Genetics and Genomics Commons^™

Evaluation Of Pediatric Genetics Clinics’ Workflows, Efficiencies, & Genetic Counselor Job Satisfaction, Ashlyn M. Keziah

USF Tampa Graduate Theses and Dissertations

The organizational structures and workflows of pediatric/general genetics clinics exhibit significant variability across institutions. However, there is a notable lack of studies exploring which structural components within pediatric clinics contribute to increased patient volumes, while concurrently upholding genetic counselor work satisfaction and mitigating burnout risks. To address this gap, this multiple case study delves into the operational dynamics of several pediatric genetics clinics located throughout the state of Florida. We employed surveys and interviews to identify shared patterns and distinctions in clinic workflows and structures, subsequently evaluating efficiency and genetic counselor job satisfaction/burnout at each site. This study includes survey …

Linking Shared Decision Making To Outcomes In Simulated Prenatal Genetic Counseling Sessions, Raquel C. Chavarria

USF Tampa Graduate Theses and Dissertations

Shared decision-making (SDM), defined as the collaborative process between patient and healthcare provider to arrive at a values-based clinical decision, may be valuable in genetic counseling (GC) given that patients are often faced with various options. Four published studies have measured or made conclusions about the use of SDM skills in GC settings, but only one study evaluated relationships between third-party observations of SDM in recorded GC sessions and patient-reported outcomes (i.e., anxiety and decisional conflict) and found no correlations between these measures. The purpose of this study was to evaluate relationships between SDM and measures of patient-reported experience (i.e., …

Analyzing The Relationship Between Preeclamptic Severity And Placental Methylation, Mackenzie C. Maggio

USF Tampa Graduate Theses and Dissertations

Preeclampsia (PE) is a life-threatening hypertensive disorder in pregnancy (HDP) characterized by high blood pressure and proteinuria after 20 weeks of gestation. PE poses significant risks to both maternal and child health. An incomplete etiopathogenesis, diverse disease heterogeneity, and limited intervention and detection strategies further exacerbate and perpetuate PE as a major public health concern. By assessing symptom severity of placental tissues from PE pregnancies and analyzing the DNA methylation differences, this thesis aimed to identify epigenetic variations contributing to disease heterogeneity. Using the publicly available dataset GSE 98224, differentially methylated region (DMR) analysis on placental samples (n=48) revealed increasing …

Metabolic Syndrome Traits Exhibit Genotype-By-Environment Interaction In Relation To Socioeconomic Status In The Mexican American Family Heart Study, Vincent P. Diego, Eron G. Manusov, Xi Mao, Marcio A. Almeida, Juan M. Peralta, Joanne E. Curran, Michael C. Mahaney, Harald H. H. Goring, John Blangero, Sarah Williams-Blangero

School of Medicine Publications

Background: Socioeconomic Status (SES) is a potent environmental determinant of health. To our knowledge, no assessment of genotype-environment interaction has been conducted to consider the joint effects of socioeconomic status and genetics on risk for metabolic disease. We analyzed data from the Mexican American Family Studies (MAFS) to evaluate the hypothesis that genotype-by-environment interaction (GxE) is an essential determinant of variation in risk factors for metabolic syndrome (MS).

Methods: We employed a maximum likelihood estimation of the decomposition of variance components to detect GxE interaction. After excluding individuals with diabetes and individuals on medication for diabetes, hypertension, or dyslipidemia, we …

Recent Progress On Gene-Deleted Liveattenuated African Swine Fever Virus Vaccines, Hiep L.X. Vu, David Scott Mcvey

Department of Animal Science: Faculty Publications

African Swine Fever (ASF) is a highly lethal viral disease in swine, with mortality rates approaching 100%. The disease has spread to many swine-producing countries, leading to significant economic losses and adversely impacting global food security. Extensive efforts have been directed toward developing effective ASF vaccines. Among the vaccinology approaches tested to date, liveattenuated virus (LAV) vaccines produced by rational deleting virulence genes from virulent African Swine Fever Virus (ASFV) strains have demonstrated promising safety and efficacy in experimental and field conditions. Many gene-deleted LAV vaccine candidates have been generated in recent years. The virulence genes targeted for deletion from …

Recent Progress On Gene-Deleted Liveattenuated African Swine Fever Virus Vaccines, Hiep Vu, David Scott Mcvey

Department of Animal Science: Faculty Publications

African Swine Fever (ASF) is a highly lethal viral disease in swine, with mortality rates approaching 100%. The disease has spread to many swine-producing countries, leading to significant economic losses and adversely impacting global food security. Extensive efforts have been directed toward developing effective ASF vaccines. Among the vaccinology approaches tested to date, liveattenuated virus (LAV) vaccines produced by rational deleting virulence genes from virulent African Swine Fever Virus (ASFV) strains have demonstrated promising safety and efficacy in experimental and field conditions. Many gene-deleted LAV vaccine candidates have been generated in recent years. The virulence genes targeted for deletion from …

A Differentially Methylated Region Analysis Between Three Disease States Of Major Depressive Disorder In Primarily African-American Cohorts, Lanie Katelynn Mullins

USF Tampa Graduate Theses and Dissertations

Major depressive disorder (MDD) is a common and debilitating disorder that affects millions of people worldwide. MDD is a multifactorial disease with no established mechanism currently able to explain all facets of the disease or its etiology. Feedback loop mechanisms have been posited to explain the interactions of psychological and physical components of the disease etiology. Epigenetics, specifically DNA-methylation analyses, can shed light on the interaction between the within-person environment resulting from MDD symptomology, the persistence of the disease, and factors influencing remission. Here, a differentially methylated region analysis was conducted using samples derived from whole blood to interrogate the …

Grb2 Stabilizes Rad51 At Reversed Replication Forks Suppressing Genomic Instability And Innate Immunity Against Cancer, Zu Ye, Shengfeng Xu, Yin Shi, Xueqian Cheng, Yuan Zhang, Sunetra Roy, Sarita Namjoshi, Michael A Longo, Todd M Link, Katharina Schlacher, Guang Peng, Dihua Yu, Bin Wang, John A Tainer, Zamal Ahmed

Faculty, Staff and Student Publications

Growth factor receptor-bound protein 2 (GRB2) is a cytoplasmic adapter for tyrosine kinase signaling and a nuclear adapter for homology-directed-DNA repair. Here we find nuclear GRB2 protects DNA at stalled replication forks from MRE11-mediated degradation in the BRCA2 replication fork protection axis. Mechanistically, GRB2 binds and inhibits RAD51 ATPase activity to stabilize RAD51 on stalled replication forks. In GRB2-depleted cells, PARP inhibitor (PARPi) treatment releases DNA fragments from stalled forks into the cytoplasm that activate the cGAS-STING pathway to trigger pro-inflammatory cytokine production. Moreover in a syngeneic mouse metastatic ovarian cancer model, GRB2 depletion in the context of PARPi treatment …

A Machine Learning Model Of Perturb-Seq Data For Use In Space Flight Gene Expression Profile Analysis, Liam F. Johnson, James Casaletto, Lauren Sanders, Sylvain Costes

Graduate Industrial Research Symposium

The genetic perturbations caused by spaceflight on biological systems tend to have a system-wide effect which is often difficult to deconvolute it into individual signals with specific points of origin. Single cell multi-omic data can provide a profile of the perturbational effects, but does not necessarily indicate the initial point of interference within the network. The objective of this project is to take advantage of large scale and genome-wide perturbational datasets by using them to train a tuned machine learning model that is capable of predicting the effects of unseen perturbations in new data. Perturb-Seq datasets are large libraries of …

Daily Injection Of The Β2 Adrenergic Agonist Clenbuterol Improved Muscle Glucose Metabolism, Glucose-Stimulated Insulin Secretion, And Hyperlipidemia In Juvenile Lambs Following Heat-Stress-Induced Intrauterine Growth Restriction, Rachel L. Gibbs, James Wilson, Rebecca M. Swanson, Joslyn K. Beard, Zena M. Hicks, Haley Beer, Eileen Marks-Nelson, Ty B. Schmidt, Jessica Lynn Petersen, Dustin T. Yates

Department of Animal Science: Faculty Publications

Stress-induced fetal programming diminishes β2 adrenergic tone, which coincides with intrauterine growth restriction (IUGR) and lifelong metabolic dysfunction. We determined if stimulating β2 adrenergic activity in IUGR-born lambs would improve metabolic outcomes. IUGR lambs that received daily injections of saline or the β2 agonist clenbuterol from birth to 60 days were compared with controls from pair-fed thermoneutral pregnancies. As juveniles, IUGR lambs exhibited systemic inflammation and robust metabolic dysfunction, including greater (p < 0.05) circulating TNF, IL-6, and non-esterified fatty acids, increased (p < 0.05) intramuscular glycogen, reduced (p < 0.05) circulating IGF-1, hindlimb blood flow, glucose-stimulated insulin secretion, and muscle glucose oxidation. Daily clenbuterol fully recovered (p < 0.05) circulating TNF, IL-6, and nonesterified fatty acids, hindlimb blood flow, muscle glucose oxidation, and intramuscular glycogen. Glucose-stimulated insulin secretion was partially recovered (p < 0.05) in clenbuterol-treated IUGR lambs, but circulating IGF-1 was not improved. Circulating triglycerides and HDL cholesterol were elevated (p < 0.05) in clenbuterol-treated IUGR lambs, despite being normal in untreated IUGR lambs. We conclude that deficient β2 adrenergic regulation is a primary mechanism for several components of metabolic dysfunction in IUGR-born offspring and thus represents a potential therapeutic target for improving metabolic outcomes. Moreover, benefits from the β2 agonist were likely complemented by its suppression of IUGR-associated inflammation.

Applicability Of Fibrous Cellulose –D In Extracting Double-Stranded Rna (Dsrna) Of Tobrfv, Raed Alkow, Reem Hijaz, Beesan Jamoos, Najah Khandaqji, We’Am Daraghmeh, Saja Salah, Alaa Bari, Rahaf Ben Ali, Osama Alabdalla

Jerash for Research and Studies Journal مجلة جرش للبحوث والدراسات

The viral replicative form double strand RNA (dsRNA) is a unique feature to the plant RNA viruses that used for non-specific detection of plant viruses. For decades; fibrous cellulose -11 (CF11) was used for dsRNA purification, but recently was no-more produced. Other fibrous celluloses (CF-A; -B; -C; -D; and –E) were suggested as alternatives to CF11. This study was to evaluate the applicability and reproducibility of using CF-D with two different dsRNA extracting methods: micro-spin column and modified Dodds extraction methods. The best results were recorded on Dodds extraction method over micro-spin one. This results also confirmed the applicability of …

Envisioning Transition From Open Landscapes To Forested Landscapes In The Routt National Forest, Colorado, United States, Brice B. Hanberry, Jacob M. Seidel

Aspen Bibliography

Globally, in remaining wildlands, tree densities and forested cover have increased in grasslands and open forests since European settlement. In the southern Rocky Mountains of Colorado, United States, we determined tree composition and tree cover from historical (years 1875 to 1896) surveys and compared them to current (2002 to 2011) tree composition and current (year 2016) forested land cover for 500,000 ha of the Routt National Forest. Additionally, we examined whether changes in precipitation occurred. Regarding composition, pine (primarily lodgepole pine; Pinus contorta) decreased from 65% to 32% of all trees, with increased subalpine fir (Abies lasiocarpa) …

Factors Impacting Genetic Test Result Recall And Adherence To Cancer Risk Management Recommendations Among Patients With Germline Pathogenic Variants, Karishma Prakash Bharwani

USF Tampa Graduate Theses and Dissertations

Only 20-60% of information from medical appointments is estimated to be retained of which about half is recalled accurately; however there remains limited information about recall following disclosure of inherited cancer genetic test results (GTR). We sought to evaluate recall of GTRs and the association of recall with adherence to recommended cancer risk management (CRM). Study participants were consented individuals with a confirmed germline pathogenic or likely pathogenic variant (GPV) in an inherited cancer predisposing genes for which there are CRM guidelines per the National Comprehensive Cancer Network (NCCN). Through information collected through self-reported surveys, adherence to CRM was defined …

Prevalence, Morbidity, And Mortality Of Men With Sex Chromosome Aneuploidy In The Million Veteran Program Cohort, Shanlee Davis, Craig Teerlink, Julie Lynch, Bryan Gorman, Meghana Pagadala, Aoxing Liu, Matthew Panizzon, Victoria Merritt, Giulio Genovese, Judith Ross, Richard Hauger

Department of Pediatrics Faculty Papers

IMPORTANCE: The reported phenotypes of men with 47,XXY and 47,XYY syndromes include tall stature, multisystem comorbidities, and poor health-related quality of life (HRQOL). However, knowledge about these sex chromosome aneuploidy (SCA) conditions has been derived from studies in the less than 15% of patients who are clinically diagnosed and also lack diversity in age and genetic ancestry.

OBJECTIVES: To determine the prevalence of clinically diagnosed and undiagnosed X or Y chromosome aneuploidy among men enrolled in the Million Veteran Program (MVP); to describe military service metrics of men with SCAs; and to compare morbidity and mortality outcomes between men with …

Species Delimitation Of Slimy Salamanders, Plethodon Kisatchie And Plethodon Mississippi, Across The Lower Mississippi River, Brock Hunter Stevenson

Master's Theses

Species are fundamental units of biodiversity yet delimiting species can be challenging. Slimy Salamanders of the Plethodon glutinosus species complex are a classic example of cryptic species for which species boundaries and relationships have proved difficult to determine. Once thought to be a single species ranging across the eastern United States, protein analysis revealed high genetic divergences among geographically distinct groups of populations, leading to 16 species being recognized within the group. Two of these species, the Louisiana Slimy Salamander (Plethodon kisatchie) and the Mississippi Slimy Salamander (Plethodon mississippi), are closely related but occur on opposite sides of the Mississippi …

Influence Of Maternal Supplementation With Vitamins, Minerals, And (Or) Protein/Energy On Placental Development And Angiogenic Factors In Beef Heifers During Pregnancy, Bethania J. Dávila Ruiz, Carl R. Dahlen, Kacie L. Mccathy, Joel S. Caton, Jennifer L. Hurlbert, Friederike Baumgaertner, Ana Clara B. Menezes, Wellison J. S. Diniz, Sarah R. Underdahl, James D. Kirsch, Kevin K. Sedivec, Kerri A. Bochantin, Pawel P. Borowicz, Sebastián Canovas, Lawrence P. Reynolds

Department of Animal Science: Faculty Publications

The effect of vitamins and minerals supplementation (VTM) and/or two rates of body weight gain (GAIN) on bovine placental vascular development and angiogenic factors gene expression were evaluated in two experiments: In Exp. 1, crossbred Angus heifers (n = 34) were assigned to VTM/NoVTM treatments at least 71 days before breeding to allow changes in the mineral status. At breeding, through artificial insemination (AI), heifers were assigned to low-gain (LG) 0.28 kg/d or moderate-gain (MG) 0.79 kg/d treatments, resulting in NoVTM-LG (Control; n = 8), NoVTM-MG (n = 8), VTM-LG (n = 9), and VTM-MG (n = …

Genetic Counseling Student Self-Efficacy, Exam Anxiety, And Opinions Related To Study Materials For The Genetic Counseling Board Certification Exam., Jessica F. Stanton

USF Tampa Graduate Theses and Dissertations

The Genetic Counseling Board Examination is a critical assessment for clinical practice in the field. However, the relationship between students’ test-related anxiety, confidence in their ability to study (i.e., self-efficacy), and the use of gamification for board examination preparation remains unexplored. This study compared gamification and traditional quiz-style study methods using two randomized groups of students preparing for the Genetic Counseling Board Examination. The primary objectives were to assess for changes in exam-related anxiety and self-efficacy after completing the respective study materials and to evaluate the acceptability and completion rates of these materials. Ninety-eight genetic counseling students or recent graduates …

Agrobacterium-Mediated Genetic Transformation And Plant Regeneration From Cotyledons In Philippine Eggplant (Solanum Melongena L.) Acc. ‘Ph 11424’, Mark Gabriel Sagarbarria, John Albert Caraan, Patrick Lipio, Ian Bien Oloc-Oloc, Kazuo Watanabe, Desiree Hautea

The Philippine Agricultural Scientist

Eggplant (Solanum melongena L.) is one of the most important vegetables grown and consumed in the Philippines hence, continuous breeding programs are vital to maintain the supply of this economically important crop. This study demonstrates the first successful Agrobacterium-mediated genetic transformation and plant regeneration of the Philippine eggplant cultivar ‘PH 11424’, also known as ‘Mistisa’. Cotyledons from 2-wk-old seedlings were used as explants, which were transformed with disarmed Agrobacterium tumefaciens strain LBA4404 harboring a binary vector for CRISPR/Cas9 expression and hygromycin phosphotransferase (HPT), an antibiotic selection marker. Growth of shoot primordia from the agro-infected explants was observed during selective culture …

Investigating The Mechanisms Of Surface Sensing Using Motility Appendages By Pseudomonas Aeruginosa Pa14, Christopher James Geiger

Dartmouth College Ph.D Dissertations

Biofilms are surfaced attached communities of cells encased in an extracellular matrix. The transition from free-swimming planktonic cells to a surface attached biofilm begins with cellular changes that occur after surface contact. This process is known as "surface sensing" and the opportunistic pathogen Pseudomonas aeruginosa PA14 uses its two motility appendages, type IV pili (T4P) and a single, polar flagellum to sense and traverse surfaces. The first cellular changes to occur within this organism upon surface contact is an increase in the second messengers cAMP and cdi- GMP. While the genes involved in surface sensing by P. aeruginosa are known, …

Genome Editing Using Crispr-Cas9 In Annual Killifish Species, Keria Moritsugu-Vandehey

University Honors Theses

CRISPR-Cas9 genome editing has been used successfully to knock out genes in model organisms such as zebrafish, turquoise killifish, and cichlid fish. CRISPR-Cas9 genome editing has not been verified in the annual killifish, Austrofundulus limnaeus. We hypothesize that targeted editing of the tyrosinase gene in embryos of A. limnaeus will lead to fish without the ability to produce black pigment. Embryos at the 1-cell stage were injected with a Cas9 cocktail containing a mix of guide RNA molecules that target the genomic sequence of the tyrosinase gene and either an mRNA coding for the Cas9 protein or Cas9 protein. …