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Description
Phosphorus (P), an essential element for life, is becoming increasingly scarce, and its global management presents a serious challenge. As urban environments dominate the landscape, we need to elucidate how P cycles in urban ecosystems to better understand how cities contribute to — and provide opportunities to solve — problems of P management. The goal of my research was to increase our understanding of urban P cycling in the context of urban resource management through analysis of existing ecological and socio-economic data supplemented with expert interviews in order to facilitate a transition to sustainable P management. Study objectives were to: I) Quantify and map P stocks and flows in the Phoenix metropolitan area and analyze the drivers of spatial distribution and dynamics of P flows; II) examine changes in P-flow dynamics at the urban agricultural interface (UAI), and the drivers of those changes, between 1978 and 2008; III) compare the UAI's average annual P budget to the global agricultural P budget; and IV) explore opportunities for more sustainable P management in Phoenix. Results showed that Phoenix is a sink for P, and that agriculture played a primary role in the dynamics of P cycling. Internal P dynamics at the UAI shifted over the 30-year study period, with alfalfa replacing cotton as the main locus of agricultural P cycling. Results also suggest that the extent of P recycling in Phoenix is proportionally larger than comparable estimates available at the global scale due to the biophysical characteristics of the region and the proximity of various land uses. Uncertainty remains about the effectiveness of current recycling strategies and about best management strategies for the future because we do not have sufficient data to use as basis for evaluation and decision-making. By working in collaboration with practitioners, researchers can overcome some of these data limitations to develop a deeper understanding of the complexities of P dynamics and the range of options available to sustainably manage P. There is also a need to better connect P management with that of other resources, notably water and other nutrients, in order to sustainably manage cities.
ContributorsMetson, Genevieve (Author) / Childers, Daniel (Thesis advisor) / Aggarwal, Rimjhim (Thesis advisor) / Redman, Charles (Committee member) / Arizona State University (Publisher)
Created2011
Description
The elaborate signals of animals are often costly to produce and maintain, thus communicating reliable information about the quality of an individual to potential mates or competitors. The properties of the sensory systems that receive signals can drive the evolution of these signals and shape their form and function. However, relatively little is known about the ecological and physiological constraints that may influence the development and maintenance of sensory systems. In the house finch (Carpodacus mexicanus) and many other bird species, carotenoid pigments are used to create colorful sexually selected displays, and their expression is limited by health and dietary access to carotenoids. Carotenoids also accumulate in the avian retina, protecting it from photodamage and tuning color vision. Analogous to plumage carotenoid accumulation, I hypothesized that avian vision is subject to environmental and physiological constraints imposed by the acquisition and allocation of carotenoids. To test this hypothesis, I carried out a series of field and captive studies of the house finch to assess natural variation in and correlates of retinal carotenoid accumulation and to experimentally investigate the effects of dietary carotenoid availability, immune activation, and light exposure on retinal carotenoid accumulation. Moreover, through dietary manipulations of retinal carotenoid accumulation, I tested the impacts of carotenoid accumulation on visually mediated foraging and mate choice behaviors. My results indicate that avian retinal carotenoid accumulation is variable and significantly influenced by dietary carotenoid availability and immune system activity. Behavioral studies suggest that retinal carotenoid accumulation influences visual foraging performance and mediates a trade-off between color discrimination and photoreceptor sensitivity under dim-light conditions. Retinal accumulation did not influence female choice for male carotenoid-based coloration, indicating that a direct link between retinal accumulation and sexual selection for coloration is unlikely. However, retinal carotenoid accumulation in males was positively correlated with their plumage coloration. Thus, carotenoid-mediated visual health and performance or may be part of the information encoded in sexually selected coloration.
ContributorsToomey, Matthew (Author) / McGraw, Kevin J. (Thesis advisor) / Deviche, Pierre (Committee member) / Smith, Brian (Committee member) / Rutowski, Ronald (Committee member) / Verrelli, Brian (Committee member) / Arizona State University (Publisher)
Created2011
Description
Molecular dynamics (MD) simulations provide a particularly useful approach to understanding conformational change in biomolecular systems. MD simulations provide an atomistic, physics-based description of the motions accessible to biomolecular systems on the pico- to micro-second timescale, yielding important insight into the free energy of the system, the dynamical stability of contacts and the role of correlated motions in directing the motions of the system. In this thesis, I use molecular dynamics simulations to provide molecular mechanisms that rationalize structural, thermodynamic, and mutation data on the interactions between the lac repressor headpiece and its O1 operator DNA as well as the ERK2 protein kinase. I performed molecular dynamics simulations of the lac repressor headpiece - O1 operator complex at the natural angle as well as at under- and overbent angles to assess the factors that determine the natural DNA bending angle. I find both energetic and entropic factors contribute to recognition of the natural angle. At the natural angle the energy of the system is minimized by optimization of protein-DNA contacts and the entropy of the system is maximized by release of water from the protein-DNA interface and decorrelation of protein motions. To identify the mechanism by which mutations lead to auto-activation of ERK2, I performed a series of molecular dynamics simulations of ERK1/2 in various stages of activation as well as the constitutively active Q103A, I84A, L73P and R65S ERK2 mutants. My simulations indicate the importance of domain closure for auto-activation and activity regulation. My results enable me to predict two loss-of-function mutants of ERK2, G83A and Q64C, that have been confirmed in experiments by collaborators. One of the powerful capabilities of MD simulations in biochemistry is the ability to find low free energy pathways that connect and explain disparate structural data on biomolecular systems. An extention of the targeted molecular dynamics technique using constraints on internal coordinates will be presented and evaluated. The method gives good results for the alanine dipeptide, but breaks down when applied to study conformational changes in GroEL and adenylate kinase.
ContributorsBarr, Daniel Alan (Author) / van der Vaart, Arjan (Thesis advisor) / Matyushov, Dmitry (Committee member) / Wolf, George (Committee member) / Shumway, John (Committee member) / Arizona State University (Publisher)
Created2011
Description
The trend towards using recycled materials on new construction projects is growing as the cost for construction materials are ever increasing and the awareness of the responsibility we have to be good stewards of our environment is heightened. While recycled asphalt is sometimes used in pavements, its use as structural fill has been hindered by concern that it is susceptible to large long-term deformations (creep), preventing its use for a great many geotechnical applications. While asphalt/soil blends are often proposed as an alternative to 100% recycled asphalt fill, little data is available characterizing the geotechnical properties of recycled asphalt soil blends. In this dissertation, the geotechnical properties for five different recycled asphalt soil blends are characterized. Data includes the particle size distribution, plasticity index, creep, and shear strength for each blend. Blends with 0%, 25%, 50%, 75% and 100% recycled asphalt were tested. As the recycled asphalt material used for testing had particles sizes up to 1.5 inches, a large 18 inch diameter direct shear apparatus was used to determine the shear strength and creep characteristics of the material. The results of the testing program confirm that the creep potential of recycled asphalt is a geotechnical concern when the material is subjected to loads greater than 1500 pounds per square foot (psf). In addition, the test results demonstrate that the amount of soil blended with the recycled asphalt can greatly influence the creep and shear strength behavior of the composite material. Furthermore, there appears to be an optimal blend ratio where the composite material had better properties than either the recycled asphalt or virgin soil alone with respect to shear strength.
ContributorsSchaper, Jeffery M (Author) / Kavazanjian, Edward (Thesis advisor) / Houston, Sandra L. (Committee member) / Zapata, Claudia E (Committee member) / Arizona State University (Publisher)
Created2011
Description
ABSTRACT Water resources in many parts of the world are subject to increasing stress because of (a) the growth in demand caused by population increase and economic development, (b) threats to supply caused by climate and land cover change, and (c) a heightened awareness of the importance of maintaining water supplies to other parts of the ecosystem. An additional factor is the quality of water management. The United States-Mexican border provides an example of poor water management combined with increasing demand for water resources that are both scarce and uncertain. This dissertation focuses on the problem of water management in the border city of Ciudad Juarez, Chihuahua. The city has attracted foreign investment during the last few decades, largely due to relatively low environmental and labor costs, and to a range of tax incentives and concessions. This has led to economic and population growth, but also to higher demand for public services such as water which leads to congestion and scarcity. In particular, as water resources have become scarce, the cost of water supply has increased. The dissertation analyzes the conditions that allow for the efficient use of water resources at sustainable levels of economic activity--i.e., employment and investment. In particular, it analyzes the water management strategies that lead to an efficient and sustainable use of water when the source of water is either an aquifer, or there is conjunctive use of ground and imported water. The first part of the dissertation constructs a model of the interactive effects of water supply, wage rates, inward migration of labor and inward investment of capital. It shows how growing water scarcity affects population growth through the impact it has on real wage rates, and how this erodes the comparative advantage of Ciudad Juarez--low wages--to the point where foreign investment stops. This reveals the very close connection between water management and the level of economic activity in Ciudad Juarez. The second part of the dissertation examines the effect of sustainable and efficient water management strategies on population and economic activity levels under two different settings. In the first Ciudad Juarez relies exclusively on ground water to meet demand--this reflects the current situation of Ciudad Juarez. In the second Ciudad Juarez is able both to import water and to draw on aquifers to meet demand. This situation is motivated by the fact that Ciudad Juarez is considering importing water from elsewhere to maintain its economic growth and mitigate the overdraft of the Bolson del Hueco aquifer. Both models were calibrated on data for Ciudad Juarez, and then used to run experiments with respect to different environmental and economic conditions, and different water management options. It is shown that for a given set of technological, institutional and environmental conditions, the way water is managed in a desert environment determines the long run equilibrium levels of employment, investment and output. It is also shown that the efficiency of water management is consistent with the sustainability of water use and economic activity. Importing water could allow the economy to operate at higher levels of activity than where it relies solely on local aquifers. However, at some scale, water availability will limit the level of economic activity, and the disposable income of the residents of Ciudad Juarez.
ContributorsGarduno Angeles, Gustavo Leopoldo (Author) / Perrings, Charles (Thesis advisor) / Holway, Jim (Thesis advisor) / Aggarwal, Rimjhim (Committee member) / Arizona State University (Publisher)
Created2011
Description
Restaurants have a cumulative impact on the environment, economy, and society. The majority of restaurants are small-to-medium enterprises (SMEs). Review of sustainability and industry literature revealed that considering restaurants as businesses with sustainable development options is the most appropriate way to evaluate their sustainable practices or lack thereof. Sustainable development is the means by which a company progresses towards achieving an identified set of sustainability goals and harnesses competitive advantage. The purpose of this thesis is to identify barriers to implementing sustainable practices in restaurants, and explore ways that restaurateurs can incorporate sustainable business practices. Energy consumption, water use, waste production, and food throughput are the four sustainability indicators addressed in this thesis. Interviews were conducted with five Tempe, Arizona restaurants, two of which consider their operations to be sustainable, and three of which are traditional restaurants. Results show that for traditional restaurants, the primary barriers to implementing sustainable business practices are cost, lack of awareness, and space. For sustainability-marketed restaurants, the barriers included a lack of knowledge or legal concerns. The sustainability-marketed restaurants have energy-efficient equipment and locally source a majority of their food purchases. There is a marked difference between the two types of restaurants in perception of barriers to sustainable business practices. I created a matrix to identify whether each indicator metric was applicable and present at a particular restaurant, and the potential barriers to implementing sustainable practices in each of the four indicator areas. Restaurants can use the assessment matrix to compare their current practices with sustainable practices and find ways to implement new or enhance existing sustainable practices. Identifying the barriers from within restaurants increases our understanding of the reasons why sustainable practices are not automatically adopted by SMEs. The assessment matrix can help restaurants overcome barriers to achieving sustainability by highlighting how to incorporate sustainable business practices.
ContributorsFreeman, Emily McConnell (Author) / Eakin, Hallie (Thesis advisor) / Basile, George (Thesis advisor) / Williams, Eric D. (Committee member) / Arizona State University (Publisher)
Created2011
Description
A synbody is a newly developed protein binding peptide which can be rapidly produced by chemical methods. The advantages of the synbody producing process make it a potential human proteome binding reagent. Most of the synbodies are designed to bind to specific proteins. The peptides incorporated in a synbody are discovered with peptide microarray technology. Nevertheless, the targets for unknown synbodies can also be discovered by searching through a protein mixture. The first part of this thesis mainly focuses on the process of target searching, which was performed with immunoprecipitation assays and mass spectrometry analysis. Proteins are pulled down from the cell lysate by certain synbodies, and then these proteins are identified using mass spectrometry. After excluding non-specific bindings, the interaction between a synbody and its real target(s) can be verified with affinity measurements. As a specific example, the binding between 1-4-KCap synbody and actin was discovered. This result proved the feasibility of the mass spectrometry based method and also suggested that a high throughput synbody discovery platform for the human proteome could be developed. Besides the application of synbody development, the peptide microarray technology can also be used for immunosignatures. The composition of all types of antibodies existing in one's blood is related to an individual's health condition. A method, called immunosignaturing, has been developed for early disease diagnosis based on this principle. CIM10K microarray slides work as a platform for blood antibody detection in immunosignaturing. During the analysis of an immunosignature, the data from these slides needs to be validated by using landing light peptides. The second part of this thesis focuses on the validation of the data. A biotinylated peptide was used as a landing light on the new CIM10K slides. The data was collected in several rounds of tests and indicated that the variation among landing lights was significantly reduced by using the newly prepared biotinylated peptide compared with old peptide mixture. Several suggestions for further landing light improvement are proposed based on the results.
ContributorsSun, Minyao (Author) / Johnston, Stephen Albert (Thesis advisor) / Diehnelt, Chris Wayne (Committee member) / Stafford, Phillip (Committee member) / Arizona State University (Publisher)
Created2011
Description
In the 1970s James Watson recognized the inability of conventional DNA replication machinery to replicate the extreme termini of chromosomes known as telomeres. This inability is due to the requirement of a building block primer and was termed the end replication problem. Telomerase is nature's answer to the end replication problem. Telomerase is a ribonucleoprotein which extends telomeres through reverse transcriptase activity by reiteratively copying a short intrinsic RNA sequence to generate 3' telomeric extensions. Telomeres protect chromosomes from erosion of coding genes during replication, as well as differentiate native chromosome ends from double stranded breaks. However, controlled erosion of telomeres functions as a naturally occurring molecular clock limiting the replicative capacity of cells. Telomerase is over activated in many cancers, while inactivation leads to multiple lifespan limiting human diseases. In order to further study the interaction between telomerase RNA (TR) and telomerase reverse transcriptase protein (TERT), vertebrate TERT fragments were screened for solubility and purity following bacterial expression. Soluble fragments of medaka TERT including the RNA binding domain (TRBD) were identified. Recombinant medaka TRBD binds specifically to telomerase RNA CR4/CR5 region. Ribonucleotide and amino acid pairs in close proximity within the medaka telomerase RNA-protein complex were identified using photo-activated cross-linking in conjunction with mass spectrometry. The identified cross-linking amino acids were mapped on known crystal structures of TERTs to reveal the RNA interaction interface of TRBD. The identification of this RNA TERT interaction interface furthers the understanding of the telomerase complex at a molecular level and could be used for the targeted interruption of the telomerase complex as a potential cancer treatment.
ContributorsBley, Christopher James (Author) / Chen, Julian (Thesis advisor) / Allen, James (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2011
Description
The greatest challenge facing humanity in the twenty-first century is our ability to reconcile the capacity of natural systems to support continued improvement in human welfare around the globe. Over the last decade, the scientific community has attempted to formulate research agendas in response to what they view as the problems of sustainability. Perhaps the most prominent and wide-ranging of these efforts has been sustainability science, an interdisciplinary, problem-driven field that seeks to address fundamental questions on human-environment interactions. This project examines how sustainability scientists grapple with and bound the deeply social, political and normative dimensions of both characterizing and pursuing sustainability. Based on in-depth interviews with leading researchers and a content analysis of the relevant literature, this project first addresses three core questions: (1) how sustainability scientists define and bound sustainability; (2) how and why various research agendas are being constructed to address these notions of sustainability; (3) and how scientists see their research contributing to societal efforts to move towards sustainability. Based on these results, the project explores the tensions between scientific efforts to study and inform sustainability and social action. It discusses the implications of transforming sustainability into the subject of scientific analysis with a focus on the power of science to constrain discourse and the institutional and epistemological contexts that link knowledge to societal outcomes. Following this analysis, sustainability science is repositioned, borrowing Herbert Simon's concept, as a "science of design." Sustainability science has thus far been too focused on understanding the "problem-space"--addressing fundamental questions about coupled human-natural systems. A new set objectives and design principles are proposed that would move the field toward a more solutions-oriented approach and the enrichment of public reasoning and deliberation. Four new research streams that would situate sustainability science as a science of design are then discussed: creating desirable futures, socio-technical change, sustainability values, and social learning. The results serve as a foundation for a sustainability science that is evaluated on its ability to frame sustainability problems and solutions in ways that make them amenable to democratic and pragmatic social action.
ContributorsMiller, Thaddeus R. (Author) / Minteer, Ben A (Thesis advisor) / Redman, Charles L. (Committee member) / Sarewitz, Daniel (Committee member) / Wiek, Arnim (Committee member) / Arizona State University (Publisher)
Created2011
Description
Individuals' experiences, environment, and education greatly impact their entire being. Similarly, a designer is affected by these elements, which impacts how, what and why they design. In order for design education to generate designers who are more socially aware problem solvers, that education must introduce complex social matters and not just design skills. Traditionally designers learned through apprenticing a master. Most design education has moved away from this traditional model and has begun incorporating a well-rounded program of study, yet there are still more improvements to be made. This research proposes a new Integrated Transformational Experience Model, ITEM, for design education which will be rooted in sustainability, cultural integration, social embeddedness, and discipline collaboration. The designer will be introduced to new ideas and experiences from the immersion of current social issues where they will gain experience creating solutions to global problems enabling them to become catalysts of change. This research is based on interviews with industrial design students to gain insights, benefits and drawbacks of the current model of design education. This research will expand on the current model for design education, combining new ideas that will shed light on the future of design disciplines through the education and motivation of designers. The desired outcome of this study is to incorporate hands on learning through social issues in design classrooms, identify ways to educate future problem solvers, and inspire more research on this issue.
ContributorsWingate, Andrea (Author) / Takamura, John (Thesis advisor) / Stamm, Jill (Committee member) / Bender, Diane (Committee member) / Arizona State University (Publisher)
Created2011