Molecular Genetics Commons^™

Exploring Competitive Dynamics Between Pseudomonas Baetica And Salmonella In A Polymicrobial System, Braxton E.M. Stout

Electronic Theses and Dissertations

The global rise in antimicrobial resistance has catalyzed a greater focus on polymicrobial research aimed at characterizing microbial interactions and uncovering new therapeutic strategies. Though it has long been of interest, environmental soil-derived bacteria remain largely under-represented in research and thus uncharacterized in this field. This project aimed to identify soil microbes that display inhibitory mechanisms to potential nosocomial pathogens. Soil sample S1S3-2 displayed inhibitory phenotypes toward numerous bacteria and was identified as Pseudomonas baetica. In both planktonic and biofilm growth, P. baetica was able to inhibit Salmonella arizonae through a contact-dependent and temperature-dependent manner. Screening of a transposon insertion …

Data Curation And Integration For Cancer Cell Line Pharmacogenomics Analysis, Meric Kinali

Graduate Masters Theses

Cancer cell lines are essential resources for connecting genomic and molecular features with drug response and identifying biomarkers. Therefore, large-scale cancer cell line resources have been growing, but this introduces challenges such as data standardization, consistent annotation, matching identifiers, cross-database integration, and a reproducible computational framework. CellMiner Cross Database (CellMinerCDB) integrates pharmacogenomic datasets from multiple resources and provides a standardized analysis of cell lines across datasets. This thesis examines cancer cell line cross-databases and their importance in pharmacogenomics, with a particular focus on CellMinerCDB. As part of this work, I developed an R package for the gCSI (Genentech Cell Line …

The Role Of Seed Mix Characteristics And Soil Amendments During Post-Agricultural Prairie Restoration, Valerie N. Thurston, Michaela J. Woods, Madelaine Gregory, Mary C. Lloyd, Ryan W. Mcewan

Biology Faculty Publications

Introduction: Prairie restoration on degraded lands may be influenced by seed mix characteristics, including species richness and legume establishment. Soil amendments may facilitate restoration; however, the practical usefulness of techniques such as applications of whole soil and leaf mulch remains relatively unclear.

Objectives: We assessed whether increasing species richness and legume content in seed mixes enhances prairie restoration success and examined how soil amendments interact with seed mix composition to influence cover, species richness, diversity, and legume establishment.

Methods: We conducted a field experiment on a 12-ha post-agricultural site in Ohio, U.S.A. Twenty 50 × 50 m plots received one …

Gene Therapy Strategies To Enhance Antifungal Immunity In Microgravity, Riley Dienna

Discovery Day - Daytona Beach

During spaceflight, the immune system of astronauts becomes impaired due to microgravity, resulting in increased susceptibility to infections caused by pathogens such as Candida albicans. One of the most common clinical treatments for aggressive candidiasis is amphotericin B, a polyene antimycotic that targeted ergosterol in the fungal cell membrane and compromised the stability of the membrane. However, due to the chemical similarities between ergosterol and cholesterol, this treatment also affects the somatic cells of patients it is administered to. A novel treatment is therefore required to combat the aggressive fungal infection while minimizing damage to the host’s cells. This project …

Validating The Expression Of Genes Potentially Involved In The Development Of Aggressive Melanoma Tumor In The Zebrafish Melanoma Model, Mayra Matos Diaz

Theses, Dissertations and Culminating Projects

Melanoma is an aggressive form of skin cancer characterized by rapid progression, metastatic potential, and the frequent development of resistance to targeted therapies. Although the Inducible cAMP Early Repressor (ICER) has been identified as a potential tumor suppressor in melanoma, the molecular mechanisms underlying its role in tumor progression remain poorly understood. Building upon the transcriptomic findings of Wheelan et al. (2025), this study investigates the relationship between ICER and ten candidate genes (gdf6a, pdgfra, col4a4, fgfr2, pdgfrb, cdkn1a, fgf5, akt1, met, and notch3) associated with BMP signaling. Quantitative polymerase chain reaction (qPCR) was used to compare gene expression between …

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 …

Vertebrate Diversity In Cave Systems Of Colombia: An Approach Based On Environmental Dna Metabarcoding Analysis, Rita Daniela Martinelli Marín, Carlos Andres Lasso, Francesco Sauro, Susana Josefina Caballero

International Journal of Speleology

There is currently limited knowledge of the biological communities inhabiting cave ecosystems in South America. This study examines the vertebrate community composition of 21 caves across diverse subterranean ecosystems in Colombia using environmental DNA (eDNA) analysis. Water was collected from water bodies inside caves and subterranean systems in six of the eight speleological regions of Colombia in eight departments. Water was filtered manually through a 0.8 m pore size filter and preserved with Longmire solution. A 170-base pair (bp) fragment of the 12s mitochondrial gene specific for vertebrate identification was amplified by PCR and sequenced by Illumina (metabarcoding). Data corresponding …

Computational Insights Into Nucleosome Dynamics In Epigenetics Using Molecular Dynamics Simulations, Rutika Patel

Dissertations, Theses, and Capstone Projects

Nucleosome core particles (NCP) are the building blocks that form a highly organized and compact chromatin structure. Nucleosomes package DNA in the nucleus of eukaryotic cells. The NCP consists of about 147 base pairs of DNA wrapped around the histone octamer, with 1.65 superhelical turns in a left-handed manner. The histone octamer is composed of two copies of H3, H4, H2A, and H2B. Together with histone H1 and linker DNA, they further assemble into a higher-order chromatin structure. The nucleosome complex is stabilized by electrostatic interactions between positively charged histone residues and the negatively charged DNA backbone. To effectively access …

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 …

Exploring Biogeographical Ancestry Inference Of New York Residents Using A 45 Indel Panel, Amanda Martinez

Student Theses

Biogeographical ancestry (BGA) inference is an important tool in forensic science, providing supplemental information when comparison/reference DNA is not available for traditional DNA analyses. Insertion/deletion polymorphisms (INDELs) have been used in the last decade as ancestry-informative markers (AIMs) for BGA inference because they can be easily adapted to forensic-type samples and are determined using low cost and easy processing methods. Limited research has attempted to estimate ancestry and admixture in United States (U.S.) populations. This study evaluated the effectiveness of a 45- and 21- INDEL panel to measure population admixture proportions of four different origins (African, European, East Asian and …

Environmental Dna (Edna) Assessment Of Fish And Decapod Diversity And Their Association With Cetacean Distribution In Matang Coastal Waters, Perak, Lim Chuan Hui

Student Works (2020-2029)

The estuarine and coastal regions of Matang, Perak, Peninsular Malaysia, are vital fishing grounds and recognised biodiversity hotspots, but are increasingly exposed to human activities. Understanding the biodiversity of marine fish and decapods is crucial for effective conservation efforts. Conventional biodiversity monitoring methods face several challenges, including invasiveness, inconsistencies in sampling techniques, reduced taxonomic accuracy, time-consuming processes, high costs, and often only providing approximate estimates. In this study, we evaluated the use of environmental DNA (eDNA) metabarcoding to assess marine fish and decapod diversity in Matang waters and to explore possible associations between fish assemblages and local cetacean occurrence. Water …

An Investigation Of Entamoeba Histolytica Chitin Synthases And Other Encystation Factors In Early Encystation, John N. Talledo

All Theses

Entamoeba histolytica is a food-and-water-borne human protozoan pathogen that relies on a two-stage life cycle for successful proliferation outside of the host. E. histolytica exists in its dormant cyst form while outside of its host and converts to the motile trophozoite (amoeba) form in the small intestine. The trophozoites colonize the large intestine to cause symptomatic disease in ~10% of infections, resulting in ~100 million cases of amoebic dysentery each year. Trophozoites can convert back to the cyst form, which is shed in feces to continue the infection cycle.

Currently, there is a lack of understanding of the exact molecular …

Maternal Toxicity: A Meta-Narrative Review Of Pfas And Epigenetic Regulation In Embryonic Development, Catherine Duong, Hayden J. Fisher, Shannon Mccauley, Danny M. Nguyen

Research Methods Poster Session 2026

No abstract provided.

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 …

Genetic Screen For Regulators Of Pol4, A Dna Repair Polymerase In Saccharomyces Cerevisiae, Pasang Dolma Sherpa

Theses and Dissertations

In Saccharomyces cerevisiae, DNA polymerase 4 (POL4) is the beta repair polymerase, the product of the POL4 gene, and is involved in base excision repair (BER) and microhomology-mediated end joining (MMEJ). Despite its involvement in these repair pathways and its conservation across eukaryotes, deletion of POL4 shows no detectable phenotype under standard laboratory conditions. I hypothesized that unknown genes act as backup systems, providing redundant activities that allow pol4Δ cells to survive. To test this, a genetic screen for mutants showing synthetic lethality with pol4Δ was implemented. I constructed a strain lacking the POL4 gene and carrying …

The Hitchhiker's Guide To The Host: Fleas And The History Of Pikas In North America, Josh Pletcher

All NMU Master's Theses

Parasite phylogenetics can offer windows into the cryptic evolutionary history of hosts, often highlighting events that are not recorded by the phylogenetics of the host. Pikas (small lagomorphs) host a diverse parasite community comprising endoparasites (e.g., coccidians, nematodes, and cestodes) and ectoparasites (e.g., fleas and mites). Phylogenetic analysis of pika endoparasites has revealed pikas evolved in Asia and colonized North America in two waves, and that contact between these two pika lineages allowed parasites to be transferred from one lineage to another and to survive the extinction of their original host. To uncover these cryptic histories, understanding the biogeography of …

Validation Of A Real-Time Pcr Laboratory Developed Test For The Detection Of Pneumocystis Jirovecii In Bronchoalveolar Lavage Samples, Caitlyn Moon

Honors Scholar Theses

Pneumocystis jirovecii is an opportunistic, host-obligate fungal pathogen responsible for causing P. jirovecii pneumonia (PJP) in humans. PJP is treated with trimethoprim-sulfamethoxazole (TMP-SMX), a strong broad-spectrum antibiotic that carries risk of renal and hepatotoxicity. Therefore, rapid diagnosis or exclusion of PJP is crucial to ensure PJP-positive patients receive effective treatment and PJP-negative patients avoid unnecessary antibiotics. Unlike most microorganisms, P. jirovecii cannot be cultured, presenting complications for the typical methods of diagnosing fungal pathogens. Historically, the gold standard for diagnosis was direct microscopic examination with stains such as methenamine silver and calcofluor white, but this diagnostic technique requires highly skilled …

Characterizing The Molecular Response Of Embryonic Zebra Finch To Acute Sound Playback, Saidat O. Adeniran-Obey Miss

All Theses

Auditory stimuli are important cues that influence developmental plasticity in animals and are important for development and adaptation to an ever-changing environment. In the zebra finch (Taeniopygia guttata), there is evidence of adaptive developmental reprogramming in response to a prenatal ‘heat call’. Embryos exposed to this heat call exhibit changes in growth rate post-hatch, increased heat resistance, and enhanced reproductive success at maturity. However, it has long been assumed that embryonic zebra finches cannot respond to sound due to the immaturity of their auditory system. These findings raise the critical question of whether late-stage zebra finch embryos can, …

Using The Flexon Approach To Rnai To Identify Essential Genes That Affect Gonadal Development In C. Elegans, Joyce S. Lefevers

Undergraduate Theses

To elucidate the molecular role of essential genes in the gonadal development of Caenorhabditis elegans (C. elegans) it is necessary to utilize specialized molecular techniques such that the phenotypic effects of gene knockdown can be studied while the viability of the organism is preserved. Shaffer and Greenwald (2022) developed the floxed exon (flexon), a tool that improves upon previous approaches to spatiotemporal control of gene expression. The flexon subunit is made up of an artificial exon with a stop cassette flanked by artificial introns which, when inserted into a gene of interest, prevents the expression of that gene. …

Quantification Of Mouse Tracheal Epithelial Cell Differentiation With Cilia Defects, Olivia V. Allen

Honors Thesis

Primary Ciliary Dyskinesia (PCD) is an autosomal recessive disorder that affects 1 in every 7,500 live births. PCD results from motile cilia defects, impairing mucociliary clearance and causing chronic respiratory infections. Our lab studies include three PCD mouse lines — bgh (Spef2), nm1054 (Cfap221), and Cfap54^gt/gt (Cfap54). Prior transcriptomic data led us to hypothesize that PCD mutant mouse tracheal epithelial cells (MTECs) exhibit reduced differentiation into ciliated cells. MTECs from the trachea of the Wild Type (WT) and the PCD mutant mouse lines were cultured at an Air Liquid Interface (ALI) to start …

Optimizing Itpa R178c Assays Via Hplc, Jared J. Reisnouer, Wally D. Pines

2026 Symposium

Two of the major nucleotide bases in DNA and RNA (Adenine and Guanine) are derived from the purine Inosine Monophosphate (IMP). IMP may occasionally form the noncanonical nucleotide Inosine Triphosphate (ITP) within the cell and become incorporated into DNA during replication, leading to potentially lethal errors. To combat this, human cells produce the “housekeeping” enzyme Inosine Triphosphatase (ITPA) to revert ITP to IMP. A mutation of this protein that replaces the 178th amino acid Arginine with Cysteine (R178C) is associated with a fatal infantile encephalopathy. Previous assessments of enzyme-substrate binding and catalysis for ITPA variants have been run at a …

Transgenic Plant Cells For The Cost-Effective Production Of Pharmaceutical Proteins, Maria Gambaro

Create@State

Plant-based systems are becoming an important method for producing pharmaceutical proteins because they can be more cost-effective, and safer compared to traditional production methods which commonly use mammalian cells. This project aims to develop a transgenic plant cell system that can produce a pharmaceutical protein using molecular cloning techniques. A transgenic plant cell has the DNA of another plant integrated into its genome, altering its gene expression to produce different proteins. To begin, a plasmid carrying the gene of interest and the DNA components needed for expression will be designed. The plasmid will then be used to introduce the gene …

Impact Of One Nucleotide On Organ Enumeration And Phyllotaxy In Arabidopsis Thaliana, Hazel R. Frans, Tara Phelps-Durr

SACAD: Scholarly Activities

Arabidopsis thaliana is a model organism used by scientists to study plant genetics, development, and physiology. CRISPR-Cas9 is a biotechnology tool adapted from a bacterial defense mechanism to precisely edit DNA using a guide mRNA and a Cas9 protein. This project aims to create CRISPR-CAS9 mutations in the APETALA3 (AP3) gene of the model plant Arabidopsis thaliana. AP3 is a class B gene critical to the petal and stamen development of Arabidopsis flowers. The AP3 protein contains a MADS domain, which binds directly to DNA and may be responsible for the expression of the CaRG-box genes. AP3 works in conjunction …

Untangling G-Quadruplexes In Dna: The Effects Of Nucleotide Excision Repair, Jaidelin Alvardo, Abiageal Riley, Erick Morales Orrante, Raynne Malik

Posters - 2026

Nucleotide Excision Repair (NER) remo ves bulky DNA lesions that are attributed to UV irradiation, environmental mutagens, and chemo-therapeutic agents (Schärer, CSH Perspectives Biology, 2013). G4- quadruplexes are formed by four guanines hydrogen bonded together to form a planar ring, and stacking of the hydrophobic G quartets stabilizes the quadruplex structure Capra et al.,PLoS Computational Biology, 2010). A surplus of this structure is linked to genomic Instability and cancer development.

Prior studies indicate that because NER eliminates large lesions of DNA, there may be a link to the removal of G4-quadruplexes through Nucleotide Excision Repair (De Magis et al, Nature,2020). …

Investigating The Endogenous & Synthetic Estrogens To The Three Estrogen Receptor Subtypes Of Teleost Fish, Ann Cyril

Posters - 2026

Estrogen and the estrogen receptors are important biological and physiological processes. The various types of estrogen include estrone, estradiol and estriol. Estradiol’s main function is to maintain the reproductive system. Estrone’s main function is to develop the female's reproductive functions. Estriol’s main function is to aid the female's sexual developments but is on the weaker side. The fish, Atlantic Croaker, has three different estrogen receptors: ERα, ERβa, and ERβb. Based on the estrogen receptors, it appears that their binding affinities do differ in strength. Each estrogen receptor has different amino acids involved that could contribute to the difference in their …

Investigating Rad14 Gene Nucleotide Excision Repair On G-Quadruplexes, Juan Pablo Olvera Rodriguez, Tyna Trevino, Yvette Gonzalez, Georgia Romike

Posters - 2026

DNA is typically found as a double-stranded helical structure; however, it can be found in different types of structures, such as G-quadruplexes (G4s). These are structures formed when DNA sequences are rich in Guanines, which interact with each other by hydrogen bonding, forming stacked G-tetrads. These guanine-rich structures are known for interacting with DNA during important cell processes, such as recombination and replication, leading to instability and DNA damage (Grey et al., 2014). If not treated properly, these structures may contribute to mutations and cancer development. To solve these issues, cells have developed maintenance pathways such as Nucleotide Excision Repair …

Exploring Base Excision Repair Using Gene Knockout, Gregory Guantos, Cailyn Brock, Kamily Visser, Dylan Vargas

Posters - 2026

•             Base Excision Repair (BER) fixes damaged 3DNA bases throughout the cell cycle by removing damaged bases and replacing either one nucleotide in short-patch BER or a short stretch of nucleotides in long-patch BER. (Hindi, 2021, Cellular and Molecular Life Sciences:CMLS)

•             4G-quadruplexes (G4s) are 4 stranded secondary DNA structures formed in guanine rich areas of DNA and RNA. (Rhodes, 2015, Nucleic Acids Research)

The URA3 plasmid was used as a PCR template to make a gene deletion construct, then yeast were transformed so APN1 was replaced by URA3. 2APN1 encodes a major DNA repair enzyme in yeast, and strains …

Phenol–Chloroform Dna Extraction For Dna Amplification From Personal Items, Aditya Rahman Ernanto, Dinda Amaliyatul Khasanah, Yunita Aldirahayu, Rizki Setiyaningrum, Arya Iswara

Makara Journal of Science

This study examined the feasibility of extracting DNA from various personal items using the phenol–chloroform–isoamyl alcohol (PCIA) method. A towel, collared shirt, toothbrush, shower puff, comb, hair tie, and buccal swabs were analyzed. The quality of the DNA extraction, along with DNA concentration, purity, and suitability for multiplex PCR amplification, were evaluated. The shower puff exhibited the highest DNA concentration (68.35 ng/µL), whereas the collared shirt yielded the lowest (26.43 ng/µL). All samples exhibited good DNA purity (A260 nm/A280 nm ranging from 1.827 to 1.985), emphasizing the potential of this method for forensic analysis. Factors influencing DNA concentration included material …

Reproductive Performance And Its Association With Esr, Prlr, Fshb Genes In Indigenous “I” Pigs, Do Duc Luc, Phan Thi Tuoi, Nguyen Thai Anh, Do Thi Hue, Nguyen Hoang Thinh

The Thai Journal of Veterinary Medicine

Improving the reproductive performance of sows plays an important role in the pig industry, and it applies not only to commercial pigs but also to indigenous pigs. In this study, the polymorphisms of three genes, namely estrogen receptor (ESR), prolactin receptor (PRLR), and follicle-stimulating hormone beta subunit (FSHB) in the “I” pig population were investigated, and their associations with reproductive performance were evaluated. Ear tissue samples were collected from 151 fattening pigs and 126 sows across breeding farms in Vietnam for polymorphisms of the ESR, PRLR and FSHB genes. Three genotypes (AA, AB, and BB) were detected at the …

Metagenomic Profiling Of Gut Microbiome Signatures Across Liver Disease Stages And Hcv-Related Hepatocellular Carcinoma In Egyptian Patients, Marwa A. Zahra

Theses and Dissertations

Dysbiosis in the gut microbiome, particularly concerning the synchronous crosstalk between the gut and the liver, has been associated with various diseases. This study profiles the gut microbiome in liver diseases among Egyptian patients, with a focus on the hepatitis C virus (HCV) and hepatocellular carcinoma (HCC), both of which are highly prevalent in Egypt. Utilizing shotgun metagenomic sequencing, we analyzed microbial gene catalogs and taxonomic profiles from 46 Egyptian patients categorized into five groups: healthy individuals, liver disease patients of different etiologies, post-HCV, treated HCV, and HCV-HCC patients. Healthy and treated HCV patients exhibited distinct microbial profiles characterized by …