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 75
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
When people look for things in their environment they use a target template - a mental representation of the object they are attempting to locate - to guide their attention around a scene and to assess incoming visual input to determine if they have found that for which they are searching. However, unlike laboratory experiments, searchers in the real-world rarely have perfect knowledge regarding the appearance of their target. In five experiments (with nearly 1,000 participants), we examined how the precision of the observer's template affects their ability to conduct visual search. Specifically, we simulated template imprecision in two ways: First, by contaminating our searchers' templates with inaccurate features, and second, by introducing extraneous features to the template that were unhelpful. In those experiments we recorded the eye movements of our searchers in order to make inferences regarding the extent to which attentional guidance and decision-making are hindered by template imprecision. We also examined a third way in which templates may become imprecise; namely, that they may deteriorate over time. Overall, our findings support a dual-function theory of the target template, and highlight the importance of examining template precision in future research.
ContributorsHout, Michael C (Author) / Goldinger, Stephen D (Thesis advisor) / Azuma, Tamiko (Committee member) / Homa, Donald (Committee member) / Reichle, Erik (Committee member) / Arizona State University (Publisher)
Created2013
Description
Two groups of cochlear implant (CI) listeners were tested for sound source localization and for speech recognition in complex listening environments. One group (n=11) wore bilateral CIs and, potentially, had access to interaural level difference (ILD) cues, but not interaural timing difference (ITD) cues. The second group (n=12) wore a single CI and had low-frequency, acoustic hearing in both the ear contralateral to the CI and in the implanted ear. These `hearing preservation' listeners, potentially, had access to ITD cues but not to ILD cues. At issue in this dissertation was the value of the two types of information about sound sources, ITDs and ILDs, for localization and for speech perception when speech and noise sources were separated in space. For Experiment 1, normal hearing (NH) listeners and the two groups of CI listeners were tested for sound source localization using a 13 loudspeaker array. For the NH listeners, the mean RMS error for localization was 7 degrees, for the bilateral CI listeners, 20 degrees, and for the hearing preservation listeners, 23 degrees. The scores for the two CI groups did not differ significantly. Thus, both CI groups showed equivalent, but poorer than normal, localization. This outcome using the filtered noise bands for the normal hearing listeners, suggests ILD and ITD cues can support equivalent levels of localization. For Experiment 2, the two groups of CI listeners were tested for speech recognition in noise when the noise sources and targets were spatially separated in a simulated `restaurant' environment and in two versions of a `cocktail party' environment. At issue was whether either CI group would show benefits from binaural hearing, i.e., better performance when the noise and targets were separated in space. Neither of the CI groups showed spatial release from masking. However, both groups showed a significant binaural advantage (a combination of squelch and summation), which also maintained separation of the target and noise, indicating the presence of some binaural processing or `unmasking' of speech in noise. Finally, localization ability in Experiment 1 was not correlated with binaural advantage in Experiment 2.
ContributorsLoiselle, Louise (Author) / Dorman, Michael F. (Thesis advisor) / Yost, William A. (Thesis advisor) / Azuma, Tamiko (Committee member) / Liss, Julie (Committee member) / Arizona State University (Publisher)
Created2013
Description
Concussion, a subset of mild traumatic brain injury (mTBI), has recently been brought to the forefront of the media due to a large lawsuit filed against the National Football League. Concussion resulting from injury varies in severity, duration, and type, based on many characteristics about the individual that research does not presently understand. Chronic fatigue, poor working memory, impaired self-awareness, and lack of attention to task are symptoms commonly present post-concussion. Currently, there is not a standard method of assessing concussion, nor is there a way to track an individual's recovery, resulting in misguided treatment for better prognosis. The aim of the following study was to determine patient specific higher-order cognitive processing deficits for clinical diagnosis and prognosis of concussion. Six individuals (N=6) were seen during the acute phase of concussion, two of whom were seen subsequently when their symptoms were deemed clinically resolved. Subjective information was collected from both the patient and from neurology testing. Each individual completed a task, in which they were presented with degraded speech, taxing their higher-order cognitive processing. Patient specific behavioral patterns are noted, creating a unique paradigm for mapping subjective and objective data for each patient's strategy to compensate for deficits and understand speech in a difficult listening situation. Keywords: concussion, cognitive processing
ContributorsBerg, Dena (Author) / Liss, Julie M (Committee member) / Azuma, Tamiko (Committee member) / Caviness, John (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
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
Previous research has shown that people can implicitly learn repeated visual contexts and use this information when locating relevant items. For example, when people are presented with repeated spatial configurations of distractor items or distractor identities in visual search, they become faster to find target stimuli in these repeated contexts over time (Chun and Jiang, 1998; 1999). Given that people learn these repeated distractor configurations and identities, might they also implicitly encode semantic information about distractors, if this information is predictive of the target location? We investigated this question with a series of visual search experiments using real-world stimuli within a contextual cueing paradigm (Chun and Jiang, 1998). Specifically, we tested whether participants could learn, through experience, that the target images they are searching for are always located near specific categories of distractors, such as food items or animals. We also varied the spatial consistency of target locations, in order to rule out implicit learning of repeated target locations. Results suggest that participants implicitly learned the target-predictive categories of distractors and used this information during search, although these results failed to reach significance. This lack of significance may have been due the relative simplicity of the search task, however, and several new experiments are proposed to further investigate whether repeated category information can benefit search.
ContributorsWalenchok, Stephen C (Author) / Goldinger, Stephen D (Thesis advisor) / Azuma, Tamiko (Committee member) / Homa, Donald (Committee member) / Hout, Michael C (Committee member) / Arizona State University (Publisher)
Created2014
Description
A multitude of individuals across the globe suffer from hearing loss and that number continues to grow. Cochlear implants, while having limitations, provide electrical input for users enabling them to "hear" and more fully interact socially with their environment. There has been a clinical shift to the bilateral placement of implants in both ears and to bimodal placement of a hearing aid in the contralateral ear if residual hearing is present. However, there is potentially more to subsequent speech perception for bilateral and bimodal cochlear implant users than the electric and acoustic input being received via these modalities. For normal listeners vision plays a role and Rosenblum (2005) points out it is a key feature of an integrated perceptual process. Logically, cochlear implant users should also benefit from integrated visual input. The question is how exactly does vision provide benefit to bilateral and bimodal users. Eight (8) bilateral and 5 bimodal participants received randomized experimental phrases previously generated by Liss et al. (1998) in auditory and audiovisual conditions. The participants recorded their perception of the input. Data were consequently analyzed for percent words correct, consonant errors, and lexical boundary error types. Overall, vision was found to improve speech perception for bilateral and bimodal cochlear implant participants. Each group experienced a significant increase in percent words correct when visual input was added. With vision bilateral participants reduced consonant place errors and demonstrated increased use of syllabic stress cues used in lexical segmentation. Therefore, results suggest vision might provide perceptual benefits for bilateral cochlear implant users by granting access to place information and by augmenting cues for syllabic stress in the absence of acoustic input. On the other hand vision did not provide the bimodal participants significantly increased access to place and stress cues. Therefore the exact mechanism by which bimodal implant users improved speech perception with the addition of vision is unknown. These results point to the complexities of audiovisual integration during speech perception and the need for continued research regarding the benefit vision provides to bilateral and bimodal cochlear implant users.
ContributorsLudwig, Cimarron (Author) / Liss, Julie (Thesis advisor) / Dorman, Michael (Committee member) / Azuma, Tamiko (Committee member) / Arizona State University (Publisher)
Created2015