Molecular Genetics Commons^™

Network Analysis Of Antimicrobial Resistance In Staphylococcus Aureus: Characterization Of Hub Genes And Their Functional Implications, Md Imran Hasan, Davida Smyth, Jeong Yang, Ashley Teufel

Masters Theses (Archived)

Antimicrobial resistance is a major cause of morbidity and mortality in patients with S. aureus infections. In this study, we analyzed genes, molecular mechanisms, and pathways driving drug resistance in S. aureus using network analysis. Using whole-genome sequencing (WGS) data and systems biology approaches, we identified 229 AMR-associated genes and constructed a protein-protein interaction network among these genes. Through network topology and functional enrichment analyses, we not only confirmed their association with resistance, but also highlighted the central roles of these genes in resistance pathways, such as efflux, target replacement, and target protection, which are directly linked to multiple drug …

Diagnostic And Clinical Utility Of Oncoscan Microarray And Ngs-Based Sequencing In Pediatric Solid Tumors: Children’S Mercy Hospital’S Experience, Aravindh Nagarajan, Lisa Lansdon, Midhat Farooqi, Lei Zhang, Elena Repnikova

Research Days

This papers attempts to evaluate the diagnostic and clinical utility of microarray-based OS+ in detecting clinically relevant genetic alterations in FFPE solid tumor samples and to compare the yield of somatic mutation detection by WGS/WES in pediatric solid tumors at Children’s Mercy Hospital - Kansas City.

Generation Of A Transgenic Vector For The Purpose Of Transforming Charcoal Rot Resistance Into Soybeans (Glycine Max), John M. Bear Jr

Electronic Theses & Dissertations

Charcoal rot, caused by Macrophomina phaseolina, is among the most devastating fungal pathogens affecting G. max, particularly in drought-susceptible regions such as the midwestern United States. Traditional agricultural practices have included crop rotation and irrigation, which have proved ineffective or economically unfeasible. Charcoal rot infects over 500 other species of plants and can overwinter as dormant sclerotia which can germinate once soybeans are re-planted and infect young plants. As a result, transgenic solutions have offered a promising alternative for the development of disease-resistant soybeans. This thesis documents the construction of a transgenic vector to express BOZO, a …

The Role Of Presynaptic Proteins In Alcohol Sensitivity And Tolerance, Madhumitha Gundluru

Honors Theses

Mammalian Unc13 (Munc13) and Drosophila Unc13 (Dunc13) are presynaptic active zone proteins essential for synaptic vesicle docking and priming in a neuron. Alcohol binds to the C1 domain of Munc13, which inhibits DAG binding. The reduction in DAG binding by Munc13 decreases the probability of vesicle fusion with the membrane, decreasing neurotransmitter release. Heterozygotes for a Dunc13 loss-of-function allele are behaviorally resistant to alcohol, physiologically resistant to alcohol, molecularly resistant to alcohol, and self-administer significantly more alcohol than control flies. Therefore, genetically reducing Dunc13 mimics a state of alcohol tolerance in the fly. The two main Dunc13 isoforms, Dunc13A and …

Genomic Structure Among Populations Of A Regionally Rare Perennial Plant Indicates The Need For Reevaluation Of Management Units, Cheyenne Moore, Angela J. Mcdonnell, Scott Schuette, Christopher T. Martine

Faculty Journal Articles

Conservation of rare species often relies on the delineation of management units and genomic tools can now be applied for this purpose. However, this is not as common on a local scale, where populations are often small and fragmented, despite the utility of informing conservation and management practice at the regional level. We use a genotyping by sequencing (GBS) approach to assess the perennial riparian plant species Baptisia australis (Fabaceae) in Pennsylvania, where the taxon is at the edge of its natural distribution and considered threatened. In this system, we investigate whether sampled subpopulations exhibit genetic structure. We find that …

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 …

Competence Protein Comea And Oxidative Stress In Bacillus Subtilis Stationary Phase Mutagenesis, Angeline Roldan, Sam Schauf

Undergraduate Research Symposium Posters

Stationary Phase Mutagenesis is a process where a bacterium can accumulate mutations in the absence of cell division. This may occur via competent DNA uptake and oxidant DNA damage and repair. ComEA is a transmembrane protein in B. subtilis that is required for the transport of exogenous DNA into the cell. (Figure 1)

Microbial Community And Water Quality Assessment Of Crassostrea Virginica Habitats In Southeast Florida, Stacy Brown

All HCAS Student Capstones, Theses, and Dissertations

Eastern oysters (Crassostrea virginica) are essential habitat-forming species that contribute significantly to coastal water quality due to their filter-feeding behavior. Unlike other coastal regions in the Gulf of Mexico and Northeastern United States, oysters are not commercially managed in Southeast Florida and as a result sparse data exists on locations of the Eastern oyster habitat. Similarly, the benefits of oyster reefs to water quality are also not fully documented in Southeast Florida. Although beneficial and often referred to as keystone habitat building species, populations of C. virginica are not currently listed as protected species so little work has …

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 …

Implications Of Type Iv Pilus Retraction For Dna Uptake By Acinetobacter Baumannii, Yafan Yu

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

Horizontal gene transfer (HGT) via natural competence allows bacteria to incorporate extracellular DNA (eDNA) into their genomes, facilitating genetic diversity and adaptation. In Acinetobacter species, natural competence depends on DNA binding and uptake mediated by type IV pili (T4P). T4P are dynamic extracellular filaments composed primarily of the major pilin subunit PilA, along with a few minor subunits. T4P drive a range of cellular functions including twitching motility, biofilm formation, and DNA uptake, with some functions dependent on pilus retraction and others not. However, how Acinetobacter T4P bind DNA and how T4P/eDNA interactions impact biofilm formation remain unclear. Here, I …

Hypoxia Induced Ribosomal Rna Fragmentation Mediated By Rnase L, Vanessa Kristina Pizutelli, Dimitri G Pestov

Rowan-Virtua Research Day

Ischemic injury contributes to a range of global pathologies. Ischemia/Reperfusion Injury (IRI) is a paradoxical phenomenon that involves an initial restriction of blood flow followed by a sudden restoration of perfusion. This type of injury takes place in conditions such as myocardial infarction, acute kidney disease, and ischemic stroke and often leads to cellular death. Additionally, IRI exacerbates post-surgical outcomes and plays a role in graft dysfunction and transplant rejection. Despite efforts to develop therapies targeting known IRI pathways, clinical trials have largely been unsuccessful, underscoring the need for alternative mechanisms and biomarkers associated with IRI-induced apoptosis. Reactive oxygen species …

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 …

Investigating The Role Of Ilv1 On Stress Response In Saccharomyces Cerevisiae, Luke H. Beachboard

Honors Theses

Saccharomyces cerevisiae, a model organism within molecular genetics, is also known for its broad role within baking, brewing, biofuel, and pharmaceutical industries. An unpublished study at The University of Tennessee at Chattanooga observed decreased cell viability in an ILV1 Knockout strain of S. cerevisiae when exposed to environmental stressors. A subsequent study at The University of Tennessee at Chattanooga found expression levels of the candidate genes to be significantly altered within the ILV1 Knockout strain relative to the BY4743 Wildtype strain, demonstrating the reality of a pleiotropic role within ILV1. Now, this study aims to further investigate this peculiar characteristic …

The Roles Of Rnt1 And Putative Endoribonucleases In Eukaryotic Mrna Degradation, Lee-Ann Notice-Sarpaning

Dissertations and Theses (Open Access)

Endoribonucleases initiate degradation by cleaving RNAs internally. Mutations in these enzymes have been shown to cause diseases such as cancer, developmental disorders, and neurodegenerative diseases. Yet, eukaryotic endoribonucleases have not been well studied, especially with regard to their role in nuclear mRNA degradation. Rnt1 is a Saccharomyces cerevisiae (budding yeast) nuclear endoribonuclease and homolog of human Drosha with well-characterized roles in the processing of ncRNAs. The enzyme recognizes and cleaves double-stranded RNA stems containing a terminal tetraloop with an AGNN consensus sequence. However, the scope and consequence of its function in mRNA degradation has heretofore been unclear. Previous studies have …

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 …

A Stakeholder-Informed Conceptual Framework For Evaluating Genomics In Precision Oncology, Julie A. Wiedower

All Dissertations

This dissertation explores the value of genomic testing in precision oncology with an emphasis on how US payers conceptualize and prioritize elements of value. This research aims to address gaps in understanding payer perspectives and proposes a stakeholder-informed framework for evaluating genomic testing in oncology. To achieve this aim, the presented research investigates payer perspectives, value-based cancer care priorities, and the conceptual understanding of the value of a genetic diagnosis to establish a framework for value with the payer audience in mind. Chapter 1 outlines relevant background information relating to the genomic revolution and challenges in translating genomic testing technologies …

The Genomic Landscape And Prognostic Impact Of Kras, Stk11, And Smarca4 Mutations And Co-Mutations On Survival Outcomes In Non-Small Cell Lung Cancer, Peter Manolakos

All Dissertations

Non-small lung cancer (NSCLC) accounts for 85% of lung cancer cases, and Kirsten rat sarcoma viral oncogene homolog (KRAS), Serine/Threonine Kinase 11 (STK11), and SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 4 (SMARCA4) mutations and co-mutations have been increasingly recognized for their potential prognostic significance. However, clear knowledge gaps remain regarding which treatments should be selected for patients who present clinically with KRAS/STK11 or KRAS/SMARCA4 co-mutations, as outlined in Chapter 1. Despite significant clinical development advancements in immunotherapy and targeted therapy, a deeper understanding of the influence of these genomic …

African Sleeping Sickness: From Basic Biology To Future Directions, Riddhi R. Patel

All Theses

African Sleeping Sickness is a Neglected Tropical Disease (NTD) which poses a significant health risk to impoverished populations in 36 Sub-Saharan African countries. It is a devastating disease caused by the protozoan parasite Trypanosoma brucei, which is transmitted to mammals via the bite of infected tsetse flies. The disease manifests in two stages: the hemolymphatic stage and the meningoencephalitic stage. In the latter stage, it invades the Central Nervous System (CNS) and can be fatal if left untreated. It is caused by morphologically indistinguishable species of Trypanosoma brucei in both humans and animals, where in humans it is known as …

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 …

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 …