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Description
Coccidioidomycosis, also known as Valley Fever, is a disease caused by the dimorphic soil-dwelling fungus, Coccidioides sp. Coccidioidomycosis is difficult to diagnose because symptoms are similar to community-acquired pneumonia. Current diagnostic tests rely on antibody responses, but immune responses can be delayed and aberrant, resulting in false negative diagnoses. Unlike

Coccidioidomycosis, also known as Valley Fever, is a disease caused by the dimorphic soil-dwelling fungus, Coccidioides sp. Coccidioidomycosis is difficult to diagnose because symptoms are similar to community-acquired pneumonia. Current diagnostic tests rely on antibody responses, but immune responses can be delayed and aberrant, resulting in false negative diagnoses. Unlike serology, detection of coccidioidal proteins or other fungal components in blood could distinguish valley fever from other pulmonary infections and provide a definitive diagnosis. Using mass spectrometry (LC-MS/MS) we examined the plasma peptidome from patients with serologically confirmed coccidioidomycosis. Mass spectra were searched using the protein database from the Coccidioides species, generated and annotated by the Broad Institute. 15 of 20 patients with serologically confirmed coccidioidomycosis demonstrated the presence of a peptide in plasma, "PGLDSKSLACTFSQV" (PGLD). The peptide is derived from an open reading frame from a "conserved hypothetical protein" annotated with 2 exons, and to date, found only in the C. posadasii strain Silviera RMSCC 3488 genomic sequence. In this thesis work, cDNA sequence analysis from polyadenylated RNA confirms the peptide sequence and genomic location of the peptide, but does not indicate that the intron in the gene prediction of C. posadasii strain Silviera RMSCC 3488 is present. A monoclonal antibody generated against the peptide bound to a 16kDa protein in T27K coccidioidal lysate. Detecting components of the fungus plasma could be a useful diagnostic tool, especially when serology does not provide a definitive diagnosis.
ContributorsDuffy, Stacy Leigh (Author) / Lake, Douglas (Thesis advisor) / Magee, Dewey Mitch (Committee member) / Antwi, Kwasi (Committee member) / Arizona State University (Publisher)
Created2013
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Description
Modified and artificial water sources can be used as a management tool for game and non-game wildlife species. State, federal, and private agencies allocate significant resources to install and maintain artificial water sources (AWS) annually. Capture mark recapture methods were used to sample small mammal communities in the vicinity of

Modified and artificial water sources can be used as a management tool for game and non-game wildlife species. State, federal, and private agencies allocate significant resources to install and maintain artificial water sources (AWS) annually. Capture mark recapture methods were used to sample small mammal communities in the vicinity of five AWS and five paired control sites (treatments) in the surrounding Sonoran desert from October 2011 to May 2012. I measured plant species richness, density, and percent cover in the spring of 2012. A Multi-response Permutation Procedure was used to identify differences in small mammal community abundance, biomass, and species richness by season and treatment. I used Principle Component Analysis to reduce 11 habitat characteristics to five habitat factors. I related rodent occurrence to habitat characteristics using multiple and logistic regression. A total of 370 individual mammals representing three genera and eight species of rodents were captured across 4800 trap nights. Desert pocket mouse (Chaetodipus penicillatus) was the most common species in both seasons and treatments. Whereas rodent community abundance, biomass, and richness were similar between seasons, community variables of AWS were greater than CS. Rodent diversity was similar between treatments. Desert pocket mouse abundance and biomass were twice as high at AWS when compared to controls. Biomass of white-throated woodrat (Neotoma albigula) was five times greater at AWS. Habitat characteristics were similar between treatments. Neither presence of water nor distance to water explained substantial habitat variation. Occurrence of rodent species was associated with habitat characteristics. Desert rodent communities are adapted for arid environments (i.e. Heteromyids) and are not dependent on "free water". Higher abundances of desert pocket mouse at AWS were most likely related to increased disturbance and debris and not the presence of water. The results of this study and previous studies suggest that more investigation is needed and that short term studies may not be able to detect interactions (if any) between AWS and desert small mammal communities.
ContributorsSwitalski, Aaron (Author) / Bateman, Heather L (Thesis advisor) / Miller, William (Committee member) / Alford, Eddie (Committee member) / Arizona State University (Publisher)
Created2013
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Description
ABSTRACT 1. Aposematic signals advertise prey distastefulness or metabolic unprofitability to potential predators and have evolved independently in many prey groups over the course of evolutionary history as a means of protection from predation. Most aposematic signals investigated to date exhibit highly chromatic patterning; however, relatives in these toxic groups

ABSTRACT 1. Aposematic signals advertise prey distastefulness or metabolic unprofitability to potential predators and have evolved independently in many prey groups over the course of evolutionary history as a means of protection from predation. Most aposematic signals investigated to date exhibit highly chromatic patterning; however, relatives in these toxic groups with patterns of very low chroma have been largely overlooked. 2. We propose that bright displays with low chroma arose in toxic prey species because they were more effective at deterring predation than were their chromatic counterparts, especially when viewed in relatively low light environments such as forest understories. 3. We analyzed the reflectance and radiance of color patches on the wings of 90 tropical butterfly species that belong to groups with documented toxicity that vary in their habitat preferences to test this prediction: Warning signal chroma and perceived chromaticity are expected to be higher and brightness lower in species that fly in open environments when compared to those that fly in forested environments. 4. Analyses of the reflectance and radiance of warning color patches and predator visual modeling support this prediction. Moreover, phylogenetic tests, which correct for statistical non-independence due to phylogenetic relatedness of test species, also support the hypothesis of an evolutionary correlation between perceived chromaticity of aposematic signals and the flight habits of the butterflies that exhibit these signals.
ContributorsDouglas, Jonathan Marion (Author) / Rutowski, Ronald L (Thesis advisor) / Gadau, Juergen (Committee member) / McGraw, Kevin J. (Committee member) / Arizona State University (Publisher)
Created2013
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Description
Random peptide microarrays are a powerful tool for both the treatment and diagnostics of infectious diseases. On the treatment side, selected random peptides on the microarray have either binding or lytic potency against certain pathogens cells, thus they can be synthesized into new antimicrobial agents, denoted as synbodies (synthetic antibodies).

Random peptide microarrays are a powerful tool for both the treatment and diagnostics of infectious diseases. On the treatment side, selected random peptides on the microarray have either binding or lytic potency against certain pathogens cells, thus they can be synthesized into new antimicrobial agents, denoted as synbodies (synthetic antibodies). On the diagnostic side, serum containing specific infection-related antibodies create unique and distinct "pathogen-immunosignatures" on the random peptide microarray distinct from the healthy control serum, and this different mode of binding can be used as a more precise measurement than traditional ELISA tests. My thesis project is separated into these two parts: the first part falls into the treatment side and the second one focuses on the diagnostic side. My first chapter shows that a substitution amino acid peptide library helps to improve the activity of a recently reported synthetic antimicrobial peptide selected by the random peptide microarray. By substituting one or two amino acids of the original lead peptide, the new substitutes show changed hemolytic effects against mouse red blood cells and changed potency against two pathogens: Staphylococcus aureus and Pseudomonas aeruginosa. Two new substitutes are then combined together to form the synbody, which shows a significantly antimicrobial potency against Staphylococcus aureus (<0.5uM). In the second chapter, I explore the possibility of using the 10K Ver.2 random peptide microarray to monitor the humoral immune response of dengue. Over 2.5 billion people (40% of the world's population) live in dengue transmitting areas. However, currently there is no efficient dengue treatment or vaccine. Here, with limited dengue patient serum samples, we show that the immunosignature has the potential to not only distinguish the dengue infection from non-infected people, but also the primary dengue infection from the secondary dengue infections, dengue infection from West Nile Virus (WNV) infection, and even between different dengue serotypes. By further bioinformatic analysis, we demonstrate that the significant peptides selected to distinguish dengue infected and normal samples may indicate the epitopes responsible for the immune response.
ContributorsWang, Xiao (Author) / Johnston, Stephen Albert (Thesis advisor) / Blattman, Joseph (Committee member) / Arntzen, Charles (Committee member) / Arizona State University (Publisher)
Created2013
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Description
Biological diversity is threatened by increasing anthropogenic modification of natural environments and increasing demands on natural resources. Sonoran desert tortoises (Gopherus morafkai) currently have Candidate status under the Endangered Species Act (ESA) based on health and habitat threats. To ensure this animal persists in the midst of multiple threats requires

Biological diversity is threatened by increasing anthropogenic modification of natural environments and increasing demands on natural resources. Sonoran desert tortoises (Gopherus morafkai) currently have Candidate status under the Endangered Species Act (ESA) based on health and habitat threats. To ensure this animal persists in the midst of multiple threats requires an understanding of the life history and ecology of each population. I looked at one physiological and one behavioral aspect of a population of tortoises at the Sugarloaf Mountain (SL) study site in central Arizona, USA. I used 21 years of capture-recapture records to estimate growth parameters of the entire population. I investigated habitat selection of juvenile tortoises by selecting 117 locations of 11 tortoises that had been tracked by radio-telemetry one to three times weekly for two years, selecting locations from both summer active season and during winter hibernation. I compared 22 microhabitat variables of tortoise locations to random SL locations to determine habitat use and availability. Male tortoises at SL reach a greater asymptotic length than females, and males and females appear to grow at the same rate. Juvenile tortoises at the SL site use steep rocky hillsides with high proportions of sand and annual vegetation, few succulents, and enclosed shelters in summer. They use enclosed shelters on steep slopes for winter hibernation. An understanding of these features can allow managers to quantify Sonoran desert tortoise habitat needs and life history characteristics and to understand the impact of land use policies.
ContributorsBridges, Andrew (Author) / Bateman, Heather L (Thesis advisor) / Miller, William (Committee member) / Ulrich, Jon (Committee member) / Arizona State University (Publisher)
Created2012
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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.,

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
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Description
Urbanization provides an excellent opportunity to examine the effects of human-induced rapid environmental change (HIREC) on natural ecosystems. Certain species can dominate in urban habitats at the expense of biodiversity. Phenotypic plasticity may be the mechanism by which these 'urban exploiters' flourish in urban areas. Color displays and condition-dependent phenotypes

Urbanization provides an excellent opportunity to examine the effects of human-induced rapid environmental change (HIREC) on natural ecosystems. Certain species can dominate in urban habitats at the expense of biodiversity. Phenotypic plasticity may be the mechanism by which these 'urban exploiters' flourish in urban areas. Color displays and condition-dependent phenotypes are known to be highly plastic. However, conspicuous color displays are perplexing in that they can be costly to produce and may increase detection by enemies. The Western black widow spider () is a superabundant pest species that forms dense aggregations throughout metropolitan Phoenix, Arizona, USA. Adult female display a red hourglass on their abdomen, which is speculated to function as a conspicuous warning signal to enemies. Here, I performed field studies to identify how widow morphology and hourglass color differ between urban and desert subpopulations. I also conducted laboratory experiments to examine the dietary sensitivity of hourglass coloration and to identify its functional role in the contexts of agonism, mating, and predator defense. My field data reveal significant spatial variation across urban and desert subpopulations in ecology and color. Furthermore, hourglass coloration was significantly influenced by environmental factors unique to urban habitats. Desert spiders were found to be smaller and less colorful than urban spiders. Throughout, I observed a positive correlation between body condition and hourglass size. Laboratory diet manipulations empirically confirm the condition-dependence of hourglass size. Additionally, widows with extreme body conditions exhibited condition-dependent coloration. However, hourglass obstruction and enlargement did not produce any effects on the outcome of agonistic encounters, male courtship, or predator deterrence. This work offers important insights into the effects of urbanization on the ecology and coloration of a superabundant pest species. While the function of the hourglass remains undetermined, my findings characterize the black widow's hourglass as extremely plastic. Plastic responses to novel environmental conditions can modify the targets of natural selection and subsequently influence evolutionary outcomes. Therefore, assuming a heritable component to this plasticity, the response of hourglass plasticity to the abrupt environmental changes in urban habitats may result in the rapid evolution of this phenotype.
ContributorsGburek, Theresa (Author) / Johnson, James C. (Thesis advisor) / McGraw, Kevin J. (Committee member) / Rutowski, Ronald L (Committee member) / Arizona State University (Publisher)
Created2014
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Description
Past research suggested that lutein (L) and zeaxanthin (Z) play a role in many aspects of cognitive functions including motor speed, working memory, executive function, psychomotor speed and verbal fluency among elderly people. Moreover, L and Z are the only carotenoids found in the eye, and they are correlated with

Past research suggested that lutein (L) and zeaxanthin (Z) play a role in many aspects of cognitive functions including motor speed, working memory, executive function, psychomotor speed and verbal fluency among elderly people. Moreover, L and Z are the only carotenoids found in the eye, and they are correlated with improved contrast sensitivity, improved temporal vision, reduced glare disability, and reduced risk of age related-macular degeneration (AMD). Animal and postmortem research suggests that MPOD may be a biomarker for predicting cognitive decline with age. The purpose of this study is to evaluate the potential relationship between MPOD and cognition in young healthy adults. There were fifty participants in the current study, 25 had low MPOD. The remaining participants exhibited high MPOD, which was measured using a macular pigment densitometer. People with low MPOD did not perform any worse than people with high MPOD. Although low MPOD in young adults may be a biomarker for future cognitive decline, the effects may lay dormant until later in life. Future research should explore this possibility by replicating this study with an older population.
ContributorsZimmerman, Daniel (Author) / Nanez, Jose E (Thesis advisor) / Shipstead, Zachary (Committee member) / Hall, Deborah (Committee member) / Arizona State University (Publisher)
Created2014
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Description
Grassland habitat restoration activities are occurring within the semi-arid grasslands of the Agua Fria National Monument located 65 km north of Phoenix, AZ. The goal of these restoration activities is to reduce woody species encroachment, remove lignified plant materials and recycle nutrients within the ecosystem thus improving range conditions for

Grassland habitat restoration activities are occurring within the semi-arid grasslands of the Agua Fria National Monument located 65 km north of Phoenix, AZ. The goal of these restoration activities is to reduce woody species encroachment, remove lignified plant materials and recycle nutrients within the ecosystem thus improving range conditions for both wildlife species and livestock. Broadcast burning, juniper thinning and slash pile burns are the principle tools used to accomplish resource objectives. Line cover, belt transect, densities, heights and biomass of vegetation data were collected to determine the response of the vegetative community to habitat restoration activities. Principal Component Analysis (PCA) was used to reduce data analysis to the more influential factors. Regression analysis was conducted for statistically significant response variables. Quadratic regression analysis found low predictive values. In broadcast burn treatment units, all important factors as identified by PCA had low predictive factors but significantly differed (R2 <0.01, p<0.05) between unburned and the years post treatment. Regression analysis found significant, albeit weak, relationships between time since treatment and independent variables. In pile burn treatment units, data reduction by PCA was not possible in a biologically meaningful way due to the high variability within treatment units. This suggests the effect of juniper encroachment on grassland vegetation persists long after junipers have been cut and burned. This study concluded that broadcast burning of the central Arizona grasslands does significantly alter many components of the vegetative community. Fuels treatments generally initially reduced both perennial woody species and grasses in number and height for two year post fire. However, palatable shrubs, in particular shrubby buckwheat, were not significantly different in broadcast burn treatment areas. The vegetative community characteristics of juniper encroached woodlands of central Arizona are unaffected by the removal and burning of junipers aside from the removal of hiding cover for predators for multiple years. It is recommended that habitat restoration activities continue provided the needs of wildlife are considered, especially pronghorn, with the incorporation of state and transition models specific to each of the respective ecological site descriptions and with the consideration of the effects of fire to pronghorn fawning habitat.
ContributorsSitzmann, Paul Roman (Author) / Miller, William (Thesis advisor) / Alford, Eddie (Committee member) / Green, Douglas (Committee member) / Arizona State University (Publisher)
Created2014
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Description
Modeling dynamic systems is an interesting problem in Knowledge Representation (KR) due to their usefulness in reasoning about real-world environments. In order to effectively do this, a number of different formalisms have been considered ranging from low-level languages, such as Answer Set Programming (ASP), to high-level action languages, such as

Modeling dynamic systems is an interesting problem in Knowledge Representation (KR) due to their usefulness in reasoning about real-world environments. In order to effectively do this, a number of different formalisms have been considered ranging from low-level languages, such as Answer Set Programming (ASP), to high-level action languages, such as C+ and BC. These languages show a lot of promise over many traditional approaches as they allow a developer to automate many tasks which require reasoning within dynamic environments in a succinct and elaboration tolerant manner. However, despite their strengths, they are still insufficient for modeling many systems, especially those of non-trivial scale or that require the ability to cope with exceptions which occur during execution, such as unexpected events or unintended consequences to actions which have been performed. In order to address these challenges, a theoretical framework is created which focuses on improving the feasibility of applying KR techniques to such problems. The framework is centered on the action language BC+, which integrates many of the strengths of existing KR formalisms, and provides the ability to perform efficient reasoning in an incremental fashion while handling exceptions which occur during execution. The result is a developer friendly formalism suitable for performing reasoning in an online environment. Finally, the newly enhanced Cplus2ASP 2 is introduced, which provides a number of improvements over the original version. These improvements include implementing BC+ among several additional languages, providing enhanced developer support, and exhibiting a significant performance increase over its predecessors and similar systems.
ContributorsBabb, Joseph (Author) / Lee, Joohyung (Thesis advisor) / Lee, Yann-Hang (Committee member) / Baral, Chitta (Committee member) / Arizona State University (Publisher)
Created2014