Genetics and Genomics Commons^™

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

Biological Sciences Undergraduate Honors Theses

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

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

Graduate Theses and Dissertations

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

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

Graduate Theses and Dissertations

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

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

Graduate Theses and Dissertations

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

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

Graduate Theses and Dissertations

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

Diverse Origins Of Near-Identical Antifreeze Proteins In Unrelated Fish Lineages Provide Insights Into Evolutionary Mechanisms Of New Gene Birth And Protein Sequence Convergence, Nathan Rives, Vinita Lamba, C.H. Christina Cheng, Xuan Zhuang

Biological Sciences Faculty Publications and Presentations

Determining the origins of novel genes and the mechanisms driving the emergence of new functions is challenging yet crucial for understanding evolutionary innovations. Recently evolved fish antifreeze proteins (AFPs) offer a unique opportunity to explore these processes, particularly the near-identical type I AFP (AFPI) found in four phylogenetically divergent fish taxa. This study tested the hypothesis of protein sequence convergence beyond functional convergence in three unrelated AFPI-bearing fish lineages. Through comprehensive comparative analyses of newly sequenced genomes of winter flounder and grubby sculpin, along with available high-quality genomes of cunner and 14 other related species, the study revealed that near-identical …

Noise Leads To The Perceived Increase In Evolutionary Rates Over Short Time Scales, Brian C. O'Meara, Jeremy M. Beaulieu

Biological Sciences Faculty Publications and Presentations

Across a variety of biological datasets, from genomes to conservation to the fossil record, evolutionary rates appear to increase toward the present or over short time scales. This has long been seen as an indication of processes operating differently at different time scales, even potentially as an indicator of a need for new theory connecting macroevolution and microevolution. Here we introduce a set of models that assess the relationship between rate and time and demonstrate that these patterns are statistical artifacts of time-independent errors present across ecological and evolutionary datasets, which produce hyperbolic patterns of rates through time. We show …

Using Machine Learning To Combine Genetic And Environmental Data For Maize Grain Yield Predictions Across Multi-Environment Trials, Igor K. Fernandes, Caio C. Vieira, Kaio O.G. Dias, Samuel B. Fernandes

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

Complementing phenotypic traits and molecular markers with high-dimensional data such as climate and soil information is becoming a common practice in breeding programs. This study explored new ways to combine non-genetic information in genomic prediction models using machine learning. Using the multi-environment trial data from the Genomes To Fields initiative, different models to predict maize grain yield were adjusted using various inputs: genetic, environmental, or a combination of both, either in an additive (genetic-and-environmental; G+E) or a multiplicative (genotype-by-environment interaction; GEI) manner. When including environmental data, the mean prediction accuracy of machine learning genomic prediction models increased up to 7% …

Identifying And Training Deep Learning Neural Networks On Biomedical-Related Datasets, Alan E. Woessner, Usman Anjum, Hadi Salman, Jacob Lear, Jeffrey T. Turner, Ross Campbell, Laura Beaudry, Justin Zhan, Lawrence E. Cornett, Susan Gauch, Kyle P. Quinn

Computer Science and Computer Engineering Faculty Publications and Presentations

This manuscript describes the development of a resources module that is part of a learning platform named 'NIGMS Sandbox for Cloud-based Learning' https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox at the beginning of this Supplement. This module delivers learning materials on implementing deep learning algorithms for biomedical image data in an interactive format that uses appropriate cloud resources for data access and analyses. Biomedical-related datasets are widely used in both research and clinical settings, but the ability for professionally trained clinicians and researchers to interpret datasets becomes difficult as the size and …

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

Biomedical Engineering Undergraduate Honors Theses

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

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

Biomedical Engineering Undergraduate Honors Theses

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

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, …

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

Biological Sciences Undergraduate Honors Theses

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

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

Graduate Theses and Dissertations

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

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

Entomology and Plant Pathology Faculty Publications and Presentations

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

Long-Term Impacts Of Conservation Pasture Management In Manuresheds On System-Level Microbiome And Antibiotic Resistance Genes, Mitiku Mihiret Seyoum, Amanda Ashworth, Kristina M. Feye, Steven C. Ricke, Phillip R. Owens, Philip A. Moore Jr., Mary Savin

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

Animal manure improves soil fertility and organic carbon, but long-term deposition may contribute to antibiotic resistance genes (ARGs) entering the soil-water environment. Additionally, long-term impacts of applying animal manure to soil on the soil-water microbiome, a crucial factor in soil health and fertility, are not well understood. The aim of this study is to assess: (1) impacts of long-term conservation practices on the distribution of ARGs and microbial dynamics in soil, and runoff; and (2) associations between bacterial taxa, heavy metals, soil health indicators, and ARGs in manures, soils, and surface runoff in a study following 15 years of continuous …

The Time-Course Of Cancer Cachexia Onset Reveals Biphasic Transcriptional Disruptions In Female Skeletal Muscle Distinct From Males, Francielly Morena, Seongkyun Lim, Ana Regina Cabrera, Eleanor R. Schrems, Ronald G. Jones, Megan E. Rosa-Caldwell, Tyrone A. Washington, Kevin A. Murach, Nicholas P. Greene

Health, Human Performance and Recreation Faculty Publications and Presentations

Background

Cancer-cachexia (CC) is a debilitating condition affecting up to 80% of cancer patients and contributing to 40% of cancer-related deaths. While evidence suggests biological sex differences in the development of CC, assessments of the female transcriptome in CC are lacking, and direct comparisons between sexes are scarce. This study aimed to define the time course of Lewis lung carcinoma (LLC)-induced CC in females using transcriptomics, while directly comparing biological sex differences.

Results

We found the global gene expression of the gastrocnemius muscle of female mice revealed biphasic transcriptomic alterations, with one at 1 week following tumor allograft and another …

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 …

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 …

Comprehensive Long- And Short- Read Sequencing Approaches To Screen The Mutational Landscape After Therapeutic Crispr-Editing For Duchenne Muscular Dystrophy, Mary Jia, Made Harumi Padmaswari, Landon Burcham, Shilpi Agrawal, Alexis Ivy, Abbey Bryan, Christopher E. Nelson

Biomedical Engineering Undergraduate Honors Theses

Duchenne muscular dystrophy (DMD) is an X-linked muscle wasting disease caused by mutations in the Dmd gene resulting in non-functional dystrophin. Adeno-associated virus (AAV)-mediated delivery of classical CRISPR systems resulting in double-stranded breaks (DSBs) has yielded promise as a curative DMD therapeutic. However, the consequences of AAV-CRISPR require more thorough characterization. PCR-enriched short-read amplicon sequencing at cut sites is the most common method of sequencing CRISPR editing, but PCR bias results in unreliable quantification of on-target edits. We analyze orthogonal long- and short-read sequencing approaches to screen the outcomes of CRISPR technologies at the DNA and RNA-level for DMD. We …

Understanding The Role Of Heterodisulfide Reductase During Nitrogen Fixation By Methanosarcina Acetivorans, Grant Shelnut

Biological Sciences Undergraduate Honors Theses

Methanosarcina acetivorans is a methanogenic archaeon (methanogen) that is important for several processes in our biosphere. A feature of interest within this methanogen is the enzyme nitrogenase which catalyzes the reduction of unusable dinitrogen gas (N₂) into a usable form of nitrogen, ammonia (NH₃). How electrons are transferred within M. acetivorans to nitrogenase during N₂ reduction is unknown. Heterodisulfide reductase (Hdr) is a key enzyme known to reduce the electron carrier protein ferredoxin, which is a direct electron donor to nitrogenase in bacteria. I hypothesized that cytoplasmic HdrA2B2C2 functions in electron transfer to nitrogenase and …

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

Entomology and Plant Pathology Faculty Publications and Presentations

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

Admixpipe V3: Facilitating Population Structure Delimitation From Snp Data, Steven M. Mussmann, Marlis R. Douglas, Tyler Chafin, Michael E. Douglas

Biological Sciences Faculty Publications and Presentations

Quantifying genetic clusters (=populations) from genotypic data is a fundamental, but non-trivial task for population geneticists that is compounded by: hierarchical population structure, diverse analytical methods, and complex software dependencies. AdmixPipe v3 ameliorates many of these issues in a single bioinformatic pipeline that facilitates all facets of population structure analysis by integrating outputs generated by several popular packages (i.e. CLUMPAK, EvalAdmix). The pipeline interfaces disparate software packages to parse Admixture outputs and conduct EvalAdmix analyses in the context of multimodal population structure results identified by CLUMPAK. We further streamline these tasks by packaging AdmixPipe v3 within a Docker container to …

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

Graduate Theses and Dissertations

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

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

Graduate Theses and Dissertations

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

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

Graduate Theses and Dissertations

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

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

Graduate Theses and Dissertations

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

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 …

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 …