ASU Electronic Theses and Dissertations
This collection includes most of the ASU Theses and Dissertations from 2011 to present. ASU Theses and Dissertations are available in downloadable PDF format; however, a small percentage of items are under embargo. Information about the dissertations/theses includes degree information, committee members, an abstract, supporting data or media.
In addition to the electronic theses found in the ASU Digital Repository, ASU Theses and Dissertations can be found in the ASU Library Catalog.
Dissertations and Theses granted by Arizona State University are archived and made available through a joint effort of the ASU Graduate College and the ASU Libraries. For more information or questions about this collection contact or visit the Digital Repository ETD Library Guide or contact the ASU Graduate College at gradformat@asu.edu.
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- All Subjects: Biology
- Creators: Wang, Xuan
- Creators: Perrings, Charles
Description
This dissertation consists of three substantive chapters. The first substantive chapter investigates the premature harvesting problem in fisheries. Traditionally, yield-per-recruit analysis has been used to both assess and address the premature harvesting of fish stocks. However, the fact that fish size often affects the unit price suggests that this approach may be inadequate. In this chapter, I first synthesize the conventional yield-per-recruit analysis, and then extend this conventional approach by incorporating a size-price function for a revenue-per-recruit analysis. An optimal control approach is then used to derive a general bioeconomic solution for the optimal harvesting of a short-lived single cohort. This approach prevents economically premature harvesting and provides an "optimal economic yield". By comparing the yield- and revenue-per-recruit management strategies with the bioeconomic management strategy, I am able to test the economic efficiency of the conventional yield-per-recruit approach. This is illustrated with a numerical study. It shows that a bioeconomic strategy can significantly improve economic welfare compared with the yield-per-recruit strategy, particularly in the face of high natural mortality. Nevertheless, I find that harvesting on a revenue-per-recruit basis improves management policy and can generate a rent that is close to that from bioeconomic analysis, in particular when the natural mortality is relatively low.
The second substantive chapter explores the conservation potential of a whale permit market under bounded economic uncertainty. Pro- and anti-whaling stakeholders are concerned about a recently proposed, "cap and trade" system for managing the global harvest of whales. Supporters argue that such an approach represents a novel solution to the current gridlock in international whale management. In addition to ethical objections, opponents worry that uncertainty about demand for whale-based products and the environmental benefits of conservation may make it difficult to predict the outcome of a whale share market. In this study, I use population and economic data for minke whales to examine the potential ecological consequences of the establishment of a whale permit market in Norway under bounded but significant economic uncertainty. A bioeconomic model is developed to evaluate the influence of economic uncertainties associated with pro- and anti- whaling demands on long-run steady state whale population size, harvest, and potential allocation. The results indicate that these economic uncertainties, in particular on the conservation demand side, play an important role in determining the steady state ecological outcome of a whale share market. A key finding is that while a whale share market has the potential to yield a wide range of allocations between conservation and whaling interests - outcomes in which conservationists effectively "buy out" the whaling industry seem most likely.
The third substantive chapter examines the sea lice externality between farmed fisheries and wild fisheries. A central issue in the debate over the effect of fish farming on the wild fisheries is the nature of sea lice population dynamics and the wild juvenile mortality rate induced by sea lice infection. This study develops a bioeconomic model that integrates sea lice population dynamics, fish population dynamics, aquaculture and wild capture salmon fisheries in an optimal control framework. It provides a tool to investigate sea lice control policy from the standpoint both of private aquaculture producers and wild fishery managers by considering the sea lice infection externality between farmed and wild fisheries. Numerical results suggest that the state trajectory paths may be quite different under different management regimes, but approach the same steady state. Although the difference in economic benefits is not significant in the particular case considered due to the low value of the wild fishery, I investigate the possibility of levying a tax on aquaculture production for correcting the sea lice externality generated by fish farms.
The second substantive chapter explores the conservation potential of a whale permit market under bounded economic uncertainty. Pro- and anti-whaling stakeholders are concerned about a recently proposed, "cap and trade" system for managing the global harvest of whales. Supporters argue that such an approach represents a novel solution to the current gridlock in international whale management. In addition to ethical objections, opponents worry that uncertainty about demand for whale-based products and the environmental benefits of conservation may make it difficult to predict the outcome of a whale share market. In this study, I use population and economic data for minke whales to examine the potential ecological consequences of the establishment of a whale permit market in Norway under bounded but significant economic uncertainty. A bioeconomic model is developed to evaluate the influence of economic uncertainties associated with pro- and anti- whaling demands on long-run steady state whale population size, harvest, and potential allocation. The results indicate that these economic uncertainties, in particular on the conservation demand side, play an important role in determining the steady state ecological outcome of a whale share market. A key finding is that while a whale share market has the potential to yield a wide range of allocations between conservation and whaling interests - outcomes in which conservationists effectively "buy out" the whaling industry seem most likely.
The third substantive chapter examines the sea lice externality between farmed fisheries and wild fisheries. A central issue in the debate over the effect of fish farming on the wild fisheries is the nature of sea lice population dynamics and the wild juvenile mortality rate induced by sea lice infection. This study develops a bioeconomic model that integrates sea lice population dynamics, fish population dynamics, aquaculture and wild capture salmon fisheries in an optimal control framework. It provides a tool to investigate sea lice control policy from the standpoint both of private aquaculture producers and wild fishery managers by considering the sea lice infection externality between farmed and wild fisheries. Numerical results suggest that the state trajectory paths may be quite different under different management regimes, but approach the same steady state. Although the difference in economic benefits is not significant in the particular case considered due to the low value of the wild fishery, I investigate the possibility of levying a tax on aquaculture production for correcting the sea lice externality generated by fish farms.
ContributorsHuang, Biao (Author) / Abbott, Joshua K (Thesis advisor) / Perrings, Charles (Thesis advisor) / Gerber, Leah R. (Committee member) / Muneepeerakul, Rachata (Committee member) / Schoon, Michael (Committee member) / Arizona State University (Publisher)
Created2014
Description
The Multiple Antibiotic Resistance Regulator Family (MarR) are transcriptional regulators, many of which forms a dimer. Transcriptional regulation provides bacteria a stabilized responding system to ensure the bacteria is able to efficiently adapt to different environmental conditions. The main function of the MarR family is to create multiple antibiotic resistance from a mutated protein; this process occurs when the MarR regulates an operon. We hypothesized that different transcriptional regulator genes have interactions with each other. It is known that Salmonella pagC transcription is activated by three regulators, i.e., SlyA, MprA, and PhoP. Bacterial Adenylate Cyclase-based Two-Hybrid (BACTH) system was used to research the protein-protein interactions in SlyA, MprA, and PhoP as heterodimers and homodimers in vivo. Two fragments, T25 and T18, that lack endogenous adenylate cyclase activity, were used for construction of chimeric proteins and reconstruction of adenylate cyclase activity was tested. The significant adenylate cyclase activities has proved that SlyA is able to form homodimers. However, weak adenylate cyclase activities in this study has proved that MprA and PhoP are not likely to form homodimers, and no protein-protein interactions were detected in between SlyA, MprA and PhoP, which no heterodimers have formed in between three transcriptional regulators.
ContributorsTao, Zenan (Author) / Shi, Yixin (Thesis advisor) / Wang, Xuan (Committee member) / Bean, Heather (Committee member) / Arizona State University (Publisher)
Created2018
Description
Lignocellulosic biomass represents a renewable domestic feedstock that can support large-scale biochemical production processes for fuels and specialty chemicals. However, cost-effective conversion of lignocellulosic sugars into valuable chemicals by microorganisms still remains a challenge. Biomass recalcitrance to saccharification, microbial substrate utilization, bioproduct titer toxicity, and toxic chemicals associated with chemical pretreatments are at the center of the bottlenecks limiting further commercialization of lignocellulose conversion. Genetic and metabolic engineering has allowed researchers to manipulate microorganisms to overcome some of these challenges, but new innovative approaches are needed to make the process more commercially viable. Transport proteins represent an underexplored target in genetic engineering that can potentially help to control the input of lignocellulosic substrate and output of products/toxins in microbial biocatalysts. In this work, I characterize and explore the use of transport systems to increase substrate utilization, conserve energy, increase tolerance, and enhance biocatalyst performance.
ContributorsKurgan, Gavin (Author) / Wang, Xuan (Thesis advisor) / Nielsen, David (Committee member) / Misra, Rajeev (Committee member) / Nannenga, Brent (Committee member) / Arizona State University (Publisher)
Created2018
Description
Emergence of multidrug resistant (MDR) bacteria is a major concern to global health. One of the major MDR mechanisms bacteria employ is efflux pumps for the expulsion of drugs from the cell. In Escherichia coli, AcrAB-TolC proteins constitute the major chromosomally-encoded drug efflux system. AcrB, a trimeric membrane protein is well-known for its substrate promiscuity. It has the ability to efflux a broad spectrum of substrates alongside compounds such as dyes, detergent, bile salts and metabolites. Newly identified AcrB residues were shown to be functionally relevant in the drug binding and translocation pathway using a positive genetic selection strategy. These residues—Y49, V127, D153, G288, F453, and L486—were identified as the sites of suppressors of an alteration, F610A, that confers a drug hypersensitivity phenotype. Using site-directed mutagenesis (SDM) along with the real-time efflux and the classical minimum inhibitory concentration (MIC) assays, I was able to characterize the mechanism of suppression.
Three approaches were used for the characterization of these suppressors. The first approach focused on side chain specificity. The results showed that certain suppressor sites prefer a particular side chain property, such as size, to overcome the F610A defect. The second approach focused on the effects of efflux pump inhibitors. The results showed that though the suppressor residues were able to overcome the intrinsic defect of F610A, they were unable to overcome the extrinsic defect caused by the efflux pump inhibitors. This showed that the mechanism by which F610A imposes its effect on AcrB function is different than that of the efflux pump inhibitors. The final approach was to determine whether suppressors mapping in the periplasmic and trans-membrane domains act by the same or different mechanisms. The results showed both overlapping and distinct mechanisms of suppression.
To conclude, these approaches have provided a deeper understanding of the mechanisms by which novel suppressor residues of AcrB overcome the functional defect of the drug binding domain alteration, F610A.
Three approaches were used for the characterization of these suppressors. The first approach focused on side chain specificity. The results showed that certain suppressor sites prefer a particular side chain property, such as size, to overcome the F610A defect. The second approach focused on the effects of efflux pump inhibitors. The results showed that though the suppressor residues were able to overcome the intrinsic defect of F610A, they were unable to overcome the extrinsic defect caused by the efflux pump inhibitors. This showed that the mechanism by which F610A imposes its effect on AcrB function is different than that of the efflux pump inhibitors. The final approach was to determine whether suppressors mapping in the periplasmic and trans-membrane domains act by the same or different mechanisms. The results showed both overlapping and distinct mechanisms of suppression.
To conclude, these approaches have provided a deeper understanding of the mechanisms by which novel suppressor residues of AcrB overcome the functional defect of the drug binding domain alteration, F610A.
ContributorsBlake, Mellecha (Author) / Misra, Rajeev (Thesis advisor) / Stout, Valerie (Committee member) / Wang, Xuan (Committee member) / Arizona State University (Publisher)
Created2016
Description
The spread of dengue worldwide currently places half of the world’s population at risk. In the absence of a dengue vaccine, control of the disease requires control of the mosquito species that transmit the virus. The most important of these is. Advances in research detailing the responsiveness of Aedes aegypti to small changes in climate enable the production of more sophisticated remote sensing and surveillance techniques for monitoring these populations. Close monitoring of global dengue activity and outbreaks likewise enables a greater specificity when determining to which human populations the virus is most likely to spread. There have been no locally acquired cases in Arizona to date, but the high abundance of Aedes aegypti in the Phoenix Metropolitan area raises concern within the Arizona Department of Health Services over the potential transmission of dengue in the city. This study develops a model that combines mosquito abundance, micro-climatic and demographic information to delineate regions in Phoenix that are most support transmission of dengue. The first chapter focuses on the impact that daytime high and low temperatures have on Aedes aegypti’s ability to become infectious with dengue. It argues that NDVI (normal difference vegetative index) imaging of the Phoenix area can be used to plot areas where mosquitoes are most likely to become competent vectors. The second chapter focuses on the areas in the city where mosquitoes are most likely to be exposed to the virus. Based on proximity to Phoenix and the high volume of traffic across the Arizona-Mexico border, I treat the Mexican state of Sonora as the source of infection. I combine these two analyses, micro-climatic and demographic, to produce maps of Phoenix that show the locations with the highest likelihood of transmission overall.
ContributorsHughes, Tyler (Author) / Perrings, Charles (Thesis advisor) / Kinzig, Ann (Committee member) / Hall, Sharon J (Committee member) / Arizona State University (Publisher)
Created2016
Description
The closer integration of the world economy has yielded many positive benefits including the worldwide diffusion of innovative technologies and efficiency gains following the widening of international markets. However, closer integration also has negative consequences. Specifically, I focus on the ecology and economics of the spread of species and pathogens. I approach the problem using theoretical and applied models in ecology and economics. First, I use a multi-species theoretical network model to evaluate the ability of dispersal to maintain system-level biodiversity and productivity. I then extend this analysis to consider the effects of dispersal in a coupled social-ecological system where people derive benefits from species. Finally, I estimate an empirical model of the foot and mouth disease risks of trade. By combining outbreak and trade data I estimate the disease risks associated with the international trade in live animals while controlling for the biosecurity measures in place in importing countries and the presence of wild reservoirs. I find that the risks associated with the spread and dispersal of species may be positive or negative, but that this relationship depends on the ecological and economic components of the system and the interactions between them.
ContributorsShanafelt, David William (Author) / Perrings, Charles (Thesis advisor) / Fenichel, Eli (Committee member) / Richards, Timorthy (Committee member) / Janssen, Marco (Committee member) / Collins, James (Committee member) / Arizona State University (Publisher)
Created2016
Characterization and Manipulation of Microbiomes From Arid Landfills for Improved Methane Production
Description
Environmentally harmful byproducts from solid waste’s decomposition, including methane (CH4) emissions, are managed through standardized landfill engineering and gas-capture mechanisms. Yet only a limited number of studies have analyzed the development and composition of Bacteria and Archaea involved in CH4 production from landfills. The objectives of this research were to compare microbiomes and bioactivity from CH4-producing communities in contrasting spatial areas of arid landfills and to tests a new technology to biostimulate CH4 production (methanogenesis) from solid waste under dynamic environmental conditions controlled in the laboratory. My hypothesis was that the diversity and abundance of methanogenic Archaea in municipal solid waste (MSW), or its leachate, play an important role on CH4 production partially attributed to the group’s wide hydrogen (H2) consumption capabilities. I tested this hypothesis by conducting complementary field observations and laboratory experiments. I describe niches of methanogenic Archaea in MSW leachate across defined areas within a single landfill, while demonstrating functional H2-dependent activity. To alleviate limited H2 bioavailability encountered in-situ, I present biostimulant feasibility and proof-of-concepts studies through the amendment of zero valent metals (ZVMs). My results demonstrate that older-aged MSW was minimally biostimulated for greater CH4 production relative to a control when exposed to iron (Fe0) or manganese (Mn0), due to highly discernable traits of soluble carbon, nitrogen, and unidentified fluorophores found in water extracts between young and old aged, starting MSW. Acetate and inhibitory H2 partial pressures accumulated in microcosms containing old-aged MSW. In a final experiment, repeated amendments of ZVMs to MSW in a 600 day mesocosm experiment mediated significantly higher CH4 concentrations and yields during the first of three ZVM injections. Fe0 and Mn0 experimental treatments at mesocosm-scale also highlighted accelerated development of seemingly important, but elusive Archaea including Methanobacteriaceae, a methane-producing family that is found in diverse environments. Also, prokaryotic classes including Candidatus Bathyarchaeota, an uncultured group commonly found in carbon-rich ecosystems, and Clostridia; All three taxa I identified as highly predictive in the time-dependent progression of MSW decomposition. Altogether, my experiments demonstrate the importance of H2 bioavailability on CH4 production and the consistent development of Methanobacteriaceae in productive MSW microbiomes.
ContributorsReynolds, Mark Christian (Author) / Cadillo-Quiroz, Hinsby (Thesis advisor) / Krajmalnik-Brown, Rosa (Thesis advisor) / Wang, Xuan (Committee member) / Kavazanjian, Edward (Committee member) / Arizona State University (Publisher)
Created2022
Description
Biomass synthesis is a competing factor in biological systems geared towards generation of commodity and specialty chemicals, ultimately limiting maximum titer and yield; in this thesis, a widely generalizable, modular approach focused on decoupling biomass synthesis from the production of the phenylalanine in a genetically modified strain of E. coli BW25113 was explored with the use of synthetic trans-encoded small RNA (sRNA) to achieve greater efficiency. The naturally occurring sRNA MicC was used as a scaffold, and combined on a plasmid with a promoter for anhydrous tetracycline (aTc) and a T1/TE terminator. The coding sequence corresponding to the target binding site for fourteen potentially growth-essential gene targets as well as non-essential lacZ was placed in the seed region of the of the sRNA scaffold and transformed into BW25113, effectively generating a unique strain for each gene target. The BW25113 strain corresponding to each gene target was screened in M9 minimal media; decreased optical density and elongated cell morphology changes were observed and quantified in all induced sRNA cases where growth-essential genes were targeted. Six of the strains targeting different aspects of cell division that effectively suppressed growth and resulted in increased cell size were then screened for viability and metabolic activity in a scaled-up shaker flask experiment; all six strains were shown to be viable during stationary phase, and a metabolite analysis showed increased specific glucose consumption rates in induced strains, with unaffected specific glucose consumption rates in uninduced strains. The growth suppression, morphology and metabolic activity of the induced strains in BW25113 was compared to the bacteriostatic additives chloramphenicol, tetracycline, and streptomycin. At this same scale, the sRNA plasmid targeting the gene murA was transformed into BW25113 pINT-GA, a phenylalanine overproducer with the feedback resistant genes aroG and pheA overexpressed. Two induction times were explored during exponential phase, and while the optimal induction time was found to increase titer and yield amongst the BW25113 pINT-GA murA sRNA variant, overall this did not have as great a titer or yield as the BW25113 pINT-GA strain without the sRNA plasmid; this may be a result of the cell filamentation.
ContributorsHerschel, Daniel Jordan (Author) / Nielsen, David R (Thesis advisor) / Torres, César I (Committee member) / Wang, Xuan (Committee member) / Arizona State University (Publisher)
Created2016
Description
Reactive oxygen species (ROS) including superoxide, hydrogen peroxide, and hydroxyl radicals occur naturally as a byproduct of aerobic respiration. To mitigate damages caused by ROS, Escherichia coli employs defenses including two cytosolic superoxide dismutases (SODs), which convert superoxide to hydrogen peroxide. Deletion of both sodA and sodB, the genes coding for the cytosolic SOD enzymes, results in a strain that is unable to grow on minimal medium without amino acid supplementation. Additionally, deletion of both cytosolic SOD enzymes in a background containing the relA1 allele, an inactive version of the relA gene that contributes to activation of stringent response by amino acid starvation, results in a strain that is unable to grow aerobically, even on rich medium. These observations point to a relationship between the stringent response and oxidative stress. To gain insight into this relationship, suppressors were isolated by growing the ∆sodAB relA1 cells aerobically on rich medium, and seven suppressors were further examined to characterize distinct colony sizes and temperature sensitivity phenotypes. In three of these suppressor-containing strains, the relA1 allele was successfully replaced by the wild type relA allele to allow further study in aerobic conditions. None of those three suppressors were found to increase tolerance to exogenous superoxides produced by paraquat, which shows that these mutations only overcome the superoxide buildup that naturally occurs from deletion of SODs. Because each of these suppressors had unique phenotypes, it is likely that they confer tolerance to SOD-dependent superoxide buildup by different mechanisms. Two of these three suppressors have been sent for whole-genome sequencing to identify the location of the suppressor mutation and determine the mechanism by which they confer superoxide tolerance.
ContributorsFlake, Melissa (Author) / Misra, Rajeev (Thesis advisor) / Shah, Dhara (Committee member) / Wang, Xuan (Committee member) / Arizona State University (Publisher)
Created2024