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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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
In this dissertation Mexican American (MA) youths environmental risk contexts, HPA axis functioning and mental health symptomatology were investigated in two separate studies. In the first study, environmental risk contexts were examined utilizing a person-centered approach and focusing on MA adolescents' family, peer, and cultural risk factors in fifth grade (N = 750). Environmental contexts were then linked to mental health symptomatology in seventh grade. Results revealed three distinct environmental contexts: Low risk, Moderate risk-language, and High risk-peer. Youth in the High-risk peer context reported the highest levels of symptomatology; greater major depressive disorder (MDD), anxiety, conduct disorder (CD)/oppositional defiant disorder (ODD), and attention deficit hyperactive disorder (ADHD) symptoms than youth experiencing Low risk or Moderate risk-language context. Females, in particular, experiencing the High risk peer context appeared at greatest risk for MDD symptoms. Finally, adolescents in the Moderate risk-language context displayed similar levels of symptoms to the individuals in the Low risk context, with the exception of higher anxiety. This study suggested that MA youth live in unique environmental contexts and these contexts are differentially related to mental health symptomatology. In the second study, 98 MA youth participated in a three-day diurnal cortisol protocol in hopes of linking perceptions of discrimination and HPA diurnal cortisol rhythms. Results revealed that discrimination was related to greater overall cortisol output and marginally related to the cortisol awakening response and evening levels of cortisol. Results suggest that important physiological processes underlie the experiences of discrimination.
ContributorsZeiders, Katharine H (Author) / Roosa, Mark W. (Thesis advisor) / Doane, Leah D. (Committee member) / Dumka, Larry (Committee member) / Enders, Craig E. (Committee member) / Updegraff, Kimberly A. (Committee member) / Arizona State University (Publisher)
Created2011
Description
Federal education policies call for school district leaders to promote classroom technology integration to prepare students with 21st century skills. However, schools are struggling to integrate technology effectively, with students often reporting that they feel like they need to power down and step back in time technologically when they enter classrooms. The lack of meaningful technology use in classrooms indicates a need for increased teacher preparation. The purpose of this study was to investigate the impact a coaching model of professional development had on school administrators` abilities to increase middle school teachers` technology integration in their classrooms. This study attempted to coach administrators to develop and articulate a vision, cultivate a culture, and model instruction relative to the meaningful use of instructional technology. The study occurred in a middle school. Data for this case study were collected via administrator interviews, the Principal`s Computer Technology Survey, structured observations using the Higher Order Thinking, Engaged Learning, Authentic Learning, Technology Use protocol, field notes, the Technology Integration Matrix, teacher interviews, and a research log. Findings concluded that cultivating change in an organization is a complex process that requires commitment over an extended period of time. The meaningful use of instructional technology remained minimal at the school during fall 2010. My actions as a change agent informed the school`s administrators about the role meaningful use of technology can play in instruction. Limited professional development, administrative vision, and expectations minimized the teachers` meaningful use of instructional technology; competing priorities and limited time minimized the administrators` efforts to improve the meaningful use of instructional technology. Realizing that technology proficient teachers contribute to student success with technology, it may be wise for administrators to incorporate technology-enriched professional development and exercise their leadership abilities to promote meaningful technology use in classrooms.
ContributorsRobertson, Kristen (Author) / Moore, David (Thesis advisor) / Cheatham, Greg (Committee member) / Catalano, Ruth (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
This study follows three secondary teachers as they facilitate a digital storytelling project with their students for the first time. All three teachers were not specifically trained in digital storytelling in order to investigate what happens when a digital storytelling novice tries to do a project like this with his or her students. The study follows two high school English teachers and one middle school math teacher. Each teacher's experience is shared in a case study, and all three case studies are compared and contrasted in a cross-case analysis. There is a discussion of the types of projects the teachers conducted and any challenges they faced. Strategies to overcome the challenges are also included. A variety of assessment rubrics are included in the appendix. In the review of literature, the history of digital storytelling is illuminated, as are historical concepts of literacy. There is also an exploration of twenty-first century skills including multiliteracies such as media and technology literacy. Both the teachers and their students offer suggestions to future teachers taking on digital storytelling projects. The dissertation ends with a discussion of future scholarship in educational uses of digital storytelling.
ContributorsGordon, Corrine (Author) / Blasingame, James (Thesis advisor) / Nilsen, Alleen P (Committee member) / Early, Jessica (Committee member) / Marsh, Josephine (Committee member) / Arizona State University (Publisher)
Created2011
Description
The cyanobacterium Synechocystis sp. PCC 6803 performs oxygenic photosynthesis. Light energy conversion in photosynthesis takes place in photosystem I (PSI) and photosystem II (PSII) that contain chlorophyll, which absorbs light energy that is utilized as a driving force for photosynthesis. However, excess light energy may lead to formation of reactive oxygen species that cause damage to photosynthetic complexes, which subsequently need repair or replacement. To gain insight in the degradation/biogenesis dynamics of the photosystems, the lifetimes of photosynthetic proteins and chlorophyll were determined by a combined stable-isotope (15N) and mass spectrometry method. The lifetimes of PSII and PSI proteins ranged from 1-33 and 30-75 hours, respectively. Interestingly, chlorophyll had longer lifetimes than the chlorophyll-binding proteins in these photosystems. Therefore, photosynthetic proteins turn over and are replaced independently from each other, and chlorophyll is recycled from the damaged chlorophyll-binding proteins. In Synechocystis, there are five small Cab-like proteins (SCPs: ScpA-E) that share chlorophyll a/b-binding motifs with LHC proteins in plants. SCPs appear to transiently bind chlorophyll and to regulate chlorophyll biosynthesis. In this study, the association of ScpB, ScpC, and ScpD with damaged and repaired PSII was demonstrated. Moreover, in a mutant lacking SCPs, most PSII protein lifetimes were unaffected but the lifetime of chlorophyll was decreased, and one of the nascent PSII complexes was missing. SCPs appear to bind PSII chlorophyll while PSII is repaired, and SCPs stabilize nascent PSII complexes. Furthermore, aminolevulinic acid biosynthesis, an early step of chlorophyll biosynthesis, was impaired in the absence of SCPs, so that the amount of chlorophyll in the cells was reduced. Finally, a deletion mutation was introduced into the sll1906 gene, encoding a member of the putative bacteriochlorophyll delivery (BCD) protein family. The Sll1906 sequence contains possible chlorophyll-binding sites, and its homolog in purple bacteria functions in proper assembly of light-harvesting complexes. However, the sll1906 deletion did not affect chlorophyll degradation/biosynthesis and photosystem assembly. Other (parallel) pathways may exist that may fully compensate for the lack of Sll1906. This study has highlighted the dynamics of photosynthetic complexes in their biogenesis and turnover and the coordination between synthesis of chlorophyll and photosynthetic proteins.
ContributorsYao, Cheng I Daniel (Author) / Vermaas, Wim (Thesis advisor) / Fromme, Petra (Committee member) / Roberson, Robert (Committee member) / Webber, Andrew (Committee member) / Arizona State University (Publisher)
Created2011
Description
Other studies have previously demonstrated that perceived stress and maladaptive stress management can lead to harmful outcomes including depression, morbidity, and mortality. College students (especially freshmen) have more difficulty dealing with stress, which can increase their susceptibility to engage in high risk behaviors. The importance of conducting this research is to discover the effects that perceived stress levels may have on depression outcomes in college students, and to evaluate the influence of health related behaviors on this relationship. This study used a retrospective cross-sectional correlational design to examine correlations between perceived stress, physical activity, and other health behaviors on clinical and perceived depression in college students. A random sample of 20,000 students was drawn from 62,476 students enrolled at Arizona State University (ASU). Participants included 2,238 students who volunteered to take the American College Health Association-National College Health Assessment (ACHA-NCHA) in spring 2009. Supplemental questions for ASU students were developed by ASU Wellness and administered as a part of the ACHA-NCHA II. The university sent an invitation email, wherein students were directed through a hyperlink to the survey website. ACHA provided institutional survey data in an SPSS file for analysis. The data were evaluated with Spearman Rho Correlation Analysis and Wilcoxon-Mann-Whitney test. There were more female participants (n = 580) than males (n = 483), both averaged 23 years of age. Men had greater height, weight, and body mass index than females, all were significant mean differences. There were more significant correlations between health factors and having perceived depression than with having real or diagnosed depression. Logistic regression showed that out of all variables and behaviors studied, only high levels of stress, poor general health, substance use, and gender (female) resulted in significant odds in predicting that a participant would be in one of the depression categories. This research suggests that addressing these factors may be important to prevent and reduce depression among college students. This study provides empirical evidence that there is a significant relationship between perceived stress and depression among college students, and that health behaviors such as substance abuse have a negative mediating effect on this relationship.
ContributorsSkipworth, Katherine (Author) / Swan, Pamela (Thesis advisor) / Woodruff, Larry (Committee member) / Moses, Karen (Committee member) / Arizona State University (Publisher)
Created2011
Description
Telomerase ribonucleoprotein is a unique reverse transcriptase that adds telomeric DNA repeats to chromosome ends. Telomerase RNA (TER) is extremely divergent in size, sequence and has to date only been identified in vertebrate, yeast, ciliate and plant species. Herein, the identification and characterization of TERs from an evolutionarily distinct group, filamentous fungi, is presented. Based on phylogenetic analysis of 69 TER sequences and mutagenesis analysis of in vitro reconstituted Neurospora telomerase, we discovered a conserved functional core in filamentous fungal TERs sharing homologous structural features with vertebrate TERs. This core contains the template-pseudoknot and P6/P6.1 domains, essential for enzymatic activity, which retain function in trans. The in vitro reconstituted Neurospora telomerase is highly processive, synthesizing canonical TTAGGG repeats. Similar to Schizosaccharomycetes pombe, filamentous fungal TERs utilize the spliceosomal splicing machinery for 3' processing. Neurospora telomerase, while associating with the Est1 protein in vivo, does not bind homologous Ku or Sm proteins found in both budding and fission yeast telomerase holoenzyme, suggesting a unique biogenesis pathway. The development of Neurospora as a model organism to study telomeres and telomerase may shed light upon the evolution of the canonical TTAGGG telomeric repeat and telomerase processivity within fungal species.
ContributorsQi, Xiaodong (Author) / Chen, Julian (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Chaput, John (Committee member) / Arizona State University (Publisher)
Created2011