Genetics Commons^™

Analysis Of Post-Traumatic Stress Disorder Gene Expression Profiles In A Prospective, Community-Based Cohort, Jan Dahrendorff

USF Tampa Graduate Theses and Dissertations

Post-traumatic stress disorder (PTSD) is a common and debilitating psychiatric disorder that may occur in individuals exposed to traumatic events such as accidents, interpersonal violence, war, combat-exposures or natural disasters. PTSD is a significant public health issue with a high disease burden associated with substantial health care costs and several comorbidities negatively affecting an individual’s quality of life. The biological underpinnings of the disorder are not well understood. Gene expression studies can shed light into the complex physiology of PTSD. However, to date, studies employing a hypothesis-free approach examining the whole transcriptome are scarce and are limited to assessment of …

Human Population History At The Crossroads Of East And Southeast Asia Since 11,000 Years Ago, Tianyi Wang, Wei Wang, Guangmao Xie, Zhen Li, Xuechun Fan, Qingping Yang, Xichao Wu, Ling Qin, Fajun Li, Melinda A. Yang

Biology Faculty Publications

Past human genetic diversity and migration between southern China and Southeast Asia have not been well characterized, in part due to poor preservation of ancient DNA in hot and humid regions. We sequenced 31 ancient genomes from southern China (Guangxi and Fujian), including two ∼12,000- to 10,000-year-old individuals representing the oldest humans sequenced from southern China. We discovered a deeply diverged East Asian ancestry in the Guangxi region that persisted until at least 6,000 years ago. We found that ∼9,000- to 6,000-year-old Guangxi populations were a mixture of local ancestry, southern ancestry previously sampled in Fujian, and deep Asian ancestry …

Successful Atac-Seq From Snap-Frozen Equine Tissues, Sichong Peng, Rebecca Bellone, Jessica L. Petersen, Theodore S. Kalbfleisch, Carrie J. Finno

Veterinary Science Faculty Publications

An assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) has become an increasingly popular method to assess genome-wide chromatin accessibility in isolated nuclei from fresh tissues. However, many biobanks contain only snap-frozen tissue samples. While ATAC-seq has been applied to frozen brain tissues in human, its applicability in a wide variety of tissues in horse remains unclear. The Functional Annotation of Animal Genome (FAANG) project is an international collaboration aimed to provide high quality functional annotation of animal genomes. The equine FAANG initiative has generated a biobank of over 80 tissues from two reference female animals and experiments to begin …

A Screen For Sleep And Starvation Resistance Identifies A Wake-Promoting Role For The Auxiliary Channel Unc79, Kazuma Murakami, Justin Palermo, Bethany A. Stanhope, Allen G. Gibbs, Alex C. Keene

Life Sciences Faculty Research

The regulation of sleep and metabolism are highly interconnected, and dysregulation of sleep is linked to metabolic diseases that include obesity, diabetes, and heart disease. Furthermore, both acute and long-term changes in diet potently impact sleep duration and quality. To identify novel factors that modulate interactions between sleep and metabolic state, we performed a genetic screen for their roles in regulating sleep duration, starvation resistance, and starvation-dependent modulation of sleep. This screen identified a number of genes with potential roles in regulating sleep, metabolism, or both processes. One such gene encodes the auxiliary ion channel UNC79, which was implicated in …

An Investigation On The Irish Population’S Attitudes And Knowledge Towards Genetic Screening For Cancer, Emer Mccarthy, Ada Fleming, Dawn Hannah Cronin

International Undergraduate Journal of Health Sciences

Genetic mutations are alterations in DNA that may result in the development of a disease later in life. A BRCA gene is a tumour suppressor gene that helps to prevent the development of some cancers, particularly breast cancer. If a mutation occurs, this gene no longer functions at preventing these cancers. Genetic screening is when a population is tested for a mutation in an attempt to identify a group of people that are positive for the mutation. This can help identify cancer in different populations as well as track their inheritance. This study was conducted online, questioning the Irish populations …

Full Issue: The International Undergraduate Journal Of Health Sciences, Volume 1, Issue 1, June 2021, Iujhs Full Issue

International Undergraduate Journal of Health Sciences

The full June 2021 issue (Volume 1, Issue 1) of the International Undergraduate Journal of Health Sciences

Patterns Of Recent Natural Selection On Genetic Loci Associated With Sexually Differentiated Human Body Size And Shape Phenotypes, Audrey M. Arner, Kathleen E. Grogan, Mark Grabowski, Hugo Reyes-Centeno, George H. Perry

Anthropology Faculty Publications

Levels of sex differences for human body size and shape phenotypes are hypothesized to have adaptively reduced following the agricultural transition as part of an evolutionary response to relatively more equal divisions of labor and new technology adoption. In this study, we tested this hypothesis by studying genetic variants associated with five sexually differentiated human phenotypes: height, body mass, hip circumference, body fat percentage, and waist circumference. We first analyzed genome-wide association (GWAS) results for UK Biobank individuals (~194,000 females and ~167,000 males) to identify a total of 114,199 single nucleotide polymorphisms (SNPs) significantly associated with at least one of …

Temperature Regulation Of Plant Hormone Signaling During Stress And Development, Christian Castroverde, Damaris Dina

Biology Faculty Publications

Global climate change has broad-ranging impacts on the natural environment and human civilization. Increasing average temperatures along with more frequent heat waves collectively have negative effects on cultivated crops in agricultural sectors and wild species in natural ecosystems. These aberrantly hot temperatures, together with cold stress, represent major abiotic stresses to plants. Molecular and physiological responses to high and low temperatures are intricately linked to the regulation of important plant hormones. In this review, we shall highlight our current understanding of how changing temperatures regulate plant hormone pathways during immunity, stress responses and development. This article will present an overview …

The Role Of Placental Genes On Intellectual Disability And Developmental Delay, Maedot A. Yidenk

Dissertations, Theses, and Capstone Projects

The complex interaction between gene expressions and environmental factors plays a key role in the pathogenesis of various diseases, including neurodevelopmental disorders (Lenroot & Giedd, 2008). This study aimed to evaluate first, the magnitude of association between placental gene Methyl-CpG Binding Protein 2 (MeCP2) and intellectual disability (ID) in the offspring and second, the synergy between placental gene Forkhead box protein 1(FOXP1) and developmental delay (DD) in the offspring. We focused on assessing two specific paradigms, i) placental gene expressions of MeCP2 among children that have ID vs. children without ID; and ii) placental gene expression of …

Transcriptional Analysis Of The Response Of C. Elegans To Ethanol Exposure, Mark G. Sterken, Marijke H. Van Wijk, Elizabeth C. Quamme, Joost A. G. Riksen, Lucinda Carnell, Laura D. Mathies, Andrew G. Davies, Jan E. Kammenga, Jill C. Bettinger

Biology Faculty Scholarship

Ethanol-induced transcriptional changes underlie important physiological responses to ethanol that are likely to contribute to the addictive properties of the drug. We examined the transcriptional responses of Caenorhabditis elegans across a timecourse of ethanol exposure, between 30 min and 8 h, to determine what genes and genetic pathways are regulated in response to ethanol in this model. We found that short exposures to ethanol (up to 2 h) induced expression of metabolic enzymes involved in metabolizing ethanol and retinol, while longer exposure (8 h) had much more profound effects on the transcriptome. Several genes that are known to be involved …

Analysis Of Symptom Expressions And Transmission Rates Caused By The Plant Pathogen Phytophthora Ramorum On Native Chaparral Plants From The Genus Arctostaphylos, Bharati Gaonker

Natural Sciences and Mathematics | Biological Sciences Master's Theses

Phytophthora ramorum is the causal agent of Sudden Oak death (SOD), ramorum dieback and ramorum leaf blight which affect both forest environments and nurseries. This oomycete pathogen has had a huge economic impact on the nursery and lumber industry. Forests in California have experienced substantial mortality of oaks affecting the forest dynamics and diversity. Our research investigates four native species and two ornamental cultivars of plants, which belong to the genus Arctostaphylos (manzanita) and are considered to be new hosts for P. ramorum in the chaparral ecosystem of California. Symptom expression and transmission rates were analyzed on Arctostaphylos glauca, …

A Forward Genetic Screen To Identify Human Genes Of Interest And Their Roles In Ovarian Cancer, Susan A. Ihejirika

Honors College Theses

Drosophila melanogaster, fruit flies, are very important for modeling and studying human diseases. This study identifies human genes of interest and their contributions to epithelial ovarian carcinogenesis and progression as well as the roles orthologs of these genes play in Drosophila melanogaster. This is important because ovarian cancer is the most common cause of death among the gynecological cancers. This identification of genes was carried out using a forward genetic screen employing the widely used GMR-Gal4 driver/UAS-transgene system. The GMR-Gal4 driver is commonly utilized to express transgenes in the developing eye of the fruit fly. Transgenes that are expressed using …

Sources Of Resistance To Common Bacterial Blight And Charcoal Rot Disease For The Production Of Mesoamerican Common Beans In The Southern United States, Daniel Ambachew, Jacqueline Joshua, Margaret T. Mmbaga, Matthew W. Blair

Agricultural and Environmental Sciences Faculty Research

The gene pool of Mesoamerican common beans (Phaseolus vulgaris L.) includes genotypes in the small-to-medium-size seeded dry beans, as well as some snap beans from hotter environments adapted to the Southeastern United States. However, the warm and humid climate of the Southeastern United States is conducive to diseases such as Common Bacterial Blight (CBB) and Charcoal Rot (CR). The pathogens for these two diseases can survive long periods in infested soil or on seeds and are difficult to control through pesticides. Hence, field-level resistance would be the best management strategy for these diseases. The goals of this study were (1) …

Identifying The Cell Composition And Clonal Diversity Of Supratentorial Ependymoma Using Single Cell Rna-Sequencing, James He

University Scholar Projects

Ependymoma is a primary solid tumor of the central nervous system. Supratentorial ependymoma (ST-EPN), a subtype of ependymomas, is driven by an oncogenic fusion between the ZFTA and RELA genes in 70% of cases. We introduced this fusion into neural progenitor cells of mice embryos via in utero electroporation of a non-viral binary piggyBac transposon system containing ZFTA-RELA. From preliminary data in the LoTurco lab, inducing the expression of ZFTA-RELA into different neural progenitor cells produces tumors of varying lethality and cellular composition. To define the cellular composition and subclonal diversity of ST-EPN tumors, we used single cell RNA-sequencing to …

The Effects Of Mapk Signaling On The Development Of Cerebellar Granule Cells, Kerry Morgan

University Scholar Projects

The granule cells are the most abundant neuronal type in the human brain. Rapid proliferation of granule cell progenitors results in dramatic expansion and folding of the cerebellar cortex during postnatal development. Mis-regulation of this proliferation process causes medulloblastoma, the most prevalent childhood brain tumor. In the developing cerebellum, granule cells are derived from Atoh1-expressing cells, which arise from the upper rhombic lip (the interface between the roof plate and neuroepithelium). In addition to granule cells, the Atoh1 lineage also gives rise to different types of neurons including cerebellar nuclei neurons. In the current study, I have investigated the …

The Effects Of Mapk Signaling On The Development Of Cerebellar Granule Cells, Kerry Morgan

Honors Scholar Theses

The granule cells are the most abundant neuronal type in the human brain. Rapid proliferation of granule cell progenitors results in dramatic expansion and folding of the cerebellar cortex during postnatal development. Mis-regulation of this proliferation process causes medulloblastoma, the most prevalent childhood brain tumor. In the developing cerebellum, granule cells are derived from Atoh1-expressing cells, which arise from the upper rhombic lip (the interface between the roof plate and neuroepithelium). In addition to granule cells, the Atoh1 lineage also gives rise to different types of neurons including cerebellar nuclei neurons. In the current study, I have investigated the …

Big Five Personality Traits And Political Orientation: An Inquiry Into Political Beliefs, Ian E. Phillips

The Downtown Review: An Interdisciplinary Journal Written and Peer-Reviewed by Mandel Honors College Students at Cleveland State University

Personality research centered on the Big Five personality traits has heavily impacted our understanding in regards to what forces orient a person on a political spectrum. Examining how personality differences interact with political orientation, this research seeks to provide information on what makes someone either more or less likely to be liberal or conservative based on their temperament. In this paper, previous personality research is synthesized into one discussion, centered on what the effects of each trait are and how they impact political orientation, the heritability of personality, and what implications there are for such research in the realm of …

Mapping And Characterization Of Mutagen Sensitivity Genes In Drosophila Malanogaster, Alexis Nystrom

Graduate Theses

The information contained within DNA is vital to directing all biological processes. All organisms have repair mechanisms in place to repair DNA damage quickly and efficiently. Without these repair pathways, DNA can acquire harmful mutations that can compromise the survival of an organism. Studies of DNA repair in Drosophila melanogaster have focused on mutagen sensitive (mus) mutants, each of which contain a mutation that renders them incapable of performing DNA repair. Since a majority of these mus genes are unmapped, the goal of this project was to determine what genes in the Drosophila melanogaster genome are mus106 and mus108. Presence …

Characterization Of A Putative Helicase In Rifampicin Resistance Of Mycobacterium Abscessus:, Aavrati Saxena

Legacy Theses & Dissertations (2009 - 2024)

Mycobacterium abscessus (Mab), a non-tuberculous environmental mycobacterium is one of the emerging pathogens. The number of Mab infections has doubled in the past decade. It is also an opportunistic pathogen usually infecting immunocompromised individuals and causing numerous skin and soft tissue infections. It commonly causes lung infections in people who are already infected with one or other lung infections such as tuberculosis. The treatment of Mab infections is difficult because of its intrinsic resistance to most of the antibiotics available. This project studies Rifampicin (RIF) resistance in Mab, as RIF is a well-established treatment for other mycobacterial infections including tuberculosis, …

Dynamics Of Hybrid Zones At A Continental Scale, Bradley T. Martin

Graduate Theses and Dissertations

Hybridization has traditionally been viewed as a happenstance that negatively impacts populations, but is now recognized as an important evolutionary mechanism that can substantially impact the evolutionary trajectories of gene pools, influence adaptive capacity, and contravene or reinforce divergence. Physiographic processes are important drivers of dispersal, alternately funneling populations into isolation, promoting divergence, or facilitating secondary contact of diverged populations, increasing the potential for hybridization. In North America, glacial-interglacial cycles and geomorphological changes have provided a dynamic backdrop over the last two million years that promoted such oscillations of population contraction and expansion. These biogeographic processes have resulted in regional …

Implementing Crispr-Cas9 Gene Editing System In Microbotryum., Stevana Reese Schauer

College of Arts & Sciences Senior Theses

Microbotryum dianthorum is a species of smut fungus which causes infection in plants in the Dianthus genus. The infection process is aided by small-secreted proteins known as effectors. Effectors may aid in the infection process because they are secreted by the fungus and can enter plant tissue, possibly to facilitate infection and/or manipulate the host. Thus, it is of interest to investigate the genes for these effectors to determine their role in the infection process. One method to study genes is through gene disruption, via the CRISPR/Cas9 gene editing system, but this has not yet been implemented in Microbotryum dianthorum …

Mapping The Domain Of Rna Helicase Ddx1 That Interacts With The Ns1 Of Influenza A Viruses, Elise Wyatt

Biomedical Engineering Undergraduate Honors Theses

Of the known influenza virus strains, influenza A viruses (IAVs) are the most catastrophic due to their highly contagious nature and possibly life-threatening symptoms. IAVs invade a host cell and enter the nucleus where they use the cell’s nuclear machinery for replication of their viral RNA genome which is then exported to neighboring cells to establish a productive infection. Host pathogen recognition receptors (PRRs) respond to viral infection by signaling the cell to produce type I interferons (IFNs) to fight the foreign invader. Non-structural protein 1 (NS1) of IAVs, a major component in the regulation of viral replication, opposes host …

Production, Evaluation, And Selection Of Elite Quality Protein Popcorn (Qpp) Hybrids, Leandra Marshall Parsons

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

In 2017, twelve Quality Protein Popcorn (QPP) inbred lines were developed and selected as premier dent by popcorn crosses fit for hybridization and testing. These QPP inbred lines were derived from specific Quality Protein dent Maize (QPM) by ConAgra Brands® popcorn line crosses to produce high lysine, vitreous popcorn lines capable of near-equal popping characteristics compared to the original popcorn parents. The QPP hybridization project commenced in the summer of 2018 utilizing these 12 inbred QPP lines and crossing them in a full diallel. Since then, the production of QPP hybrids has employed a diverse set of selection factors evaluating …

Discovery Of Novel Ubiquitin- And Methylation-Dependent Interactions Using Protein Domain Microarrays, Jianji Chen

Dissertations and Theses (Open Access)

Post-translational modifications (PTMs) drive signal transduction by interacting with "reader" proteins. Protein domain microarray is a high throughput platform to identify novel readers for PTMs. In this dissertation, I applied two protein domain microarrays identifying novel readers for histone H2Aub1 and H2Bub1, and H3TM K4me3. Ubiquitinations of histone H2A at K119 (H2Aub1) and histone H2B at K120 (H2Bub1) function in distinct transcription regulation and DNA damage repair pathways, likely mediated by specific "reader" proteins. There are only two H2Aub1-specific readers identified and no known H2Bub1-specific readers. Using a ubiquitin-binding domain microarray, I discovered the phospholipase A2-activating protein (PLAA) PFU domain …

Assessing Genetic Counselors' Clinical Approach And Practices Regarding Pathogenic/Likely Pathogenic Variant Downgrades, Grant Bonesteele

Dissertations and Theses (Open Access)

Although rare, variant downgrades from a pathogenic/likely pathogenic (P/LP) variant to a variant of uncertain significance can have a significant impact on patients and their families in the clinical cancer setting. However, there is a lack of literature about how to approach these potentially challenging cases as a genetic counselor. Therefore, we aimed to characterize genetic counselors’ experiences, approach, and practices to variant downgrade cases using an online survey. The survey asked participants how they would approach variant downgrade scenarios involving the CDH1 or ATM genes with variable family histories. Genetic counselors appear to be united in whether they would …

Genomic Analysis Of Paenibacillus Larvae Bacteriophages, Casey Stamereilers

UNLV Theses, Dissertations, Professional Papers, and Capstones

American Foulbrood is the most destructive bacterial infection of the honeybee (Apis mellifera) and is caused by the Gram-positive, spore forming bacterium Paenibacillus larvae. Current treatment methods rely on antibiotics, but antibiotics treatments are experiencing a reduction in efficacy due to the recent rise in antibiotic resistant strains of P. larvae. This has been a major catalyst for exploration of alternative treatment methods. Phage therapy is an alternative treatment method that uses viruses that exclusively infect bacteria, known as bacteriophages (phages), to combat bacterial infections. Several experimental studies have shown that phages P. larvae phages are effective at lysing P. …

Determination Of Human Shedding Propensity Based On Str Results, Genevieve Trapani

Student Theses

Trace DNA evidence may be discovered at a crime scene after having been deposited by a person of interest via active or passive transfer. Based on previous studies, passive transfer of one’s DNA is influenced by their shedding propensity, or probability of depositing a detectable amount of DNA through touch. Determining the shedding propensity of a person of interest can aid in trace DNA interpretation in forensic casework. This study explored STR profile quality and the presence of a DNA mixture for different skin surface locations, including fingertips before and after handwashing. As expected, unwashed fingers showed a higher prevalence …

Genetic Pathway Analysis Of Abnormal Facial Development In Nonsyndromic Cleft Lip And Palate, Lorena Maili

Dissertations and Theses (Open Access)

Nonsyndromic cleft lip with or without cleft palate (NSCLP) is the most common craniofacial birth defect resulting from incomplete fusion of the facial prominences during development, which leaves a gap in the lip, primary palate and/or the secondary palate. NSCLP affects 135,000 NSCLP newborns worldwide each year based on a birth prevalence of 1 per 700 live births. While surgical treatments have dramatically improved, many long-term health issues persist, imposing significant medical, psychosocial and economic burdens. Familial aggregation and segregation analyses suggest genetic contributions underlie NSCLP, but despite decades of study, only a small portion of the NSCLP genetic liability …

Investigating Barriers Experienced By Underrepresented Minorities In Becoming A Competitive Genetic Counseling Applicant, Katie Huang

Dissertations and Theses (Open Access)

Representation for both racial/ethnic and gender identity minorities in genetic counseling (GC) remains the lowest among similar healthcare professions. Barriers that underrepresented minority (URM) individuals face in becoming a competitive GC applicant have not yet been described. Academic capital (AC) is a theoretical framework describing the social processes necessary for individuals to navigate and succeed in higher education. This study aimed to characterize barriers experienced by applicants who self-identify as underrepresented and to explore how AC could identify areas for intervention. Prospective GC applicants for the 2021/2022 cycles were recruited to complete an anonymous online survey in Qualtrics through a …

Rare Variant Association Studies In Crohn’S Disease And Colorectal Cancer: Methods And Applications, Jiun-Sheng Chen

Dissertations and Theses (Open Access)

Genetic factors account for a substantial portion of Crohn’s disease and colorectal cancer (CRC) risk. Patients with Crohn’s disease, a condition that causes chronic inflammation of the gastrointestinal tract, are at increased risk of colorectal cancer morbidity and mortality. Genome-wide association studies using single marker approaches have identified loci responsible for these diseases, but disease susceptibility from rare variants is incompletely understood. This dissertation includes three chapters, two association studies for Crohn’s disease and CRC, and a statistical method to improve the power of statistical tests.

For Crohn’s disease, we performed targeted sequencing of 101 genes in 205 children with …