Matching Items (107)
Description
With a quantum efficiency of nearly 100%, the electron transfer process that occurs within the reaction center protein of the photosynthetic bacteria Rhodobacter (Rh.) sphaeroides is a paragon for understanding the complexities, intricacies, and overall systemization of energy conversion and storage in natural systems. To better understand the way in which photons of light are captured, converted into chemically useful forms, and stored for biological use, an investigation into the reaction center protein, specifically into its cascade of cofactors, was undertaken. The purpose of this experimentation was to advance our knowledge and understanding of how differing protein environments and variant cofactors affect the spectroscopic aspects of and electron transfer kinetics within the reaction of Rh. sphaeroides. The native quinone, ubiquinone, was extracted from its pocket within the reaction center protein and replaced by non-native quinones having different reduction/oxidation potentials. It was determined that, of the two non-native quinones tested—1,2-naphthaquinone and 9,10- anthraquinone—the substitution of the anthraquinone (lower redox potential) resulted in an increased rate of recombination from the P+QA- charge-separated state, while the substitution of the napthaquinone (higher redox potential) resulted in a decreased rate of recombination.
ContributorsSussman, Hallie Rebecca (Author) / Woodbury, Neal (Thesis director) / Redding, Kevin (Committee member) / Lin, Su (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2015-12
Description
Advances in peptide microarray technology have allowed for the creation of fast-paced and modular experiments within affinity ligand discovery. Previously, low density peptide arrays of 10,000 peptides were used to identify low affinity peptide ligands for a target protein; an approach that can be subsequently improved upon with a number of techniques. VDAP[a] offers more information about the relative affinity of protein-peptide interactions via signal intensity in contrast to high throughput screening (HTS) and display technologies which offer binary data. Now, high density peptide arrays with 130,000 to 330,000 peptides are available that allow screening across peptide libraries of greater diversity. With this increase in scale and diversity, faster analytical tools are needed to adequately characterize array data. Using the statistical power available in the R programming language, we have created a flexible analysis package that efficiently processes high density peptide array data from a variety of layouts, rank existing peptide hits, and utilize signal intensity data to generate new hits. This analysis provides a user-friendly method to efficiently analyze high density peptide array data, generate peptide leads for targeted therapeutic development, and further improve peptide array technologies.
ContributorsMoore, Cody Allen (Author) / Woodbury, Neal (Thesis director) / Diehnelt, Chris (Committee member) / Barrett, The Honors College (Contributor)
Created2015-12
Description
Photosynthesis is the process by which plants, algae, and bacteria use light energy to synthesize organic compounds to use as energy. Among these organisms are a kind of purple photosynthetic bacteria called Rhodobacter sphaeroides, a non-sulfur purple bacteria that grows aerobically in the dark by respiration. There have been many contributions throughout the history of this group of bacteria. Rhodobacter sphaeroides is metabolically very diverse as it has many different ways to obtain energy--aerobic respiration and anoxygenic photosynthesis being just a couple of the ways to do so. This project is part of a larger ongoing project to study different mutant strains of Rhodobacter and the different ways in which carries out electron transfer/photosynthesis. This thesis focused on the improvements made to protocol (standard procedure of site directed mutagenesis) through a more efficient technique known as infusion.
ContributorsNucuta, Diana Ileana (Author) / Woodbury, Neal (Thesis director) / Lin, Su (Committee member) / Loskutov, Andrey (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-05
Description
Collaborative learning has been found to enhance student learning experiences through interaction with peers and instructors in a way that typically does not occur in a traditional lecture course. However, more than half of all collaborative learning structures have failed to last very long after their initial introductions which makes understanding the factors of collaboration that make it successful very important. The purpose of this study was to evaluate collaborative learning in a blended learning course to gauge student perceptions and the factors of collaboration and student demographics that impact that perception. This was done by surveying a sample of students in BIO 282 about their experiences in the BIO 281 course they took previously which was a new introductory Biology course with a blended learning structure. It was found that students agree that collaboration is beneficial as it provides an opportunity to gain additional insight from peers and improve students' understanding of course content. Also, differences in student gender and first generation status have less of an effect on student perceptions of collaboration than differences in academic achievement (grade) bracket.
ContributorsVu, Bethany Thao-Vy (Author) / Stout, Valerie (Thesis director) / Brownell, Sara (Committee member) / Wright, Christian (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-05
Description
The influenza virus is the main cause of thousands of deaths each year in the United States, and far more hospitalizations. Immunization has helped in protecting people from this virus and there are a number of therapeutics which have proven effective in aiding people infected with the virus. However, these therapeutics are subject to various limitations including increased resistance, limited supply, and significant side effects. A new therapeutic is needed which addresses these problems and protects people from the influenza virus. Synbodies, synthetic antibodies, may provide a means to achieve this goal. Our group has produced a synbody, the 5-5 synbody, which has been shown to bind to and inhibit the influenza virus. The direct pull down and western blot techniques were utilized to investigate how the synbody bound to the influenza virus. Our research showed that the 5-5 synbody bound to the influenza nucleoprotein (NP) with a KD of 102.9 ± 74.48 nM. It also showed that the synbody bound strongly to influenza viral extract from two different strains of the virus, the Puerto Rico (H1N1) and Sydney (H3N2) strains. This research demonstrated that the 5-5 synbody binds with high affinity to NP, which is important because influenza NP is highly conserved between various strains of the virus and plays an important role in the replication of the viral genome. It also demonstrated that this binding is conserved between various strains of the virus, indicating that the 5-5 synbody potentially could bind many different influenza strains. This synbody may have potential as a therapeutic in the future if it is able to demonstrate similar binding in vivo.
ContributorsKombe, Albert E. (Author) / Diehnelt, Chris (Thesis director) / Woodbury, Neal (Committee member) / Legutki, Bart (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of International Letters and Cultures (Contributor)
Created2014-05
Description
One of the major challenges that were yet to be solved for solid phase peptide synthesis was the lack of an efficient peptide sequencing technique that was less hazardous, easier to perform , and was more cost-effective. Sequencing peptides were held important in the field of Chemistry and Biochemistry because it aided in drug discovery, finding ligands that bind to a specific target protein and finding alternative agents in transporting molecules to its desired location. Therefore, the overall purpose of this experiment was to develop a method of solid phase sequencing technique that was more environmental friendly, sequences at a faster rate, and was more cost-effective.
ContributorsCordovez, Lalaine Anne Ordiz (Author) / Woodbury, Neal (Thesis director) / Zhao, Zhan-Gong (Committee member) / Legutki, Joseph Barten (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor)
Created2014-05
Description
We, a team of students and faculty in the life sciences at Arizona State University (ASU), currently teach an Introduction to Biology course in a Level 5, or maximum-security unit with the support of the Arizona Department of Corrections and the Prison Education Program at ASU. This course aims to enhance current programs at the unit by offering inmates an opportunity to practice literacy and math skills, while also providing exposure to a new academic field (science, and specifically biology). Numerous studies, including a 2005 study from the Arizona Department of Corrections (ADC), have found that vocational programs, including prison education programs, reduce recidivism rates (ADC 2005, Esperian 2010, Jancic 1988, Steurer et al. 2001, Ubic 2002) and may provide additional benefits such as engagement with a world outside the justice system (Duguid 1992), the opportunity for inmates to revise personal patterns of rejecting education that they may regret, and the ability of inmate parents to deliberately set a good example for their children (Hall and Killacky 2008). Teaching in a maximum security prison unit poses special challenges, which include a prohibition on most outside materials (except paper), severe restrictions on student-teacher and student-student interactions, and the inability to perform any lab exercises except limited computer simulations. Lack of literature discussing theoretical and practical aspects of teaching science in such environment has prompted us to conduct an ongoing study to generate notes and recommendations from this class through the use of surveys, academic evaluation of students' work and ongoing feedback from both teachers and students to inform teaching practices in future science classes in high-security prison units.
ContributorsLarson, Anika Jade (Author) / Mor, Tsafrir (Thesis director) / Brownell, Sara (Committee member) / Lockard, Joe (Committee member) / Barrett, The Honors College (Contributor) / School of Politics and Global Studies (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
As the world energy demand increases, semiconductor devices with high energy conversion efficiency become more and more desirable. The energy conversion consists of two distinct processes, namely energy generation and usage. In this dissertation, novel multi-junction solar cells and light emitting diodes (LEDs) are proposed and studied for high energy conversion efficiency in both processes, respectively. The first half of this dissertation discusses the practically achievable energy conversion efficiency limit of solar cells. Since the demonstration of the Si solar cell in 1954, the performance of solar cells has been improved tremendously and recently reached 41.6% energy conversion efficiency. However, it seems rather challenging to further increase the solar cell efficiency. The state-of-the-art triple junction solar cells are analyzed to help understand the limiting factors. To address these issues, the monolithically integrated II-VI and III-V material system is proposed for solar cell applications. This material system covers the entire solar spectrum with a continuous selection of energy bandgaps and can be grown lattice matched on a GaSb substrate. Moreover, six four-junction solar cells are designed for AM0 and AM1.5D solar spectra based on this material system, and new design rules are proposed. The achievable conversion efficiencies for these designs are calculated using the commercial software package Silvaco with real material parameters. The second half of this dissertation studies the semiconductor luminescence refrigeration, which corresponds to over 100% energy usage efficiency. Although cooling has been realized in rare-earth doped glass by laser pumping, semiconductor based cooling is yet to be realized. In this work, a device structure that monolithically integrates a GaAs hemisphere with an InGaAs/GaAs quantum-well thin slab LED is proposed to realize cooling in semiconductor. The device electrical and optical performance is calculated. The proposed device then is fabricated using nine times photolithography and eight masks. The critical process steps, such as photoresist reflow and dry etch, are simulated to insure successful processing. Optical testing is done with the devices at various laser injection levels and the internal quantum efficiency, external quantum efficiency and extraction efficiency are measured.
ContributorsWu, Songnan (Author) / Zhang, Yong-Hang (Thesis advisor) / Menéndez, Jose (Committee member) / Ponce, Fernando (Committee member) / Belitsky, Andrei (Committee member) / Schroder, Dieter (Committee member) / Arizona State University (Publisher)
Created2010
Description
Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We demonstrate its use to determine the first room-temperature structure of RNA polymerase II at high resolution, revealing new structural details. Moreover, the double flow-focusing nozzles were successfully tested with three other protein samples and the first room temperature structure of an extradiol ring-cleaving dioxygenase was solved by utilizing the improved operation and characteristics of these devices.
ContributorsOberthuer, Dominik (Author) / Knoska, Juraj (Author) / Wiedorn, Max O. (Author) / Beyerlein, Kenneth R. (Author) / Bushnell, David A. (Author) / Kovaleva, Elena G. (Author) / Heymann, Michael (Author) / Gumprecht, Lars (Author) / Kirian, Richard (Author) / Barty, Anton (Author) / Mariani, Valerio (Author) / Tolstikova, Aleksandra (Author) / Adriano, Luigi (Author) / Awel, Salah (Author) / Barthelmess, Miriam (Author) / Dorner, Katerina (Author) / Xavier, P. Lourdu (Author) / Yefanov, Oleksandr (Author) / James, Daniel (Author) / Nelson, Garrett (Author) / Wang, Dingjie (Author) / Calvey, George (Author) / Chen, Yujie (Author) / Schmidt, Andrea (Author) / Szczepek, Michael (Author) / Frielingsdorf, Stefan (Author) / Lenz, Oliver (Author) / Snell, Edward (Author) / Robinson, Philip J. (Author) / Sarler, Bozidar (Author) / Belsak, Grega (Author) / Macek, Marjan (Author) / Wilde, Fabian (Author) / Aquila, Andrew (Author) / Boutet, Sebastien (Author) / Liang, Mengning (Author) / Hunter, Mark S. (Author) / Scheerer, Patrick (Author) / Lipscomb, John D. (Author) / Weierstall, Uwe (Author) / Kornberg, Roger D. (Author) / Spence, John (Author) / Pollack, Lois (Author) / Chapman, Henry N. (Author) / Bajt, Sasa (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor)
Created2017-03-16
Description
X-ray free-electron lasers provide novel opportunities to conduct single particle analysis on nanoscale particles. Coherent diffractive imaging experiments were performed at the Linac Coherent Light Source (LCLS), SLAC National Laboratory, exposing single inorganic core-shell nanoparticles to femtosecond hard-X-ray pulses. Each facetted nanoparticle consisted of a crystalline gold core and a differently shaped palladium shell. Scattered intensities were observed up to about 7 nm resolution. Analysis of the scattering patterns revealed the size distribution of the samples, which is consistent with that obtained from direct real-space imaging by electron microscopy. Scattering patterns resulting from single particles were selected and compiled into a dataset which can be valuable for algorithm developments in single particle scattering research.
ContributorsLi, Xuanxuan (Author) / Chiu, Chun-Ya (Author) / Wang, Hsiang-Ju (Author) / Kassemeyer, Stephan (Author) / Botha, Sabine (Author) / Shoeman, Robert L. (Author) / Lawrence, Robert (Author) / Kupitz, Christopher (Author) / Kirian, Richard (Author) / James, Daniel (Author) / Wang, Dingjie (Author) / Nelson, Garrett (Author) / Messerschmidt, Marc (Author) / Boutet, Sebastien (Author) / Williams, Garth J. (Author) / Hartman, Elisabeth (Author) / Jafarpour, Aliakbar (Author) / Foucar, Lutz M. (Author) / Barty, Anton (Author) / Chapman, Henry (Author) / Liang, Mengning (Author) / Menzel, Andreas (Author) / Wang, Fenglin (Author) / Basu, Shibom (Author) / Fromme, Raimund (Author) / Doak, R. Bruce (Author) / Fromme, Petra (Author) / Weierstall, Uwe (Author) / Huang, Michael H. (Author) / Spence, John (Author) / Schlichting, Ilme (Author) / Hogue, Brenda (Author) / Liu, Haiguang (Author) / ASU Biodesign Center Immunotherapy, Vaccines and Virotherapy (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Department of Physics (Contributor) / School of Life Sciences (Contributor)
Created2017-04-11