Genetics and Genomics Commons^™

The History And Future Of Cystic Fibrosis, Randall Combs, Che Fung Andy Chan, Daisy Sahagun

Undergraduate Research Symposium Posters

The purpose of this research timeline is to highlight the tumultuous yet inspiring history of Cystic Fibrosis disease and treatment to give us a more pragmatic understanding of its current state. Cystic Fibrosis is an autosomal recessive disease, most often caused by a single amino-acid deletion of phenylalanine at position 508 in the nucleotide binding domain, which results in a loss of the cystic fibrosis transmembrane conductance regulator (CFTR). Symptomatology varies considerably but a buildup of mucus in the respiratory tract leading to lung failure, and exocrine pancreatic insufficiency which results in digestive and metabolic dysfunction are commonly, if not …

Retinoblastoma: Past, Present, And Future, Izabela Daneva, Crysty-Ann Olaco, Albert Tran

Undergraduate Research Symposium Posters

The purpose of this research timeline is to synthesize the natural history of retinoblastoma to understand its societal effects and develop a public health message to raise awareness of the disease. We used literature-based research in order to gain an understanding about the discovery of this disease and investigate its most current state of knowledge. Retinoblastoma is an intraocular cancer that manifests early in childhood. It is typically linked to a somatic or germline insertion, deletion, or single-base substitution mutation on both alleles of RB1, a tumor-suppressor gene. Retinoblastoma was first identified in 1809 by James Wardrop, and since then, …

Study Of Sickle Cell Disease, Aaron Guevarra, Carlos Herrera, Faysal Ali

Undergraduate Research Symposium Posters

The purpose of this research timeline is to explore the history, prevalence, and effects of Sickle Cell Disease (SCD) so that treatments and possible future experiments or cures may be discussed. In SCD, abnormal red blood cells appear as sickle shaped as opposed to the round shape of normal red blood cells. It is inherited in an autosomal recessive pattern, so an individual must inherit two copies of the allele. The gene mutation is a single nucleotide mutation in the gene which codes for β-globin. In 1910, James B. Herrick first described the disease, and in 1949, its inheritance pattern …

An Exploration Of The Genetic Counselor’S Role In The Individualized Education Program, Naomi Jean Barker

Theses and Dissertations

Purpose: This exploratory study aimed to assess the knowledge of school psychologists and special education teachers regarding genetic conditions and the resources used in the development of individualized education programs (IEP) for students with genetic disorders. While the IEP process has been described for children with disabilities, literature explicitly focusing on children with genetic conditions is lacking. The rarity of genetic conditions often leaves school personnel with limited information. Methods: School psychologists (N=29) and special education teachers (N =14) throughout the United States participated in an online questionnaire. School psychologists were recruited from research committee listservs of state associations, and …

Exploration Of Patient Communication Preference Regarding Reclassified Genetic Test Results, Cooper Nicole Hall

Theses and Dissertations

Genetic testing is becoming increasingly used to detect individuals who are predisposed to developing cancer. If genetic testing identifies a variant in an individual’s DNA, the testing laboratory uses available data to classify the variant as either disease-causing or benign. When limited data is available regarding a variant’s pathogenicity and the risk of cancer for an individual is not clear, the variant is classified as a “variant of uncertain significance” (VUS). If new data is discovered, the VUS may be reclassified. There is a gap in current literature regarding desired communication for a reclassified genetic test result. There are no …

Genomic Studies Of Beaf-32 In Drosophila, John Keller Mckowen Iii

LSU Doctoral Dissertations

Compared to humans, the model organism Drosophila melanogaster is particularly gene dense and encodes several insulator binding proteins (IBP) to aid in its genome organization. Our focus of research is a particular IBP, Boundary Element-Associated Factor of 32kD (BEAF). BEAF primarily binds near the promoters of constitutively active housekeeping genes. It is thought to help maintain the active state of these genes by preventing the spread of repressive chromatin. Additionally, the enhancer blocking activity of BEAF is thought to prevent aberrant activation or silencing of genes. BEAF appears to be ubiquitously expressed among cells and tissues, albeit at varying levels. …

Morphological And Microsatellite-Based Molecular Characterization Of Locally Collected Sugarcane (Saccharum Officinarum L.), Carl F. Libayao, Carmina C. Manuel Ma., Eureka Teresa M. Ocampo, Antonio G. Lalusin

The Philippine Agricultural Scientist

Fifty-three sugarcane accessions from Aklan, Iloilo, Cagayan, Nueva Vizcaya, Isabela, and Bohol were characterized using forty-two morphometric parameters and forty microsatellite markers. Twenty-six morphological characters using the Shannon-Weaver diversity index showed high variability (H’ = > 0.76) and were able to characterize the fifty-three sugarcane accessions. Cluster analysis of morphological traits based on sequential agglomerative hierarchical test and Euclidean distance revealed two groupings at 0.3 coefficient of dissimilarity. The clustering of some accessions was irrespective of their geographical origin indicating a high degree of phenotypic similarity in some accessions. Out of the forty microsatellite markers, twenty-five (63%) have a PIC value …

Phenotypic Characters And Expression Of Cytokinin Oxidase 2 (Osckx2) Gene In Rice Genotypes With Enhanced Grain Filling Traits, Cielo Luz C. Mondejar, Maria Genaleen Q. Diaz, Teresita H. Borromeo, Tonette P. Laude, Arlen A. Dela Cruz, Roel Rodriguez Suralta

The Philippine Agricultural Scientist

Poor grain filling is still a major problem in rice production. Recent attention in crop varietal improvement is focused on heritable delayed foliar senescence, enhanced root system, and fast-synchronous grain filling pattern. Nine genotypes were characterized for these three enhanced grain-filling traits to determine the role of these traits on grain yield. Based on heritable delayed foliar senescence, NSIC Rc436 and NSIC Rc512 were characterized as Type A, while PSB Rc18 and NSIC Rc514 as Type B. These genotypes had a significantly higher yield than IR64, owing to their high spikelets number. Data suggested a positive correlation between the delayed …

16s Rrna Gene Sequence Analysis Of Acetic And Lactic Acid Bacteria Isolated From Philippine Sugarcane Wine (Basi) [Research Note], John Russel G. Sevilla, Michael Angelo S. Esteban, Honey Bhabes R. Iñigo, Audrey May V. Orillaza, Baby Richard R. Navarro

The Philippine Agricultural Scientist

Basi, a traditional sugarcane wine of the Philippines, was studied. Here, we used molecular- and cultural-based methods to isolate, identify and characterize acid-producing bacteria, specifically acetic and lactic acid bacteria, from basi. Acid producers were focused on owing to the rapid spoilage of basi via acidification with air exposure. Two strains each of acetic and lactic acid bacteria were isolated. DNA was extracted from these isolates. PCR-amplified DNA products were subjected to 16S rRNA gene sequencing. The sequences of the isolates were then aligned with BLAST database sequences and found to have high similarities to Acetobacter malorum (99%), …

“Adopt-A-Tissue” Initiative Advances Efforts To Identify Tissue-Specific Histone Marks In The Mare, N. B. Kingsley, Natasha A. Hamilton, Gabriella Lindgren, Ludovic Orlando, Ernest Bailey, Samantha Brooks, Molly Mccue, Theodore S. Kalbfleisch, James N. Macleod, Jessica L. Petersen, Carrie J. Finno, Rebecca R. Bellone

Maxwell H. Gluck Equine Research Center Faculty Publications

No abstract provided.

Variation In Genes Responsible For Melanism In Sciurus Carolinensis And Sciurus Niger, Ibrahim Hussain

UNO Student Research and Creative Activity Fair

During the past few years, the population of melanistic squirrels in Nebraska has increased. These color variations have been associated with variation in the Melanocortin 1 Receptor (MC1R) and Agouti Signaling Protein (ASIP) genes, which are responsible for pigment production. DNA was isolated from 3 grey and 46 fox squirrels collected from Eastern Nebraska; 8 of the fox squirrels were melanistic in color. Primers were designed to amplify and sequence MC1R and three portions of ASIP to examine the extent of variation in these genes in local squirrels. The sequences were aligned to the grey squirrel reference …

Comparison Of Gray Squirrel (Sciurus Carolinensis) And Fox Squirrel (Sciurus Niger) In Order To Explore Genes That Confer A Fitness Advantage, Joshua Franzen

UNO Student Research and Creative Activity Fair

Mutations in the MC1R gene is associated with melanism, or black fur, and the presence of a 24 base pair deletion in the MC1R gene of fox and gray squirrels suggests a shared ancestry between the two species. This could be due to a mutation in a common ancestor or previous mating between species. Evidence has shown that the most likely cause for the presence of MC1R in both species is previous mating between species. If this did occur, then it is possible that other genes traveled between species along with the mutated MC1R gene. Conserved genes shared between species …

The Perceived Utility Of Direct-To-Consumer Genetic Testing Marketed For Athletic Ability, Katherine L. Zimmerman

USF Tampa Graduate Theses and Dissertations

Factors that influence the public’s interest in pursuing genetic testing to determine athletic ability are not yet known. The purpose of this study is to compare interest in genetic testing marketed for athletic ability and susceptibility to sports-related injuries among athletes and the general public. Additionally, this study aims to determine if genetic determinism, knowledge and elements of perceived utility influence their overall intention to use the results of such genetic testing. Participants were recruited through social media platforms to complete an online survey measuring their intention to pursue testing under various circumstances, intention to use the results to change …

Defining Codes Based On The Consolidated Framework For Implementation Research In The Context Of The Implementing Universal Lynch Syndrome Screening, Jasmine A. Burton-Akright

USF Tampa Graduate Theses and Dissertations

Lynch syndrome (LS) is the most common hereditary cause of both colorectal cancer (CRC) and endometrial cancer (EC). Universal tumor screening (UTS) of newly diagnosed EC and CRC patients has been shown to be both an effective and economical approach to identify patients with LS and subsequently reduce future cancer s for patients and their family members. Despite its efficacy, LS UTS has not been consistently adopted across hospital systems and existing programs vary widely in their structure and execution. The Implementing Universal Lynch Syndrome Screening (IMPULSS) study aims to determine the critical factors necessary for successful implementation of LS …

Novel Educational Material For Patients With A Variant Of Uncertain Significance (Vus) In A Cancer Risk Gene, Meghan E. Kelley

USF Tampa Graduate Theses and Dissertations

The number of individuals being tested for hereditary cancer syndromes has greatly increased in the last several years and many people receive Variants of Uncertain Significance (VUS) as a test result. Although VUS results should not guide medical management, patients and even some healthcare providers continue to use a VUS to alter or receive unnecessary medical care.

We conducted a needs assessment via literature review and analyzed VUS patient interviews from a previous study with the goal of identifying various themes that could help determine content, layout, and messaging to incorporate into online educational materials. The needs assessment found few …

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 …