Matching Items (98)
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 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
Bdellovibrio bacteriovorus (B. bacteriovorus) is a predatory bacterium that preys on other gram-negative bacteria. In order to survive and reproduce, B. bacteriovorus invades the periplasm of other bacterial cells creating the potential for it to act as a “living antibiotic”. In this work, a comparison was made between the rates of predation of B. bacteriovorus in vitro and in vivo. In vitro, the behavior of B. bacteriovorus was examined in the presence of prey. In vivo, the behavior of B. bacteriovorus was examined in the presence of prey and a living host, Caenorhabditis elegans (C. elegans). C. elegans were infected with Escherichia coli (E. coli) and treated with B. bacteriovorus. In previous studies that analyzed B. bacteriovorus in vitro, a decrease in concentrations of bacteria has been observed after introduction of B. bacteriovorus. In vivo, B. bacteriovorus were found to not have a net reduction of E. coli but to reproducibly raise the level of fluctuations in E. coli concentrations.
ContributorsPerry, Nicole (Author) / Presse, Steve (Thesis director) / Mangone, Marco (Committee member) / Barrett, The Honors College (Contributor) / Economics Program in CLAS (Contributor) / School of Molecular Sciences (Contributor)
Created2023-05
Description
The RNA editing enzyme adenosine deaminase acting on double stranded RNA 2 (ADAR2) converts adenosine into inosine in regions of double stranded RNA. Here, it was discovered that this critical function of ADAR2 was dysfunctional in amyotrophic lateral sclerosis (ALS) mediated by the C9orf72 hexanucleotide repeat expansion, the most common genetic abnormality associated with ALS. Typically a nuclear protein, ADAR2 was localized in cytoplasmic accumulations in postmortem tissue from C9orf72 ALS patients. The mislocalization of ADAR2 was confirmed using immunostaining in a C9orf72 mouse model and motor neurons differentiated from C9orf72 patient induced pluripotent stem cells. Notably, the cytoplasmic accumulation of ADAR2 coexisted in neurons with cytoplasmic accumulations of TAR DNA binding protein 43 (TDP-43). Interestingly, ADAR2 overexpression in mammalian cell lines induced nuclear depletion and cytoplasmic accumulation of TDP-43, reflective of the pathology observed in ALS patients. The mislocalization of TDP-43 was dependent on the catalytic activity of ADAR2 and the ability of TDP-43 to bind directly to inosine containing RNA. In addition, TDP-43 nuclear export was significantly elevated in cells with increased RNA editing. Together these results describe a novel cellular mechanism by which alterations in RNA editing drive the nuclear export of TDP-43 leading to its cytoplasmic mislocalization. Considering the contribution of cytoplasmic TDP-43 to the pathogenesis of ALS, these findings represent a novel understanding of how the formation of pathogenic cytoplasmic TDP-43 accumulations may be initiated. Further research exploring this mechanism will provide insights into opportunities for novel therapeutic interventions.
ContributorsMoore, Stephen Philip (Author) / Sattler, Rita (Thesis advisor) / Zarnescu, Daniela (Committee member) / Brafman, David (Committee member) / Van Keuren-Jensen, Kendall (Committee member) / Mangone, Marco (Committee member) / Arizona State University (Publisher)
Created2021
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 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
Description
This dissertation describes a series of four studies on cognitive aging, working memory, and cognitive flexibility in dogs (Canis lupus familiaris) and their wild relatives. In Chapters 2 and 3, I designed assessments for age-related cognitive deficits in pet dogs which can be deployed rapidly using inexpensive and accessible materials. These novel tests can be easily implemented by owners, veterinarians, and clinicians and therefore, may improve care for elderly dogs by aiding in the diagnosis of dementia. In addition, these widely deployable tests may facilitate the use of dementia in pet dogs as a naturally occurring model of Alzheimer’s Disease in humans.In Chapters 4 and 5, I modified one of these tests to demonstrate for the first time that coyotes (Canis latrans) and wolves (Canis lupus lupus) develop age-related deficits in cognitive flexibility. This was an important first step towards differentiating between the genetic and environmental components of dementia in dogs and in turn, humans. Unexpectedly, I also detected cognitive deficits in young, adult dogs and wolves but not coyotes. These finding add to a recent shift in understanding cognitive development in dogs which may improve cognitive aging tests as well as training, care, and use of working and pet dogs. These findings also suggest that the ecology of coyotes may select for flexibility earlier in development.
In Chapter 5, I piloted the use of the same cognitive flexibility test for red and gray foxes so that future studies may test for lifespan changes in the cognition of small-bodied captive canids. More broadly, this paradigm may accommodate physical and behavioral differences between diverse pet and captive animals. In Chapters 4 and 5, I examined which ecological traits drive the evolution of behavioral flexibility and in turn, species resilience. I found that wolves displayed less flexibility than dogs and coyotes suggesting that species which do not rely heavily on unstable resources may be ill-equipped to cope with human habitat modification. Ultimately, this comparative work may help conservation practitioners to identify and protect species that cannot cope with rapid and unnatural environmental change.
ContributorsVan Bourg, Joshua (Author) / Wynne, Clive D (Thesis advisor) / Aktipis, C. Athena (Committee member) / Gilby, Ian C (Committee member) / Young, Julie K (Committee member) / Arizona State University (Publisher)
Created2022
Description
The partitioning of photosynthates between their sites of production (source) and their sites of utilization (sink) is a major determinant of crop yield and the potential of regulating this translocation promises substantial opportunities for yield increases. Ubiquitous overexpression of the plant type I proton pyrophosphatase (H+-PPase) in crops improves several valuable traits including salt tolerance and drought resistance, nutrient and water use efficiencies, and increased root biomass and yield. Originally, type I H+-PPases were described as pyrophosphate (PPi)-dependent proton pumps localized exclusively in vacuoles of mesophyll and meristematic tissues. It has been proposed that in the meristematic tissues, the role of this enzyme would be hydrolyzing PPi originated in biosynthetic reactions and favoring sink strength. Interestingly, this enzyme has been also localized at the plasma membrane of companion cells in the phloem which load and transport photosynthates from source leaves to sinks. Of note, the plasma membrane-localized H+-PPase could only function as a PPi-synthase in these cells due to the steep proton gradient between the apoplast and cytosol. The generated PPi would favor active sucrose loading through the sucrose/proton symporter in the phloem by promoting sucrose hydrolysis through the Sucrose Synthase pathway and providing the ATP required to maintain the proton gradient. To better understand these two different roles of type I H+-PPases, a series of Arabidopsis thaliana transgenic plants were generated. By expressing soluble pyrophosphatases in companion cells of Col-0 ecotype and H+-PPase mutants, impaired photosynthates partitioning was observed, suggesting phloem-localized H+-PPase could generate the PPi required for sucrose loading. Col-0 plants expressed with either phloem- or meristem-specific AVP1 overexpression cassette and the cross between the two tissue specific lines (Cross) were generated. The results showed that the phloem-specific AVP1-overexpressing plants had increased root hair elongation under limited nutrient conditions and both phloem- and meristem-overexpression of AVP1 contributed to improved rhizosphere acidification and drought resistance. It was concluded that H+-PPases localized in both sink and source tissues regulate plant growth and performance under stress through its versatile enzymatic functions (PPi hydrolase and synthase).
ContributorsLi, Lin (Author) / Park, Yujin (Thesis advisor) / Mangone, Marco (Committee member) / Roberson, Robert (Committee member) / Vermaas, Willem (Committee member) / Arizona State University (Publisher)
Created2022
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 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
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 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
Description
Precise modulation of gene expression is essential for proper tissue and cell-specific differentiation and function. Multiple distinct post-transcriptional regulatory mechanisms, such as miRNA (microRNA)-based regulation and alternative polyadenylation (APA), are an intrinsic part of this modulation and orchestrate intricate pathways to achieve and maintain balanced gene expression.MiRNA-based regulation and APA function through sequence motifs located in the 3’ Untranslated Region (3’UTR) of mRNA transcripts. MiRNAs are short (~22 nt) non-coding RNA molecules that bind target sequences within the 3’UTR of an mRNA transcript, inhibiting its translation or promoting its degradation. APA occurs during RNA transcription termination and leads to the preparation of mature mRNAs with different 3’UTR lengths, allowing shorter 3’UTRs to bypass miRNA regulation.
In addition to these two post-transcriptional forms of regulation, co-transcriptional mechanisms such as alternative RNA splicing, which produces distinct gene products from a precursor mRNA, are also important in controlling gene expression.
While miRNA-based regulation, APA, and alternative RNA splicing are important regulatory mechanisms, there is a lack of comprehensive understanding of how they interact and communicate with each other. This thesis studies these three forms of gene regulation in the nematode C. elegans, with the goal of extracting rules and mechanisms used by each of them in development to establish and maintain somatic tissue identity.
After isolating miRNA targets in multiple C. elegans somatic tissues, it was found that miRNAs can modulate the abundance of hnRNPs and SR proteins, which are known to control alternative RNA splicing in a dosage-dependent manner.To identify tissue-specific miRNAs, a nuclear fluorescent cell sorting (FACS)-based methodology named Nuc-Seq, was developed to isolate and sequence tissue-specific miRNAs from body muscle tissue. Nuc-Seq identified 2,848 muscle-specific protein-coding genes and 16 body muscle-specific miRNAs. This data was used to develop a high-quality body muscle-specific miRNA-APA Interactome which allows studies in regulatory processes in detail.
Taken together, this work highlights some of the complexity of pre- and post-transcriptional gene regulation and sheds light on how miRNA-based regulation, APA, and alternative RNA splicing are interconnected and are responsible for the establishment and maintenance of tissue identity.
ContributorsSchorr, Anna L (Author) / Mangone, Marco (Thesis advisor) / Harris, Robin (Committee member) / Sharma, Shalini (Committee member) / Varsani, Arvind (Committee member) / Arizona State University (Publisher)
Created2023
Description
Most protein-coding mRNAs in eukaryotes must undergo a series of processing steps so they can be exported from the nucleus and translated into protein. Cleavage and polyadenylation are vital steps in this maturation process. Improper cleavage and polyadenylation results in variation in the 3′ UTR length of genes, which is a hallmark of various human diseases. Previous data have shown that the majority of 3’UTRs of mRNAs from the nematode Caenorhabditis elegans terminate at an adenosine nucleotide, and that mutating this adenosine disrupts the cleavage reaction. It is unclear if the adenosine is included in the mature mRNA transcript or if it is cleaved off. To address this question, we are developing a novel method called the Terminal Adenosine Methylation (TAM) assay which will allow us to precisely define whether the cleavage reaction takes place upstream or downstream of this terminal adenosine. The TAM Assay utilizes the ability of the methyltransferase domain (MTD) of the human methyltransferase METTL16 to methylate the terminal adenosine of a test mRNA transcript prior to the cleavage reaction in vivo. The presence or absence of methylation at the terminal adenosine will then be identified using direct RNA sequencing. This project focuses on 1) preparing the chimeric construct that positions the MTD on the mRNA cleavage site of a test mRNA transcript, and 2) testing the functionality of this construct in vitro and developing a transgenic C. elegans strain expressing it. The TAM assay has the potential to be a valuable tool for elucidating the role of the terminal adenosine in cleavage and polyadenylation.
ContributorsKeane, Sara (Author) / Mangone, Marco (Thesis director) / Lapinaite, Audrone (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / Department of English (Contributor)
Created2023-05