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
Induced pluripotent stem cells (iPSCs) are an intriguing approach for neurological disease modeling, because neural lineage-specific cell types that retain the donors' complex genetics can be established in vitro. The statistical power of these iPSC-based models, however, is dependent on accurate diagnoses of the somatic cell donors; unfortunately, many neurodegenerative diseases are commonly misdiagnosed in live human subjects. Postmortem histopathological examination of a donor's brain, combined with premortem clinical criteria, is often the most robust approach to correctly classify an individual as a disease-specific case or unaffected control. We describe the establishment of primary dermal fibroblasts cells lines from 28 autopsy donors. These fibroblasts were used to examine the proliferative effects of establishment protocol, tissue amount, biopsy site, and donor age. As proof-of-principle, iPSCs were generated from fibroblasts from a 75-year-old male, whole body donor, defined as an unaffected neurological control by both clinical and histopathological criteria. To our knowledge, this is the first study describing autopsy donor-derived somatic cells being used for iPSC generation and subsequent neural differentiation. This unique approach also enables us to compare iPSC-derived cell cultures to endogenous tissues from the same donor. We utilized RNA sequencing (RNA-Seq) to evaluate the transcriptional progression of in vitro-differentiated neural cells (over a timecourse of 0, 35, 70, 105 and 140 days), and compared this with donor-identical temporal lobe tissue. We observed in vitro progression towards the reference brain tissue, supported by (i) a significant increasing monotonic correlation between the days of our timecourse and the number of actively transcribed protein-coding genes and long intergenic non-coding RNAs (lincRNAs) (P < 0.05), consistent with the transcriptional complexity of the brain, (ii) an increase in CpG methylation after neural differentiation that resembled the epigenomic signature of the endogenous tissue, and (iii) a significant decreasing monotonic correlation between the days of our timecourse and the percent of in vitro to brain-tissue differences (P < 0.05) for tissue-specific protein-coding genes and all putative lincRNAs. These studies support the utility of autopsy donors' somatic cells for iPSC-based neurological disease models, and provide evidence that in vitro neural differentiation can result in physiologically progression.
ContributorsHjelm, Brooke E (Author) / Craig, David W. (Thesis advisor) / Wilson-Rawls, Norma J. (Thesis advisor) / Huentelman, Matthew J. (Committee member) / Mason, Hugh S. (Committee member) / Kusumi, Kenro (Committee member) / Arizona State University (Publisher)
Created2013
Description
Speciation is the fundamental process that has generated the vast diversity of life on earth. The hallmark of speciation is the evolution of barriers to gene flow. These barriers may reduce gene flow either by keeping incipient species from hybridizing at all (pre-zygotic), or by reducing the fitness of hybrids (post-zygotic). To understand the genetic architecture of these barriers and how they evolve, I studied a genus of wasps that exhibits barriers to gene flow that act both pre- and post-zygotically. Nasonia is a genus of four species of parasitoid wasps that can be hybridized in the laboratory. When two of these species, N. vitripennis and N. giraulti are mated, their offspring suffer, depending on the generation and cross examined, up to 80% mortality during larval development due to incompatible genic interactions between their nuclear and mitochondrial genomes. These species also exhibit pre-zygotic isolation, meaning they are more likely to mate with their own species when given the choice. I examined these two species and their hybrids to determine the genetic and physiological bases of both speciation mechanisms and to understand the evolutionary forces leading to them. I present results that indicate that the oxidative phosphorylation (OXPHOS) pathway, an essential pathway that is responsible for mitochondrial energy generation, is impaired in hybrids of these two species. These results indicate that this impairment is due to the unique evolutionary dynamics of the combined nuclear and mitochondrial origin of this pathway. I also present results showing that, as larvae, these hybrids experience retarded growth linked to the previously observed mortality and I explore possible physiological mechanisms for this. Finally, I show that the pre-mating isolation is due to a change in a single pheromone component in N. vitripennis males, that this change is under simple genetic control, and that it evolved neutrally before being co-opted as a species recognition signal. These results are an important addition to our overall understanding of the mechanisms of speciation and showcase Nasonia as an emerging model for the study of the genetics of speciation.
ContributorsGibson, Joshua D (Author) / Gadau, Jürgen (Thesis advisor) / Harrison, Jon (Committee member) / Pratt, Stephen (Committee member) / Verrelli, Brian (Committee member) / Willis, Wayne (Committee member) / Arizona State University (Publisher)
Created2013
Description
The principle of Darwinian evolution has been applied in the laboratory to nucleic acid molecules since 1990, and led to the emergence of in vitro evolution technique. The methodology of in vitro evolution surveys a large number of different molecules simultaneously for a pre-defined chemical property, and enrich for molecules with the particular property. DNA and RNA sequences with versatile functions have been identified by in vitro selection experiments, but many basic questions remain to be answered about how these molecules achieve their functions. This dissertation first focuses on addressing a fundamental question regarding the molecular recognition properties of in vitro selected DNA sequences, namely whether negatively charged DNA sequences can be evolved to bind alkaline proteins with high specificity. We showed that DNA binders could be made, through carefully designed stringent in vitro selection, to discriminate different alkaline proteins. The focus of this dissertation is then shifted to in vitro evolution of an artificial genetic polymer called threose nucleic acid (TNA). TNA has been considered a potential RNA progenitor during early evolution of life on Earth. However, further experimental evidence to support TNA as a primordial genetic material is lacking. In this dissertation we demonstrated the capacity of TNA to form stable tertiary structure with specific ligand binding property, which suggests a possible role of TNA as a pre-RNA genetic polymer. Additionally, we discussed the challenges in in vitro evolution for TNA enzymes and developed the necessary methodology for future TNA enzyme evolution.
ContributorsYu, Hanyang (Author) / Chaput, John C (Thesis advisor) / Chen, Julian (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2013
Description
This philosophical inquiry explores the work of philosophers Gilles Deleuze and Félix Guattari and posits applications to music education. Through the concepts of multiplicities, becoming, bodies without organs, smooth spaces, maps, and nomads, Deleuze and Guattari challenge prior and current understandings of existence. In their writings on art, education, and how might one live, they assert a world consisting of variability and motion. Drawing on Deleuze and Guattari's emphasis on time and difference, I posit the following questions: Who and when are we? Where are we? When is music? When is education? Throughout this document, their philosophical figuration of a rhizome serves as a recurring theme, highlighting the possibilities of complexity, diverse connections, and continual processes. I explore the question "When and where are we?" by combining the work of Deleuze and Guattari with that of other authors. Drawing on these ideas, I posit an ontology of humans as inseparably cognitive, embodied, emotional, social, and striving multiplicities. Investigating the question "Where are we?" using Deleuze and Guattari's writings as well as that of contemporary place philosophers and other writers reveals that humans exist at the continually changing confluence of local and global places. In order to engage with the questions "When is music?" and "When is education?" I inquire into how humans as cognitive, embodied, emotional, social, and striving multiplicities emplaced in a glocalized world experience music and education. In the final chapters, a philosophy of music education consisting of the ongoing, interconnected processes of complicating, considering, and connecting is proposed. Complicating involves continually questioning how humans' multiple inseparable qualities and places integrate during musical and educative experiences. Considering includes imagining the multiple directions in which connections might occur as well as contemplating the quality of potential connections. Connecting involves assisting students in forming variegated connections between themselves, their multiple qualities, and their glocal environments. Considering a rhizomatic philosophy of music education includes continually engaging in the integrated processes of complicating, considering, and connecting. Through such ongoing practices, music educators can promote flourishing in the lives of students and the experiences of their multiple communities.
ContributorsRicherme, Lauren Kapalka (Author) / Stauffer, Sandra (Thesis advisor) / Gould, Elizabeth (Committee member) / Schmidt, Margaret (Committee member) / Sullivan, Jill (Committee member) / Tobias, Evan (Committee member) / Arizona State University (Publisher)
Created2013
Description
Synechocystis sp PCC 6803 is a photosynthetic cyanobacterium that can be easily transformed to produce molecules of interest; this has increased Synechocystis’ popularity as a clean energy platform. Synechocystis has been shown to produce and excrete molecules such as fatty acids, isoprene, etc. after appropriate genetic modification. Challenges faced for large–scale growth of modified Synechocystis include abiotic stress, microbial contamination and high processing costs of product and cell material. Research reported in this dissertation contributes to solutions to these challenges. First, abiotic stress was addressed by overexpression of the heat shock protein ClpB1. In contrast to the wild type, the ClpB1 overexpression mutant (Slr1641+) tolerated rapid temperature changes, but no difference was found between the strains when temperature shifts were slower. Combination of ClpB1 overexpression with DnaK2 overexpression (Slr1641+/Sll0170+) further increased thermotolerance. Next, we used a Synechocystis strain that carries an introduced isoprene synthase gene (IspS+) and that therefore produces isoprene. We attempted to increase isoprene yields by overexpression of key enzymes in the methyl erythritol phosphate (MEP) pathway that leads to synthesis of the isoprene precursor. Isoprene production was not increased greatly by MEP pathway induction, likely because of limitations in the affinity of the isoprene synthase for the substrate. Finally, two extraction principles, two–phase liquid extraction (e.g., with an organic and aqueous phase) and solid–liquid extraction (e.g., with a resin) were tested. Two–phase liquid extraction is suitable for separating isoprene but not fatty acids from the culture medium. Fatty acid removal required acidification or surfactant addition, which affected biocompatibility. Therefore, improvements of both the organism and product–harvesting methods can contribute to enhancing the potential of cyanobacteria as solar–powered biocatalysts for the production of petroleum substitutes.
ContributorsGonzalez Esquer, Cesar Raul (Author) / Vermaas, Willem (Thesis advisor) / Chandler, Douglas (Committee member) / Bingham, Scott (Committee member) / Nielsen, David (Committee member) / Arizona State University (Publisher)
Created2013
Description
ABSTRACT Two qualitative studies described the effects of parent's participation in the music therapy session on parent-child interaction during home-based musical experiences learned in music therapy session. Home-based musical play was based on two current programs: Sing & Grow (Abad & Williams, 2007; Nicolson, 2008 Abad, 2011; Williams, et al; 2012) and Musical Connection Programme(Warren & Nugent, 2010). The researcher utilized the core elements of these programs, such as session structures and parenting strategies for improving parent-child interaction during music therapy interventions. Several questions emerged as a result of these case studies as follows 1) does parent's participation affect parent-child interaction during music therapy interventions 2) does musical parenting strategies promote parent-child interaction while practicing musical play at home 3) does parent's interaction increase when they practice parental strategies listed on parent's self-check list. Music therapy session was provided once per week during an eight week period. The participants were referred by Arizona State University (ASU) music therapy clinic. Sessions took place either in the ASU music therapy treatment room or the participant's home. There were four participants- one diagnosed with Down syndrome and the other with Autism Spectrum Disorder (ASD) and two parents or caregivers (each subject was counted as one participant). The parent/caregiver filled out the parental self-checklist 3-4 times per week and the survey after the end of the program. The case study materials were gathered through with parent/caregiver. The case studies revealed that all of the parents responded that the parent's participation in music therapy helped to improve their interactions with their child. Furthermore, all parents became more responsive in interacting with their child through musical play, such as sing-a-long and movements. Second, musical parenting strategies encouraged parent-child interaction when practicing musical play at home. Third, the parent's self-checklist was shown to be effective material for increasing positive parent-child interaction. The self-checklist reminded the parents to practice using strategies in order to promote interaction with their child. Overall, it was found that the parent's participation in home-based musical play increased parent-child interaction and the musical parenting strategies enhanced parent-child interaction.
ContributorsChoi, Yoon Kyoung (Author) / Crowe, Barbara J. (Thesis advisor) / Rio, Robin (Committee member) / Sullivan, Jill (Committee member) / Arizona State University (Publisher)
Created2013
Description
This mixed methods research study explores the experiences of Board Certified music therapists who completed a university-affiliated (UA) internship as part of their education and clinical training in music therapy. The majority of music therapy students complete a national roster (NR) internship as the final stage in clinical training. Limited data and research is available on the UA internship model. This research seeks to uncover themes identified by former university-affiliated interns regarding: (1) on-site internship supervision; (2) university support and supervision during internship; and (3) self-identified perceptions of professional preparedness following internship completion. The quantitative data was useful in creating a profile of interns interviewed. The qualitative data provided a context for understanding responses and experiences. Fourteen Board Certified music therapists were interviewed (N=14) and asked to reflect on their experiences during their university-affiliated internship. Commonalities discovered among former university-affiliated interns included: (1) the desire for peer supervision opportunities in internship; (2) an overall perception of being professionally prepared to sit for the Board Certification exam following internship; (3) a sense of readiness to enter the professional world after internship; and (4) a current or future desire to supervise university-affiliated interns.
ContributorsEubanks, Kymla (Author) / Rio, Robin (Thesis advisor) / Crowe, Barbara (Committee member) / Sullivan, Jill (Committee member) / Arizona State University (Publisher)
Created2013
Description
The purpose of the current study was to use structural equation modeling-based quantitative genetic models to characterize latent genetic and environmental influences on proneness to three discrete negative emotions in middle childhood, according to mother-report, father-report and in-home observation. One primary aim was to test the extent to which covariance among the three emotions could be accounted for by a single, common genetically- and environmentally-influenced negative emotionality factor. A second aim was to examine the extent to which different reporters appeared to be tapping into the same genetically- and environmentally-influenced aspects of each emotion. According to mother- and father-report, moderate to high genetic influences were evident for all emotions, with mother- and father-report of fear and father-report of anger showing the highest heritability. Significant common environmental influences were also found for mother-report of anger and sadness in both univariate and multivariate models. For observed emotion, anger was moderately heritable with no evidence for common environmental variance, but sadness, object fear and social fear all showed modest to moderate common environmental influences and no significant genetic variance. In addition, cholesky decompositions examining genetic and environmental influences across reporter suggested that despite considerable overlap between mother-report and father-report, there was also reporter-specific variance on anger, sadness, and fear. Specifically, there were significant common environmental influences on mother-report of anger- and sadness that were not shared with father-report, and genetic influences on father-report of sadness and fear that were not shared with mother-report. In-home observations were not highly correlated enough with parent-report to support multivariate analysis for any emotion. Finally, according to both mother- and father-report, a single set of genetic and environmental influences was sufficient to account for covariance among all three negative emotions. However, fear was primarily explained by genetic influences not shared with other emotions, and anger also showed considerable emotion-specific genetic variance. In both cases, findings support the value of a more emotion-specific approach to temperament, and highlight the need to consider distinctions as well as commonalities across emotions, reporters and situations.
ContributorsClifford, Sierra (Author) / Lemery, Kathryn (Thesis advisor) / Shiota, Michelle (Committee member) / Eisenberg, Nancy (Committee member) / Arizona State University (Publisher)
Created2013
Description
Jazz continues, into its second century, as one of the most important musics taught in public middle and high schools. Even so, research related to how students learn, especially in their earliest interactions with jazz culture, is limited. Weaving together interviews and observations of junior and senior high school jazz players and teachers, private studio instructors, current university students majoring in jazz, and university and college jazz faculty, I developed a composite sketch of a secondary school student learning to play jazz. Using arts-based educational research methods, including the use of narrative inquiry and literary non-fiction, the status of current jazz education and the experiences by novice jazz learners is explored. What emerges is a complex story of students and teachers negotiating the landscape of jazz in and out of early twenty-first century public schools. Suggestions for enhancing jazz experiences for all stakeholders follow, focusing on access and the preparation of future jazz teachers.
ContributorsKelly, Keith B (Author) / Stauffer, Sandra (Thesis advisor) / Tobias, Evan (Committee member) / Kocour, Michael (Committee member) / Sullivan, Jill (Committee member) / Schmidt, Margaret (Committee member) / Arizona State University (Publisher)
Created2013
Description
Well-established model systems exist in four out of the seven major classes of vertebrates. These include the mouse, chicken, frog and zebrafish. Noticeably missing from this list is a reptilian model organism for comparative studies between the vertebrates and for studies of biological processes unique to reptiles. To help fill in this gap the green anole lizard, Anolis carolinensis, is being adapted as a model organism. Despite the recent release of the complete genomic sequence of the A. carolinensis, the lizard lacks some resources to aid researchers in their studies. Particularly, the lack of transcriptomic resources for lizard has made it difficult to identify genes complete with alternative splice forms and untranslated regions (UTRs). As part of this work the genome annotation for A. carolinensis was improved through next generation sequencing and assembly of the transcriptomes from 14 different adult and embryonic tissues. This revised annotation of the lizard will improve comparative studies between vertebrates, as well as studies within A. carolinensis itself, by providing more accurate gene models, which provide the bases for molecular studies. To demonstrate the utility of the improved annotations and reptilian model organism, the developmental process of somitogenesis in the lizard was analyzed and compared with other vertebrates. This study identified several key features both divergent and convergent between the vertebrates, which was not previously known before analysis of a reptilian model organism. The improved genome annotations have also allowed for molecular studies of tail regeneration in the lizard. With the annotation of 3' UTR sequences and next generation sequencing, it is now possible to do expressional studies of miRNA and predict their mRNA target transcripts at genomic scale. Through next generation small RNA sequencing and subsequent analysis, several differentially expressed miRNAs were identified in the regenerating tail, suggesting miRNA may play a key role in regulating this process in lizards. Through miRNA target prediction several key biological pathways were identified as potentially under the regulation of miRNAs during tail regeneration. In total, this work has both helped advance A. carolinensis as model system and displayed the utility of a reptilian model system.
ContributorsEckalbar, Walter L (Author) / Kusumi, Kenro (Thesis advisor) / Huentelman, Matthew (Committee member) / Rawls, Jeffery (Committee member) / Wilson-Rawls, Norma (Committee member) / Arizona State University (Publisher)
Created2012