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Deciphering The Functional Connections Between The Nuclear Paraspeckle And Rad51 Homologous Recombination Proteins Using A Yeast Protein Interaction System, Eric J. Nutz

Senior Theses

Homologous recombination (HR) is a repair pathway for DNA double-stranded breaks. Mutations in HR genes contribute to genomic instability and increase the prevalence of cancer. Exploiting HR deficiency in tumor cells has led to improved synthetic lethality outcomes. RAD51 paralogue protein complexes are known to be involved with HR. Proteomic analysis of RAD51 paralogues reveals a connection to the nuclear paraspeckle. A paraspeckle is a little-known, specialized organelle found in the interchromatin space of the nucleus in mammalian cells. Its three central protein components include SFPQ, NONO, and PSPC1. RAD51D is an HR protein shown previously to interact with SFPQ …

The Evolution And Development Of Awns In The Grass Subfamily Pooideae, Erin L. Patterson

Doctoral Dissertations

This research focuses on a specific example of replicated evolution: the grass awn. Awns are typically extensions of the lemma, but may also appear on glumes or paleas. The lemma is a leaf-like organ on the exterior of the grass flower, the glumes are a pair of bracts subtending the basic unit of grass inflorescences, the spikelet, and the palea is the floral organ opposite the lemma. Awns are often described as "hair-" or "bristle-" like, but appear in many different shapes. Many awns are “twisted & geniculate", in which the awn has two sections, a lower twisted column, and …

Comparative Animal Mucomics, Antonio R. Cerullo

Dissertations, Theses, and Capstone Projects

Mucus is one of Nature’s most abundant and versatile biomaterials. These secretions are present in all animals, from the lowly garden snail to the great blue whale, and fulfill a multitude of functions, acting as antimicrobial barriers, moisturizers, adhesive glues, surface lubricants, and mineralizing agents. Despite their importance, very little is known about mucus compositions or properties. The largest challenge precluding the greater understanding of mucus function is its complexity; a single mucus contains complex mixtures of proteins, glycans, and ions that all have important roles in function. Therefore, understanding mucus function necessitates analysis that compares different mucus from one …

Exploring A Gene Panel For Parkinson’S Disease In An Egyptian Cohort, Asmaa Saeed Gabr

Theses and Dissertations

Parkinson’s disease is a highly heterogeneous disorder characterized by diverse neuropathological features, clinical presentations and progression patterns. In Egypt, Parkinson’s disease incidence rates lie outside the range reported elsewhere. The genetic background to the pathogenesis of Parkinson's disease has been postulated for a long time. However, Parkinson’s disease has never been systematically investigated in Egypt. This study aimed to explore genetic variants and interactions that are associated with the familial and sporadic forms of Parkinson's disease in an Egyptian cohort. This includes examining variants in PD-related genes, exploring the role of specific genes like MAPT and adjacent genomic regions, and …

A Case Of Incipient Budding Speciation In The California Floristic Province, Infraspecific Divergence In Abronia Villosa, Eli J. Allen

Cal Poly Humboldt theses and projects

Physical barriers to gene flow are the traditional evidence for species divergence. Conversely, there has been increasing acknowledgment of speciation in the face of gene flow as an evolutionary process. Budding speciation involves peripheral populations adapting to local ecological conditions, thereby budding off from a widespread progenitor species. Budding speciation is distinguished by ecological divergence and is generally evidenced by asymmetrical range size and nested phylogenetic relationships of sister species. The narrow endemic Abronia villosa var. aurita is adapted to montane sandy washes adjacent to its widespread sister variety, the desert dwelling var. villosa. Here, I tested the hypothesis …

The Genetic Basis Of Two Reproductive Traits In Monkeyflowers: Stigma Closure And Corolla Carotenoids, Rachel Anne Halperin

Undergraduate Theses, Professional Papers, and Capstone Artifacts

Abstract

The interactions between pollinators and flowers have long been a driving force for the evolution of many physical floral traits. Traits such as flower shape, size, color, and smell are just some of these traits that evolve because of these interactions. This evolution does not only occur in the more obvious morphological floral traits, however, but also in more subtle traits like touch sensitive stigma closure. In hundreds of Lamiales species, the bilobed stigma, the organ that receives pollen from pollinators, closes rapidly upon touch. Theory and experiments show that this novel dynamic reproductive trait increases pollen export and …

Towards Understanding The Interactions Between Ospreys And Human-Made Structures In The Tennessee River Valley, Natasha Karina Murphy

Theses and Dissertations

Raptor nests on human-built structures represent a significant source of conflict as they can result in bird mortality, fires, structure damage, service distribution, or power outages when falling nest materials or animals connect with energized conductors. Power companies, such as the Tennessee Valley Authority (TVA), wish to mitigate these conflicts to avoid service disruptions. In this dissertation, I present my work towards understanding and mitigating the interactions between Ospreys (Pandion haliaetus) and human-made structures. To achieve this, I explored multiple elements of conflict identification, monitoring, and basic ecology of the target species to better inform conflict mitigation. In Chapter I, …

Characterization Of The Immunoglobulin Lambda Chain Across Diverse Human Populations., William Gibson

Electronic Theses and Dissertations

The adaptive immune system relies on a diverse set of over one hundred immunoglobulin (IG) genes across three genomic loci that are variably combined to form antibodies (Ab). The IG Lambda locus is one of two loci which encodes the IG light chain. The complexity of the IGL locus severely limits the effective use of standard short-read sequencing, limiting our knowledge of population diversity in these loci. We leveraged single molecule real-time (SMRT) long-read sequencing in conjunction with IGL-targeted DNA capture to develop the method IG-Cap for accurate and high-throughput sequencing of the IGL locus. We benchmarked this method using …

Annotation Of Non-Model Species’ Genomes, Taiya Jarva

Master's Theses

The innovations in high throughput sequencing technologies in recent decades has allowed unprecedented examination and characterization of the genetic make-up of both model and non-model species, which has led to a surge in the use of genomics in fields which were previously considered unfeasible. These advances have greatly expanded the realm of possibilities in the fields of ecology and conservation. It is now possible to the identification of large cohorts of genetic markers, including single nucleotide polymorphisms (SNPs) and larger structural variants, as well as signatures of selection and local adaptation. Markers can be used to identify species, define population …

Genetic Population Structure And Effective Number Of Breeders In Systems Across The Range Of The Gulf Sturgeon, Jacob Zona

Master's Theses

Gulf sturgeon (Acipenser oxyicnhus desotoi) are a large, anadromous fish belonging to an ancient lineage that diverged as early as 400 MYA. Overfishing for meat and caviar during the early 1900’s reduced their range and abundance and continued habitat destruction and mortality have limited their ability to recover, leading to their listing under the Endangered Species Act. This study uses genetic techniques to determine the effective number of breeders for multiple spawning groups of Gulf sturgeon in river systems across their range to set a baseline for tracking reproductive success of the species. Accompanying genetic information relevant to …

Migratory Material: Epigenetics & Weaving At The Us-Mexico Border, Valerie Navarrete

Masters Theses

Discourse often sutures the body shut, disallowing representations of identity to outgrow sociopolitical interests. This issue may originate from borders, but also from the unnamable pathology that generational colonial trauma transmits to the mind, body, and environment. Without a direct form of translatability, this thesis proposes a new materialism that deviates from any object-oriented ontology. Untethered and intra-active, epigenetics and weaving represent objects that transform typical ways of knowing and seeing. Their sensitivity to the environment, in addition to their mobility across generations of time, broaden the spatiotemporal loci of the body and its embodiment. Proposing new materials that expand …

The Opioid Epidemic: How Genetics Play A Role In Addiction And Treatment, Kirsten Houston

Honors College Theses

The opioid epidemic is an issue within the pharmaceutical industry in the United States of America due to prescription and non-prescription substances being made available to the population. Opioids include chemical substances that affect the body and brain through opioid receptors, including the mu, kappa, and delta receptors. These substances are derived and synthesized from the poppy plant. Multiple causes have been linked to opioid abuse disorder, including but not limited to employment, income, housing, nutrition, mental health disorders, and genetics. By gathering information from previous literature, genetics may be the main cause of narcotic analgesic tolerance and abuse. Specific …

Reverse Genetics: Downregulating Chk-1 And Fasn-1 In The Gonads Of C. Elegans, Sam Thompson

Undergraduate Theses

Despite its widespread use in research, the model organism C. elegans has several biological processes like gonadal development with potentially unexplored genetic regulators. Previous transcriptome analysis has identified several genes that are upregulated in a specific tissue or sex during the development of the somatic gonad in C. elegans (Kroetz et al. 2015) that have not been previously connected to this process. Of these genes, this research is concerned with chk-1 and fasn-1. Abrogating the expression of these genes in gonadal tissue during gonadogenesis could cause a change in phenotype for affected C. elegans that would aid in understanding these …

Understanding Host-Microbe Interactions In Maize Kernel And Sweetpotato Leaf Metagenomic Profiles., Alison K. Adams

Doctoral Dissertations

Functional and quantitative metagenomic profiling remains challenging and limits our understanding of host-microbe interactions. This body of work aims to mediate these challenges by using a novel quantitative reduced representation sequencing strategy (OmeSeq-qRRS), development of a fully automated software for quantitative metagenomic/microbiome profiling (Qmatey: quantitative metagenomic alignment and taxonomic identification using exact-matching) and implementing these tools for understanding plant-microbe-pathogen interactions in maize and sweetpotato. The next generation sequencing-based OmeSeq-qRRS leverages the strengths of shotgun whole genome sequencing and costs lower that the more affordable amplicon sequencing method. The novel FASTQ data compression/indexing and enhanced-multithreading of the MegaBLAST in Qmatey allows …

Targeting Metabolic Alterations Associated With Smooth Muscle Α-Actin Pathogenic Variant Attenuates Moyamoya-Like Cerebrovascular Disease, Anita Kaw

Dissertations & Theses (Open Access)

Heterozygous pathogenic variants in ACTA2, encoding smooth muscle α-actin (α-SMA), predispose to thoracic aortic aneurysms and dissections. De novo missense variants disrupting ACTA2 arginine 179 (p.Arg179) cause a multisystemic disease termed smooth muscle dysfunction syndrome (SMDS), which is characterized by early onset thoracic aortic disease and moyamoya disease-like (MMD) cerebrovascular disease. The MMD-like cerebrovascular disease in SMDS patients is marked by bilateral steno-occlusive lesions in the distal internal carotid arteries (ICAs) and their branches. To study the molecular mechanisms that underlie the ACTA2 p.Arg179 variants, a smooth muscle-specific Cre-lox knock-in mouse model of the heterozygous Acta2 R179C variant, termed …

Involvement Of Chromosome Remodeling Complexes On Chromosome Segregation, Adelle Warford

Biological Sciences Undergraduate Honors Theses

Errors in chromosome segregation during cell replication are detrimental to the health of living cells. These errors cause aneuploidy: daughter cells with an incorrect number of chromosomes, as well as polyploidy: the complete duplication of a genome. In humans, these segregation errors are responsible for many harmful diseases and disorders. Using the model organism S. cerevisiae, a double mutant was created by removing two key chromosome remodeling complexes, SWR1 and INO80, both known to independently cause aneuploidy, decreased fitness, and damages the sensitivity of a cell's DNA (Andalis et al. 2004). By creating a double mutant strain, genetic cell …

Gonads Without Glp-1: Silencing Glp-1 In The Male Somatic Gonad In Caenorhabditis Elegans, Matthew Titus

Undergraduate Theses

In C. elegans, the gene glp-1 encodes for a Notch receptor called GLP-1, one of two found in C. elegans’ genome. The gene has been previously implicated in the development of the hermaphroditic germline as well as playing a role in the mitosis/meiosis decision. Genetic screening has further identified it as potentially playing a role in the development of the male somatic gonad, making it an ideal candidate for a reverse genetic. We did this by silencing glp-1 and observing if any alterations to the gonad’s phenotype occur.

Normally this could be done by performing a gene knockout. …

Understanding The Expression And Role Of Pros-1 In The Male Gonad Of C. Elegans, Jack Bozik

Undergraduate Theses

The gene pros-1 is a transcription factor that is highly expressed within neuronal sheath cells, glial cells, and excretory canal cells. pros-1 plays a role in cell determination of those cell types in the nematode C. elegans, which promotes organismal development. But the degree to which pros-1 presence is important is still not fully understood, because there are many genes involved in development that when mutated or damaged can result in unexpected phenotypes or even total loss of function to a certain developmental mechanism. What makes pros-1 valuable to research is that it is a functional homologue to a …

Epigenetics In Forensic Science, Reagan Faunce

Honors Projects

DNA methylation can be useful for forensic scientists because it can be used to differentiate between the DNA of identical twins, determine the age of a contributor of a DNA sample, and help us understand the actions and tendencies of violent criminals. Research shows that DNA methylation changes over time and can be caused by traumatic events, suggesting that methylation increases with age. Prior studies of DNA methylation at the promoters of the EDARADD, TOM1L1, and NPTX2 genes have been able to predict age within 5.2 years and a study of the ASPA, EDARADD, PDE4C, and ELOVL2 genes predicted age …

The Genomics Of Autism-Related Genes Il1rapl1 And Il1rapl2: Insights Into Their Cortical Distribution, Cell-Type Specificity, And Developmental Trajectories, Jacob Weaver

MUSC Theses and Dissertations

Neuropsychiatric disorders have a significant impact on modern society. These disorders affect a large percentage of the population: schizophrenia has a world-wide prevalence of 1% and autism spectrum disorders (ASD) affects 1 in 59 school-aged children in the US. There is substantial evidence that most neuropsychiatric disorders have a genetic component. Thus, with the advent of high throughput sequencing much effort has gone into identifying genetic variants associated with these disorders. The emerging picture from these studies is a complex one where hundreds of genes with small effects interact with a varied landscape of common variants to result in disease. …

Gaming To Learn Genetics, Sarah Wolfe

Undergraduate Honors Thesis Projects

Digital game-based learning is an alternative to traditional lecture learning. It involves active engagement with concepts in a digital game setting and can apply to a variety of subjects, including STEM fields. We examined this type of learning in the context of an undergraduate introductory genetics course: specifically, use of a genetics video game for teaching. There were two groups: an experimental group that played the genetics game Geniventure, and a control group that read and studied Powerpoint lecture slides. Both groups took a pretest and posttest, as well as completed an I/D (interest/deprivation) scale and workload scale. There …

Incorporating Sex Chromosomes In Transcriptome Prediction Models And Improving Cross-Population Prediction Performance, Daniel S. Araujo

Master's Theses

Transcriptome prediction models built with data from European-descent individuals are less accurate when applied to different populations because of differences in linkage disequilibrium patterns and allele frequencies. We hypothesized multivariate adaptive shrinkage may improve cross-population transcriptome prediction, as it leverages effect size estimates across different conditions - in this case, different populations. To test this hypothesis, we made transcriptome prediction models for use in transcriptome-wide association studies (TWAS) using different methods (Elastic Net, Matrix eQTL and Multivariate Adaptive Shrinkage in R (MASHR)) and tested their out-of-sample transcriptome prediction accuracy in population-matched and cross-population scenarios. Additionally, to evaluate model applicability in …

Alzheimer’S Disease Genetics And Short-Chain Fatty Acid Treatment In Studies Of The Murine Gut Microbiome, Diana Zajac

Theses and Dissertations--Physiology

Elucidating the relationship of the gut microbiome in Alzheimer's Disease (AD) risk and pathogenesis is an area of intense interest. Since 60 to 80% of AD risk is related to genetics and APOE alleles represent the most impactful genetic risk factors for AD, their mechanism(s) of action are under intense scrutiny.

First, I conducted a study on APOE targeted replacement mice to investigate the impact of APOE alleles on the murine gut microbiome. The relative abundance of bacteria from the family Ruminococacceae and related genera increased with APOE2 status. The relative abundance of the class Erysipelotrichia increased with APOE4 status, …

Molecular Genetic Studies Of Horses, Especially With Reference To Aggrecan And Dwarfism, John Edmund Eberth

Theses and Dissertations--Veterinary Science

This work consists of studies on dwarfism in Miniature horses and a study on breakdowns in Thoroughbreds in relation to gene aggrecan. A correction of the description and designation of D3 dwarf variant in aggrecan (ACAN) from the master’s thesis Chondrodysplasia-like dwarfism in the Miniature horse (2013). Commercial sequencing showed previous sequencing reads presented an artifact and not a single base deletion. Analysis showed a single base missense mutation in exon 8 identified as D3* was the actual cause. Multiple alleles of ACAN associated with chondrodysplastic dwarfism in Miniature horses by Eberth et al. (2018), corrected the …

Molecular Investigation Of Minor Genomic Populations And Biological Exposures In Human Health, Brandon Ned Johnson

Dissertations and Theses

The study of genetics has contributed to countless discoveries related to human health and disease. However, the complexities of human biology reside not only in the genome but also in the contributions from environmental exposures, as measured via the classical twin design. To understand the influence of biological exposures, I implemented study designs to explore both the health associations and propagation of foreign genetic material. Microchimerism has been studied for association with several clinical conditions, and I further investigated if male microchimerism could elucidate the etiology of Mayer-Rokitansky-Küster-Hauser syndrome. Prevalence of male microchimerism in women with no history of pregnancy …

Extension Of The Ergot Alkaloid Gene Cluster, Samantha Joy Fabian

Graduate Theses, Dissertations, and Problem Reports

Specialized metabolites produced by fungi impact human health. A large portion of the pharmaceuticals currently on the market are derived from metabolites biosynthesized by microbes. Ergot alkaloids are a class of fungal metabolites that are important in the interactions of environmental fungi with insects and mammals and also are used in the production of pharmaceuticals. In animals, ergot alkaloids can act as partial agonists or antagonists at receptors for 5-hydroxytryptamine (serotonin), dopamine, and noradrenaline as ergot alkaloids have chemical structures similar to those neurotransmitters. Therefore, they affect insects and mammals that consume them and can be used to produce drugs …

Quantitative Song Variety In Relation To Genotype In A Hybridizing Chickadee Population, Shelby Madison Palmer

MSU Graduate Theses

The Black-capped chickadee (Poecile atricapillus) and Carolina chickadee (P. carolinensis) are North American songbird species that hybridize in a narrow contact zone stretching latitudinally from New Jersey to Kansas, USA. The association between genetic ancestry and song type in this hybrid zone has been studied independently several times and found to be minimal or absent, likely due to the influence of cultural transmission on learned song in the oscine passerine clade to which the chickadees belong. Despite this, the song of both species remains remarkably distinct in allopatry, suggesting a genetic constraint on certain qualities of …

Examining Genetically-Informed Etiologic Models Of Co-Occurring Posttraumatic Stress Disorder And Recreational Cannabis Use Among College Students, Terrell A. Hicks

Theses and Dissertations

The college years encompass a period of increased risk recreational cannabis use (RCU), as well as a time of increased risk for trauma exposure and developing posttraumatic stress disorder (PTSD). Given the high co-occurrence between RCU and PTSD, and the potentially negative consequences of the two (e.g., worse academic outcomes), there is a need to understand the etiologic mechanisms of these commonly co-occurring conditions. Two primary phenotypic models exist: self-medication model (i.e., PTSD to RCU) and the high-risk model (i.e., RCU to PTSD). To date, there are two existing studies longitudinally examining the etiologic models proposed to explain co-occurring RCU …

Advancing Methods Of Diet Analysis: A Case Study Using Degraded Merlin (Falco Columbarius) Prey Remains, Taylor A. Coon

Undergraduate Theses, Professional Papers, and Capstone Artifacts

Prey remains have long been used as a mechanism to approach diet analyses. As understanding diet is key to comprehending ecosystem dynamics, prey remains identification requires a unique methodological approach to determine diversity within a sample. With the advancement of technology, molecular protocols designed for species-specific identification have improved to incredible accuracy and precision. Yet, the visual identification method has remained a predominant technique within diet studies. With entry-level observers, we matched visual identifications with molecular-based methods to quantify the accuracy of the visual identification method. This study determined what fraction of visually identified prey remains could be correctly identified …

Revolutionary Advances In The Treatment Of Genetic Disease, Emma Kaitlyn Carrigan

Honors Theses and Capstones

No abstract provided.