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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 …

Understanding The Relationship Between B Chromosomes And Nondisjunction In Drosophila Melanogaster, Ayushi Patel

Honors Scholar Theses

B chromosomes are supernumerary, heterochromatic genetic elements that are found in hundreds of different plant and animal species. Recently, B chromosomes were discovered in a stock of Drosophila melanogaster and are carried at a high copy number of 10-12 B chromosomes per cell. B chromosomes are not known to carry any active genes, but when placed in a wild-type genetic background, they cause a significant increase in the frequency of chromosome 4 missegregation during meiosis. This project aimed to understand the relationship between a female’s B chromosome copy number and how often she passes on too many (or too few) …

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 …

Protocol To Identify The Core Gene Supported By An Essential Gene In E. Coli Bacteria Using A Genome-Wide Suppressor Screen, Isao Masuda, Ya-Ming Hou

Department of Biochemistry and Molecular Biology Faculty Papers

We describe here a genome-wide screening approach to identify the most critical core reaction among a network of many that are supported by an essential gene to establish cell viability. We describe steps for maintenance plasmid construction, knockout cell construction, and phenotype validation. We then detail isolation of suppressors, whole-genome sequencing analysis, and reconstruction of CRISPR mutants. We focus on E. coli trmD, which encodes an essential methyl transferase that synthesizes m1G37 on the 3'-side of the tRNA anticodon. For complete details on the use and execution of this protocol, please refer to Masuda et al. (2022).

Detecting Multiple Paternity In Mule Deer: Variations Among Populations And The Ecological Significance, Madeline K. Martin, Sydney Lamb, Anna K. Monson, Paul B. Frandsen, Brock R. Mcmillan

Library/Life Sciences Undergraduate Poster Competition 2023

We are interested in detecting the absence or rate of multiple paternity within mule deer populations (Odocoileus hemionus) due to 1) their unique breeding system where males mate-guard females from other males[2], and 2) the highly skewed male-biased sex ratios in populations as a result of harvest management. Comparing the rate of multiple paternity to sex ratio will suggest if harvest management is influencing long-term population genetics.

A Transcriptomic Analysis Of Triple Negative Breast Cancer Revealing Alternative Drug Therapeutics, Mauri Dobbs Spendlove, Jenna Birchall Poulsen, Naomi Rapier-Sharman, Brett Pickett

Library/Life Sciences Undergraduate Poster Competition 2023

Breast cancer is the most common tumor type in men and women combined this year the National Cancer Institute estimates there will be 290 560 new cases in the United States and 43 780 deaths 1 Triple Negative Breast Cancer ( lacks three typical surface markers of breast cancer estrogen receptor ( progesterone receptor ( and human epidermal growth factor receptor 2 (HER 2 which are common targets for endocrine or drug therapy, severely limiting TNBC treatment options 40 of TNBC patients will die within five years of diagnosis 2 Additionally, it has heightened risk for metastasis after neoadjuvant chemotherapy …

Identifying Deep Brain Photoreceptors In The Larval Zebrafish Optic Tectum, Emalie A. Christensen, Allison G. Pickens, Sarah Y. Jarrett, Maurice Hunt, Arminda Suli

Library/Life Sciences Undergraduate Poster Competition 2023

Deep brain photoreceptors (DBPs) are light sensing neurons present in mammals and non-mammalian vertebrates. In non-mammalian vertebrates, studies have shown DBP involvement in various time and light dependent behaviors including circadian rhythm, phototaxis, and seasonal reproduction. In adult teleosts, DBPs are present throughout the brain, including the optic tectum (OT). While their approximate location in teleosts is known, DBP’s function is relatively unknown. In this study, we focused on DBPs present in the larval zebrafish OT, a multilaminated midbrain structure responsible for multisensory integration. Single-cell RNA sequencing of the larval zebrafish OT showed the presence of several opsins. We focused …

Effects Of Post-Translational Histone Modifications On Transcription Rate, Aaron Bohn, Sarah Hodson, Sarah Ricks, David Bates Ph.D, Steven M. Johnson Ph.D

Library/Life Sciences Undergraduate Poster Competition 2023

The structural organization of DNA in eukaryotic cells is greatly implicated in the regulation of gene expression and thus cellular properties and behavior. At the most fundamental unit of this organization, ~147 bp of DNA wraps 1.7 times around a histone octamer core, forming a collective unit called the nucleosome. The positioning and occupancy of these nucleosomes around the promoter elements of genes is known to be a strong regulator of transcription in eukaryotic nuclei, and post-translational modifications (PTM’s) to the protruding N-terminal tails of histone proteins are known to influence chromatin structure and thus gene expression; however, relatively little …

Genetic Characteristics Required In Dairy And Beef Cattle For Temperate Grazing Systems, F. Buckley, C. Holmes, M. G. Keane

IGC Proceedings (1997-2023)

Key points

1. Only about 10% of the world’s milk is produced from grazing systems. Consequently the majority of dairy cattle have not been selected under grazing, nor on seasonal systems. This is not true for beef cattle, for which the majority, especially the dams, are managed under seasonal grazing systems.

2. In grazing systems daily feed intake is limited to lower levels than are achievable on concentrate plus conserved forage rations. Consequently, cows most suited to grazing environments are likely to have a lower genetic potential for milk production than cows selected in high concentrate systems, to minimise their relative energy …

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Paternal Ages And Genetic Diseases And Congenital Anomalies, Neda Hamood

The Pegasus Review: UCF Undergraduate Research Journal

he purpose of this research is to investigate the link between Advanced Paternal Ages (APA) (i.e., APA ≥ 35 years and APA ≥ 50 years) and genetic diseases and congenital anomalies. Currently, the relationship between both APA and genetic diseases and congenital anomalies remains unclear. There is room for improvement, however, to investigate systematically the relationship between specific congenital anomalies in newborns and APA. More recently, the link between APA (as opposed to existing studies analyzing Advanced Maternal Age alone) and genetic diseases has been recognized by researchers, epidemiologists, and various health experts. Thus, this study serves to examine the …

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 …

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

Honors Theses and Capstones

No abstract provided.

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 …

Utilizing Markov Chains To Estimate Allele Progression Through Generations, Ronit Gandhi

Honors Theses

All populations display patterns in allele frequencies over time. Some alleles cease to exist, while some grow to become the norm. These frequencies can shift or stay constant based on the conditions the population lives in. If in Hardy-Weinberg equilibrium, the allele frequencies stay constant. Most populations, however, have bias from environmental factors, sexual preferences, other organisms, etc. We propose a stochastic Markov chain model to study allele progression across generations. In such a model, the allele frequencies in the next generation depend only on the frequencies in the current one.

We use this model to track a recessive allele …

Multi-Ancestry Genome-Wide Association Analyses Improve Resolution Of Genes And Pathways Influencing Lung Function And Chronic Obstructive Pulmonary Disease Risk, Nick Shrine, Abril G. Izquierdo, Jing Chen, Richard Packer, Robert J. Hall, Anna L. Guyatt, Chiara Batini, Rebecca J. Thompson, Chandan Puvuluri, Vidhi Malik, Brian D. Hobbs, Matthew Moll, Wonji Kim, Ruth Tal-Singer, Per Bakke, Katherine A. Fawcett, Catherine John, Kayesha Coley, Noemi Nicole Piga, Sinjini Sikdar, Martin D. Tobin, Et Al.

Mathematics & Statistics Faculty Publications

Lung-function impairment underlies chronic obstructive pulmonary disease (COPD) and predicts mortality. In the largest multi-ancestry genome-wide association meta-analysis of lung function to date, comprising 580,869 participants, we identified 1,020 independent association signals implicating 559 genes supported by ≥2 criteria from a systematic variant-to-gene mapping framework. These genes were enriched in 29 pathways. Individual variants showed heterogeneity across ancestries, age and smoking groups, and collectively as a genetic risk score showed strong association with COPD across ancestry groups. We undertook phenome-wide association studies for selected associated variants as well as trait and pathway-specific genetic risk scores to infer possible consequences of …

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 …

Dfhic: A Dilated Full Convolution Model To Enhance The Resolution Of Hi-C Data, Bin Wang, Kun Liu, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation: Hi-C technology has been the most widely used chromosome conformation capture(3C) experiment that measures the frequency of all paired interactions in the entire genome, which is a powerful tool for studying the 3D structure of the genome. The fineness of the constructed genome structure depends on the resolution of Hi-C data. However, due to the fact that high-resolution Hi-C data require deep sequencing and thus high experimental cost, most available Hi-C data are in low-resolution. Hence, it is essential to enhance the quality of Hi-C data by developing the effective computational methods.

Results: In this work, we propose …

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 …

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 …

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 …