Single Cell Pharmacodynamic Modeling Of Cancer Cell Lines, Arnab Mutsuddy

All Dissertations

Cancer is one of the leading causes of disease related death worldwide. Since the discovery of the genomic origins of cancer, targeted therapy has been developed towards specific mutations implicated for oncogenic transformation. However, current standard-of-care for mapping cancer patients to efficacious drug combination is often inadequate. The pathophysiology of tumor progression relies on the dysregulation of biomolecular pathways of which the topology and the dynamics challenge prognosis. Moreover, the overall genomic instability involved in disease states and the resulting inter-patient as well as intra-tumoral heterogeneity challenge rationalization of therapy and clinical decision-making. It highlights the need for the use …

Investigating The Potential Of A Cell-Based Gene Editing Therapy For Inherited Metabolic Liver Disease, Ilayda Ates

All Dissertations

Inherited metabolic diseases (IMDs) affecting the liver are relatively rare but collectively have a prevalence of 1 in 800 live births. These diseases result from autosomal recessive single-gene mutations, leading to organ dysfunction and potentially fatal consequences if left untreated. One potential therapeutic strategy for IMDs of the liver involves using CRISPR-Cas9-induced loss of function mutations. However, translating this approach into the clinic is limited by the need for safe and effective CRISPR delivery methods. Adeno-associated viral vectors (AAVs), commonly used for CRISPR delivery, are associated with significant safety and efficacy concerns, including risks for immunogenicity, off-target mutagenesis, and genotoxicity …

A Systems Genetics Approach To Drosophila Melanogaster Models Of Rare And Common Neurodevelopmental Disorders, Rebecca Macpherson

All Dissertations

Fetal Alcohol Spectrum Disorders are a group of disorders resulting from prenatal alcohol exposure, presenting with neurodevelopmental and facial abnormalities of varying severity. SSRIDDs and CdLS are rare disorders of chromatin modification, resulting in patients with a wide range of craniofacial, digit and/or neurodevelopmental abnormalities. All of these disorders have a wide range of clinical phenotypes and disease severity, yet the role of potential genetic modifiers and gene-gene or gene-environment interactions in disease pathogenesis is largely unknown and cannot be studied in humans. Insufficient numbers of patients with a single rare disorder prevent investigation of genetic factors beyond the focal …

Assesment Of Structure, Function, And Microevolutionary Dynamics Of Extrachromosomal Circular Dna In Chinese Hamster Ovary Cells, Dylan Chitwood

All Dissertations

Chinese hamster ovary (CHO) cell lines are among the most popular expression hosts used in biopharmaceutical manufacturing due to relative ease of culture, capacity to perform human-like post-translational modifications, and non-susceptibility to viruses. However, the intrinsic plasticity of the CHO genome can lead to undesired genetic rearrangements, phenotypic shifts, reduced product quality, and early culture termination that prevents continuous biomanufacturing. A characteristic of plastic and unstable genomes that is poorly understood in CHO cells is extrachromosomal circular DNA (eccDNA). EccDNAs are focal amplifications of the genome that reside in the extranuclear space. These plasmid-like entities are structurally complex and are …

Diagnosis Of Urinary Tract Infections And Rapid Molecular Characterization Of Antibiotic Resistance, Mohammed Harris

All Dissertations

Urinary tract infections (UTIs) are one of the most common infectious clinical entities in both community and hospital settings. They have a broad range of clinical severity yet inflict large epidemiological burden of morbidity and mortality on patients and the healthcare system with billions of dollars in cost of treatment. Understanding what methods are optimal for diagnosing UTIs are critical to mitigate the marked impact and cost of these infections.

Chapter 1 and 2 in this work surveys the broad array of diagnostic modalities for UTIs and highlights their advantages and limitations in the context of the current standard of …

A Multi-Pronged Investigation To Identify Genes Affecting The Autoregulation Of Nodulation: Lasercapture Microdissection And The Barely Any Meristem Gene Family In Medicago Truncatula, Jacklyn Thomas

All Dissertations

The unique evolutionary adaptation of legumes for nitrogen-fixing symbiosis leading to nodulation is tightly regulated by the host plant. One pathway negatively regulates the number of nodules formed in response to the metabolic status of the shoot (carbon) and root (nitrogen); this long-distance systemic regulation is the autoregulation of nodulation (AON) pathway. AON is a root to shoot pathway that allows the plant to limit the number of nodules formed on roots. Central to the receptor complex in the shoots is a leucine-rich-repeat receptor-like kinase (LRR-RLK) called MtSUNN mutation of which results in plants with too many nodules. SUNN …

Methyltransferase, Glucose Adaptation, And Import Complex In Trypanosoma Brucei, Emily Knight

All Dissertations

Trypanosoma brucei is a kinetoplastid parasite responsible for human African trypanosomiasis (HAT) and nagana, a livestock wasting disease, which both endemic to sub-Saharan Africa. Unique to kinetoplastids are the specialized peroxisomes, named glycosomes, which compartmentalize the first several steps of glycolysis and gluconeogenesis, nucleotide sugar biosynthesis, and many other metabolic processes. Kinetoplastids are unique in that they have a single mitochondrion. In this work, I present the first study into SET domain proteins in any kinetoplastid parasites. We have characterized a predicted SET domain protein, TbSETD3, that localizes to the mitochondrion and a depletion of the protein results in growth …

Acetate Metabolism In The Fungal Pathogen Cryptococcus Neoformans, Oly Ahmed

All Dissertations

Cryptococcus neoformans is an environmental basidiomycetous fungus with a worldwide distribution and a wide range of habitats. Inhalation of the desiccated yeasts or spores of C. neoformans often leads to opportunistic pulmonary infections in immunocompromised individuals, and in severe cases causes lethal meningitis following hematogenous dissemination. During infection, depending on the tissue and disease state, the invading fungi experience a range of nutrient microenvironments within the host body. As a result, rapid metabolic adaptations geared towards efficient utilization of carbon sources alternative to glucose become one of the prime determinants of survival and growth for the pathogen. Incidentally, cryptococcal infection …

Large Genomes Assembly Using Mapreduce Framework, Yuehua Zhang

All Dissertations

Knowing the genome sequence of an organism is the essential step toward understanding its genomic and genetic characteristics. Currently, whole genome shotgun (WGS) sequencing is the most widely used genome sequencing technique to determine the entire DNA sequence of an organism. Recent advances in next-generation sequencing (NGS) techniques have enabled biologists to generate large DNA sequences in a high-throughput and low-cost way. However, the assembly of NGS reads faces significant challenges due to short reads and an enormously high volume of data. Despite recent progress in genome assembly, current NGS assemblers cannot generate high-quality results or efficiently handle large genomes …

Data-Driven Biomarker Panel Discovery In Ovarian Cancer Using Heterogenous Data Fusion On Exosomal And Non-Exosomal Microrna Expression Data, Paritra Mandal

All Dissertations

Ovarian cancer (OC) is an aggressive gynecological cancer and is currently the 5th leading cause of deaths due to cancer in women. High mortality rates are attributable to the vague pathogenesis and asymptomatic nature of the early stages. The development of a liquid biopsy for routine OC screening could help identify the disease at an earlier stage, making treatments more likely to be effective thereby increasing survival rates. Exosomes, small (~100nm) extracellular vesicles present in body fluids, have been shown to contain cancer-progression, onset, and related factors, making them good candidates for use in liquid biopsies. However, to date, only …

Deciphering Medicago Truncatula Nodulation Using Time-Series Transcriptomic Data At Multiple Levels Of Resolution: Organ, Tissue, And Single-Cell, Yueyao Gao

All Dissertations

Use of chemical nitrogen fertilizers has environmental repercussions such as global warming, soil contamination, and aquatic eutrophication. Legumes form a symbiotic association with nitrogen-fixing bacteria (rhizobia sp.) to obtain atmospheric nitrogen through the formation of a specialized root structure called a nodule. Understanding the transcriptional reprogramming during nodulation is a powerful approach to decipher the genetic control of nodulation, with the goal of engineering nitrogen-fixing symbiosis into non-leguminous crops. This dissertation focuses on the analytics of bulk, tissue-specific, and single-cell RNA-seq technologies and how I utilized them to discover a collection of genes to aid in deciphering nodulation mechanisms in …

Modeling Electrostatics In Molecular Biology And Its Relevance With Molecular Mechanisms Of Diseases, Mahesh Koirala

All Dissertations

Electrostatics plays an essential role in molecular biology. Modeling electrostatics in molecular biology is complicated due to the water phase, mobile ions, and irregularly shaped inhomogeneous biological macromolecules. This dissertation presents the popular DelPhi package that solves PBE and delivers the electrostatic potential distribution of biomolecules. We used the newly developed DelPhiForce steered Molecular Dynamics (DFMD) approach to model the binding of barstar to barnase and demonstrated that the first-principles method could also model the binding. This dissertation also reflects the use of existing computational approaches to model the effects of Single Amino Acid Variations (SAVs) to reveal molecular mechanisms …

Heat Stress Response And Excystation In Entamoeba Histolytica, Irem Bastuzel

All Dissertations

Entamoeba histolytica is a water- and food-borne intestinal protozoan parasite that causes amoebiasis and liver abscess and is responsible for symptomatic disease in approximately 100 million people each year leading to ~ 100,000 deaths. The most common disease transmission follows the oral-fecal route, but it can also be transmitted by mechanical vectors such as animals carrying the amoeba from contaminated sources to water systems. In rare cases, disease transmission has been recorded in some patients in which men-to-men sexual practices were preferred.

The life cycle of E. histolytica starts through ingestion of infectious cysts, which are non-dividing, quadri-nucleated structures surrounded …

Clinical And Molecular Characterization Of Key Features Of Phelan-Mcdermid Syndrome And Potential Approaches To Clinical Trials, Bridgette Moffitt

All Dissertations

Phelan-McDermid Syndrome (PMS) is a rare neurodevelopmental disorder that involves chromosomal abnormalities on 22q13.3 and pathogenic variants with the SHANK3 gene. SHANK3 encodes for a critical scaffolding protein that is important in post-synaptic density, function, and maintenance of excitatory synapses. Haploinsufficiency of SHANK3 is considered the major cause of the neurological phenotype of PMS. These studies focused on further characterizing the neurologic phenotype of sleep disturbances in individuals with PMS.

Sleep disturbances are a common feature of PMS, however there is little research available on the subject matter. We reviewed the literature on sleep disturbances and used the Phelan-McDermid Syndrome …

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 …

Characterization Of Mef2c-Related Disorders: Genotype, Phenotype, And Gene Pathway Dysregulation, Jessica Ann Cooley Coleman

All Dissertations

MEF2C­-related disorders are characterized by intellectual disability, developmental delay, lack of speech, seizures, stereotypic movements, hypotonia, and brain abnormalities and are caused by pathogenic alterations involving the MEF2C gene. Despite published cases, MEF2C­-related disorders are difficult to recognize clinically. These studies sought to further characterize MEF2C­-related disorders by investigating the genotypes, phenotypes, and gene functions (or dysfunctions) associated with the disorder.

Tremors have been reported in some patients with MEF2C­-related disorders, but the concept of tremors has been complicated by vague definitions and numerous categorization methods. We performed a concept analysis following the Walker and Avant …

Effects Of Continuous In Situ Low-Dose Ionizing Radiation On Microorganisms, Molly E. Wintenberg

All Dissertations

Precise detection and monitoring of nuclear fuel cycle, enrichment, and weapon development activities are critical for supporting warfighter preparation in chemical, biological, radiological, nuclear, and explosives (CBRNE) operations, clandestine activities, and nuclear compliance. A biological sensing system could serve as an alternative to traditional detection methods by using organic material naturally present in the environment to discreetly detect residual trace nuclear material. Microorganisms provide an optimal platform for an alternative sensing system; however, their response to low levels of ionizing radiation is poorly characterized. Combining the power of next-generation sequencing and transcriptomic analysis, this dissertation takes an approach to obtain …

Identification Of Genetic Factors Underlying Megaesophagus And Startle Disease In Dogs, Sarah M. Bell

All Dissertations

Dogs provide an excellent model for human hereditary disease research; thus, the development of canine genomic tools has been prioritized in recent years. Today, SNP arrays, multiple genome assemblies, and multi-breed reference panels containing whole genome resequencing (WGS) data from hundreds of canids are available to facilitate genome-wide genotyping in the dog. Herein, a variety of genome-wide techniques are employed to identify the genetic factors underlying congenital idiopathic megaesophagus (CIM) in two breeds, German shepherd dogs (GSDs) and Great Danes, and startle disease in Spanish greyhounds.

CIM is a complex canine esophageal motility disorder characterized by ineffective peristalsis and esophageal …

Identification Of Biomarker Systems Of Autism Spectrum Disorder And Uterine Cancer, Allison Hickman

All Dissertations

Complex diseases and disorders pose a challenge to scientists due to their variable and often inconsistent genetic and environmental underpinnings across affected individuals. Because of this variability, large condition-specific datasets and corresponding analytical tools and approaches are being curated as resources to investigate potential genetic trends in complex diseases and disorders. In this Dissertation, I used DNA- and RNA-based resources to discover polygenic biosignatures associated with Autism Spectrum Disorder (ASD) or uterine cancer. To explore the intersection of small-effect common DNA variants and regulation in ASD, I discovered and analyzed trends in allelic associations at eQTLs within ASD-affected individuals. Association …

Genetic And Mirna Transcriptomic Analysis Of Autoregulation Of Nodulation Signaling In Medicago Truncatula, Diptee Chauligain

All Dissertations

Legumes can source nitrogen from the air through biological nitrogen fixation inside root nodules formed in a symbiosis with rhizobia. A complex root-to-shoot-to-root signaling pathway called Autoregulation of Nodulation (AON) controls the number of nodules formed depending on the plant’s nitrogen requirements. In Medicago truncatula, the MtSUNN receptor complex in the shoot binds to the root-generated AON signals, peptides called MtCLEs, resulting in downregulation of miR2111 expression in the shoot, with the effect of decreased transport of miR2111 to the roots. Decreased miR2111 levels in the roots then cause an increase in transcript levels of the miR2111 targets MtTML1 …

Development Of New Bioinformatic Approaches For Human Genetic Studies, Jose Andres Guevara Coto

All Dissertations

The development of bioinformatics methods for human genetic studies utilizes the vast amount of data to generate new valuable information. Machine learning and statistical coupling analysis can be used in the study of human diseases. These diseases include intellectual disabilities (ID), prevalent in 1-3% of the population and caused primarily by genetics. Although many cases of ID are caused by mutations in protein-coding genes, the possible involvement of long non-coding RNAs (lncRNAs) in ID due to their role in gene expression regulation, has been explored. In this study, we used machine learning to develop a new expression-based model trained using …

The Role The N-Terminal Domain Plays In Spidroin Assembly, Krystal Audrey Cadle

All Dissertations

One of the most interesting biomaterials known to man is spider silk. These fibers, composed primarily of protein, show beneficial mechanical and biological properties that have many uses in medical and industrial fields. Spider silk proteins (spidroins) are composed of three core components that consists of a C-terminal domain (CTD), repeat domain (R), and N-terminal domain (NTD). The NTD and CTD are highly conserved and are believed to form “multimeric strands” that make up spider silk. Although it is known that the NTD undergoes a conformational change that results in stable homodimer formation at acidic pH , the way in …

Exploring The Interface Of Genetics, Genomics, And Older Adults, Scott Emory Moore

All Dissertations

This dissertation addresses the interface of genetics, genomics, and older adults through a collection of three manuscripts that examine genetic and genomic testing and decision-making across age groups. The dissertation offers evaluations of a new lens for decision-making in genetics and genomics, a contextualization of the differences and similarities of perceptions and beliefs that exist among age groups engaging in direct-to-consumer personal genetic testing (DTC PGT), an identification of two factors that influence the decision to engage in DTC PGT, and an expansion of the current applications of Protection Motivation Theory to include disclosure, finance, and advance directive-management behaviors related …

Tackling Adverse Environment—Molecular Mechanism Of Plant Stress Response And Biotechnology Tool Development, Ning Yuan

All Dissertations

Abiotic and biotic stresses such as drought, salt, nutrition starvation, and pathogen infection are major factors threatening our agricultural production. With the rapidly increasing population and limited arable land area, genetic engineering of crops for new products with more stable and higher yield than conventional cultivars under adverse environment provides a powerful new tool for use in developing novel GMOs (Genetically Modified Organisms) to feed the large population in the immediate future. To develop novel GMOs with enhanced performance under adverse conditions, we need first to understand molecular mechanisms underlying plant stress response. To better understand how signaling transduction pathway …

Microrna-Mediated Plant Development And Response To Environmental Stress In Perennial Grasses, Shuangrong Yuan

All Dissertations

World population will pass nine billion by 2050, while the agricultural land area will not increase dramatically in the coming decades. To meet the ever-increasing food demand, genetically engineered crops have been rapidly adopted for crop productivity. MicroRNAs have become increasingly attractive as targets in crop genetic modification due to their regulatory role in fine-tuning many essential biological processes. My research explores the potentials of microRNA528 (miR528) and miR396 for use in genetic modifications of the important agronomic traits of plant development, abiotic stress response, and/or flowering time control in an economically and environmentally important perennial monocot species, creeping bentgrass …

Phosphotransacetylase And Xylulose 5-Phosphate/Fructose 6-Phosphate Phosphoketolase: Two Eukaryotic Partners Of Acetate Kinase, Tonya Taylor

All Dissertations

Although acetate is a predominant metabolite produced by many eukaryotic microbes, far less attention has been given to acetate metabolism in eukaryotes than in bacteria and archaea. Acetate kinase (Ack), which catalyzes the reversible phosphorylation of acetate from ATP, is a key enzyme in bacterial acetate metabolism. Ack primarily partners with phosphotransacetylase (Pta), which catalyzes the generation of acetyl phosphate from acetyl-CoA, but can also partner with xylulose 5-phosphate/fructose 6-phosphate phosphoketolase (Xfp), which produces acetyl phosphate from either xylulose 5-phosphate or fructose 6-phosphate. The Ack-Pta pathway, found primarily in bacteria, is also present in lower eukaryotes such as the green …

Genetic Dissection Of Neuromuscular Diseases Affecting Domestic Dogs, Caitlin Rinz

All Dissertations

The domestic dog, Canis familiaris, has a unique population structure that lends itself to the study of hereditary diseases. Purebred dogs populations are genetically isolated and as a result are affected by more than 400 naturally occurring diseases, many of which have human counterparts. In the last 15 years, dogs have emerged as a model for the study of human hereditary diseases, fueling the development of resources including a 7.6X coverage reference genome and single nucleotide polymorphism (SNP) genotyping arrays.

Congenital myasthenic syndrome (CMS) is a neuromuscular disorder of both humans and dogs in which transmission across the neuromuscular …

Conserved Noncoding Sequences Regulate Steady-State Mrna Levels In Arabidopsis Thaliana, Jacob Spangler

All Dissertations

Arabidopsis thaliana has undergone three whole genome duplications within its ancestry, and these events have dramatically affected its gene complement. Of the most recent whole genome duplication events (&alpha event), there remain 11,452 conserved noncoding sequences (CNSs) that have been retained proximal to &alpha duplicate gene pairs. As functional DNA elements are expected to diverge in sequence at a slower rate than nonfunctional DNA elements, the retained CNSs likely encode gene regulatory function. Within this dissertation I provide evidence for the regulatory role of CNSs within Arabidopsis thaliana. Using a collection of over 5,000 microarray RNA expression profiling datasets, I …

Molecular Genetics Of Nodule Number Regulation: Cloning, Characterization And Functional Studies Of The Root Determined Nodulator1 (Rdn1) Gene In Medicago Truncatula, Tessema Kassaw

All Dissertations

Nitrogen is critical to life. However, the majority of nitrogen on earth (in the atmosphere) is inert and unavailable to nearly all organisms. Metabolically diverse prokaryotes are the only organisms capable of fixing atmospheric nitrogen; rhizobia set up a symbiosis with legume plants allowing the plants to benefit from this ability. Since nodulation and the subsequent nitrogen fixation processes are energy intensive, the host plant must balance hosting of the rhizobia by limiting the number of nodules it forms through a mechanism called Autoregulation of Nodulation (AON). My study of mutants in the model legume Medicago truncatula defective in AON …

Family Cancer History And Pedigrees As A Public Health Intervention For Promoting Health And Preventing Prostate Cancer In African American Men, Holisa Wharton

All Dissertations

ABSTRACT
Prostate cancer is the most common cancer diagnosed in men and the second leading cause of cancer death among men in the United States. African-American men have substantially higher prostate cancer incidence and mortality than European-American men. It is unclear whether this incidence is due to acquired DNA changes (sporadic cancer) or if germline Mendelian genetics/genomics (inherited cancer) is the source of this health disparity. To explore this cause, the focus of this dissertation paper is family health history and hereditary prostate cancer. A family history tool is the most commonly used predictive instrument for hereditary prostate cancer. The …