Genetics and Genomics Commons^™

Towards Understanding The Function Of An Ets-Like Gene In Nematostella Vectensis: Generation Of A Knockout Mutant Line And A Transgenic Reporter Line, Emily Bullock

Biological Sciences Undergraduate Honors Theses

Due to their unique phylogenic position as sister to Bilateria, Cnidaria are often credited with the utility of allowing for reconstruction of ancestral biology based on characteristics shared with bilaterians and other animals. This factor makes investigation into the nervous systems of cnidarians critical in understanding early neural evolution. Wamides, a class of neuropeptides, have been shown to play a regulatory role in life cycle transitions across many different species. The cnidarian specific Wamide neuropeptide, GLWamide, has previously been identified to play an accelerator role in the metamorphic timing of a specific species of sea anemone, Nematostella vectensis. However, …

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 …

Sequence Analysis Of Herbicide Target Genes In Herbicide-Tolerant Rice, Jonathan Kearney, Nilda R. Burgos, Gulab D. Rangani

Biological Sciences Undergraduate Honors Theses

The tolerance of mutagenized rice (Oryza sativa) lines to selector herbicides was investigated and the sequence of ALS gene was analyzed in plants that survived treatment with 4x the label rate of imazethapyr herbicide. This was done to determine if insensitivity to imazethapyr is due to mutation(s) in the herbicide binding site. Seedlots previously treated with ethyl-methyl sulfonate were planted in the field and 3-leaf seedlings were treated with various herbicides to screen for herbicide-tolerant mutants. Seeds from survivors composed the rice lines tested in the current research. Seeds were planted in the greenhouse and 3-leaf seedlings were …

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 …

Identification Of Genomic, Proteomic, And Metabolomic Signatures Associated With Pulmonary Hypertension Syndrome In Broilers, Duaa Almansaf

Graduate Theses and Dissertations

The present dissertation contains a collection of studies that examine the genomic, proteomic, and metabolomic association to pulmonary hypertension or ascites phenotype in fast-growing broilers. Pulmonary hypertension is a multifactorial metabolic disease influenced by physiological, environmental, and nutritional factors. It is characterized by a number of structural changes including, thrombosis and adverse pulmonary vascular remodeling. Thus, the atrial pressure is increased, and the right ventricle becomes hypertrophied, resulting in heart failure and the death of the bird. Pulmonary hypertension or ascites is a global problem that has negatively impacted the economy. The increased mortality rate of broilers (25%) is estimated …

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 …

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 …

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 …

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 …

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 …

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 …

Impact Of Genetic Variation And Timescale On Diatom Salinity Stress Response, Kala M. Downey

Graduate Theses and Dissertations

Natural environments are dynamic, and organisms must sense and respond to changing conditions. One common way organisms deal with stressful environments is through gene expression changes, allowing for stress acclimation and resistance which occurs over varying time spans in different species. The recent evolutionary history of populations could greatly influence their ability to respond successfully. An evolutionary history in disturbed or fluctuating conditions could promote increased resistance or a more rapid response to these environmental stressors. To understand the impact of genotypic variation and timescales on response and acclimation to salinity changes, we have been exploiting the abilities of euryhaline …

The Role Of Ccaat Binding Factor In The Regulation Of Catalase Gene Expression In Candida Albicans, Zahra Al-Rumaih

Graduate Theses and Dissertations

Candida albicans is a fungal opportunistic human pathogen. Its infections range from surficial infections like skin rash to fatal systemic infections. Filamentation growth mode is associated with C. albicans virulence because it helps penetration of the host’s epithelial cells. The CCAAT-binding factor (CBF) is a conserved heterooligomeric transcription factor found in 30% of eukaryotes genes. In C. albicans it is composed of 4 major subunits, including Hap2, Hap3, Hap4, and Hap5. Hap2 and Hap5 are essential for DNA binding and function. Hap4 has 3 homologous subunits: Hap41 and Hap42 are putative subunits of CBP. Hap43 is the only Hap4 subunit …

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 …

Development Of A Long-Read Sequencing Protocol To Assess The Precision And Efficacy Of Gene Editing For Duchenne Muscular Dystrophy, Landon Andrew Burcham

Graduate Theses and Dissertations

This work establishes a method for assessing on-target precision due to CRISPR-Cas9 gene editing, especially within the context of exon skipping therapy for Duchenne Muscular Dystrophy. The proposed method utilizes an Oxford nanopore long-read sequencing approach to sequence amplified regions of DNA that have been edited using CRISPR-Cas9. NIH3T3 and C2C12 cell lines were treated with a dual-guide CRISPR-Cas9 system, that targets and deletes exon 23 from the DMD gene in mouse samples. Deletion PCR revealed deletion of exon 23 in both DNA and cDNA samples. Additionally, sequencing using Oxford Nanopore revealed targeted exon 23 deletion as the most prevalent …

The Effects Of Deletion Of The Cytoplasmic Domain Of Robo3 On Drosophila, Jessie Agcaoili

Biological Sciences Undergraduate Honors Theses

My research project examines how the deletion of the cytoplasmic domain affects the function of Robo3. If Robo3 is signaling repulsion in response to SLIT this activity should require the cytoplasmic domain. I investigated the functional importance of Robo3 by deleting the cytoplasmic domain of Robo3 using a CRISPR-based technique. This modified gene was then injected into Drosophila embryos where it replaced the normal copy of the gene. Embryos expressing the modified version of robo3 in place of normal robo3 were dissected and examined.

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. …

Genome-Wide Analyses Of Genomic Variation Regulating Differential Stress Responses In Japanese Quail, Steven Anthony Shumaker

Graduate Theses and Dissertations

As consumer demands for poultry grow, producers work to improve bird productivity in both meat and egg production. This endeavor is multifaceted, as many different factors play a part in influencing the productivity of birds, including environmental conditions, overall health, and genetic potential. One aspect controlled for in all aspects of poultry production optimization is stress management. Mitigation of stress is of primary concern to producers, as improper stress management can have many deleterious effects on chickens. Stress management requires an understanding of poultry stress responses and their physiological mechanisms, which can be more deeply understood through genomic analysis. Chapter …

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 …

Identification Of Proteins That Contribute To Yeast Heat Stress By Lysine Acetylation, Weijia Shi

Biological Sciences Undergraduate Honors Theses

Evidence is emerging that protein lysine acetylation may be a novel type of post-translational modification (PTM) contributing to the mechanisms of yeast heat stress responses. Proteomics studies including ours have identified over 1,000 acetylated proteins in the yeast proteomes that are composed of about 6,000 proteins. Our lab recently identified 596 proteins that underwent acetylation changes during heat shock by mass spectrometry. However, the role of lysine acetylation on specific residues of specific proteins in yeast thermotolerance remains largely unknown. This study selected 43 proteins from our lab’s previous work and examined their possible contributions to yeast heat stress responses. …

Validation Of Anti-Oxidative Stress Genes From Genome-Wide Screening Of Escherichia Coli, Carson Ercanbrack

Chemistry & Biochemistry Undergraduate Honors Theses

The primary purpose of this project is to evaluate the genes that play a role in the oxidative stress response in Escherichia coli. In doing so, the entire genome of E. coli was subject to throughput in which individual genes were determined to have a role in the bacteria’s oxidative stress response. Moreover, this project focused on the validation of the genes that were able to pass the initial throughput stage. The genes were subject to two forms of validation. In the first validation technique, candidate genes were overexpressed and minimum inhibitory concentrations of hypochlorous acid were taken. Following, a …

Involvement Of The Ino80 Chromatin Remodeling Complex In Cell Division And Genomic Stability, Ethan Chen

Biomedical Engineering Undergraduate Honors Theses

Cell division is a vital biological process for growth and development in both single and multi-cellular organisms—whereby the cell must duplicate its organelles and genome in entirety and appropriately distribute the copied contents to the daughter cells. Cells undergo a cycle of two distinct phases: interphase and mitosis. During interphase, the cell replicates its genomic DNA (in the form of chromosomes) located within the nucleus. DNA replication is carried out in a euchromatin state, where the chromosome structure is loose and easily accessible by DNA polymerase and other replication enzymes. Upon the completion of replication, chromatin is condensed into highly …

Gene Set Testing By Distance Correlation, Sho-Hsien Su

Graduate Theses and Dissertations

Pathways are the functional building blocks of complex diseases such as cancers. Pathway-level studies may provide insights on some important biological processes. Gene set test is an important tool to study the differential expression of a gene set between two groups, e.g., cancer vs normal. The differential expression of a gene set could be due to the difference in mean, variability, or both. However, most existing gene set tests only target the mean difference but overlook other types of differential expression. In this thesis, we propose to use the recently developed distance correlation for gene set testing. To assess the …

Estimation Of Additive And Dominance Effects Of A Mutant Glutathione S-Transferase Gene On Anthocyanin And Proanthocyanidin Content In Muscadine Grape (Vitis Rotundifolia), Autumn Brown

Horticulture Undergraduate Honors Theses

The skin color of muscadine grapes (Vitis rotundifolia) is typically classified as black or bronze. A glutathione S-transferase, VrunGST4, has been identified as a candidate gene for berry skin color in muscadine grapes. A molecular marker was developed within VrunGST4 to distinguish between muscadine genotypes (cultivars and selections) with bronze (T:T), heterozygote black (C:T), and homozygote black (C:C) berries. The objectives of this study were to determine whether there was a correlation between berry skin color and total anthocyanin content and to calculate additive and dominance effects of VrunGST4 in determining total anthocyanins in the berries and …

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, …

Development Of Arkansas Net Energy Equation, Katie Hilton

Graduate Theses and Dissertations

The modern broiler is growing at a rapid rate generating tremendous amounts of heat. A sensitive Net Energy (NE) system is needed to measure body heat production (HP) generated primarily by daily maintenance and synthesis and degradation of myofibrillar and sarcoplasmic protein. The first two chapters present evaluation of the classic way to calculate NE versus a new methodology; the Arkansas NE (Ark NE) system, with birds from two genetic lines fed diets with different AA content or different ME content in two different environmental temperatures.

Utilizing together the Net Energy maintenance (NEm), determined from indirect calorimetry, and Net Energy …