Matching Items (201)
ContributorsRockmaker, Jody (Composer)
ContributorsRockmaker, Jody (Composer)
ContributorsRockmaker, Jody (Composer)
ContributorsRockmaker, Jody (Composer)
ContributorsRockmaker, Jody (Composer)
ContributorsRockmaker, Jody (Composer)
ContributorsRockmaker, Jody (Composer)
ContributorsRockmaker, Jody (Composer)
ContributorsRockmaker, Jody (Composer)
ContributorsRockmaker, Jody (Composer)
ContributorsRockmaker, Jody (Composer)
ContributorsRockmaker, Jody (Composer)
ContributorsRockmaker, Jody (Composer)
Description
The ASU School of Dance presents Lyric Reflections, November 15-18, with works by dance faculty, undergraduates, graduates, and visiting artists, performed at Galvin Playhouse Theatre.
ContributorsHergerber Institute School of Dance (Publisher) / Ammerman, Mark C. (Set designer) / Bernard, Jacqueline (Costume designer) / Britt, Melissa (Dancer) / Burnett, Cherie (Dancer) / DeBoer, Andrew (Musician) / Doherty, Kelley (Dancer) / Dostal, Michael (Lighting designer) / Fitzgerald, Mary (Choreographer) / Harriosn, Christina (Dancer) / Ingalls, Todd (Composer) / Kirwan, Molly (Dancer) / Kroon, Anjuli (Dancer) / Lee, Yeongwen (Dancer) / Limon, Jose (Choreographer) / Ma, Shouze (Choreographer, Dancer) / Malan-McDonald, Sara Jean (Dancer) / Manners, Robin (Dancer) / Manus, Nicole (Dancer) / Mapes, Aileen (Choreographer, Conductor, Dancer) / McHale, Samantha (Dancer) / Mihaleva, Galina (Costume designer, Set designer) / Mooney, Elina (Choreographer) / Mumford, Jessica (Dancer) / Norman, Katie (Musician) / Ouper, Jeffery (Composer) / Raymond, Kelley (Musician) / Rockmaker, Jody (Composer) / Schupp, Karen (Choreographer) / Shipley, Samantha (Dancer) / Spenceley, Jenni (Dancer) / Stein, Derek (Musician) / Sephens, Jr. Sanny (Dancer) / Tomlinson, Charles (Costume designer) / Tovson, Kristin (Dancer) / Trujillo, David (Dancer) / Vessey, Julia (Dancer) / Watt, Nina (Director) / Wernsman, David (Dancer) / Williams, LaShonda L. (Dancer) / Wooldridge, Holly (Dancer)
Created2007
Description
The ASU School of Dance presents Elina's LINEage, September 19-21, with works by Elina Mooney and Cliff Keuter, performed at Galvin Playhouse.
ContributorsAmmerman, Mark C. (Set designer) / Basting, Samantha (Dancer) / Benard, Jacqueline (Set designer, Costume designer) / Britt, Melissa (Dancer) / Canto, Melissa (Dancer) / Davis, Paul (Set designer, Costume designer) / Gonzales, Casey (Dancer) / Keuter, Cliff (Choreographer, Costume designer, Artist) / Lundell, Eva (Musician) / Martinez, Brandt (Dancer) / McDowell, John Herbert (Composer) / McGloin, Aaron (Dancer) / Mihaleva, Galina (Set designer, Costume designer) / Mooney, Elina (Choreographer, Dancer) / Naimark, Steven (Musician) / Nuber, Gregory (Dancer) / Radcliffe, Elisa (Dancer) / Rockmaker, Jody (Composer) / Teachout, Kim (Musician) / Herberger Institute School of Dance (Publisher)
Created2008
ContributorsGarrett, Jennifer (Conductor) / FitzPatrick, Carole (Performer) / Aspnes, Lynne (Performer) / Campbell, Andrew (Pianist) (Performer) / Ryan, Russell (Performer) / Rockmaker, Jody (Performer) / Kocour, Mike (Performer) / McLin, Katherine (Performer) / Larson, Brook Carter (Conductor) / Women's Chorus (Performer) / Men's Chorus (Performer) / ASU Library. Music Library (Publisher)
Created2009-05-04
Description
In eukaryotes, DNA is packed in a highly condensed and hierarchically organized structure called chromatin, in which DNA tightly wraps around the histone octamer consisting of one histone 3-histone 4 (H3-H4) tetramer and two histone 2A- histone 2B (H2A-H2B) dimers with 147 base pairs in an almost two left handed turns. Almost all DNA dependent cellular processes, such as DNA duplication, transcription, DNA repair and recombination, take place in the chromatin form. Based on the critical importance of appropriate chromatin condensation, this thesis focused on the folding behavior of the nucleosome array reconstituted using different templates with various controllable factors such as histone tail modification, linker DNA length, and DNA binding proteins. Firstly, the folding behaviors of wild type (WT) and nucleosome arrays reconstituted with acetylation on the histone H4 at lysine 16 (H4K16 (Ac)) were studied. In contrast to the sedimentation result, atomic force microscopy (AFM) measurements revealed no apparent difference in the compact nucleosome arrays between WT and H4K16 (Ac) and WT. Instead, an optimal loading of nucleosome along the template was found necessary for the Mg2+ induced nucleosome array compaction. This finding leads to the further study on the role of linker DNA in the nucleosome compaction. A method of constructing DNA templates with varied linker DNA lengths was developed, and uniformly and randomly spaced nucleosome arrays with average linker DNA lengths of 30 bp and 60 bp were constructed. After comprehensive analyses of the nucleosome arrays' structure in mica surface, the lengths of the linker DNA were found playing an important role in controlling the structural geometries of nucleosome arrays in both their extended and compact forms. In addition, higher concentration of the DNA binding domain of the telomere repeat factor 2 (TRF2) was found to stimulate the compaction of the telomeric nucleosome array. Finally, AFM was successfully applied to investigate the nucleosome positioning behaviors on the Mouse Mammary Tumor Virus (MMTV) promoter region, and two highly positioned region corresponded to nucleosome A and B were identified by this method.
ContributorsFu, Qiang (Author) / Lindsay, Stuart M (Thesis advisor) / Yan, Hao (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2010
Description
A novel small metal-binding protein (SmbP), with only 93 residues and no similarity to other known proteins, has been isolated from the periplasm of Nitrosomonas europaea. It is characterized by its high percentage (17%) of histidines, a motif of ten repeats of seven residues, a four α-helix bundle structure, and a high binding affinity to about six equivalents of Cu2+. The goal of this study is to investigate the Cu2+ binding sites in SmbP and to understand how Cu2+ stabilizes the protein. Preliminary folding experiments indicated that Cu2+ greatly stabilizes SmbP. In this study, protein folding data from circular dichroism (CD) spectroscopy was used to elucidate the role of Cu2+ in stabilizing SmbP structure against unfolding induced by decreased pH, increased temperature, and chemical denaturants. The significant stabilization effects of Cu2+ were demonstrated by the observation that Cu2+-SmbP remained fully folded under extreme environmental conditions, such as acidic pH, 96 °C, and 8 M urea. Also, it was shown that Cu2+ is able to induce the refolding of unfolded SmbP in acidic solutions. These findings imply that the coordination of Cu2+ to histidine residues is responsible for the stabilization effects. The crystal structure of SmbP without Cu2+ has been determined. However, attempts to crystallize Cu2+-SmbP have not been successful. In this study, multidimensional NMR experiments were conducted in order to gain additional information regarding the Cu2+-SmbP structure, in particular its metal binding sites. Unambiguous resonance assignments were successfully made. Cα secondary chemical shifts confirmed that SmbP has a four α-helical structure. A Cu2+-protein titration experiment monitored by NMR indicated a top-to-bottom, sequential metal binding pattern for SmbP. In addition, several bioinformatics tools were used to complement the experimental approach and identity of the ligands in Cu2+-binding sites in SmbP is proposed.
ContributorsYan, Qin (Author) / Francisco, Wilson A (Thesis advisor) / Allen, James (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2010
Description
Enzymes which regulate the metabolic reactions for sustaining all living things, are the engines of life. The discovery of molecules that are able to control enzyme activity is of great interest for therapeutics and the biocatalysis industry. Peptides are promising enzyme modulators due to their large chemical diversity and the existence of well-established methods for library synthesis. Microarrays represent a powerful tool for screening thousands of molecules, on a small chip, for candidates that interact with enzymes and modulate their functions. In this work, a method is presented for screening high-density arrays to discover peptides that bind and modulate enzyme activity. A viscous polyvinyl alcohol (PVA) solution was applied to array surfaces to limit the diffusion of product molecules released from enzymatic reactions, allowing the simultaneous measurement of enzyme activity and binding at each peptide feature. For proof of concept, it was possible to identify peptides that bound to horseradish peroxidase (HRP), alkaline phosphatase (APase) and â-galactosidase (â-Gal) and substantially alter their activities by comparing the peptide-enzyme binding levels and bound enzyme activity on microarrays. Several peptides, selected from microarrays, were able to inhibit â-Gal in solution, which demonstrates that behaviors selected from surfaces often transfer to solution. A mechanistic study of inhibition revealed that some of the selected peptides inhibited enzyme activity by binding to enzymes and inducing aggregation. PVA-coated peptide slides can be rapidly analyzed, given an appropriate enzyme assay, and they may also be assayed under various conditions (such as temperature, pH and solvent). I have developed a general method to discover molecules that modulate enzyme activity at desired conditions. As demonstrations, some peptides were able to promote the thermal stability of bound enzyme, which were selected by performing the microarray-based enzyme assay at high temperature. For broad applications, selected peptide ligands were used to immobilize enzymes on solid surfaces. Compared to conventional methods, enzymes immobilized on peptide-modified surfaces exhibited higher specific activities and stabilities. Peptide-modified surfaces may prove useful for immobilizing enzymes on surfaces with optimized orientation, location and performance, which are of great interest to the biocatalysis industry.
ContributorsFu, Jinglin (Author) / Woodbury, Neal W (Thesis advisor) / Johnston, Stephen A. (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2010
Description
From Marathon to Athens was inspired by the legend of Pheidippides, a Greek messenger who ran approximately twenty-six miles between the cities of Marathon and Athens in ancient Greece to deliver an important wartime message. According to the legend, he died shortly after completing the journey. The marathon races of today were inspired by his story, though it may be more myth than reality. There is a great deal of inherent drama in the undertaking of such a feat, whether it be a marathon or any other test of strength and endurance. There is the rush of adrenaline when it begins, followed by the excitement and exhilaration of the first few miles. Then, there is a period of settling in and finding a groove - when the runner realizes that there is a long way to go, but is determined to pace him or herself and stay strong. All too often, there is the "wall" that appears about three-quarters of the way through, when it seems that there is no strength left to finish the race. Finally, there is the final push to the finish line - where the runner decides that they are going to make it, in spite of fatigue, pain, or any other obstacle. In this piece, I used a simple melody that was very loosely modeled after a melody from ancient Greece (the tune inscribed on the Epitaph of Seikilos). I used both Phrygian and Dorian modes, which, according to Plato, were most appropriate for soldiers. Throughout the piece, I used different instruments, mostly percussion, to represent the heartbeat of the runner. In the legend, the runner dies - in the piece, the heartbeat becomes very fast and then rather erratic. It then slows and, finally, stops. Though I find the story of Pheidippides inspiring, I wish all marathon runners and athletes of every kind (myself included) a safer and happier outcome!
ContributorsOsteen-Petreshock, Kimberly (Composer) / Hackbarth, Glenn (Thesis advisor) / Rockmaker, Jody (Committee member) / Levy, Benjamin (Committee member) / Norton, Kay (Committee member) / Arizona State University (Publisher)
Created2010
Description
Despite a quickly growing repertoire list for the brass quintet, the music of the early Argentine tango has remained relatively neglected by brass quintet arrangers and performers. With the goal of bringing a neglected art form to the brass quintet repertoire, three arrangements based on early twentieth century Argentine tango songs are presented here: "Elegante Papirusa" by Tito Roccatagliata, "A La Gran Muñeca" by Jesús Ventura, and "La Cotorrita" by Samuel Castriota. The arrangements follow the style of three early recordings produced by The Victor Talking Machine in 1920 and 1922, as performed by two authentic Argentine orquesta típicas: Orquesta Típica Select and Orquesta Típica Fresedo. A brief history of the style and instrumental evolution of tango music from its influences and origins up until 1920 is discussed, followed by a detailed account of the musicians and circumstances involved in the three early recordings. An explanation of the issues encountered by the author in adapting the early tango style to the brass quintet setting is discussed, along with the solutions realized in order to make the project successful and practical for a moderately advanced brass quintet. The full brass quintet scores are provided as part of the Appendix.
ContributorsCamacho, Gustavo (Musician) (Author) / Ericson, John Q (Thesis advisor) / Pilafian, Samuel (Committee member) / Schuring, Martin (Committee member) / Campbell, Andrew (Committee member) / Rockmaker, Jody (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
Description
A systematic approach to composition has been used by a variety of composers to control an assortment of musical elements in their pieces. This paper begins with a brief survey of some of the important systematic approaches that composers have employed in their compositions, devoting particular attention to Pierre Boulez's Structures Ia . The purpose of this survey is to examine several systematic approaches to composition by prominent composers and their philosophy in adopting this type of approach. The next section of the paper introduces my own systematic approach to composition: the Take-Away System. The third provides several musical applications of the system, citing my work, Octulus for two pianos, as an example. The appendix details theorems and observations within the system for further study.
ContributorsHarbin, Doug (Author) / Hackbarth, Glenn (Thesis advisor) / DeMars, James (Committee member) / Etezady, Roshanne, 1973- (Committee member) / Rockmaker, Jody (Committee member) / Rogers, Rodney (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
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 composition was commissioned by the Orgelpark to be performed in Amsterdam in September 2011 during Gaudeamus Muziekweek. It will be performed by the vocal group VocaalLab Nederland. It is scored for four vocalists, organ, tanpura, and electronic sound. The work is a culmination of my studies in South Indian Carnatic rhythm, North Indian classical singing, and American minimalism. It is a meditation on the idea that the drone and pulse are micro/macro aspects of the same phenomenon of vibration. Cycles are created on the macroscale through a mathematically defined scale of harmonic/pitch relationships. Cycles are created on the microscale through the subdivision and addition of rhythmic pulses.
ContributorsAdler, Jacob (Composer) / Rockmaker, Jody (Thesis advisor) / Feisst, Sabine (Committee member) / Etezady, Roshanne, 1973- (Committee member) / Arizona State University (Publisher)
Created2011
Description
ABSTRACT études; written for violin ensemble, which include violin duets, trios, and quartets, are less numerous than solo études.; These works rarely go by the title "étude;," and have not been the focus of much scholarly research. Ensemble études; have much to offer students, teachers and composers, however, because they add an extra dimension to the learning, teaching, and composing processes. This document establishes the value of ensemble études; in pedagogy and explores applications of the repertoire currently available. Rather than focus on violin duets, the most common form of ensemble étude;, it mainly considers works for three and four violins without accompaniment. Concentrating on the pedagogical possibilities of studying études; in a group, this document introduces creative ways that works for violin ensemble can be used as both études; and performance pieces. The first two chapters explore the history and philosophy of the violin étude; and multiple-violin works, the practice of arranging of solo études; for multiple instruments, and the benefits of group learning and cooperative learning that distinguish ensemble étude; study from solo étude; study. The third chapter is an annotated survey of works for three and four violins without accompaniment, and serves as a pedagogical guide to some of the available repertoire. Representing a wide variety of styles, techniques and levels, it illuminates an historical association between violin ensemble works and pedagogy. The fourth chapter presents an original composition by the author, titled Variations on a Scottish Folk Song: étude; for Four Violins, with an explanation of the process and techniques used to create this ensemble étude.; This work is an example of the musical and technical integration essential to étude; study, and demonstrates various compositional traits that promote cooperative learning. Ensemble études; are valuable pedagogical tools that deserve wider exposure. It is my hope that the information and ideas about ensemble études; in this paper and the individual descriptions of the works presented will increase interest in and application of violin trios and quartets at the university level.
ContributorsLundell, Eva Rachel (Contributor) / Swartz, Jonathan (Thesis advisor) / Rockmaker, Jody (Committee member) / Buck, Nancy (Committee member) / Koonce, Frank (Committee member) / Norton, Kay (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
A major goal of synthetic biology is to recapitulate emergent properties of life. Despite a significant body of work, a longstanding question that remains to be answered is how such a complex system arose? In this dissertation, synthetic nucleic acid molecules with alternative sugar-phosphate backbones were investigated as potential ancestors of DNA and RNA. Threose nucleic acid (TNA) is capable of forming stable helical structures with complementary strands of itself and RNA. This provides a plausible mechanism for genetic information transfer between TNA and RNA. Therefore TNA has been proposed as a potential RNA progenitor. Using molecular evolution, functional sequences were isolated from a pool of random TNA molecules. This implicates a possible chemical framework capable of crosstalk between TNA and RNA. Further, this shows that heredity and evolution are not limited to the natural genetic system based on ribofuranosyl nucleic acids. Another alternative genetic system, glycerol nucleic acid (GNA) undergoes intrasystem pairing with superior thermalstability compared to that of DNA. Inspired by this property, I demonstrated a minimal nanostructure composed of both left- and right-handed mirro image GNA. This work suggested that GNA could be useful as promising orthogonal material in structural DNA nanotechnology.
ContributorsZhang, Su (Author) / Chaut, John C (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Yan, Hao (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
The following project is an audition preparation handbook for double bass players. The materials and techniques included are designed for use by advanced collegiate bass players seeking work as freelance or contracted musicians. Subjects ranging from finding an opening, becoming mentally and physically prepared, and developing the skills and experience necessary to be successful will be examined. The most frequently requested audition excerpts are included in this document, carefully extracted from the original orchestra parts and notated with efficient fingerings. Elements of style and performance are discussed. Each of the excerpts is recorded on the enclosed CD, performed by the author as examples to the readers. It is the hope of the author that the study and use of this text will better prepare the readers for entrance into the working world of the music industry. Ideas, processes, and materials that are often neglected in a degree program are examined with the hope that students will be better prepared to audition for, and win orchestral positions.
ContributorsRose, Christopher S. (Author) / Rotaru, Catalin (Thesis advisor) / Landschoot, Thomas (Committee member) / Rockmaker, Jody (Committee member) / Russell, Timothy (Committee member) / Arizona State University (Publisher)
Created2011
Description
This research paper creates a modern score transcription of selected choral works by composer Alexander Chesnokov. The life and works of Alexander Chesnokov are almost completely unknown in the United States. A collection of his works is housed in the New York Public Library (NYPL). Selected transcripts from this collection provide insight into the works and style of Alexander Chesnokov. They may also serve as a study guide and point for further research and explorations into the life and compositions of this Russian composer. The sets of transcriptions within this paper were created from a microfilm copy from the NYPL's archival holdings. This study comprises transcriptions of selected scores, a discussion of errors and editorial choices, text translations, and a brief history of choral performance and style during pre-revolutionary Russia, the time period during which this composer lived and wrote.
ContributorsSmolnik, Carric (Author) / Gentry, Gregory (Thesis advisor) / Reber, William (Committee member) / Rockmaker, Jody (Committee member) / Campbell, Andrew (Committee member) / Saucier, Catherine (Committee member) / Arizona State University (Publisher)
Created2011
Description
Spinal muscular atrophy (SMA) is a neurodegenerative disease that results in the loss of lower body muscle function. SMA is the second leading genetic cause of death in infants and arises from the loss of the Survival of Motor Neuron (SMN) protein. SMN is produced by two genes, smn1 and smn2, that are identical with the exception of a C to T conversion in exon 7 of the smn2 gene. SMA patients lacking the smn1 gene, rely on smn2 for production of SMN. Due to an alternative splicing event, smn2 primarily encodes a non-functional SMN lacking exon 7 (SMN D7) as well as a low amount of functional full-length SMN (SMN WT). SMN WT is ubiquitously expressed in all cell types, and it remains unclear how low levels of SMN WT in motor neurons lead to motor neuron degradation and SMA. SMN and its associated proteins, Gemin2-8 and Unrip, make up a large dynamic complex that functions to assemble ribonucleoproteins. The aim of this project was to characterize the interactions of the core SMN-Gemin2 complex, and to identify differences between SMN WT and SMN D7. SMN and Gemin2 proteins were expressed, purified and characterized via size exclusion chromatography. A stable N-terminal deleted Gemin2 protein (N45-G2) was characterized. The SMN WT expression system was optimized resulting in a 10-fold increase of protein expression. Lastly, the oligomeric states of SMN and SMN bound to Gemin2 were determined. SMN WT formed a mixture of oligomeric states, while SMN D7 did not. Both SMN WT and D7 bound to Gemin2 with a one-to-one ratio forming a heterodimer and several higher-order oligomeric states. The SMN WT-Gemin2 complex favored high molecular weight oligomers whereas the SMN D7-Gemin2 complex formed low molecular weight oligomers. These results indicate that the SMA mutant protein, SMN D7, was still able to associate with Gemin2, but was not able to form higher-order oligomeric complexes. The observed multiple oligomerization states of SMN and SMN bound to Gemin2 may play a crucial role in regulating one or several functions of the SMN protein. The inability of SMN D7 to form higher-order oligomers may inhibit or alter those functions leading to the SMA disease phenotype.
ContributorsNiday, Tracy (Author) / Allen, James P. (Thesis advisor) / Wachter, Rebekka (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2012
Description
Throughout the history of Western art music, political and religious institutions have exerted powerful influence through their patronage and censorship. This is especially relevant to the organ, an elaborate and expensive instrument which has always depended on institutional support. The fascinating story of Polish organ culture, which has existed since the Middle Ages, reflects the dramatic changes in Polish politics throughout the centuries. An understanding of this country's history helps to construct a comprehensive view of how politics influenced the developments in organ building and organ playing. This paper describes the dynamics of the Church, government and art institutions in Poland during the years 1945-2012. A brief summary of the history of Polish organ culture sets the stage for the changes occurring after WWII. The constant struggle between the Church and the communist regime affected music making and organ culture in Poland from 1945-1989. The political détente that occurred after 1989 led to a flowering of new instruments, restorations and performance opportunities for organists. By exploring the relationship between Polish organ culture and prevailing agendas in the 20th century, the author demonstrates how a centuries-old tradition adapted to survive political and economic hardships.
ContributorsKubiaczyk-Adler, Ilona (Author) / Marshall, Kimberly (Thesis advisor) / Micklich, Albie (Committee member) / Rockmaker, Jody (Committee member) / Rogers, Rodney (Committee member) / Ryan, Russell (Committee member) / Arizona State University (Publisher)
Created2012
Description
The organ is in a continued state of evolution, tonally and mechanically, designed by the builder to meet certain expectations related to the musical aesthetics of the time. Organ building in the United States has been influenced by both European organ building traditions and American innovations. During the early twentieth century, Ernest M. Skinner emerged as one of the greatest organ builders in America. Throughout his life, Skinner's quest was to create an "ideal organ," capable of playing a variety of music. Skinner's vision was rooted in the Romantic Movement and influenced by the dynamic gradations and rich, colorful sonorities of orchestral and operatic music of the era. A number of technological developments were applied to the design of the organ which made the romantic organ possible. The prominent European organ builders of the nineteenth century created organs that defined the romantic-style instrument in their respective countries. By the end of the century, American organ builders were creating their own versions. Skinner traveled to Europe to learn what he could from the foreign builders. Skinner built organs that synthesized European and American elements, along with his own innovations, as continuation of nineteenth-century trends that brought the romantic-symphonic organ to its fullest realization. Additionally, Skinner developed many new organ timbres, including a number of stops that imitate various orchestral instruments. The result of Skinner's creative work is the the American symphonic organ. This paper attempts to illustrate how the tonal designs of organs built by Walcker, Cavaillé-Coll, and Willis influenced the work of Skinner and the American symphonic organ. The work of each builder is discussed with descriptions of their designs. The designs and innovations of Skinner are examined as related to these European builders. A number of organ specifications are provided to supplement the information presented here. Today, American symphonic organs, particularly those built by Skinner, are revered for their warmth and charm and are inspiring the work of present day organ builders who are incorporating elements of this style into their own designs.
ContributorsGerber, James Theodore (Author) / Marshall, Kimberly (Thesis advisor) / Pagano, Caio (Committee member) / Ryan, Russell (Committee member) / Rogers, Rodney (Committee member) / Rockmaker, Jody (Committee member) / Arizona State University (Publisher)
Created2012
Description
Acquisition of fluorescence via autocatalytic processes is unique to few proteins in the natural world. Fluorescent proteins (FPs) have been integral to live-cell imaging techniques for decades; however, mechanistic information is still emerging fifty years after the discovery of the original green fluorescent protein (GFP). Modification of the fluorescence properties of the proteins derived from GFP allows increased complexity of experiments and consequently, information content of the data acquired. The importance of arginine-96 in GFP has been widely discussed. It has been established as vital to the kinetics of chromophore maturation and to the overall fold of GFP before post-translational self-modification. Its value during chromophore maturation has been demonstrated by mutational studies and a hypothesis proposed for its catalytic function. A strategy is described herein to determine its pKa value via NMR to determine whether Arg96 possesses the chemical capacity to function as a general base during GFP chromophore biosynthesis. Förster resonance energy transfer (FRET) techniques commonly employ Enhanced Cyan Fluorescent Proteins (ECFPs) and their derivatives as donor fluorophores useful in real-time, live-cell imaging. These proteins have a tryptophan-derived chromophore that emits light in the blue region of the visible spectrum. Most ECFPs suffer from fluorescence instability, which, coupled with their low quantum yield, makes data analysis unreliable. The structural heterogeneity of these proteins also results in undesirable photophysical characteristics. Recently, mCerulean3, a ten amino acid mutant of ECFP, was introduced as an optimized FRET-donor protein (1). The amino acids changed include a mobile residue, Asp148, which has been mutated to a glycine in the new construct, and Thr65 near the chromophore has been mutated to a serine, the wild-type residue at this location. I have solved the x-ray crystal structure of mCerulean3 at low pH and find that the pH-dependent isomerization has been eliminated. The chromophore is in the trans-conformation previously observed in Cerulean at pH 8. The mutations that increase the quantum yield and improve fluorescence brightness result in a stable, bright donor fluorophore well-suited for use in quantitative microscopic imaging.
ContributorsWatkins, Jennifer L (Author) / Wachter, Rebekka M. (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Allen, James P. (Committee member) / Arizona State University (Publisher)
Created2012
Description
The craft of improvisation at the organ has survived a long period of dormancy and is experiencing a strong resurgence in the twenty-first century. This project seeks to establish a precedence for the value of notated music as a resource in learning improvisation, and then, through music analysis, provide examples of how that process can develop. The result of the ideas presented here is a pathway whereby any disciplined organist can learn to imitate composed music, assimilate the musical ideas, and innovate through the act of spontaneous improvisation.
ContributorsHoward, Devon (Author) / Marshall, Kimberly (Thesis advisor) / Ryan, Russell (Committee member) / Kocour, Michael (Committee member) / Norton, Kay (Committee member) / Rockmaker, Jody (Committee member) / Arizona State University (Publisher)
Created2012
Description
Hydrogenases, the enzymes that reversibly convert protons and electrons to hydrogen, are used in all three domains of life. [NiFe]-hydrogenases are considered best suited for biotechnological applications because of their reversible inactivation with oxygen. Phylogenetically, there are four groups of [NiFe]-hydrogenases. The best characterized group, "uptake" hydrogenases, are membrane-bound and catalyze hydrogen oxidation in vivo. In contrast, the group 3 [NiFe]-hydrogenases are heteromultimeric, bifunctional enzymes that fulfill various cellular roles. In this dissertation, protein film electrochemistry (PFE) is used to characterize the catalytic properties of two group 3 [NiFe]-hydrogenases: HoxEFUYH from Synechocystsis sp. PCC 6803 and SHI from Pyrococcus furiosus. First, HoxEFUYH is shown to be biased towards hydrogen production. Upon exposure to oxygen, HoxEFUYH inactivates to two states, both of which can be reactivated on the timescale of seconds. Second, we show that PfSHI is the first example of an oxygen tolerant [NiFe]-hydrogenase that produces two inactive states upon exposure to oxygen. Both inactive states are analogous to those characterized for HoxEFUYH, but oxygen exposed PfSHI produces a greater fraction that reactivates at high potentials, enabling hydrogen oxidation in the presence of oxygen. Third, it is shown that removing the NAD(P)-reducing subunits from PfSHI leads to a decrease in bias towards hydrogen oxidation and renders the enzyme oxygen sensitive. Both traits are likely due to impaired intramolecular electron transfer. Mechanistic hypotheseses for these functional differences are considered.
ContributorsMcIntosh, Chelsea Lee (Author) / Jones, Anne K (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Buttry, Daniel (Committee member) / Arizona State University (Publisher)
Created2012
Description
This thesis discusses the use of mass spectrometry and polymerase chain reaction (PCR), among other methods, to detect biomarkers of microorganisms in the environment. These methods can be used to detect bacteria involved in the degradation of environmental pollutants (bioremediation) or various single-celled pathogens, including those posing potential threats as bioterrorism agents. The first chapter introduces the hurdles in detecting in diverse environmental compartments in which they could be found, a select list of single-celled pathogens representing known or potential bioterrorism agents. These hurdles take the form of substances that interfere either directly or indirectly with the detection method. In the case of mass spectrometry-based detection, many of these substances (interferences) can be removed via effective sample pretreatment. Chapters 2 through 4 highlight specific methods developed to detect bioremediation or bioterrorism agents in environmental matrices. These methods are qualitative mass spectrometry, quantitative PCR, and quantitative mass spectrometry, respectively. The targeted organisms in these methods include several bioremediation agents, e.g. Pseudomonas putida F1 and Sphingomonas wittichii RW1, and bioterrorism agents, e.g. norovirus and Cryptosporidium parvum. In Chapter 2, I identify using qualitative mass spectrometry, biomarkers for three bacterial species involved in bioremediation. In Chapter 3, I report on a new quantitative PCR method suitable for monitoring of a key gene in yet another bioremediation agent, Sphingomonas wittichii RW1; furthermore, I apply this method to track the efficacy of bioremediation in bioaugmented environmental microcosms. In Chapter 4, I report on the development of new quantitative mass spectrometry methods for two organisms, S. wittichii RW1 and Cryptosporidium parvum, and evaluate two previously published methods for their applicability to the analysis of complex environmental samples. In Chapter 5, I review state-of-the-art methods for the detection of emerging biological contaminants, specifically viruses, in environmental samples. While this summary deals exclusively with viral pathogens, the advantages and remaining challenges identified are also applicable to all single-celled organisms in environmental settings. The suggestions I make at the end of this chapter are expected to be valid not only for future needs for emerging viruses but also for bacteria, eukaryotic pathogens, and prions. In general, it is advisable to continue the trend towards quantification and to standardize methods to facilitate comparison of results between studies.
ContributorsHartmann, Erica Marie (Author) / Halden, Rolf U. (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Nelson, Randall W. (Committee member) / Arizona State University (Publisher)
Created2012
ContributorsCampbell, Andrew (Pianist) (Performer) / Mancuso, Simone (Performer) / Fusi, Marco (Performer) / Spring, Robert (Performer) / Buck, Nancy (Performer) / Kuo, Sunny (Performer) / Standley, Eileen (Performer) / Rex, Melissa S. (Performer) / Cosand, Walter, 1950- (Performer) / McAllister, Timothy (Performer) / Mastrian, Stacey (Performer) / Lilly, Stephen (Performer) / Rockmaker, Jody (Speaker) / Levy, Ben (Speaker) / ASU Library. Music Library (Publisher)
Created2012-04-17
Description
De Oriendo is a project devoted to a better understanding of the word "original" as it pertains to musical composition. It began as a way for me to try to tackle a twofold fascination that has been with me for the duration of my time at ASU, though I have not always been aware of it. The first half of this fascination is an enduring interest in tracing borrowed material used by composers and other artists throughout history. It seems that almost every research project I have undertaken in the last four years has had something to do with this concept. Scholars like Winton Dean, J. Peter Burkholder, and Sigmund Spaeth have spent parts of their careers charting out the genealogy of historical compositions, uncovering reused melodies and harmonic progressions in the process; the cases of it are countless, even among the most identifiable composers and songwriters. Since there is scholarship clearly demonstrating secondhand ideas in music, it becomes problematic to assume that the word "original" simply describes something completely new, that is, something that does not use material heard or seen before. The second half is more of a personal ambition: I thought that if I truly knew what composers and critics meant when they labeled a piece or an artist as original, then I could somehow find a way to achieve this distinction in my own attempts at composition and avoid that uninteresting, derivative sound I have always feared.
ContributorsLang, Jonathan (Author) / Levy, Benjamin (Thesis director) / Mook, Richard (Committee member) / Rockmaker, Jody (Committee member) / Barrett, The Honors College (Contributor) / Herberger Institute for Design and the Arts (Contributor)
Created2012-12
Description
Cyanovirin-N (CV-N) is a naturally occurring lectin originally isolated from the cyanobacteria Nostoc ellipsosporum. This 11 kDa lectin is 101 amino acids long with two binding sites, one at each end of the protein. CV-N specifically binds to terminal Manα1-2Manα motifs on the branched, high mannose Man9 and Man8 glycosylations found on enveloped viruses including Ebola, Influenza, and HIV. wt-CVN has micromolar binding to soluble Manα1-2Manα and also inhibits HIV entry at low nanomolar concentrations. CV-N's high affinity and specificity for Manα1-2Manα makes it an excellent lectin to study for its glycan-specific properties. The long-term aim of this project is to make a variety of mutant CV-Ns to specifically bind other glycan targets. Such a set of lectins may be used as screening reagents to identify biomarkers and other glycan motifs of interest. As proof of concept, a T7 phage display library was constructed using P51G-m4-CVN genes mutated at positions 41, 44, 52, 53, 56, 74, and 76 in binding Domain B. Five CV-N mutants were selected from the library and expressed in BL21(DE3) E. coli. Two of the mutants, SSDGLQQ-P51Gm4-CVN and AAGRLSK-P51Gm4-CVN, were sufficiently stable for characterization and were examined by CD, Tm, ELISA, and glycan array. Both proteins have CD minima at approximately 213 nm, indicating largely β-sheet structure, and have Tm values greater than 40°C. ELISA against gp120 and RNase B demonstrate both proteins' ability to bind high mannose glycans. To more specifically determine the binding specificity of each protein, AAGRLSK-P51Gm4-CVN, SSDGLQQ-P51Gm4-CVN, wt-CVN, and P51G-m4-CVN were sent to the Consortium for Functional Glycomics (CFG) for glycan array analysis. AAGRLSK-P51Gm4-CVN, wt-CVN, and P51G-m4-CVN, have identical specificities for high mannose glycans containing terminal Manα1-2Manα. SSDGLQQ-P51Gm4-CVN binds to terminal GlcNAcα1-4Gal motifs and a subgroup of high mannose glycans bound by P51G-m4-CVN. SSDGLQQ-wt-CVN was produced to restore anti-HIV activity and has a high nanomolar EC50 value compared to wt-CVN's low nanomolar activity. Overall, these experiments show that CV-N Domain B can be mutated and retain specificity identical to wt-CVN or acquire new glycan specificities. This first generation information can be used to produce glycan-specific lectins for a variety of applications.
ContributorsRuben, Melissa (Author) / Ghirlanda, Giovanna (Thesis advisor) / Allen, James (Committee member) / Wachter, Rebekka (Committee member) / Arizona State University (Publisher)
Created2013
Description
Bright Summer, a one-movement piece for orchestra, was composed in Arizona, and completed in February 2013. The piece is approximately twelve minutes long. The motivation for writing this piece was the death of my mother the year before, in 2012. The prevailing mood of this work is bright and pleasant, expressing my mother's cheerful personality when she was alive. It also portrays bright summer days which resemble my mother's spirit. Thus, soundscape plays an important role in this work. It depicts summer breeze, rustling sounds of leaves, and, to translate a Korean saying, "high blue skies." This soundscape opens the piece as well as closes it. In the middle section, the fast upbeat themes represent my mother's witty and optimistic personality. The piece also contains the presence of a hymn tune, The Love of God is Greater Far, which informs the motivic content and also functions as the climax of the piece. It was my mother's favorite hymn and we used to sing it together following her conversion to Christianity. The piece contains three main sections, which are held together by transitional material based on the soundscape and metric modulations. Unlike my earlier works, Bright Summer is tonal, with upper tertian harmonies prevailing throughout the piece. However, the opening and closing soundscapes do not have functional harmonies. For example, tertian chords appear and vanish silently, leaving behind some resonant sounds without any harmonic progression. Overall, the whole piece is reminiscent of my mother who lived a beautiful life.
ContributorsKim, JeeYeon (Composer) / DeMars, James (Thesis advisor) / Hackbarth, Glenn (Committee member) / Rogers, Rodney (Committee member) / Levy, Benjamin (Committee member) / Rockmaker, Jody (Committee member) / Arizona State University (Publisher)
Created2013
Description
Norwegian composer Ola Gjeilo (b. 1978) is highly regarded as an accomplished and prolific composer of choral music. His creative output includes works for chorus, solo piano, and wind symphony. His unique style infuses elements of cinematic music, jazz and improvisation, with particularly intriguing selections of text. This study examines the factors that influence Gjeilo's compositional techniques, and the musical interpretations of conductor Charles Bruffy in his preparation for The Phoenix Chorale's recording Northern Lights: Choral Works by Ola Gjeilo. The eleven works discussed in this study are: The Ground, Evening Prayer, Ubi caritas, Prelude, Northern Lights, The Spheres, Tota pulchra es, Serenity, Phoenix (Agnus Dei), Unicornis captivatur, and Dark Night of the Soul. As a relatively new and young composer, there is very little published literature on Gjeilo and his works. This study provides an intimate glance into the creative process of the composer. By composing in multiple styles and with a variety of inspirational sources, Gjeilo creates a fresh approach toward composition of new choral music. His style is revealed through interviews and numerous collaborations with conductors and performers who have prepared and performed his music, as well through an examination of the eleven works recorded by The Phoenix Chorale.
ContributorsGarrison, Ryan Derrick (Author) / Reber, William (Thesis advisor) / Saucier, Catherine (Committee member) / Rockmaker, Jody (Committee member) / Doan, Jerry (Committee member) / Arizona State University (Publisher)
Created2013
Description
This thesis presents a new arrangement of Richard Peaslee's trombone solo "Arrows of Time" for brass band. This arrangement adapts Peaslee's orchestration - and subsequent arrangement by Dr. Joshua Hauser for wind ensemble - for the modern brass band instrumentation and includes a full score. A brief biography of Richard Peaslee and his work accompanies this new arrangement, along with commentary on the orchestration of "Arrows of Time", and discussion of the evolution and adaptation of the work for wind ensemble by Dr. Hauser. The methodology used to adapt these versions for the brass band completes the background information.
ContributorsMalloy, Jason Patrick (Author) / Ericson, John (Thesis advisor) / Oldani, Robert (Committee member) / Rockmaker, Jody (Committee member) / Arizona State University (Publisher)
Created2013
Description
The German pianist and composer Johannes Brahms (1883-1897) wrote more than 122 works for a wide variety of ensembles and genres. Despite this remarkable productivity, and his widely heralded talent for innovation and technique as a composer, few of his works have been arranged for solo guitar, and these have focused primarily on his simpler, more melodic works. Conventional wisdom is that his music is "too dense" to be played on the guitar. As a result, there are no arrangements of orchestral works by Brahms in the standard repertoire for the guitar. In arranging Brahms's Serenade in D Major, movt. 1 for the guitar, I provide a counter argument that not all of Brahms's orchestral music is too dense all of the time. In Part I, I provide a brief overview of the history of, and sources for, the Serenade. Part II describes a step-by-step guide through the process of arranging orchestral repertoire for the solo guitar. Part III is an examination of the editing process that utilizes examples from the guitar arrangement of the Serenade in order to illustrate the various techniques and considerations that are part of the editing process. Part IV is a performance edition of the arrangement. In summary, the present arrangement of Brahms's Serenade, op.11 is the beginning of a conversation about why the "guitar world" should be incorporating the music of Brahms into the standard repertoire. The lessons learned, and the technical challenges discovered, should help inform future arrangers and guitar performers for additional compositions by Brahms.
ContributorsLanier, William Hudson (Author) / Koonce, Frank (Thesis advisor) / Micklich, Albie (Committee member) / Rockmaker, Jody (Committee member) / Arizona State University (Publisher)
Created2013
Interactions driving the collapse of islet amyloid polypeptide: implications for amyloid aggregation
Description
Human islet amyloid polypeptide (hIAPP), also known as amylin, is a 37-residue intrinsically disordered hormone involved in glucose regulation and gastric emptying. The aggregation of hIAPP into amyloid fibrils is believed to play a causal role in type 2 diabetes. To date, not much is known about the monomeric state of hIAPP or how it undergoes an irreversible transformation from disordered peptide to insoluble aggregate. IAPP contains a highly conserved disulfide bond that restricts hIAPP(1-8) into a short ring-like structure: N_loop. Removal or chemical reduction of N_loop not only prevents cell response upon binding to the CGRP receptor, but also alters the mass per length distribution of hIAPP fibers and the kinetics of fibril formation. The mechanism by which N_loop affects hIAPP aggregation is not yet understood, but is important for rationalizing kinetics and developing potential inhibitors. By measuring end-to-end contact formation rates, Vaiana et al. showed that N_loop induces collapsed states in IAPP monomers, implying attractive interactions between N_loop and other regions of the disordered polypeptide chain . We show that in addition to being involved in intra-protein interactions, the N_loop is involved in inter-protein interactions, which lead to the formation of extremely long and stable β-turn fibers. These non-amyloid fibers are present in the 10 μM concentration range, under the same solution conditions in which hIAPP forms amyloid fibers. We discuss the effect of peptide cyclization on both intra- and inter-protein interactions, and its possible implications for aggregation. Our findings indicate a potential role of N_loop-N_loop interactions in hIAPP aggregation, which has not previously been explored. Though our findings suggest that N_loop plays an important role in the pathway of amyloid formation, other naturally occurring IAPP variants that contain this structural feature are incapable of forming amyloids. For example, hIAPP readily forms amyloid fibrils in vitro, whereas the rat variant (rIAPP), differing by six amino acids, does not. In addition to being highly soluble, rIAPP is an effective inhibitor of hIAPP fibril formation . Both of these properties have been attributed to rIAPP's three proline residues: A25P, S28P and S29P. Single proline mutants of hIAPP have also been shown to kinetically inhibit hIAPP fibril formation. Because of their intrinsic dihedral angle preferences, prolines are expected to affect conformational ensembles of intrinsically disordered proteins. The specific effect of proline substitutions on IAPP structure and dynamics has not yet been explored, as the detection of such properties is experimentally challenging due to the low molecular weight, fast reconfiguration times, and very low solubility of IAPP peptides. High-resolution techniques able to measure tertiary contact formations are needed to address this issue. We employ a nanosecond laser spectroscopy technique to measure end-to-end contact formation rates in IAPP mutants. We explore the proline substitutions in IAPP and quantify their effects in terms of intrinsic chain stiffness. We find that the three proline mutations found in rIAPP increase chain stiffness. Interestingly, we also find that residue R18 plays an important role in rIAPP's unique chain stiffness and, together with the proline residues, is a determinant for its non-amyloidogenic properties. We discuss the implications of our findings on the role of prolines in IDPs.
ContributorsCope, Stephanie M (Author) / Vaiana, Sara M (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Ros, Robert (Committee member) / Lindsay, Stuart M (Committee member) / Ozkan, Sefika B (Committee member) / Arizona State University (Publisher)
Created2013
Description
Nelson Rolihlahla Mandela was born July 18, 1918 into the Madiba clan in Mvezo, Transkei, South Africa. Mandela was a lawyer by trade and a freedom fighter who envisioned freedom and equality for all South Africans regardless of race. In 1965, Mandela was imprisoned at Robben Island for twenty-seven years for treason and terrorist activities against the South African apartheid regime: he was assigned prison numbers 46664. In 1992, Mandela was released from prison and two years later not only became the first democratically elected president of South Africa, but also its first black president. "Madiba 46664" is an eight-minute chamber work scored for flute, oboe, clarinet in B-flat, and bassoon; vibraphone, and two percussionists; piano; violins, violas, and celli. The work blends traditional South African rhythms of the drumming culture with elements of Western harmony and form in contrasting textures of homophony, polyphony and antiphony. "Madiba 46664" utilizes Mandela's prison number, birthdate and age (at the time the composition process began in 2013) for the initial generation of meter, rhythm, harmony, melody, and form. The work also shares intercultural concepts that can be seen in the works of three contemporary African composers, South Africans Jeanne Zaidel-Rudolph and Andile Khumalo, and Nigerian Ayo Oluranti. Each section represents a period of Mandela's life as a freedom fighter, a prisoner, and a president. The inspiration stems from the composer's discussions with Mandela soon after his release from prison and prior to his presidency. These lively discussions pertained to the state of traditional music in then apartheid South Africa and led to this creation. The conversations also played a role in the creative process.
ContributorsMabingnai, Collette Sipho (Composer) / DeMars, James (Thesis advisor) / Hackbarth, Glenn (Committee member) / Humphreys, Jere (Committee member) / Rockmaker, Jody (Committee member) / Rogers, Rodney (Committee member) / Arizona State University (Publisher)
Created2014
Description
This thesis explores a wide array of topics related to the protein folding problem, ranging from the folding mechanism, ab initio structure prediction and protein design, to the mechanism of protein functional evolution, using multi-scale approaches. To investigate the role of native topology on folding mechanism, the native topology is dissected into non-local and local contacts. The number of non-local contacts and non-local contact orders are both negatively correlated with folding rates, suggesting that the non-local contacts dominate the barrier-crossing process. However, local contact orders show positive correlation with folding rates, indicating the role of a diffusive search in the denatured basin. Additionally, the folding rate distribution of E. coli and Yeast proteomes are predicted from native topology. The distribution is fitted well by a diffusion-drift population model and also directly compared with experimentally measured half life. The results indicate that proteome folding kinetics is limited by protein half life. The crucial role of local contacts in protein folding is further explored by the simulations of WW domains using Zipping and Assembly Method. The correct formation of N-terminal β-turn turns out important for the folding of WW domains. A classification model based on contact probabilities of five critical local contacts is constructed to predict the foldability of WW domains with 81% accuracy. By introducing mutations to stabilize those critical local contacts, a new protein design approach is developed to re-design the unfoldable WW domains and make them foldable. After folding, proteins exhibit inherent conformational dynamics to be functional. Using molecular dynamics simulations in conjunction with Perturbation Response Scanning, it is demonstrated that the divergence of functions can occur through the modification of conformational dynamics within existing fold for β-lactmases and GFP-like proteins: i) the modern TEM-1 lactamase shows a comparatively rigid active-site region, likely reflecting adaptation for efficient degradation of a specific substrate, while the resurrected ancient lactamases indicate enhanced active-site flexibility, which likely allows for the binding and subsequent degradation of different antibiotic molecules; ii) the chromophore and attached peptides of photocoversion-competent GFP-like protein exhibits higher flexibility than the photocoversion-incompetent one, consistent with the evolution of photocoversion capacity.
ContributorsZou, Taisong (Author) / Ozkan, Sefika B (Thesis advisor) / Thorpe, Michael F (Committee member) / Woodbury, Neal W (Committee member) / Vaiana, Sara M (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2014
Description
Telomerase is a unique reverse transcriptase that has evolved specifically to extend the single stranded DNA at the 3' ends of chromosomes. To achieve this, telomerase uses a small section of its integral RNA subunit (TR) to reiteratively copy a short, canonically 6-nt, sequence repeatedly in a processive manner using a complex and currently poorly understood mechanism of template translocation to stop nucleotide addition, regenerate its template, and then synthesize a new repeat. In this study, several novel interactions between the telomerase protein and RNA components along with the DNA substrate are identified and characterized which come together to allow active telomerase repeat addition. First, this study shows that the sequence of the RNA/DNA duplex holds a unique, single nucleotide signal which pauses DNA synthesis at the end of the canonical template sequence. Further characterization of this sequence dependent pause signal reveals that the template sequence alone can produce telomerase products with the characteristic 6-nt pattern, but also works cooperatively with another RNA structural element for proper template boundary definition. Finally, mutational analysis is used on several regions of the protein and RNA components of telomerase to identify crucial determinates of telomerase assembly and processive repeat synthesis. Together, these results shed new light on how telomerase coordinates its complex catalytic cycle.
ContributorsBrown, Andrew F (Author) / Chen, Julian J. L. (Thesis advisor) / Jones, Anne (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2014