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Novel mechanisms of autophagy-lysosome dysfunction in GBA1 Parkinson disease
Get PDFParkinson disease (PD) is the most common neurodegenerative movement disorder, with clinical manifestations of motor impairments and pathologic manifestations of accumulated alpha-synuclein in vulnerable neuronal populations. Mutations in the GBA1 gene, which encodes the lysosomal enzyme glucocerebrosidase (GCase), are the most common genetic risk factor for PD and drive disease progression through lysosomal dysfunction and impaired proteostasis. However, optimal strategies for restoring autophagy-lysosome function and mitigating alpha-synuclein proteotoxicity in GBA1 PD remain incompletely defined, and progress has been hindered by the limitations of non-human and non-neuronal models. To address these gaps, we developed a novel human neuron model of GBA1 PD using patient-derived induced pluripotent stem cells (iPSCs) that express the N370S GCase mutation. GBA1 PD neurons exhibited multiple markers of autophagy-lysosomal dysfunction, including impaired autophagic flux, alpha-synuclein accumulation, and increased cell death. Broad reduction in the expression of autophagy- and lysosome-related genes in GBA1 PD cells implicated dysfunction in transcriptional regulation as a potential disease mechanism. In line with this, we found that GBA1 PD neurons harbor altered expression and localization of TFEB and ZKSCAN3, which function as master transcriptional activator and repressor, respectively, of hundreds of autophagy and lysosomal genes. Overexpressing TFEB improved autophagic flux, reduced alpha-synuclein burden, and rescued cell viability in GBA1 PD neurons and knocking down ZKSCAN3 also decreased alpha-synuclein accumulation and increased cell viability, directly implicating the critical roles each factor in the molecular pathogenesis of GBA1 PD. Altogether, our engineered cell lines demonstrate molecular fidelity for modeling GBA1 PD and have unraveled novel insights and molecular targets to enhance therapy development for GBA1 PD and related lysosomal disorders
EVALUATING HUMAN PAPILLOMAVIRUS VACCINE UPTAKE AND EFFECTIVENESS IN U.S. WOMEN LIVING WITH HIV AND AT-RISK FOR HIV
No full textPersistent infection with the human papillomavirus (HPV) causes cervical cancer and is associated with other anogenital and oral cancers. Infection with the human immunodeficiency virus (HIV) increases the risk for HPV infections. There are over two hundred strains of HPV, but two strains (HPV16 and HPV18) are responsible for most of the human cancers caused by HPV. Women living with HIV (WLH) face approximately six times the risk of developing cervical cancer compared to those without HIV. At-risk women living without HIV (WLOH) are also more vulnerable to HPV infections. Variables such as poverty and living in areas with a higher prevalence of HIV infections play a role in increasing the risk of sexually transmitted human viral infections in some women compared to women without these predisposing variables. Available HPV vaccines are prophylactic and offer benefits to some women. HPV vaccination coverage among WLH and WLOH in the United States (U.S.) remains unclear--a gap this dissertation sought to address.
This dissertation was conducted in two phases. The first phase was a critical synthesis of research on HPV vaccine response in people living with HIV, while also quantifying the differences in immunogenicity by HIV serostatus, and between HPV16 and HPV18 genotypes. The second phase employed a retrospective data analysis approach to estimate HPV vaccine uptake in WLH and WLOH by HIV serostatus, and to examine both the socioeconomic and clinical variables associated with uptake.
Findings showed promising outcomes in vaccinating women without HPV vaccine-specific genotypes. HPV vaccine uptake is suboptimal in both WLH and WLOH, estimated at 18.5% and 12.4%, respectively. Results suggested that provider-level factors and insurance coverage are the critical socioeconomic variables in determining HPV vaccine uptake in WLH. A history of a serious cardiovascular event (such as myocardial infarction) facilitated HPV vaccine uptake. As for WLOH, drivers of HPV vaccination could not be identified from the results of this study
MECHANISMS OF MICROBIOME MODULATION BY NON-NUTRITIVE SWEETENERS AND THE IMPLICATIONS FOR METABOLIC HEALTH
No full textConsumption of non-nutritive sweeteners (NNS) has grown increasingly popular in recent decades. As they contain little to no calories and do not induce a postprandial glycemic response, NNS have been frequently used as a sugar substitute to reduce the risk of metabolic diseases. However, accumulating evidence indicates that NNS may contribute to these very issues they were intended to prevent. Nonetheless, interventional human trials show heterogeneous results on whether NNS consumption can mitigate the risk of metabolic diseases. A major cause of the variability can be attributed to the interpersonal difference in the gut microbiome, which can be altered by NNS and cause worsened metabolic health. While a few studies support the gut microbiome’s role in mediating the personalized metabolic responses to NNS, the mechanisms underlying microbiome alterations by NNS and the NNS-modulated microbiome’s impact on host metabolic health remain obscure. Filling these knowledge gaps is essential for elucidating how the microbiome mediates personalized responses to NNS, and eventually, facilitating well-informed public health decisions regarding the usage of NNS to reduce the prevalence of metabolic diseases. In this thesis, I explored the mechanisms through which NNS modulate the gut microbiome by anaerobically screening individual gut bacterial taxa against direct exposure to saccharin and sucralose, two prototypical NNS. The screen revealed that the two NNS impact the individual bacteria’s growth in a species-dependent manner with shared and distinct mechanisms. To explore molecular mechanistic insights underlying NNS’s varying impact on individual taxa, I conducted evolution experiments, inducing adaptations in bacterial monocultures. Through analyzing the genome of the adapted bacteria, I identified sucralose’s potential bacterial targets and proposed a mechanism of sucralose-driven inhibition. To investigate how NNS-modulated microbiomes contribute to worsened metabolic health, I conducted an NNS-feeding trial using specific pathogen-free mice fed a high-fat diet. Future analysis of this experiment can help validate the physiological relevance of findings discovered in germ-free mouse experiments previously conducted in the Suez lab. Collectively, this thesis provides valuable mechanistic insights underlying the microbiome’s mediation of personalized responses to NNS, promoting a better understanding of the impact of NNS consumption on metabolic health
DEVELOPING AND APPLYING SEQUENCING-BASED TOOLS TO UNDERSTAND ADAPTIVE IMMUNE RESPONSES IN MYOSITIS
No full textIdiopathic inflammatory myopathies (IIMs) are a group of heterogeneous, systemic diseases characterized by skeletal muscle pathologies, which most commonly result in chronic, progressive muscle weakness. Immune infiltrates, which includes B and T cells, are often found in the muscle of IIM patients. Currently, autoantibodies help stratify IIMs into clinical subtypes, however disease heterogeneity persists within subtypes of IIMs and the etiologies of IIMs remain unknown. Through the application of adaptive immune profiling methods: 1) Phage Immunoprecipitation Sequencing (PhIP-Seq) to understand antibody reactivities at cohort-scale and 2) B cell receptor sequencing, I have further characterized the antibody repertoires in IIMs. Using PhIP-Seq, I identified novel environmental and autoantibody reactivities in subtypes of IIMs. These findings may generate hypotheses about IIM etiologies, and improve IIM disease classifications. Using both PhIP-Seq and BCR sequencing, I characterized the diversity of the local antibody repertoire in muscle tissue of IIM patients, improving our understanding of the adaptive immune response within muscle. To improve our ability to perform immune receptor repertoire sequencing in a low-cost, high-throughput manner, I developed a method, INtraCEllular Reverse Transcription with Sorting and sequencing, or INCERTS, to efficiently link T cell phenotypes with T cell receptor sequencies. INCERTS is complementary to single-cell sequencing. Through the application of these sequencing- based methods, I have increased our understanding of the B cell immune response in IIMs. Through the development of INCERTS, I have improved our ability to perform immune receptor repertoire sequencing, which can be applied to further increase our understanding of the adaptive immune response in IIMs
REGIONAL PERSPECTIVES ON GLOBAL GEOBIOLOGICAL TRANSITIONS ACROSS THE NEOPROTEROZOIC ERA
No full textIn this dissertation, I build and interpret regional bio- and chemostratigraphic records of global geobiological transitions across the Neoproterozoic Era (1000 – 538 Ma).
In Chapter 2, I apply U–Pb zircon geochronology and geochemistry to constrain the age and tectonic setting of a late Tonian microfossil assemblage from southern Kazakhstan. In addition to improving regional tectonic and biostratigraphic understanding, this work constrains the timing of test acquisition by single-celled eukaryotes.
Chapters 3, 4, and 5 concern the terminal Ediacaran Period. In Chapter 3, I describe, image, and chemically analyze a new fossil horizon from terminal Ediacaran strata in southwestern Laurentia. On a morphological basis, I suggest that the fossils belong to the problematicum Vendotaenia, a putative macroaglae previously unreported from the region. This finding extends the paleogeographic range of eukaryotic primary producers during the terminal Ediacaran diversity crisis.
In Chapters 4 and 5, I evaluate controls on the generation and preservation of an extreme negative carbon isotope excursion that roughly coincides with the end-Ediacaran mass extinction. Chapter 4 centers on the record of this excursion in southwestern Laurentia, where it is clearly reproduced down the continental margin. Through the combination of geochemical proxies and sedimentological analysis, I demonstrate that this record reflects a shift in the carbon isotope composition of dissolved inorganic carbon (DIC) in terminal Ediacaran platform seawater, and that this shift is unrelated to diagenetic processes. However, I also find that the geochemical fingerprint of early marine diagenesis is ubiquitous, which may indicate the influence of local carbon cycling on platform DIC.
In Chapter 5, I further explore controls on terminal Ediacaran carbon isotope records, with a focus on terminal Ediacaran strata from southwestern Mongolia. These strata enigmatically record spatially heterogeneous carbon isotope trends. To test hypotheses to explain this heterogeneity, I (1) determine the spatial scale at which it occurs, (2) develop a basin-wide depositional model for the strata that record it, and (3) assess the influence of diagenesis. I find that tectonically-influenced diachronous deposition across the basin can largely explain the observed carbon isotope variation, but suggest dolomitization plays a secondary role in producing regional heterogeneity
DESCRIPTION OF A MICROSIMULATION MODEL OF HIV TRANSMISSION IN BALTIMORE CITY
No full textBackground: Baltimore City bears a high HIV burden with persistent disparities in viral suppression and new infections. Long-acting injectable pre-exposure prophylaxis (LAI-PrEP) offers superior efficacy and adherence compared to daily oral PrEP, but its population-level impact remains largely unknown due to limited uptake.
Methods: We developed a microsimulation model of HIV transmission and progression among adults (≥18 years) in Baltimore City, stratified by demographics, HIV risk exposure, treatment status, and viral suppression. The model was calibrated to 2017–2021 surveillance data using the L-BFGS-B algorithm, and was validated against published estimates from 2022–2023.
Results: The model closely reproduced observed trends from 2017 to 2023, with mean absolute errors in incidence rates <0.0002 overall, and ≤0.0005 across racial groups. Viral suppression rates were slightly overestimated but remained within acceptable bounds.
Conclusion: Our validated model reflects relatively well HIV dynamics in Baltimore City and can be used to assess the health and economic impacts of HIV prevention and treatment strategies
Characterization of exposure to elements detected in infant formula and the implications of consuming milk from cows fed seaweed
Get PDFThe infant population is uniquely sensitive and their exposure to environmental contaminants can affect health and disease risk in later life. While breastfeeding is recommended, most infants consume some formula. Prior studies have detected metals and other elements of potential concern in infant formula. In addition, seaweed-based supplements for dairy cows are emerging as a potential greenhouse gas mitigation strategy as their use can reduce the production of methane. Seaweeds contain beneficial elements, but also metals. The goal of this dissertation was to characterize exposures to elements detected in current infant formula and explore the implications of consuming milk from cows fed seaweed supplements.
In Aim 1, we measured element concentrations in infant formula and performed a risk factor analysis of variables that could be associated with these element concentrations. Based on univariable regression modeling, we found that products that were made with cow’s milk, did not include carrageenan as an ingredient, were powder composition, were purchased in Europe, or were labeled as organic had significantly lower concentrations of elements than alternative products.
In Aim 2, we estimated a distribution of element exposures that could be experienced by an infant who consumes these formula products. We then characterized these exposures by comparing to a diet of human milk, and to regulatory limits or guidance for drinking water and foods. Our simulation estimated that dietary exposures to elements from the formula product samples included here were generally similar to exposures expected from human milk and in compliance with drinking water and dietary guidance.
In Aim 3, we measured element concentrations in samples of milk from cows fed seaweed. We estimated a distribution of element exposures under the assumption that an infant could consume this milk directly as they would infant formula. We found that milk from cows fed seaweed consistently had greater concentrations of arsenic and iodine than milk from cows who were not given seaweed. Dietary exposures to elements from the consumption of milk from cows fed seaweeds were generally below or similar to exposures from cow’s milk infant formula and human milk, and in compliance with regulatory limits or guidance
The Complexity-Simplicity Trade-Off: Strategic Fit and Firm Viability in the Security-First Economy
Get PDFIn an era where national security concerns increasingly shape economic governance, global industries are undergoing a structural shift from market-driven selection to policy-driven constraints. This thesis develops the Complexity–Simplicity Balance (CSB) Framework to explain why some firms thrive while others struggle under evolving selection pressures. Traditional theories of strategic management offer useful insights, but they often overlook the role of policy as a selector — particularly in environments marked by geopolitical fragmentation and industrial intervention. CSB introduces three interlocking concepts: embedded strategic traits, selection fit, and firm viability.
The study uses process-tracing and comparative case methods to analyze Samsung Electronics and SK-Hynix, two South Korean semiconductor firms that have diverged sharply in their strategic responses to U.S. security-first policies, including the CHIPS Act and export controls on China. Samsung, a complexity-embedded firm, pursued vertical integration and global scale but encountered coordination friction and adaptation lags. SK-Hynix, with structurally simpler operations, aligned more quickly with shifting policy logics and capitalized on high-growth niches like AI-focused memory.
Findings show that in policy-fragmented environments, selection fit is dynamic, not fixed. Strategic complexity can become a liability when the selector changes, while structural simplicity may enable faster realignment. Two factors shape firm viability: strategic agility, which allows favored firms to exploit alignment; and structural resilience, which determines whether constrained firms can survive until pressures shift. The CSB framework also highlights the growing importance of selector volatility — where policy signals themselves are unstable, especially amid overlapping technological and geopolitical disruptions.
The thesis extends CSB to global firms (e.g., Intel, TSMC) and Korea’s EV battery sector to test its generalizability across other security-sensitive industries. It offers new insights for strategy, IPE, and GVC research by foregrounding firm heterogeneity and the limits of policy-driven adaptation. In a security-first economy, sustained competitiveness requires more than compliance — it requires the capacity to reconfigure embedded traits in pursuit of moving targets
INVESTIGATING THE ESTABLISHMENT AND INHIBITION OF IMMUNOLOGICAL MEMORY FORMATION BY CRISPR-CAS SYSTEMS
No full textDespite the ubiquity of CRISPR-Cas technology for use in contemporary biomedical research, relatively little is known about CRISPR-Cas systems in natural models of infection by bacterial viruses, known as (bacterio)phages. In prokaryotes, CRISPR-Cas systems provide adaptive immunity by memorizing foreign nucleic acids as DNA-encoded memories called “spacers” and storing them in genomic repositories known as CRISPR arrays. In conjunction with other CRISPR-Cas effector proteins, non-coding crRNAs transcribed from spacers in the CRISPR array enable sequence-specific defense against re-encountered pathogens. Given the requirements for memory formation, we sought to explore how CRISPR systems could defend against a rapid phage infection quickly enough to memorize the invader and clear the infection.
This thesis work first describes how CRISPR-Cas systems exploit the programmed viral dormancy of temperate phages, a process known as lysogeny, to carry out CRISPR immunity. During a naïve phage infection, CRISPR-Cas immunizations are significantly enhanced against phages which choose to enter lysogeny. Further, in a population of lysogens, spacers are constantly acquired from superinfecting phages produced during spontaneous prophage induction of neighboring lysogens. Acquired spacers targeting a resident prophage cause Cas9-induced curing of the prophage, generating a population of cells heterogeneous in both spacer and prophage content. Altogether, we propose a model where the lysogenic lifecycle of temperate phages allows CRISPR-Cas immunization to occur over larger temporal windows, affording time for all steps of CRISPR-Cas immunity to take place.
Next, we analyzed how phages can overcome CRISPR immunity using anti-CRISPR (Acr) proteins. I describe a bioinformatic screen for Acrs and the functional validation and characterization of putative hits. Preliminary data on several of the putative Acrs suggest novel mechanisms for CRISPR-Cas9 inhibition.
Finally, I describe the beginnings of a project analyzing the regulation of a CRISPR-Cas system by another CRISPR-Cas locus in the same bacterium. I describe the preliminary experiments justifying further study, as well as efforts to establish assays for probing the CRISPR-based interactions in the native bacterial species
SUBZERO PRESERVATION TECHNOLOGIES TO EXTEND PRESERVATION TIME FOR VASCULARIZED COMPOSITE ALLOGRAFTS (VCA)
No full textVascularized composite allotransplantation (VCA) offers a reconstructive option for patients with severe tissue defects, yet its clinical application remains constrained due to further limited ischemic tolerance of grafts compared to solid organs. Conventional preservation methods, primarily static cold storage (SCS) at 4˚C, provide only a narrow ischemic time window, suggesting the necessity to develop alternative strategies.
This project investigated subzero preservation techniques under both isobaric and isochoric approaches, with the combined use of machine perfusion and a novel cryostasis cocktail to prevent ice formation and to extend preservation time. The feasibility and effects of extended high-subzero preservations were evaluated by characterizing perfusion parameters as well as an in vivo assessment using a syngeneic orthotopic rat forelimb transplantation, followed by long-term functional evaluation.
We were thus able to demonstrate the first in vivo evidence of successful prolonged subzero preservation of VCA forelimb grafts for up to 72 hours with functional recovery. This proof-of-concept study provided critical insights into the effects of extended high-subzero preservation in VCA grafts and established a platform for further optimization of preservation conditions and strategies, together contributing to the advancement of VCA preservation techniques and their clinical translation