Genetics Commons^™

Americans’ Familiarity, Interest, And Actions With Direct-To-Consumer Genetic Testing, Riley L. Carroll

USF Tampa Graduate Theses and Dissertations

Background: In 2013, 36% of the U.S. public was aware of Direct-to-Consumer (DTC) genetic tests, but updated studies are needed to identify whether this has changed over time. Objective: The aims are to determine current awareness and utilization of DTC tests and to identify demographic factors that influence testing uptake. Methods: An online panel survey of 543 U.S. adults was conducted using age- and sex-based quotas. Descriptive statistics and binary regression identified factors associated with undergoing DTC testing and linear regression was conducted to identify factors associated with likelihood of using DTC testing for athletic ability to …

Evaluation Of A Spanish-Language Educational Tool For Inherited Cancer, Stefania Alastre

USF Tampa Graduate Theses and Dissertations

A web-based educational tool designed to cover pre-test genetic counseling elements for multi-gene hereditary cancer panel testing increased knowledge and decisional empowerment among an English-speaking cohort actively seeking information about genetic testing. The purpose of this study was to pilot a Spanish-language version of this tool using a pre- post- survey design to assess for changes in knowledge and informed decision making about genetic testing and obtain additional feedback using semi-structured interviews. Spanish-speaking individuals were recruited online. Although several participants expressed that the tool was informative, interesting, and that they liked it, time stamps for the post-survey suggested that most …

Reducing Seed Coat Fiber Content And Pod Shatter, And Engineering Medium Chain Fatty Acids-Containing Oil, In The Oilseed Crop Pennycress ( Thlaspi Arvense L. ), Maliheh Esfahanian

Theses and Dissertations

The overall goal of this thesis was to genetically improve agronomic traits of pennycress (Thlaspi arvense L.; Field Pennycress) and demonstrate the production of value-added designer seed oils to domesticate pennycress and enable its establishment as a new winter annual oilseed/meal/cover crop to be grown in temperate regions of the world. In the U.S. Midwest, pennycress can be double cropped on existing farmland during the time between corn harvest and subsequent planting of soybeans the following spring. Pennycress has the potential to produce 2,000 lbs/acre seeds, which at 33% by weight oil content and 20% protein, would yield 85 gallons/acre …

Using Crispr-Cas9 To Construct Knockout Mutants In Dna-Repair Genes In Arabidopsis Thaliana, David Campbell

Honors Program: Senior Projects (Public)

The mitochondria are known as the powerhouse of the cell, and just like a real powerhouse, it can be a dangerous place to store sensitive information. Energy generation and redox reactions in the mitochondria can cause damage to the DNA stored there, resulting in a higher mutation rate. Compared to their animal counterparts, however, plant mitochondria exhibit a lower mutation rate and a higher recombination rate. It is hypothesized that the unique DNA repair methods present in plant mitochondria are responsible for the phenomena observed there. To study the mechanics of DNA-repair in this organelle, however, researchers must be able …

The Dna Cloud: Is It Alive?, Theodoros Bargiotas

LSU Doctoral Dissertations

In this analysis, I will firstly be presenting the current knowledge concerning the materiality of the internet based Cloud, which I will henceforth be referring to as simply the Cloud. For organisation purposes I have created two umbrella categories under which I place the ongoing research in the field. Scholars have been addressing the issue of Cloud materiality through broadly two prisms: sociological materiality and geopolitical materiality. The literature of course deals with the intricacies of the Cloud based on its present ferromagnetic storage functionality. However, developments in synthetic biology have caused private tech companies and University spin-offs to flirt …

Changes In Both Trans- And Cis-Regulatory Elements Mediate Insecticide Resistance In A Lepidopteron Pest, Spodoptera Exigua, Bo Hu, He Huang, Songzhu Hu, Miaomiao Ren, Qi Wei, Xiangrui Tian, Mohammed Esmail Abdalla Elzaki, Chris Bass, Jianya Su, Subba Reddy Palli

Entomology Faculty Publications

The evolution of insect resistance to insecticides is frequently associated with overexpression of one or more cytochrome P450 enzyme genes. Although overexpression of CYP450 genes is a well-known mechanism of insecticide resistance, the underlying regulatory mechanisms are poorly understood. Here we uncovered the mechanisms of overexpression of the P450 gene, CYP321A8 in a major pest insect, Spodoptera exigua that is resistant to multiple insecticides. CYP321A8 confers resistance to organophosphate (chlorpyrifos) and pyrethroid (cypermethrin and deltamethrin) insecticides in this insect. Constitutive upregulation of transcription factors CncC/Maf are partially responsible for upregulated expression of CYP321A8 in the resistant strain. Reporter gene assays …

Recent Genetic Connectivity And Clinal Variation In Chimpanzees, Jack D. Lester, Linda Vigilant, Paolo Gratton, Maureen S. Mccarthy, Christopher D. Barratt, Paula Dieguez, Anthony Agbor, Paula Alvarez-Varona, Samuel Angedakin, Emmanuel Ayuk Ayimisin, Emma Bailey, Mattia Bessone, Gregory Brazzola, Rebecca Chancellor, Heather Cohen, Emmanuel Danquah, Tobias Deschner, Villard Ebot Egbe, Manasseh Eno-Nku, Annemarie Goedmakers, Anne-Celine Granjon, Josephine Head, Daniela Hedwig, R. Adriana Hernandez-Aguilar, Kathryn J. Jeffery, Sorrel Jones, Jessica Junker, Parag Kadam, Michael Kaiser, Ammie K. Kalan, Laura Kehoe, Ivonne Kienast, Kevin E. Langergraber, Juan Lapuente, Anne Laudisoit, Kevin Lee, Sergio Marrocoli, Vianet Mihindou, David Morgan, Geoffrey Muhanguzi, Emily Neil, Sonia Nicholl, Christopher Orbell, Lucy Jayne Ormsby, Liliana Pacheco, Alex Piel, Martha M. Robbins, Aaron S. Rundus, Crickette Sanz, Lilah Sciaky, Alhaji M. Siaka, Veronika Staedele, Fiona Stewart, Nikki Tagg, Els Ton, Joost Van Schijndel, Magloire Kambale Vyalengerera, Erin G. Wessling, Jacob Willie, Roman M. Wittig, Yisa Ginath Yuh, Kyle Yurkiw, Klaus Zuberbuehler, Christophe Boesch, Hjalmar S. Kuehl, Mimi Arandjelovic

Psychology Faculty Publications

Much like humans, chimpanzees occupy diverse habitats and exhibit extensive behavioural variability. However, chimpanzees are recognized as a discontinuous species, with four subspecies separated by historical geographic barriers. Nevertheless, their range-wide degree of genetic connectivity remains poorly resolved, mainly due to sampling limitations. By analyzing a geographically comprehensive sample set amplified at microsatellite markers that inform recent population history, we found that isolation by distance explains most of the range-wide genetic structure of chimpanzees. Furthermore, we did not identify spatial discontinuities corresponding with the recognized subspecies, suggesting that some of the subspecies-delineating geographic barriers were recently permeable to gene flow. …

Stategra: Multi-Omics Data Integration - A Conceptual Scheme With A Bioinformatics Pipeline, Nuria Planell, Vincenzo Lagani, Patricia Sebastian-Leon, Frans Van Der Kloet, Ewoud Ewing, Nestoras Karathanasis, Arantxa Urdangarin, Imanol Arozarena, Maja Jagodic, Ioannis Tsamardinos, Sonia Tarazona, Ana Conesa, Jesper Tegner, David Gomez-Cabrero

Computational Medicine Center Faculty Papers

Technologies for profiling samples using different omics platforms have been at the forefront since the human genome project. Large-scale multi-omics data hold the promise of deciphering different regulatory layers. Yet, while there is a myriad of bioinformatics tools, each multi-omics analysis appears to start from scratch with an arbitrary decision over which tools to use and how to combine them. Therefore, it is an unmet need to conceptualize how to integrate such data and implement and validate pipelines in different cases. We have designed a conceptual framework (STATegra), aiming it to be as generic as possible for multi-omics analysis, combining …

Spatio-Temporal Selection Of Reference Genes In The Two Congeneric Species Of Glycyrrhiza, Yuping Li, Xiaoju Liang, Xuguo Zhou, Yu An, Ming Li, Ling Yuan, Yongqing Li, Ying Wang

Entomology Faculty Publications

Glycyrrhiza, a genus of perennial medicinal herbs, has been traditionally used to treat human diseases, including respiratory disorders. Functional analysis of genes involved in the synthesis, accumulation, and degradation of bioactive compounds in these medicinal plants requires accurate measurement of their expression profiles. Reverse transcription quantitative real-time PCR (RT-qPCR) is a primary tool, which requires stably expressed reference genes to serve as the internal references to normalize the target gene expression. In this study, the stability of 14 candidate reference genes from the two congeneric species G. uralensis and G. inflata, including ACT, CAC, CYP, …

Ectopic Expression Of Pericentric Hsatii Rna Results In Nuclear Rna Accumulation, Mecp2 Recruitment, And Cell Division Defects, C. C. Landers, Christina Rabeler, E. K. Ferrari, Lia R. D'Alessandro , '21, D. D. Kang, J. Malisa, Safia M. Bashir , '20, Dawn M. Carone

Biology Faculty Works

Within the pericentric regions of human chromosomes reside large arrays of tandemly repeated satellite sequences. Expression of the human pericentric satellite HSATII is prevented by extensive heterochromatin silencing in normal cells, yet in many cancer cells, HSATII RNA is aberrantly expressed and accumulates in large nuclear foci in cis. Expression and aggregation of HSATII RNA in cancer cells is concomitant with recruitment of key chromatin regulatory proteins including methyl-CpG binding protein 2 (MeCP2). While HSATII expression has been observed in a wide variety of cancer cell lines and tissues, the effect of its expression is unknown. We tested the effect …

Recent Advances In The Application Of Crispr/Cas9 Gene Editing System In Poultry Species, Collins N. Khwatenge, Samuel N. Nahashon

Agricultural and Environmental Sciences Faculty Research

CRISPR/Cas9 system genome editing is revolutionizing genetics research in a wide spectrum of animal models in the genetic era. Among these animals, is the poultry species. CRISPR technology is the newest and most advanced gene-editing tool that allows researchers to modify and alter gene functions for transcriptional regulation, gene targeting, epigenetic modification, gene therapy, and drug delivery in the animal genome. The applicability of the CRISPR/Cas9 system in gene editing and modification of genomes in the avian species is still emerging. Up to date, substantial progress in using CRISPR/Cas9 technology has been made in only two poultry species (chicken and …

Insights Into Leptopilina Spp. Immune-Suppressive Strategies Using Mixed-Omics And Molecular Approaches, Brian Wey

Dissertations, Theses, and Capstone Projects

Host-parasite interactions influence the biology of each over the course of evolution. Parasite success allows for the passage of potent virulence strategies from generation to generation. Host success passes stronger immunity and resistance strategies to the following generations as well. Only by studying both partners within their natural contexts can we begin to understand the relationship between the two and how immune mechanisms and virulence strategies interact as a molecular arms race.

In this work, we focus on a natural host-parasite pair, the Drosophila-Leptopilina model. Leptopilina species are parasites of several fruit fly species, including Drosophila melanogaster. This model …

Epigenetic Evolution Of Ace2 And Il-6 Genes: Non-Canonical Interferon-Stimulated Genes Correlate To Covid-19 Susceptibility In Vertebrates, Eric R. Sang, Yun Tian, Laura C. Miller, Yongming Sang

Agricultural and Environmental Sciences Faculty Research

The current novel coronavirus disease (COVID-19) has spread globally within a matter of months. The virus establishes a success in balancing its deadliness and contagiousness, and causes substantial differences in susceptibility and disease progression in people of different ages, genders and pre-existing comorbidities. These host factors are subjected to epigenetic regulation; therefore, relevant analyses on some key genes underlying COVID-19 pathogenesis were performed to longitudinally decipher their epigenetic correlation to COVID-19 susceptibility. The genes of host angiotensin-converting enzyme 2 (ACE2, as the major virus receptor) and interleukin (IL)-6 (a key immuno-pathological factor triggering cytokine storm) were shown to evince active …

A Pathogenic Ufsp2 Variant In An Autosomal Recessive Form Of Pediatric Neurodevelopmental Anomalies And Epilepsy, Min Ni, Bushra Afroze, Chao Xing, Chunxiao Pan, Yanqiu Shao, Ling Cai, Brandi L. Cantarel, Jimin Pei, Nick V. Grishin, Stacy Hewson

Department of Paediatrics and Child Health

Purpose: Neurodevelopmental disabilities are common and genetically heterogeneous. We identified a homozygous variant in the gene encoding UFM1-specific peptidase 2 (UFSP2), which participates in the UFMylation pathway of protein modification. UFSP2 variants are implicated in autosomal dominant skeletal dysplasias, but not neurodevelopmental disorders. Homozygosity for the variant occurred in eight children from four South Asian families with neurodevelopmental delay and epilepsy. We describe the clinical consequences of this variant and its effect on UFMylation.
Methods: Exome sequencing was used to detect potentially pathogenic variants and identify shared regions of homozygosity. Immunoblotting assessed protein expression and post-translational modifications in patient-derived fibroblasts. …

Genetic Variability And Genome-Wide Association Analysis Of Flavor And Texture In Cooked Beans (Phaseolus Vulgaris L.), Amber Bassett, Kelvin Kamfwa, Daniel Ambachew, Karen Cichy

Agricultural and Environmental Sciences Student Research

Key message

Cooked bean flavor and texture vary within and across 20 Andean seed types; SNPs are significantly associated with total flavor, beany, earthy, starchy, bitter, seed-coat perception, and cotyledon texture.

Abstract

Common dry beans are a nutritious food recognized as a staple globally, but their consumption is low in the USA. Improving bean flavor and texture through breeding has the potential to improve consumer acceptance and suitability for new end-use products. Little is known about genetic variability and inheritance of bean sensory characteristics. A total of 430 genotypes of the Andean Diversity Panel representing twenty seed types were grown …

Forensic Genealogy: A Tool In Dna Analysis, Samantha Olsen

Undergraduate Honors College Theses 2016-

DNA is the basic unit of which differentiates one individual to the next. Short Tandem Repeats and Single Nucleotide Polymorphisms are two locations of DNA that have been the most successful in DNA analysis. Unique DNA profiles can be created so that interpretations can be made about the individual who contributed to the DNA sample. Systems like STRmix are currently being employed to give unbiased assumptions about the DNA profiles. There are several different statistical approaches in assigning probabilities to DNA evidence, likelihood ratio and random match probability are two common approaches. After assumptions are made, comparisons can be made …

A Zugunruhe Data Collection System Using Passive Infrared Sensors, Ryan Terry, Luis E. Ramirez, Carol Carrera, Abigail Kimmitt, Kira Delmore, Ana Goulart

Pursue: Undergraduate Research Journal

When engineers and biologists work together, there is a lot to learn on both sides. For instance, our work introduced us to zugunruhe, which is a German word that means “unrest”. It is used in the context of migratory birds, as they become restless at night, inside their cages, during their migratory period. When does zugunruhe start? It usually starts when the weather becomes cold and the days shorter, but it varies for different bird species. Moreover, global warming has caused changes in zungunruhe’s timing, which made it even harder to predict. Another question is about genetics: is …

Viropana (Vna) 5, Abijeet Singh Mehta, Panagiotis A. Tsonis, Amit Singh

Components of a Regeneration Toolkit: Notophthalmus viridescens

Viropana (vna) 5

• ID – vna 5
• Details – Gene from a novel protein family belonging to the regeneration toolkit of Notophthalmus viridescens
• Base pairs – 391

Viropana (Vna) 1, Abijeet Singh Mehta, Panagiotis A. Tsonis, Amit Singh

Components of a Regeneration Toolkit: Notophthalmus viridescens

Viropana (vna) 1

• ID – vna 1

• Details – Gene from a novel protein family belonging to the regeneration toolkit of Notophthalmus viridescens

• Base pairs – 492

Efficacy Of Aav-Mediated Gene Replacement Therapy For Mybpc3- Associated Hcm In Ipscms, Marian Henderson, Josh Meisner, Sabrina Friedline, Yao-Chang Tsan, Adam Helms

Summer Research

• Hypertrophic cardiomyopathy (HCM) is a highly morbid myocardial disease occurring in 1:200 people in the general population
• Most common genetic cause of HCM are mutations in MYBPC3, encoding for MyBP-C, a critical protein for regulating cardiac muscle contractility
• Limited treatments available primarily focus on symptomatic management and cannot reverse cardiomyopathy
• Haploinsufficiency - one allele is unable to produce sufficient protein to maintain normal cardiac function
• Adeno-associated virus (AAV) mediated gene replacement therapy recently emerged as a therapeutic option for genetic diseases due to loss of function variants causing haploinsufficiency

Viropana (Vna) 2, Abijeet Singh Mehta, Panagiotis A. Tsonis, Amit Singh

Components of a Regeneration Toolkit: Notophthalmus viridescens

Viropana (vna) 2

• ID – vna 2
• Details – Gene from a novel protein family belonging to the regeneration tool kit of Notophthalmus viridescens
• Base pairs – 396

Viropana (Vna) 4, Abijeet Singh Mehta, Panagiotis A. Tsonis, Amit Singh

Components of a Regeneration Toolkit: Notophthalmus viridescens

Viropana (vna) 4

• ID – vna 4
• Details – Gene from a novel protein family belonging to the regeneration toolkit of Notophthalmus viridescens
• Base pairs – 501

A Multispecies Perspective Into Dietary Genetic Adaptations And Ancient Migration In The Peruvian Andes, Kelsey Jorgensen

Wayne State University Dissertations

Successful adaptation to the high-elevation Andes would have required both cultural and biological adaptations by early human populations. These past adaptations continue to shape the evolutionary outcomes of both humans and non-human species today. A multispecies perspective was used to examine how humans and non-human creatures, specifically insects, were shaped by past human adaptations. This dissertation asked two primary questions: 1) Given the importance and evolutionary history of potato consumption in the Peruvian Andes, is a genetic adaptation to better digest potato starch detectable in present-day Peruvians? and 2) Using the Andean Potato Weevil (APW) phylogeny as a proxy, what …

Using Genetic Approaches To Understand Tumorigenesis In Drosophila, Shawna Defreitas

College of Graduate Studies: Theses & Dissertations

The large number of conserved molecular and signaling pathways between Drosophila melanogaster and humans, makes Drosophila an effective model organism to better understand human diseases, including cancers. Previous studies by clinicians and researchers have identified PTEN, BRCA2, P53, NF1, and RB1 as key mutational drivers in High Grade Serous Ovarian Cancer (HGSOC), the most malignant form of ovarian cancer in humans. The objective of this study was to develop a tumor model in the follicle cell epithelium of the Drosophila ovary and to use immunohistochemistry to study the molecular mechanisms behind tumor development. First, the Drosophila …

Mimicking The Effect Of Prolactin On Stat3/Stat5 Activity In Breast Cancer, Jennifer N. Barbuto, Sarah R. Walker

Honors Theses and Capstones

Signal transducers and activators of transcription (STAT) 3 and 5 are commonly constitutively activated in breast cancer. STAT5 can outcompete STAT3 and reduce cell proliferation and metastasis. STAT5 activation is stimulated by prolactin, a natural hormone that can be harmful at high levels. The aim of this study is to identify some possible previously developed drugs that mimic the effect of prolactin and STAT5 without the added risk in MDA-MB231 breast cancer cells. Using the CLUE database query app and STAT5 up- and downregulation signatures, three drugs (X, K, and M) were chosen based on their similarity in signatures to …

Examining A Functional Interaction Between Chromatin Remodeler Chd1 And Histone H1 In D. Melanogaster, Breanna Kim

Scripps Senior Theses

Chromodomain-helicase-DNA-binding-protein-1 (CHD1) is a highly conserved ATP- dependent remodeling protein. It is localized to active genes and directs nucleosome spacing, while its loss has been linked to various human diseases, such as human prostate cancer. In Drosophila, CHD1 is important for fertility and wing development, and overexpression of CHD1 leads to severe wing vein defect phenotypes. The Linker Histone H1, which is known for maintaining heterochromatin and is associated with inactive genes, had been previously identified as a possible functional partner of CHD1, though the exact nature of their interaction is unclear. I undertook a genetic approach to examining the …

Retrotransposon-Mediated Transduction Of An Environmental Cue To Regulate Centrosome Fate, Shawn Patrick Murphy

Legacy Theses & Dissertations (2009 - 2024)

In 1969, the enrichment of mobile element repeat sequences led Britton and Davidson to propose the hypothesis that gene expression in higher eukaryotes is regulated through the exaptation of mobile elements. In this work, I have explored the hypothesis that mobile elements can also be harnessed by the host to regulate asymmetric cell division, thereby determining cell fate. Retrotransposons are ubiquitous eukaryotic mobile elements that transpose through an RNA intermediate. They are often active in cell types that divide asymmetrically to yield daughter cells with different fates, such as embryonic stem cells, germline stem cells, neuronal stem cells and the …

Will There Be Changes In Sexually Differentiated Behaviors In Mice Manipulated For The Sry Gene As They Mature Into Adultood?, Subin Joo

CMC Senior Theses

Sexually differentiated behavior has been shown to be affected by both genes and hormones. The discovery of the SRY gene, which codes for the development of testes, lead to the development of the Four Core Genotypes model of mice, and the separation of sex chromosomes and its resulting gonadal hormones. Using the FCG model, this study aims to look at the development of sexually differentiated behavior in mice, and track how it changes throughout their life. FCG mice will be divided into individual and social housing, and repeated experiments carried out to test their reaction to both intact female and …

Functional Characterization Of Threonine 49 Phosphorylation Of Cytochrome C, Antoine Khobeir

Wayne State University Theses

Cytochrome c (Cytc) is a pivotal multifunctional mitochondrial protein that serves as a single electron carrier between complexes III and IV of the electron transport chain. It has important roles in both cellular respiration and apoptosis. The novel Thr49 (T49) phosphorylation of Cytc likely affects mitochondrial respiration, membrane potential, ROS production, ATP production, and apoptosis. Based on the functional characterization of previously mapped phosphorylation sites (Tyr97, Tyr48, Thr28, Ser47, Thr58) of the lab, we hypothesize that T49 phosphorylation will lead to controlled respiration, optimal intermediate mitochondrial membrane potential, lower ROS production, and inhibition of apoptosis compared to unphosphorylated Cytc. Here …

Novel Role Of Endoplasmic Reticulum-Associated Degradation In The Regulation Of Ceruloplasmin, Stephen William Hippleheuser

Wayne State University Theses

Ceruloplasmin (Cp) is a secreted ferroxidase produced by the hepatocytes that assists in the transport of iron throughout the human body. In human aceruloplasminemia patients, due to Cp deficiency excess intracellular iron buildup leads to ailments like liver cirrhosis, neurodegeneration, and blindness. We recently found that the biogenesis of Cp in the endoplasmic reticulum (ER) is regulated by a principal ER quality-control process, ER-associated degradation (ERAD). ERAD clears misfolded ER proteins for cytosolic proteasomal degradation, with the Sel-1 suppressor of lin-12-like (Sel1L)-HMG-CoA reductase degradation 1 (Hrd1) protein complex representing the most conserved branch in mammals. Interestingly, we found that Sel1L-Hrd1 …