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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
The world faces significant environmental and social challenges due to high economic development, population growth, industrialization, rapid urbanization, and unsustainable consumption. Global communities are taking the necessary measures to confront these international challenges and applying sustainable development principles across all sectors. Construction is a critical driving instrument of economic activity, and to achieve sustainable development, it is vital to transform conventional construction into a more sustainable model. The research investigated sustainable construction perceptions in Kuwait, a rapidly growing country with a high volume of construction activities. Kuwait has ambitious plans to transition into a more sustainable economic development model, and the construction industry needs to align with these plans. This research aims to identify the characteristics of sustainable construction applications in the Kuwaiti construction market, such as awareness, current perceptions, drivers and barriers, and the construction regulations' impact. The research utilized a qualitative approach to answer research questions and deliver research objectives by conducting eleven Semi-structured interviews with experienced professionals in the Kuwaiti construction market to collect rich data that reflects insights and understandings of the Kuwaiti construction industry. The Thematic analysis of the data resulted in six themes and one sub-theme that presented reflections, insights, and perspectives on sustainable construction perceptions in the Kuwaiti construction market. The research findings reflected poor sustainable construction awareness and poor environmental and social application in the construction industry, the determinant role of construction regulations in promoting sustainable construction. and barriers and drivers to sustainable construction applications. The research concluded with answers to research questions, delivery of research objectives, and an explanation of sustainable construction perceptions in the Kuwaiti construction market.
Contributorsalsalem, mohammad salem (Author) / Duran, Melanie (Thesis advisor) / Chong, Oswald (Committee member) / Sullivan, Kenneth (Committee member) / Grau, David (Committee member) / Arizona State University (Publisher)
Created2023
Description
During the rapid growth of infrastructure projects globally, countries pay high environmental and social costs as a result of the impacts caused from utilizing the traditional open-cut utility installation method that still widely being used in Egypt. For that, it was essential to have alternatives to reduce these environmental impacts and social costs; however, there are some obstacles that prevent the implementation and the realization of these alternatives.This research is conducted mainly to evaluate the environmental impacts of open-cut excavation vs. trenchless technology in Egypt, through two main methodologies. Firstly, a field survey that aims to measure knowledge of people working in the Egyptian construction industry of trenchless technology, and the harms caused from keeping utilizing open-cut for installing all kinds of underground utilities. In addition to investigating the reasons behind not relying on trenchless technology as a safe alternative for open-cut in Egypt.
Furthermore, in order to compare the greenhouse gases emissions resulted from both open-cut vs trenchless technology, a real case study is applied quantifying the amounts of the resulted greenhouse gases from each method. The results show that greenhouse gases emissions generated from open-cut were extremely higher than that of horizontal directional drilling as a trenchless installation method.
ContributorsKhedr, Ahmed Mossad Saeed Hafez (Author) / Ariaratnam, Samuel (Thesis advisor) / El Asmar, Mounir (Committee member) / Chong, Oswald (Committee member) / Arizona State University (Publisher)
Created2023
Description
The United States building sector was the most significant carbon emission contributor (over 40%). The United States government is trying to decrease carbon emissions by enacting policies, but emissions increased by approximately 7 percent in the U.S. between 1990 and 2013. To reduce emissions, investigating the factors affecting carbon emissions should be a priority. Therefore, in this dissertation, this research examine the relationship between carbon emissions and the factors affecting them from macro and micro perspectives. From a macroscopic perspective, the relationship between carbon dioxide, energy resource consumption, energy prices, GDP (gross domestic product), waste generation, and recycling waste generation in the building and waste sectors has been verified. From a microscopic perspective, the impact of non-permanent electric appliances and stationary and non-stationary occupancy has been investigated. To verify the relationships, various kinds of statistical and data mining techniques were applied, such as the Granger causality test, linear and logarithmic correlation, and regression method. The results show that natural gas and electricity prices are higher than others, as coal impacts their consumption, and electricity and coal consumption were found to cause significant carbon emissions. Also, waste generation and recycling significantly increase and decrease emissions from the waste sector, respectively. Moreover, non-permanent appliances such as desktop computers and monitors consume a lot of electricity, and significant energy saving potential has been shown. Lastly, a linear relationship exists between buildings’ electricity use and total occupancy, but no significant relationship exists between occupancy and thermal loads, such as cooling and heating loads. These findings will potentially provide policymakers with a better understanding of and insights into carbon emission manipulation in the building sector.
ContributorsLee, Seungtaek (Author) / Chong, Oswald (Thesis advisor) / Sullivan, Kenneth (Committee member) / Tang, Pingbo (Committee member) / Arizona State University (Publisher)
Created2018
Description
Signal transduction networks comprising protein-protein interactions (PPIs) mediate homeostatic, diseased, and therapeutic cellular responses. Mapping these networks has primarily focused on identifying interactors, but less is known about the interaction affinity, rates of interaction or their regulation. To better understand the extent of the annotated human interactome, I first examined > 2500 protein interactions within the B cell receptor (BCR) signaling pathway using a current, cutting-edge bioluminescence-based platform called “NanoBRET” that is capable of analyzing transient and stable interactions in high throughput. Eighty-three percent (83%) of the detected interactions have not been previously reported, indicating that much of the BCR pathway is still unexplored. Unfortunately, NanoBRET, as with all other high throughput methods, cannot determine binding kinetics or affinities. To address this shortcoming, I developed a hybrid platform that characterizes > 400 PPIs quantitatively and simultaneously in < 1 hour by combining the high throughput and flexible nature of nucleic programmable protein arrays (NAPPA) with the quantitative abilities of surface plasmon resonance imaging (SPRi). NAPPA-SPRi was then used to study the kinetics and affinities of > 12,000 PPIs in the BCR signaling pathway, revealing unique kinetic mechanisms that are employed by proteins, phosphorylation and activation states to regulate PPIs. In one example, activation of the GTPase RAC1 with nonhydrolyzable GTP-γS minimally affected its binding affinities with phosphorylated proteins but increased, on average, its on- and off-rates by 4 orders of magnitude for one-third of its interactions. In contrast, this phenomenon occurred with virtually all unphosphorylated proteins. The majority of the interactions (85%) were novel, sharing 40% of the same interactions as NanoBRET as well as detecting 55% more interactions than NanoBRET. In addition, I further validated four novel interactions identified by NAPPA-SPRi using SDS-PAGE migration and Western blot analyses. In one case, we have the first evidence of a direct enzyme-substrate interaction between two well-known proto-oncogenes that are abnormally regulated in > 30% of cancers, PI3K and MYC. Herein, PI3K is demonstrated to phosphorylate MYC at serine 62, a phosphosite that increases the stability of MYC. This study provides valuable insight into how PPIs, phosphorylation, and GTPase activation regulate the BCR signal transduction pathway. In addition, these methods could be applied toward understanding other signaling pathways, pathogen-host interactions, and the effect of protein mutations on protein interactions.
ContributorsPetritis, Brianne Ogata (Author) / LaBaer, Joshua (Thesis advisor) / Lake, Douglas (Committee member) / Wang, Shaopeng (Committee member) / Arizona State University (Publisher)
Created2018
Description
Multicellular organisms use precise gene regulation, executed throughout development, to build and sustain various cell and tissue types. Post-transcriptional gene regulation is essential for metazoan development and acts on mRNA to determine its localization, stability, and translation. MicroRNAs (miRNAs) and RNA binding proteins (RBPs) are the principal effectors of post-transcriptional gene regulation and act by targeting the 3'untranslated regions (3'UTRs) of mRNA. MiRNAs are small non-coding RNAs that have the potential to regulate hundreds to thousands of genes and are dysregulated in many prevalent human diseases such as diabetes, Alzheimer's disease, Duchenne muscular dystrophy, and cancer. However, the precise contribution of miRNAs to the pathology of these diseases is not known.
MiRNA-based gene regulation occurs in a tissue-specific manner and is implemented by an interplay of poorly understood and complex mechanisms, which control both the presence of the miRNAs and their targets. As a consequence, the precise contributions of miRNAs to gene regulation are not well known. The research presented in this thesis systematically explores the targets and effects of miRNA-based gene regulation in cell lines and tissues.
I hypothesize that miRNAs have distinct tissue-specific roles that contribute to the gene expression differences seen across tissues. To address this hypothesis and expand our understanding of miRNA-based gene regulation, 1) I developed the human 3'UTRome v1, a resource for studying post-transcriptional gene regulation. Using this resource, I explored the targets of two cancer-associated miRNAs miR-221 and let-7c. I identified novel targets of both these miRNAs, which present potential mechanisms by which they contribute to cancer. 2) Identified in vivo, tissue-specific targets in the intestine and body muscle of the model organism Caenorhabditis elegans. The results from this study revealed that miRNAs regulate tissue homeostasis, and that alternative polyadenylation and miRNA expression patterns modulate miRNA targeting at the tissue-specific level. 3) Explored the functional relevance of miRNA targeting to tissue-specific gene expression, where I found that miRNAs contribute to the biogenesis of mRNAs, through alternative splicing, by regulating tissue-specific expression of splicing factors. These results expand our understanding of the mechanisms that guide miRNA targeting and its effects on tissue-specific gene expression.
MiRNA-based gene regulation occurs in a tissue-specific manner and is implemented by an interplay of poorly understood and complex mechanisms, which control both the presence of the miRNAs and their targets. As a consequence, the precise contributions of miRNAs to gene regulation are not well known. The research presented in this thesis systematically explores the targets and effects of miRNA-based gene regulation in cell lines and tissues.
I hypothesize that miRNAs have distinct tissue-specific roles that contribute to the gene expression differences seen across tissues. To address this hypothesis and expand our understanding of miRNA-based gene regulation, 1) I developed the human 3'UTRome v1, a resource for studying post-transcriptional gene regulation. Using this resource, I explored the targets of two cancer-associated miRNAs miR-221 and let-7c. I identified novel targets of both these miRNAs, which present potential mechanisms by which they contribute to cancer. 2) Identified in vivo, tissue-specific targets in the intestine and body muscle of the model organism Caenorhabditis elegans. The results from this study revealed that miRNAs regulate tissue homeostasis, and that alternative polyadenylation and miRNA expression patterns modulate miRNA targeting at the tissue-specific level. 3) Explored the functional relevance of miRNA targeting to tissue-specific gene expression, where I found that miRNAs contribute to the biogenesis of mRNAs, through alternative splicing, by regulating tissue-specific expression of splicing factors. These results expand our understanding of the mechanisms that guide miRNA targeting and its effects on tissue-specific gene expression.
ContributorsKotagama, Kasuen Indrajith Bandara (Author) / Mangone, Marco (Thesis advisor) / LaBaer, Joshua (Committee member) / Newbern, Jason (Committee member) / Rawls, Alan (Committee member) / Arizona State University (Publisher)
Created2019
Description
Biomarkers find a wide variety of applications in oncology from risk assessment to diagnosis and predicting and monitoring recurrence and response to therapy. Developing clinically useful biomarkers for cancer is faced with several challenges, including cancer heterogeneity and factors related to assay development and biomarker performance. Circulating biomarkers offer a rapid, cost-effective, and minimally-invasive window to disease and are ideal for population-based screening. Circulating immune biomarkers are stable, measurable, and can betray the underlying antigen when present below detection levels or even no longer present. This dissertation aims to investigate potential circulating immune biomarkers with applications in cancer detection and novel therapies. Over 600,000 cancers each year are attributed to the human papillomavirus (HPV), including cervical, anogenital and oropharyngeal cancers. A key challenge in understanding HPV immunobiology and developing immune biomarkers is the diversity of HPV types and the need for multiplexed display of HPV antigens. In Project 1, nucleic acid programmable protein arrays displaying the proteomes of 12 HPV types were developed and used for serum immunoprofiling of women with cervical lesions or invasive cervical cancer. These arrays provide a valuable high-throughput tool for measuring the breadth, specificity, heterogeneity, and cross-reactivity of the serologic response to HPV. Project 2 investigates potential biomarkers of immunity to the bacterial CRISPR/Cas9 system that is currently in clinical trials for cancer. Pre-existing B cell and T cell immune responses to Cas9 were detected in humans and Cas9 was modified to eliminate immunodominant epitopes while preserving its function and specificity. This dissertation broadens our understanding of the immunobiology of cervical cancer and provides insights into the immune profiles that could serve as biomarkers of various applications in cancer.
ContributorsEwaisha, Radwa Mohamed Emadeldin Mahmoud (Author) / Anderson, Karen S (Thesis advisor) / LaBaer, Joshua (Committee member) / Lake, Douglas F (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2018
Description
Biological fluids, in particular blood plasma, provide a vital source of information on the state of human health. While specific detection of biomarker species can aid in disease diagnostics, the complexity of plasma makes analysis challenging. Despite the challenge of complex sample analysis, biomarker quantification has become a primary interest in biomedical analysis. Due to the extremely specific interaction between antibody and analyte, immunoassays are attractive for the analysis of these samples and have gained popularity since their initial introduction several decades ago. Current limitations to diagnostics through blood testing include long incubation times, interference from non-specific binding, and the requirement for specialized instrumentation and personnel. Optimizing the features of immunoassay for diagnostic testing and biomarker quantification would enable early and accurate detection of disease and afford rapid intervention, potentially improving patient outcomes. Improving the limit of quantitation for immunoassay has been the primary goal of many diverse experimental platforms. While the ability to accurately quantify low abundance species in a complex biological sample is of the utmost importance in diagnostic testing, models illustrating experimental limitations have relied on mathematical fittings, which cannot be directly related to finite analytical limits or fundamental relationships. By creating models based on the law of mass action, it is demonstrated that fundamental limitations are imposed by molecular shot noise, creating a finite statistical limitation to quantitative abilities. Regardless of sample volume, 131 molecules are necessary for quantitation to take place with acceptable levels of uncertainty. Understanding the fundamental limitations of the technique can aid in the design of immunoassay platforms, and assess progress toward the development of optimal diagnostic testing. A sandwich-type immunoassay was developed and tested on three separate human protein targets: myoglobin, heart-type fatty acid binding protein, and cardiac troponin I, achieving superior limits of quantitation approaching ultimate limitations. Furthermore, this approach is compatible with upstream sample separation methods, enabling the isolation of target molecules from a complex biological sample. Isolation of target species prior to analysis allows for the multiplex detection of biomarker panels in a microscale device, making the full optimization of immunoassay techniques possible for clinical diagnostics.
ContributorsWoolley, Christine F (Author) / Hayes, Mark A. (Thesis advisor) / Ros, Alexandra (Committee member) / LaBaer, Joshua (Committee member) / Arizona State University (Publisher)
Created2015
Description
Quiescin sulfhydryl oxidase 1 (QSOX1) is a highly conserved disulfide bond-generating enzyme that represents the ancient fusion of two major thiol-disulfide oxidoreductase gene families: thioredoxin and ERV. QSOX1 was first linked with cancer after being identified as overexpressed in pancreatic ductal adenocarcinoma (but not in adjacent normal ductal epithelia, infiltrating lymphocytes, or chronic pancreatitis). QSOX1 overexpression has been confirmed in a number of other histological tumor types, such as breast, lung, kidney, prostate, and others. Expression of QSOX1 supports a proliferative and invasive phenotype in tumor cells, and its enzymatic activity is critical for promoting an invasive phenotype. An in vivo tumor growth study utilizing the pancreatic tumor cell line MIAPaCa-2 containing a QSOX1-silencing shRNA construct revealed that QSOX1 expression supports a proliferative phenotype. These preliminary studies suggest that suppressing the enzymatic activity of QSOX1 could represent a novel therapeutic strategy to inhibit proliferation and invasion of malignant neoplasms.
The goal of this research was to identify and characterize biologically active small molecule inhibitors for QSOX1. Chemical inhibition of QSOX1 enzymatic activity was hypothesized to reduce growth and invasion of tumor cells. Recombinant QSOX1 was screened against libraries of small molecules using an enzymatic activity assay to identify potential QSOX1 inhibitors. Two lead QSOX1 inhibitors were confirmed, 2-phenyl-1, 2-benzisoselenazol-3-one (ebselen), and 3-methoxy-n-[4-(1 pyrrolidinyl)phenyl]benzamide. The biological activity of these compounds is consistent with QSOX1 knockdown in tumor cell lines, reducing growth and invasion in vitro. Treatment of tumor cells with these compounds also resulted in specific ECM defects, a phenotype associated with QSOX1 knockdown. Additionally, these compounds were shown to be active in pancreatic and renal cancer xenografts, reducing tumor growth with daily treatment. For ebselen, the molecular mechanism of inhibition was determined using a combination of biochemical and mass spectrometric techniques. The results obtained in these studies provide proof-of-principle that targeting QSOX1 enzymatic activity with chemical compounds represents a novel potential therapeutic avenue worthy of further investigation in cancer. Additionally, the utility of these small molecules as chemical probes will yield future insight into the general biology of QSOX1, including the identification of novel substrates of QSOX1.
The goal of this research was to identify and characterize biologically active small molecule inhibitors for QSOX1. Chemical inhibition of QSOX1 enzymatic activity was hypothesized to reduce growth and invasion of tumor cells. Recombinant QSOX1 was screened against libraries of small molecules using an enzymatic activity assay to identify potential QSOX1 inhibitors. Two lead QSOX1 inhibitors were confirmed, 2-phenyl-1, 2-benzisoselenazol-3-one (ebselen), and 3-methoxy-n-[4-(1 pyrrolidinyl)phenyl]benzamide. The biological activity of these compounds is consistent with QSOX1 knockdown in tumor cell lines, reducing growth and invasion in vitro. Treatment of tumor cells with these compounds also resulted in specific ECM defects, a phenotype associated with QSOX1 knockdown. Additionally, these compounds were shown to be active in pancreatic and renal cancer xenografts, reducing tumor growth with daily treatment. For ebselen, the molecular mechanism of inhibition was determined using a combination of biochemical and mass spectrometric techniques. The results obtained in these studies provide proof-of-principle that targeting QSOX1 enzymatic activity with chemical compounds represents a novel potential therapeutic avenue worthy of further investigation in cancer. Additionally, the utility of these small molecules as chemical probes will yield future insight into the general biology of QSOX1, including the identification of novel substrates of QSOX1.
ContributorsHanavan, Paul D (Author) / Lake, Douglas (Thesis advisor) / LaBaer, Joshua (Committee member) / Mangone, Marco (Committee member) / Borges, Chad (Committee member) / Arizona State University (Publisher)
Created2015
Description
Given the importance of buildings as major consumers of resources worldwide, several organizations are working avidly to ensure the negative impacts of buildings are minimized. The U.S. Green Building Council's (USGBC) Leadership in Energy and Environmental Design (LEED) rating system is one such effort to recognize buildings that are designed to achieve a superior performance in several areas including energy consumption and indoor environmental quality (IEQ). The primary objectives of this study are to investigate the performance of LEED certified facilities in terms of energy consumption and occupant satisfaction with IEQ, and introduce a framework to assess the performance of LEED certified buildings.
This thesis attempts to achieve the research objectives by examining the LEED certified buildings on the Arizona State University (ASU) campus in Tempe, AZ, from two complementary perspectives: the Macro-level and the Micro-level. Heating, cooling, and electricity data were collected from the LEED-certified buildings on campus, and their energy use intensity was calculated in order to investigate the buildings' actual energy performance. Additionally, IEQ occupant satisfaction surveys were used to investigate users' satisfaction with the space layout, space furniture, thermal comfort, indoor air quality, lighting level, acoustic quality, water efficiency, cleanliness and maintenance of the facilities they occupy.
From a Macro-level perspective, the results suggest ASU LEED buildings consume less energy than regional counterparts, and exhibit higher occupant satisfaction than national counterparts. The occupant satisfaction results are in line with the literature on LEED buildings, whereas the energy results contribute to the inconclusive body of knowledge on energy performance improvements linked to LEED certification. From a Micro-level perspective, data analysis suggest an inconsistency between the LEED points earned for the Energy & Atmosphere and IEQ categories, on one hand, and the respective levels of energy consumption and occupant satisfaction on the other hand. Accordingly, this study showcases the variation in the performance results when approached from different perspectives. This contribution highlights the need to consider the Macro-level and Micro-level assessments in tandem, and assess LEED building performance from these two distinct but complementary perspectives in order to develop a more comprehensive understanding of the actual building performance.
This thesis attempts to achieve the research objectives by examining the LEED certified buildings on the Arizona State University (ASU) campus in Tempe, AZ, from two complementary perspectives: the Macro-level and the Micro-level. Heating, cooling, and electricity data were collected from the LEED-certified buildings on campus, and their energy use intensity was calculated in order to investigate the buildings' actual energy performance. Additionally, IEQ occupant satisfaction surveys were used to investigate users' satisfaction with the space layout, space furniture, thermal comfort, indoor air quality, lighting level, acoustic quality, water efficiency, cleanliness and maintenance of the facilities they occupy.
From a Macro-level perspective, the results suggest ASU LEED buildings consume less energy than regional counterparts, and exhibit higher occupant satisfaction than national counterparts. The occupant satisfaction results are in line with the literature on LEED buildings, whereas the energy results contribute to the inconclusive body of knowledge on energy performance improvements linked to LEED certification. From a Micro-level perspective, data analysis suggest an inconsistency between the LEED points earned for the Energy & Atmosphere and IEQ categories, on one hand, and the respective levels of energy consumption and occupant satisfaction on the other hand. Accordingly, this study showcases the variation in the performance results when approached from different perspectives. This contribution highlights the need to consider the Macro-level and Micro-level assessments in tandem, and assess LEED building performance from these two distinct but complementary perspectives in order to develop a more comprehensive understanding of the actual building performance.
ContributorsChokor, Abbas (Author) / El Asmar, Mounir (Thesis advisor) / Chong, Oswald (Committee member) / Parrish, Kristen (Committee member) / Arizona State University (Publisher)
Created2015