Theses and Dissertations
This collection includes both ASU Theses and Dissertations, submitted by graduate students, and the Barrett, Honors College theses submitted by undergraduate students.
Displaying 1 - 10 of 135
Description
The principle of Darwinian evolution has been applied in the laboratory to nucleic acid molecules since 1990, and led to the emergence of in vitro evolution technique. The methodology of in vitro evolution surveys a large number of different molecules simultaneously for a pre-defined chemical property, and enrich for molecules with the particular property. DNA and RNA sequences with versatile functions have been identified by in vitro selection experiments, but many basic questions remain to be answered about how these molecules achieve their functions. This dissertation first focuses on addressing a fundamental question regarding the molecular recognition properties of in vitro selected DNA sequences, namely whether negatively charged DNA sequences can be evolved to bind alkaline proteins with high specificity. We showed that DNA binders could be made, through carefully designed stringent in vitro selection, to discriminate different alkaline proteins. The focus of this dissertation is then shifted to in vitro evolution of an artificial genetic polymer called threose nucleic acid (TNA). TNA has been considered a potential RNA progenitor during early evolution of life on Earth. However, further experimental evidence to support TNA as a primordial genetic material is lacking. In this dissertation we demonstrated the capacity of TNA to form stable tertiary structure with specific ligand binding property, which suggests a possible role of TNA as a pre-RNA genetic polymer. Additionally, we discussed the challenges in in vitro evolution for TNA enzymes and developed the necessary methodology for future TNA enzyme evolution.
ContributorsYu, Hanyang (Author) / Chaput, John C (Thesis advisor) / Chen, Julian (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2013
Description
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
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
Solution conformations and dynamics of proteins and protein-DNA complexes are often difficult to predict from their crystal structures. The crystal structure only shows a snapshot of the different conformations these biological molecules can have in solution. Multiple different conformations can exist in solution and potentially have more importance in the biological activity. DNA sliding clamps are a family of proteins with known crystal structures. These clamps encircle the DNA and enable other proteins to interact more efficiently with the DNA. Eukaryotic PCNA and prokaryotic β clamp are two of these clamps, some of the most stable homo-oligomers known. However, their solution stability and conformational equilibrium have not been investigated in depth before. Presented here are the studies involving two sliding clamps: yeast PCNA and bacterial β clamp. These studies show that the β clamp has a very different solution stability than PCNA. These conclusions were reached through various different fluorescence-based experiments, including fluorescence correlation spectroscopy (FCS), Förster resonance energy transfer (FRET), single molecule fluorescence, and various time resolved fluorescence techniques. Interpretations of these, and all other, fluorescence-based experiments are often affected by the properties of the fluorophores employed. Often the fluorescence properties of these fluorophores are influenced by their microenvironments. Fluorophores are known to sometimes interact with biological molecules, and this can have pronounced effects on the rotational mobility and photophysical properties of the dye. Misunderstanding the effect of these photophysical and rotational properties can lead to a misinterpretation of the obtained data. In this thesis, photophysical behaviors of various organic dyes were studied in the presence of deoxymononucleotides to examine more closely how interactions between fluorophores and DNA bases can affect fluorescent properties. Furthermore, the properties of cyanine dyes when bound to DNA and the effect of restricted rotation on FRET are presented in this thesis. This thesis involves studying fluorophore photophysics in various microenvironments and then expanding into the solution stability and dynamics of the DNA sliding clamps.
ContributorsRanjit, Suman (Author) / Levitus, Marcia (Thesis advisor) / Lindsay, Stuart (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2013
Description
This dissertation explores the role of smart home service provisions (SHSP) as motivational agents supporting goal attainment and human flourishing. Evoking human flourishing as a lens for interaction encapsulates issues of wellbeing, adaptation and problem solving within the context of social interaction. To investigate this line of research a new, motivation-sensitive approach to design was implemented. This approach combined psychometric analysis from motivational psychology's Personal Project Analysis (PPA) and Place Attachment theory's Sense of Place (SoP) analysis to produce project-centered motivational models for environmental congruence. Regression analysis of surveys collected from 150 (n = 150) young adults about their homes revealed PPA motivational dimensions had significant main affects on all three SoP factors. Model one indicated PPA dimensions Fearful and Value Congruency predicted the SoP factor Place Attachment (p = 0.012). Model two indicated the PPA factor Positive Affect and PPA dimensions Value Congruency, Self Identity and Autonomy predicted Place Identity (p = .0003). Model three indicated PPA dimensions Difficulty and Likelihood of Success predicted the SoP factor Place Dependency. The relationships between motivational PPA dimensions and SoP demonstrated in these models informed creation of a set of motivational design heuristics. These heuristics guided 20 participants (n = 20) through co-design of paper prototypes of SHSPs supporting goal attainment and human flourishing. Normative analysis of these paper prototypes fashioned a design framework consisting of the use cases "make with me", "keep me on task" and "improve myself"; the four design principles "time and timing", "guidance and accountability", "project ambiguity" and "positivity mechanisms"; and the seven interaction models "structuring time", "prompt user", "gather resources", "consume content", "create content", "restrict and/or restore access to content" and "share content". This design framework described and evaluated three technology probes installed in the homes of three participants (n = 3) for field-testing over the course of one week. A priori and post priori samples of psychometric measures were inconclusive in determining if SHSP motivated goal attainment or increased environmental congruency between young adults and their homes.
ContributorsBrotman, Ryan Scott (Author) / Burleson, Winsow (Thesis advisor) / Heywood, William (Committee member) / Forlizzi, Jodi (Committee member) / Arizona State University (Publisher)
Created2013
Description
There is a lack of music therapy services for college students who have problems with depression and/or anxiety. Even among universities and colleges that offer music therapy degrees, there are no known programs offering music therapy to the institution's students. Female college students are particularly vulnerable to depression and anxiety symptoms compared to their male counterparts. Many students who experience mental health problems do not receive treatment, because of lack of knowledge, lack of services, or refusal of treatment. Music therapy is proposed as a reliable and valid complement or even an alternative to traditional counseling and pharmacotherapy because of the appeal of music to young women and the potential for a music therapy group to help isolated students form supportive networks. The present study recruited 14 female university students to participate in a randomized controlled trial of short-term group music therapy to address symptoms of depression and anxiety. The students were randomly divided into either the treatment group or the control group. Over 4 weeks, each group completed surveys related to depression and anxiety. Results indicate that the treatment group's depression and anxiety scores gradually decreased over the span of the treatment protocol. The control group showed either maintenance or slight worsening of depression and anxiety scores. Although none of the results were statistically significant, the general trend indicates that group music therapy was beneficial for the students. A qualitative analysis was also conducted for the treatment group. Common themes were financial concerns, relationship problems, loneliness, and time management/academic stress. All participants indicated that they benefited from the sessions. The group progressed in its cohesion and the participants bonded to the extent that they formed a supportive network which lasted beyond the end of the protocol. The results of this study are by no means conclusive, but do indicate that colleges with music therapy degree programs should consider adding music therapy services for their general student bodies.
ContributorsAshton, Barbara (Author) / Crowe, Barbara J. (Thesis advisor) / Rio, Robin (Committee member) / Davis, Mary (Committee member) / Arizona State University (Publisher)
Created2013
Description
Single molecule DNA Sequencing technology has been a hot research topic in the recent decades because it holds the promise to sequence a human genome in a fast and affordable way, which will eventually make personalized medicine possible. Single molecule differentiation and DNA translocation control are the two main challenges in all single molecule DNA sequencing methods. In this thesis, I will first introduce DNA sequencing technology development and its application, and then explain the performance and limitation of prior art in detail. Following that, I will show a single molecule DNA base differentiation result obtained in recognition tunneling experiments. Furthermore, I will explain the assembly of a nanofluidic platform for single strand DNA translocation, which holds the promised to be integrated into a single molecule DNA sequencing instrument for DNA translocation control. Taken together, my dissertation research demonstrated the potential of using recognition tunneling techniques to serve as a general readout system for single molecule DNA sequencing application.
ContributorsLiu, Hao (Author) / Lindsay, Stuart M (Committee member) / Yan, Hao (Committee member) / Levitus, Marcia (Committee member) / Arizona State University (Publisher)
Created2013
Description
Research has shown that the ability to smell is the most direct sense an individual can experience. With every breath a person takes, the brain recognizes thousands of molecules and makes connections with our memories to determine their composition. With the amount of research looking into how and why we smell, researchers still have little understanding of how the nose and brain process an aroma, and how emotional and physical behavior is impacted. This research focused on the affects smell has on a caregiver in a simulated Emergency Department setting located in the SimET of Banner Good Samaritan Medical Center in Phoenix, Arizona. The study asked each participant to care for a programmed mannequin, or "patient", while performing simple computer-based tasks, including memory and recall, multi-tasking, and mood-mapping to gauge physical and mental performance. Three different aromatic environments were then introduced through diffusion and indirect inhalation near the participants' task space: 1) a control (no smell), 2) an odor (simulated dirty feet), and 3) an aroma (one of four true essential oils plus a current odor-eliminating compound used in many U.S. Emergency Departments). This study was meant to produce a stressful environment by leading the caregiver to stay in constant movement throughout the study through timed tasks, uncooperative equipment, and a needy "patient". The goal of this research was to determine if smells, and of what form of pleasantness and repulsiveness, can have an effect on the physical and mental performance of emergency caregivers. Findings from this study indicated that the "odor eliminating" method currently used in typical Emergency Departments, coffee grounds, is more problematic than helpful, and the introduction of true essential oils may not only reduce stress, but increase efficiency and, in turn, job satisfaction.
ContributorsClark, Carina M (Author) / Bernardi, Jose (Thesis advisor) / Heywood, William (Committee member) / Watts, Richard (Committee member) / Rosso, Rachel (Committee member) / Arizona State University (Publisher)
Created2013
Description
The F1Fo ATP synthase is required for energy conversion in almost all living organisms. The F1 complex is a molecular motor that uses ATP hydrolysis to drive rotation of the γ–subunit. It has not been previously possible to resolve the speed and position of the γ–subunit of the F1–ATPase as it rotates during a power stroke. The single molecule experiments presented here measured light scattered from 45X91 nm gold nanorods attached to the γ–subunit that provide an unprecedented 5 μs resolution of rotational position as a function of time. The product of velocity and drag, which were both measured directly, resulted in an average torque of 63±8 pN nm for the Escherichia coli F1-ATPase that was determined to be independent of the load. The rotational velocity had an initial (I) acceleration phase 15° from the end of the catalytic dwell, a slow (S) acceleration phase during ATP binding/ADP release (15°–60°), and a fast (F) acceleration phase (60°–90°) containing an interim deceleration (ID) phase (75°–82°). High ADP concentrations decreased the velocity of the S phase proportional to 'ADP-release' dwells, and the F phase proportional to the free energy derived from the [ADP][Pi]/[ATP] chemical equilibrium. The decreased affinity for ITP increased ITP-binding dwells by 10%, but decreased velocity by 40% during the S phase. This is the first direct evidence that nucleotide binding contributes to F1–ATPase torque. Mutations that affect specific phases of rotation were identified, some in regions of F1 previously considered not to contribute to rotation. Mutations βD372V and γK9I increased the F phase velocity, and γK9I increased the depth of the ID phase. The conversion between S and F phases was specifically affected by γQ269L. While βT273D, βD305E, and αR283Q decreased the velocity of all phases, decreases in velocity due to βD302T, γR268L and γT82A were confined to the I and S phases. The correlations between the structural locations of these mutations and the phases of rotation they affect provide new insight into the molecular basis for F1–ATPase γ-subunit rotation.
ContributorsMartin, James (Author) / Frasch, Wayne D (Thesis advisor) / Chandler, Douglas (Committee member) / Gaxiola, Roberto (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2012
Description
A growing body of research shows that characteristics of the built environment in healthcare facilities impact patients' well-being. Research findings suggest that patients form judgments of perceived quality care based on environmental characteristics. Patient outcomes and ratings of quality of care are linked to the environments' ability to reduce patient stress as well as influence perceptions of quality of care. Historically, this research has been focused in the hospital environment. The United States healthcare system heavily relies on hospitals to treat (rather than prevent) illness, leading to a high per capita healthcare expenditure. Currently, this healthcare system is shifting to rely heavily on ambulatory care settings and primary care providers to detect, prevent, and manage expensive medical conditions. The highest rates of preventable disease and the lowest rates of primary care usage are found in the young adult population (ages 18 to 24). More than any other patient population, this segment rates their satisfaction with healthcare significantly low. For this population education, early detection, and monitoring will be key for a primary care focused model to have the greatest impact on care and long-term savings. Strong patient-physician connections ensure the success of a primary care focused model. The physical environment has the opportunity to provide a message consistent with a physician's practice values and goals. Environmental cues in the waiting area have the potential to relay these messages to the patient prior to physician contact. Through an understanding and optimization of these cues patient perception of quality of care may be increased, thus improving the patient-physician relationship. This study provides insight on how to optimize environmental impact on the healthcare experience. This descriptive exploratory study utilized a non-verbal self-report instrument to collect demographic information and measure participant's responses to two panoramic photos of primary care provider waiting areas. Respondents were asked to identify physical elements in the photos that contributed to their perceptions of the quality of care to be expected. The sample population consisted of 33, 18 to 24 year-olds leaving a total of 234 emotional markers and comments. Qualitative and quantitative revealed three key themes of appeal, comfort, and regard. Physical elements, in the photos, related to the themes include: General areas that were important to the respondents were the seating and reception areas, as well as the overall appearance of the waiting area. Key elements identified to be significant characteristics influencing perceptions of quality of care are presented in this study.
ContributorsBadura, Kerri (Author) / Lamb, Gerri (Thesis advisor) / Heywood, William (Committee member) / Wolf, Peter (Committee member) / Arizona State University (Publisher)
Created2012