Matching Items (114)
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 study of bacterial resistance to antimicrobial peptides (AMPs) is a significant area of interest as these peptides have the potential to be developed into alternative drug therapies to combat microbial pathogens. AMPs represent a class of host-mediated factors that function to prevent microbial infection of their host and serve as a first line of defense. To date, over 1,000 AMPs of various natures have been predicted or experimentally characterized. Their potent bactericidal activities and broad-based target repertoire make them a promising next-generation pharmaceutical therapy to combat bacterial pathogens. It is important to understand the molecular mechanisms, both genetic and physiological, that bacteria employ to circumvent the bactericidal activities of AMPs. These understandings will allow researchers to overcome challenges posed with the development of new drug therapies; as well as identify, at a fundamental level, how bacteria are able to adapt and survive within varied host environments. Here, results are presented from the first reported large scale, systematic screen in which the Keio collection of ~4,000 Escherichia coli deletion mutants were challenged against physiologically significant AMPs to identify genes required for resistance. Less than 3% of the total number of genes on the E. coli chromosome was determined to contribute to bacterial resistance to at least one AMP analyzed in the screen. Further, the screen implicated a single cellular component (enterobacterial common antigen, ECA) and a single transporter system (twin-arginine transporter, Tat) as being required for resistance to each AMP class. Using antimicrobial resistance as a tool to identify novel genetic mechanisms, subsequent analyses were able to identify a two-component system, CpxR/CpxA, as a global regulator in bacterial resistance to AMPs. Multiple previously characterized CpxR/A members, as well as members found in this study, were identified in the screen. Notably, CpxR/A was found to transcriptionally regulate the gene cluster responsible for the biosynthesis of the ECA. Thus, a novel genetic mechanism was uncovered that directly correlates with a physiologically significant cellular component that appears to globally contribute to bacterial resistance to AMPs.
ContributorsWeatherspoon-Griffin, Natasha (Author) / Shi, Yixin (Thesis advisor) / Clark-Curtiss, Josephine (Committee member) / Misra, Rajeev (Committee member) / Nickerson, Cheryl (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2013
Description
Consideration of both biological and human-use dynamics in coupled social-ecological systems is essential for the success of interventions such as marine reserves. As purely human institutions, marine reserves have no direct effects on ecological systems. Consequently, the success of a marine reserve depends on managers` ability to alter human behavior in the direction and magnitude that supports reserve objectives. Further, a marine reserve is just one component in a larger coupled social-ecological system. The social, economic, political, and biological landscape all determine the social acceptability of a reserve, conflicts that arise, how the reserve interacts with existing fisheries management, accuracy of reserve monitoring, and whether the reserve is ultimately able to meet conservation and fishery enhancement goals. Just as the social-ecological landscape is critical at all stages for marine reserve, from initial establishment to maintenance, the reserve in turn interacts with biological and human use dynamics beyond its borders. Those interactions can lead to the failure of a reserve to meet management goals, or compromise management goals outside the reserve. I use a bio-economic model of a fishery in a spatially patchy environment to demonstrate how the pre-reserve fisheries management strategy determines the pattern of fishing effort displacement once the reserve is established, and discuss the social, political, and biological consequences of different patterns for the reserve and the fishery. Using a stochastic bio-economic model, I demonstrate how biological and human use connectivity can confound the accurate detection of reserve effects by violating assumptions in the quasi-experimental framework. Finally, I examine data on recreational fishing site selection to investigate changes in response to the announcement of enforcement of a marine reserve in the Gulf of California, Mexico. I generate a scale of fines that would fully or partially protect the reserve, providing a data-driven way for managers to balance biological and socio-economic goals. I suggest that natural resource managers consider human use dynamics with the same frequency, rigor, and tools as they do biological stocks.
ContributorsFujitani, Marie (Author) / Abbott, Joshua (Thesis advisor) / Fenichel, Eli (Thesis advisor) / Gerber, Leah (Committee member) / Anderies, John (Committee member) / Arizona State University (Publisher)
Created2014
Description
I travelled and worked in international fisheries policy for 7 months in preparation for this thesis. During this time I completed one internship in Rome, Italy with the Food and Agriculture Organization of the United Nations (UNFAO) and another internship on the island of Pohnpei with the Secretariat of the Western and Central Pacific Fisheries Commission (WCPFC). From these experiences, I selected the subject of this thesis. My thesis analyzes the management system for South Pacific albacore tuna, the source stock for brands like "Chicken of the Sea" and "Starkist". South Pacific albacore tuna pass through international waters and the waters of several Pacific Island countries and territories, necessitating States to cooperate and coordinate to sustain the future viability of the stock. A case study for transboundary natural resource management, I discuss the institutional complexity that arises from managing such a resource. I use common-pool resource (CPR) theory to describe this complexity, which frames natural resource management as a collective-action problem among resource users. I first conceptualize the management system as having multiple institutional scales and multiple levels of organization. Then, employing Ostrom's 8 design principles for successful CPR management, I conduct a multi-institution analysis of the international, regional, and subregional institutions that participate in the management system. Finally, I also conduct a cross-institution analysis by examining the interactions between these institutions. I find that significant space for theoretical development exists in CPR theory for understanding complex management systems for transboundary natural resources. Furthermore, I find that interactions between institutions create linkages that could be retooled to improve the performance of the South Pacific albacore tuna management system.
ContributorsAbolhassani, Angela Maryam (Author) / Abbott, Kenneth (Thesis director) / Schoon, Michael (Committee member) / Barrett, The Honors College (Contributor) / School of Politics and Global Studies (Contributor) / School of Life Sciences (Contributor) / Department of English (Contributor)
Created2015-05
Description
This paper explores two areas of study: Colony Collapse Disorder and urban apiculture--the practice of keeping bees in urban areas. Additionally, this paper discusses the ways in which Colony Collapse Disorder has encouraged an increase in urban beekeeping, and the possible role of urban apiculture as a means of combatting the negative effects of Colony Collapse Disorder. The symptoms, history, and possible causes of Colony Collapse Disorder are presented, as well as the important role that honey bees play in human agriculture. Following the discussion of Colony Collapse Disorder is a description of my urban beekeeping apprenticeship at Desert Marigold School where I kept bees, researched various hives, attended a beekeeping workshop in Tucson, and eventually built a hive and established a colony with my mentor. This paper includes a guide to beekeeping basics, as well as a guide to starting a hive based upon the lessons learned during my apprenticeship.
ContributorsRomero, Madelyn Rattan (Author) / Schoon, Michael (Thesis director) / Silcox, Holly (Committee member) / Barrett, The Honors College (Contributor) / School of Sustainability (Contributor) / School of Geographical Sciences and Urban Planning (Contributor)
Created2015-05
Description
Hepatitis C virus (HCV) is a globally prevalent infection which is a main contributor to the global burden of liver disease. Due to its ability to establish a chronic infection, and the lack of usefulness of traditional neutralizing antibody vaccine design in producing a protective immune response, a preventative vaccine has been notoriously difficult to produce. To overcome this, a vaccine using non-structural protein 3 (NS3) as a target to elicit a T cell specific immune response is thought to be a possible strategy for eliciting a protective immune response against hepatitis C infection. In this paper, a recombinant strain of measles virus (MV) that expresses HCV NS3 protein was analyzed. The replication fitness of this recombinant virus also indicates that this construct replicates at a higher rate than parental measles strain. It is also demonstrated through western blot analysis of protein expression and immunofluorescence that this recombinant virus expresses both the inserted HCV NS3 protein, as well as native measles proteins.
ContributorsWoell, Dana Marie (Author) / Reyes del Valle, Jorge (Thesis director) / Nickerson, Cheryl (Committee member) / Julik, Emily (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Human Evolution and Social Change (Contributor)
Created2015-05
Description
South Mountain is the largest municipal park in the nation. It is a bundled amenity, providing a series of linked services to the surrounding communities. A dataset of 19,209 homes in 155 neighborhoods within three miles of the park was utilized in order to complete a hedonic estimation for two nearby urban villages, Ahwatukee Foothills and South Mountain Village. Measures of access include proximity to the park, trailhead access, and adjacency to the park. Two regressions were estimated, the first including lot characteristics and subdivision fixed effects and the second using the coefficients for each subdivision as the dependent variable. These estimates describe how the location of a house in a subdivision contributes to its conditional mean price. As a result they offer a direct basis for capturing amenities measured at the neighborhood scale on home values. Park proximity, trailhead access and adjacency were found to significantly influence the price of homes at the 5% confidence level in Ahwatukee, but not in South Mountain Village. The results of this study can be applied to issues of environmental justice and park access in determining which areas and attributes of the park are associated with a high premium. Though South Mountain was preserved some time ago, development and future preservation in the City of Phoenix can be informed by such studies.
ContributorsRamakrishna, Saritha Kambhampati (Author) / Abbott, Joshua (Thesis director) / Smith, V. Kerry (Committee member) / Schoon, Michael (Committee member) / Barrett, The Honors College (Contributor) / School of Sustainability (Contributor) / Economics Program in CLAS (Contributor) / Department of English (Contributor)
Created2015-05
Hiking and Hegemony: Destabilizing the nature/culture and gender binaries through outdoor recreation
Description
This paper explores the contested relationships between nature, culture, and gender. In order to analyze these relationships, we look specifically at outdoor recreation. Furthermore, we employ poststructuralist feminist theory in order to produce three frameworks; the first of which is titled Mother Nature’s Promiscuous Past. Rooted in Old World and colonial values, this framework illustrates the flawed feminization of nature by masculinity, and its subsequent extortion of anything related to femininity — including women and nature itself. This belief barred women from nature, resulting in a lack of access for women to outdoor recreation.
Our second framework, titled The Pleasurable Potential of Outdoor Recreation, cites second-wave feminism as a catalyst for women’s participation in wilderness exploration and outdoor recreation. The work of radical feminists and the women’s liberation movement in 1960s and 1970s empowered women at home, in the workplace, and eventually, in the outdoors; women reclaimed their wilderness, yet they continued to employ Framework One’s feminization of nature. Ecofeminsim brought together nature and women, seeking to bring justice to two groups wronged by the same entity: masculinity. In this context, outdoor recreation is empowering for women.
Despite the potential of Framework Two to reinscribe and better the experiences of women in outdoor recreation, we argue that both Frameworks One and Two perpetuate the gender binary and the nature/culture binary, because they are based upon the notion that women are in fact fundamentally different and separate from men, the notion that nature is an entity separate from culture, or human society, as well as the notion that nature is in fact a feminine entity.
Our third framework, Deer Pay No Mind to Your Genitals, engages poststructuralism, asserting that outdoor recreation and activities that occur in nature can serve to destabilize and deconstruct notions of the gender binary. However, we argue that care must be exercised during this process as not to perpetuate the problematic nature/culture binary, a phenomenon that is unproductive in terms of both sustainability and gender liberation. Outdoor recreation has been used by many as a tool to deconstruct numerous societal constraints, including the gender binary; this, however, continues to attribute escapist and isolationist qualities toward nature, and therefore perpetuating the nature/culture divide. Ultimately, we argue outdoor recreation can and should be used as a tool deconstruct the gender binary, however needs to account for the fact that if nature is helping to construct elements of culture, then the two cannot be separate.
Our second framework, titled The Pleasurable Potential of Outdoor Recreation, cites second-wave feminism as a catalyst for women’s participation in wilderness exploration and outdoor recreation. The work of radical feminists and the women’s liberation movement in 1960s and 1970s empowered women at home, in the workplace, and eventually, in the outdoors; women reclaimed their wilderness, yet they continued to employ Framework One’s feminization of nature. Ecofeminsim brought together nature and women, seeking to bring justice to two groups wronged by the same entity: masculinity. In this context, outdoor recreation is empowering for women.
Despite the potential of Framework Two to reinscribe and better the experiences of women in outdoor recreation, we argue that both Frameworks One and Two perpetuate the gender binary and the nature/culture binary, because they are based upon the notion that women are in fact fundamentally different and separate from men, the notion that nature is an entity separate from culture, or human society, as well as the notion that nature is in fact a feminine entity.
Our third framework, Deer Pay No Mind to Your Genitals, engages poststructuralism, asserting that outdoor recreation and activities that occur in nature can serve to destabilize and deconstruct notions of the gender binary. However, we argue that care must be exercised during this process as not to perpetuate the problematic nature/culture binary, a phenomenon that is unproductive in terms of both sustainability and gender liberation. Outdoor recreation has been used by many as a tool to deconstruct numerous societal constraints, including the gender binary; this, however, continues to attribute escapist and isolationist qualities toward nature, and therefore perpetuating the nature/culture divide. Ultimately, we argue outdoor recreation can and should be used as a tool deconstruct the gender binary, however needs to account for the fact that if nature is helping to construct elements of culture, then the two cannot be separate.
ContributorsPolick-Kirkpatrick, Kaelyn (Co-author) / Downing, Haley Marie (Co-author) / Dove-Viebahn, Aviva (Thesis director) / Schoon, Michael (Committee member) / School of Sustainability (Contributor) / School of Social Transformation (Contributor) / Economics Program in CLAS (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Cancer remains one of the leading killers throughout the world. Death and disability due to lung cancer in particular accounts for one of the largest global economic burdens a disease presents. The burden on third-world countries is especially large due to the unusually large financial stress that comes from late tumor detection and expensive treatment options. Early detection using inexpensive techniques may relieve much of the burden throughout the world, not just in more developed countries. I examined the immune responses of lung cancer patients using immunosignatures – patterns of reactivity between host serum antibodies and random peptides. Immunosignatures reveal disease-specific patterns that are very reproducible. Immunosignaturing is a chip-based method that has the ability to display the antibody diversity from individual sera sample with low cost. Immunosignaturing is a medical diagnostic test that has many applications in current medical research and in diagnosis. From a previous clinical study, patients diagnosed for lung cancer were tested for their immunosignature vs. healthy non-cancer volunteers. The pattern of reactivity against the random peptides (the ‘immunosignature’) revealed common signals in cancer patients, absent from healthy controls. My study involved the search for common amino acid motifs in the cancer-specific peptides. My search through the hundreds of ‘hits’ revealed certain motifs that were repeated more times than expected by random chance. The amino acids that were the most conserved in each set include tryptophan, aspartic acid, glutamic acid, proline, alanine, serine, and lysine. The most overall conserved amino acid observed between each set was D - aspartic acid. The motifs were short (no more than 5-6 amino acids in a row), but the total number of motifs I identified was large enough to assure significance. I utilized Excel to organize the large peptide sequence libraries, then CLUSTALW to cluster similar-sequence peptides, then GLAM2 to find common themes in groups of peptides. In so doing, I found sequences that were also present in translated cancer expression libraries (RNA) that matched my motifs, suggesting that immunosignatures can find cancer-specific antigens that can be both diagnostic and potentially therapeutic.
ContributorsShiehzadegan, Shima (Author) / Johnston, Stephen (Thesis director) / Stafford, Phillip (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2015-12
Description
Clean water for drinking, food preparation, and bathing is essential for astronaut health and safety during long duration habitation of the International Space Station (ISS), including future missions to Mars. Despite stringent water treatment and recycling efforts on the ISS, it is impossible to completely prevent microbial contamination of onboard water supplies. In this work, we used a spaceflight analogue culture system to better understand how the microgravity environment can influence the pathogenesis-related characteristics of Burkholderia cepacia complex (Bcc), an opportunistic pathogen previously recovered from the ISS water system. The results of the present study suggest that there may be important differences in how this pathogen can respond and adapt to spaceflight and other low fluid shear environments encountered during their natural life cycles. Future studies are aimed at understanding the underlying mechanisms responsible for these phenotypes.
ContributorsKang, Bianca Younseon (Author) / Nickerson, Cheryl (Thesis director) / Barrila, Jennifer (Committee member) / Ott, Mark (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05