Genetics and Genomics Commons^™

Discovering The Genetics Underlying Speciation Traits In Heuchera (Coral Bells), Tajinder Singh

Honors Theses

Hybridization is a key evolutionary mechanism for generating biological diversity, ultimately shaping diversification and adaptation of plant lineages in natural and agroecosystems.  Our understanding of the frequency, distribution, and significance of hybridization is rapidly increasing, but the external driving forces that dictate why certain species hybridize, and others do not remain obscure. The physical traits that shape gene flow and trait sharing among species are likely to be among the key factors that directly control hybridization. Gene flow in most plants is mediated by pollinating insects and thus by pollination syndromes, which are suites of floral traits that have evolved …

Cleft Palate And The Coordination Of Wnt Signaling And Pax9 In Murine Palatogenesis, Landon Wyatt

Honors Theses

Cleft palate is a common craniofacial birth defect that arises when the molecular and morphogenetic events guiding secondary palate formation lose coordination during a narrow developmental window. In mice, successful palatogenesis requires the paired palatal shelves to grow vertically, elevate above the tongue, and fuse at the midline; disruption of any of these steps can result in clefting. Two important regulators of this process are canonical Wnt signaling and the transcription factor Pax9, both of which contribute to normal palatal mesenchymal growth and patterning during early development. This paper first examines whether altered Dkk1/Wnt signaling contributes to the Pax9-null palate …

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. …

Cross-Sectional Associations Of Metabolically Healthy Obesity, Lifestyle Factors, And Steatotic Liver Disease In Adults From The Fels Longitudinal Study, Ariana L. Garza, Audrey C. Choh, John Blangero, Cici X. Bauer, Stefan A. Czerwinski, Miryoung Lee

School of Medicine Publications

Objective: To examine the associations of metabolic health and obesity phenotypes with liver fat accumulation and hepatic steatosis in adults. Methods: We analyzed 676 non-Hispanic white adults (18–95 years; 55.8% female) from the Fels Longitudinal Study using a cross-sectional design. Participants were classified into metabolically healthy normal weight (MHNW), metabolically healthy obesity (MHO), metabolically unhealthy normal weight (MUNW), and metabolically unhealthy obesity (MUO) phenotypes. Metabolically unhealthy status was defined as the presence of ≥1 metabolic dysfunction, consistent with prior epidemiological definitions; secondary analyses using ≥2 were also performed. Obesity was defined using DXA-derived body fat percentage. Liver fat (%) was …

From Bench To Bedside: Unraveling The Role Of Sarm1 In Chronic Human Neurodegenerative Disease, Caitlin Dingwall

Arts & Sciences Graduate Student Theses and Dissertations

Axon degeneration (AxD) is an early and often causative event in many neurodegenerative diseases, yet no treatments exist to halt the breakdown of axons. In healthy axons, the axon survival factor NMNAT2 inhibits SARM1, the central executioner of programmed axon degeneration. NMNAT2 is a highly labile protein produced in the soma and trafficked into the axon. Nerve injury blocks axonal transport and leads to rapid depletion of axonal NMNAT2, causing NMN buildup and NAD+ loss. Recent breakthroughs led to the discovery that SARM1 is activated by an increase in the NMN to NAD+ ratio. While the SARM1 axon degeneration pathway …

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 …

Identification Of Lipid Quantitative Trait Loci Linked With Cardiometabolic Disease In Asian Indians And Europeans: A Genome-Wide Association Study And Mendelian Randomization, Madhusmita Rout, Christopher E. Aston, Ravindranath Duggirala, Harald H. H. Goring, Oliver Fiehn, Dharambir K. Sanghera

School of Medicine Publications

Background: Genetic mechanisms that predispose people to type 2 diabetes (T2D) and cardiovascular disease (CVD) remain poorly understood, partly because of a lack of sufficient data on non-European ethnic groups. Extending these evaluations to diverse cohorts is essential for gaining insights into the molecular pathways involved in disease development among human populations. In this study, we aimed to evaluate the genetic connection between the human lipidome and cardiometabolic disorders. We conducted a metabolite genome-wide association study (mGWAS) in a Punjabi population from India, along with multi-layer replication studies using the UK Biobank and other independent European and non-European cohorts.

Methods …

Biomechanical Effects Of Bilateral Torsion And Skeletal Fusion: A Case Study, Linnéa Forbes

Honors Projects

As part of both a personal endeavor and an academic project, I have investigated the aetiology and treatment of seemingly idiopathic and debilitating leg pain in a patient over the past 10 years. Via collaboration with medical professionals at Cincinnati Children’s Hospital, Cincinnati Premier Physical Therapy, and Cincinnati Women’s TriHealth, I have identified sources of pain at the anatomical level. The combination of internal femoral torsion, external tibial torsion, pes planus, and bony fusions appear to be major perpetuators of the pain. An effective treatment continues to be evasive. To date, I have attempted to find answers through genetic approaches, …

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 …

Amyloid Beta-42 Neurotoxicity In Drosophila Retinal Development, Shay O. Sims, Pierce Duncan, Malachi Abon, Jacob G. Smith

Create@State

Alzheimer's disease (AD) represents one of the most prevalent neurodegenerative disorders globally. Thus far, the underlying mechanisms associated with the pathogenesis of AD are innately elusive. Two hallmarks associated with the progression of AD exist, including Amyloid-Beta 42 (Aβ42) protein plaque formation and hyperphosphorylation of tau proteins in neurons. Amyloid-beta is known to concentrate with other neuronal proteins as complexes form, including the cytoskeletal protein actin. However, whether actin contributes to neuronal decline in AD is unknown. To further understand the cellular cascades associated with AD, we investigated the role of cytoskeleton dynamics in modulating oxidative stress and neuroinflammation within …

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 …

Variation In Infection Prevalence Of Splendidofilaria Pectoralis Across Alaskan Grouse Populations, Anahi Garcia Valdez, Diego Martinez

Create@State

In recent years, rapid climate change has altered species distributions worldwide and influenced parasite transmission dynamics in wildlife systems. Parasite infections play an important role in shaping patterns of disease distribution across species and populations. Understanding variation in infection prevalence across geographic regions and host demographic groups is essential for interpreting these patterns. Splendidofilaria pectoralis is a filarial nematode that infects the connective tissues of grouse (Aves: Tetraonini) in Alaska and has been moving northward as the climate warms. However, relatively little is known about the variation in prevalence of the nematode across geography and demography. This project examines variation …

The Genetics Of Sex, Fortis Brown

The Agora

Sex is a complex biological process that begins in the womb and lasts into puberty and beyond. It is often presented to society as a binary, chromosome-based system where XX means female and XY means male. In reality, chromosomes are just the beginning of a lifelong process involving hormones that influence biological changes. This process becomes apparent with its errors, known as Differences in Sexual Development (DSDs). DSDs can be caused in two main ways: through changes in either meiosis or in gene expression. While many consider these changes as ‘errors’, the processes that cause them to have been intentionally …

A Computational Assessment Of Halobacterium Salinarum Glutamate Dehydrogenase Enzymes, Maaz Abdalla

Thesis/ Dissertation Defenses

Glutamate dehydrogenase (GDH) is a hexameric enzyme. GDH is involved in several pathways and cellular processes such as oxidation-reduction homeostasis, ammonia metabolism, lipid biosynthesis, insulin and lactate production, and acid-base equilibrium. The main objective of this thesis is to understand the structural and biochemical properties of this enzyme and why some organisms, for e.g., Halobacterium salinarum, have more than one GDH with different coenzyme specificities. The catabolism of glutamate is linked to NAD+-specific GDHs, meanwhile, NADP+-specific GDHs play an anabolic role in ammonia assimilation. Molecular docking and binding free energy calculations were employed followed by long-scale (500 nanoseconds) comparative molecular …

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 …

Ultrasonography Accompanied By Genetic Testing In Feline Polycystic Kidney Disease, Thao Phuong Vu, Thong Quang Le, Ha Nguyen Nhat Tran, Khoa Hoang Dang Le, Anh Phu Nam Bui

The Thai Journal of Veterinary Medicine

Autosomal dominant polycystic kidney disease (ADPKD), caused by the PKD1 c.10063C>A mutation, is a prevalent inherited feline disorder, but its allele frequency in Vietnam remains unidentified. This study aimed to determine the carrier frequency of this variant in British Shorthair, Maine Coon, and Ragdoll cats in Ho Chi Minh City and to correlate genotype with ultrasonographic phenotype. Ninety-seven client-owned cats were genotyped for the pkd1 mutation using PCR-RFLP. A subset of 47 cats also underwent abdominal ultrasonography to detect renal cysts. Genotypic results were correlated with sonographic findings, and risk factors were analyzed using chi-square tests and odds ratios …

Unpacking Developmental Programming: A Conceptual And Historical Analysis In The Context Of Dohad, Andrea Gretchev, Heide S. Temples, Gillian England-Mason, Deborah Dewey, Sara M. Sarasua, Christopher Farrell, Vivian Haley-Zitlin

Publications

The Developmental Origins of Health and Disease (DOHaD) paradigm posits that early environmental factors may influence a child’s development and long-term health outcomes. Developmental programming (DP) is central to this paradigm, whereby specific early life exposures during critical periods of development are associated with changes to physiological and metabolic pathways, potentially predisposing individuals to disease. However, no standard definition of DP exists, and various terms have been used to describe similar processes. This analysis aimed to develop a conceptual definition for DP to inform interdisciplinary research, education, and practice. Walker and Avant’s eight-step method was employed to analyze the literature, …

G-Quadruplex Dna-Driven Genomic Instability Under Ber Loss, Addison Belick, Claryssa Gutierrez, Joslynn Rosas, Andrea Vargas

Posters - 2026

Base Excision Repair (BER) is a cellular tool that can repair damaged DNA (Hindi et al., 2022, Cellular and Molecular Life Sciences). G-quadruplexes (G4s) are unique 4-stranded structures in DNA or RNA that are rich in guanine (Gray et al., 2023, Nat. Chem. Biol). The purpose of this study is to understand whether BER contributes to the removal of G4s in DNA. This will determine if the BER-deficient yeast is more sensitive to treatment with G4-binding drugs than the BER-proficient yeast. We will replace the APN1 gene in the yeast genome with the URA3 gene, because the wild type yeast …

Understanding P53 Regulation On Transposable Elements In Cancer, Xuan Qu

Arts & Sciences Graduate Student Theses and Dissertations

Transposable elements (TEs), traditionally known as “jumping genes”, are known to have the ability to move in the genome and alter the activation of transcriptions from nearby genes. Taking up nearly half of the human genome, TEs have evolved, and some have been selected to play important roles in biological processes. We found that in human diseases such as cancer, global hypomethylation resurrects many ordinarily silenced TEs. These TEs can often serve as alternative promoters for oncogenes and play functionally meaningful roles in driving disease processes. One of the top genetic mutation status that correlates with differential numbers of TE …

Dissecting The Etiology Of Alcohol Use Disorder By An Integrative Heritable Component Approach, Ivy Garrenton

Computer Science Theses & Dissertations

Alcohol Use Disorder (AUD) is a pervasive condition characterized by complex interplay among genetic, phenotypic, and environmental factors. Although previous studies have identi fied genetic loci associated with alcohol consumption, these efforts have not captured the genetic heterogeneity and gene-environment interactions underlying AUD pathogenesis. To address this critical gap, we developed a novel statistical methodology that integrates phenotypic, genotypic, and environmental data through an environmentally modified Genetic Relationship Matrix (GRM) to derive AUD-related traits with enhanced heritability.

This approach demonstrated superior performance in both simulated and real-world datasets. Traits derived using the environmentally modified GRM exhibited significantly higher estimated heritability …