1983 research outputs found
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Developing Uniform, Photon-Emitting Nanoprobes for Multi-Color Electron Microscopy
No full textStudying cellular processes relies on an understanding of subcellular protein interactions, often facilitated by cellular features. Unfortunately, there are no well-established methods for nanoscale imaging of these features alongside proteins. Existing bioimaging methods require complicated correlation methods or have complex sample preparation protocols. Electron microscopy (EM) has the highest resolution of all microscopy methods and can reveal cellular morphology with a nanoscale resolution. However, the resulting images are grayscale and do not label specific proteins. Inspired by probes in fluorescence imaging, this thesis developed a library of nine multi-colored nanoprobes for EM to permit protein visualization. The nanoprobes were composed of rare-earth elements that emit detectable photons of different wavelengths when excited by an electron beam. Photon emissions were spatially correlated with a simultaneously collected high-resolution EM image, producing a colorized EM image that labels tagged proteins with different colors. Each nanoprobe generated detectable photons with a high signal-to-noise ratio. They were small and uniformly shaped, making them ideal for bioimaging. Up to seven probes were simultaneously in a sample to demonstrate their distinct colors. This thesis illustrates, for the first time to our knowledge, multicolor EM, unlocking the potential to visualize proteins in their cellular context
Multi-omics interrogation of metabolic stress in cancer
No full textCancer is associated with alterations to many pathways and cellular processes, including activation of pro-growth cell signaling pathways, resistance to cell death, activation of metastasis, and evasion of the immune system. Another key change in cancer is rewiring of cellular and mitochondrial metabolism to support cellular growth via energy generation, intake of molecular building blocks, and increased anabolic synthesis. While general metabolic changes in cancer are well characterized, the effect of cancer type-specific changes on metabolism are poorly understood. The goal of this dissertation was to identify metabolic vulnerabilities in specific cancer subtypes using data-driven approaches.
In this dissertation, I present three studies that each utilize multi-omics approaches to characterize metabolic changes present in cancer. In the first project, we performed combined transcriptional and metabolic profiling of the mitochondrial stress response. Using integrated data analysis, we then generated mitochondrial stress signatures that describe discrete nodes of the mitochondrial stress response. Finally, we generated a workflow for quantifying these mitochondrial stress signatures in outside datasets, and utilized this to probe mitochondrial dysfunction in IDH1-mutant glioma. In the second project, we investigated the changes in lung tumorigenesis associated with aging using combined transcriptional and metabolic profiling of human patient samples. While we identified many shared genetic and metabolic changes in lung tumors independent of age, we identified age-dependent changes in metabolism that differ between tumors and healthy tissue. Furthermore, we identified the glutathione synthesis gene GCLC as differentially-regulated in young tumors compared to old tumors. Metabolic analysis highlighted changes to redox metabolism in tumors and with age, and identified changes in glutathione production associated with increased GCLC expression in young tumors. Using integrated multi-omics analysis, we then validated that GCLC expression is closely linked to glutathione levels in young patients, but not in old patients. In the final study, we investigated glutamate metabolism in triple negative breast cancer (TNBC). Given TNBC shows reduced expression of the glutamate enzyme GLUD1, we utilized bioinformatics approaches, combining human patient expression data and human-derived cell line metabolic data, to identify trends in TNBC with regard to GLUD1 expression and glutamate levels. We identified that the neurotransmitter GABA, alongside several of the genes encoding its receptors, were elevated in TNBC and specifically in concert with reduced GLUD1 expression. Together, these studies present methodologies for integrating transcriptional and metabolic changes in cancer to identify metabolic pathways that could be potential targets for cancer treatments.Medical SciencesMedical Science
The dream of trauma-related nightmares: Can physiological and subjective within-subjects measures help elucidate sleep-related mechanisms involved in PTSD symptoms?
No full textPosttraumatic stress disorder (PTSD) poses significant challenges to individuals, impacting interpersonal relationships, work performance, and overall health outcomes. Treatment can be challenging due to the heterogeneity of PTSD, which is characterized by four distinct symptom clusters: intrusion, avoidance, negative cognition and mood (NegCog), and hyperarousal. Sleep disturbances, inherent to the intrusion and hyperarousal symptom cluster criteria, pervade all clusters. Interventions targeting daytime symptoms offer limited relief for nighttime disturbances, while interventions addressing sleep disruptions appear promising for alleviating both daytime and nighttime symptoms of PTSD. This study aims to elucidate sleep disruption differences across heterogeneous PTSD symptom clusters to inform personalized therapeutic approaches.
The data were generously contributed from a larger study in Dr. Edward Pace-Schott's lab examining sleep measures and different prolonged exposure therapy exposure stimuli in a population of trauma-exposed individuals. The variables included in the analysis fall into four categories: (1) sleep architecture, quality, and continuity measures; (2) daytime and sleep measures of arousal; (3) spectral power sleep measures; and (4) self-report assessment measures. These were analyzed in relation to both symptom cluster severity and cluster membership (based on symptom cluster questions in which each participant scored the highest). Additional exploratory analyses using multidimensional scaling (MDS) and investigating relationships between REM density (REMD) and spectral power were conducted.
Despite numerous observed trends, few correlations and pairwise comparisons achieved statistical significance after correcting for multiple comparisons in the main analyses. Significant differences were observed in sleep architecture, quality, and continuity measures. There was a notable association between total sleep time and intrusion cluster scores. In pairwise comparisons, the hyperarousal cluster displayed significantly higher mean scores on the Insomnia Severity Index (ISI) compared to the avoidance and intrusion cluster; the avoidance cluster also had a significantly higher mean ISI scores compared to the intrusion cluster. Both the avoidance and hyperarousal clusters exhibited higher mean Pittsburgh Sleep Quality Index (PSQI) scores than the intrusion cluster. The avoidance cluster also demonstrated significantly longer mean sleep onset latency (SOL) compared to the hyperarousal cluster.
These findings underscore the importance of examining nuanced PTSD-related sleep disruptions from a dimensional, symptom-based perspective. Despite the modest sample size, notable relationships between sleep patterns emerged depending on cluster membership and cluster symptom severity. The findings suggest hyperarousal symptoms may manifest in sleep maintenance issues, while intrusion symptoms may correlate with difficulties initiating sleep. Future research with larger cohorts is warranted to fully discern these associations, potentially paving the way for targeted interventions that ameliorate both daytime and nighttime PTSD symptoms
Ministers, Martyrs, and Mystics: Religious Antiwar Activists in the Vietnam Era
No full textThis thesis is a biographical exploration of the lives and experiences of five individuals who came to protest the Vietnam War due to their religious beliefs: A.J. Muste, who was ordained as a Dutch Reform minister but later came to describe himself as a Christian pacifist; Norman Morrison, who was a Quaker; Abraham Heschel, who was Jewish; William Sloane Coffin, Jr., who was Presbyterian; and Daniel Berrigan, who was Catholic. Examining the lives, experiences, actions, and writings of each of these men illuminates the subset of activists of the Vietnam period who came to protest the war due to their religious beliefs. In addition to their different religious identities, these men varied widely in age and background, and yet they all shared in the prophetic tradition of concern for suffering in the world. Their actions, writings, and examples influenced countless people both then and now
Cocreating Property Value and Energy Justice: A Framework to Leverage Investor Self-Interest to Overcome the Renewable Energy Split-Incentive in Rental Property
No full textRenewable energy deployment over the past two decades has been undeniably successful in many facets of the national economy. Its mass deployment can create positive economic, environmental, and energy justice impacts. In the built environment, which accounts for up to 40% of the U.S. greenhouse gasses, renewable energy has made significant inroads in adoption. Unfortunately, the benefits have not been evenly shared among all economic demographics and in all property types. Specifically, renters in existing multifamily workforce apartments are lagging far behind single-family homeowners in access to photovoltaic solar renewable energy as apartments currently have adoption rates below one percent. A primary reason cited for this stubbornly low adoption rate is the existence of the split-incentive where landlords must make the financial investments, but tenants receive the benefits of the energy systems.
The ramifications of this situation manifest themselves in economic, environmental, and health outcomes that are demonstrably worse for residents of workforce multifamily rental housing. The negative impacts are most acutely experienced in socioeconomically marginalized communities, but the effects can extend beyond local and state borders and have far-reaching negative consequences.
This study evaluated the financial and environmental benefits available with photovoltaic solar when deployed on a large scale on multifamily properties in various locations across the country. I therefore created a model to quantify the financial return and decarbonization potential of installing photovoltaic solar systems on multifamily apartments. I correlated these results with energy burden data across seven U.S. cities to create a geographic index for property owners and policy makers to understand how to develop and implement measures to incentivize increased renewable energy adoption.
The results of the study demonstrated that positive economic results can accrue to landlords after making photovoltaic solar investments in the form of both increased annual net income and property values beyond the value of the initial system investments. The property value increases were available in almost all geographic jurisdictions studied and reached above an eight-fold increase over the system cost in Lahaina, HI. Similarly, the annual cash flow enjoyed by the investors attained over a four-fold increase in the best-performing city, Lahaina, HI. These financial results were buttressed with significant positive environmental outcomes in many states when a reasonable photovoltaic solar adoption rate was modeled. Over half a million metric tons of CO2e could be avoided annually in six states, and in Texas, over two million metric tons of GHGs could be eliminated annually.
The study hopes to facilitate renewable energy adoption in rental housing in a wide variety of locations by providing the information necessary for property investors to determine the financial outcome of making renewable energy investments. Additionally, by using the three-dimensional index developed in the study, regulators could incentivize private property owners to unleash the financial and environmental results identified in the study by targeting policies to the locations that offer the best opportunities. This public-private schema could have the effect of allowing a private market mechanism to address both environmental and energy justice challenges creating a virtuous system where landlords, tenants, and community interests are all simultaneously promoted
Structured slow deep breathing: Comparing the differences between practicing in an individual setting versus a group setting and its impact on well-being
No full textThis study investigated whether a 5-day slow deep breathing (SDB) protocol (between 4-10 cycles of breath per minute) with extended exhalations, a type of body-oriented psychotherapy (BOP), impacted short-term (5 days post-intervention), and long-term (30 days post-intervention) well-being. Additionally, this study examined the impact of environment (e.g., individual vs. group) on the efficacy of the SDB protocol. BOP utilizes verbal and non-verbal body techniques to enhance self-awareness and foster patient communication. Group-based BOP has been shown to be particularly effective at promoting self-understanding and interpersonal connection. SDB has been associated with positive physiological changes and improved emotional regulation, immune function, heart rate variability, stress, anxiety, depression, and overall well-being. To assess the impact of (SDB) in individual and group environments, a between-subjects study was conducted comprised of 134 participants from multiple countries. Multiple aspects of the participants’ well-being were measured, including self-reported anxiety, depression, stress, mental and physical quality of life, and sleep. These standardized questionnaires were carried out at three different time points: pre-intervention, post-intervention, and after 30 days. The analysis involved examining the entire participant sample independently and comparing the effects within two distinct environments, group versus individual. The study's findings revealed that after five consecutive days of a 20-minute slow deep breathing (SDB) protocol with extended exhalations, perceived states of well-being significantly increased across all participants, regardless of the intervention environment. Furthermore, these results remained significant 30 days post-intervention. However, comparing the group to the individual setting did not yield significant results for performing better within a particular environment. Substantially higher compliance rates in the group setting suggest that social dynamics, including shared experiences and support, may enhance commitment to therapeutic practices and, by extension, yield better outcomes. Future research should aim to incorporate a broader range of methods, participant demographics, and an extended duration of study to fully understand the long-term effects and potential advantages of somatic interventions in varied settings
Sacrificing Cities Modernity, Religions, and Urban Spatial Dynamics in Dhaka, Bangladesh
No full textThis dissertation examines the complex interactions between urban religiosity and modernity in the context of Dhaka, Bangladesh, focusing on the celebration of Eid ul Adha. As a South Asian megacity, Dhaka undergoes significant transformations during this annual religious festival, temporarily disrupting the city's usual modernist development trajectory. The thesis introduces the concept of "Sacrificing Cities" to describe how Dhaka, like several other South Asian cities, tends to sacrifice its modern development mandates temporarily to accommodate traditional religious practices. These sacrifices manifest in various urban domains, including infrastructure, institutions, markets, and technology.
The study is based on three years of ethnographic fieldwork in Dhaka, exploring how the city manages the influx of millions of rural cattle farmers and traders, the transformation of urban spaces into makeshift cattle markets, and the temporary suspension of regular urban activities during Eid ul Adha. The research highlights the adaptability of Dhaka's urban infrastructure and institutions to non-secular functions and the role of the informal economic sector in managing the festival's demands. It also discusses the challenges posed by digitalization in maintaining traditional communal practices and religious sentiments.
By situating Dhaka within the broader frameworks of postcolonial, modern, and global city discourses, the thesis argues that the city's temporary disruptions during Eid ul Adha challenge conventional understandings of urban modernity. The concept of "Sacrificing Cities" provides a new lens for analyzing how cities in the Global South negotiate between tradition and modernity, revealing the unique ways in which urban religiosity shapes economic and political pathways.
Through detailed case studies, the thesis explores the justifications and mechanisms that enable Dhaka to temporarily deviate from its modern development goals, emphasizing the importance of understanding these practices within the context of South Asian urbanism. The findings contribute to broader discussions in critical urban development, postcolonialism, modernism, and developmental studies, offering insights into the evolution, development, and functioning of cities like Dhaka
The role of aging and metabolism in the regulation of T cell immunity
No full textFunctional deterioration of the adaptive immune system is a cardinal feature of the natural aging process and coincides with a sharp increase in the incidence of cancer. Although immune checkpoint blockade (ICB) has revolutionized the landscape of cancer therapy by providing durable tumor regression and overall survival, how aging impacts anti-tumor immunity and the activity of ICB is poorly understood. In addition to age-associated T cell dysfunction, metabolic barriers play a prominent role in the subversion of anti-tumor immune responses. However, the metabolic pathways required for effective anti-tumor immunity and successful re-invigoration of T cell function following ICB therapy are largely unknown.
By systemically dissecting the consequences of aging on anti-tumor immunity, we identified the loss of tumor antigen-specific CD8+ T cells as a primary feature driving tumor progression and resistance to immunotherapy in aged mice. Provision of tumor-matching clones elicits anti-tumor activity and sensitizes aged mice to ICB with anti-PD-1 therapy. Our results resolve a long standing mystery as to why mice beyond a certain age are recalcitrant to ICB therapy and highlight the importance of considering antigen specificity in studies of anti-tumor T cell responses in aged animals.
Additionally, we identify and functionally validate asparagine (Asn) metabolism as a novel regulator of the anti-tumor T cell response to PD-1 blockade. Remarkably, therapeutic Asn supplementation provides metabolic support to CD8+ T cells reinvigorated by anti-PD-1, resulting in enhanced tumor eradication and increased survival. We show that extracellular Asn bioavailability also represents a metabolic vulnerability for CD4+ helper T cells. Depletion of extracellular Asn impairs the activation, proliferation and differentiation of CD4+ T cells into helper lineages by restricting protein synthesis and dysregulating mitochondrial fitness. We demonstrate that Asn depletion through asparaginase treatment therapeutically ameliorates autoimmunity driven by pathogenic CD4+ T helper cells. These results identify Asn metabolism a key metabolic node for functional responses of T cells.
Taken together, our studies resolve an important conceptual gap in the aging cancer immunology field by identifying the loss of tumor antigen-specific T cells as a fundamental barrier for eliciting protective anti-tumor immunity in aged mice and reveal a requisite role for Asn metabolism in the propagation of functional T cell responses.Medical SciencesMedical Science
A House to Grow In: A Proposal for the Contemporary Re-Pioneering of the Iowa Prairie
No full textWhile the complexities of contemporary life have many considering a rural relocation, the current American imagination of a desirable rural life has contributed to uninformed urbanite settlement and a lack of population growth in agricultural rural communities. The thesis seeks to write promise and adventure back into these agricultural communities by proposing a contemporary re-pioneering of current farmland. In Clinton, Iowa, a new farmhouse typology and site strategy will aid in the incremental establishment of the former Iowa prairie and a pioneering family; this will become the foundation of a new rural narrative based on the resources of rural America: ecology, tradition, and the transcendent. In this reformed rural narrative, the transcendent value of stewardship will guide the design and is made manifest through the hidden abundance of the native prairie and a contemporary reimagining of traditional building and agricultural practices
Drug-Responsive Regulation and Comparison of Engineered Transcription Factors Containing Different Activation Domains
No full textThe pursuit of effective tools for probing biological systems has led to a growing
interest in approaches that offer both rapid, reversible, and accurate methods.
Specifically, the ability to perturb the function of specific proteins with precision is
highly sought after, as it contributes significantly to our capacity to unravel the intricacies
of complex biological processes. Effective methods to regulate gene expression or protein
function within mammalian hosts are essential for understanding basic biological
mechanisms (Banaszynski 2008). Examples of these methods include generating animal
knockouts, siRNA, the Cre-loxP system, and small molecule activators or inhibitors.
However, these methods are limited because they may not be reversible, are non-specific,
or—in the case of animal knockouts—the gene being knockout out is essential for
development thus confounding the study of the protein’s function. Another method
involves synthetic transcription factors paired with destabilizing-domain fusion proteins
that target a gene of interest. The destabilizing-domain are stabilized in the presence of a
ligand, thus providing the ability to control and regulate gene expression. This technique
can provide the regulatability, specificity, and ease of use in understanding complex
biological mechanisms. One component of synthetic transcription factors is the design of
activation domains utilized. Activation domains promote recruitment of chromatin
modifiers, which cause chromatin decondensation and accumulation of histone marks,
thus promoting transcription (Martella 2021). The variability of transcription efficacy is
based on the properties of different activation domains. In this study, three different
domains are investigated: VPR, VP64, and p65, with the goal of determining which one
provides the highest dynamic range in a lentiviral-transduced mammalian cell system
using a synthetic transcription factor fused to a drug-dependent destabilizing protein
domain