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.
Displaying 1 - 10 of 84
Description
Reductive dechlorination by members of the bacterial genus Dehalococcoides is a common and cost-effective avenue for in situ bioremediation of sites contaminated with the chlorinated solvents, trichloroethene (TCE) and perchloroethene (PCE). The overarching goal of my research was to address some of the challenges associated with bioremediation timeframes by improving the rates of reductive dechlorination and the growth of Dehalococcoides in mixed communities. Biostimulation of contaminated sites or microcosms with electron donor fails to consistently promote dechlorination of PCE/TCE beyond cis-dichloroethene (cis-DCE), even when the presence of Dehalococcoides is confirmed. Supported by data from microcosm experiments, I showed that the stalling at cis-DCE is due a H2 competition in which components of the soil or sediment serve as electron acceptors for competing microorganisms. However, once competition was minimized by providing selective enrichment techniques, I illustrated how to obtain both fast rates and high-density Dehalococcoides using three distinct enrichment cultures. Having achieved a heightened awareness of the fierce competition for electron donor, I then identified bicarbonate (HCO3-) as a potential H2 sink for reductive dechlorination. HCO3- is the natural buffer in groundwater but also the electron acceptor for hydrogenotrophic methanogens and homoacetogens, two microbial groups commonly encountered with Dehalococcoides. By testing a range of concentrations in batch experiments, I showed that methanogens are favored at low HCO3 and homoacetogens at high HCO3-. The high HCO3- concentrations increased the H2 demand which negatively affected the rates and extent of dechlorination. By applying the gained knowledge on microbial community management, I ran the first successful continuous stirred-tank reactor (CSTR) at a 3-d hydraulic retention time for cultivation of dechlorinating cultures. I demonstrated that using carefully selected conditions in a CSTR, cultivation of Dehalococcoides at short retention times is feasible, resulting in robust cultures capable of fast dechlorination. Lastly, I provide a systematic insight into the effect of high ammonia on communities involved in dechlorination of chloroethenes. This work documents the potential use of landfill leachate as a substrate for dechlorination and an increased tolerance of Dehalococcoides to high ammonia concentrations (2 g L-1 NH4+-N) without loss of the ability to dechlorinate TCE to ethene.
ContributorsDelgado, Anca Georgiana (Author) / Krajmalnik-Brown, Rosa (Thesis advisor) / Cadillo-Quiroz, Hinsby (Committee member) / Halden, Rolf U. (Committee member) / Rittmann, Bruce E. (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2013
Description
Microbial mat communities that inhabit hot springs in Yellowstone National Park have been studied for their biodiversity, energetics and evolutionary history, yet little is know about how these communities cope with nutrient limitation. In the present study the changes in assimilatory gene expression levels for nitrogen (nrgA), phosphorus (phoA), and iron (yusV) were measured under various nutrient enrichment experiments. While results for nrgA and phoA were inconclusive, results for yusV showed an increase in expression with the addition of N and Fe. This is the first data that shows the impact of nutrients on siderophore uptake regulation in hot spring microbes.
ContributorsThorne, Michele (Author) / Elser, James J (Thesis advisor) / Touchman, Jeffrey (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2012
Description
Creative design lies at the intersection of novelty and technical feasibility. These objectives can be achieved through cycles of divergence (idea generation) and convergence (idea evaluation) in conceptual design. The focus of this thesis is on the latter aspect. The evaluation may involve any aspect of technical feasibility and may be desired at component, sub-system or full system level. Two issues that are considered in this work are: 1. Information about design ideas is incomplete, informal and sketchy 2. Designers often work at multiple levels; different aspects or subsystems may be at different levels of abstraction Thus, high fidelity analysis and simulation tools are not appropriate for this purpose. This thesis looks at the requirements for a simulation tool and how it could facilitate concept evaluation. The specific tasks reported in this thesis are: 1. The typical types of information available after an ideation session 2. The typical types of technical evaluations done in early stages 3. How to conduct low fidelity design evaluation given a well-defined feasibility question A computational tool for supporting idea evaluation was designed and implemented. It was assumed that the results of the ideation session are represented as a morphological chart and each entry is expressed as some combination of a sketch, text and references to physical effects and machine components. Approximately 110 physical effects were identified and represented in terms of algebraic equations, physical variables and a textual description. A common ontology of physical variables was created so that physical effects could be networked together when variables are shared. This allows users to synthesize complex behaviors from simple ones, without assuming any solution sequence. A library of 16 machine elements was also created and users were given instructions about incorporating them. To support quick analysis, differential equations are transformed to algebraic equations by replacing differential terms with steady state differences), only steady state behavior is considered and interval arithmetic was used for modeling. The tool implementation is done by MATLAB; and a number of case studies are also done to show how the tool works. textual description. A common ontology of physical variables was created so that physical effects could be networked together when variables are shared. This allows users to synthesize complex behaviors from simple ones, without assuming any solution sequence. A library of 15 machine elements was also created and users were given instructions about incorporating them. To support quick analysis, differential equations are transformed to algebraic equations by replacing differential terms with steady state differences), only steady state behavior is considered and interval arithmetic was used for modeling. The tool implementation is done by MATLAB; and a number of case studies are also done to show how the tool works.
ContributorsKhorshidi, Maryam (Author) / Shah, Jami J. (Thesis advisor) / Wu, Teresa (Committee member) / Gel, Esma (Committee member) / Arizona State University (Publisher)
Created2014
Description
The prevalence of antibiotic resistant bacterial pathogens has increased since the introduction of penicillin in the 1940s. Insufficient development of novel antibacterial agents is leaving us with a failing arsenal of therapies to combat these pathogenic organisms. We have identified a clay mineral mixture (designated CB) that exhibits in vitro antibacterial activity against a broad spectrum of bacterial pathogens, yet the antibacterial mechanism of action remains unknown. Antibacterial susceptibility testing of four different clay samples collected from the same source revealed that these natural clays had markedly different antibacterial activity. X-ray diffraction analyses of these minerals revealed minor mineralogical differences across the samples; however, ICP analyses demonstrated that the concentrations of many elements, Fe, Co, Cu, Ni, and Zn in particular, vary greatly across the four clay mixture leachates. Supplementation of a non-antibacterial leachate containing lower concentrations of Fe, Co, Ni, Cu, and Zn to final ion concentrations and a pH equivalent to that of the antibacterial leachate resulted in antibacterial activity against E. coli and MRSA, confirming the role of these ions in the in vitro antibacterial clay mixture leachates. The prevailing hypothesis is that metal ions participate in redox cycling and produce ROS, leading to oxidative damage to macromolecules and resulting in cellular death. However, E. coli cells showed no increase in DNA or protein oxidative lesions and a slight increase in lipid peroxidation following exposure to CB-L. Supplementation of CB-L with ROS scavengers eliminated oxidative damage in E. coli, but did not rescue the cells from killing, indicating that in vitro killing is due to direct metal toxicity and not to indirect oxidative damage. Finally, we ion-exchanged non-antibacterial clays with Fe, Co, Cu, and Zn and established antibacterial activity in these samples. Treatment of MRSA skin infections with both natural and ion-exchanged clays significantly decreased the bacterial load after 7 days of treatment. We conclude that 1) in vitro clay-mediated killing is due to toxicity associated directly with released metal ions and not to indirect oxidative damage and 2) that in vivo killing is due to the physical properties of the clays rather than metal ion toxicity.
ContributorsOtto, Caitin Carol (Author) / Haydel, Shelley (Thesis advisor) / Stout, Valerie (Committee member) / Roberson, Robby (Committee member) / Sandrin, Todd (Committee member) / Rege, Kaushal (Committee member) / Arizona State University (Publisher)
Created2014
Description
Pathogenic Gram-negative bacteria employ a variety of molecular mechanisms to combat host defenses. Two-component regulatory systems (TCR systems) are the most ubiquitous signal transduction systems which regulate many genes required for virulence and survival of bacteria. In this study, I analyzed different TCR systems in two clinically-relevant Gram-negative bacteria, i.e., oral pathogen Porphyromonas gingivalis and enterobacterial Escherichia coli. P. gingivalis is a major causative agent of periodontal disease as well as systemic illnesses, like cardiovascular disease. A microarray study found that the putative PorY-PorX TCR system controls the secretion and maturation of virulence factors, as well as loci involved in the PorSS secretion system, which secretes proteinases, i.e., gingipains, responsible for periodontal disease. Proteomic analysis (SILAC) was used to improve the microarray data, reverse-transcription PCR to verify the proteomic data, and primer extension assay to determine the promoter regions of specific PorX regulated loci. I was able to characterize multiple genetic loci regulated by this TCR system, many of which play an essential role in hemagglutination and host-cell adhesion, and likely contribute to virulence in this bacterium. Enteric Gram-negative bacteria must withstand many host defenses such as digestive enzymes, low pH, and antimicrobial peptides (AMPs). The CpxR-CpxA TCR system of E. coli has been extensively characterized and shown to be required for protection against AMPs. Most recently, this TCR system has been shown to up-regulate the rfe-rff operon which encodes genes involved in the production of enterobacterial common antigen (ECA), and confers protection against a variety of AMPs. In this study, I utilized primer extension and DNase I footprinting to determine how CpxR regulates the ECA operon. My findings suggest that CpxR modulates transcription by directly binding to the rfe promoter. Multiple genetic and biochemical approaches were used to demonstrate that specific TCR systems contribute to regulation of virulence factors and resistance to host defenses in P. gingivalis and E. coli, respectively. Understanding these genetic circuits provides insight into strategies for pathogenesis and resistance to host defenses in Gram negative bacterial pathogens. Finally, these data provide compelling potential molecular targets for therapeutics to treat P. gingivalis and E. coli infections.
ContributorsLeonetti, Cori (Author) / Shi, Yixin (Thesis advisor) / Stout, Valerie (Committee member) / Nickerson, Cheryl (Committee member) / Sandrin, Todd (Committee member) / Arizona State University (Publisher)
Created2013
Description
The advent of new high throughput technology allows for increasingly detailed characterization of the immune system in healthy, disease, and age states. The immune system is composed of two main branches: the innate and adaptive immune system, though the border between these two states is appearing less distinct. The adaptive immune system is further split into two main categories: humoral and cellular immunity. The humoral immune response produces antibodies against specific targets, and these antibodies can be used to learn about disease and normal states. In this document, I use antibodies to characterize the immune system in two ways: 1. I determine the Antibody Status (AbStat) from the data collected from applying sera to an array of non-natural sequence peptides, and demonstrate that this AbStat measure can distinguish between disease, normal, and aged samples as well as produce a single AbStat number for each sample; 2. I search for antigens for use in a cancer vaccine, and this search results in several candidates as well as a new hypothesis. Antibodies provide us with a powerful tool for characterizing the immune system, and this natural tool combined with emerging technologies allows us to learn more about healthy and disease states.
ContributorsWhittemore, Kurt (Author) / Sykes, Kathryn (Thesis advisor) / Johnston, Stephen A. (Committee member) / Jacobs, Bertram (Committee member) / Stafford, Phillip (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2014
Description
Bacteria of the Legionella genus are a water-borne pathogen of increasing concern due to being responsible for more annual drinking water related disease outbreaks in the United States than all other microbes combined. Unfortunately, the development of public health policies concerning Legionella has impeded by several key factors, including a paucity of data on their interactions and growth requirements in water distribution networks, a poor understanding of potential transmission sources for legionellosis, and limitations in current methodology for the characterization of these pathogens. To address these issues, a variety of research approaches were taken. By measuring Legionella survival in tap water, association in pipe material biofilms, population dynamics in a model distribution system, and occurrence in drinking water distribution system biofilms, key aspects of Legionella ecology in drinking water systems were revealed. Through a series of experiments qualitatively and quantitatively examining the growth of Legionella via nutrients obtained from several water sources, environmental nutritional requirements and capability for growth in the absence of host organisms were demonstrated. An examination of automobile windshield washer fluid as a possible source of legionellosis transmission revealed Legionella survival in certain windshield washer fluids, growth within washer fluid reservoirs, high levels and frequency of contamination in washer fluid reservoirs, and the presence of viable cells in washer fluid spray, suggesting the potential for exposure to Legionella from this novel source. After performing a systematic and quantitative analysis of methodology optimization for the analysis of Legionella cells via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, several strains of this microbe isolated from separated and varied environmental water sampling sites were distinctly typed, demonstrating a potential application of this technology for the characterization of Legionella. The results from this study provide novel insight and methodology relevant to the development of programs for the monitoring and treatment of Legionella in drinking water systems.
ContributorsSchwake, David Otto (Author) / Abbaszadegan, Morteza (Thesis advisor) / Alum, Absar (Committee member) / Fox, Peter (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2014
Description
Network traffic analysis by means of Quality of Service (QoS) is a popular research and development area among researchers for a long time. It is becoming even more relevant recently due to ever increasing use of the Internet and other public and private communication networks. Fast and precise QoS analysis is a vital task in mission-critical communication networks (MCCNs), where providing a certain level of QoS is essential for national security, safety or economic vitality. In this thesis, the details of all aspects of a comprehensive computational framework for QoS analysis in MCCNs are provided. There are three main QoS analysis tasks in MCCNs; QoS measurement, QoS visualization and QoS prediction. Definitions of these tasks are provided and for each of those, complete solutions are suggested either by referring to an existing work or providing novel methods.
A scalable and accurate passive one-way QoS measurement algorithm is proposed. It is shown that accurate QoS measurements are possible using network flow data.
Requirements of a good QoS visualization platform are listed. Implementations of the capabilities of a complete visualization platform are presented.
Steps of QoS prediction task in MCCNs are defined. The details of feature selection, class balancing through sampling and assessing classification algorithms for this task are outlined. Moreover, a novel tree based logistic regression method for knowledge discovery is introduced. Developed prediction framework is capable of making very accurate packet level QoS predictions and giving valuable insights to network administrators.
A scalable and accurate passive one-way QoS measurement algorithm is proposed. It is shown that accurate QoS measurements are possible using network flow data.
Requirements of a good QoS visualization platform are listed. Implementations of the capabilities of a complete visualization platform are presented.
Steps of QoS prediction task in MCCNs are defined. The details of feature selection, class balancing through sampling and assessing classification algorithms for this task are outlined. Moreover, a novel tree based logistic regression method for knowledge discovery is introduced. Developed prediction framework is capable of making very accurate packet level QoS predictions and giving valuable insights to network administrators.
ContributorsSenturk, Muhammet Burhan (Author) / Li, Jing (Thesis advisor) / Baydogan, Mustafa G (Committee member) / Wu, Teresa (Committee member) / Arizona State University (Publisher)
Created2014
Description
This thesis presents a meta-analysis of lead-free solder reliability. The qualitative analyses of the failure modes of lead- free solder under different stress tests including drop test, bend test, thermal test and vibration test are discussed. The main cause of failure of lead- free solder is fatigue crack, and the speed of propagation of the initial crack could differ from different test conditions and different solder materials. A quantitative analysis about the fatigue behavior of SAC lead-free solder under thermal preconditioning process is conducted. This thesis presents a method of making prediction of failure life of solder alloy by building a Weibull regression model. The failure life of solder on circuit board is assumed Weibull distributed. Different materials and test conditions could affect the distribution by changing the shape and scale parameters of Weibull distribution. The method is to model the regression of parameters with different test conditions as predictors based on Bayesian inference concepts. In the process of building regression models, prior distributions are generated according to the previous studies, and Markov Chain Monte Carlo (MCMC) is used under WinBUGS environment.
ContributorsXu, Xinyue (Author) / Pan, Rong (Thesis advisor) / Montgomery, Douglas C. (Committee member) / Wu, Teresa (Committee member) / Arizona State University (Publisher)
Created2014
Description
The main objective of this research is to develop an approach to PV module lifetime prediction. In doing so, the aim is to move from empirical generalizations to a formal predictive science based on data-driven case studies of the crystalline silicon PV systems. The evaluation of PV systems aged 5 to 30 years old that results in systematic predictive capability that is absent today. The warranty period provided by the manufacturers typically range from 20 to 25 years for crystalline silicon modules. The end of lifetime (for example, the time-to-degrade by 20% from rated power) of PV modules is usually calculated using a simple linear extrapolation based on the annual field degradation rate (say, 0.8% drop in power output per year). It has been 26 years since systematic studies on solar PV module lifetime prediction were undertaken as part of the 11-year flat-plate solar array (FSA) project of the Jet Propulsion Laboratory (JPL) funded by DOE. Since then, PV modules have gone through significant changes in construction materials and design; making most of the field data obsolete, though the effect field stressors on the old designs/materials is valuable to be understood. Efforts have been made to adapt some of the techniques developed to the current technologies, but they are too often limited in scope and too reliant on empirical generalizations of previous results. Some systematic approaches have been proposed based on accelerated testing, but no or little experimental studies have followed. Consequently, the industry does not exactly know today how to test modules for a 20 - 30 years lifetime.
This research study focuses on the behavior of crystalline silicon PV module technology in the dry and hot climatic condition of Tempe/Phoenix, Arizona. A three-phase approach was developed: (1) A quantitative failure modes, effects, and criticality analysis (FMECA) was developed for prioritizing failure modes or mechanisms in a given environment; (2) A time-series approach was used to model environmental stress variables involved and prioritize their effect on the power output drop; and (3) A procedure for developing a prediction model was proposed for the climatic specific condition based on accelerated degradation testing
This research study focuses on the behavior of crystalline silicon PV module technology in the dry and hot climatic condition of Tempe/Phoenix, Arizona. A three-phase approach was developed: (1) A quantitative failure modes, effects, and criticality analysis (FMECA) was developed for prioritizing failure modes or mechanisms in a given environment; (2) A time-series approach was used to model environmental stress variables involved and prioritize their effect on the power output drop; and (3) A procedure for developing a prediction model was proposed for the climatic specific condition based on accelerated degradation testing
ContributorsKuitche, Joseph Mathurin (Author) / Pan, Rong (Thesis advisor) / Tamizhmani, Govindasamy (Thesis advisor) / Montgomery, Douglas C. (Committee member) / Wu, Teresa (Committee member) / Arizona State University (Publisher)
Created2014