Matching Items (124)
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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
Description

One of the identified health risk areas for human spaceflight is infectious disease, particularly involving environmental microorganisms already found on the International Space Station (ISS). In particular, bacteria belonging to the Burkholderia cepacia complex (Bcc) which can cause human disease in those who are immunocompromised, have been identified in the

One of the identified health risk areas for human spaceflight is infectious disease, particularly involving environmental microorganisms already found on the International Space Station (ISS). In particular, bacteria belonging to the Burkholderia cepacia complex (Bcc) which can cause human disease in those who are immunocompromised, have been identified in the ISS water supply. This present study characterized the effect of spaceflight analog culture conditions on Bcc to certain physiological stresses (acid and thermal as well as intracellular survival in U927 human macrophage cells). The NASA-designed Rotating Wall Vessel (RWV) bioreactor was used as the spaceflight analogue culture system in these studies to grow Bcc bacterial cells under Low Shear Modeled Microgravity (LSMMG) conditions. Results show that LSMMG culture increased the resistance of Bcc to both acid and thermal stressors, but did not alter phagocytic uptake in 2-D monolayers of human monocytes.

ContributorsVu, Christian-Alexander (Author) / Nickerson, Cheryl (Thesis director) / Barrila, Jennifer (Committee member) / Ott, Mark (Committee member) / Barrett, The Honors College (Contributor) / Harrington Bioengineering Program (Contributor)
Created2023-05
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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
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Description
Exposure of liquid biospecimens like plasma and serum (P/S) to improper handling and storage can impact the integrity of biomolecules, potentially leading to apparent quantitative changes of important clinical proteins. An accurate and quick estimate of the quality of biospecimens employed in biomarker discovery and validation studies is essential to

Exposure of liquid biospecimens like plasma and serum (P/S) to improper handling and storage can impact the integrity of biomolecules, potentially leading to apparent quantitative changes of important clinical proteins. An accurate and quick estimate of the quality of biospecimens employed in biomarker discovery and validation studies is essential to facilitating accurate conclusions. ΔS-Cys-Albumin is a marker of blood P/S exposure to thawed conditions that can quantitatively track the exposure of P/S to temperatures greater than their freezing point of -30 C. Reported here are studies carried out to evaluate the potential of ΔS-Cys-Albumin to track the stability of clinically important analytes present in P/S upon their exposure to thawed conditions. P/S samples obtained from both cancer-free donors and cancer patients were exposed to 23 C (room temperature), 4 C and -20 C degrees, and the degree to which the apparent concentrations of clinically relevant biomolecules present in P/S were impacted during the time it took ΔS-Cys-Albumin to reach zero was measured. Analyte concentrations measured by molecular interaction-based assays were significantly impacted when samples were exposed to the point where average ΔS-Cys-Albumin fell below 12% at each temperature. Furthermore, the percentage of proteins that became unstable with time under thawed conditions exhibited a strong inverse linear relationship to ΔS-Cys-Albumin, indicating that ΔS-Cys-Albumin can serve as an effective surrogate marker to track the stability of other clinically relevant proteins in plasma as well as to estimate the fraction of proteins that have been destabilized by exposure to thawed conditions, regardless of what the exposure temperature(s) may have been. These results indicated that P/S exposure to thawed conditions disrupts epitopes required for clinical protein quantification via molecular interaction-based assays. In continuation of this theme, a spurious binding event between two clinically important proteins, Apolipoprotein E (ApoE) and Interferon-  (IFN) present in human plasma under in vitro experimental conditions is also reported. The interaction was confirmed to be evident only when ApoE was expressed in vitro with a Glutathione-S-Transferase (GST) fusion tag. Future steps required to find the exact manner in which the GST fusion tag facilitated the association between ApoE and IFNγ are discussed with emphasis on the possible pitfalls associated with using fusion proteins for studying novel protein-protein interactions.
ContributorsKapuruge, Erandi Prasadini (Author) / Borges, Chad R (Thesis advisor) / LaBaer, Joshua (Committee member) / Van Horn, Wade (Committee member) / Arizona State University (Publisher)
Created2021
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Description
As the construction industry in Saudi Arabia was on its way to thriving again. Their growth was due to the unprecedented volume of planned projects such as large-scale and unique projects. Suddenly, the world was faced with one of the most disrupting events in the last century which had a

As the construction industry in Saudi Arabia was on its way to thriving again. Their growth was due to the unprecedented volume of planned projects such as large-scale and unique projects. Suddenly, the world was faced with one of the most disrupting events in the last century which had a devastating impact on the construction industry specifically. This paper explores mainly the impact of the COVID-19 pandemic on construction projects in Saudi Arabia. Particularly, this paper explores how the pandemic and its related events contributed to the projects' schedule disturbances. This is because most of the projects rely on manpower and supply chains which were heavily disrupted due to the protective measures. For that, a study was conducted to evaluate the impact on the construction projects in Saudi Arabia, to what extent the schedule projects were affected, and what were the main reasons for the schedule delays. The research relied on a field survey and schedule analysis for 12 projects which resulted in identifying several causes of delays and the delayed durations that the projects in Saudi Arabia were facing. This research allows those in construction fields to identify the main causes of delays in order to avoid or minimize the impact of these issues on future projects.
ContributorsObeid, Muhammad Hasan Hani (Author) / Ariaratnam, Samuel (Thesis advisor) / El Asmar, Mounir (Committee member) / Chong, Oswald (Committee member) / Arizona State University (Publisher)
Created2021
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Description
Osteocalcin (Oc) is the most abundant non-collagen protein found in the bone, but its precise function is still not completely understood. Three glutamic acid (Glu) residues within its sequence are sites for vitamin K-dependent post-translational modification, replacing a hydrogen with a carboxylate located at the γ-carbon position, converting these to

Osteocalcin (Oc) is the most abundant non-collagen protein found in the bone, but its precise function is still not completely understood. Three glutamic acid (Glu) residues within its sequence are sites for vitamin K-dependent post-translational modification, replacing a hydrogen with a carboxylate located at the γ-carbon position, converting these to γ-carboxyglutamic acid (Gla) residues. This modification confers increased binding of Oc to Ca2+ and hydroxyapatite matrix. Presented here, novel metal binding partners Mn2+, Fe3+, and Cr3+ of human Oc were determined, while the previously identified binders to (generally) non-human Oc, Ca2+, Mg2+, Pb2+ and Al3+ were validated as binders to human Oc by direct infusion mass spectrometry with all metals binding with higher affinity to the post-translationally modified form (Gla-Oc) compared to the unmodified form (Glu-Oc). Oc was also found to form pentamer (Gla-Oc) and pentamer and tetramer (Glu-Oc) homomeric self-assemblies in the absence of NaCl, which disassembled to monomers in the presence of near physiological Na+ concentrations. Additionally, Oc was found to form filamentous structures in vitro by negative stain TEM in the presence of increased Ca2+ titrations in a Gla- and pH-dependent manner. Finally, by combining circular dichroism spectroscopy to determine the fraction of Gla-Oc bound, and inductively-coupled plasma mass spectrometry to quantify total Al concentrations, the data were fit to a single-site binding model and the equilibrium dissociation constant for Al3+ binding to human Gla-Oc was determined (Kd = 1.0 ± 0.12 nM). Including citrate, a known competitive binder of Al3+, maintained Al in solution and enabled calculation of free Al3+ concentrations using a Matlab script to solve the complex set of linear equations. To further improve Al solubility limits, the pH of the system was lowered to 4.5, the pH during bone resorption. Complementary binding experiments with Glu-Oc were not possible due to the observed precipitation of Glu-Oc at pH 4.5, although qualitatively if Glu-Oc binds Al3+, it is with much lower affinity compared to Gla-Oc. Taken together, the results presented here further support the importance of post-translational modification, and thus adequate nutritional intake of vitamin K, on the binding and self-assembly properties of human Oc.
ContributorsThibert, Stephanie (Author) / Borges, Chad R (Thesis advisor) / LaBaer, Joshua (Committee member) / Chiu, Po-Lin (Committee member) / Arizona State University (Publisher)
Created2021
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Description

The 5-year survival rate for late-stage metastatic melanoma is only ~30%. A major reason for this low survival rate is that one of the most commonly mutated genes in melanoma, NRAS, has no FDA-approved targeted therapies. Because the RAS protein does not have any targeted therapies, patients with RAS mutant

The 5-year survival rate for late-stage metastatic melanoma is only ~30%. A major reason for this low survival rate is that one of the most commonly mutated genes in melanoma, NRAS, has no FDA-approved targeted therapies. Because the RAS protein does not have any targeted therapies, patients with RAS mutant tumors have an ongoing need for treatments that indirectly target RAS. This thesis project aims to identify expression and phosphorylation levels of proteins downstream of RAS in melanoma cell lines with the most common driver mutations. By analyzing the protein-level differences between these genetic mutants, we hope to identify additional indirect RAS protein targets for the treatment of NRAS mutant melanoma. RAS has several downstream effector proteins involved in oncogenic signaling pathways including FAK, Paxillin, AKT, and ERK. 5 melanoma cell lines (2 BRAF mutant, 2 NRAS mutant, and 1 designated wildtype) were analyzed using western bloting for FAK, Paxillin, AKT, and ERK phosphorylation and total expression levels. The results of western blot analysis showed that NRAS mutant cell lines had increased expression of phosphorylated Paxillin. Increased Paxillin phosphorylation corresponds to increased Paxillin binding at the FAT domain of FAK. Therefore, cell lines with increased FAK FAT – Paxillin interaction would be more sensitive to FAK FAT domain inhibition. The data presented provide an an explanation for the reduction in cell viability in NRAS mutant cell lines infected with Ad-FRNK. This information also has significant clinical relevance as researchers work to develop synthetic FAK FAT domain inhibitors, such as cyclic peptides. Additionally, cell lines with high levels of phosphorylated AKT showed a significant reduction in the amount of phosphorylated ERK. The identification of this inverse relationship may help to explain why BRAF and NRAS mutations are mutually exclusive. To conclude, NRAS mutant cell lines have increased expression of phosphorylated Paxillin and AKT which may explain why NRAS mutant cell lines are more sensitive to FAK FAT domain inhibition.

ContributorsSherwood, Nicole (Author) / Gould, Ian (Thesis director) / LaBaer, Joshua (Committee member) / Marlowe, Timothy (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2022-05
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Description
Emerging pathogens present several challenges to medical diagnostics. Primarily, the exponential spread of a novel pathogen through naïve populations require a rapid and overwhelming diagnostic response at the site of outbreak. While point-of-care (PoC) platforms have been developed for detection of antigens, serologic responses, and pathogenic genomes, only nucleic acid

Emerging pathogens present several challenges to medical diagnostics. Primarily, the exponential spread of a novel pathogen through naïve populations require a rapid and overwhelming diagnostic response at the site of outbreak. While point-of-care (PoC) platforms have been developed for detection of antigens, serologic responses, and pathogenic genomes, only nucleic acid diagnostics currently have the potential to be developed and manufactured within weeks of an outbreak owing to the speed of next-generation sequencing and custom DNA synthesis. Among nucleic acid diagnostics, isothermal amplification strategies are uniquely suited for PoC implementation due to their simple instrumentation and lack of thermocycling requirement. Unfortunately, isothermal strategies are currently prone to spurious nonspecific amplification, hindering their specificity and necessitating extensive empirical design pipelines that are both time and resource intensive. In this work, isothermal amplification strategies are extensively compared for their feasibility of implementation in outbreak response scenarios. One such technology, Loop-mediated Amplification (LAMP), is identified as having high-potential for rapid development and PoC deployment. Various approaches to abrogating nonspecific amplification are described including a novel in silico design tool based on coarse-grained simulation of interactions between thermophilic DNA polymerase and DNA strands in isothermal reaction conditions. Nonspecific amplification is shown to be due to stabilization of primer secondary structures by high concentrations of Bst DNA polymerase and a mechanism of micro-complement-mediated cross-priming is demonstrated as causal via nanopore sequencing of nonspecific reaction products. The resulting computational model predicts primer set background in 64% of 67 test assays and its usefulness is illustrated further by determining problematic primers in a West Nile Virus-specific LAMP primer set and optimizing primer 3’ nucleotides to eliminate micro-complements within the reaction, resulting in inhibition of background accumulation. Finally, the emergence of Orthopox monkeypox (MPXV) as a recurring threat is discussed and SimCycle is utilized to develop a novel technique for clade-specific discrimination of MPXV based on bridging viral genomic rearrangements (Bridging LAMP). Bridging LAMP is implemented in a 4-plex microfluidic format and demonstrates 100% sensitivity in detection of 100 copies of viral lysates and 45 crude MPXV-positive patient samples collected during the 2022 Clade IIb outbreak.
ContributorsKnappenberger, Mark Daniel (Author) / Anderson, Karen S (Thesis advisor) / LaBaer, Joshua (Committee member) / Roberson, Robert (Committee member) / Lindsay, Stuart (Committee member) / Arizona State University (Publisher)
Created2023
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Description
The consequences of failures from large-diameter water pipelines can be severe. Results can include significant property damage, damage to adjacent infrastructure such as roads and bridges resulting in transportation delays or shutdowns, adjacent structural damage to buildings resulting in loss of business, service disruption to a significant number of

The consequences of failures from large-diameter water pipelines can be severe. Results can include significant property damage, damage to adjacent infrastructure such as roads and bridges resulting in transportation delays or shutdowns, adjacent structural damage to buildings resulting in loss of business, service disruption to a significant number of customers, loss of water, costly emergency repairs, and even loss of life. The American Water Works Association’s (AWWA) 2020 “State of the Water Industry” report states the top issue facing the water industry since 2016 is aging infrastructure, with the second being financing for improvements. The industry must find innovative ways to extend asset life and reduce maintenance expenditures. While are many different assets comprise the drinking water industry, pipelines are a major component and often neglected because they are typically buried. Reliability Centered Maintenance (RCM) is a process used to determine the most effective maintenance strategy for an asset, with the ultimate goal being to establish the required function of the asset with the required reliability at the lowest operations and maintenance costs. The RCM philosophy considers Preventive Maintenance, Predictive Maintenance, Condition Based Monitoring, Reactive Maintenance, and Proactive Maintenance techniques in an integrated manner to increase the probability an asset will perform its designed function throughout its design life with minimal maintenance. In addition to determining maintenance tasks, the timely performance of those tasks is crucial. If performed too late an asset may fail; if performed too early, resources that may be used better elsewhere are expended. Utility agencies can save time and money by using RCM analysis for their drinking water infrastructure. This dissertation reviews industries using RCM, discusses the benefits of an RCM analysis, and goes through a case study of an RCM at a large aqueduct in the United States. The dissertation further discusses the consequence of failure of large diameter water pipelines and proposes a regression model to help agencies determine the optimum time to perform maintenance tasks on large diameter prestressed concrete pipelines using RCM analysis.
ContributorsGeisbush, James R (Author) / Ariaratnam, Samuel T (Thesis advisor) / Grau, David (Committee member) / Chong, Oswald (Committee member) / Arizona State University (Publisher)
Created2024
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Description
MicroRNAs (miRNAs) are 17-22 nucleotide non-coding RNAs that regulate gene expression by targeting non-complementary elements in the 3’ untranslated regions (3’UTRs) of mRNAs. miRNAs, which form complex networks of interaction that differ by tissue and developmental stage, display conservation in their function across metazoan species. Yet much remains unknown regarding

MicroRNAs (miRNAs) are 17-22 nucleotide non-coding RNAs that regulate gene expression by targeting non-complementary elements in the 3’ untranslated regions (3’UTRs) of mRNAs. miRNAs, which form complex networks of interaction that differ by tissue and developmental stage, display conservation in their function across metazoan species. Yet much remains unknown regarding their biogenesis, localization, strand selection, and their absolute abundance due to the difficulty of detecting and amplifying such small molecules. Here, I used an updated HT qPCR-based methodology to follow miRNA expression of 5p and 3p strands for all 190 C. elegans miRNAs described in miRBase throughout all six developmental stages in triplicates (total of 9,708 experiments), and studied their expression levels, tissue localization, and the rules underlying miRNA strand selection. My study validated previous findings and identified novel, conserved patterns of miRNA strand expression throughout C. elegans development, which at times correlate with previously observed developmental phenotypes. Additionally, my results highlighted novel structural principles underlying strand selection, which can be applied to higher metazoans. Though optimized for use in C. elegans, this method can be easily adapted to other eukaryotic systems, allowing for more scalable quantitative investigation of miRNA biology and/or miRNA diagnostics.
ContributorsMeadows, Dalton Alexander (Author) / Mangone, Marco (Thesis advisor) / LaBaer, Joshua (Committee member) / Murugan, Vel (Committee member) / Wilson-Rawls, Jeanne (Committee member) / Arizona State University (Publisher)
Created2023