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- Genre: Doctoral Dissertation
Description
The ribosome is a ribozyme and central to the biosynthesis of proteins in all organisms. It has a strong bias against non-alpha-L-amino acids, such as alpha-D-amino acids and beta-amino acids. Additionally, the ribosome is only able to incorporate one amino acid in response to one codon. It has been demonstrated that reengineering of the peptidyltransferase center (PTC) of the ribosome enabled the incorporation of both alpha-D-amino acids and beta-amino acids into full length protein. Described in Chapter 2 are five modified ribosomes having modifications in the peptidyltrasnferase center in the 23S rRNA. These modified ribosomes successfully incorporated five different beta-amino acids (2.1 - 2.5) into E. coli dihydrofolate reductase (DHFR). The second project (Chapter 3) focused on the study of the modified ribosomes facilitating the incorporation of the dipeptide glycylphenylalanine (3.25) and fluorescent dipeptidomimetic 3.26 into DHFR. These ribosomes also had modifications in the peptidyltransferase center in the 23S rRNA of the 50S ribosomal subunit. The modified DHFRs having beta-amino acids 2.3 and 2.5, dipeptide glycylphenylalanine (3.25) and dipeptidomimetic 3.26 were successfully characterized by the MALDI-MS analysis of the peptide fragments produced by "in-gel" trypsin digestion of the modified proteins. The fluorescent spectra of the dipeptidomimetic 3.26 and modified DHFR having fluorescent dipeptidomimetic 3.26 were also measured. The type I and II DNA topoisomerases have been firmly established as effective molecular targets for many antitumor drugs. A "classical" topoisomerase I or II poison acts by misaligning the free hydroxyl group of the sugar moiety of DNA and preventing the reverse transesterfication reaction to religate DNA. There have been only two classes of compounds, saintopin and topopyrones, reported as dual topoisomerase I and II poisons. Chapter 4 describes the synthesis and biological evaluation of topopyrones. Compound 4.10, employed at 20 µM, was as efficient as 0.5 uM camptothecin, a potent topoisomerase I poison, in stabilizing the covalent binary complex (~30%). When compared with a known topoisomerase II poison, etoposide (at 0.5 uM), topopyorone 4.10 produced similar levels of stabilized DNA-enzyme binary complex (~34%) at 5 uM concentration.
ContributorsMaini, Rumit (Author) / Hecht, Sidney M. (Thesis advisor) / Gould, Ian (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2013
Description
Photosynthesis, one of the most important processes in nature, has provided an energy basis for nearly all life on Earth, as well as the fossil fuels we use today to power modern society. This research aims to mimic the photosynthetic process of converting incident solar energy into chemical potential energy in the form of a fuel via systems capable of carrying out photo-induced electron transfer to drive the production of hydrogen from water. Herein is detailed progress in using photo-induced stepwise electron transfer to drive the oxidation of water and reduction of protons to hydrogen. In the design, use of more blue absorbing porphyrin dyes to generate high-potential intermediates for oxidizing water and more red absorbing phthalocyanine dyes for forming the low potential charge needed for the production of hydrogen have been utilized. For investigating water oxidation at the photoanode, high potential porphyrins such as, bis-pyridyl porphyrins and pentafluorophenyl porphyrins have been synthesized and experiments have aimed at the co-immobilization of this dye with an IrO2-nH2O catalyst on TiO2. To drive the cathodic reaction of the water splitting photoelectrochemical cell, utilization of silicon octabutoxy-phthalocyanines have been explored, as they offer good absorption in the red to near infrared, coupled with low potential photo-excited states. Axially and peripherally substituted phthalocyanines bearing carboxylic anchoring groups for the immobilization on semiconductors such as TiO2 has been investigated. Ultimately, this work should culminate in a photoelectrochemical cell capable of splitting water to oxygen and hydrogen with the only energy input from light. A series of perylene dyes bearing multiple semi-conducting metal oxide anchoring groups have been synthesized and studied. Results have shown interfacial electron transfer between these perylenes and TiO2 nanoparticles encapsulated within reverse micelles and naked nanoparticles. The binding process was followed by monitoring the hypsochromic shift of the dye absorption spectra over time. Photoinduced electron transfer from the singlet excited state of the perylenes to the TiO2 conduction band is indicated by emission quenching of the TiO2-bound form of the dyes and confirmed by transient absorption measurements of the radical cation of the dyes and free carriers (injected electrons) in the TiO2.
ContributorsBergkamp, Jesse J (Author) / Moore, Ana L (Thesis advisor) / Mariño-Ochoa, Ernesto (Thesis advisor) / Gust, Devens J (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2013
Description
Developing a system capable of using solar energy to drive the conversion of an abundant and available precursor to fuel would profoundly impact humanity's energy use and thereby the condition of the global ecosystem. Such is the goal of artificial photosynthesis: to convert water to hydrogen using solar radiation as the sole energy input and ideally do so with the use of low cost, abundant materials. Constructing photoelectrochemical cells incorporating photoanodes structurally reminiscent of those used in dye sensitized photovoltaic solar cells presents one approach to establishing an artificial photosynthetic system. The work presented herein describes the production, integration, and study of water oxidation catalysts, molecular dyes, and metal oxide based photoelectrodes carried out in the pursuit of developing solar water splitting systems.
ContributorsSherman, Benjamin D (Author) / Moore, Thomas (Thesis advisor) / Moore, Ana (Committee member) / Buttry, Daniel (Committee member) / Arizona State University (Publisher)
Created2013
Description
The biological and chemical diversity of protein structure and function can be greatly expanded by position-specific incorporation of non-natural amino acids bearing a variety of functional groups. Non-cognate amino acids can be incorporated into proteins at specific sites by using orthogonal aminoacyl-tRNA synthetase/tRNA pairs in conjunction with nonsense, rare, or 4-bp codons. There has been considerable progress in developing new types of amino acids, in identifying novel methods of tRNA aminoacylation, and in expanding the genetic code to direct their position. Chemical aminoacylation of tRNAs is accomplished by acylation and ligation of a dinucleotide (pdCpA) to the 3'-terminus of truncated tRNA. This strategy allows the incorporation of a wide range of natural and unnatural amino acids into pre-determined sites, thereby facilitating the study of structure-function relationships in proteins and allowing the investigation of their biological, biochemical and biophysical properties. Described in Chapter 1 is the current methodology for synthesizing aminoacylated suppressor tRNAs. Aminoacylated suppressor tRNACUAs are typically prepared by linking pre-aminoacylated dinucleotides (aminoacyl-pdCpAs) to 74 nucleotide (nt) truncated tRNAs (tRNA-COH) via a T4 RNA ligase mediated reaction. Alternatively, there is another route outlined in Chapter 1 that utilizes a different pre-aminoacylated dinucleotide, AppA. This dinucleotide has been shown to be a suitable substrate for T4 RNA ligase mediated coupling with abbreviated tRNA-COHs for production of 76 nt aminoacyl-tRNACUAs. The synthesized suppressor tRNAs have been shown to participate in protein synthesis in vitro, in an S30 (E. coli) coupled transcription-translation system in which there is a UAG codon in the mRNA at the position corresponding to Val10. Chapter 2 describes the synthesis of two non-proteinogenic amino acids, L-thiothreonine and L-allo-thiothreonine, and their incorporation into predetermined positions of a catalytically competent dihydrofolate reductase (DHFR) analogue lacking cysteine. Here, the elaborated proteins were site-specifically derivitized with a fluorophore at the thiothreonine residue. The synthesis and incorporation of phosphorotyrosine derivatives into DHFR is illustrated in Chapter 3. Three different phosphorylated tyrosine derivatives were prepared: bis-nitrobenzylphosphoro-L-tyrosine, nitrobenzylphosphoro-L-tyrosine, and phosphoro-L-tyrosine. Their ability to participate in a protein synthesis system was also evaluated.
ContributorsNangreave, Ryan Christopher (Author) / Hecht, Sidney M. (Thesis advisor) / Yan, Hao (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2013
Description
The thesis studies new methods to fabricate optoelectronic Ge1-ySny/Si(100) alloys and investigate their photoluminescence (PL) properties for possible applications in Si-based photonics including IR lasers. The work initially investigated the origin of the difference between the PL spectrum of bulk Ge, dominated by indirect gap emission, and the PL spectrum of Ge-on-Si films, dominated by direct gap emission. It was found that the difference is due to the supression of self-absorption effects in Ge films, combined with a deviation from quasi-equilibrium conditions in the conduction band of undoped films. The latter is confirmed by a model suggesting that the deviation is caused by the shorter recombination lifetime in the films relative to bulk Ge. The knowledge acquired from this work was then utilized to study the PL properties of n-type Ge1-ySny/Si (y=0.004-0.04) samples grown via chemical vapor deposition of Ge2H6/SnD4/P(GeH3)3. It was found that the emission intensity (I) of these samples is at least 10x stronger than observed in un-doped counterparts and that the Idir/Iind ratio of direct over indirect gap emission increases for high-Sn contents due to the reduced gamma-L valley separation, as expected. Next the PL investigation was expanded to samples with y=0.05-0.09 grown via a new method using the more reactive Ge3H8 in place of Ge2H6. Optical quality, 1-um thick Ge1-ySny/Si(100) layers were produced using Ge3H10/SnD4 and found to exhibit strong, tunable PL near the threshold of the direct-indirect bandgap crossover. A byproduct of this study was the development of an enhanced process to produce Ge3H8, Ge4H10, and Ge5H12 analogs for application in ultra-low temperature deposition of Group-IV semiconductors. The thesis also studies synthesis routes of an entirely new class of semiconductor compounds and alloys described by Si5-2y(III-V)y (III=Al, V= As, P) comprising of specifically designed diamond-like structures based on a Si parent lattice incorporating isolated III-V units. The common theme of the two thesis topics is the development of new mono-crystalline materials on ubiquitous silicon platforms with the objective of enhancing the optoelectronic performance of Si and Ge semiconductors, potentially leading to the design of next generation optical devices including lasers, detectors and solar cells.
ContributorsGrzybowski, Gordon (Author) / Kouvetakis, John (Thesis advisor) / Chizmeshya, Andrew (Committee member) / Menéndez, Jose (Committee member) / Arizona State University (Publisher)
Created2013
Description
This study sought to analyze the messages being conveyed through the discourse utilized in presenting the public face of The Arizona Early Childhood Development and Health Board, popularly known as First Things First (FTF) and to reveal how the different discourses and ideologies within FTF have been in the past and currently are "contending and struggling for dominance (Wodak, 2007)." FTF is located within the policy realm of Early Childhood Education and Care (ECEC). The people and the system have been very influential in guiding the course and policies set forth in Arizona since the citizen initiative, Proposition 203, passed in 2006, which allowed for the creation of the Early Childhood Development and Health Board. Lakoff's techniques for analyzing frames of discourse were utilized in conjunction with critical discourse analysis in order to tease out frames of reference, shifts in both discourse and frames, specific modes of messaging, and consistencies and inconsistencies within the public face presented by FTF.
ContributorsMiller, Lisa (Author) / Swadener, Elizabeth B (Thesis advisor) / Nakagawa, Kathy (Committee member) / Romero, Mary (Committee member) / Arizona State University (Publisher)
Created2013
Description
As digital media practices become readily available in today's classrooms, literacy and literacy instruction are changing in profound ways (Alvermann, 2010). Professional organizations emphasize the importance of integrating new literacies (New London Group, 1996) practices into language-arts instruction (IRA, 2009; NCTE, 2005). As a result, teachers search for effective ways to incorporate the new literacies in an effort to engage students. Therefore, this study was designed to investigate the potential of digital storytelling as participatory media for writing instruction. This case study was conducted during the fall semester of 2012 in one first-grade classroom and one second-grade classroom in the Southwestern United States. The study addressed ten interrelated research questions relating to how primary-grade students performed in relation to the Common Core writing standards, how they were motivated, how they formed a meta- language to talk about their writing, how they developed identities as writers, and how they were influenced by their teachers' philosophies and instructional approaches. Twenty-two first-grade students and 24 second-grade students used the MovieMaker software to create digital stories of personal narratives. Data included field notes, interviews with teachers and students, teacher journals, my own journal, artifacts of teachers' lesson plans, photographs, students' writing samples, and their digital stories. Qualitative data were analyzed by thematic analysis (Patton, 1990) and discourse analysis (Gee, 2011). Writing samples were scored by rubrics based on the Common Core State Standards. The study demonstrated how digital storytelling can be used to; (a) guide teachers in implementing new literacies in primary grades; (b) illustrate digital storytelling as writing; (c) develop students' meta-language to talk about writing; (d) impact students' perceptions as writers; (e) meet Common Core State Standards for writing; (f) improve students' skills as writers; (g) build students' identities as writers; (h) impact academic writing; (i) engage students in the writing process; and (j) illustrate the differences in writing competencies between first- and second-grade students. The study provides suggestions for teachers interested in incorporating digital storytelling in primary-grade classrooms.
ContributorsFoley, Leslie M (Author) / Guzzetti, Barbara J. (Thesis advisor) / Hayes, Elisabeth R. (Committee member) / Gee, James P (Committee member) / Arizona State University (Publisher)
Created2013
Description
The purpose of this study was to investigate critical literacy practices in two prehistoric exhibits in a natural history museum. Bourdieu's habitus and Bakhtin's dialogism served as theoretical frames to collect and analyze data. Data were collected and triangulated using field notes, interview transcriptions, archives, and other data sources to critically scrutinize textual meaning and participant responses. Spradley's (1979) domain analysis was used to sort and categorize data in the early stage. Glaser and Strauss's (1967) constant comparative method was used to code data. My major findings were that museum texts within this context represent embedded beliefs and values that were interwoven with curators` habitus, tastes and capital, as well as institutional policies. The texts in the two Hohokam exhibits endorse a certain viewpoint of learning. Teachers and the public were not aware of the communicative role that the museum played in the society. In addition, museum literacy/ies were still practiced in a fundamental way as current practices in the classroom, which may not support the development of critical literacy. In conclusion, the very goal for critical museum literacy is to help students and teachers develop intellectual strategies to read the word and the world in informal learning environments.
ContributorsLiang, Sheau-yann (Author) / Mccarty, Teresa (Thesis advisor) / Marsh, Josephine (Committee member) / Blumenfeld-Jones, Donald (Committee member) / Welsh, Peter (Committee member) / Arizona State University (Publisher)
Created2013
Description
Chemistry as a subject is difficult to learn and understand, due in part to the specific language used by practitioners in their professional and scientific communications. The language and ways of representing chemical interactions have been grouped into three modes of representation used by chemistry instructors, and ultimately by students in understanding the discipline. The first of these three modes of representation is the symbolic mode, which uses a standard set of rules for chemical nomenclature set out by the IUPAC. The second mode of representation is that of microscopic, which depicts chemical compounds as discrete units made up of atoms and molecules, with a particular ratio of atoms to a molecule or formula unit. The third mode of representation is macroscopic, what can be seen, experienced, or measured directly, like ice melting or a color change during a chemical reaction. Recent evidence suggests that chemistry instructors can assist their students in making the connections between the modes of representation by incorporating all three modes into their teaching and discussions, and overtly connecting the modes during instruction. In this research, chemistry teachers at the community college level were observed over the course of an entire semester, to evaluate their instructional use of mode of representation. The students of these teachers were tested prior to and after a semester's worth of instruction, and changes in the basic chemistry conceptual knowledge of these students were compared. Additionally, a subset of the overall population that was pre- and post-tested was interviewed at length using demonstrations of chemical phenomenon that students were asked to translate using all three modes of representation. Analysis of the instruction of three community college teachers shows there were significant differences among these teachers in their instructional use of mode of representation. Additionally, the students of these three teachers had differential and statistically significant achievement over the course of the semester. This research supports results of other similar studies, as well as providing some unexpected results from the students involved.
ContributorsWood, Lorelei (Author) / Baker, Dale (Thesis advisor) / Ganesh, Tirupalavanam G. (Committee member) / Colleen, Megowan (Committee member) / Sujatha, Krishnaswamy (Committee member) / Arizona State University (Publisher)
Created2013
Description
Researchers have postulated that math academic achievement increases student success in college (Lee, 2012; Silverman & Seidman, 2011; Vigdor, 2013), yet 80% of universities and 98% of community colleges require many of their first-year students to be placed in remedial courses (Bettinger & Long, 2009). Many high school graduates are entering college ill prepared for the rigors of higher education, lacking understanding of basic and important principles (ACT, 2012). The desire to increase academic achievement is a wide held aspiration in education and the idea of adapting instruction to individuals is one approach to accomplish this goal (Lalley & Gentile, 2009a). Frequently, adaptive learning environments rely on a mastery learning approach, it is thought that when students are afforded the opportunity to master the material, deeper and more meaningful learning is likely to occur. Researchers generally agree that the learning environment, the teaching approach, and the students' attributes are all important to understanding the conditions that promote academic achievement (Bandura, 1977; Bloom, 1968; Guskey, 2010; Cassen, Feinstein & Graham, 2008; Changeiywo, Wambugu & Wachanga, 2011; Lee, 2012; Schunk, 1991; Van Dinther, Dochy & Segers, 2011). The present study investigated the role of college students' affective attributes and skills, such as academic competence and academic resilience, in an adaptive mastery-based learning environment on their academic performance, while enrolled in a remedial mathematics course. The results showed that the combined influence of students' affective attributes and academic resilience had a statistically significant effect on students' academic performance. Further, the mastery-based learning environment also had a significant effect on their academic competence and academic performance.
ContributorsFoshee, Cecile Mary (Author) / Atkinson, Robert K (Thesis advisor) / Elliott, Stephen N. (Committee member) / Horan, John (Committee member) / Arizona State University (Publisher)
Created2013