Genetics and Genomics Commons^™

The Study Of Dmrt1 In Zebrafish And How It Impacts Sex Determination, Raymond Michael Poirier

Graduate Masters Theses

The dmrt1 gene is common amongst most animals and functions to determine or maintain male sex during development. Similarly, in zebrafish dmrt1 is important for male sex determination and maintaining proper testis morphology. This gene is expressed in two different cell types of the testis in zebrafish, germ cells and Sertoli cells. While we know where this gene is expressed and what its role is, it is not known if it is sufficient to drive male fate. If so, then in which cells is it sufficient to drive male fate in the testis? I aimed to answer this question by …

Characterization Of Ato Family Transporters In The Fungal Pathogen Cryptococcus Neoformans, Will Betsill

All Theses

Fungal pathogens are a significant threat to public health as they are becoming increasingly common and more resistant to treatment. Cryptococcus neoformans contributes greatly to this threat annually by causing an estimated 278,000 cases of cryptococcal meningitis resulting in approximately 181,000 deaths globally according to the CDC. C. neoformans is ubiquitous across most of the globe and can be found in such places as in trees or soil. Exposure to this fungus is especially dangerous to individuals who are immunocompromised or immunosuppressed. In these cases, inhalation of spores can lead to infection in the lungs. Once in the lungs, C. …

A Phylogenetic Analysis Of The Population Dynamics Of A Captive Colony Of Diploptera Punctata., Nick Peterson

Theses/Capstones/Creative Projects

The unique milk production of Diploptera punctata makes this species a promising model species in entomology for studying the evolution of milk production and for insect endocrinology. Despite this, the genetic diversity of captive populations of the species is not well studied. To better evaluate the captive diversity and population dynamics of Diploptera punctata at UNO we extracted the DNA of 20 random individuals and amplified their DNA using 4 different primers before cleaning the amplified products and sequencing the genes of the samples for use in both individual and concatenated phylogenetic trees. Our results indicate the UNO colony of …

The Anti-Diabetic Drug Metformin Disrupts Feeding And Sleeping Behaviors In Drosophila Melanogaster., Lucas Fitzgerald

College of Arts & Sciences Senior Theses

Dimethylbiguanide, also known as metformin, is the single most prescribed oral treatment for non-insulin dependent diabetes mellitus, or type 2 diabetes, in Western countries. The primary mechanism of action that metformin acts through is the activation of AMP kinase, an important regulator of energy homeostasis. While the anti-diabetic effects of metformin are well documented, its effects on feeding and sleeping behaviors are not well characterized. Using the model organism Drosophila melanogaster, the mean daily quantity of food consumed was measured and compared between groups treated with several dosages of metformin. Feeding interactions such as meal frequency and length were …

Conserving One Of Hawai'i'S Last Endemic Ducks: Genetics And Habitat Associations Of Koloa, Feral Mallards, And Their Hybrids, Kristi Fukunaga

Open Access Theses & Dissertations

Increases in anthropogenic hybridization through introduced species have accelerated the loss of genetic diversity and reductions in population size of native species that are already threatened by population and genetic diversity decline. Fertile hybrids that are common among waterfowl (order Anseriformes) are especially worrisome. A prime example is the endangered Hawaiian duck (Anas wyvilliana; “koloa maoli”), which is the remaining endemic duck species on the main Hawaiian Islands and is threatened by genetic extinction through ongoing hybridization with feral mallards (Anas platyrhynchos). Of note, koloa populations are known to be strongly male-biased (3:1), and this sex bias is known to …

Understanding The Role Of Minor Intron Splicing In Spermatogenesis, Jade Rosado, Kazumasa Takemoto, Rahul Kanadia

Honors Scholar Theses

The minor spliceosome is composed of the unique small nuclear RNAs (snRNA), U11, U12, U4atac, and U6atac, and is necessary for the splicing of less than 0.5% of introns, termed minor introns. Minor intron containing genes (MIGs) regulate diverse processes, one of which is spermatogenesis. Specifically, 111 testis-specific MIGs have been identified, suggesting that minor splicing is necessary for spermatogenesis. To interrogate the role of minor splicing in spermatogenesis, we conditionally ablated the Rnu11 gene, which encodes for the U11 snRNA, in the developing testes via Stra8-iCre, creating a Rnu11^Flx/Flx::Stra8-Cre⁺ mutant. We found, at postnatal …

Archaeal Diversity In The Anna's Hummingbird Microbiome, Lauren E. Chance

Honors Scholar Theses

The microbial communities that are present in and on vertebrates are collectively called the microbiome. The composition of a microbiome is dependent upon the host, the environment, and evolution. There has been extensive research on the bacterial composition of host-associated microbiomes, however, there has been much less work on the archaeal composition of host-associated microbiomes. Archaea have previously been assumed to primarily exist in extreme environments, but this may not be true and has been influenced by their generally low abundance and methodological difficulties in detection. It is possible they are consistent members of diverse host-associated microbiomes.

Archaea-specific PCR primers …

Exploring Genomic Convergence For Adaptations To Freezing Environments In Polar Fish, Ethan Talley

Biological Sciences Undergraduate Honors Theses

Convergent evolution provides valuable insights into how natural selection shapes species traits. Genomic analysis of lineages that display convergent traits has the potential to identify candidate genes for environmental adaptations across the scope of entire genomes. One remarkable example of convergent evolution is the independent development of antifreeze proteins (AFPs) in phylogenetically distant polar fish lineages. While AFPs themselves are relatively well studied, the full genomic context of adaptation to freezing conditions in these fish lineages remains largely unexplored. Leveraging the whole genome sequences previously assembled in our lab, along with other high-quality genomes available in GenBank, I examined the …

Characterizing The Role Of Pa5189 Of Pseudomonas Aeruginosa In Deletion And Overexpression Mutants, Seh Na Mellick

Theses/Capstones/Creative Projects

In the context of rising multidrug resistance in biofilm-forming pathogens like Pseudomonas aeruginosa, this study investigates the role of the understudied transcription factor PA5189 in antibiotic resistance and biofilm formation. PA5189 deletion and overexpression mutants were created in a parent P. aeruginosa strain using pEX18Tc-based recombinant suicide vectors, with genotypic verification of putative triparental conjugants achieved through restriction digestion and PCR. The study revealed that PA5189 overexpression significantly increases resistance to commonly used broad spectrum antibiotics such as ciprofloxacin and imipenem. Additionally, differential expression of PA5189 was found to notably affect biofilm formation, with variations contingent on the nutrient …

Survey Of The Bolctes From Fish River Nature Preserve, Noah T. Nelson

Honors Theses

Boletes are a special kind of mushroom inside of the Kingdom Fungi that are distinguished from other mushrooms by their uniquely pored hymenium, as opposed to gills. Many boletes are ectomycorrhizal, meaning they are mutualists with vascular plants, and thus beneficial to the overall health of the terrestrial ecosystem. Some are well-known for their edibility and are of economic importance. In the United States 59 genus-level clades comprising 290 operational taxonomic units have been reported. The southeastern US and Gulf Coast regions however are less researched and recorded for their mushroom ecology. In Alabama, only 56 bolete species have been …

An Investigation Of Information Structures In Dna, Joel Mohrmann

Department of Electrical and Computer Engineering: Dissertations, Theses, and Student Research

The information-containing nature of the DNA molecule has been long known and observed. One technique for quantifying the relationships existing within the information contained in DNA sequences is an entity from information theory known as the average mutual information (AMI) profile. This investigation sought to use principally the AMI profile along with a few other metrics to explore the structure of the information contained in DNA sequences.

Treating DNA sequences as an information source, several computational methods were employed to model their information structure. Maximum likelihood and maximum a posteriori estimators were used to predict missing bases in DNA sequences. …

Elucidation Of The Overexpression Of Taf2 In Eukaryotic Cells, Morgan Osborn

Honors Theses

Through several studies, Taf2 has been found to be upregulated in various cancer cells. However, the mechanism through which this increased expression of Taf2 occurs remains unknown. As evolutionarily conserved ubiquitin-proteasome system (UPS) maintains protein homeostasis for normal cellular function, we hypothesized that stability of Taf2 may be regulated by this UPS and this UPS may be dysregulated in cancer cells causing overexpression of Taf2. To test our hypothesis, we assessed the role of the UPS in the regulation of the stability of Taf2 by 26S proteasome-mediated degradation. To do so, we performed molecular experiments mainly through two steps: 1st …

The Role Of The Transcription Factor Cebpa In Regulating Lung Alveolar Type 2 Cell Fate In Vivo, Dalia Hassan

Dissertations and Theses (Open Access)

Cell plasticity can extend across all possible cell types, yet it naturally diminishes as cells progress through differentiation. This plasticity can be reactivated during injury repair, engaging developmental flexibility. Our investigations reveal the critical role of the transcription factor (TF) CEBPA, specific to lung alveolar type 2 (AT2) cells, in modulating AT2 cell plasticity within the mouse lung. We demonstrate that CEBPA constrains AT2 cell plasticity by promoting the AT2 differentiation program and recruiting the lineage-specific TF NKX2-1. Without CEBPA, AT2 cells, in both neonatal and mature, show a diminished AT2 program; however, only neonatal cells re-activate the SOX9 progenitor …

Mismatch Repair Deficient Neoantigen And Associated Circulating T-Cell Receptor Repertoires In Lynch Syndrome, Ana Bolivar

Dissertations and Theses (Open Access)

Lynch Syndrome (LS) is the most common inherited colorectal cancer (CRC) syndrome. It constitutes the perfect model to understand DNA mismatch repair deficient (MMRd) carcinogenesis, which underlies 15% of early-stage CRC. LS patients develop MMRd tumors with high loads of shared neoantigens (neoAgs), which are recognized by the immune system. Previous research has concentrated on discovering neoAgs and their potential as targets for vaccines in LS patients. However, these studies have primarily identified shared neoAgs from cancers, lacking detailed information on targetable neoAgs present in precancerous lesions. Understanding this landscape of pre-cancer derived neoAgs is crucial for intercepting cancer development …

Uncovering Capillary Endothelial Cells Response During Lung Injury-Repair, Celine Shuet Lin Kong

Dissertations and Theses (Open Access)

Once thought to be a homogenous population, capillary endothelial cells (ECs) have embodied organotypic specialization and heterogenous properties, both during homeostasis and tissue injury. In the lung, capillary ECs consist of two distinct populations, CAP1 and CAP2s; how each population responds to diverse tissue injury is incompletely understood. In this thesis, I report the induction and function of a truncated isoform of Ntrk2, Ntrk2^-tk (lacking the tyrosine kinase domain) in multiple injury models. Using a combinatorial approach of single-cell multiome, mouse genetics and viral infection models, I found that Ntrk2^-tk is broadly induced in CAP1s after the initial …

Genomic Characterization Of Enterococcus Spp Infecting Chicken Embryo, Aishat Olaoluwa Lawal

Graduate Theses and Dissertations

Chicken embryo mortality has been attributed to bacterial infections and can lead to a decline in hatchability, posing potential losses in the broiler industry. This study aims to investigate the vertical transmission of specific bacterial pathogens from breeder hens to subsequent broiler flocks through MGEs and their association with host specificity. In our sampling of 360 eggs from a broiler flock, we isolated various Enterococcus species, including E. gallinarum and E. faecalis, from incubated egg yolks or aborted embryos. E. avium was found in unincubated bad yolks. Other species like Streptococcus, Lactobacillus, and Bacillus were observed but presumed to be …

Plant Model Of Α-Synucleinopathy: Expression Of Α-Synuclein A53t Variant In Hairy Root Cultures Leads To Proteostatic Stress And Dysregulation Of Iron Metabolism, Jasmina Kurepa, Kristen A. Bruce, Greg A. Gerhardt, Jan A. Smalle

Neurology Faculty Publications

Synucleinopathies, typified by Parkinson’s disease (PD), entail the accumulation of α- synuclein (αSyn) aggregates in nerve cells. Various αSyn mutants, including the αSyn A53T variant linked to early-onset PD, increase the propensity for αSyn aggregate formation. In addition to disrupting protein homeostasis and inducing proteostatic stress, the aggregation of αSyn in PD is associated with an imbalance in iron metabolism, which increases the generation of reactive oxygen species and causes oxidative stress. This study explored the impact of αSyn A53T expression in transgenic hairy roots of four medicinal plants (Lobelia cardinalis, Artemisia annua, Salvia miltiorrhiza, and Polygonum multiflorum). In all …

Key Variants Via The Alzheimer's Disease Sequencing Project Whole Genome Sequence Data, Yanbing Wang, Chloé Sarnowski, Honghuang Lin, Achilleas N Pitsillides, Nancy L Heard-Costa, Seung Hoan Choi, Dongyu Wang, Joshua C Bis, Elizabeth E Blue, Eric Boerwinkle, Philip L De Jager, Myriam Fornage, Ellen M Wijsman, Sudha Seshadri, Josée Dupuis, Gina M Peloso, Anita L Destefano

Faculty, Staff and Student Publications

INTRODUCTION: Genome-wide association studies (GWAS) have identified loci associated with Alzheimer's disease (AD) but did not identify specific causal genes or variants within those loci. Analysis of whole genome sequence (WGS) data, which interrogates the entire genome and captures rare variations, may identify causal variants within GWAS loci.

METHODS: We performed single common variant association analysis and rare variant aggregate analyses in the pooled population (N cases = 2184, N controls = 2383) and targeted analyses in subpopulations using WGS data from the Alzheimer's Disease Sequencing Project (ADSP). The analyses were restricted to variants within 100 kb of 83 previously …

Retinal Dystrophies Associated With Peripherin-2: Genetic Spectrum And Novel Clinical Observations In 241 Patients, Rachael C. Heath Jeffery, Jennifer A. Thompson, Johnny Lo, Enid S. Chelva, Sean Armstrong, Jose S. Pulido, Rebecca Procopio, Andrea L. Vincent, Lorenzo Bianco, Maurizio Battaglia Parodi, Lucia Ziccardi, Giulio Antonelli, Lucilla Barbano, João P. Marques, Sara Geada, Ana L. Carvalho, Wei C. Tang, Choi M. Chan, Camiel J. F. Boon, Jonathan Hensman, Ta-Ching Chen, Chien-Yu Lin, Pei-Lung Chen, Ajoy Vincent, Anupreet Tumber, Elise Heon, John R. Grigg, Robyn V. Jamieson, Elisa E. Cornish, Benjamin M. Nash, Shyamanga Borooah, Lauren N. Ayton, Alexis Ceecee Britten-Jones, Thomas L. Edwards, Jonathan B. Ruddle, Abhishek Sharma, Rowan G. Porter, Tina M. Lamey, Terri L. Mclaren, Samuel Mclenachan, Danial Roshandel, Fred K. Chen

Wills Eye Hospital Papers

PURPOSE: To describe the clinical, electrophysiological and genetic spectrum of inherited retinal diseases associated with variants in the PRPH2 gene.

METHODS: A total of 241 patients from 168 families across 15 sites in 9 countries with pathogenic or likely pathogenic variants in PRPH2 were included. Records were reviewed for age at symptom onset, visual acuity, full-field ERG, fundus colour photography, fundus autofluorescence (FAF), and SD-OCT. Images were graded into six phenotypes. Statistical analyses were performed to determine genotype-phenotype correlations.

RESULTS: The median age at symptom onset was 40 years (range, 4-78 years). FAF phenotypes included normal (5%), butterfly pattern dystrophy, …

Examining Population Structure Of Cismontane And Desert Populations Of Zebra-Tailed Lizards (Callisaurus Draconoides) Using Mitochondrial And Nuclear Intron Dna., Lauren Nicole Morrison

Electronic Theses, Projects, and Dissertations

Callisaurus draconoides, also known as the Zebra-Tailed lizard, belongs to the family Phrynosomatidae family (Pianka, et al. 1972). C. draconoides is a widespread desert lizard found western North America. In California, this species can be found in the Mojave and Colorado Deserts. There are currently several populations that reside in the San Bernardino basin on the cismontane side of the Transverse and Peninsular ranges. These mountain ranges have the potential to have isolated the cismontane populations from their typical desert ranges. In addition, geological passes have the potential to serve as migration corridor between the Deserts and cismontane regions. The …

Epigenetic Modification As A Therapeutic Target In Brafv600e-Mutated Metastatic Colorectal Cancer, Hey Min Lee

Dissertations and Theses (Open Access)

Patients with BRAF^V600E-mutated metastatic colorectal cancer (mCRC) experience a worse prognosis and demonstrate only a 5% response rate to BRAF inhibitor treatment. In this study, adaptive resistance, and a potential combination of standard therapies in BRAF^V600E CRC were unveiled. Intriguingly, a robust association of BRAF^V600E mutation and DNA hypermethylation suggests this is a unique subgroup harboring aberrant epigenetic phenotype. Firstly, DNA methyltransferase (DNMT) inhibitor treatment induced profound DNA hypomethylation in vivo, but minimal change in gene expression due to adaptive elevation of the repressive histone methylation, H3K27me3, leading to compensatory suppression of key tumor suppressor genes, …

Patient Preferences For Ultrasound Soft Sign Disclosure With Prior Negative Cfdna Screening, Disha Patel

Dissertations and Theses (Open Access)

Soft signs are nonstructural fetal anomalies that can be identified by the second-trimester comprehensive ultrasound examination. In isolation, soft signs are insufficient to diagnose chromosome conditions but can adjust an individual's risk for aneuploidy, primarily Down syndrome. In the age of noninvasive cell-free DNA (cfDNA) prenatal screening, which exhibits superior sensitivity and specificity for aneuploidy compared to what can be provided by soft sign risk adjustment, the utility of these soft signs is arguably waning. Thus, this study aimed to establish patient preferences for whether and how soft signs are disclosed in pregnancy to inform recommendations for disclosure. A survey …

Acute Pain Prediction In Oral Cavity And Oropharyngeal Cancer Patients Receiving Radiation Therapy, Vivian Salama

Dissertations and Theses (Open Access)

Oral-Cavity and oropharyngeal cancers (OC/OPC) are types of head and neck cancers that are increasing in incidence domestically. Radiation therapy (RT) is crucial in OC/OPC management. Pain is a common and challenging symptom for most patients during therapy, as nearly all patients undergoing locoregional RT in OC/OPC require analgesia for acute iatrogenic pain. Moreover, about 45% of long-term survivors report chronic pain, with more than 10% exhibiting severe chronic pain. Pain control is challenging due to the multifactorial clinical, molecular, and cellular etiology of cancer/therapy pain, as well as variation in pain assessment and the non-uniform management of pain between …

Patient Understanding Of Fetal Sex Versus Gender In The Context Of Routine Cell-Free Dna Screening, Mindy Kolodziejski

Dissertations and Theses (Open Access)

Non-invasive prenatal testing (NIPT) is the current standard of care to screen for fetal aneuploidy using cell-free DNA (cfDNA). NIPT screens for sex chromosome aneuploidies (SCAs) and in doing so, can predict fetal chromosomal sex. Despite sex and gender being distinct concepts, many patients refer to NIPT as “the gender test” and elect testing in order to find out predicted fetal sex and assume gender. Our study aimed to evaluate and describe patient understanding of sex and gender in the context of receiving routine prenatal genetics education (PGE) on NIPT. A survey was developed with the goal of assessing patient …

Influential Factors For Disclosing A Tuberous Sclerosis Complex Diagnosis To Romantic Partners, Laura Gorecki

Dissertations and Theses (Open Access)

Tuberous sclerosis complex (TSC) is a highly variable genetic condition characterized by multi-organ tumor predisposition. Due to the heritability, variability, and severity of this condition, individuals with TSC may face unique psychosocial challenges in dating and romantic relationships, specifically related to disclosing their diagnosis to romantic partners. Despite disclosure within romantic relationships being explored in the context of other genetic conditions, this area has not yet been explored in the TSC community who face unique challenges related to physical and mental health, educational performance, and overall quality of life. This study surveyed 117 independent adults with TSC regarding the following …

Efficacy Of Genetic Testing Methodologies For Prenatal Detection Of Skeletal Anomalies And Craniosynostosis Syndromes, Nicolette Murphey

Dissertations and Theses (Open Access)

Prenatal ultrasound findings suggestive of skeletal dysplasia often have a wide differential with over 450 skeletal dysplasia syndromes described to date. Specific phenotypic features on ultrasound provide guidance, though we noted in this study that molecular testing is most informative in making a diagnosis. Prenatal genetic testing ranges from screening tests using cell-free fetal DNA to diagnostic tests which include next generation sequencing panels and whole exome or genome sequencing. We aimed to determine which prenatal genetic tests were capable of identifying disease causing variants in pregnancies suspected to have skeletal dysplasia and craniosynostosis syndromes. This multi-center retrospective chart review …

The In4mer Crispr/Cas12a Multiplex Knockout Platform And Its Applications, Nazanin Esmaeili Anvar

Dissertations and Theses (Open Access)

Discovering synthetic lethal interactions between genes holds the key to uncovering cancer vulnerabilities, enabling the development of more effective drugs for patients. However, identifying these vulnerabilities in the complex genome of human, which comprises thousands of genes, poses a significant challenge. One alternative approach to investigate these interactions involves exploring enriched sources of synthetic lethal interactions, such as paralog pairs. In recent years, a couple of studies have conducted dual-gene knockout experiments on paralog pairs using different approaches to identify synthetic lethal interactions. In this study, we conducted a meta-analysis of CRISPR genetic interaction screens. We identified a candidate set …

Dysmorphology Training And Utility In Genetic Counseling, Maria G. Hernandez

Dissertations and Theses (Open Access)

Before the availability of comprehensive genetic testing, dysmorphology was critical for developing a differential for individuals suspected of having a genetic disorder. Literature suggests that the availability of whole exome and whole genome sequencing (ES/GS) has shifted the use of dysmorphology from a forward to backward approach. There is no literature describing the continued use of dysmorphology within the genetic counseling field or the training that genetic counseling students receive. The study aims to describe the dysmorphology training that genetic counselors (GC) and GC students reported receiving, to explore the involvement of GCs in evaluating dysmorphic features and identify factors …

Inclusion Of Adoption As A Pregnancy Management Option In Prenatal Genetic Counseling Practice, Emma Billings

Dissertations and Theses (Open Access)

Prenatal genetic counselors are essential to providing education, psychosocial support, and guidance on pregnancy options to patients who receive a fetal diagnosis of an anomaly or genetic condition. Therefore, genetic counselors should be well-educated on comprehensive pregnancy management options consisting of parenting, abortion, and adoption. The landscape of adoption education in genetic counseling practice was last characterized in 2010 by Perry and Henry, revealing substantial variability in both the inclusion of adoption-specific education in genetic counseling program (GCP) curricula and the discussion of pregnancy options with patients in prenatal practice. As a result, the authors published a call to action …

Fraud In Genetic Testing: Swindling The System, Rachel Notestine, Rachel Notestine, Claire N. Singletary

Dissertations and Theses (Open Access)

Healthcare fraud comprises a sizable portion of the United States healthcare expenditure and inflicts strain on payors, patients, and the healthcare system overall. The genetic testing industry is rapidly growing which provides a multitude of fraud opportunities. There is limited research exploring genetic testing fraud, although federal organizations have highlighted it as an issue. In this study, a retrospective review of federal websites, news articles, and a legal database identified 42 cases of fraud involving outpatient genetic testing published between February 2019 and December 2023. These cases were analyzed for themes via inductive conventional content analysis. Themes of fraudulent activity …