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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- Creators: Ghirlanda, Giovanna
- Creators: Redkar, Sangram
Description
The purpose of this project was to commission, perform, and discuss a new work for an instrument pairing not often utilized, oboe and percussion. The composer, Alyssa Morris, was selected in June 2009. Her work, titled Forecast, was completed in October of 2009 and premiered in February of 2010, as part of a program showcasing music for oboe and percussion. Included in this document is a detailed biography of the composer, a description of the four movements of Forecast, performance notes for each movement, a diagram for stage set-up, the full score, the program from the premiere performance with biographies of all the performers involved, and both a live recording and MIDI sound file. The performance notes discuss issues that arose during preparation for the premiere and should help avoid potential pitfalls. TrevCo Music, publisher of the work, graciously allowed inclusion of the full score. This score is solely for use in this document; please visit the publisher's website for purchasing information. The commission and documentation of this composition are intended to add to the repertoire for oboe in an unusual instrument pairing and to encourage further exploration of such combinations.
ContributorsCreamer, Caryn (Author) / Schuring, Martin (Thesis advisor) / Hill, Gary (Committee member) / Holbrook, Amy (Committee member) / Micklich, Albie (Committee member) / Spring, Robert (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
In nearly all commercially successful internal combustion engine applications, the slider crank mechanism is used to convert the reciprocating motion of the piston into rotary motion. The hypocycloid mechanism, wherein the crankshaft is replaced with a novel gearing arrangement, is a viable alternative to the slider crank mechanism. The geared hypocycloid mechanism allows for linear motion of the connecting rod and provides a method for perfect balance with any number of cylinders including single cylinder applications. A variety of hypocycloid engine designs and research efforts have been undertaken and produced successful running prototypes. Wiseman Technologies, Inc provided one of these prototypes to this research effort. This two-cycle 30cc half crank hypocycloid engine has shown promise in several performance categories including balance and efficiency. To further investigate its potential a more thorough and scientific analysis was necessary and completed in this research effort. The major objective of the research effort was to critically evaluate and optimize the Wiseman prototype for maximum performance in balance, efficiency, and power output. A nearly identical slider crank engine was used extensively to establish baseline performance data and make comparisons. Specialized equipment and methods were designed and built to collect experimental data on both engines. Simulation and mathematical models validated by experimental data collection were used to better quantify performance improvements. Modifications to the Wiseman prototype engine improved balance by 20 to 50% (depending on direction) and increased peak power output by 24%.
ContributorsConner, Thomas (Author) / Redkar, Sangram (Thesis advisor) / Rogers, Bradley (Committee member) / Georgeou, Trian (Committee member) / Arizona State University (Publisher)
Created2011
Description
During the twentieth-century, the dual influence of nationalism and modernism in the eclectic music from Latin America promoted an idiosyncratic style which naturally combined traditional themes, popular genres and secular music. The saxophone, commonly used as a popular instrument, started to develop a prominent role in Latin American classical music beginning in 1970. The lack of exposure and distribution of the Latin American repertoire has created a general perception that composers are not interested in the instrument, and that Latin American repertoire for classical saxophone is minimal. However, there are more than 1100 works originally written for saxophone in the region, and the amount continues to grow. This Modern Latin American Repertoire for Classical Saxophone: Recording Project and Performance Guide document establishes and exhibits seven works by seven representative Latin American composers.The recording includes works by Carlos Gonzalo Guzman (Colombia), Ricardo Tacuchian (Brazil), Roque Cordero (Panama), Luis Naón (Argentina), Andrés Alén-Rodriguez (Cuba), Alejandro César Morales (Mexico) and Jose-Luis Maúrtua (Peru), featuring a range of works for solo alto saxophone to alto saxophone with piano, alto saxophone with vibraphone, and tenor saxophone with electronic tape; thus forming an important selection of Latin American repertoire. Complete recorded performances of all seven pieces are supplemented by biographical, historical, and performance practice suggestions. The result is a written and audio guide to some of the most important pieces composed for classical saxophone in Latin America, with an emphasis on fostering interest in, and research into, composers who have contributed in the development and creation of the instrument in Latin America.
ContributorsOcampo Cardona, Javier Andrés (Author) / McAllister, Timothy (Thesis advisor) / Spring, Robert (Committee member) / Hill, Gary (Committee member) / Pilafian, Sam (Committee member) / Rogers, Rodney (Committee member) / Gardner, Joshua (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
Description
Telomerase is a specialized enzyme that adds telomeric DNA repeats to the chromosome ends to counterbalance the progressive telomere shortening over cell divisions. It has two essential core components, a catalytic telomerase reverse transcriptase protein (TERT), and a telomerase RNA (TR). TERT synthesizes telomeric DNA by reverse transcribing a short template sequence in TR. Unlike TERT, TR is extremely divergent in size, sequence and structure and has only been identified in three evolutionarily distant groups. The lack of knowledge on TR from important model organisms has been a roadblock for vigorous studies on telomerase regulation. To address this issue, a novel in vitro system combining deep-sequencing and bioinformatics search was developed to discover TR from new phylogenetic groups. The system has been validated by the successful identification of TR from echinoderm purple sea urchin Strongylocentrotus purpuratus. The sea urchin TR (spTR) is the first invertebrate TR that has been identified and can serve as a model for understanding how the vertebrate TR evolved with vertebrate-specific traits. By using phylogenetic comparative analysis, the secondary structure of spTR was determined. The spTR secondary structure reveals unique sea urchin specific structure elements as well as homologous structural features shared by TR from other organisms. This study enhanced the understanding of telomerase mechanism and the evolution of telomerase RNP. The system that was used to identity telomerase RNA can be employed for the discovery of other TR as well as the discovery of novel RNA from other RNP complex.
ContributorsLi, Yang (Author) / Chen, Julian Jl (Thesis advisor) / Yan, Hao (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2011
Description
Finger motion and hand posture of six professional clarinetists (defined by entrance into or completion of a doctorate of musical arts degree in clarinet performance) were recorded using a pair of CyberGloves® in Arizona State University's Center for Cognitive Ubiquitous Computing Laboratory. Performance tasks included performing a slurred three-octave chromatic scale in sixteenth notes, at sixty quarter-note beats per minute, three times, with a metronome and a short pause between repetitions, and forming three pedagogical hand postures. Following the CyberGloves® tasks, each subject completed a questionnaire about equipment, playing history, practice routines, health practices, and hand usage during computer and sports activities. CyberGlove® data were analyzed to find average hand/finger postures and differences for each pitch across subjects, subject variance in the performance task and differences in ascending and descending postures of the chromatic scale. The data were also analyzed to describe generalized finger posture characteristics based on hand size, whether right hand thumb position affects finger flexion, and whether professional clarinetists use similar finger/hand postures when performing on clarinet, holding a tennis ball, allowing hands to hang freely by the sides, or form a "C" shape. The findings of this study suggest an individual approach based on hand size is necessary for teaching clarinet hand posture.
ContributorsHarger, Stefanie (Author) / Spring, Robert (Thesis advisor) / Hill, Gary (Committee member) / Koonce, Frank (Committee member) / Norton, Kay (Committee member) / Stauffer, Sandy (Committee member) / Arizona State University (Publisher)
Created2011
Description
Owen Middleton (b. 1941) enjoys an established and growing reputation as a composer of classical guitar music, but his works for piano are comparatively little known. The close investigation offered here of Middleton's works for piano reveals the same impressive craftsmanship, compelling character, and innovative spirit found in his works for guitar. Indeed, the only significant thing Middleton's piano music currently lacks is the well-deserved attention of professional players and a wider audience. Middleton's piano music needs to be heard, not just discussed, so one of this document's purposes is to provide a recorded sample of his piano works. While the overall repertoire for solo piano is vast, and new works become established in that repertoire with increasing difficulty, Middleton's piano works have a significant potential to find their way into the concert hall as well as the private teaching studio. His solo piano music is highly effective, well suited to the instrument, and, perhaps most importantly, fresh sounding and truly original. His pedagogical works are of equal value. Middleton's piano music offers something for everyone: there one finds daring virtuosity, effusions of passion, intellectual force, colorful imagery, poetry, humor, and even a degree of idiomatic innovation. This study aims to reveal key aspects of the composer's musical style, especially his style of piano writing, and to provide pianists with helpful analytical, technical, and interpretive insights. These descriptions of the music are supported with recorded examples, selected from the works for solo piano written between 1962 and 1993: Sonata for Piano, Childhood Scenes, Katie's Collection, and Toccata for Piano. The complete scores of the recorded works are included in the appendix. A chapter briefly describing the piano pieces since 1993 concludes the study and invites the reader to further investigations of this unique and important body of work.
ContributorsMoreau, Barton Andrew (Author) / Hamilton, Robert (Thesis advisor) / Holbrook, Amy (Committee member) / Campbell, Andrew (Committee member) / Spring, Robert (Committee member) / Gardner, Joshua (Committee member) / Arizona State University (Publisher)
Created2011
Description
Natural products that target the DNA of cancer cells have been an important source of knowledge and understanding in the development of anticancer chemotherapeutic agents. Bleomycin (BLM) exemplifies this class of DNA damaging agent. The ability of BLM to chelate metal ions and effect oxidative damage of the deoxyribose sugar moiety of DNA has been studied extensively for four decades. Here, the study of BLM A5 was conducted using a previously isolated library of hairpin DNAs found to bind strongly to metal free BLM. The ability of BLM to effect single-stranded was then extensively characterized on both the 3′ and 5′-arms of the hairpin DNAs. The strongly bound DNAs were found to be efficient substrates for Fe·BLM A5-mediated cleavage. Surprisingly, the most prevalent site of damage by BLM was found to be a 5′-AT-3′ dinucleotide sequence. This dinucleotide sequence and others generally not cleaved by BLM when examined using arbitrarily chosen DNA substrate were found in examining the library of ten hairpin DNAs. In total, 111 sites of DNA damage were found to be produced by exposure of the hairpin DNA library to Fe·BLM A5. Also, an assay was developed with which to test the propensity of the hairpin DNAs to undergo double stranded DNA damage. Adapting methods previously described by the Povirk laboratory, one hairpin was characterized using this method. The results were in accordance with those previously reported.
ContributorsSegerman, Zachary (Author) / Hecht, Sidney M. (Thesis advisor) / Levitus, Marcia (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2011
Description
The properties of materials depend heavily on the spatial distribution and connectivity of their constituent parts. This applies equally to materials such as diamond and glasses as it does to biomolecules that are the product of billions of years of evolution. In science, insight is often gained through simple models with characteristics that are the result of the few features that have purposely been retained. Common to all research within in this thesis is the use of network-based models to describe the properties of materials. This work begins with the description of a technique for decoupling boundary effects from intrinsic properties of nanomaterials that maps the atomic distribution of nanomaterials of diverse shape and size but common atomic geometry onto a universal curve. This is followed by an investigation of correlated density fluctuations in the large length scale limit in amorphous materials through the analysis of large continuous random network models. The difficulty of estimating this limit from finite models is overcome by the development of a technique that uses the variance in the number of atoms in finite subregions to perform the extrapolation to large length scales. The technique is applied to models of amorphous silicon and vitreous silica and compared with results from recent experiments. The latter part this work applies network-based models to biological systems. The first application models force-induced protein unfolding as crack propagation on a constraint network consisting of interactions such as hydrogen bonds that cross-link and stabilize a folded polypeptide chain. Unfolding pathways generated by the model are compared with molecular dynamics simulation and experiment for a diverse set of proteins, demonstrating that the model is able to capture not only native state behavior but also partially unfolded intermediates far from the native state. This study concludes with the extension of the latter model in the development of an efficient algorithm for predicting protein structure through the flexible fitting of atomic models to low-resolution cryo-electron microscopy data. By optimizing the fit to synthetic data through directed sampling and context-dependent constraint removal, predictions are made with accuracies within the expected variability of the native state.
ContributorsDe Graff, Adam (Author) / Thorpe, Michael F. (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Matyushov, Dmitry (Committee member) / Ozkan, Sefika B. (Committee member) / Treacy, Michael M. J. (Committee member) / Arizona State University (Publisher)
Created2011