Theses and Dissertations
This collection includes both ASU Theses and Dissertations, submitted by graduate students, and the Barrett, Honors College theses submitted by undergraduate students.
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Description
The relationship between biodiversity and ecosystem functioning (BEF) is a central issue in ecology, and a number of recent field experimental studies have greatly improved our understanding of this relationship. Spatial heterogeneity is a ubiquitous characterization of ecosystem processes, and has played a significant role in shaping BEF relationships. The first step towards understanding the effects of spatial heterogeneity on the BEF relationships is to quantify spatial heterogeneity characteristics of key variables of biodiversity and ecosystem functioning, and identify the spatial relationships among these variables. The goal of our research was to address the following research questions based on data collected in 2005 (corresponding to the year when the initial site background information was conducted) and in 2008 (corresponding to the year when removal treatments were conducted) from the Inner Mongolia Grassland Removal Experiment (IMGRE) located in northern China: 1) What are the spatial patterns of soil nutrients, plant biodiversity, and aboveground biomass in a natural grassland community of Inner Mongolia, China? How are they related spatially? and 2) How do removal treatments affect the spatial patterns of soil nutrients, plant biodiversity, and aboveground biomass? Is there any change for their spatial correlations after removal treatments? Our results showed that variables of biodiversity and ecosystem functioning in the natural grassland community would present different spatial patterns, and they would be spatially correlated to each other closely. Removal treatments had a significant effect on spatial structures and spatial correlations of variables, compared to those prior to the removal treatments. The differences in spatial pattern of plant and soil variables and their correlations before and after the biodiversity manipulation may not imply that the results from BEF experiments like IMGRE are invalid. However, they do suggest that the possible effects of spatial heterogeneity on the BEF relationships should be critically evaluated in future studies.
ContributorsYuan, Fei (Author) / Wu, Jianguo (Thesis advisor) / Smith, Andrew T. (Committee member) / Rowe, Helen I (Committee member) / Arizona State University (Publisher)
Created2011
Description
Membrane proteins are very important for all living cells, being involved in respiration, photosynthesis, cellular uptake and signal transduction, amongst other vital functions. However, less than 300 unique membrane protein structures have been determined to date, often due to difficulties associated with the growth of sufficiently large and well-ordered crystals. This work has been focused on showing the first proof of concept for using membrane protein nanocrystals and microcrystals for high-resolution structure determination. Upon determining that crystals of the membrane protein Photosystem I, which is the largest and most complex membrane protein crystallized to date, exist with only a hundred unit cells with sizes of less than 200 nm on an edge, work was done to develop a technique that could exploit the growth of the Photosystem I nanocrystals and microcrystals. Femtosecond X-ray protein nanocrystallography was developed for use at the first high-energy X-ray free electron laser, the LCLS at SLAC National Accelerator Laboratory, in which a liquid jet would bring fully hydrated Photosystem I nanocrystals into the interaction region of the pulsed X-ray source. Diffraction patterns were recorded from millions of individual PSI nanocrystals and data from thousands of different, randomly oriented crystallites were integrated using Monte Carlo integration of the peak intensities. The short pulses ( 70 fs) provided by the LCLS allowed the possibility to collect the diffraction data before the onset of radiation damage, exploiting the diffract-before-destroy principle. At the initial experiments at the AMO beamline using 6.9- Å wavelength, Bragg peaks were recorded to 8.5- Å resolution, and an electron-density map was determined that did not show any effects of X-ray-induced radiation damage. Recently, femtosecond X-ray protein nanocrystallography experiments were done at the CXI beamline of the LCLS using 1.3- Å wavelength, and Bragg reflections were recorded to 3- Å resolution; the data are currently being processed. Many additional techniques still need to be developed to explore the femtosecond nanocrystallography technique for experimental phasing and time-resolved X-ray crystallography experiments. The first proof-of-principle results for the femtosecond nanocrystallography technique indicate the incredible potential of the technique to offer a new route to the structure determination of membrane proteins.
ContributorsHunter, Mark (Author) / Fromme, Petra (Thesis advisor) / Wolf, George (Committee member) / Levitus, Marcia (Committee member) / Arizona State University (Publisher)
Created2011
Description
Molecular dynamics (MD) simulations provide a particularly useful approach to understanding conformational change in biomolecular systems. MD simulations provide an atomistic, physics-based description of the motions accessible to biomolecular systems on the pico- to micro-second timescale, yielding important insight into the free energy of the system, the dynamical stability of contacts and the role of correlated motions in directing the motions of the system. In this thesis, I use molecular dynamics simulations to provide molecular mechanisms that rationalize structural, thermodynamic, and mutation data on the interactions between the lac repressor headpiece and its O1 operator DNA as well as the ERK2 protein kinase. I performed molecular dynamics simulations of the lac repressor headpiece - O1 operator complex at the natural angle as well as at under- and overbent angles to assess the factors that determine the natural DNA bending angle. I find both energetic and entropic factors contribute to recognition of the natural angle. At the natural angle the energy of the system is minimized by optimization of protein-DNA contacts and the entropy of the system is maximized by release of water from the protein-DNA interface and decorrelation of protein motions. To identify the mechanism by which mutations lead to auto-activation of ERK2, I performed a series of molecular dynamics simulations of ERK1/2 in various stages of activation as well as the constitutively active Q103A, I84A, L73P and R65S ERK2 mutants. My simulations indicate the importance of domain closure for auto-activation and activity regulation. My results enable me to predict two loss-of-function mutants of ERK2, G83A and Q64C, that have been confirmed in experiments by collaborators. One of the powerful capabilities of MD simulations in biochemistry is the ability to find low free energy pathways that connect and explain disparate structural data on biomolecular systems. An extention of the targeted molecular dynamics technique using constraints on internal coordinates will be presented and evaluated. The method gives good results for the alanine dipeptide, but breaks down when applied to study conformational changes in GroEL and adenylate kinase.
ContributorsBarr, Daniel Alan (Author) / van der Vaart, Arjan (Thesis advisor) / Matyushov, Dmitry (Committee member) / Wolf, George (Committee member) / Shumway, John (Committee member) / Arizona State University (Publisher)
Created2011
Description
This dissertation examines associations between religious affiliation, religious community context and health of women and their children in Mozambique focusing on the following issues: (1) attending prenatal consultations and delivering children in a health facility; (2) women's symptoms of STDs; and (3) under-five mortality. Estimation of random intercept Poisson regression for the outcome about attending prenatal consultations demonstrated a favorable effect of affiliation to Catholic or Mainline Protestant and Apostolic religious groups. The concentration of Zionist churches in the community had a negative influence. Random intercept logistic regression was used to estimate the relationship between religion and institutional child delivery. Affiliation to Catholic or Mainline Protestant denominations as well as concentration of Catholic or Mainline Protestant churches in the community had some beneficial effect on giving birth in health clinics. The presence of Zionist churches in the community had some negative effect and that of other groups no significant influence. Random intercept logistic regression was also employed for investigating the influence of religion on women's symptoms of STDs. Belonging to the Catholic or Mainline Protestant church had some protective effect on reporting symptoms of STDs. There was no effect of religious context, except that the concentration of Other Pentecostal churches had a positive effect on reporting symptoms of SDTs. Event-history analysis was conducted for examining relationships between maternal religious affiliation with under-five mortality. Affiliation to Catholic or Mainline Protestant churches and to Apostolic denominations increased the odds of child survival, although, the influence of having a mother belonging to Catholic or Mainline Protestant churches lost statistical significance after accounting particularly for the average level of education in the community, for the period of 5 years preceding the survey date. Taken together, the results in this dissertation show some protective effect of religion that varies primarily by denominational group to which women are affiliated. They also indicate that religious community context may have some negative effect on health of women and children. The nature of the effect of religious community context varies with the type of outcome considered and the type of religious mixture in the community.
ContributorsCau, Boaventura Manuel (Author) / Agadjanian, Victor (Thesis advisor) / Hayford, Sarah (Committee member) / Yabiku, Scott (Committee member) / Arizona State University (Publisher)
Created2011
Description
This thesis describes several approaches to next generation DNA sequencing via tunneling current method based on a Scanning Tunneling Microscope system. In chapters 5 and 6, preliminary results have shown that DNA bases could be identified by their characteristic tunneling signals. Measurements taken in aqueous buffered solution showed that single base resolution could be achieved with economic setups. In chapter 7, it is illustrated that some ongoing measurements are indicating the sequence readout by making linear scan on a piece of short DNA oligomer. However, to overcome the difficulties of controlling DNA especially ssDNA movement, it is much better to have the tunneling measurement incorporated onto a robust nanopore device to realize sequential reading of the DNA sequence while it is being translocated.
ContributorsHuang, Shuo (Author) / Lindsay, Stuart (Thesis advisor) / Sankey, Otto (Committee member) / Tao, Nongjian (Committee member) / Drucker, Jeff (Committee member) / Ros, Robert (Committee member) / Arizona State University (Publisher)
Created2011
Description
Worldwide, riverine floodplains are among the most endangered landscapes. In response to anthropogenic impacts, riverine restoration projects are considerably increasing. However, there is a paucity of information on how riparian rehabilitation activities impact non-avian wildlife communities. I evaluated herpetofauna abundance, species richness, diversity (i.e., Shannon and Simpson indices), species-specific responses, and riparian microhabitat characteristics along three reaches (i.e., wildland, urban rehabilitated, and urban disturbed) of the Salt River, Arizona. The surrounding uplands of the two urbanized reaches were dominated by the built environment (i.e., Phoenix metropolitan area). I predicted that greater diversity of microhabitat and lower urbanization would promote herpetofauna abundance, richness, and diversity. In 2010, at each reach, I performed herpetofauna visual surveys five times along eight transects (n=24) spanning the riparian zone. I quantified twenty one microhabitat characteristics such as ground substrate, vegetative cover, woody debris, tree stem density, and plant species richness along each transect. Herpetofauna species richness was the greatest along the wildland reach, and the lowest along the urban disturbed reach. The wildland reach had the greatest diversity indices, and diversity indices of the two urban reaches were similar. Abundance of herpetofauna was approximately six times lower along the urban disturbed reach compared to the two other reaches, which had similar abundances. Principal Component Analysis (PCA) reduced microhabitat variables to five factors, and significant differences among reaches were detected. Vegetation structure complexity, vegetation species richness, as well as densities of Prosopis (mesquite), Salix (willow), Populus (cottonwood), and animal burrows had a positive correlation with at least one of the three herpetofauna community parameter quantified (i.e., herpetofauna abundance, species richness, and diversity indices), and had a positive correlation with at least one herpetofauna species. Overall, rehabilitation activities positively influenced herpetofauna abundance and species richness, whereas urbanization negatively influenced herpetofauna diversity indices. Based on herpetofauna/microhabitat correlations established, I developed recommendations regarding microhabitat features that should be created in order to promote herpetofauna when rehabilitating degraded riparian systems. Recommendations are to plant vegetation of different growth habit, provide woody debris, plant Populus, Salix, and Prosopis of various ages and sizes, and to promote small mammal abundance.
ContributorsBanville, Mélanie Josianne (Author) / Bateman, Heather L (Thesis advisor) / Brady, Ward (Committee member) / Stromberg, Juliet (Committee member) / Arizona State University (Publisher)
Created2011
Description
A right to the city is a human right that is overlooked in American cities. Cities reflect humanity in collective form, but are manipulated by the powerful at the expense of the powerless. Landscapes of cities tell the city's stories, as historical inequalities become imprinted on the city's physical and symbolic landscapes. In Detroit, Michigan, over forty square miles of the city are vacant, unemployment might be as high as fifty percent, and the city has lost about sixty percent of its population since the mid-1950s. Detroit must now solve its spatial problems in the context of depopulation; the city's planners, nonprofits, and scholars are now debating "planned shrinking" or "right-sizing." Simultaneously, a blooming arts scene is also slowly revitalizing parts of the city. This thesis will critically examine the possibilities of planned shrinking and the arts movement in Detroit, as well as suggest theoretical explanations for the city's dilemmas. Detroit has been the subject of a myopic popular narrative, one that isolates the city from modern America rather than critically examines its place in modern America. Redefining regional healing through honest discourse and developing a more appropriate narrative for Detroit are among the solutions proposed. Finally, the importance of establishing a human right for the city is discussed.
ContributorsMarotta, Stephen J (Author) / Casper, Monica J (Thesis advisor) / Murphy-Erfani, Julie (Committee member) / Stancliff, Michael (Committee member) / Arizona State University (Publisher)
Created2011
Description
With the ongoing drought surpassing a decade in Arizona, scholars, water managers and decision-makers have heightened attention to the availability of water resources, especially in rapidly growing regions where demand may outgrow supplies or outpace the capacity of the community water systems. Community water system managing entities and the biophysical and social characteristics of a place mediate communities' vulnerability to hazards such as drought and long-term climate change. The arid southwestern Phoenix metropolitan area is illustrative of the challenges that developed urban areas in arid climates face globally as population growth and climate change stress already fragile human-environmental systems. This thesis reveals the factors abating and exacerbating differential community water system vulnerability to water scarcity in communities simultaneously facing drought and rapid peri-urban growth. Employing a grounded, qualitative comparative case study approach, this thesis explores the interaction of social, biophysical and institutional factors as they effect the exposure, sensitivity and adaptive capacity of community water systems in Cave Creek and Buckeye, Arizona. Buckeye, once a small agricultural town in the West Valley, is wholly dependent on groundwater and currently planning for massive development to accommodate 218,591 new residents by 2020. Amid desert hills and near Tonto National Forest in the North Valley, Cave Creek is an upscale residential community suffering frequent water outages due to aging infrastructure and lack of system redundancy. Analyzing interviews, media accounts and policy documents, a narrative was composed explaining how place based factors, nested within a regional institutional water management framework, impact short and long-term vulnerability. This research adds to the library of vulnerability assessments completed using Polsky et al.'s Vulnerability Scoping Diagram and serves a pragmatic need assisting in the development of decision making tools that better represent the drivers of placed based vulnerability in arid metropolitan regions.
ContributorsZautner, Lilah (Author) / Larson, Kelli (Thesis advisor) / Bolin, Bob (Committee member) / Chhetri, Netra (Committee member) / Arizona State University (Publisher)
Created2011
Description
This thesis describes several experiments based on carbon nanotube nanofludic devices and field-effect transistors. The first experiment detected ion and molecule translocation through one single-walled carbon nanotube (SWCNT) that spans a barrier between two fluid reservoirs. The electrical ionic current is measured. Translocation of small single stranded DNA oligomers is marked by large transient increases in current through the tube and confirmed by a PCR (polymerase chain reaction) analysis. Carbon nanotubes simplify the construction of nanopores, permit new types of electrical measurement, and open new avenues for control of DNA translocation. The second experiment constructed devices in which the interior of a single-walled carbon nanotube field-effect transistor (CNT-FET) acts as a nanofluidic channel that connects two fluid reservoirs, permitting measurement of the electronic properties of the SWCNT as it is wetted by an analyte. Wetting of the inside of the SWCNT by water turns the transistor on, while wetting of the outside has little effect. This finding may provide a new method to investigate water behavior at nanoscale. This also opens a new avenue for building sensors in which the SWCNT functions as an electronic detector. This thesis also presents some experiments that related to nanofabrication, such as construction of FET with tin sulfide (SnS) quantum ribbon. This work demonstrates the application of solution processed IV-VI semiconductor nanostructures in nanoscale devices.
ContributorsCao, Zhai (Author) / Lindsay, Stuart (Thesis advisor) / Vaiana, Sara (Committee member) / Ros, Robert (Committee member) / Marzke, Robert (Committee member) / Shumway, John (Committee member) / Arizona State University (Publisher)
Created2011
Description
This study was designed to produce a comprehensive flora of Usery Mountain Regional Park and Pass Mountain of the Tonto National Forest. A total of 168 vascular plant species representing 46 families and 127 genera were collected or documented at this study area. Sixteen species were not native to the flora of Arizona and represent 9.5% of the flora. Nevertheless, the study area does not appear to be significantly damaged or degraded in spite of its historical and current land use. The location and types of invasive species recorded in this study will assist with implementing preventative measures to prevent further spreading of certain species. The complete list of all vascular species recorded in this study will provide a valuable tool for land management decisions and future restoration projects that may occur at this area or similar sites and invasive species control. The distribution of the saguaro (Carnegiea gigantea) population on Pass Mountain was documented through the measurement of saguaros by random sampling. ArcGIS was used to generate 50 random points for sampling the saguaro population. Analysis to determine saguaro habitat preferences based on the parameters of aspect, slope and elevation was conducted through ArcGIS. The saguaro population of Pass Mountain significantly favored the southern aspects with the highest concentration occurring in the southwest aspects at an average density of 42.66 saguaros per hectare. The large numbers of saguaros recorded in the younger size classes suggests a growing populations.
ContributorsMarshall, Laura Lee (Author) / Steele, Kelly P (Thesis advisor) / Miller, William H. (Committee member) / Alford, Eddie J (Committee member) / Arizona State University (Publisher)
Created2011