ASU Electronic Theses and Dissertations
This collection includes most of the ASU Theses and Dissertations from 2011 to present. ASU Theses and Dissertations are available in downloadable PDF format; however, a small percentage of items are under embargo. Information about the dissertations/theses includes degree information, committee members, an abstract, supporting data or media.
In addition to the electronic theses found in the ASU Digital Repository, ASU Theses and Dissertations can be found in the ASU Library Catalog.
Dissertations and Theses granted by Arizona State University are archived and made available through a joint effort of the ASU Graduate College and the ASU Libraries. For more information or questions about this collection contact or visit the Digital Repository ETD Library Guide or contact the ASU Graduate College at gradformat@asu.edu.
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Description
Since Darwin popularized the evolution theory in 1895, it has been completed and studied through the years. Starting in 1990s, evolution at molecular level has been used to discover functional molecules while studying the origin of functional molecules in nature by mimicing the natural selection process in laboratory. Along this line, my Ph.D. dissertation focuses on the in vitro selection of two important biomolecules, deoxynucleotide acid (DNA) and protein with binding properties. Chapter two focuses on in vitro selection of DNA. Aptamers are single-stranded nucleic acids that generated from a random pool and fold into stable three-dimensional structures with ligand binding sites that are complementary in shape and charge to a desired target. While aptamers have been selected to bind a wide range of targets, it is generally thought that these molecules are incapable of discriminating strongly alkaline proteins due to the attractive forces that govern oppositely charged polymers. By employing negative selection step to eliminate aptamers that bind with off-target through charge unselectively, an aptamer that binds with histone H4 protein with high specificity (>100 fold)was generated. Chapter four focuses on another functional molecule: protein. It is long believed that complex molecules with different function originated from simple progenitor proteins, but very little is known about this process. By employing a previously selected protein that binds and catalyzes ATP, which is the first and only protein that was evolved completely from random pool and has a unique α/β-fold protein scaffold, I fused random library to the C-terminus of this protein and evolved a multi-domain protein with decent properties. Also, in chapter 3, a unique bivalent molecule was generated by conjugating peptides that bind different sites on the protein with nucleic acids. By using the ligand interactions by nucleotide conjugates technique, off-the shelf peptide was transferred into high affinity protein capture reagents that mimic the recognition properties of natural antibodies. The designer synthetic antibody amplifies the binding affinity of the individual peptides by ∼1000-fold to bind Grb2 with a Kd of 2 nM, and functions with high selectivity in conventional pull-down assays from HeLa cell lysates.
ContributorsJiang, Bing (Author) / Chaput, John C (Thesis advisor) / Chen, Julian (Committee member) / Liu, Yan (Committee member) / Arizona State University (Publisher)
Created2013
Description
Researchers across a variety of fields are often interested in determining if data are of a random nature or if they exhibit patterning which may be the result of some alternative and potentially more interesting process. This dissertation explores a family of statistical methods, i.e. space-time interaction tests, designed to detect structure within three-dimensional event data. These tests, widely employed in the fields of spatial epidemiology, criminology, ecology and beyond, are used to identify synergistic interaction across the spatial and temporal dimensions of a series of events. Exploration is needed to better understand these methods and determine how their results may be affected by data quality problems commonly encountered in their implementation; specifically, how inaccuracy and/or uncertainty in the input data analyzed by the methods may impact subsequent results. Additionally, known shortcomings of the methods must be ameliorated. The contributions of this dissertation are twofold: it develops a more complete understanding of how input data quality problems impact the results of a number of global and local tests of space-time interaction and it formulates an improved version of one global test which accounts for the previously identified problem of population shift bias. A series of simulation experiments reveal the global tests of space-time interaction explored here to be dramatically affected by the aforementioned deficiencies in the quality of the input data. It is shown that in some cases, a conservative degree of these common data problems can completely obscure evidence of space-time interaction and in others create it where it does not exist. Conversely, a local metric of space-time interaction examined here demonstrates a surprising robustness in the face of these same deficiencies. This local metric is revealed to be only minimally affected by the inaccuracies and incompleteness introduced in these experiments. Finally, enhancements to one of the global tests are presented which solve the problem of population shift bias associated with the test and better contextualize and visualize its results, thereby enhancing its utility for practitioners.
ContributorsMalizia, Nicholas (Author) / Anselin, Luc (Thesis advisor) / Murray, Alan (Committee member) / Rey, Sergio (Committee member) / Arizona State University (Publisher)
Created2013
Description
The objective of this dissertation is to empirically analyze the results of the retail location decision making process and how chain networks evolve given their value platform. It employs one of the largest cross-sectional databases of retailers ever assembled, including 50 US retail chains and over 70,000 store locations. Three closely related articles, which develop new theory explaining location deployment and behaviors of retailers, are presented. The first article, "Regionalism in US Retailing," presents a comprehensive spatial analysis of the domestic patterns of retailers. Geographic Information Systems (GIS) and statistics examine the degree to which the chains are deployed regionally versus nationally. Regional bias is found to be associated with store counts, small market deployment, and the location of the founding store, but not the age of the chain. Chains that started in smaller markets deploy more stores in other small markets and vice versa for chains that started in larger markets. The second article, "The Location Types of US Retailers," is an inductive analysis of the types of locations chosen by the retailers. Retail locations are classified into types using cluster analysis on situational and trade area data at the geographical scale of the individual stores. A total of twelve distinct location types were identified. A second cluster analysis groups together the chains with the most similar location profiles. Retailers within the same retail business often chose similar types of locations and were placed in the same clusters. Retailers generally restrict their deployment to one of three overall strategies including metropolitan, large retail areas, or market size variety. The third article, "Modeling Retail Chain Expansion and Maturity through Wave Analysis: Theory and Application to Walmart and Target," presents a theory of retail chain expansion and maturity whereby retailers expand in waves with alternating periods of faster and slower growth. Walmart diffused gradually from Arkansas and Target grew from the coasts inward. They were similar, however, in that after expanding into an area they reached a point of saturation and opened fewer stores, then moved on to other areas, only to revisit the earlier areas for new stores.
ContributorsJoseph, Lawrence (Author) / Kuby, Michael (Thesis advisor) / Matthews, Richard (Committee member) / Ó Huallacháin, Breandán (Committee member) / Kumar, Ajith (Committee member) / Arizona State University (Publisher)
Created2013
Description
The principle of Darwinian evolution has been applied in the laboratory to nucleic acid molecules since 1990, and led to the emergence of in vitro evolution technique. The methodology of in vitro evolution surveys a large number of different molecules simultaneously for a pre-defined chemical property, and enrich for molecules with the particular property. DNA and RNA sequences with versatile functions have been identified by in vitro selection experiments, but many basic questions remain to be answered about how these molecules achieve their functions. This dissertation first focuses on addressing a fundamental question regarding the molecular recognition properties of in vitro selected DNA sequences, namely whether negatively charged DNA sequences can be evolved to bind alkaline proteins with high specificity. We showed that DNA binders could be made, through carefully designed stringent in vitro selection, to discriminate different alkaline proteins. The focus of this dissertation is then shifted to in vitro evolution of an artificial genetic polymer called threose nucleic acid (TNA). TNA has been considered a potential RNA progenitor during early evolution of life on Earth. However, further experimental evidence to support TNA as a primordial genetic material is lacking. In this dissertation we demonstrated the capacity of TNA to form stable tertiary structure with specific ligand binding property, which suggests a possible role of TNA as a pre-RNA genetic polymer. Additionally, we discussed the challenges in in vitro evolution for TNA enzymes and developed the necessary methodology for future TNA enzyme evolution.
ContributorsYu, Hanyang (Author) / Chaput, John C (Thesis advisor) / Chen, Julian (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2013
Description
Cyanovirin-N (CV-N) is a naturally occurring lectin originally isolated from the cyanobacteria Nostoc ellipsosporum. This 11 kDa lectin is 101 amino acids long with two binding sites, one at each end of the protein. CV-N specifically binds to terminal Manα1-2Manα motifs on the branched, high mannose Man9 and Man8 glycosylations found on enveloped viruses including Ebola, Influenza, and HIV. wt-CVN has micromolar binding to soluble Manα1-2Manα and also inhibits HIV entry at low nanomolar concentrations. CV-N's high affinity and specificity for Manα1-2Manα makes it an excellent lectin to study for its glycan-specific properties. The long-term aim of this project is to make a variety of mutant CV-Ns to specifically bind other glycan targets. Such a set of lectins may be used as screening reagents to identify biomarkers and other glycan motifs of interest. As proof of concept, a T7 phage display library was constructed using P51G-m4-CVN genes mutated at positions 41, 44, 52, 53, 56, 74, and 76 in binding Domain B. Five CV-N mutants were selected from the library and expressed in BL21(DE3) E. coli. Two of the mutants, SSDGLQQ-P51Gm4-CVN and AAGRLSK-P51Gm4-CVN, were sufficiently stable for characterization and were examined by CD, Tm, ELISA, and glycan array. Both proteins have CD minima at approximately 213 nm, indicating largely β-sheet structure, and have Tm values greater than 40°C. ELISA against gp120 and RNase B demonstrate both proteins' ability to bind high mannose glycans. To more specifically determine the binding specificity of each protein, AAGRLSK-P51Gm4-CVN, SSDGLQQ-P51Gm4-CVN, wt-CVN, and P51G-m4-CVN were sent to the Consortium for Functional Glycomics (CFG) for glycan array analysis. AAGRLSK-P51Gm4-CVN, wt-CVN, and P51G-m4-CVN, have identical specificities for high mannose glycans containing terminal Manα1-2Manα. SSDGLQQ-P51Gm4-CVN binds to terminal GlcNAcα1-4Gal motifs and a subgroup of high mannose glycans bound by P51G-m4-CVN. SSDGLQQ-wt-CVN was produced to restore anti-HIV activity and has a high nanomolar EC50 value compared to wt-CVN's low nanomolar activity. Overall, these experiments show that CV-N Domain B can be mutated and retain specificity identical to wt-CVN or acquire new glycan specificities. This first generation information can be used to produce glycan-specific lectins for a variety of applications.
ContributorsRuben, Melissa (Author) / Ghirlanda, Giovanna (Thesis advisor) / Allen, James (Committee member) / Wachter, Rebekka (Committee member) / Arizona State University (Publisher)
Created2013
Description
The dynamics of urban water use are characterized by spatial and temporal variability that is influenced by associated factors at different scales. Thus it is important to capture the relationship between urban water use and its determinants in a spatio-temporal framework in order to enhance understanding and management of urban water demand. This dissertation aims to contribute to understanding the spatio-temporal relationships between single-family residential (SFR) water use and its determinants in a desert city. The dissertation has three distinct papers to support this goal. In the first paper, I demonstrate that aggregated scale data can be reliably used to study the relationship between SFR water use and its determinants without leading to significant ecological fallacy. The usability of aggregated scale data facilitates scientific inquiry about SFR water use with more available aggregated scale data. The second paper advances understanding of the relationship between SFR water use and its associated factors by accounting for the spatial and temporal dependence in a panel data setting. The third paper of this dissertation studies the historical contingency, spatial heterogeneity, and spatial connectivity in the relationship of SFR water use and its determinants by comparing three different regression models. This dissertation demonstrates the importance and necessity of incorporating spatio-temporal components, such as scale, dependence, and heterogeneity, into SFR water use research. Spatial statistical models should be used to understand the effects of associated factors on water use and test the effectiveness of certain management policies since spatial effects probably will significantly influence the estimates if only non-spatial statistical models are used. Urban water demand management should pay attention to the spatial heterogeneity in predicting the future water demand to achieve more accurate estimates, and spatial statistical models provide a promising method to do this job.
ContributorsOuyang, Yun (Author) / Wentz, Elizabeth (Thesis advisor) / Ruddell, Benjamin (Thesis advisor) / Harlan, Sharon (Committee member) / Janssen, Marcus (Committee member) / Arizona State University (Publisher)
Created2013
Description
There is a critical need for the development of clean and efficient energy sources. Hydrogen is being explored as a viable alternative to fuels in current use, many of which have limited availability and detrimental byproducts. Biological photo-production of H2 could provide a potential energy source directly manufactured from water and sunlight. As a part of the photosynthetic electron transport chain (PETC) of the green algae Chlamydomonas reinhardtii, water is split via Photosystem II (PSII) and the electrons flow through a series of electron transfer cofactors in cytochrome b6f, plastocyanin and Photosystem I (PSI). The terminal electron acceptor of PSI is ferredoxin, from which electrons may be used to reduce NADP+ for metabolic purposes. Concomitant production of a H+ gradient allows production of energy for the cell. Under certain conditions and using the endogenous hydrogenase, excess protons and electrons from ferredoxin may be converted to molecular hydrogen. In this work it is demonstrated both that certain mutations near the quinone electron transfer cofactor in PSI can speed up electron transfer through the PETC, and also that a native [FeFe]-hydrogenase can be expressed in the C. reinhardtii chloroplast. Taken together, these research findings form the foundation for the design of a PSI-hydrogenase fusion for the direct and continuous photo-production of hydrogen in vivo.
ContributorsReifschneider, Kiera (Author) / Redding, Kevin (Thesis advisor) / Fromme, Petra (Committee member) / Jones, Anne (Committee member) / Arizona State University (Publisher)
Created2013
Description
Two critical limitations for hyperspatial imagery are higher imagery variances and large data sizes. Although object-based analyses with a multi-scale framework for diverse object sizes are the solution, more data sources and large amounts of testing at high costs are required. In this study, I used tree density segmentation as the key element of a three-level hierarchical vegetation framework for reducing those costs, and a three-step procedure was used to evaluate its effects. A two-step procedure, which involved environmental stratifications and the random walker algorithm, was used for tree density segmentation. I determined whether variation in tone and texture could be reduced within environmental strata, and whether tree density segmentations could be labeled by species associations. At the final level, two tree density segmentations were partitioned into smaller subsets using eCognition in order to label individual species or tree stands in two test areas of two tree densities, and the Z values of Moran's I were used to evaluate whether imagery objects have different mean values from near segmentations as a measure of segmentation accuracy. The two-step procedure was able to delineating tree density segments and label species types robustly, compared to previous hierarchical frameworks. However, eCognition was not able to produce detailed, reasonable image objects with optimal scale parameters for species labeling. This hierarchical vegetation framework is applicable for fine-scale, time-series vegetation mapping to develop baseline data for evaluating climate change impacts on vegetation at low cost using widely available data and a personal laptop.
ContributorsLiau, Yan-ting (Author) / Franklin, Janet (Thesis advisor) / Turner, Billie (Committee member) / Myint, Soe (Committee member) / Arizona State University (Publisher)
Created2013
Description
Sustainable development in an American context implies an ongoing shift from quantitative growth in energy, resource, and land use to the qualitative development of social-ecological systems, human capital, and dense, vibrant built environments. Sustainable urban development theory emphasizes locally and bioregionally emplaced economic development where the relationships between people, localities, products, and capital are tangible to and controllable by local stakeholders. Critical theory provides a mature understanding of the political economy of land development in capitalist economies, representing a crucial bridge between urban sustainability's infill development goals and the contemporary realities of the development industry. Since its inception, Phoenix, Arizona has exemplified the quantitative growth paradigm, and recurring instances of land speculation, non-local capital investment, and growth-based public policy have stymied local, tangible control over development from Phoenix's territorial history to modern attempts at downtown revitalization. Utilizing property ownership and sales data as well as interviews with development industry stakeholders, the political economy of infill land development in downtown Phoenix during the mid-2000s boom-and-bust cycle is analyzed. Data indicate that non-local property ownership has risen significantly over the past 20 years and rent-seeking land speculation has been a significant barrier to infill development. Many speculative strategies monopolize the publicly created value inherent in zoning entitlements, tax incentives and property assessment, indicating that political and policy reforms targeted at a variety of governance levels are crucial for achieving the sustainable development of urban land. Policy solutions include reforming the interconnected system of property sales, value assessment, and taxation to emphasize property use values; replacing existing tax incentives with tax increment financing and community development benefit agreements; regulating vacant land ownership and deed transfers; and encouraging innovative private development and tenure models like generative construction and community land trusts.
ContributorsStanley, Benjamin W (Author) / Boone, Christopher G. (Thesis advisor) / Redman, Charles (Committee member) / Bolin, Robert (Committee member) / Arizona State University (Publisher)
Created2013
Description
This dissertation explores vulnerability to extreme heat hazards in the Maricopa County, Arizona metropolitan region. By engaging an interdisciplinary approach, I uncover the epidemiological, historical-geographical, and mitigation dimensions of human vulnerability to extreme heat in a rapidly urbanizing region characterized by an intense urban heat island and summertime heat waves. I first frame the overall research within global climate change and hazards vulnerability research literature, and then present three case studies. I conclude with a synthesis of the findings and lessons learned from my interdisciplinary approach using an urban political ecology framework. In the first case study I construct and map a predictive index of sensitivity to heat health risks for neighborhoods, compare predicted neighborhood sensitivity to heat-related hospitalization rates, and estimate relative risk of hospitalizations for neighborhoods. In the second case study, I unpack the history and geography of land use/land cover change, urban development and marginalization of minorities that created the metropolitan region's urban heat island and consequently, the present conditions of extreme heat exposure and vulnerability in the urban core. The third study uses computational microclimate modeling to evaluate the potential of a vegetation-based intervention for mitigating extreme heat in an urban core neighborhood. Several findings relevant to extreme heat vulnerability emerge from the case studies. First, two main socio-demographic groups are found to be at higher risk for heat illness: low-income minorities in sparsely-vegetated neighborhoods in the urban core, and the elderly and socially-isolated in the expansive suburban fringe of Maricopa County. The second case study reveals that current conditions of heat exposure in the region's urban heat island are the legacy of historical marginalization of minorities and large-scale land-use/land cover transformations of natural desert land covers into heat-retaining urban surfaces of the built environment. Third, summertime air temperature reductions in the range 0.9-1.9 °C and of up to 8.4 °C in surface temperatures in the urban core can be achieved through desert-adapted canopied vegetation, suggesting that, at the microscale, the urban heat island can be mitigated by creating vegetated park cool islands. A synthesis of the three case studies using the urban political ecology framework argues that climate changed-induced heat hazards in cities must be problematized within the socio-ecological transformations that produce and reproduce urban landscapes of risk. The interdisciplinary approach to heat hazards in this dissertation advances understanding of the social and ecological drivers of extreme heat by drawing on multiple theories and methods from sociology, urban and Marxist geography, microclimatology, spatial epidemiology, environmental history, political economy and urban political ecology.
ContributorsDeclet-Barreto, Juan (Author) / Harlan, Sharon L (Thesis advisor) / Bolin, Bob (Thesis advisor) / Hirt, Paul (Committee member) / Boone, Christopher (Committee member) / Arizona State University (Publisher)
Created2013