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- Member of: Theses and Dissertations
Description
The entire history of HIV-1 is hidden in its ten thousand bases, where information regarding its evolutionary traversal through the human population can only be unlocked with fine-scale sequence analysis. Measurable footprints of mutation and recombination have imparted upon us a wealth of knowledge, from multiple chimpanzee-to-human transmissions to patterns of neutralizing antibody and drug resistance. Extracting maximum understanding from such diverse data can only be accomplished by analyzing the viral population from many angles. This body of work explores two primary aspects of HIV sequence evolution, point mutation and recombination, through cross-sectional (inter-individual) and longitudinal (intra-individual) investigations, respectively. Cross-sectional Analysis: The role of Haiti in the subtype B pandemic has been hotly debated for years; while there have been many studies, up to this point, no one has incorporated the well-known mechanism of retroviral recombination into their biological model. Prior to the use of recombination detection, multiple analyses produced trees where subtype B appears to have first entered Haiti, followed by a jump into the rest of the world. The results presented here contest the Haiti-first theory of the pandemic and instead suggest simultaneous entries of subtype B into Haiti and the rest of the world. Longitudinal Analysis: Potential N-linked glycosylation sites (PNGS) are the most evolutionarily dynamic component of one of the most evolutionarily dynamic proteins known to date. While the number of mutations associated with the increase or decrease of PNGS frequency over time is high, there are a set of relatively stable sites that persist within and between longitudinally sampled individuals. Here, I identify the most conserved stable PNGSs and suggest their potential roles in host-virus interplay. In addition, I have identified, for the first time, what may be a gp-120-based environmental preference for N-linked glycosylation sites.
ContributorsHepp, Crystal Marie, 1981- (Author) / Rosenberg, Michael S. (Thesis advisor) / Hedrick, Philip (Committee member) / Escalante, Ananias (Committee member) / Kumar, Sudhir (Committee member) / Arizona State University (Publisher)
Created2013
Description
Four Souvenirs for Violin and Piano was composed by Paul Schoenfeld (b.1947) in 1990 as a showpiece, spotlighting the virtuosity of both the violin and piano in equal measure. Each movement is a modern interpretation of a folk or popular genre, re- envisioned over intricate jazz harmonies and rhythms. The work was commissioned by violinist Lev Polyakin, who specifically requested some short pieces that could be performed in a local jazz establishment named Night Town in Cleveland, Ohio. The result is a work that is approximately fifteen minutes in length. Schoenfeld is a respected composer in the contemporary classical music community, whose Café Music (1986) for piano trio has recently become a staple of the standard chamber music repertoire. Many of his other works, however, remain in relative obscurity. It is the focus of this document to shed light on at least one other notable composition; Four Souvenirs for Violin and Piano. Among the topics to be discussed regarding this piece are a brief history behind the genesis of this composition, a structural summary of the entire work and each of its movements, and an appended practice guide based on interview and coaching sessions with the composer himself. With this project, I hope to provide a better understanding and appreciation of this work.
ContributorsJanczyk, Kristie Annette (Author) / Ryan, Russell (Thesis advisor) / Campbell, Andrew (Committee member) / Norton, Kay (Committee member) / Arizona State University (Publisher)
Created2015
Description
Recent technology advancements in photovoltaics have enabled crystalline silicon (c-Si) solar cells to establish outstanding photoconversion efficiency records. Remarkable progresses in research and development have been made both on the silicon feedstock quality as well as the technology required for surface passivation, the two dominant sources of performance loss via recombination of photo-generated charge carriers within advanced solar cell architectures.
As these two aspects of the solar cell framework improve, the need for a thorough analysis of their respective contribution under varying operation conditions has emerged along with challenges related to the lack of sensitivity of available characterization techniques. The main objective of my thesis work has been to establish a deep understanding of both “intrinsic” and “extrinsic” recombination processes that govern performance in high-quality silicon absorbers. By studying each recombination mechanism as a function of illumination and temperature, I strive to identify the lifetime limiting defects and propose a path to engineer the ultimate silicon solar cell.
This dissertation presents a detailed description of the experimental procedure required to deconvolute surface recombination contributions from bulk recombination contributions when performing lifetime spectroscopy analysis. This work proves that temperature- and injection-dependent lifetime spectroscopy (TIDLS) sensitivity can be extended to impurities concentrations down to 109 cm-3, orders of magnitude below any other characterization technique available today. A new method for the analysis of TIDLS data denominated Defect Parameters Contour Mapping (DPCM) is presented with the aim of providing a visual and intuitive tool to identify the lifetime limiting impurities in silicon material. Surface recombination velocity results are modelled by applying appropriate approaches from literature to our experimentally evaluated data, demonstrating for the first time their capability to interpret temperature-dependent data. In this way, several new results are obtained which solve long disputed aspects of surface passivation mechanisms. Finally, we experimentally evaluate the temperature-dependence of Auger lifetime and its impact on a theoretical intrinsically limited solar cell. These results decisively point to the need for a new Auger lifetime parameterization accounting for its temperature-dependence, which would in turn help understand the ultimate theoretical efficiency limit for a solar cell under real operation conditions.
As these two aspects of the solar cell framework improve, the need for a thorough analysis of their respective contribution under varying operation conditions has emerged along with challenges related to the lack of sensitivity of available characterization techniques. The main objective of my thesis work has been to establish a deep understanding of both “intrinsic” and “extrinsic” recombination processes that govern performance in high-quality silicon absorbers. By studying each recombination mechanism as a function of illumination and temperature, I strive to identify the lifetime limiting defects and propose a path to engineer the ultimate silicon solar cell.
This dissertation presents a detailed description of the experimental procedure required to deconvolute surface recombination contributions from bulk recombination contributions when performing lifetime spectroscopy analysis. This work proves that temperature- and injection-dependent lifetime spectroscopy (TIDLS) sensitivity can be extended to impurities concentrations down to 109 cm-3, orders of magnitude below any other characterization technique available today. A new method for the analysis of TIDLS data denominated Defect Parameters Contour Mapping (DPCM) is presented with the aim of providing a visual and intuitive tool to identify the lifetime limiting impurities in silicon material. Surface recombination velocity results are modelled by applying appropriate approaches from literature to our experimentally evaluated data, demonstrating for the first time their capability to interpret temperature-dependent data. In this way, several new results are obtained which solve long disputed aspects of surface passivation mechanisms. Finally, we experimentally evaluate the temperature-dependence of Auger lifetime and its impact on a theoretical intrinsically limited solar cell. These results decisively point to the need for a new Auger lifetime parameterization accounting for its temperature-dependence, which would in turn help understand the ultimate theoretical efficiency limit for a solar cell under real operation conditions.
ContributorsBernardini, Simone (Author) / Bertoni, Mariana I (Thesis advisor) / Coletti, Gianluca (Committee member) / Bowden, Stuart (Committee member) / Alford, Terry (Committee member) / Arizona State University (Publisher)
Created2018
Description
The ability to edit chromosomal regions is an important tool for the study of gene function and the ability to engineer synthetic gene networks. CRISPR-Cas systems, a bacterial RNA-guided immune system against foreign nucleic acids, have recently been engineered for a plethora of genome engineering and transcriptional regulation applications. Here we employ engineered variants of CRISPR systems in proof-of-principle experiments demonstrating the ability of CRISPR-Cas derived single-DNA-strand cutting enzymes (nickases) to direct host-cell genomic recombination. E.coli is generally regarded as a poorly recombinogenic host with double-stranded DNA breaks being highly lethal. However, CRISPR-guided nickase systems can be easily programmed to make very precise, non-lethal, incisions in genomic regions directing both single reporter gene and larger-scale recombination events deleting up to 36 genes. Genome integrated repetitive elements of variable sizes can be employed as sites for CRISPR induced recombination. We project that single-stranded based editing methodologies can be employed alongside preexisting genome engineering techniques to assist and expedite metabolic engineering and minimalized genome research.
ContributorsStandage-Beier, Kylie S (Author) / Wang, Xiao (Thesis director) / Haynes, Karmella (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-05
Description
Samuel Máynez Prince (1886-1966), was a prolific and important Mexican musician. Prince’s musical style followed the trends of the nineteenth-century salon music genre. His compositions include lullabies, songs, dances, marches, mazurkas, waltzes, and revolutionary anthems. Prince’s social status and performances in the famed Café Colón in Mexico City increased his popularity among high-ranking political figures during the time of the Mexican Revolution as well as his status in the Mexican music scene.
Unfortunately there is virtually no existing scholarship on Prince and even basic information regarding his life and works is not readily available. The lack of organization of the manuscript scores and the absence of dates of his works has further pushed the composer into obscurity. An investigation therefore was necessary in order to explore the neglected aspects of the life and works of Prince as a violinist and composer. This document is the result of such an investigation by including extensive new biographical information, as well as the first musical analysis and edition of the complete recovered works for violin and piano.
In order to fill the gaps present in the limited biographical information regarding Prince’s life, investigative research was conducted in Mexico City. Information was drawn from archives of the composer’s grandchildren, the Palacio de Bellas Artes, the Conservatorio Nacional de Música de México, and the Orquesta Sinfónica Nacional. The surviving relatives provided first-hand details on events in the composer’s life; one also offered the researcher access to their personal archive including, important life documents, photographs, programs from concert performances, and manuscript scores of the compositions. Establishing connections with the relatives also led the researcher to examining the violins owned and used by the late violinist/composer.
This oral history approach led to new and updated information, including the revival of previously unpublished music for violin and piano. These works are here compiled in an edition that will give students, teachers, and music-lovers access to this unknown repertoire. Finally, this research seeks to promote the beauty and nuances of Mexican salon music, and the complete works for violin and piano of Samuel Máynez Prince in particular.
Unfortunately there is virtually no existing scholarship on Prince and even basic information regarding his life and works is not readily available. The lack of organization of the manuscript scores and the absence of dates of his works has further pushed the composer into obscurity. An investigation therefore was necessary in order to explore the neglected aspects of the life and works of Prince as a violinist and composer. This document is the result of such an investigation by including extensive new biographical information, as well as the first musical analysis and edition of the complete recovered works for violin and piano.
In order to fill the gaps present in the limited biographical information regarding Prince’s life, investigative research was conducted in Mexico City. Information was drawn from archives of the composer’s grandchildren, the Palacio de Bellas Artes, the Conservatorio Nacional de Música de México, and the Orquesta Sinfónica Nacional. The surviving relatives provided first-hand details on events in the composer’s life; one also offered the researcher access to their personal archive including, important life documents, photographs, programs from concert performances, and manuscript scores of the compositions. Establishing connections with the relatives also led the researcher to examining the violins owned and used by the late violinist/composer.
This oral history approach led to new and updated information, including the revival of previously unpublished music for violin and piano. These works are here compiled in an edition that will give students, teachers, and music-lovers access to this unknown repertoire. Finally, this research seeks to promote the beauty and nuances of Mexican salon music, and the complete works for violin and piano of Samuel Máynez Prince in particular.
ContributorsEkenes, Spencer Arvin (Author) / McLin, Katherine (Thesis advisor) / Feisst, Sabine (Committee member) / Jiang, Danwen (Committee member) / Arizona State University (Publisher)
Created2016
Description
Previous recombination rate estimation studies in rhesus macaques have been mostly restricted to a singular approach (e.g., using microsatellite loci). Here, we employ a bilateral method in estimating recombination rates—pedigree-based and linkage-disequilibrium-based—from whole-genome data of rhesus macaques to estimate CO and NCO recombination events and to compare contemporary and historical rates of recombination.
ContributorsWeiss, Sarah (Author) / Pfeifer, Susanne (Thesis director) / Versoza, Cyril (Committee member) / Barrett, The Honors College (Contributor) / School of Art (Contributor) / School of Life Sciences (Contributor)
Created2023-05
ContributorsWeiss, Sarah (Author) / Pfeifer, Susanne (Thesis director) / Versoza, Cyril (Committee member) / Barrett, The Honors College (Contributor) / School of Art (Contributor) / School of Life Sciences (Contributor)
Created2023-05
ContributorsWeiss, Sarah (Author) / Pfeifer, Susanne (Thesis director) / Versoza, Cyril (Committee member) / Barrett, The Honors College (Contributor) / School of Art (Contributor) / School of Life Sciences (Contributor)
Created2023-05
ContributorsWeiss, Sarah (Author) / Pfeifer, Susanne (Thesis director) / Versoza, Cyril (Committee member) / Barrett, The Honors College (Contributor) / School of Art (Contributor) / School of Life Sciences (Contributor)
Created2023-05