Genetics and Genomics Commons^™

The Role Of Nitric Oxide In Inter- And Intra- Cellular Signaling In Plant Defense, Fan Xia

Theses and Dissertations--Plant Pathology

Plants have evolved a sophisticated immune system to defend themselves against pathogens. This immune response can be triggered in response to pathogen-associated molecular patterns (PAMP) or specialized effectors that are recognized by the plant resistance (R) proteins. The latter, commonly referred to as effector-triggered immunity (ETI), is well known to induce broad-spectrum resistance throughout the plants. This phenomenon known as systemic acquired resistance (SAR) is regulated by several chemical signals including salicylic acid (SA), and free radical nitric oxide (NO) and reactive oxygen species (ROS). These signals operate in two parallel branches with NO/ROS functioning downstream of pipecolic acid (Pip) …

A Functional Genomics Approach To Overwintering Mechanisms In Insects, Emily Allison Wheeler Nadeau

Theses and Dissertations--Entomology

Insects living in temperate and polar environments have developed numerous adaptations to increase survival at low temperatures. A majority of insects are freeze-intolerant and die from internal ice formation, but some are freeze-tolerant and can survive ice formation in extracellular spaces. Both categories of insects prepare for winter with a combination of seasonal and rapid acclimation responses, which differ both in time course and in underlying mechanisms. In this dissertation, I examine adaptations for winter survival in several insect species with a specific focus on molecular mechanisms. To better understand the underpinning mechanisms of these adaptations, I leverage functional genomics …

Analysis Of Root System Architecture And Qtl Identification In Grapevines, Sujan Thapa

Graduate Theses/Dissertations

The root system of the plant plays a vital role in water and nutrient uptake. Native North American grapevines adapted to a broad range of climatic and soil conditions, which led to the evolution of diverse root system architecture (RSA) within the Vitis genus. Despite the importance of RSA in viticulture, little is known about the genetic basis of the RSA in grapevine. I used novel root phenotyping tool, RhizoVision Analyzer to characterize the root system of 208 genotypes of an F₁ grapevine progeny obtained from a cross between Vitis rupestris Scheele B38 and Vitis riparia Michx. HP-1. Dormant …

Development Of Genetic Manipulation Techniques For The Fish Pathogen Flavobacterium Psychrophilum, Seada Sloboda

All Graduate Theses, Dissertations, and Other Capstone Projects

Flavobacterium psychrophilum is a known fish pathogen, causing bacterial cold-water disease (BCWD) and rainbow trout fry syndrome (RTFS), predominantly in salmonids. The disease causes tissue damage and tail rot in young and adult fish. The issue is prevalent in fisheries in the Pacific Northwest and the treatments often entail the use of antibiotics. Genetic manipulations in F. psychrophilum are scarce, due to most of the strains’ ability to destroy foreign DNA via restriction enzymes. The virulence mechanisms of F. psychrophilum are not well understood. Lack of genetic manipulation tools in F. psychrophilum has also hampered the development of live attenuated …

Characterizing Drought Adaptations, Phenotypic Plasticity, And Fixed Gene Expression Patterns Within Quercus, James K. Rauschendorfer

Dissertations, Master's Theses and Master's Reports

This dissertation was written on topics related to the genus Quercus with a primary focus on Quercus ellipsoidalis (northern pin oak) and Quercus rubra (northern red oak). Within this dissertation are chapters related to the setup of experimental common gardens within the Ford and Kellogg experimental forest, a literature review describing drought adaptations of Quercus sect. Lobatae (red oak group), identification of transcription factors within the Q. robur (English oak) and Q. rubra genomes, a study comparing leaf trait phenotypic plasticity of Q. ellipsoidalis and Q. rubra, and an RNA-seq experiment studying ecological speciation between Q. ellipsoidalis and Q. …

Comparative Transcriptomic Analysis Of Cancer Testis Genes In Ovarian Cancer, Zayne Knuth

Dissertations, Master's Theses and Master's Reports

Cancer testis genes are common targets for the development of immunotherapy for cancer treatment. Ovarian cancer is one of the leading causes of death in women cancer patients. Cancer testis genes play a role in tumorigenesis, but it is not clear how these genes are activated. This study utilized differential expression analysis between The Cancer Genome Atlas (TCGA) ovarian cancer data, Genotype-Tissue Expression (GTEx) non-cancerous ovary and testis data, and cell line data to identify a list of cancer testis genes that have a novel expression profile. To identify ovarian cancer testis genes, we obtained normal ovary tissue data and …

Prevalence Of Mutations In The Pfdhfr, Pfdhps, And Pfmdr1 Genes Of Malarial Parasites Isolated From Symptomatic Patients In Dogondoutchi, Niger, Ibrahima Issa, Mahaman Moustapha Lamine, Veronique Hubert, Amadou Ilagouma, Eric Adehossi, Aboubacar Mahamadou, Neil F. Lobo, Demba Sarr, Lisa M. Shollenberger, Houze Sandrine, Ronan Jambou, Ibrahim Maman Laminou

Biological Sciences Faculty Publications

The effectiveness of artemisinin-based combination therapies (ACTs) depends not only on that of artemisinin but also on that of partner molecules. This study aims to evaluate the prevalence of mutations in the Pfdhfr, Pfdhps, and Pfmdr1 genes from isolates collected during a clinical study. Plasmodium genomic DNA samples extracted from symptomatic malaria patients from Dogondoutchi, Niger, were sequenced by the Sanger method to determine mutations in the Pfdhfr (codons 51, 59, 108, and 164), Pfdhps (codons 436, 437, 540, 581, and 613), and Pfmdr1 (codons 86, 184, 1034, and 1246) genes. One hundred fifty-five (155) pre-treatment samples were …

Cpf1-Based Crispr Genome Editing In The Cyanobacterium N. Punctiforme, Soohan Woo

University of the Pacific Theses and Dissertations

CRISPR systems have been growing in their utility and their application throughout the biological field as researchers continue to grow in their understanding of the relatively novel genome editing technology. However, despite the potential of CRISPR as a genome editing tool, the complexity of applying this technology to a specific organism calls for custom modifications to the system to improve its success rate. In this project, a CRISPR-Cpf1 system that can be effectively employed in the cyanobacterium Nostoc punctiforme was designed, with a focus on the hormogonium development of this species. Multiple plasmids containing the CRISPR system and targeting different …

Reduction Of Plasmid Vector Backbone Length Enhances Reporter Gene Expression, Carly Boye, Sezgi Arpag, Michael Francis, Scott Declemente, Aislin West, Richard Heller, Anna Bulysheva

Electrical & Computer Engineering Faculty Publications

Gene therapy has a wide range of applications for various types of pathologies. Viral methods of gene delivery provide high levels of gene expression but have various safety concerns. Non-viral methods are largely known to provide lower levels of expression. We aim to address this issue by using plasmid DNA with smaller backbones to increase gene expression levels when delivered using non-viral methods. In this study we compare gene expression levels between two vectors with firefly luciferase encoding gene insert using liposome complexes and gene electrotransfer as delivery methods. A 2-fold reduction in plasmid vector backbone size, disproportionately enhanced gene …

Amelioration Of Mitochondrial Bioenergetic Dysfunction In Diabetes Mellitus: Delving Into Specialized And Non-Specific Therapeutics For The Ailing Heart, Andrya Jean Durr

Graduate Theses, Dissertations, and Problem Reports (ETD)

Morbidity and mortality of the diabetic population is influenced by many confounding factors, but cardiovascular disease (CVD), remains the leading cause of death. Mitochondrial dysfunction is central in the development of cardiac contractile dysfunction, with decreased mitochondrial bioenergetic function, increased dependence on free fatty acid utilization, and a decrease in glucose utilization having been shown to contribute to contractile dysfunction. Strategies targeting the amelioration of mitochondrial bioenergetic function are attractive for limiting diabetes-induced heart failure, and preserving health-span. The goals of this dissertation were to assess two mitochondrial-centric approaches for the amelioration of mitochondrial and cardiac contractile dysfunction in diabetes …

Getting To The Root Cause: The Genetic Underpinnings Of Root System Architecture And Rhizodeposition In Sorghum, Farren Smith

Graduate Theses, Dissertations, and Problem Reports (ETD)

Plants are some of the most diverse organisms on earth, consisting of more than 350,000 different species. To understand the underlying processes that contributed to plant diversification, it is fundamental to identify the genetic and genomic components that facilitated various adaptations over evolutionary history. Most studies to date have focused on the underlying controls of above-ground traits such as grain and vegetation; however, little is known about the “hidden half” of plants. Root systems comprise half of the total plant structure and provide vital functions such as anchorage, resource acquisition, and storage of energy reserves. The execution of these key …

Genetic Underpinnings Of Novel Trait Development In A Euwallacea-Fusarium Mutualism, Elaina J. Spahr

Graduate Theses, Dissertations, and Problem Reports (ETD)

Evolutionary Developmental Biology seeks to answer fundamental questions about the mechanisms underlying the evolution and innovation towards increasing structural complexity within the body plan. The ambrosia symbiosis, a polyphyletic group of xylem-feeding beetles, provides a wealth of diversity in novel pouch-like structures called mycangia. This diversity could serve as a rich model for understanding how mutualisms may prompt structural innovation and diversification in a host organism. The ambrosia symbiosis has become a fast-growing research subject in entomology and forest pathology but has yet to experience the same attention under the lens of evolutionary developmental genetics.

Development of mycangia was examined …

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

College of Graduate Studies: Theses & 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 …

Florida Sand Skink And Blue-Tailed Mole Skink: Expanding Geographic Coverage Of Genetic Analysis For Conservation, Emma Simpson

College of Graduate Studies: Theses & Dissertations

The Lake Wales Ridge is important scrub habitat that has been increasingly altered since the post-Columbian settlement in Florida. This loss of habitat has caused extreme anthropogenic fragmentation within the Lake Wales Ridge resulting in isolation among extant scrub patches. To expand the geographic scope of previous studies and answer questions concerning population connectivity, we characterized genetic diversity and differentiation using cytochrome-b and microsatellite genetic markers for two endemic skink species: the Florida Sand Skink (Plestiodon reynoldsi) and Blue-tailed Mole Skink (Plestiodon egregius lividus). Both species display historical isolation between central and southern Lake Wales Ridge …

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

College of Graduate Studies: Theses & 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 …

Factors Impacting Genomic Testing Rates Among Epithelial Ovarian Cancer Patients Across A Large Community-Based Healthcare System, Nicole M. Kretzer, Christopher J. Darus, Nancy Biery, Roshanthi Weerasinghe, Grace Li, Ann Vita, Shwetha Pindikuri, Amy S. Parrish, Charles W Drescher, Fernanda B. Musa

All Podium Presentations

Background: Epithelial ovarian cancer (EOC) accounts for the highest mortality of all gynecological cancers. NCCN guidelines recommend germline and somatic testing for all women with invasive EOC. Despite this recommendation, there is a large diversity in the types of testing patients receive even within a single healthcare system. Reported data of genetic testing for epithelial ovarian cancer (EOC) patients is largely based on patients treated at academic medical centers or patients who participate in clinical trials.

Purpose: This study sought to determine the rates of germline and somatic testing for epithelial ovarian cancer patients and identify factors that impact testing …

Patterns Of Genomic Testing For Epithelial Ovarian Cancer Across A Large Community-Based Health Care Network- A Real World Experience, Nicole M. Kretzer, Fernanda B. Musa, Christopher Darus, Nancy Biery, Roshanthi Weerasinghe, Grace Li, Ann Vita, Shwetha Pindikuri, Amy S. Parrish, Charles W Drescher

All Podium Presentations

Background: NCCN guidelines recommend germline and somatic tumor testing for all women with invasive epithelial ovarian cancer (EOC). Despite this recommendation, testing rates remain low and an optimal strategy to achieve the recommended testing has not been defined.

Purpose: We elected to review the patterns of germline and somatic tumor testing for patients with EOC across a large health care network to identify barriers to testing.

Methods: Clinical, pathologic, demographic and genomic testing (GT) information including involvement of a genetic counselor, specific test(s) ordered, test vendor, test turn-around time, and test results were obtained from the diverse dataset within the …

Identifying The Role Of Cholesterol And The Cholesterol Transfer Protein, Ysp1-2, In Cell-Cell Fusion In Tetrahymena Thermophila, Natasha D. Kusibab

Honors Program Theses

A cell’s shape directly affects how it behaves as one’s structure directly correlates to its function. The shape of cells and organelles is driven in part by the lipid bilayer that makes up their membranes. The process by which cells systematically adjust the types of lipids in membranes to facilitate changes in membrane shape remain uncertain. In our research, we aimed to address this issue by studying the role of lipid transfer proteins in the ciliate, Tetrahymena thermophilia. Specifically, we focus on the process of cell-cell fusion during mating in Tetrahymena as this requires a drastic change in membrane shape …

Protein Charge Parameters That Influence Stability And Cellular Internalization Of Polyelectrolyte Complex Micelles, Rachel A. Kapelner, Rachel S. Fisher, Shana Elbaum-Garfinkle, Allie C. Obermeyer

Advanced Science Research Center

Proteins are an important class of biologics, but there are several recurring challenges to address when designing protein-based therapeutics. These challenges include: the propensity of proteins to aggregate during formulation, relatively low loading in traditional hydrophobic delivery vehicles, and inefficient cellular uptake. This last criterion is particularly challenging for anionic proteins as they cannot cross the anionic plasma membrane. Here we investigated the complex coacervation of anionic proteins with a block copolymer of opposite charge to form polyelectrolyte complex (PEC) micelles for use as a protein delivery vehicle. Using genetically modified variants of the model protein green fluorescent protein (GFP), …

An Integrative Investigation Of The Synechococcus A/B Clade During Adaptive Radiation At The Upper Thermal Limit Of Phototrophy, Christopher L. Pierpont

Graduate Student Theses, Dissertations, & Professional Papers

Thermophilic microorganisms have been scientifically observed since the early nineteenth century and have spurred many questions about the limits of life and the capacity of organisms to survive extreme conditions. Decades of research on thermophile proteins and genomes have yielded several proposed correlates of temperature that may contribute to adaptation of bacteria and archaea to high temperature. However, many of the generalizations reported are drawn from analyses of deeply divergent taxa or from individual case studies in isolation from mesophilic relatives. Members of the Synechococcus A/B (SynAB) group are the only cyanobacteria with members able to grow above 65 °C …

Genetic Variants Associated With Circulating Liver Injury Markers In Mexican Americans, A Population At Risk For Non-Alcoholic Fatty Liver Disease, Caroline M Sabotta, Suet-Ying Kwan, Lauren E Petty, Jennifer E Below, Aron Joon, Peng Wei, Susan P Fisher-Hoch, Joseph B Mccormick, Laura Beretta

Faculty, Staff and Student Publications

Objective: Mexican Americans are disproportionally affected by non-alcoholic fatty liver disease (NAFLD), liver fibrosis and hepatocellular carcinoma. Noninvasive means to identify those in this population at high risk for these diseases are urgently needed. Approach: The Cameron County Hispanic Cohort (CCHC) is a population-based cohort with high rates of obesity (51%), type 2 diabetes (28%) and NAFLD (49%). In a subgroup of 564 CCHC subjects, we evaluated 339 genetic variants previously reported to be associated with liver injury markers aspartate aminotransferase (AST) and alanine aminotransferase (ALT) in United Kingdom and Japanese cohorts. Results: Association was confirmed for 86 variants. Among …

Robust Meta-Analysis For Large-Scale Genomic Experiments Based On An Empirical Approach, Sinjini Sikdar

Mathematics & Statistics Faculty Publications

BACKGROUND: Recent high-throughput technologies have opened avenues for simultaneous analyses of thousands of genes. With the availability of a multitude of public databases, one can easily access multiple genomic study results where each study comprises of significance testing results of thousands of genes. Researchers currently tend to combine this genomic information from these multiple studies in the form of a meta-analysis. As the number of genes involved is very large, the classical meta-analysis approaches need to be updated to acknowledge this large-scale aspect of the data.

METHODS: In this article, we discuss how application of standard theoretical null distributional assumptions …

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 …

Identifying Epidermal Enriched Genes Required For Planarian Regeneration- Sp. Schmidtea Mediterranea, Pallob Barai

Theses and Dissertations--Biology

The outer epithelial layer covering an organism, commonly known as the epidermis, is crucial for maintaining homeostasis and for the wound healing processes after injury. The planarian epidermis allows flatworms to heal their wounds and virtually restore any missing tissues. Immediately after amputation, planarians contract their muscle and stretch their epidermis to heal the wound area. However, how the planarian epidermis coordinates with other tissues and mechanisms after the initial wound healing processes begins is not understood in detail. I hypothesized that epidermal cell stretching upon wound healing induces transcriptional changes that are required for effective regeneration. To test this …

Determinants Of Virus Variation, Evolution, And Host Adaptation, Katherine Latourrette, Hernan Garcia-Ruiz

Nebraska Center for Virology: Faculty Publications

Virus evolution is the change in the genetic structure of a viral population over time and results in the emergence of new viral variants, strains, and species with novel biological properties, including adaptation to new hosts. There are host, vector, environmental, and viral factors that contribute to virus evolution. To achieve or fine tune compatibility and successfully establish infection, viruses adapt to a particular host species or to a group of species. However, some viruses are better able to adapt to diverse hosts, vectors, and environments. Viruses generate genetic diversity through mutation, reassortment, and recombination. Plant viruses are exposed to …

Immunogenicity And Protective Efficacy Of A Recombinant Pichinde Viral-Vectored Vaccine Expressing Influenza Virus Hemagglutinin Antigen In Pigs, Sushmita Kumari, Jayeshbhai Chaudhari, Qinfeng Huang, Phillip Gauger, Marcelo Nunes De Almeida, Yuying Liang, Hinh Ly, Hiep Vu

Nebraska Center for Virology: Faculty Publications

Influenza A virus of swine (IAV-S) is an economically important swine pathogen. The IAV-S hemagglutinin (HA) surface protein is the main target for vaccine development. In this study, we evaluated the feasibility of using the recombinant tri-segmented Pichinde virus (rPICV) as a viral vector to deliver HA antigen to protect pigs against IAV-S challenge. Four groups of weaned pigs (T01–T04) were included in the study. T01 was injected with PBS to serve as a non-vaccinated control. T02 was inoculated with rPICV expressing green fluorescence protein (rPICV-GFP). T03 was vaccinated with rPICV expressing the HA antigen of the IAV-S H3N2 strain …

Increased Signal Complexity Is Associated With Increased Mating Success, Noori Choi, Matt Adams, Kasey Fowler-Finn, Elise Knowlton, Malcolm Rosenthal, Aaron Rundus, Roger D. Santer, Dustin J. Wilgers, Eileen Hebets

Eileen Hebets Publications

The evolution of complex signals has often been explored by testing multiple functional hypotheses regarding how independent signal components provide selective benefits to offset the costs of their production. In the present study, we take a different approach by exploring the function of complexity per se. We test the hypothesis that increased vibratory signal complexity— based on both proportional and temporal patterning—provides selective benefits to courting male Schizocosa stridulans wolf spiders. In support of this hypothesis, all of our quantified metrics of vibratory signal complexity predicted the mating success of male S. stridulans. The rate of visual signalling, which is …

Description Of The Courtship And Copulation Behaviours Of The Wall Spider Oecobius Concinnus (Oecobiidae), Diego Solano-Brenes, Laura Segura-Hernández, Gilbert Barrantes

Eileen Hebets Publications

Courtship and copulation behaviours are yet scantily described in many spider families, and this lack of information limits our understanding of the evolution of such behaviours within and across families. Here, we provide a detailed description of both courtship and copulation behaviour for Oecobius concinnus Simon, 1893. A striking characteristic of the male courtship is the construction of a tubular web (mating web) in which most courtship and copulation occurs. This web likely functions to restrain the female in a reduced space and as a substrate for male pheromones. The courtship consists of a complex web of interactions between both …

Modeling The Evolution Of Herbicide Resistance In Weed Species With A Complex Life Cycle, K. Harrison Holmes, John L. Lindquist, Richard Rebarber, Rodrigo Werle, Melinda K. Yerka, Brigitte Tenhumberg

Brigitte Tenhumberg Papers

A growing number of weed species have evolved resistance to herbicides in recent years, which causes an immense financial burden to farmers. An increasingly popular method of weed control is the adoption of crops that are resistant to specific herbicides, which allows farmers to apply the herbicide during the growing season without harming the crop. If such crops are planted in the presence of closely related weed species, it is possible that resistance genes could transfer from the crop species to feral populations of the wild species via gene flow and become stably introgressed under ongoing selective pressure by the …

Genomic Approaches To Uncovering The Coevolutionary History Of Parasitic Lice [Review], Kevin P. Johnson

Harold W. Manter Laboratory of Parasitology: Library Materials

Next-generation sequencing technologies are revolutionizing the fields of genomics, phylogenetics, and population genetics. These new genomic approaches have been extensively applied to a major group of parasites, the lice (Insecta: Phthiraptera) of birds and mammals. Two louse genomes have been assembled and annotated to date, and these have opened up new resources for the study of louse biology. Whole genome sequencing has been used to assemble large phylogenomic datasets for lice, incorporating sequences of thousands of genes. These datasets have provided highly supported trees at all taxonomic levels, ranging from relationships among the major groups of lice to those among …