Matching Items (128)
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Description
Transient Receptor Potential Vanilloid-1 (TRPV1) is an integral membrane polymodal cation channel involved in various essential biological functions, including thermosensing, thermoregulation, and nociception. Discrete TRPV1 activation modes such as ligand, heat, and proton have been challenging to disentangle. However, dissecting the polymodal nature of TRPV1 is essential for therapeutic development.

Transient Receptor Potential Vanilloid-1 (TRPV1) is an integral membrane polymodal cation channel involved in various essential biological functions, including thermosensing, thermoregulation, and nociception. Discrete TRPV1 activation modes such as ligand, heat, and proton have been challenging to disentangle. However, dissecting the polymodal nature of TRPV1 is essential for therapeutic development. The human TRPV1 (hTRPV1) voltage-sensing like domain (VSLD; transmembrane helices S1-S4) contains the canonical vanilloid ligand binding site and significantly contributes to thermosensing. Nuclear magnetic resonance (NMR)-detected studies probe the role of the hTRPV1-VSLD in TRPV1 polymodal function. The hTRPV1-VSLD is identified as an allosteric hub for all three primary TRPV1 activation modes and demonstrates plasticity in chemical ligand modulation. The presented results underscore molecular features in the VSLD that dictate TRPV1 function, highlighting important considerations for future therapeutic design.
ContributorsOwens, Aerial M. (Author) / Van Horn, Wade D. (Thesis advisor) / Levitus, Marcia (Committee member) / LaBaer, Joshua (Committee member) / Arizona State University (Publisher)
Created2023
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Description
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic, declared in March 2020 resulted in an unprecedented scientific effort that led to the deployment in less than a year of several vaccines to prevent severe disease, hospitalizations, and death from coronavirus disease 2019 (COVID-19). Most vaccine models focus on the

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic, declared in March 2020 resulted in an unprecedented scientific effort that led to the deployment in less than a year of several vaccines to prevent severe disease, hospitalizations, and death from coronavirus disease 2019 (COVID-19). Most vaccine models focus on the production of neutralizing antibodies against the spike (S) to prevent infection. As the virus evolves, new variants emerge that evade neutralizing antibodies produced by natural infection and vaccination, while memory T cell responses are long-lasting and resilient to most of the changes found in variants of concern (VOC). Several lines of evidence support the study of T cell-mediated immunity in SARS-CoV-2 infections. First, T cell reactivity against SARS-CoV-2 is found in both (cluster of differentiation) CD4+ and CD8+ T cell compartments in asymptomatic, mild, and severe recovered COVID-19 patients. Second, an early and stronger CD8+ T cell response correlates with less severe COVID-19 disease [1-4]. Third, both CD4+ and CD8+ T cells that are reactive to SARS-CoV-2 viral antigens are found in healthy unexposed individuals suggesting that cross-reactive and conserved epitopes may be protective against infection. The current study is focused on the T cell-mediated response, with special attention to conserved, non-spike-cross-reactive epitopes that may be protective against SARS-CoV-2. The first chapter reviews the importance of epitope prediction in understanding the T cell-mediated responses to a pathogen. The second chapter centers on the validation of SARS-CoV-2 CD8+ T cell predicted peptides to find conserved, immunodominant, and immunoprevalent epitopes that can be incorporated into the next generation of vaccines against severe COVID-19 disease. The third chapter explores pre-existing immunity to SARS-CoV-2 in a pre-pandemic cohort and finds two highly immunogenic epitopes that are conserved among human common cold coronaviruses (HCoVs). To end, the fourth chapter explores the concept of T cell receptor (TCR) cross-reactivity by isolating SARS-CoV-2-reactive TCRs to elucidate the mechanisms of cross-reactivity to SARS-CoV-2 and other human coronaviruses (HCoVs).
ContributorsCarmona, Jacqueline (Author) / Anderson, Karen S (Thesis advisor) / Lake, Douglas (Thesis advisor) / Maley, Carlo (Committee member) / Mangone, Marco (Committee member) / LaBaer, Joshua (Committee member) / Arizona State University (Publisher)
Created2023
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Description
Wastewater-based epidemiology (WBE) has emerged as a powerful tool for community health assessment, using wastewater-borne biological and chemical markers as analytical targets. This study investigates the critical influence of sampling frequency on the resultant estimates of opioid consumption and the prevalence of SARS-CoV-2 infections at the neighborhood level using common

Wastewater-based epidemiology (WBE) has emerged as a powerful tool for community health assessment, using wastewater-borne biological and chemical markers as analytical targets. This study investigates the critical influence of sampling frequency on the resultant estimates of opioid consumption and the prevalence of SARS-CoV-2 infections at the neighborhood level using common WBE biomarkers including fentanyl, norfentanyl, and the SARS-CoV-2 N1 gene as targets. The goal was to assess sampling methodologies that include the impact of the day of the week and of the sampling frequency. Wastewater samples were collected two or three times per week over the course of five months (n=525) and analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) or reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) for target chemical or molecular indicators of interest. Results showed no statistically significant differences for days of the week (i.e., Tuesday vs. Thursday vs. Saturday) for 24-hour composite samples analyzed for fentanyl or SARS-CoV-2; however, concentrations of the human metabolite of fentanyl, norfentanyl, were statistically different between Tuesday and Saturday (p < 0.05). When data were aggregated either by Tuesday/Thursday or Tuesday/Thursday/Saturday to examine sensitivity to sampling frequency, data were not statistically different except for the Tuesday/Thursday weekly average and Saturday for norfentanyl (p < 0.05). These results highlight how sample collection and data handling methodologies can impact wastewater-derived public health assessments. Care should be taken when selecting an approach to the sampling frequency based on the public health concerns under investigation.
ContributorsAJDINI, ARIANNA (Author) / Halden, Rolf (Thesis advisor) / Driver, Erin (Committee member) / Conroy-Ben, Otakuye (Committee member) / Arizona State University (Publisher)
Created2023
Description
Current methods for quantifying microplastics via LC-MS/MS analysis have been adapted from environmental monitoring protocols and are often inadequate for sampling within complex matrices. This study explores the application of liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the detection of microplastics. The initial phase of this research utilized pork kidney

Current methods for quantifying microplastics via LC-MS/MS analysis have been adapted from environmental monitoring protocols and are often inadequate for sampling within complex matrices. This study explores the application of liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the detection of microplastics. The initial phase of this research utilized pork kidney samples to establish a baseline for background and efficacy of sample processing. These findings underscore the complexity of developing a sensitive and specific analytical technique for microplastics in tissues. The observed discrepancies in contamination and replicability between samples emphasize the need for continual method optimization.
ContributorsBabbrah, Ayesha (Author) / Halden, Rolf (Thesis director) / Newell, Melanie (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2023-12
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Description
This dissertation focused on studying risks associated with emerging drinking water contaminants and tradeoffs related to water management interventions. The built environment impacts health, as humans on average spend ~90% of their time indoors. Federal regulations generally focus on drinking water at the water treatment plant and within the distribution

This dissertation focused on studying risks associated with emerging drinking water contaminants and tradeoffs related to water management interventions. The built environment impacts health, as humans on average spend ~90% of their time indoors. Federal regulations generally focus on drinking water at the water treatment plant and within the distribution system as opposed to when it enters buildings after crossing the property line. If drinking water is not properly managed in buildings, it can be a source or amplifier of microbial and chemical contaminants. Unlike regulations for chemical contaminants that are risk-based, for pathogens, regulations are either based on recommended treatment technologies or designated as zero, which is not achievable in practice. Practice-based judgments are typically made at the building level to maintain water quality. This research focuses on two drinking water opportunistic pathogens of public health concern, Legionella pneumophila and Mycobacterium avium complex (MAC). Multiple aspects of drinking water quality in two green buildings were monitored in tandem with water management interventions. Additionally, a quantitative microbial risk assessment framework was used to predict risk-based critical concentrations of MAC for drinking water-related exposures in the indoor environment corresponding to a 1 in 10,000 annual infection target risk benchmark. The overall goal of this work was to inform the development of water management plans and guidelines for buildings that will improve water quality in the built environment and promote better public health. It was determined that a whole building water softening system with ion exchange softening resin and expansion tanks were unexplored reservoirs for the colonization of L. pneumophila. Furthermore, it was observed that typical water management interventions such as flushing and thermal disinfection did not always mitigate water quality issues. Thus, there was a need to implement several atypical interventions such as equipment replacement to improve the building water quality. This work has contributed comprehensive field studies and models that have highlighted the need for additional niches, facility management challenges, and risk tradeoffs for focus in water safety plans. The work also informs additional risk-based water quality policy approaches for reducing drinking water risks.
ContributorsJoshi, Sayalee (Author) / Hamilton, Kerry A (Thesis advisor) / Abbaszadegan, Morteza (Committee member) / Conroy-Ben, Otakuye (Committee member) / Halden, Rolf (Committee member) / Arizona State University (Publisher)
Created2023
Description

Redox homeostasis is described as the net physiologic balance between inter-convertible oxidized and reduced equivalents within subcellular compartments that remain in a dynamic equilibrium. This equilibrium is impacted by reactive oxygen species (ROS), which are natural by-products of normal cellular activity. Studies have shown that cancer cells have high ROS

Redox homeostasis is described as the net physiologic balance between inter-convertible oxidized and reduced equivalents within subcellular compartments that remain in a dynamic equilibrium. This equilibrium is impacted by reactive oxygen species (ROS), which are natural by-products of normal cellular activity. Studies have shown that cancer cells have high ROS levels and altered redox homeostasis due to increased basal metabolic activity, mitochondrial dysfunction, peroxisome activity, as well as the enhanced activity of NADPH oxidase, cyclooxygenases, and lipoxygenases. Glioblastoma (GBM) is the most prevalent primary brain tumor in adults with a median survival of 15 months. GBM is characterized by its extreme resistance to therapeutic interventions as well as an elevated metabolic rate that results in the exacerbated production of ROS. Therefore, many agents with either antioxidant or pro-oxidant mechanisms of action have been rigorously employed in preclinical as well as clinical settings for treating GBM by inducing oxidative stress within the tumor. Among those agents are well-known antioxidant vitamin C and small molecular weight SOD mimic BMX-001, both of which are presently in clinical trials on GBM patients. Despite the wealth of investigations, limited data is available on the response of normal brain vs glioblastoma tissue to these therapeutic interventions. Currently, a sensitive and rapid liquid chromatography tandem mass spectrometry (LC-MS/MS) method was established for the quantification of a panel of oxidative stress biomarkers: glutathione (GSH), cysteine (Cys), glutathione disulfide (GSSG), and cysteine disulfide in human-derived brain tumor and mouse brain samples; this method will be enriched with additional oxidative stress biomarkers homocysteine (Hcy), methionine (Met), and cystathionine (Cyst). Using this enriched method, we propose to evaluate the thiol homeostasis and the redox state of both normal brain and GBM in mice after exposure with redox-active therapeutics. Our results showed that, compared to normal brain (in intact mice), GBM tissue has significantly lower GSH/GSSG and Cys/CySS ratios indicating much higher oxidative stress levels. Contralateral “normal” brain tissue collected from the mice with intracranial GBM were also under significant oxidative stress compared to normal brains collected from the intact mice. Importantly, normal brain tissue in both studies retained the ability to restore redox homeostasis after treatment with a redox-active therapeutic within 24 hours while glioblastoma tissue does not. Ultimately, elucidating the differential redox response of normal vs tumor tissue will allow for the development of more redox-active agents with therapeutic benefit.

ContributorsShaik, Kamal (Author) / LaBaer, Joshua (Thesis director) / Tovmasyan, Artak (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / Historical, Philosophical & Religious Studies, Sch (Contributor) / Dean, W.P. Carey School of Business (Contributor)
Created2022-12
Description

Synthetic plastics are ubiquitously used in a broad range of applications, including food and drink packaging. Plastics often contain chemical additives, including bisphenols, phthalates, and terephthalic acid, which can degrade under thermal stress. The environmental presence of these chemicals is cause for public concern, especially in consumer products that utilize

Synthetic plastics are ubiquitously used in a broad range of applications, including food and drink packaging. Plastics often contain chemical additives, including bisphenols, phthalates, and terephthalic acid, which can degrade under thermal stress. The environmental presence of these chemicals is cause for public concern, especially in consumer products that utilize plastic packaging, as many have been identified as endocrine disruptors. This study sought to determine exposure to phthalates, bisphenols, and terephthalic acid by quantifying a broad spectrum of these analytes within three bottled water brands at varying temperature exposure levels using the combination of solid phase extraction followed by isotope dilution liquid chromatography-tandem mass spectrometry. Monobenzyl phthalate was detected in two of the three brands after bottles were heated to ~100 °C, ranging from 98 – 107 ng/L, and bisphenol A was detected in one brand at ~100 °C at an average concentration of 748 ± 36 ng/L. Subsequent mass loading calculations demonstrated that bioaccumulation of BPA from Brand C after high levels of temperature exposure well exceeded the tolerable daily intake (TDI). Findings in this study indicate that consumers should not be expected to incur harmful exposures to the target compounds under normal conditions as analytes were not measured in water bottle samples at 25 °C or 60 °C. Further studies should explore a more nuisance approach to heating over long durations, including that of ultraviolet exposure.

ContributorsZevitz, Jacob (Author) / Halden, Rolf (Thesis director) / Driver, Erin (Committee member) / Barrett, The Honors College (Contributor) / School of International Letters and Cultures (Contributor) / School of Life Sciences (Contributor)
Created2022-12
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Description
DNA methylation (DNAm) is an epigenetic mark with a critical role in regulating gene expression. Altered clinical states, including toxin exposure and viral infections, can cause aberrant DNA methylation in cells, which may persist during cell division. Current methods to study genome-wide methylome profiles of the cells require a long

DNA methylation (DNAm) is an epigenetic mark with a critical role in regulating gene expression. Altered clinical states, including toxin exposure and viral infections, can cause aberrant DNA methylation in cells, which may persist during cell division. Current methods to study genome-wide methylome profiles of the cells require a long processing time and are expensive. Here, a novel technique called Multiplexed Methylated DNA Immunoprecipitation Sequencing (Mx-MeDIP-Seq), which is amenable to automation. Up to 15 different samples can be combined into the same run of Mx-MeDIP-Seq, using only 25 ng of DNA per sample. Mx-MeDIP-Seq was used to study DNAm profiles of peripheral blood mononuclear cells (PBMCs) in two biologically distinct RNA viral infections with different modes of transmission, symptoms, and interaction with the host immune system: human immunodeficiency virus1 (HIV-1) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Analysis of 90 hospitalized patients with SARS-CoV-2 and 57 healthy controls revealed that SARS-CoV-2 infection led to alterations in 920 methylated regions in PBMCs, resulting in a change in transcription that affects host immune response and cell survival. Analysis of publicly available RNA-Sequencing data in COVID-19 correlated with DNAm in several key pathways. These findings provide a mechanistic view toward further understanding of viral infections. Genome-wide DNAm changes post HIV-1-infection from 37 chronically ill patients compared to 17 controls revealed dysregulation of the actin cytoskeleton, which could contribute to the establishment of latency in HIV-1 infections. Longitudinal DNAm analysis identified several potentially protective and harmful genes that could contribute to disease suppression or progression.
ContributorsRidha, Inam (Author) / LaBaer, Joshua (Thesis advisor) / Murugan, Vel (Thesis advisor) / Plaisier, Christopher (Committee member) / Nikkhah, Mehdi (Committee member) / Vernon, Brent (Committee member) / Arizona State University (Publisher)
Created2022
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Description
Type 1 diabetes (T1D) is the result of an autoimmune attack against the insulin-producing β-cells of the pancreas causing hyperglycemia and requiring the individual to rely on life-long exogenous insulin. With the age of onset typically occurring in childhood, there is increased physical and emotional stress to the child as

Type 1 diabetes (T1D) is the result of an autoimmune attack against the insulin-producing β-cells of the pancreas causing hyperglycemia and requiring the individual to rely on life-long exogenous insulin. With the age of onset typically occurring in childhood, there is increased physical and emotional stress to the child as well as caregivers to maintain appropriate glucose levels. The majority of T1D patients have antibodies to one or more antigens: insulin, IA-2, GAD65, and ZnT8. Although antibodies are detectable years before symptoms occur, the initiating factors and mechanisms of progression towards β-cell destruction are still not known. The search for new autoantibodies to elucidate the autoimmune process in diabetes has been slow, with proteome level screenings on native proteins only finding a few minor antigens. Post-translational modifications (PTM)—chemical changes that occur to the protein after translation is complete—are an unexplored way a self-protein could become immunogenic. This dissertation presents the first large sale screening of autoantibodies in T1D to nitrated proteins. The Contra Capture Protein Array (CCPA) allowed for fresh expression of hundreds of proteins that were captured on a secondary slide by tag-specific ligand and subsequent modification with peroxynitrite. The IgG and IgM humoral response of 48 newly diagnosed T1D subjects and 48 age-matched controls were screened against 1632 proteins highly or specifically expressed in pancreatic cells. Top targets at 95% specificity were confirmed with the same serum samples using rapid antigenic protein in situ display enzyme-linked immunosorbent assay (RAPID ELISA) a modified sandwich ELISA employing the same cell-free expression as the CCPA. For validation, 8 IgG and 5 IgM targets were evaluated with an independent serum sample set of 94 T1D subjects and 94 controls. The two best candidates at 90% specificity were estrogen receptor 1 (ESR1) and phosphatidylinositol 4-kinase type 2 beta (PI4K2B) which had sensitivities of 22% (p=.014) and 25% (p=.045), respectively. Receiver operating characteristic (ROC) analyses found an area under curve (AUC) of 0.6 for ESR1 and 0.58 for PI4K2B. These studies demonstrate the ability and value for high-throughput autoantibody screening to modified antigens and the frequency of Type 1 diabetes.
ContributorsHesterman, Jennifer (Author) / LaBaer, Joshua (Thesis advisor) / Borges, Chad (Committee member) / Sweazea, Karen (Committee member) / Mangone, Marco (Committee member) / Arizona State University (Publisher)
Created2022
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Description
Antibodies are the immunoglobulins which are secreted by the B cells after a microbial invasion. They are stable and stays in the serum for a long time which makes them an excellent biomarker for disease diagnosis. Inflammatory bowel disease is a type of autoimmune disease where the immune system mistakenly

Antibodies are the immunoglobulins which are secreted by the B cells after a microbial invasion. They are stable and stays in the serum for a long time which makes them an excellent biomarker for disease diagnosis. Inflammatory bowel disease is a type of autoimmune disease where the immune system mistakenly attacks the commensal bacteria and leads to inflammation. We studied antibody response of 100 Crohn’s disease (CD), 100 ulcerative colitis (UC) and 100 healthy controls against 1,173 bacterial and 397 viral proteins. We found some anti-bacterial antibodies higher in CD compared to controls while some antibodies lower in UC compared to controls. We were able to build biomarker panels with AUCs of 0.81, 0.87, and 0.82 distinguishing CD vs. control, UC vs. control, and CD vs. UC, respectively. Subgroup analysis based on the Montreal classification revealed that penetrating CD behavior (B3), colonic CD location (L2), and extensive UC (E3) exhibited highest antibody reactivity among all patients. We also wanted to study the reason for the presence of autoantibodies in the sera of healthy individuals. A meta-analysis of 9 independent biomarker study was performed to find 77 common autoantibodies shared by healthy individuals. There was no gender bias; however, the number of autoantibodies increased with age, plateauing around adolescence. Molecular mimicry likely contributed to the elicitation of a subset of these common autoantibodies as 21 common autoantigens had 7 or more ungapped amino acid matches with viral proteins. Intrinsic properties of protein like hydrophilicity, basicity, aromaticity, and flexibility were enriched for common autoantigens. Subcellular localization and tissue expression analysis indicated the sequestration of some autoantigens from circulating autoantibodies can explain the absence of autoimmunity in these healthy individuals.
ContributorsShome, Mahasish (Author) / LaBaer, Joshua (Thesis advisor) / Borges, Chad (Committee member) / Stephanopoulos, Nicholas (Committee member) / Arizona State University (Publisher)
Created2021