Genetics Commons^™

Development Of The Ark Assay For Quantitating Dna- Protein Crosslink Accumulation And Fanconi Anemia Pathway Involvement In The Repair Process, Naeh Klages-Mundt

Dissertations and Theses (Open Access)

DNA-protein crosslinks (DPCs) are a common DNA lesion naturally arising in cells, wherein protein becomes covalently and irreversibly bound to the DNA. Given their excessive size, these adducts present a significant challenge to replication and transcription, thus requiring timely and efficient repair. However, the precise mechanisms involved with processing DPC removal remain unclear. Moreover, current methodologies to quantitate DPC accumulation and removal are restrained by a range of limitations. Here, we describe and discuss a new DPC detection assay – the ARK assay – capable of overcoming the limitations incurred by prior assays. The design, which uses dual chaotropic lysis …

Functional Role Of Ppal And Potential For Moss In Industrial Applications., Susana Perez Martinez

Electronic Theses and Dissertations

This dissertation is an examination and characterization of the functional roles of PPAL. PROTEIN PRENYLTRANSFERASE ALPHA SUBUNIT-LIKE (PPAL) is a recently discovered gene. PPAL homologs are present in all plants and many animals, where its function is largely unknown. It is possible that PPAL could participate in prenylation processes since it shares similarity to the α subunits of known prenylation enzymes. Prenylation is a post-translational modification of proteins that involves the addition of a lipid moiety to proteins to facilitate membrane targeting and association and promote protein-protein interactions. Prenylation has important roles in plant growth and development, including …

When Problems Become Solutions: Harnessing The Osteogenic Capacity Of Disease-Causing Stem Cells To Repair Bone Fractures, Mehreen Pasha

Honors Scholar Theses

While we often perceive disease as negative, there is potential to engineer seemingly negative biological phenomena into therapeutics to treat a variety of human illnesses. Fibrodysplasia ossificans progressiva (FOP) is a genetic disorder involving uncontrolled, widespread, extraskeletal bone growth, or heterotopic ossification (HO). In FOP patients, stem cells called fibro/adipogenic progenitors (FAPs) follow an abnormal, osteogenic pathway. In the present study, we investigate whether we can adapt these Acvr1 mutant FAPs, which are exceptional at producing bone, to repair bone fractures in otherwise normal patients. The primary aims of this study are (1) to devise and optimize a novel method …

Transcriptome-Wide Identification Of Rna-Binding Protein Binding Sites Using Seclip-Seq, Steven M Blue, Brian A Yee, Gabriel A Pratt, Jasmine R Mueller, Samuel S Park, Alexander A Shishkin, Anne C Starner, Eric L Van Nostrand, Gene W Yeo

Faculty, Staff and Students Publications

Discovery of interaction sites between RNA-binding proteins (RBPs) and their RNA targets plays a critical role in enabling our understanding of how these RBPs control RNA processing and regulation. Cross-linking and immunoprecipitation (CLIP) provides a generalizable, transcriptome-wide method by which RBP/RNA complexes are purified and sequenced to identify sites of intermolecular contact. By simplifying technical challenges in prior CLIP methods and incorporating the generation of and quantitative comparison against size-matched input controls, the single-end enhanced CLIP (seCLIP) protocol allows for the profiling of these interactions with high resolution, efficiency and scalability. Here, we present a step-by-step guide to the seCLIP …

Improving Self-Efficacy And Knowledge While Reducing Anxiety In High-Risk Breast Cancer Patients Through Standardized Education, Shelley Miles

UNLV Theses, Dissertations, Professional Papers, and Capstones

Breast cancer is the leading cause of death of women in the United States. Patients at high risk for developing cancer are more easily identified in today’s world. Early identification might be due to strong family history or genetic mutations, such as BRCA1 or BRCA2. Screening and risk reduction guidelines have been developed over recent years for these patients. Adherence to these guidelines continues to be a problem. The factors stemming from this problem include lack of knowledge about being high-risk, understanding the guidelines, and anxiety and depression about the perceived risk of developing breast cancer. These factors can cause …

Experiences Of Racial And Ethnic Minority Patients With Genetic Counseling, Emile Moura Coelho Da Silva

Dissertations and Theses (Open Access)

Racial and ethnic minority patients in the United States undoubtedly suffer from inequalities in healthcare. While some studies have explored these inequalities in the field of genetic counseling specifically, research relating to genetic counseling outcomes in diverse patient populations is still limited. With the number of non-Hispanic White individuals in the United States projected to decrease by 20 million by 2060, it becomes imperative to better understand the experiences of racial and ethnic minority patients to meet their needs. Therefore, this study aimed to further describe the experiences of racial and ethnic minority patients who received genetic counseling services. In …

Invisible Disabilities, Academic Capital And Competitiveness Of Genetic Counseling Applicants, Natalie E. Stoner, Meagan Choates, Carla Mcgruder, Debra Murray, Theresa Wittman, Sara Wofford, Claire N. Singletary

Dissertations and Theses (Open Access)

The field of genetic counseling has historically lacked diversity. Recent research has begun to explore how visible diversity may present barriers to a genetic counseling applicant becoming competitive, but has not yet characterized potential barriers with invisible diversities, such as being a first-generation college student, or a part of the LBGTQ+ community. Therefore, this study aimed to address this gap among those with invisible diversities, as well as explore their academic capital (AC), a theoretical framework used to identify factors that make students more likely to succeed in post-secondary work including supportive networks, trustworthy information, family uplift, college knowledge, overcoming …

Unraveling The Genetic Architecture Of Somatic Embryogenesis In Upland Cotton, Adam M. Canal

All Theses

Somatic embryogenesis is the de novo development of asexual embryos because of the plasticity of the plant cell. In tissue culture, the biochemical and genetic mechanisms of dedifferentiated callus tissues can be reprogrammed to transdifferentiate into developed, polarized embryos, which can ultimately regenerate into whole plants. Although this rarely occurs in nature, scientists have exploited this process for decades to regenerate whole plants following gene transformation or for micropropagation. While some species are amenable to in vitro regeneration, upland cotton is particularly recalcitrant, with regenerative potential being confined to only several genotypes. The lack of elite, regenerable genotypes greatly restricts …

Heritability Of Maxillary Dental Arch Dimensions In A Pedigreed Sample Of Hamadryas Baboons, Samuel Park

Crop, Soil and Environmental Sciences Undergraduate Honors Theses

This thesis presents a study of heritability of maxillary dental arch dimensions in a captive baboon colony. Arch dimensions are important subject because they influence the entirety of the craniofacial and masticatory complex. The goal of this study was to quantify the relative genetic influence on arch dimensions and the nature of this influence at different points along the maxillary arcade. Referencing virtual, three-dimensional dental cast scans, widths were measured at different points between the a) maxillary left and right canines, and b) maxillary left and right first molars (M1). Specifically, measurements were taken at the inner (lingual) gingival margin, …

Development Of Cloning Vehicles For Expression Of Gc-Maf In Yeast, Tammy Tran, Seohyun Lee, Jane Yu, Wilson Wu

Pacific Undergraduate Research and Creativity Conference (PURCC)

No abstract provided.

Proteomic Analysis Of The Expression Of Masp1 Dragline Silk Protein In E. Coli, Sophie Rae Pazzo, Rajan Amit Patel, Kamrin Athwal, Edward Kim

Pacific Undergraduate Research and Creativity Conference (PURCC)

No abstract provided.

Utilizing Pharmacology To Target Transcription Factors Involved With Cancer Onset And Development, Tristan D. Sanders

Mountaineer Undergraduate Research Review

Transcription factors (TFs) are a vital part of every living organism on earth, as they allow for the correct genes to be expressed while much of the genome is never used. They can fall victim to mutations or manipulations that lead to the deregulation of many genes within a cell. If specific genes are over/under-expressed, a cell may become cancerous and begin replicating into a tumor. It has been demonstrated that common TFs associated with cancer can be targeted using small molecule drugs, and a popular target of these drugs is the DNA binding site on the TF along with …

Covid Susceptibility And Severity Correlation With The Ace2 Gene, Natalie Taylor

Thinking Matters Symposium

A wide spectrum of susceptibility and severity of infection has been observed among COVID-19 patients. While some individuals remain unaffected by the Sars-Cov-2 virus, others have contracted the virus multiple times with varying levels of severity. This poster reviews some of the research demonstrating a link between the susceptibility of the Sars-Cov- 2 virus and the severity of infection, and a specific gene called ACE2. The ACE2 gene encodes an angiotensin-converting enzyme that acts as a functional receptor for the spike glycoprotein receptor binding domain of the coronavirus and severe acute respiratory syndrome coronaviruses. ACE2 presents numerous amino acid variants …

Alzheimer's Disease: A Comprehensive Review Including Personal Experience From Retirement Home Patients, Sydney Fox

Honors Theses

Alzheimer’s Disease is a neurodegenerative illness and disease, the most common type of dementia, and the sixth leading cause of death (Sá et al., 2012). The disease was discovered in 1906 and named after Dr. Alois Alzheimer, a psychiatrist and neuropathologist. Over time, a variety of hypotheses have developed regarding the cause behind this multifactorial disease, and these will be disclosed in a later section. Nonetheless, the disease was first observed in changes of the brain tissue of a woman who was said to have die from an unusual mental illness with many abnormal bumps. These bumps are now recognized …

The Synthesis And Purification Methodology Of An Intermolecular Pyrophosphate Sensor: Applications For The Quantitative Polymerase Chain Reaction, Ethan Gevedon

Honors Projects

The optimized synthesis and purification methodology for an intermolecular pyrophosphate sensor scaffold molecule was performed: high performance liquid chromatography afforded the scaffold in excellent purity and yield. The applications of the sensor assembly in the quantitative polymerase chain reaction were discussed, and preliminary results show that

Metabolism, Cognition, And Male Coloration In Eastern Mosquitofish, Katelyn Ashleigh Giltner

Honors Capstone Projects and Theses

No abstract provided.

Polydactyly In Cats, Rosa Benson, Cassie Morris, Leaha Mancuso, Bernardo Mesa

Harrisburg University Research Symposium: Highlighting Research, Innovation, & Creativity

Polydactyly is a genetic condition in which a cat is born with more than the typical number of toes. It is a dominant genetic mutation and is fairly common in cats. (Class Project)

Editorial: Accelerating Genetic Gains In Pulses, Aditya Pratap, Shiv Kumar, Patricia L. Polowick, Matthew W. Blair, Michael Baum

Agricultural and Environmental Sciences Faculty Research

No abstract provided.

Sex And Starvation Influences Latrotoxin Expression In The Brown Widow Spider, Mattie Harris

Honors College Theses

Widow spiders (genus Latrodectus) are well-known for their potent venom. Seven latrotoxin proteins constitute the main components of widow spider venom. The vertebrate specific (α-latrotoxin) and insect specific (α-latroinsectotoxin) latrotoxins have been well-characterized with respect to structure and function. Regulation of latrotoxin gene expression is not well understood but sex and feeding could be factors influencing production. In this study, I used quantitative qPCR to (1) characterize the expression patterns of both the insect and vertebrate specific latrotoxins in male and female brown widow spiders (Latrodectus geometricus) to characterize sex-biased expression and to (2) study expression patterns …

Host-Pathogen Coevolution Between Tasmanian Devils (Sarcophilus Harrisii) And Devil Facial Tumor Disease, Dylan Garret Gallinson

USF Tampa Graduate Theses and Dissertations

Coevolution is a driving force of rapid evolution, yet the complexity of coevolutionary interactions has made it difficult to characterize the genomic basis of traits mediating such relationships. Coevolutionary dynamics are especially important in host-pathogen systems where the host and pathogen must constantly adapt to one another. The Tasmanian devil and its species-specific transmissible cancer, devil facial tumor disease (DFTD), provide the rare opportunity to study host-pathogen coevolution in a complex natural system. Extensive spatiotemporal devil sampling, high linkage disequilibrium in devils, and a large selective pressure imposed by DFTD facilitate a system tractable for study. Here, we characterized devil …

Exploring The Functionality Of Putative Bop3 Post-Translational Modifications, Liliya Tkachuk

Honors Scholars Collaborative Projects

All eukaryotic cells require that transcribed mRNAs undergo export form the nucleus to the cytoplasm where they can be translated into proteins. This process requires a host of proteins which are conserved between the unicellular budding yeast, S. cerevisiae, and humans. During this process, Mex67 and other associated proteins facilitate the mRNA to travel across the nuclear pore complex (NPC), doorways embedded in the nuclear envelope. Upon the exit of mRNA, Mex67 is released and recycled back into the nucleus to facilitate the export of more mRNA. This occurs through the action of Dbp5, whose activity is regulated through …

Comparative Modeling And Evolutionary Comparison Of Serine Protease, A Timber Rattlesnake Venom Protein, Qawer Ayaz

Theses

The aim of this study is to create a homology model of VG35 serine protease and evaluate the evolutionary comparison of secondary structure on basis of protein model using YASARA. This method was furthermore used to predict the potential epitopes which can help in the investigation of future studies.

The VG35 was used to run a BLAST search which gave most resembled serine protease of different species which was then translated and modeled in YASARA. The modeled protein data was then used to determine the secondary structure. This was then used for evolutionary comparison of all proteins to VG35. Then …

Molecular Evidence Of Cryptic Hybridization In The Japanese Nezasa Bamboos (Pleioblastus Section Nezasa), Ryan Long

Theses

The genus Pleioblastus is a complex group of Southeast Asian temperate bamboos with 7-21 species, depending on taxonomic authority. This study tests the hypothesis that taxonomic complexity in this group is due in part to hybridization and subsequent backcrossing in natural populations, resulting in a reticulate evolutionary history and a contemporary species assemblage that includes cryptic hybrids. This hypothesis is supported by recent research on the temperate bamboos that revealed intergeneric hybrids involving Pleioblastus and other genera of temperate bamboos (Triplett and Clark, 2021). The objective of the current study was to use data from Amplified Fragment Length Polymorphism (AFLP) …

The Roles Of Individual Proteins In De Novo Recruitment Of Pcg Repressive Complexes To Giant, Anni Kum

Biological Sciences Theses and Dissertations

Epigenetic gene regulation is the process by which external factors regulate the genome. This research studies Polycomb Group (PcG) proteins which function as epigenetic agents that work together in complexes to maintain gene silencing for multiple cellular generations. Drosophila melanogaster PcG proteins can be organized into three canonical complexes: Pho-RC, PRC1, and PRC2. Though there are multiple proposed models for the order of recruitment, it is generally accepted that PhoRC, PRC1, and PRC2 interact with each other to stably recruit to a target gene. Since these proteins are highly conserved, this project studies PcG proteins in the model organism, Drosophila …

Characterization Of Hemocytes In Amblyomma Americanum And Investigation Of Traf6’S Role In Proliferation Of Hemocytes In Response To Infection, Jacquelyn T. May

Electronic Theses and Dissertations

Amblyomma americanum is a medically important vector in the southeast United States. Cellular and molecular aspects of the immune system of this species were examined. To investigate cellular processes, hemocytes produced in response to gram-negative infection were characterized according to their ultrastructure. Four hemocyte types were identified: prohemocytes, plasmatocytes, type-I granulocytes, and type-II granulocytes. To elucidate molecular processes, we investigated AamTRAF as an immune-related gene by silencing the gene using RNAi then quantifying the hemocytes after inoculation with gram-negative and positive bacteria. It was found that silencing AamTRAF caused a decrease in hemocyte proliferation in response to gram-positive but not …

Cryptic Hybridization In The Temperate Bamboos: Is Pleioblastus Simonii A Species Of Hybrid Origin?, Morgan Brown

Theses

Japanese river bamboo (Pleioblastus simonii, ‘medake,’‘kawadake’) is an ecologically important species of temperate bamboo native to Japan. This species is widely known and historically important in Japanese rural farm life. Based on morphological data, Japanese river bamboo is classified in Pleioblastus section Medakea (Poaceae: Bambusoideae) along with five other Japanese species, which are collectively considered to represent a phylogenetically distinct lineage. However, recent studies suggest that Japanese river bamboo may have arisen as a result of previously undetected hybridization (i.e., cryptic hybridization), while also calling into question the diversity of section Medakea. The role of hybridization in natural plant populations …

Characterization Of A Medium-Dependent Streptomyces Developmental Mutant, Dylan Gray, Jennifer A. Bennett

Undergraduate Distinction Papers

Streptomyces coelicolor is a soil-dwelling, Gram-positive Actinobacteria. Streptomyces species produce thousands of secondary metabolites which include many antibiotics used in medicine today. In Streptomyces development, as colonies grow, secondary metabolites are produced, and ultimately mature spores are dispersed. The production of each of these secondary metabolites in wild-type Streptomyces is determined by a distinct biosynthetic pathway. In order to identify new genes for antibiotic production and other aspects of development, an engineered Tn5-derived transposon was used to mutagenize wild-type cells in vivo and produce single, stable insertions.

Colonies that were visually distinct from the wild type were selected for further …

Fragile Foal Syndrome: Its Past, Present, And Future, Alena Martin, Alena M. Martin

Honors College Theses

Though Fragile Foal Syndrome (FFS) has been around for some time, the public interest in FFS is recent. The hype spread rapidly from a public media announcement that a stallion at a prominent North American stud farm was a carrier (Brooks, 2021). As with most genetic mutations, FFS likely arose due to the increased inbreeding that results from human selection (Orlando & Librado, 2019). Fragile Foal Syndrome affects the enzyme responsible for developing the connective tissues. Two recent case studies highlighted the devastating effect of FFS on every part of the equine body (Metzger, et al., 2020; Grillos, 2021). So …

Investigation Of Oncogenic Ras And Endoplasmic Reticulum-Mitochondria Calcium Flux And Their Relationship In The Context Of Tumorigenesis, Emma Anderson

Senior Honors Theses

Intracellular calcium as a signaling molecule is a pervasive feature of cellular pathways, especially those that manage internal homeostasis and transitions through the cell cycle, so much so that regulated, responsive calcium flux between the endoplasmic reticulum (ER) and the mitochondria has been suggested to play a major role in cancer development. Another factor commonly implicated in tumorigenesis is RAS, an oncogene that controls signaling for many pathways that are also regulated by calcium. While both calcium and oncogenic RAS signaling are implicated in cancer development, possible links between them have yet to be determined. The identification of these links …

Determining The Role Of High-Sugar Diets On Ovarian Function In Drosophila Melanogaster, Emma Otey

Senior Theses

The prevalence of obesity in the United States has increased drastically and the effects of obesity on human physiology are not fully known at this point. It has been noted that there is a significant decrease of fertility rates in obese women. In order to study how exactly these high-sugar or high-fat diets are impacting fertility, Drosophila can be used as a model organism. The use of Drosophila as a model organism for humans is due to the many conserved molecular and systematic mechanisms, namely ovarian function, as well as conserved physiological responses to obesity and obesogenic diets. This study …