Genetics Commons^™

The Genetic Basis Of High Transformation Efficiency In The Model Yeast Saccharomyces Cerevisiae, Mary Kathryn E. Cheek

Biological Sciences Undergraduate Honors Theses

Transformation, a type of horizontal gene transfer, describes the uptake, maintenance, and integration of environmental DNA by cells. Despite the known effects of transformation on evolutionary processes, little is known about the genetic basis of this phenomenon. Saccharomyces cerevisiae is a eukaryote able to transform at quantifiable rates when made chemically competent and treated with a heat shock. S. cerevisiae also has variation in transformation efficiencies between various strains, and high recombination rates allow for sufficient allele “shuffling” in intercross populations. This project utilizes a bulk segregant analysis approach to compare sequencing data between transformant pools and non-transformant pools of …

Dissecting The Complex Genomic Landscape Underlying Oxidative Stress Resistance Using Natural Variation In Yeast, Sonali Lakshika Anne Lenaduwe

Graduate Theses and Dissertations

Stress is experienced across the tree of life. Survival in fluctuating environments depends on a robust genetic architecture. This dissertation examines the genetic and metabolic determinants underlying one such adaptive response: cross-protection. Leveraging natural variation in the stress responses of budding yeast, Saccharomyces cerevisiae, I examine the genetic variation contributing to ethanol-induced cross-protection against oxidative stress. Acquired stress resistance, in which mild pre-exposure improves survival to subsequent stresses, is prevalent across diverse organisms and can involve both same-stress and cross-protection. Using high-throughput bulk segregant analysis (BSA-seq) and advanced intercross mapping populations derived from natural yeast isolates, I identify quantitative trait …

The Genetic And Environmental Determinants Of Stress Resilience Across Model Systems, Carson Len Stacy

Graduate Theses and Dissertations

Survival in fluctuating environments demands that organisms effectively anticipate and respond to future challenges. This capacity is shaped by both genetic background and environmental context. In this dissertation, I apply a population aware lens to explore how genetic diversity and environmental conditions intersect to shape stress survival. Integrating functional genomics and transcriptomics in Saccharomyces cerevisiae (brewer’s yeast) and a vertebrate (common canary) system, I dissect gene-by-environment (GE) interactions that underpin resilience. First, I move beyond a single reference genome by using a pan-genomic CRISPR knockout screen to assess osmotic stress survival across diverse S. cerevisiae isolates. This analysis reveals a …

Gene Expression And Transfection Of C15orf57 In Chicken Show Clear Correlation To The Function Of The Ap2 Complex, E. Ashton Magdich

Graduate Theses and Dissertations

Discovering the functions of functionally unknown genes has made a huge impact on biological understanding including poultry species. In this thesis, C15orf57 (or C5H15orf57, chicken chromosome 5 human ortholog H15 open reading frame 57), was studied to understand its genetic characteristics and function. Chapter one is literature reviews on annotation of genes, the gene information on C15orf57, the importance of characterizing unknown genes in the genome, and what is known now about C15orf57. The Chapter 2 is for the structural characterization of C15orf57, gene expression of C15orf57 in various organ tissues using the qPCR method and effect of overexpression of …

Crispr-Cas9 Integration Of Salmon Elovl2 In Zebrafish Enhances Lc-Pufa Biosynthesis And Growth Across Diets, Waleed Sami J. Al-Bachry

Graduate Theses and Dissertations

Fish are a rich source of EPA and DHA, which are well-known long-chain polyunsaturated fatty acids (LC-PUFAs). The sustainable production of these essential fatty acids poses significant challenges, mainly due to our dependence on marine fish and certain nuts. CRISPR-Cas system was utilized to insert the elongation of long-chain fatty acids-like2 (Elovl2) gene from Salmo salar into Danio rerio. Elovl2 was introduced at 10-15-minute post-fertilization, and successful integration confirmed by PCR genotyping, sequencing and expression of EGFP. Approximately 67% of injected embryos successfully exhibited EGFP and sequence results verified the gene integration of Salmo salar Elovl2 at the first start …

Evaluation Of The Efficiency Of Muscle-Specific Promoters To Express Non-Endogenous Proteins In Skeletal Muscle, Gabrielle Bulliard, Made Harumi Padmaswari, Christopher E. Nelson

Biomedical Engineering Undergraduate Honors Theses

Gene therapies are emerging as powerful tools for treating genetic diseases and cancers, offering the potential for a permanent cure. Hemophilia B, affecting approximately 6,000 men in the U.S., results from a deficiency in coagulation factor IX protein (FIX), which is crucial for blood clotting. A substantial portion of patients, over 40%, suffer from severe hemophilia B, experiencing spontaneous, prolonged bleeding. Current prophylactic treatments involve frequent coagulation factor infusions, yet a curative approach would alleviate this burden. Gene editing technologies like CRISPR-Cas systems show promise for correcting genetic mutations, but the diverse nature of factor IX gene (F9) …

Transcriptomic Profiling Of Engineered Human Gene Integration In The Mouse Genome Following In Vitro Gene Editing, Ethan Potts, Made Harumi Padmaswari, Christopher Nelson

Biomedical Engineering Undergraduate Honors Theses

Gene replacement is a promising method of therapy for genetic diseases. However, safety and efficacy are areas that need more research. This experiment aims to use RNA sequencing and bioinformatic techniques to provide answers to these questions and provide direction to future studies to develop a gene replacement therapeutic. C2C12 mouse myoblast cells were transfected with a vector containing a CRISPR-Cas9 system and the Human Factor IX (hF9) gene in order to hijack target genes and integrate the hF9 gene. The two target genes, myoglobin (Mb) and creatine kinase (Ckm), were chosen for their high rate of expression and low …

Exploring Genomic Convergence For Adaptations To Freezing Environments In Polar Fish, Ethan Talley

Biological Sciences Undergraduate Honors Theses

Convergent evolution provides valuable insights into how natural selection shapes species traits. Genomic analysis of lineages that display convergent traits has the potential to identify candidate genes for environmental adaptations across the scope of entire genomes. One remarkable example of convergent evolution is the independent development of antifreeze proteins (AFPs) in phylogenetically distant polar fish lineages. While AFPs themselves are relatively well studied, the full genomic context of adaptation to freezing conditions in these fish lineages remains largely unexplored. Leveraging the whole genome sequences previously assembled in our lab, along with other high-quality genomes available in GenBank, I examined the …

Genomic Characterization Of Enterococcus Spp Infecting Chicken Embryo, Aishat Olaoluwa Lawal

Graduate Theses and Dissertations

Chicken embryo mortality has been attributed to bacterial infections and can lead to a decline in hatchability, posing potential losses in the broiler industry. This study aims to investigate the vertical transmission of specific bacterial pathogens from breeder hens to subsequent broiler flocks through MGEs and their association with host specificity. In our sampling of 360 eggs from a broiler flock, we isolated various Enterococcus species, including E. gallinarum and E. faecalis, from incubated egg yolks or aborted embryos. E. avium was found in unincubated bad yolks. Other species like Streptococcus, Lactobacillus, and Bacillus were observed but presumed to be …

Robust Phylogenetic Regression, Richard Adams, Zoe Cain, Raquel Assis, Michael Degiorgio

Entomology and Plant Pathology Faculty Publications and Presentations

Modern comparative biology owes much to phylogenetic regression. At its conception, this technique sparked a revolution that armed biologists with phylogenetic comparative methods (PCMs) for disentangling evolutionary correlations from those arising from hierarchical phylogenetic relationships. Over the past few decades, the phylogenetic regression framework has become a paradigm of modern comparative biology that has been widely embraced as a remedy for shared ancestry. However, recent evidence has shown doubt over the efficacy of phylogenetic regression, and PCMs more generally, with the suggestion that many of these methods fail to provide an adequate defense against unreplicated evolution—the primary justification for using …

Molar Macrowear As A Proxy For Age In A Captive Sample Of Papio Hamadryas, Lauren Conrad

Biological Sciences Undergraduate Honors Theses

This study is methods-focused, centering around molar crown macrowear and its performance as a proxy for age in a sample of pedigreed, non-human primates. It analyzes the correlation between age-structured variables and molar wear among both males and females in a captive group of baboons. Here, I examined whether wear is significantly correlated with age-related variables (i.e., generations/cohorts) and whether the structure of the “age” dataset differed across wear categories. Because chronological age is unknown, I used documented pedigrees and parent-offspring relationships to group individuals into possible generations. I then used dental development charts to group individuals into cohorts based …

Biology, Genetic Diversity, And Conservation Of Wild Bees In Tree Fruit Orchards, Olivia Mae Kline, Ngoc T. Phan, Mitzy F. Porras, Joshua Chavana, Coleman Z. Little, Lilia Stemet, Roshani S. Acharya, David J. Biddinger, Gadi V.P. Reddy, Edwin G. Rajotte, Neelendra K. Joshi

Entomology and Plant Pathology Faculty Publications and Presentations

Honey bees (Apis mellifera) are the most economically important agricultural pollinator in North America, as well as being the most frequently studied bee species. Many agricultural systems, such as fruit tree orchards, benefit from having a diversity of bee species present. In this article, we present information about the types of bees that can be found in orchards and explore their mating behaviors, life cycles, genetic differences, flower preferences, and foraging activities. Many orchard-pollinating bees, including bumble bees (Bombus spp.), mason bees (Osmia spp.), and mining bees (Andrena spp.), are often less studied than honey …

The Effect Of Spirulina Platensis Algae Inclusion In Feed Of Commercial Broilers Subjected To Cyclic Heat Stress, Kirsten Shafer

Graduate Theses and Dissertations

The effect of Spirulina platensis inclusion in feed of commercial broilers was evaluated over one experiment. The study aimed to investigate the effects of Spirulina platensis freshwater algae inclusion on live performance and processing characteristics of commercial broilers subjected to daily cyclic heat stress. Day old Ross 708 male broilers were placed into 8 environmentally controlled chambers. At d 21, four chambers remained on a control diet containing no algae (CON) while 4 chambers received a diet that included algae at an inclusion rate of 2.5% (ALG). An 8 hour daily cyclic heat stress (24°C to 36°C) was applied to …

Mitochondrial Dna Diversity, Parasite And Pathogen Occurrence, And A Potential Disease Vector In Managed And Unmanaged Honey Bee, Apis Mellifera L. Populations, Dylan Cleary

Graduate Theses and Dissertations

The western honey bee, Apis mellifera L., is a globally important pollinator plagued by several harmful stressors impacting colony health and survival. At least eight A. mellifera subspecies were imported and continue to be the genetic ancestors of U.S. honey bee populations today. Successive genetic bottle-neck events have led to reduced genetic diversity in U.S. honey bees. First, the subset of subspecies imported into the U.S. represents only a third of A. mellifera subspecies. Next, the parasitic varroa mite reduced managed and feral populations. Third, ongoing breeding practices have selected for traits from a single genetic lineage and bred from …

The Effects Of Physical Function And Genetics On Cognition And Blood Biomarkers In Individuals At-Risk For Alzheimer’S Disease And Related Dementias, Joshua Louis Gills

Graduate Theses and Dissertations

Alzheimer’s disease and related dementia (ADRD) rates are expected to triple by the year 2050. Early detection and specific mitigation efforts are warranted to blunt the alarming rate. Physical function (PF) declines with age, but higher physical function is associated with better cognitive functioning in middle-to- older age individuals. Moreover, greater physical activity (PA) is associated with better global cognition; however, Apoliporotein e4 carriers may not gain the same benefits with exercise. Additionally, plasma phosphorylated tau 217 (p-tau217) has been identified as a novel diagnostic ADRD biomarker which needs further research to examine associations with risk factors. Therefore, the aims …

Characterization Of Genetic Pathways Involved In Resistance To A Novel Antifungal Peptide, Kayla L. Haberman

Graduate Theses and Dissertations

Antibiotic resistance is increasing prevalence, particularly in Candida glabrata. This opportunistic pathogen is closely phylogenetically related to Saccharomyces cerevisiae; however, its characterization is limited. C. glabrata is only second to Candida albicans as a fungal pathogen in immunocompromised patients. Commonly resistant to azoles, the most common fungal therapy, it has become costly and challenging to treat. A histatin 5 derived antifungal peptide, KM29, has a high degree of efficacy in Candida species and S. cerevisiae. The objective of this work is to advance our understanding of the mechanism of action of KM29 against C. glabrata. Previous work in the lab …

Riverscape Community Genomics Of Ozark Fishes: A Comparative Framework To Infer Ecological And Evolutionary Determinants Of Genetic Diversity, Zachery D. Zbinden

Graduate Theses and Dissertations

Genetic variation is a crucial component of biodiversity and represents the variability and spatial structure of alleles within and among organisms. Evolution modulates this variability over time through mutation, selection, gene flow, and genetic drift. However, our capacity to test foundational theories of population genetics has always been at the mercy of molecular approaches available to quantify patterns of genetic diversity. Initially, techniques for empirical DNA studies were in their infancy and limited by technologies and the price per unit of genetic information. Because of these constraints, our pursuits have generally been limited to investigations of one or a few …

Validation Of Whole Genome Resequencing For Mapping The Genetics Of Ascites In Broilers And Viral Susceptibility In Layers, Katherine Pepper Lee

Graduate Theses and Dissertations

This dissertation focused on the efficacy and validity of whole genome resequencing (WGR) for fine mapping genetic determinants of particular traits in a given organism. Previously, our research group used WGR to identify haplotype blocks of single nucleotide polymorphisms associated with ascites resistance with some as strong candidates for use in marker-assisted selection (MAS). Chapter 2 discusses the completion of a MAS project through evaluation of ascites incidence as well as production traits of economic value to poultry producers. Thus, the MAS project also covered viability of this methodology in the industry. The MAS significantly reduced ascites incidence in broilers …

Effects Of Sunrise/Sunset Lighting On Corticosterone Levels In Coturnix Quail (Coturnix Coturnix), Hannah Feuerborn

Poultry Science Undergraduate Honors Theses

Both genetics and environment play an important role in the growth, performance and overall welfare of poultry species. Current commercial production practices typically do not mimic the natural environmental conditions of ancestral poultry species, specifically lighting requirements. In nature, poultry species are subjected to natural day length and the slow rising and setting of the sun. This is compared to commercial conditions in which lights are sudden on/off, not mimicking the natural trajectory of the sun in terms of light intensity and exposure. The current study aimed to evaluate the impact of genetics and the effect of sunrise/sunset lighting on …

Root Phenotyping Of Peptide-Treated Glycine Max, Salem Jackson

Biological Sciences Undergraduate Honors Theses

Plant elicitor peptides (Peps) – endogenous chains of amino acids involved in natural plant defense – have been shown to decrease damage from herbivores and pathogens by inducing an immune response, increasing the emission of volatile organic compounds (VOCS), transcripts, and metabolites. Exogenous treatment of soybean seeds with plant elicitor peptide GmPep3 has been shown to induce these broad-spectrum defenses and offers a new method for increasing crop yield. However, the effects of GmPep3 on indicators of soybean health – root characteristics, growth stages, etc. – have not been fully realized.

Using the root-phenotyping platform RhizoVision Explorer, several root traits …

Characterizing The Expression Pattern And Function Of Tartan During Drosophila Development, Alaina Baggett

Biomedical Engineering Undergraduate Honors Theses

The development of complex structures and organs by multicellular organisms relies on the ability of epithelial cells to self-organize. Epithelia are sheets of connected cells, and compartment boundaries are formed between certain epithelial cells to create distinct tissue compartments. Compartment boundaries are specialized cell-cell interfaces that are enriched for the cytoskeletal proteins actin and myosin, leading to straight cell edges under relatively high tension that act as fences keep cells from moving between compartments. In the model organism Drosophila melanogaster (fruit fly), compartment boundaries in the early embryo are established in response to the non-uniform striped expression of the cell-surface …

Heritability Of Maxillary Dental Arch Dimensions In A Pedigreed Sample Of Hamadryas Baboons, Samuel Park

Crop, Soil and Environmental Sciences Undergraduate Honors Theses

This thesis presents a study of heritability of maxillary dental arch dimensions in a captive baboon colony. Arch dimensions are important subject because they influence the entirety of the craniofacial and masticatory complex. The goal of this study was to quantify the relative genetic influence on arch dimensions and the nature of this influence at different points along the maxillary arcade. Referencing virtual, three-dimensional dental cast scans, widths were measured at different points between the a) maxillary left and right canines, and b) maxillary left and right first molars (M1). Specifically, measurements were taken at the inner (lingual) gingival margin, …

Response To A Water Bolus In Long Term Oral Contraceptive Users, Whitley C. Atkins, Brendon P. Mcdermott, Abigail T. Colburn, Stavros A. Kavouras

Health, Human Performance and Recreation Faculty Publications and Presentations

The purpose of our study was to determine the responses to an acute water bolus in long-term oral contraception (OCP) users. Seventeen female volunteers (27 ± 5 y, 64.1 ± 13.7 kg, 39.6 ± 5.9 kg/LBM) provided consent and enrolled in our study. All were long-term OCP users and participated in two trials, one during the active pill (High Hormone, HH) dose of their prescribed OCP and one during the sham pill (Low Hormone, LH) dose. Participants reported to the laboratory euhydrated, were fed breakfast, remained seated for 60 min and were provided a bolus of room temperature water in …

Effects Of Sunrise/Sunset Lighting On Corticosterone Levels In Coturnix Quail (Coturnix Coturnix), Hannah M. Feuerborn, Sara K. Orlowski

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

Both genetics and environment play important roles in the growth, performance, and overall welfare of poultry species. Current commercial production practices typically do not mimic the natural environmental conditions of ancestral poultry species, specifically lighting. The current study aimed to evaluate the impact of genetics and the effect of sunrise/sunset lighting on the stress response of 4 genetic lines of Coturnix quail. The 4 lines utilized in this study included high stress (H), low stress (L), stress control (R), and Arkansas randombred (A) quail lines. Day old chicks from these lines were placed in one of two environmentally controlled rooms. …

Divergent Selection For Water Conversion Ratio In Broiler Populations, Joseph Hiltz

Graduate Theses and Dissertations

Water scarcity is a global reality and with the anticipated population growth, freshwater resources will be further strained to meet both human needs and agriculture applications. To ensure a water sustainable and food secure future, all aspects of agriculture must become more efficient. Two strategies were explored. The potential of improving water efficiency in broilers was examined. The first strategy was to develop a more efficient and accurate method for measuring water consumption/inputs in agriculture. To date, water measuring technology has lacked the necessary sophistication to assure accuracy and repeatability of low flow water usage.

After establishing a low flow …

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

Biomedical Engineering Undergraduate Honors Theses

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

Molecular And Genetic Studies Of Robo2 Transcriptional Regulation In The Central Nervous System Of Drosophila Melanogaster, Muna Abdal Rahim Abdal Rhida

Graduate Theses and Dissertations

Drosophila Robo2 axon guidance receptor is a member of the evolutionarily conserved Roundabout (Robo) protein family that is involved in directing axons that cross the midline to the other side of the animal body. Robo2 roles mainly depend on two factors: The functional domains of the Robo2 protein, which is extensively studied, and the dynamic transcription of robo2 in various subsets of cells throughout embryogenesis which is not fully understood. Thus, knowing robo2 enhancers that transcriptionally regulate robo2 during embryogenesis is significant. To investigate robo2 potential enhancers, we screened 17 transgenic lines of Drosophila that were generated by Janelia Research …

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

Graduate Theses and Dissertations

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

Neogene And Quaternary Events Shaped Diversification And Speciation In Bhutanese Rheophilic Fishes Of The Family Nemacheilidae (Cypriniformes) And Sisoridae (Siluriformes), Karma Wangchuk

Graduate Theses and Dissertations

Biogeography of the Himalayan region [to include the Qinghai-Tibetan Plateau (QTP)] evolved over a ~30M year span, catalyzed by the collision of the Indian and Eurasian plates. The resulting uplift produced major ecological and climatic effects, that in turn drove the diversification of biodiversity. As a result, the QTP is designated as a global biodiversity hotspot particularly vulnerable to cumulative climatic effects, including shrinking distributions, declining numbers, and local extinctions. Understanding how the biodiversity within the Himalaya/ QTP was established and maintained is a necessary first step in prioritizing conservation efforts.

Fishes in global montane regions, such as the Himalaya, …

Comparative Genomics Of Human Mesenchymal Stem Cells And Human Mesenchymal Stem Cells Derived Vascular Smooth Muscle Cells, Samia Ismail

Biomedical Engineering Undergraduate Honors Theses

As of 2017, vascular diseases contributed to 23.1% of all deaths in America. To address the need for more effective and sustainable treatment options for these ailments, stem cell differentiation and implantation has emerged as a viable alternative to standard bypass and graft insertions. A completely autologous treatment can be achieved by extracting adult stem cells, differentiating them into vascular smooth muscle cells (VSMCs), and then reimplanting these cells at the affected tissue site. This study aims to investigate the efficiency of the VSMC differentiation from human mesenchymal stem cells (hMSCs) by comparing 4 cell lines of untreated hMSCs with …