Doctor of Philosophy, Miami University, 2016, Biology

The ocular lens is an excellent model to study cell signaling, cell survival and cell differentiation. The lens is comprised of only two cell types: proliferative lens epithelial cells and terminally differentiated lens fiber cells. The lens fiber differentiation process involves specific changes in gene expression between the two cell types. However, a comprehensive understanding of gene expression changes during lens fiber differentiation remains incomplete. Furthermore, despite the wealth of knowledge of transcription factors involved in lens cell proliferation, survival and lens fiber differentiation, little information exists about the role of DNA methylation and miRNAs in these processes. This study presents the first application of RNA-seq to provide a comprehensive view of both the relative abundance and differential expression of mRNAs and long intergenic non-coding RNAs from lens epithelial cells and lens fiber cells. We also investigated the role of DNA methylation in lens development. We found that while Dnmt1 inactivation at the lens placode stage led to lens DNA hypomethylation and severe lens epithelial apoptosis, lens fiber cell differentiation remained largely unaffected. The simultaneous deletion of phosphatase and tensin homolog (Pten) elevated the level of phosphorylated AKT and rescued many of the morphological defects and cell death in DNMT1- deficient lenses. With a different Cre driver (MLR10) we demonstrated that a small number of lens epithelial cells escaped Dnmt1-deletion and over-proliferated to compensate for the loss of Dnmt1-deleted cells, suggesting that lens epithelium possess a substantial capacity for self- renewal. Inactivation of both Dnmt3a and Dnmt3b by either the Le-Cre or MLR10-Cre transgene did not result in any obvious lens phenotype prior to 10 months of age, indicating that de novo DNA methylation, at least as mediated by both DNMT3A and DNMT3B, is dispensable for normal lens development. Our comparative miRNA-Seq data a (open full item for complete abstract)

Committee: Michael Robinson (Advisor) Subjects: Biology; Biomedical Research; Genetics; Zoology

Doctor of Philosophy (Ph.D.), University of Dayton, 2011, Biology

1: Silver nanoparticles (Ag Np's) have an interesting surface chemistry and unique plasmonic properties. They are used in a wide variety of applications ranging from consumer products like socks, medical dressing, computer chips and it is also shown to have antimicrobial, anti bacterial activity and wound healing. Ag Np toxicity studies have been limited to date which needs to be critically addressed due to its wide applications. Mouse embryonic stem (MES) cells represent a unique cell population with the ability to undergo both self renewal and differentiation. They exhibit very stringent and tightly regulated mechanisms to circumvent DNA damage and stress response. We used 10 nm coated (polysaccharide) and uncoated Ag Np's to test its toxic effects on MES cells. MES cells and embryoid bodies (EB's) were treated with two concentrations of Ag Np's: 5 µg/ml and 50 ug/ml and exposed for 24, 48 and 72 hours. Increased cell death, ROS production and loss of mitochondrial membrane potential and alkaline phosphatase (AP) occur in a time and a concentration dependant manner. Due to increased cell death, there is a progressive increase in Annexin V (apoptosis) and Propidium Iodide (PI) staining (necrosis). Oct4 and Nanog undergo ubiquitination and dephosphorylation post-translational modifications in MES cells thereby altering gene expression of pluripotency factors and differentiation of EB's into all the three embryonic germ layers with specific growth factors were also inhibited after Ag Np exposure. Flow cytometry analysis revealed Ag Np's treated cells had altered cell cycle phases correlating with altered self renewal capacity. Our results suggest that Ag Np's effect MES cell self renewal, pluripotency and differentiation and serves as a perfect model system for studying toxicity induced by engineered Ag Np's. ABSTRACT 2: The reprogramming of fibroblasts to pluripotent stem cells and the direct conversion of fibroblasts to functional neurons has been successfully man (open full item for complete abstract)

Committee: Hong Yiling (Advisor); Shirley J. Wright (Committee Member); Mark G. Nielsen (Committee Member); Tsonis A. Panagiotis (Committee Member); Shawn M. Swavey (Committee Member) Subjects: Biology

PhD, University of Cincinnati, 2020, Medicine: Molecular Genetics, Biochemistry, and Microbiology

The goal of this dissertation is to improve our understanding of two important processes in carcinogenesis: First, the resistance mechanisms to tyrosine kinase inhibitors in glioblastoma (GBM). Second, the mechanisms involved in the metastatic spread of non-small cell lung cancer (NSCLC) to the brain. Malignant gliomas have a poor prognosis, as recurrence remains nearly inevitable despite aggressive treatment with a median survival time of 12-15 months. Primary GBM usually displays amplification or mutation of at least one receptor tyrosine kinase, most often the epidermal growth factor receptor (EGFR). Targeting EGFR for inhibition often provides an initial tumor response in patients, but recurrence is a main limitation of these therapies because secondary mutations emerge that lead to drug resistance. In this work, we identified a receptor tyrosine kinase, proto-oncogene ROS1 fusion, that drives the resistance to therapy and leads to tumorigenesis in GBM. In parallel, the aggressive metastatic phenotype is one of the hallmarks of recurrent tumors, and its estimated that 90% of all cancer deaths arise from the metastatic spread of primary tumors. Of all the processes involved in carcinogenesis, local invasion and the formation of metastases are clinically the most relevant, but the least well understood at the molecular level. This work also provides evidence for the use of circulating tumor cells as a biomarker for the metastatic spread of cancer, specifically in lung cancer. To uncover the molecular changes that govern the transition from a primary lung tumor to a secondary metastasis and specifically the mechanisms by which circulating tumor cells (CTCs) survive in circulation, we carried out whole genome sequencing of normal lung tissue, primary tumors, and the corresponding brain metastases from five patients with progressive metastatic NSCLC. We also isolated CTCs from patients with metastatic cancer and subjected them to whole genome amplification and Sanger (open full item for complete abstract)

Committee: Peter Stambrook Ph.D. (Committee Chair); El Mustapha Bahassi Ph.D. (Committee Member); Pankaj Desai Ph.D. (Committee Member); Rhett Kovall Ph.D. (Committee Member); William Miller Ph.D. (Committee Member) Subjects: Biochemistry

Master of Science (MS), Wright State University, 2018, Biochemistry and Molecular Biology

Ras proteins were the first human oncogenes discovered. Although Ras has been found to be the most frequently mutated oncogene, there are currently no anti-Ras-specific drugs available in the clinic. Ras is responsible for initiating cellular pathways that include proliferation, survival, and apoptosis. There are three ubiquitously expressed Ras isoforms in mammalian cells: H-, N-, and K-Ras. Interaction with the plasma membrane is required for Ras biological activity. When Ras interaction with the plasma membrane is blocked, Ras activity is inhibited. Two compounds (from Dr. Ketcha, WSU Chemistry Department) were tested and shown to dissociate K-Ras, but not H-Ras from the plasma membrane. The molecular mechanism was found to be through phosphorylation of K-Ras Ser181. Furthermore, these compounds block signal output of K-Ras, but not H-Ras, and inhibit the growth of K-Ras-driven non-small cell lung cancer cells. Further characterization of these compounds could lead to the development of anti-K-Ras drugs.

Committee: Kwang-Jin Cho Ph.D. (Advisor); Daniel Ketcha Ph.D. (Committee Member); Weiwen Long Ph.D. (Committee Member); Michael Markey Ph.D. (Committee Member); Hongmei Ren Ph.D. (Committee Member) Subjects: Biochemistry; Molecular Biology

Master of Sciences, Case Western Reserve University, 2017, Systems Biology and Bioinformatics

In this study, we have explored the challenges present in piRNA functional annotation and regulation. We outline here the usage of genomic and transcriptomic references to define the properties and biogenesis of piRNA. We further examine possible methods for piRNA post-transcriptional regulation. This pipeline will help identify and classify both previously discovered and novel piRNA to help scientists define and research piRNA.

Committee: Gurkan Bebek Ph.D (Advisor); Yu Jennifer MD, Ph.D (Committee Member); Ahmad Khalil Ph.D (Committee Member) Subjects: Bioinformatics

Doctor of Philosophy, The Ohio State University, 2014, Computer Science and Engineering

The increasing popularity of handheld devices, such as smartphones and tablets, has made the demand for high-data-rate wireless access more urgent than ever. Due to the scarcity of wireless spectrum and the limitation of physical size of handheld devices, Small-Cell based solutions are being widely adopted. The concept of small cells encompasses WiFi access points, femtocells and microcells, etc. Small cells can be categorized as Managed and Unmanaged. While managed small cells allow access to all users, it is cost prohibitive for large-scale blanket deployment. On the other hand, unmanaged small cells are cost-efficient to expand, but they only provide service to dedicated users. Therefore, the issues of budgeted deployment and resource allocation for managed small cells and access acquisition of unmanaged small cells are critical and challenging to study. This dissertation studies those problems and makes the following contributions: 1. Sparse Deployment of Large Scale Managed Small Cell Networks. This dissertation first examines the deployment problem in large scale managed small cell networks. It presents a new metric, called Contact Opportunity, as a characterization of roadside WiFi networks. Contact opportunity measures the fraction of distance or time that a mobile user is in contact with some APs when moving on a certain trajectory. Our objective is to find a deployment that ensures a required level of contact opportunity with the minimum cost. This is the first work that addresses the challenges in achieving a sparse wireless infrastructure that provides QoS assurance to mobile users in the face of uncertainty. 2. Resource Management in Managed Dense Small Cell Networks. Fast expansion of small cells makes the problem of resource management in urban dense networks challenging. To achieve both high throughput and fairness among users, the second part of this dissertation studies two dynamic resource allocation problems: 1) Achieve max-min fairness (open full item for complete abstract)

Committee: Prasun Sinha Prof. (Advisor); Dong Xuan Prof. (Committee Member); Peng Chunyi Prof. (Committee Member) Subjects: Computer Science

Doctor of Philosophy, The Ohio State University, 2013, Biophysics

Myocardial infarction (MI), pulmonary hypertension (PH), and cardiomyopathy belong to a class of diseases collectively described as cardiovascular disease, the leading cause of death worldwide. Assessment of the left and right ventricular (LV, RV) structural and functional changes concomitant with the aforementioned pathologies is vital, particularly when evaluating the efficacy of a potential cardiac therapy. High-field in vivo cardiac magnetic resonance imaging (CMRI) provides high-resolution anatomical images without use of ionizing radiation and is thus uniquely suited to accurately assess the LV and RV. This dissertation reports the use of CMRI at 9.4T in precisely monitoring the LV and RV structural and functional adaptations in murine models of heart disease, specifically, MI, PH, and diabetic cardiomyopathy. As the first application, CMRI was utilized to quantify LV structure and function in an ischemia-reperfusion (IR) model of rat MI following treatment with mesenchymal stem cells (MSC) and hyperbaric oxygen (Ox). MRI results were compared to data acquired using histology and echocardiography. Although echocardiography was able to establish significant improvements in cardiac structure and function following MSC, Ox, and MSC+Ox therapies, CMRI revealed little improvement in LV structure or function, relative to MI animals. CMRI was also used to assess the LV in rat model of MI following human induced pluripotent stem (hiPS) cell-derived cardiomyocyte therapy, in direct comparison to human MSC (hMSC) therapy. MI was induced by permanent ligation of the left anterior descending (LAD) coronary artery. CMRI structural and functional data were compared to echocardiographic findings. While CMRI revealed significant improvements, relative to MI, in LV structure and function for the hiPS group, but not the hMSC group, echocardiography revealed little difference between the cell-treated groups. The effects of hypoxia-induced pulmonary hypertension (PH) on LV (open full item for complete abstract)

Committee: Periannan Kuppusamy Ph.D., M.D. (h.c.), D. Litt. (Advisor); Govindasamy Ilangovan Ph.D. (Committee Member); Kimerly Powell Ph.D. (Committee Member); Mahmood Khan Ph.D. (Committee Member) Subjects: Biophysics