvarez-Coiradas, Pablo Garrido, Laureano Simón, Joseph Kim

Markey Cancer Center Faculty Publications

The relative failure of immune checkpoint inhibitors in pancreatic ductal adenocarcinoma (PDAC) despite having a dense, immunosuppressive tumor microenvironment highlights the need to target alternate/escape pathways. We have previously examined C–C chemokine receptor type 9 (CCR9) as a candidate immune checkpoint and developed a targeted, humanized monoclonal antibody (SRB2). Cytotoxicity of SRB2 was evaluated in vitro and in vivo. CCR9 expression on PDAC cells/tissues, immune components of patient-derived organoids (PDOs), and antibody-dependent cell-mediated cytotoxicity were examined. In PANC-1 and MIA PaCa-2 cell lines, we demonstrated highest CCR9 expression; however, no direct cytotoxic effect was observed with SRB2 treatment. In PANC-1 …

Evaluating Cancer Rates, Cancer Types, And Variant Hotspots Between Different Races And Ethnicities In Individuals With Li-Fraumeni Syndrome, Hillary Esplen

Dissertations and Theses (Open Access)

Li Fraumeni Syndrome (LFS) is a cancer predisposition syndrome that increases the risk for numerous cancer types in both children and adults. In the general population, incidence rates for various cancer types differ among races and ethnicities. Although a few germline TP53 pathogenic/likely pathogenic (P/LP) variants in those with LFS have been studied and associated with specific populations, such as the South and Southeast Brazil founder variant, p.Arg337His, there still lacks research on the variable expressivity of cancers within the LFS population based on specific variant, race and/or ethnicity. This study aims to describe the specific TP53 germline variants, the …

Elucidating The Multi-Omics Of Early-Onset Colorectal Cancer, Jumanah Alshenaifi

Dissertations and Theses (Open Access)

The incidence and mortality rates of sporadic early-onset colorectal cancer have increased in recent decades, but there is no clear etiological basis for this trend. EOCRC is commonly defined as colon and rectal cancers diagnosed before the age of 50 years. The rising incidence of EOCRC has made it the second most common cancer and the third leading cause of cancer death in this age group. The rising incidence of EOCRC is also documented internationally in more than 20 countries across different continents. Clinically, EOCRC has a distinct, more aggressive clinical profile than LOCRC. While approximately 15% of EOCRC cases …

The Influence Of Scientific, Genetic, And Health Literacy On Carrier Screening Decision-Making, Brenna D. Albracht

Dissertations and Theses (Open Access)

For those wishing to assess their reproductive risks and make informed decisions in their reproductive planning, carrier screening for autosomal recessive and X-linked conditions, as well as cell-free DNA (cfDNA) screening for aneuploidy, are recommended during pregnancy. Despite similarities in purpose, sample requirements, insurance coverage, and safety, a lower percentage of individuals elect carrier screening than cfDNA screening, suggesting there may be a disconnect in what patients perceive as valuable information for their pregnancy. Previous studies have attempted to explain the factors associated with carrier screening uptake or decline; however, no models have yet accounted for a patient’s literacy level …

"Magic Computer In The Sky" - Participant Perspectives On Control And The Genetic Counseling Admissions Match, Jessica Clark

Dissertations and Theses (Open Access)

Since the 2018 admissions cycle, genetic counseling graduate programs in North America have utilized the Genetic Counseling Admissions Match (GCAM), a Match algorithm to place applicants. While a study prior to implementation found that most students were uninterested in a Match due to concerns of control, there has been no investigation into matched applicants’ experiences since its inception. A mixed-methods study explored the experiences and perceptions of control of genetic counselors and genetic counseling (GC) students who entered a program following the GCAM. An anonymous survey documenting GCAM experience and a validated measure for locus of control (LOC) was disseminated …

Evaluating Triage To Genetic Counseling Using An Online Reproductive Genetics Module, Grace Ra

Dissertations and Theses (Open Access)

The American College of Obstetricians and Gynecologists recommends genetic screening for all pregnant women. As clinical recommendations broaden and demand for prenatal screening increases, obstetric practitioners report time constraints and lack of genetics knowledge as challenges to providing sufficient pretest education. These challenges in offering routine screening are further compounded by the inequities in access to genetic counseling and testing. Thus, alternative education and service delivery models have emerged to meet the demands for prenatal genetics education and help mitigate challenges surrounding access. At UTHealth Houston, an online triage and education module, the Prenatal Genetics Education Program (PGEP), was created …

Gene Expression And Transfection Of C15orf57 In Chicken Show Clear Correlation To The Function Of The Ap2 Complex, E. Ashton Magdich

Graduate Theses and Dissertations

Discovering the functions of functionally unknown genes has made a huge impact on biological understanding including poultry species. In this thesis, C15orf57 (or C5H15orf57, chicken chromosome 5 human ortholog H15 open reading frame 57), was studied to understand its genetic characteristics and function. Chapter one is literature reviews on annotation of genes, the gene information on C15orf57, the importance of characterizing unknown genes in the genome, and what is known now about C15orf57. The Chapter 2 is for the structural characterization of C15orf57, gene expression of C15orf57 in various organ tissues using the qPCR method and effect of overexpression of …

Investigation Into Mycorrhizae Associated With Native Venus' Flytrap Root Tissue, Anna Carnaggio

Electronic Theses and Dissertations

Dionaea muscipula, a plant commonly known as the Venus' flytrap, is found native to the southeast corner of North Carolina and the northeast corner of South Carolina. Several populations of native Venus' flytraps are known to exist in the nutrient-poor peat bog conditions in and around Lewis Ocean Bay Heritage Preserve (LOBHP) in Northeastern South Carolina. Anthropogenic pressures in Horry County, specifically surrounding LOBHP, have resulted in a loss of habitat for several native and endangered species. As a result, conservation efforts are focused on relocating native Venus' flytraps into adjacent habitats to ensure survival. This is only a temporary …

Crispr-Cas9 Integration Of Salmon Elovl2 In Zebrafish Enhances Lc-Pufa Biosynthesis And Growth Across Diets, Waleed Sami J. Al-Bachry

Graduate Theses and Dissertations

Fish are a rich source of EPA and DHA, which are well-known long-chain polyunsaturated fatty acids (LC-PUFAs). The sustainable production of these essential fatty acids poses significant challenges, mainly due to our dependence on marine fish and certain nuts. CRISPR-Cas system was utilized to insert the elongation of long-chain fatty acids-like2 (Elovl2) gene from Salmo salar into Danio rerio. Elovl2 was introduced at 10-15-minute post-fertilization, and successful integration confirmed by PCR genotyping, sequencing and expression of EGFP. Approximately 67% of injected embryos successfully exhibited EGFP and sequence results verified the gene integration of Salmo salar Elovl2 at the first start …

Gonadal Absence Of Ceh-22: Degradation Of Ceh-22 In The Gonads Of Caenorhabditis Elegans, Andreya C. White

Undergraduate Theses

The reproductive system of hermaphrodite Caenorhabditis elegans (C. elegans) comprises two gonadal arms, each with a terminating distal tip cell (DTC), connected by a common uterus. The DTC has two functions: leader and niche. In C. elegans, ceh-22/nkx2,5 has been found to work together with Wnt signaling to determine the fates of the DTC (Lam et al., 2006). This is an indication that ceh-22 aids in the specification of DTCs. Our research aims to determine the specific function of ceh-22 in the gonad of both male and hermaphrodite C. elegans. This will be accomplished by observing …

The Role And Expression Of Pros-1 In The C. Elegans Gonad, Brandon W. Thomas, Mary B. Kroetz, Roberta Challener

Undergraduate Theses

The nematode, formally known as Caenorhabditis elegans, has served as an excellent model organism in understanding fundamental biological processes, including those governed by conserved genes like pros-1. pros-1 is partially responsible for the formation of tubular structures within the organism. Glial cells and excretory canals are both examples of tubular structures governed by pros-1. pros-1 orchestrates the embryonic development of these cell types by modulating cell proliferation and differentiation, thus ensuring proper morphogenesis and organogenesis. Its regulatory influence likely extends beyond embryogenesis, potentially affecting reproductive processes as well. Furthermore, the evolutionary conservation of pros-1 underscores its significance …

Investigating Genetic Regulators Of Crystal Cell Development In Drosophila Melanogaster, Andrea Feria, Nyla Walbrook, Anisa Turaeva, Rebecca Spokony

Publications and Research

Crystal cells, a subset of Drosophila melanogaster hemocytes, are important for melanization, a crucial immune response. While the genetic regulation of crystal cell develop remains incompletely understood, this study investigates the functions of five candidate genes: ACXB, ACXA, Gp210, CG4390, and Cyp4s3; identidied through previous genome-wide association studies. Using the Gal4/UAS system along with RNA interference (RNAi), we exclusively knocked down each gene in third instar larvae and quantified crystal cell populations following heat shock-induced melanization. Our results imply that the knockdown of ACXB and ACXA significantly increased crystal cell counts in both sexes, suggesting these genes either act as …

Args & Chronic Disease: How Antibiotic Resistance Genes Impact The Progression Of Type Ii Diabetes, Paige Imperato

Thinking Matters Symposium

Antibiotics are typically offered to patients with no warning of long-term consequences, though increasing evidence suggests this may not be entirely true. When antibiotics enter the body, they kill both good and bad bacterial populations in the gut - collectively known as the human microbiome. Repeated use of these drugs encourages mutations in this bacterial population [2]. This leads to the creation of antibiotic-resistant genes (ARGs) in antibiotic resistant bacteria (ARB). The causal relationship between antibiotic use and bacterial resistance is well established. However, recent research suggests a newly discovered relationship between the presence of specific ARGs in the microbiome …

Functional Protein Biomarkers Based On Distributions Of Expression Levels In Single-Cell Imaging Data, Misung Yi, Tingting Zhan, Hallgeir Rui, Inna Chervoneva

Department of Pharmacology, Physiology, and Cancer Biology Faculty Papers

MOTIVATION: The intra-tumor heterogeneity of protein expression is well recognized and may provide important information for cancer prognosis and predicting treatment responses. Analytic methods that account for spatial heterogeneity remain methodologically complex and computationally demanding for single-cell protein expression. For many functional proteins, single-cell expressions vary independently of spatial localization in a substantial proportion of the tumor tissues, and incorporation of spatial information may not affect the prognostic value of such protein biomarkers.

RESULTS: We developed a new framework for using the distributions of functional single-cell protein expression levels as cancer biomarkers. The quantile functions of single-cell expressions are used …

The Roles Of Cup1, Ssu1, And Mitochondrial Dna In Copper Tolerance In Wild Yeasts, Madeleine Panek

Undergraduate Honors Theses

Understanding the genetic basis of complex traits remains a central challenge in biology. In Saccharomyces cerevisiae, copper resistance is a multifactorial trait shaped by both genetic and environmental influences, yet its underlying mechanisms are not fully understood. The genes CUP1 and SSU1 are known to influence copper resistance, though how these genes interact with each other and with mitochondrial DNA (mtDNA) variation in wild yeast populations is unknown. I hypothesized that the genes CUP1 and SSU1 and variation in mtDNAs contribute to copper resistance in wild yeasts independently and through genetic interactions. To test this, I measured copper resistance …

Missense Mutation Of Msh6 Leucine 696 Has No Apparent Effect On The Dna Mismatch Repair Process, Razan H. Hammad, Rafia Rashid, Essence Tarrence, Christopher Bolden, Joanna E. Haye-Bertolozzi

XULAneXUS

Lynch Syndrome and Constitutional Mismatch Repair Deficiency are human diseases implicated in mutations of DNA mismatch repair (MMR) genes. This experiment tested a mutation of an MMR gene, MSH6, and evaluated how the mutation affected overall MMR effectiveness. Using the yeast Saccharomyces cerevisiae, we performed the CAN1 forward mutation assay to study msh6-L696F and its implications in the MMR process. We hypothesized that there would be a significant change in molecular function in the Msh6 protein in the presence of this mutation. Bioinformatic tools predicted that this amino acid change would have deleterious effects on MMR function. However, …

Leveraging Attention Mechanism To Unlock Gene And Protein Attributes, Ala Jararweh

Computer Science ETDs

Advancing personalized medicine depends on effectively integrating and interpreting the vast, heterogeneous landscape of biological data, from genomic sequences and transcriptomics to the insights embedded in scientific literature. Current machine learning models often focus on single data modalities, limiting their capacity to capture the multifaceted nature of biological systems. We address this gap by developing three attention-based machine-learning models integrating diverse data modalities. Firstly, DeepVul is a multi-task model that leverages cancer transcriptome data to predict genes critical for cancer survival and their corresponding drugs. Subsequently, LitGene refines gene representations by integrating textual information from the scientific literature. Finally, Protein2Text …

Discovery Of Suitable Habitat For Freshwater Mussel Species In The Appomattox River Through The Use Of Environmental Dna., Nicholas Duellman

Longwood Senior Thesis Proposal

Freshwater mussels are a keystone species providing crucial ecosystem services and river composition resiliency. Anecdotal evidence suggests the presence of freshwater mussels within the Appomattox river, the specifics of population sizes and suitable habitat remains an open question. Environmental DNA (eDNA) usage in conservation ecology has exploded in use within the past two decades, being far less invasive and cost-demanding than traditional methods. An eDNA metabarcoding pipeline of the 16s mitochondrial ribosomal subunit was built in R v. 4.4.2, using dada2 v. 3.2.1 package to trim MinION single read ASV outputs for freshwater mussel species identification in the interest of …

Characterizing Kmt2d In Endometrial Cancer, Katherine R. Davanzo

Medical Student Research Symposium

Endometrial cancer is rising in incidence in the United States, notably among premenopausal women. This increase and the trend of delayed childbearing warrant the need for further advancement in fertility-sparing treatment for endometrial cancer. A gene left widely unexplored in its possible clinical utility as a target for fertility-sparing treatment is KMT2D, a lysine-specific methyltransferase and tumor suppressor. Preliminary gene set enrichment analysis on a 12Z endometriotic epithelial cell line identified TIMP3 as a gene that is possibly regulated by KMT2D expression. TIMP3 encodes an irreversible inhibitor of matrix metalloproteinases (MMPs), a well-recognized class of proteins as contributing to the …

Fisheries Management Paper No.286: Western Australian Octopus Resource Harvest Strategy, Department Of Primary Industries And Regional Development, Western Australia

Fisheries Management Papers

Harvest strategies for Western Australia’s (WA) aquatic resources are formal documents developed to support decision-making processes that ensure the outcomes are consistent with the principles of Ecologically Sustainable Development (ESD; Fletcher 2002a) and Ecosystem Based Fisheries Management (EBFM; Fletcher et al. 2012). Harvest strategies are a key component of all contemporary fishery management systems and a requirement for certification under the Marine Stewardship Council (MSC). The objectives of ESD are reflected in the objectives of the Fish Resources Management Act 1994 (FRMA).

This Octopus Resource Harvest Strategy (Harvest Strategy) has been developed and revised in line with the Harvest Strategy …

Investigating Sk-3 Based Spore Killing In Neurospora Crassa Through Deletion Analysis Of Dna Intervals I383 And I394, Paulina Paulikas

Senior Theses – Biological Sciences

Neurospora fungi are found around the world. The species N. crassa is a popular model for use in genetics research. N. crassa produces sexual spores, called ascospores, during mating between strains of opposite mating types. N. crassa also produces spore sacs called asci, and each ascus typically contains eight viable ascospores. However, some Neurospora fungi carry selfish genetic elements called Spore killers, and when a strain carrying a Spore killer mates with a spore killing-susceptible strain, asci contain four black viable ascospores and four white inviable ascospores. In this project, I investigated a Spore killer called Sk-3. To act as …