Genetics and Genomics Commons^™

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 …

Variation In The Genome And Transcriptome Associated With Beef Cattle Production And Investigation Of The Metabolic Consequences Of Beta-Adrenergic Agonist Supplementation, Renae L. Sieck

Department of Animal Science: Dissertations, Theses, and Student Research

Beta-adrenergic agonists (β-AA) are widely used supplements in livestock production to improve feed efficiency and increase lean muscle mass. Heat stress is one of the largest economic burdens to the livestock industry due to production efficiency losses and morbidity and mortality of animals. Both β-AA and catecholamines released in response to heat stress bind to β-adrenoceptors on the skeletal muscle cell surface to activate downstream signaling pathways. The purpose of this study was to determine if β-AA supplementation and heat stress have an additive effect on the skeletal muscle transcriptome. 3’ RNA sequencing of samples of the longissimus dorsi was …

Bipolar Multiplex Families Have An Increased Burden Of Common Risk Variants For Psychiatric Disorders, Till F.M. Andlauer, Jose Guzman-Parra, Fabian Streit, Jana Strohmaier, Ney Alliey Rodriguez

School of Medicine Publications

Multiplex families with a high prevalence of a psychiatric disorder are often examined to identify rare genetic variants with large effect sizes. In the present study, we analysed whether the risk for bipolar disorder (BD) in BD multiplex families is influenced by common genetic variants. Furthermore, we investigated whether this risk is conferred mainly by BD-specific risk variants or by variants also associated with the susceptibility to schizophrenia or major depression. In total, 395 individuals from 33 Andalusian BD multiplex families (166 BD, 78 major depressive disorder, 151 unaffected) as well as 438 subjects from an independent, BD case/control cohort …

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 …

Previvor And High-Risk Breast Cancer Patients’ Opinions On A Specialized Management Clinic, Madeleine Nicole Tjoelker

Theses and Dissertations

Approximately 5-10% of cancers are thought to be hereditary, caused by pathogenic variants in genes associated with inherited cancer syndromes. Previvors, individuals who have a higher predisposition to cancer due to genetic or other risk factors, have specific healthcare and psychological needs that may be better served by a specialized management clinic. This study compared the experiences of previvors who had access to a specialized management clinic with those who did not, in order to better understand the unique needs of previvors. This study utilized a mixed methods design including an online survey (N=26) and semi-structured phone interview …

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 …

Mitochondrial Transfer From Mesenchymal Stem Cells Improves Neuronal Metabolism After Oxidant Injury In Vitro: The Role Of Miro1, Nancy Tseng, Scott C Lambie, Christopher Q Huynh, Bridget Sanford, Manisha Patel, Paco S Herson, D Ryan Ormond

Faculty, Staff and Students Publications

Stroke-induced cerebral ischemia is a major cause of death and disability. The disruption of blood flow results in neuronal and glial cell death leading to brain injury. Reperfusion restores oxygen to the affected tissue, but can also cause damage through an enhanced oxidative stress and inflammatory response. This study examines mitochondrial transfer from MSC to neurons and the role it plays in neuronal preservation after oxidant injury. We observed the transfer of mitochondria from MSC to mouse neurons in vitro following hydrogen peroxide exposure. The observed transfer was dependent on cell-to-cell contact and led to increased neuronal survival and improved …

Determination Of The Presence Of Rickettsia Spp. And Borrelia Spp. Carried By Tortoise Ticks From Madagascar, Anna Phan

Biological Sciences Theses & Dissertations

Ticks were removed from three species of Malagasy tortoises, Astrochelys yniphora, A. radiata, and Pyxis arachnoides (comprising two subspecies P. a. arachnoides and P. a. oblonga), between 2012 and 2015. The ticks were presumed to be from the genus Amblyomma. Ticks were morphologically identified and then checked molecularly to confirm their classification or identify any ticks that could not be morphologically identified. Molecular identification was done via end-point PCR that amplified tick cytochrome oxidase (CO1) and tick 12S rRNA genes. Ticks were screened via a real-time polymerase chain reaction assay for the presence of Rickettsia spp. …

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. …

Henry V. Howe And His Collection Of Foraminifera At Louisiana State University, Lorene E. Smith, Barun K. Sen Gupta

Occasional Papers of the Museum of Natural Science, Louisiana State University

Henry V. Howe, the founder of the current academic program in geology at Louisiana State University (LSU), and a renowned ostracod specialist, was also a distinguished foraminiferal paleontologist. His best work in that field, involving the discovery of many new species, was on the taxonomy of Eocene Foraminifera of Louisiana. The present H.V. Howe Type Collection of Microfossils began with Howe’s gift of slides to LSU. This collection, enriched by contributions from later workers, now includes over 580 slides of foraminiferal primary type specimens, with holotypes and syntypes of 361 species and 15 taxa labeled as “varieties.” Information regarding these …

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 Influence Of Autism Linked Gene Topoisomerase 3b (Top3b) On Neural Development In Zebrafish, Sydney Doolittle

Honors College Theses

Autism Spectrum Disorder is a class of developmental disabilities characterized by a spectrum of social, communication, and behavioral impairments in affected individuals. Studies have shown these defects stem from abnormal brain development during critical periods during early development. The underlying genetic cause of these impairments is not well understood but is believed to be a combination of a complex pairing of genetic and environmental factors. One of the genetic factors that has been recognized to influence the phenotypic symptoms of ASD is the enzyme topoisomerase 3β (top3β.) Topoisomerases are responsible for the prevention of supercoiling during DNA replication. Top3β is …

Investigation Of The State Of Dna Methylation In High And Low Protein Accumulating Maize Lines, Akash Lal

Student Theses and Dissertations

Transgenic plant-based production for industrial enzymes is an evolutionary tool. Green bio- factories have powerful potential to produce desirable product on the most economical and efficient level. Seed itself provides protein a very stable environment, solving the problem of storage. Transgenic plants easily scale up production. Increasing population, climate change and low amounts of arable land create a damaging situation for which a plant-based production system is beneficial. The transgenic plant-based production system rather than microbial fermentation is a solution for this rising scenario. Epigenetics is a natural phenomenon which causes heritable changes in gene expression alternative to the involvement …

Induction And Characterization Of Microspore Embryogenesis In Soybean (Glycine Max [L.] Merrill), Bretton M. Hale

Student Theses and Dissertations

Gametophytic embryogenesis is a method used to achieve homozygosity in plant breeding programs. However, its application is limited within the Fabaceae, which has historically demonstrated morphogenic recalcitrance in comparison to other plant families (i.e., Brassicaceae and Poaceae). Here, the immature male gametophyte — or microspore — was used to investigate gametophytic embryogenesis in soybean (Glycine max [L.] Merrill). In so doing, an induction regimen was optimized to support embryogenic growth through pretreatment temperature shock, a nitrogen starvation medium, and other post-isolation culture conditions. In addition, parallels were drawn between soybean microspore cytology and that which has been reported in model …

Pando: Charismatic Megaflora And The Populus Paradox, Paul C. Rogers, Lance Oditt

Aspen Bibliography

Within the field of landscape ecology, the Pando aspen grove on the Fishlake National Forest of Utah is legendary—and it is in danger of dying from hotter, drier temperatures and other threats. Pando is one of the largest and oldest known still-living organisms on Earth. Quaking aspen are an important tree species in Greater Yellowstone and the Rocky Mountain West. Enjoy this essay written by a scientist who studies Pando and a photographer who celebrates this arboreal mega-being.

Micro- And Macroevolution Of Drab Plumage Color In Birds, Rafael Marcondes

LSU Doctoral Dissertations

I address the evolution of drab bird colors at micro- and macroevolutionary scales. I use as a study system the Furnariida, a clade of >600 Neotropical passerine species that, despite tremendous ecological and morphological diversity, are colored almost exclusively in shades of brown and grey produced by melanin pigments.

In chapters two and three, I took a macroevolutionary approach and showed that (1) plumage colors in the Furnariida evolve at similar rates in a monochromatic clade, males of a dichromatic clade, and females of a dichromatic clade; (2) ventral plumage color evolves faster than dorsal; (3) bird species that occupy …

The Annual Rhythmic Differentiation Of Populus Davidiana Growth–Climate Response Under A Warming Climate In The Greater Hinggan Mountains, Ruixin Yun, Yuting Jin, Junxia Li, Zhenju Chen, Zhaoyang Lyu, Ying Zhao, Di Cui

Aspen Bibliography

The stability and balance of forest ecosystems have been seriously affected by climate change. Herein, we use dendrochronological methods to investigate the radial growth and climate response of pioneer tree species in the southern margin of cold temperate coniferous forest based on Populus davidiana growing on the Greater Hinggan Mountains in northeastern China. Correlations of P. davidiana growth with temperature and precipitation in a year (October–September) were rhythmically opposed: while temperatures in previous October–June (winter and spring) and in May–September (growing season) respectively inhibited and promoted radial growth on P. davidiana (p < 0.01), precipitation in the same periods respectively promoted and inhibited of growth (p < 0.01). High temperature or less rain/snow in winter and early spring, and low temperature or excess rainfall in summer, are inconducive to P. davidiana growth and vice versa …

Open-Source Computational Framework For Studying Drosophila Behavioral Phase, Boyan Kostadinov, Hannah Lee Pettibone, Evardra Valerie Bell, Xiaona Zhou, Ausra Pranevicius, Orie Thomas Shafer, Maria Paz Fernandez

Publications and Research

This protocol describes a standardized method for analyzing Drosophila behavioral rhythmicity under light dark cycles, temperature ramps, and free running conditions. The protocol constitutes a step-by-step guide from generation of appropriate Drosophila genetic crosses to behavioral experiments. We also provide an opensource computational framework using R for the analysis of the phase of behavior using circular statistics. An extended method for complete use is also provided. For complete details on the use and execution of this protocol, please refer to Fernandez et al. (2020).

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 …