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- Genre: Masters Thesis
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
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
Description
Vertebrate genomes demonstrate a remarkable range of sizes from 0.3 to 133 gigabase pairs. The proliferation of repeat elements are a major genomic expansion. In particular, long interspersed nuclear elements (LINES) are autonomous retrotransposons that have the ability to "cut and paste" themselves into a host genome through a mechanism called target-primed reverse transcription. LINES have been called "junk DNA," "viral DNA," and "selfish" DNA, and were once thought to be parasitic elements. However, LINES, which diversified before the emergence of many early vertebrates, has strongly shaped the evolution of eukaryotic genomes. This thesis will evaluate LINE abundance, diversity and activity in four anole lizards. An intrageneric analysis will be conducted using comparative phylogenetics and bioinformatics. Comparisons within the Anolis genus, which derives from a single lineage of an adaptive radiation, will be conducted to explore the relationship between LINE retrotransposon activity and causal changes in genomic size and composition.
ContributorsMay, Catherine (Author) / Kusumi, Kenro (Thesis advisor) / Gadau, Juergen (Committee member) / Rawls, Jeffery A (Committee member) / Arizona State University (Publisher)
Created2013
Description
Gene-centric theories of evolution by natural selection have been popularized and remain generally accepted in both scientific and public paradigms. While gene-centrism is certainly parsimonious, its explanations fall short of describing two patterns of evolutionary and social phenomena: the evolution of sex and the evolution of social altruism. I review and analyze current theories on the evolution of sex. I then introduce the conflict presented to gene-centric evolution by social phenomena such as altruism and caste sterility in eusocial insects. I review gene-centric models of inclusive fitness and kin selection proposed by Hamilton and Maynard Smith. Based their assumptions, that relatedness should be equal between sterile workers and reproductives, I present several empirical examples that conflict with their models. Following that, I introduce a unique system of genetic caste determination (GCD) observed in hybrid populations of two sister-species of seed harvester ants, Pogonomyrmex rugosus and Pogonomyrmex barbatus. I review the evidence for GCD in those species, followed by a critique of the current gene-centric models used to explain it. In chapter two I present my own theoretical model that is both simple and extricable in nature to explain the origin, evolution, and maintenance of GCD in Pogonomyrmex. Furthermore, I use that model to fill in the gaps left behind by the contributing authors of the other GCD models. As both populations in my study system formed from inter-specific hybridization, I review modern discussions of heterosis (also called hybrid vigor) and use those to help explain the ecological competitiveness of GCD. I empirically address the inbreeding depression the lineages of GCD must overcome in order to remain ecologically stable, demonstrating that as a result of their unique system of caste determination, GCD lineages have elevated recombination frequencies. I summarize and conclude with an argument for why GCD evolved under selective mechanisms which cannot be considered gene-centric, providing evidence that natural selection can effectively operate on non-heritable genotypes appearing in groups and other social contexts.
ContributorsJacobson, Neal (Author) / Gadau, Juergen (Thesis advisor) / Laubichler, Manfred (Committee member) / Pratt, Stephen (Committee member) / Arizona State University (Publisher)
Created2012
Description
Here I present a phylogeographic study of at least six reproductively isolated lineages of harvester ants within the Pogonomyrmex barbatus and P. rugosus species group. The genetic and geographic relationships within this clade are complex: four of the identified lineages are divided into two pairs, and each pair has evolved under a mutualistic system that necessitates sympatry. These paired lineages are dependent upon one another because interlineage matings within each pair are the sole source of hybrid F1 workers; these workers build and sustain the colonies, facilitating the production of the reproductive caste, which results solely from intralineage fertilizations. This system of genetic caste determination (GCD) maintains genetic isolation among these closely related lineages, while simultaneously requiring co-expansion and emigration as their distributions have changed over time. Previous studies have also demonstrated that three of the four lineages displaying this unique genetic caste determination phenotype are of hybrid origin. Thus, reconstructing the phylogenetic and geographic history of this group allows us to evaluate past insights and plan future inquiries in a more complete historical biogeographic context. Using mitochondrial DNA sequences sampled across most of the morphospecies' ranges in the U.S. and Mexico, I employed several methods of phylogenetic and DNA sequence analysis, along with comparisons to geological, biogeographic, and phylogeographic studies throughout the sampled regions. These analyses on Pogonomyrmex harvester ants reveal a complex pattern of vicariance and dispersal that is largely concordant with models of late Miocene, Pliocene, and Pleistocene range shifts among various arid-adapted taxa in North America.
ContributorsMott, Brendon (Author) / Gadau, Juergen (Thesis advisor) / Fewell, Jennifer (Committee member) / Anderson, Kirk (Committee member) / Arizona State University (Publisher)
Created2012
Description
Communications around sustainability have been found to be incongruent with eliciting the transformative change required to address global climate change and its' repercussions. Recent research has been exploring storytelling in sustainability, specifically with an emphasis on reflexive and emancipatory methods. These methods encourage embracing and contextualizing complexity and intend to target entire cognitive hierarchies. This study explores the possibility of using emancipatory and reflexive storytelling as a tool to change attitudes pertaining to the Valley Metro Light Rail, an example of a complex sustainability mitigation effort. I explore this in four steps: 1) Conducted a pre-survey to gauge preexisting attitudes and predispositions; 2) Provided a narrative that uses storytelling methodologies of reflexivity and emancipation through a story about the light rail; 3) Conducted a post-survey to gauge attitude shift resulting from the narrative intervention; 4) Facilitated a focus group discussion to examine impact qualitatively. These steps intended to provide an answer to the question: How does emancipatory and reflexive storytelling impact affective, cognitive and conative attitudes regarding local alternative transportation? By using tripartite attitude model, qualitative and quantitative analysis this paper determines that reflexive and emancipatory storytelling impacts attitudinal structures. The impact is marginal in the survey response, though the shift indicated a narrowing of participant responses towards one another, indicative of participants subscribing to emancipation and reflexivity of their held attitudes. From the group discussion, it was evident from qualitative responses that participants engaged in emancipating themselves from their held attitudes and reflected upon them. In doing so they engaged in collaboration to make suggestions and suggest actions to help those with experiences that differed from their own. Though this research doesn’t provide conclusive evidence, it opens the door for future research to assess these methodologies as a tool to elicit shared values, beliefs and norms, which are necessary for collective action leading to transformative change in response to global climate change.
ContributorsSwanson, Jake Ryan (Author) / Roseland, Mark (Thesis advisor) / Larson, Kelli (Committee member) / Calhoun, Craig (Committee member) / Schoon, Michael (Committee member) / Arizona State University (Publisher)
Created2023
Description
University-level sustainability education in Western academia attempts to focus on eliminating future harm to people and the planet. However, Western academia as an institution upholds systems of oppression and reproduces settler colonialism. This reproduction is antithetical to sustainability goals as it continues patterns of Indigenous erasure and extractive relationships to the Land that perpetuate violence towards people and the planet. Sustainability programs, however, offer several frameworks, including resilience, that facilitate critical interrogations of social-ecological systems. In this thesis, I apply the notion of resilience to the perpetuation of settler colonialism within university-level sustainability education. Specifically, I ask: How is settler colonialism resilient in university-level sustainability education? How are, or could, sustainability programs in Western academic settings address settler colonialism? Through a series of conversational interviews with faculty and leadership from Arizona State University School of Sustainability, I analyzed how university-level sustainability education is both challenging and shaped by settler colonialism. These interviews focused on faculty perspectives on the topic and related issues; the interviews were analyzed using thematic coding in NVivo software. The results of this project highlight that many faculty members are already concerned with and focused on challenging settler colonialism, but that settler colonialism remains resilient in this system due to feedback loops at the personal level and reinforcing mechanisms at the institutional level. This research analyzes these feedback loops and reinforcing mechanisms, among others, and supports the call for anti-colonial and decolonial reconstruction of curriculum, as well as a focus on relationship building, shifting of mindset, and school-wide education on topics of white supremacy, settler colonialism, and systems of oppression in general.
ContributorsBills, Haven (Author) / Klinsky, Sonja (Thesis advisor) / Goebel, Janna (Committee member) / Schoon, Michael (Committee member) / Arizona State University (Publisher)
Created2022
Description
Wildlife rehabilitation as a practice in the United States exists in a complicated ethical landscape. The Wildlife Rehabilitator's Code of Ethics exists to guide the profession and states that rehabilitators must respect the wildness and maintain the dignity of an animal in their care. This thesis explores the question: How do the attitudes and actions of wildlife rehabilitators exemplify the ways in which they understand and enact respect for an animal’s dignity and wildness while in their care? Additionally, in what circumstances do rehabilitators align and diverge from each other in their interpretation and demonstration of this respect? These questions were answered through a literature review, interviews with rehabilitators, and site visits to wildlife rehabilitation centers in the Phoenix metropolitan area. My results suggest that rehabilitators are aligned in their understanding of respect for wildness and dignity as it applies to the animals in their care that are actively undergoing rehabilitation. Rehabilitators achieved consensus on the idea that they should interact with the animals as little as possible while providing their medically necessary care. Rehabilitators began to diverge when considering the animals in their sanctuary spaces. Specifically, they varied in their perception of wildness in sanctuary animals, which informed how some saw their responsibilities to the animals. Lesser perceived wildness correlated to increased acceptance of forming affectionate relationships with the sanctuary animals, and even feelings of obligation to form these relationships. Based on my research, I argue that the Wildlife Rehabilitator's Code of Ethics should be revised to reflect the specific boundary that wildlife rehabilitators identified in the rehabilitation space and provide substantive guidance as to what respecting wildness and dignity means in this field.
ContributorsBernat, Isabella Elyse (Author) / Minteer, Ben (Thesis advisor) / Ellison, Karin (Committee member) / Schoon, Michael (Committee member) / Arizona State University (Publisher)
Created2023
Description
Amongst the most studied of the social insects, the honey bee has a prominent place due to its economic importance and influence on human societies. Honey bee colonies can have over 50,000 individuals, whose activities are coordinated by chemical signals called pheromones. Because these pheromones are secreted from various exocrine glands, the proper development and function of these glands are vital to colony dynamics. In this thesis, I present a study of the developmental ontogeny of the exocrine glands found in the head of the honey bee. In Chapter 2, I elucidate how the larval salivary gland transitions to an adult salivary gland through apoptosis and cell growth, differentiation and migration. I also explain the development of the hypopharyngeal and the mandibular gland using apoptotic markers and cytoskeletal markers like tubulin and actin. I explain the fundamental developmental plan for the formation of the glands and show that apoptosis plays an important role in the transformation toward an adult gland.
ContributorsNath, Rachna (Author) / Gadau, Juergen (Thesis advisor) / Rawls, Alan (Committee member) / Harrison, Jon (Committee member) / Arizona State University (Publisher)
Created2018
Description
Many Fic domain proteins, through catalyzing post translational modifications (PTM) of protein substrates, functionally contribute to bacterial pathogenesis and the regulation of bacterial growth. Furthermore, one form of Fic-mediated regulation is the Fic toxin-antitoxin system, whereby an antitoxin interacts with and inhibits the Fic toxin. This study sought to determine the functional importance of Mycobacterium tuberculosis Fic and its putative antitoxin protein, Rv3642c. Using M. tuberculosis H37Rv genetic deletion mutants, fic and Rv3642c were demonstrated to promote intracellular survival in human THP-1 macrophage-like cells. Unlike other Fic toxins, of Fic toxin-antitoxin systems, Fic did not inhibit bacterial growth in vitro in the absence of Rv3642c. Notably, Fic demonstrated in vitro AMPylation of a THP-1 cell extract protein as shown by immunodetection. Fic also exhibited auto-AMPylation activity. Interestingly, a mutation of the conserved histidine in the Fic domain motif, a residue previously shown to be critical for AMPylation, had no effect on Fic-mediated ATP hydrolysis or AMPylation activity. Rv3642c was demonstrated to form a complex with Fic when co-expressed in Escherichia coli, indicating a toxin-antitoxin interaction. Screening M. tuberculosis protein fractions and culture filtrate with α-Fic and α-Rv3642c rabbit antisera did not detect monomers of Fic or Rv3642c, thus the cellular localization of Fic and the Rv3642c-Fic complex remains unclear. The results of this study provide insight into the function of M. tuberculosis Fic, and suggest that Fic and Rv3642c are important for M. tuberculosis survival in the intracellular macrophage environment. Furthermore, these findings challenge the current dogma that Fic domain catalysis is dependent on the conserved histidine of the Fic motif.
ContributorsLaMarca, Ryan (Author) / Haydel, Shelley (Thesis advisor) / Lake, Douglas (Committee member) / Nickerson, Cheryl (Committee member) / Arizona State University (Publisher)
Created2017