Genetics and Genomics Commons^™

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 …

The Genomics Of Champ1: Insights Into Their Cell-Type Specificity And Developmental Trajectories, Zoe Marie Van Caugherty

MUSC Theses and Dissertations

Chromosome alignment maintaining phosphoprotein 1(CHAMP1) is a gene that encodes a zinc finger protein that is involved in in the maintenance of kinetochore-microtubule attachment and regulating chromosome segregation in mitosis. (Itoh et al., 2011) CHAMP1 mutations have been shown to be major risk factors for neurodevelopmental disorders (NDDs) and autism spectrum disorder (ASD).(Asakura et al., 2021; Isidor et al., 2016; Levy et al., 2022) Although there is information on the link between CHAMP1 mutations and NDD, the role of CHAMP1 in regulating processes of human cortical development, namely, neurogenesis, proliferation, and electrophysiological properties of newly born neurons, is unknown. This …

Investigating The Impact Of Transcription On Mutation Rates, Sarah Patterson

Theses and Dissertations

tRNA genes are highly transcribed and perform one of the most fundamental cellular functions. Although a universal pattern observed across all three domains of life is that highly transcribed genes tend to evolve slowly, tRNA genes have been shown previously to evolve rapidly. This rapid sequence evolution could result from relaxed selection, increased mutation rate, or a combination of both. Here, we use mutation-accumulation line sequencing data to show that tRNA genes accumulate more mutations than other gene types. Our results indicate that this elevated mutation rate is a consequence of both elevated transcription-associated mutagenesis and a lack of transcription-coupled …

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 …

The Evolution Of Transposable Elements As Cis-Regulatory Elements In Mammals, Alan Y. Du

Arts & Sciences Electronic Theses and Dissertations

Transposable elements (TEs) are mobile genetic elements that make up a large proportion of mammalian genomes. Although TEs are highly prevalent genomic sequences, they have been understudied as they were once labeled as “junk DNA.” Despite their initial status as simple genomic parasites, recent studies have implicated TEs as cis-regulatory elements, supplying promoters, enhancers, and boundary elements. Functional testing of regulatory activity, however, remains a significant bottleneck. Nonetheless, due to their repetitive nature, TEs provide a unique model to examine the evolution of cis-regulatory elements, which has traditionally been difficult to study due to lack of homology at the sequence …

Assessing Genomic Literacy In Advanced Practice Nursing Students Before And After An Intervention, Guiselle Palomera

Doctor of Nursing Practice Final Manuscripts

Introduction

The purpose of this evidence-based Doctor of Nursing Practice (DNP) project was to examine genetics and genomics literacy in advanced practice nursing students before and after an intervention.

Background

As genomics continue to play an emerging role in healthcare, and advancements are introduced into clinical practice, it is critical that nurses be competent in genetics and genomics concepts. There is a fundamental need to incorporate genomics education into nursing school curriculum. However, studies have shown that the majority of faculty across nursing schools in the United States are ill-equipped to teach genetics and genomics concepts. Furthermore, many interventions to …

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. …

The Genomic Dynamics Of Fermented Food Microbes, Katherine Chacón-Vargas

Doctoral Dissertations

Along with the agriculture and domestication revolution, humans have utilized bacteria, yeasts, and molds for millennia in the production of traditionally fermented foods and beverages. Fermentation is a very ancient practice of high relevance nowadays since it contributes with a great variety of foods worldwide. Microbial fermentation allows metabolic transformation of the raw food materials leading to biochemical changes that played a key role in food preservation, health benefits, nutrition, flavors, and texture, among others. Food fermentation practices could diverge from traditional artisanal spontaneous fermentation to industrialize methods with specialized microbial starters and although fermented environments tend to be very …

Genetic Evaluation Of The Current Distribution And Possible Diffrentations Between Lasiurus Borealis And Lasiurus Frantzii In Southwestern North America, Zeinab M. Haidar

Cal Poly Humboldt theses and projects

Several recent accounts of overlap and historic misidentifications regarding two species of the genus Lasiurus, Western red bat (Lasiurus frantzii) and Eastern red bat (Lasiurus borealis), have cast doubt on our understanding of their distribution, assumed spatial allopatry, and interactions in the United States Southwest. With the use of morphometrics and genetic sequencing, utilizing tissue collected from specimens throughout California and adjoining states, we have reassessed the current distribution, best practices for field identification, and genetic differentiation between both species. Appropriate species classification by region was achieved utilizing mitochondrial DNA, targeting the cytochrome c oxidase …

Effects Of Riverine Barriers On Avian Evolution In The Amazon Basin, Andre Eugene Moncrieff

LSU Doctoral Dissertations

The high biodiversity found in the Amazon Basin has long captivated the attention of naturalists and evolutionary biologists seeking to explain its origins. Early observations by Alfred Wallace highlighted the role of rivers in delimiting the geographic ranges of many species; furthermore, where rivers narrow towards their headwaters, he noted that some species cross rivers freely. A major goal of this dissertation is to investigate how these and other observations about riverine barriers might inform our understanding of how speciation unfolds in Amazonia. My approach involved generating genomic data with dense geographic sampling for manakins in the genus Lepidothrix, …

Methods And Tools To Improve Performance Of Plant Genome Analysis, Drew Ferrell

Theses and Dissertations

Multi -omics data analysis and integration facilitates hypothesis building toward an understanding of genes and pathway responses driven by environments. Methods designed to estimate and analyze gene expression, with regard to treatments or conditions, can be leveraged to understand gene-level responses in the cell. However, genes often interact and signal within larger structures such as pathways and networks. Complex studies guided toward describing dynamic genetic pathways and networks require algorithms or methods designed for inference based on gene interactions and related topologies. Classes of algorithms and methods may be integrated into generalized workflows for comparative genomics studies, as multi -omics …

A Genomic Investigation Of Divergence Between Tuna Species, Pavel V. Dimens

Dissertations

Effective management and conservation of marine pelagic fishes is heavily dependent on a robust understanding of their population structure, their evolutionary history, and the delineation of appropriate management units. The Yellowfin tuna (Thunnus albacares) and the Blackfin tuna (Thunnus atlanticus) are two exploited epipelagic marine species with overlapping ranges in the tropical and sub-tropical Atlantic Ocean. This work analyzed genome-wide genetic variation of both species in the Atlantic basin to investigate the occurrence of population subdivision and adaptive variation. A de novo assembly of the Blackfin tuna genome was generated using Illumina paired-end sequencing data and …

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 …

Decoding The Tumor And Immune Microenvironment In Pdac And Breast Cancer By Single Cell Sequencing., Aislyn Schalck

Dissertations & Theses (Open Access)

This work utilizes single cell RNA sequencing to identify transcriptional populations and gene changes for the purpose of immune-related cancer therapies. First we have characterized the T cell populations of the normal and malignant human pancreas. Furthermore, we utilized single cell TCR sequencing to track transcriptional states of T cell clones from human PDACs into a T cell culture product for adoptive cell therapy. Second, we examined the potential role of radiotherapy in inducing an immune response in hormone receptor positive breast tumors.

Development Of Graphical Models And Statistical Physics Motivated Approaches To Genomic Investigations, Yashwanth Lagisetty

Dissertations & Theses (Open Access)

Identifying genes involved in disease pathology has been a goal of genomic research since the early days of the field. However, as technology improves and the body of research grows, we are faced with more questions than answers. Among these is the pressing matter of our incomplete understanding of the genetic underpinnings of complex diseases. Many hypotheses offer explanations as to why direct and independent analyses of variants, as done in genome-wide association studies (GWAS), may not fully elucidate disease genetics. These range from pointing out flaws in statistical testing to invoking the complex dynamics of epigenetic processes. In the …

Genetics And Genomics Education Among Physician Assistants, Wesley Patterson

All Dissertations

This dissertation comprises five chapters to describe genetics and genomics education among physician assistant/associate (PA) students and practicing PAs. Chapter I introduces the gap in supply and demand of genetic services, the need for non-genetics healthcare providers to fill the gap, and the PA profession as a solution.

Chapter II is a rapid literature review that summarizes the available literature regarding genetics and genomics education for PAs. A paucity of literature exists to describe the current state of PA genetics-genomics education. The few studies retrieved describe content being taught in PA programs, the number of genetics-genomics contact hours PA students …

Strategic Plan For Genomic Competencies Into Undergraduate Nursing Curriculum, Myerann Royce M. Mangalino

UNLV Theses, Dissertations, Professional Papers, and Capstones

Problem: As genomics research continues to grow in medicine and in popular culture, an educational gap in nursing is inevitable. Nurses must have a strong understanding of genetics and genomics to effectively integrate them into current practice.Objectives: The objective is to identify gaps in the current undergraduate curriculum and build threads that may be incorporated into the current curriculum to fill the identified gaps. Methods: The foundation of this project was the Essentials of Genetic and Genomic Nursing: Competencies, Curricula Guidelines, and Outcome Indicators, 2nd Edition (Consensus Panel on Genetic/Genomic Nursing Competencies, 2008). A strategic plan was created to increase …

Mechanisms By Which Xenorhabdus Nematophila Interacts With Hosts Using Integrated -Omics Approaches, Nicholas C. Mucci

Doctoral Dissertations

Nearly all organisms exist in proximity to microbes. These microbes perform most of the essential metabolic processes necessary for homeostasis, forming the nearly hidden support system of Earth. Microbial symbiosis, which is defined as the long-term physical association between host and microbes, relies on communication between the microbial community and their host organism. These interactions among higher order organisms (such as animals, plants, and fungi) and their bacteria links metabolic processes between interkingdom consortia. Many questions on microbial behavior within a host remain poorly understood, such as the colonization efficiency among different microbial species, or how environmental context changes their …

An Investigation Of Epigenetic Mechanisms Driving The Biology Of Head And Neck Squamous Cell Carcinoma, Scot Carson Callahan

Dissertations & Theses (Open Access)

Head and neck squamous cell carcinoma (HNSCC) is the 6th most common cancer worldwide and is associated with significant morbidity and mortality. To date, the majority of work in the field has focused on genomic alterations such as mutations and copy number alterations. However, the clinical success of targeted therapies that exploit known genomic alterations, such as EGFR mutations, has remained mixed. Over the past decade, the importance of epigenetic regulators has come to the forefront, with the realization that many of these genes are mutated in cancer. Despite this realization, the role of epigenetics in regulating tumorigenesis, progression and …

The Influence Of Climate Change On The Ecology Of The Arctic Ground Squirrel In Denali National Park, Ak., Nigel A. Golden

Doctoral Dissertations

This dissertation research focuses on the ecology of the Arctic ground squirrel (Urocitellus parryii) in Denali National Park and Preserve, AK. The Arctic ground squirrels is a species of interest for monitoring efforts under the National Park Services’ Vital Signs Monitoring Program under the Vital Signs Monitoring program. The focus of this program is to monitor what is considered to be the most significant indicators of ecological conditions of the specific park resources that are of the greatest concern. The CAKN designated the Arctic ground squirrel (Urocitellus parryii) as one indicator species of park ecosystems. Despite being easy to observe …

Genomic Organization And Expression Of The Wc1 Hybrid Coreceptor And Pattern Recognition Receptor On Porcine Gamma Delta T Cells, Lauren Le Page

Doctoral Dissertations

gd T cells are a crucial component of the immune response to a number of increasingly relevant and largely zoonotic pathogens to which efficacious vaccination is lacking. In ruminants and swine, gd T cells represent a major population of peripheral blood and epithelial tissue-resident lymphocytes. gdT cells respond to both protein and non-protein antigens independently of MHC presentation and possess immunological memory. Upon activation, gamma delta T cells illicit a variety of effector functions and play an indispensable role of orchestrating the downstream immune response. These characteristics make gamma delta T cells a promising candidate for recruitment by vaccination, however, …

Single Cell Lineage Tracing Reveals Mechanisms Of Tumor Initiation And Chemoresistance In Small Cell Lung Cancer, Hannah Wollenzien

Dissertations and Theses

Small Cell Lung Cancer (SCLC) is a devastating disease characterized by a very low two-year survival rate and almost universal acquisition of chemoresistance. Nearly all patients have tumors driven by functional inactivation of the tumor suppressors Rb and p53, but despite the uniform origins of this tumor, not all patients are genetically or phenotypically identical. SCLC can be subtyped into four unique molecular subtypes, determined by the expression of ASCL1, NEUROD1, POU2F3, or YAP1. These subtypes are plastic, and subtype switching after chemotherapy has been documented. Without the understanding of how tumor heterogeneity arises, we cannot solve the challenge of …

Quantifying Contributions Of Climate, Geography, And Gene Flow To Divergence: A Case Study For Three North American Pines, Constance E. Bolte

Theses and Dissertations

Long-lived species of trees, especially conifers, often display weak patterns of reproductive isolation, but clear patterns of local adaptation and phenotypic divergence. Discovering the evolutionary history of these patterns is paramount to a generalized understanding of speciation and the processes that confer population persistence versus those that compromise adaptive potential under rapidly changing environments. Forest trees have long generation times and low migratory potential making them especially vulnerable to population fragmentation and reductions of genetic diversity due to insufficient tracking of niche optima and adaptational lags. Within clades of the genus Pinus, evolutionary histories appear to be riddled with hybridization …

Examination Of Common And Rare Variant Genetic Architecture Of Psychiatric Disorders, Mohammad Ahangari

Theses and Dissertations

Psychiatric disorders are often heterogenous in their manifestation and genome-wide association studies have identified many common risk variants involved in their polygenic architectures with varying degrees of pleiotropy. In recent years, large-scale biobanks have also begun sequencing the genome of their participants to elucidate the role of rare risk variation in the genetic architecture of complex phenotypes, including psychiatric traits. This dissertation sought to better understand the role of both common and rare risk variation in the genetic architecture of psychiatric disorders with a particular focus on schizophrenia and alcohol problems. In the first three analyses, we focused on characterizing …

Population Genomics Of Redbreast Sunfish (Lepomis Auritus): Exploring Gene Flow And Local Adaptation In A Widely Distributed Freshwater Fish, Garret J. Strickland

Electronic Theses and Dissertations

Little information is available concerning the distribution of genetic diversity in non-salmonid, non-imperiled, freshwater fish. In order to fill in this knowledge gap, I conducted a population genomics survey in Redbreast Sunfish (Lepomis auritus; RBS), a widespread, generalist species distributed along the Atlantic slope rivers of eastern North America. I sampled four basins (ACF, Savannah, Roanoke, and James) at eight sites each with a factorial experimental design. Sites were distributed among coastal plain, Piedmont, or mountain ecoregions in order to capture the greatest range of environmental states experienced by RBS, with the intention of finding evidence for local adaptation to …

Applying Conservation Genomic Techniques To Guide Management Of The Reticulated Flatwoods Salamander (Ambystoma Bishopi), Miranda Gaupp

Electronic Theses and Dissertations

The Reticulated flatwoods salamander (Ambystoma bishopi) is a federally endangered amphibian endemic to the longleaf-pine ecosystem of the southeastern U.S. This study used analyses of single-nucleotide polymorphism (SNP) data, collected from 2,255 unique individuals across 5 breeding seasons, spread across the known extant range of A. bishopi, to characterize the genetic diversity and demographics of populations, genetic relationships among populations, and patterns and spatial extents of gene flow, and to evaluate potential effects of management on A. bishopi’s resiliency. Population structure was strongly hierarchical, with individual breeding ponds (n = 38) acting as semi-connected subpopulations …

Impact Of Intratumor Heterogeneity And The Tumor Microenvironment In Shaping Tumor Evolution And Response To Therapy, Akash Mitra

Dissertations & Theses (Open Access)

Intratumor heterogeneity (ITH) is a crucial challenge in cancer treatment. The genotypic and phenotypic heterogeneity underlying diverse cancer types leads to subclonal variation, which may result in mixed or failed response to therapy. The heterogeneity at the tumor level, along with the tumor microenvironment (TME), often shapes tumor evolution and ultimately clinical outcome. Given that modern treatment paradigms increasingly expose patients with metastatic disease to multiple treatment modalities through the course of their disease, there exists a need to characterize robust and predictive biomarkers of response to therapy. In order to accurately characterize tumor evolution, we need to account for …

Analysis Of Structural Variation And Mtdna Copy Number In Finns, Liron Ganel

Arts & Sciences Electronic Theses and Dissertations

Cardiovascular disease (CVD) is a complex disease responsible for more deaths worldwide than any other cause according to the World Health Organization. Genetic association studies for CVD and related risk factors have successfully identified hundreds of loci associated with these complex diseases and traits, although much of their heritability remains unexplained. Structural variants (SVs) - including insertions, deletions, duplications, and inversions - are an understudied class of genomic variation that have the potential to explain much of the missing heritability of CVD and other complex traits. Here, we discuss advances emerging from the study of SVs in the context of …

Development Of In-Silico Pipelines For Identification And Characterization Of Biomarker Panels And Therapeutic Interventions In Gastro-Intestinal (Gi) Cancers, Pranita Atri

Theses & Dissertations

Gastro-intestinal (GI) malignancies, including gastric, colorectal, and pancreatic cancers, have maintained their high overall mortality due to a lack of prognostic and diagnostic biomarkers and potential therapeutic modalities. While efforts have been made to improve both early detection and therapeutic interventions in these cancers, failure of conventional approaches have proven to be a big challenge, and alternate approaches are needed. Computational biology approaches owing to lesser time and more per target success rate offer a unique solution here. The current study explored the use of computational biology techniques to study the various aspects relating to GI malignancies. First, we sought …

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 …