Theses and Dissertations from UMD
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New submissions to the thesis/dissertation collections are added automatically as they are received from the Graduate School. Currently, the Graduate School deposits all theses and dissertations from a given semester after the official graduation date. This means that there may be up to a 4 month delay in the appearance of a give thesis/dissertation in DRUM
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Item Understanding Allosteric Communication in Biological Systems using Molecular Dynamics Simulations(2024) Samanta, Riya; Matysiak, Silvina; Biophysics (BIPH); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Allostery is critical to survival in living organisms due to its biological relevance in signal transduction, metabolism, and drug discovery. However, the molecular details of this phenomenon remain unclear. In this thesis, I present my work on two allosteric protein systems, each representative of structure-based (E. coli Biotin Protein Ligase) and dynamics-based (B. taurus S100B) allostery. I examined the structural and dynamic features of the proteins and associated variants subjected to various allosteric triggers (ligand/salt/mutations) to study how external/internal perturbations transmit across large distances using Molecular Dyanmic simulations in conjunction with the experiments carried out by our collaborators. Additionally, I carried out Network analyses on the two systems to characterize communication pathways on the protein/ protein family levels. Together, the structural and dynamic features would help us elucidate the underlying mechanism of allostery. The first chapter introduces the two systems with a brief dive into the history of allostery. In the second chapter, my work on E. coli Biotin Protein Ligase and its variants reveal one possible mechanism by which disorder-to-order transitions at the functional surfaces transmit via local changes around the critical residues in the allosteric network. The third chapter explores how the protein network reconfigures to adopt a new allosteric function by studying the allosteric and non-allosteric Biotin Protein Ligases. The fourth chapter elucidates the structural and dynamical markers in bovine S100B, which help to relay information about an allosteric signal by varying two allosteric triggers - ionic strength and target peptide. The final chapter sums up my conclusions, where I propose additional experiments and computational analyses that could be carried out to further our understanding of allostery.Item STATE-LEVEL STRUCTURAL RACISM AND ALCOHOL AND TOBACCO USE BEHAVIORS IN A NATIONAL PROBABILITY SAMPLE OF AFRICAN AMERICANS(2023) Woodard, Nathaniel; Knott, Cheryl L; Public and Community Health; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Structural racism is how society maintains and promotes racial discrimination through established and interconnected systems. Structural racism is a historical driver of health disparities, including those in the area of cancer. One pathway posited for this effect is through the promotion of maladaptive coping behaviors, such as alcohol and tobacco use. This dissertation empirically assessed the association between state-level structural racism and alcohol and tobacco use behaviors among African Americans, including within various subgroups of African Americans based on age, gender, and household income. This project analyzed secondary self-report data collected from a national probability sample of 1,946 African Americans in the Religion and Health in African Americans (RHIAA) Study. Existing measures of state level structural racism were merged into the RHIAA dataset including a composite index of structural racism assessed using five dimensions (i.e., residential segregation, and economic, employment, education, and incarceration disparities). Analyses were performed in SPSS Version 28 using hierarchical linear and logistic regression models. In the first study, two models (Model A and Model B) were constructed for each of four outcomes, frequency of alcohol consumption (measured in days per month), frequency of binge drinking (measured in the number of occurrences per month), smoking status (current smoker or not a current smoker), and smoking frequency (never smoked, former smoker, currently smoke on some days, and currently smoke every day). Model A used the composite structural racism index measure to model the four alcohol and tobacco use measures and Model B analyzed the disaggregated dimensions of structural racism rather than the composite measure. All hierarchical analyses controlled for confounding variables (i.e., participant gender, age, education, income, and employment status). In the second study, analyses using the dimension-level approach in Model B from study one were repeated in subgroups stratified by participant age, gender, and income for the frequency of binge drinking and smoking status behaviors. Statistical comparisons of the slope estimates between corresponding subgroups (e.g., younger and older age) were used to test the moderation effects of age, gender, and income on the association between structural racism and alcohol and tobacco use behaviors. Results from these studies generally indicated a positive association between state level structural racism, especially in the incarceration dimension, and binge drinking and tobacco use behaviors. Stratified analyses generally did not support age, gender, or income as moderating variables of the association between structural racism and binge drinking and tobacco use behaviors. Current findings demonstrate a need for further research on structural racism and health and progress in structural racism measurement, including further emphasis of dimension-level measurement and analysis. Findings from the current dissertation highlight the importance of addressing structural racism, especially in incarceration, to reduce alcohol and tobacco use behaviors among African Americans and help address existing health disparities.Item High Resolution Mapping of Intracellular Mechanical Properties during Key Stages of Cancer Progression(2022) Nikolic, Milos; Scarcelli, Giuliano; Tanner, Kandice; Biophysics (BIPH); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The mechanical phenotype of the living cell is critical for survival following deformations due to confinement and fluid flow. Furthermore, in recent years mechanical interaction between cells and the cellular environment has been implicated as one of the key regulators of cancer progression and malignant transformation. Due to the need to better understand the mechanical properties of invasive cells and how the mechanical phenotype plays a role in cancer progression, several microrheology techniques have been applied to study cell mechanics in a range of in vitro environments. However, many of these techniques have been limited either to studying cells in only one type of environment (e.g. 2D), with limited resolution, or with invasive probes. To begin to address this question, in this dissertation we aim to quantify the mechanical state of cells in a broader range of different contexts and geometries. To do this we use Brillouin microscopy, a non-contact, label free, non-invasive technique which enables us to probe the mechanical response of cells in a wide range of complex microenvironments. Here we introduce an improved Brillouin microscope with improved signal and acquisition speed which enables us to perform biological studies at the single cell level. Using the improved Brillouin microscopy, we find that individual cells can be softer as function of the invasive potential, but that cells are able to dynamically change their mechanical properties across many different contexts. We validate our results using complementary microrheology methods such as atomic force microscopy and broadband optical tweezer microrheology. We directly observe changes in cell mechanics in key processes relevant for metastatic migration, as well as a function of external and internal parameters like morphology, ECM properties, intracellular factors, and cell-cell cooperativity during multicellular tissue organization. These results support the paradigm that the mechanical state of a cell is a dynamic parameter that varies as a consequence of the microenvironmental and functional context, in addition to the observable changes in cell’s mechanical properties due to malignant transformation.Item Leveraging Biomaterials to Direct Immune Function in Cancer and Autoimmunity(2022) Tsai, Shannon Joanne; Jewell, Christopher M; Bioengineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Immune dysregulation and difficulties in directing immune function in cancer and autoimmune disease pose complex challenges for existing vaccines and immunotherapies. In cancer, tumor cells exploit processes to evade the immune system. Conversely, autoimmune diseases such as multiple sclerosis (MS) occur when immune cells incorrectly attack healthy host tissue and cells. To address the dichotomy of dysregulated immune responses that can arise, next generation vaccines and immunotherapies demand better control over the specificity and types of immune of responses generated within lymph nodes (LNs). This dissertation investigated two approaches to improve immune signal delivery for precision control over immune responses. In the first approach, self-assembling vaccine nanoparticles were engineered with tunable charge and cargo loading to efficiently deliver immune signals in specific combinations and doses without compromising function. These studies offer new insight into biomaterial design for therapeutic cancer vaccines and demonstrate that the physiochemical properties of biomaterials - particularly the interplay between charge, uptake, and affinity - play an important role in the immune signals that can promote T cell expansion against tumor antigens. In the second approach, a biomaterial-based platform is used to control immune signal delivery to LNs during autoimmunity. Direct injections of therapeutic vaccine carriers into the LNs of mice offer new insight into how the localized combination of myelin peptide (MOG) and rapamycin (Rapa) - an immunomodulatory signal, promote potent and selective immune tolerance. This body of work demonstrates that immune function is highly localized to the signals delivered to the LNs, requiring an idealized combination of both self-antigen and immunomodulatory signal to promote the proliferation, retention, and polarization of antigen specific T cells towards regulatory T cells that can selectively limit inflammatory T cell phenotypes and combat autoimmunity. Together, these two approaches offer new insight into how biomaterials can be rationally harnessed to direct immune function across cancer and autoimmune disease.Item Structural and Biophysical Characterization of Homo Sapiens RIOK2 in Complex with Selective Prostate Cancer Inhibitors and its Transition State Complex(2021) Seraj, Nishat; LaRonde, Nicole; Biochemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Homo sapiens Riok2 (HsRiok2) is an atypical, Ser/Thr protein kinase that has been implicated in a number of cancers, including Prostate Cancer. More recently, evidence has shown that HsRiok2 plays a biological role in the upregulation of ERG-positive cancer cells, thus presenting itself as an attractive drug target. The first known prostate cancer inhibitor against HsRiok2 has been identified, as well as select derivative inhibitors and has been shown both in vitro and in vivo to target HsRiok2. Here, the first ever Homo sapiens Riok2 in complex with two known Prostate Cancer inhibitors at 1.75 Å resolution and 2.70 Å resolution is reported, respectively. To evaluate conformational changes upon inhibitor binding, the first ever Homo sapiens Riok2 transition state complex is reported, capturing a snapshot of the kinase poised for phosphoryl transfer, at 2.80 Å resolution. These structural insights reveal the influence of the phosphate-binding loop (P-loop) in HsRiok2’s dimerization and potentially a catalytically inactive state, mediated by the presence of the drug candidate. Its dimerization interface is prevented from interacting with the Pre-40S ribosome, preventing HsRiok2 from carrying out its function as an ATPase/Kinase to further mature the pre-40S particle. These findings provide the first blueprint for a structure-based drug design approach to facilitate the development of more selective prostate cancer inhibitors.Item Novel Immunotherapy Agents in Oncology: Generalizability of Trial Results and Drivers of Clinical Utilization(2021) Mishkin, Grace; Franzini, Luisa; Health Services Administration; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Cancer is the second most common cause of death in the United States after heart disease. Novel immunotherapy agents such as nivolumab and pembrolizumab have become an essential, albeit extremely expensive, component of oncology care since their first approvals in melanoma in 2014 and lung cancer in 2015. However, little is known about differences between immunotherapy clinical trial participants and the real-world patient population, or about the drivers of provider utilization of these agents. The first objective of this dissertation used the SEER-Medicare linked database with claims data from 2014-2016 to conduct two aims analyzing potential disparities between Medicare beneficiaries on active treatment for melanoma and lung cancer and Medicare clinical trial participants. Aim one compared the characteristics of Medicare patients on active cancer treatment to Medicare patients on active cancer treatment clinical trials. Aim two compared Medicare patients receiving the novel immunotherapy agents nivolumab or pembrolizumab to Medicare patients participating in trials of these two immunotherapy agents. Because of the demographic differences in the melanoma and lung cancer patient populations, these aims were analyzed separately in melanoma and lung cancer. As hypothesized, patients in clinical trials were significantly younger and had fewer comorbid conditions than patients undergoing active cancer treatment not in clinical trials. Underrepresentation of non-White and female patients in clinical trials was hypothesized, but these results were less consistent. The second objective used Medicare Open Payments data from 2016 and Medicare provider utilization data from 2017 to analyze 1) if industry payments promoting nivolumab or pembrolizumab were positively associated with whether a provider was a high utilizer of the agent, and 2) among these high utilizers, if industry payments were positively associated with greater utilization amounts. The hypothesized results, that industry payments were associated with greater likelihood of high utilization and more utilization among high utilizers, were seen in some of the analyses but not consistently throughout the study. Through unique analyses of recent datasets, this dissertation advances our understanding of potential disparities in clinical trial representativeness and the generally positive relationship between promotional payments and provider utilization of immunotherapy agents in the Medicare cancer patient population.Item DISSECTING THE GENE REGULATORY FUNCTION OF THE MYC ONCOGENE WITH SINGLE-MOLECULE IMAGING(2020) Patange, Simona; Larson, Daniel R; Girvan, Michelle; Biophysics (BIPH); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The MYC oncogene contributes to an estimated 100,000 cancer-related deaths annually in the United States and is associated with aggressive tumor progression and poor clinical outcome. MYC is a nuclear transcription factor that regulates a myriad of cellular activities and has direct interactions with hundreds of proteins, which has made a unified understanding of its function historically difficult. In recent years, several groups have put forth a new hypothesis that questions the prevailing view of MYC as a gene-specific transcription factor and instead envision it as a global amplifier of gene expression. Instead of being an on/off switch for transcription, MYC is proposed to act as a `volume knob' to amplify and sustain the active gene expression program in a cell. The scope of the amplifier model remains controversial in part because studies of MYC largely consist of cell population-based measurements obtained at fixed timepoints, which makes distinguishing direct from indirect consequences on gene expression difficult. A high-temporal, high-spatial precision viewpoint of how MYC acts in single living cells does not exist. To evaluate the competing hypotheses of MYC function, we developed a single-cell assay for precisely controlling MYC and interrogating the effects on transcription in living cells. We engineered `Pi-MYC,' an optogenetic variant of MYC that is biologically active, can be visualized under the microscope, and can be controlled with light. We combined Pi-MYC with single-molecule imaging methods to obtain the first real-time observations of how MYC affects RNA production and transcription factor mobility in single cells. We show that MYC increases the duration of active periods of genes population-wide, and globally affects the binding dynamics of core transcription factors involved in RNA Polymerase II transcription complex assembly and productive elongation. These findings provide living, single-cell evidence of MYC as a global amplifier of gene expression, and suggests the mechanism is by stabilizing the active period of a gene through interactions with core transcription machinery.Item DOES PATIENT-CENTERED COMMUNICATION AND TRUST IN PHYSICIAN INFORMATION VARY BY CANCER SURVIVORSHIP STATUS? AN ANALYSIS OF THE HEALTH INFORMATION NATIONAL TRENDS SURVEY (HINTS) 2017(2019) Al-Nassir, Marwa Fawzi; Dallal, Cher M; Epidemiology and Biostatistics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Trust is the foundation of the patient-physician relationship. Patients’ trust in a physician has been associated with patient satisfaction, adherence to treatment, continuity of care, and improved health outcomes. Trust in a physician is especially important for health-vulnerable populations, such as cancer survivors, as they tend to endure complex emotional needs related to re-acclimating to the new normal post cancer diagnosis. The patient-physician relationship also relies heavily on effective patient-centered communication (PCC), however, associations between PCC and trust in physician information overall and by cancer survivorship status is not well understood. Using nationally representative data (N = 2604) ascertained from Cycle 1 of the fifth iteration of the 2017 Health Information National Trends Survey (HINTS), a cross-sectional analysis was conducted to examine PCC in relation to trust in physician information. PCC was assessed on a 4-point Likert scale using responses from seven sub-questions that address the main functions of PCC: 1) fostering healing relationships, 2) exchanging clinical information, 3) responding to emotional needs, 4) managing uncertainty, 5) facilitating shared decision-making, and 6) enabling patient self-management. Trust in physician information was analyzed dichotomously (high versus low) based on responses from a single item question. PCC was analyzed as individual components (optimal versus sub-optimal) and as an overall score. Confounders included age, sex, race/ethnicity, education, and household annual income. Odds ratios (OR) and 95% confidence intervals (CI) for the relationship between PCC and trust in physician information were estimated using multivariable logistic regression. Analyses of cancer survivorship status (cancer survivor versus never had cancer) as an effect modifier of the relationship between PCC and trust in physician information was also conducted using an interaction term. Results from the weighted multivariable models revealed that for every one-unit increase in the overall PCC score (range 1 to 100), the odds of having high trust in physician information increased by 4% (adj OR = 1.04, 95% CI = 1.03–1.05). The odds of reporting high level of trust in physician information were significantly associated with each individual component of PCC when comparing those who felt their communication component was optimal versus sub-optimal (PCC components: exchanging clinical information (adj OR = 2.57, 95% CI = 1.82–3.62), responding to emotional needs (adj OR = 2.34, 95% CI = 1.65–3.30), facilitating in shared decision-making (adj OR = 2.35, 95% CI = 1.70–3.26), enabling patient self-management (adj OR = 2.88, 95% CI = 2.11–3.92), managing uncertainty (adj OR = 2.45, 95% CI = 1.74–3.44), fostering healing relationships (adj OR = 2.79, 95% CI = 2.18–3.57), and spending enough time with you (adj OR = 2.09, 95% CI = 1.49–2.93)). When examining relationships by cancer survivorship status, estimates among cancer survivors were of greater magnitude compared to persons who reported never having cancer, however, no significant interactions were observed in the weighted multivariable models (all p-interaction>0.05). These findings provide insight on how optimal experiences of PCC influence trust in physician information and can help inform the development of PCC strategies to ultimately improve health outcomes and reduce consequences related to poor patient-physician trust overall and among cancer survivors.Item ESTIMATION AND ANALYSIS OF CELL-SPECIFIC DNA METHYLATION FROM BISULFITE-SEQUENCING DATA(2018) Dorri, Faezeh; Bravo Corrada, Hector; Computer Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)DNA methylation is the best understood heritable gene regulatory mechanism that does not involve direct modification of DNA sequence itself. Cells with different methylation profiles (over temporal or micro-environmental dimensions) may exhibit different phenotypic properties. In cancer, heterogeneity across cells in the tumor microenvironment presents significant challenges to treatment. In particular, epigenetic heterogeneity is discernible among tumor cells, and it is believed to impact the growth properties and treatment resistance of tumors. Existing computational methods used to study the epigenetic composition of cell populations are based on the analysis of DNA methylation modifications at multiple consecutive genomic loci spanned by single DNA sequencing reads. These approaches have yielded great insight into how cell populations differ epigenetically across different tissues. However, they only provide a general summary of the epigenetic composition of these cell populations without providing cell-specific methylation patterns over longer genomic spans to perform a comprehensive analysis of the epigenetic heterogeneity of cell populations. In this dissertation, we address this challenge by proposing two computational methods called methylFlow and MCFDiff. In methylFlow, we propose a novel method based on network flow algorithms to reconstruct cell-specific methylation profiles using reads obtained from sequencing bisulfite-converted DNA.We reveal the methylation profile of underlying clones in a heterogeneous cell population including the methylation patterns and their corresponding abundance within the population. In MCFDiff, we propose a statistical model that leverages the identified cell-specific methylation profiles (from methylFlow) to determine regions of differential methylation composition (RDMCs) between multiple phenotypic groups, in particular, between tumor and paired normal tissue. In MCFDiff, we can systematically exclude the tumor tissue impurities and increase the accuracy in detecting the regions with differential methylation composition in normal and tumor samples. Profiling the changes between normal and tumor samples according to the reconstructed methylation profile of underling clone in different samples leads us to the discovery of de novo epigenetic markers and a better understanding about the effect of epigenetic heterogeneity in cancer dynamics from the initiation, progression to metastasis, and relapse.Item Couples Coping with Li-Fraumeni Syndrome: A Mixed-Methods Study of Family Strengths(2018) Young, Jennnifer Louise; Epstein, Norman B; Family Studies; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Using mixed methodology involving qualitative and quantitative data, this dissertation fills gaps in knowledge regarding psychosocial implications for families living with the genetically-transmitted Li-Fraumeni cancer susceptibility syndrome, specifically targeting couple dyads. An initial review of the existing literature on couples coping with heritable cancer syndromes identified gaps in knowledge, and pointed to future directions for research in this area. The three papers that comprise this dissertation provide multiple perspectives on the levels of distress, coping styles, and social support patterns of couples in which one partner is at high risk of cancer. The first paper investigates spousal distress and coping styles in relation to cancer worry for individuals with Li-Fraumeni Syndrome, using quantitative data from one of the largest existing collections of Li-Fraumeni Syndrome cases. The second paper identifies couples’ coping and communication processes regarding cancer stressors, using semi-structured qualitative interviews of individuals with Li-Fraumeni Syndrome and their partners. The third paper utilizes a social network approach to illustrate shared patterns of emotional, tangible, and informational support that couples report accessing. The integrated findings from these three studies indicate that these subjects are low in general distress but high in cancer-specific worry. Couples cope with this worry by balancing multiple roles, exercising flexibility in family dynamics, and utilizing extensive social support networks. This research provides significant information that can aid in development of effective interventions for couples as they face their ongoing threat of cancer. Recommendations for clinical work with this population include an integrated blend of couple therapy, genetic counseling, and oncology practice that is sensitive to the unique needs of individuals with heritable cancer syndromes and their partners.