Matching Items (185)
Filtering by
- All Subjects: Computer Science
- Creators: Barrett, The Honors College
- Member of: Theses and Dissertations
Description
Synechocystis sp PCC 6803 is a photosynthetic cyanobacterium that can be easily transformed to produce molecules of interest; this has increased Synechocystis’ popularity as a clean energy platform. Synechocystis has been shown to produce and excrete molecules such as fatty acids, isoprene, etc. after appropriate genetic modification. Challenges faced for large–scale growth of modified Synechocystis include abiotic stress, microbial contamination and high processing costs of product and cell material. Research reported in this dissertation contributes to solutions to these challenges. First, abiotic stress was addressed by overexpression of the heat shock protein ClpB1. In contrast to the wild type, the ClpB1 overexpression mutant (Slr1641+) tolerated rapid temperature changes, but no difference was found between the strains when temperature shifts were slower. Combination of ClpB1 overexpression with DnaK2 overexpression (Slr1641+/Sll0170+) further increased thermotolerance. Next, we used a Synechocystis strain that carries an introduced isoprene synthase gene (IspS+) and that therefore produces isoprene. We attempted to increase isoprene yields by overexpression of key enzymes in the methyl erythritol phosphate (MEP) pathway that leads to synthesis of the isoprene precursor. Isoprene production was not increased greatly by MEP pathway induction, likely because of limitations in the affinity of the isoprene synthase for the substrate. Finally, two extraction principles, two–phase liquid extraction (e.g., with an organic and aqueous phase) and solid–liquid extraction (e.g., with a resin) were tested. Two–phase liquid extraction is suitable for separating isoprene but not fatty acids from the culture medium. Fatty acid removal required acidification or surfactant addition, which affected biocompatibility. Therefore, improvements of both the organism and product–harvesting methods can contribute to enhancing the potential of cyanobacteria as solar–powered biocatalysts for the production of petroleum substitutes.
ContributorsGonzalez Esquer, Cesar Raul (Author) / Vermaas, Willem (Thesis advisor) / Chandler, Douglas (Committee member) / Bingham, Scott (Committee member) / Nielsen, David (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
Teleosts have the most primitive adaptive immune system. However, in terms of functionality the teleost immune system is similar to birds and mammals. On the other hand, enteric bacterial pathogens of mammals and birds present conserved regulatory mechanisms that control virulence factors. In this context, deletion of conserved genes that control virulence factors have been successfully used as measure to construct live attenuated bacterial vaccines for mammals and birds. Here, I hypothesize that evolutionary conserved genes, which control virulence factors or are essential for bacterial physiology in Enterobacteriaceae, could be used as universal tools to design live attenuated recombinant bacterial vaccines from fish to mammals. The evolutionary conserved genes that control virulence factors, crp and fur, and the essential gene for the synthesis of the cell wall, asd, were studied in Edwardsiella ictaluri to develop a live recombinant vaccine for fish host. The genus Edwardsiella is one of the most ancient represent of the Enterobacteriaceae family. E. ictaluri, a host restricted pathogen of catfish (Ictalurus punctatus), is the causative agent of the enteric septicemia and one of the most important pathogens of this fish aquaculture. Although, crp and fur control different virulence factors in Edwardsiella, in comparison to other enterics, individual deletion of these genes triggered protective immune response at the systemic and mucosal level of the fish. Deletion of asdA gene allowed the creation of a balanced-lethal system to syntheses heterologous antigens. I concluded that crp, fur and asd could be universally used to develop live attenuate recombinant Enterobacteriaceae base vaccines for different hosts.
ContributorsSantander Morales, Javier Alonso (Author) / Curtiss, Roy Iii (Thesis advisor) / Chandler, Douglas (Committee member) / Chang, Yung (Committee member) / Shi, Yixin (Committee member) / Arizona State University (Publisher)
Created2012
Description
Skeletal muscle (SM) mitochondria generate the majority of adenosine triphosphate (ATP) in SM, and help regulate whole-body energy expenditure. Obesity is associated with alterations in SM mitochondria, which are unique with respect to their arrangement within cells; some mitochondria are located directly beneath the sarcolemma (i.e., subsarcolemmal (SS) mitochondria), while other are nested between the myofibrils (i.e., intermyofibrillar (IMF) mitochondria). Functional and proteome differences specific to SS versus IMF mitochondria in obese individuals may contribute to reduced capacity for muscle ATP production seen in obesity. The overall goals of this work were to (1) isolate functional muscle SS and IMF mitochondria from lean and obese individuals, (2) assess enzyme activities associated with the electron transport chain and ATP production, (3) determine if elevated plasma amino acids enhance SS and IMF mitochondrial respiration and ATP production rates in SM of obese humans, and (4) determine differences in mitochondrial proteome regulating energy metabolism and key biological processes associated with SS and IMF mitochondria between lean and obese humans.
Polarography was used to determine functional differences in isolated SS and IMF mitochondria between lean (37 ± 3 yrs; n = 10) and obese (35 ± 3 yrs; n = 11) subjects during either saline (control) or amino acid (AA) infusions. AA infusion increased ADP-stimulated respiration (i.e., coupled respiration), non-ADP stimulated respiration (i.e., uncoupled respiration), and ATP production rates in SS, but not IMF mitochondria in lean (n = 10; P < 0.05). Neither infusion increased any of the above parameters in muscle SS or IMF mitochondria of the obese subjects.
Using label free quantitative mass spectrometry, we determined differences in proteomes of SM SS and IMF mitochondria between lean (33 ± 3 yrs; n = 16) and obese (32 ± 3 yrs; n = 17) subjects. Differentially-expressed mitochondrial proteins in SS versus IMF mitochondria of obese subjects were associated with biological processes that regulate: electron transport chain (P<0.0001), citric acid cycle (P<0.0001), oxidative phosphorylation (P<0.001), branched-chain amino acid degradation, (P<0.0001), and fatty acid degradation (P<0.001). Overall, these findings show that obesity is associated with redistribution of key biological processes within the mitochondrial reticulum responsible for regulating energy metabolism in human skeletal muscle.
Polarography was used to determine functional differences in isolated SS and IMF mitochondria between lean (37 ± 3 yrs; n = 10) and obese (35 ± 3 yrs; n = 11) subjects during either saline (control) or amino acid (AA) infusions. AA infusion increased ADP-stimulated respiration (i.e., coupled respiration), non-ADP stimulated respiration (i.e., uncoupled respiration), and ATP production rates in SS, but not IMF mitochondria in lean (n = 10; P < 0.05). Neither infusion increased any of the above parameters in muscle SS or IMF mitochondria of the obese subjects.
Using label free quantitative mass spectrometry, we determined differences in proteomes of SM SS and IMF mitochondria between lean (33 ± 3 yrs; n = 16) and obese (32 ± 3 yrs; n = 17) subjects. Differentially-expressed mitochondrial proteins in SS versus IMF mitochondria of obese subjects were associated with biological processes that regulate: electron transport chain (P<0.0001), citric acid cycle (P<0.0001), oxidative phosphorylation (P<0.001), branched-chain amino acid degradation, (P<0.0001), and fatty acid degradation (P<0.001). Overall, these findings show that obesity is associated with redistribution of key biological processes within the mitochondrial reticulum responsible for regulating energy metabolism in human skeletal muscle.
ContributorsKras, Katon Anthony (Author) / Katsanos, Christos (Thesis advisor) / Chandler, Douglas (Committee member) / Dinu, Valentin (Committee member) / Mor, Tsafrir S. (Committee member) / Arizona State University (Publisher)
Created2017
Description
The original version of Helix, the one I pitched when first deciding to make a video game
for my thesis, is an action-platformer, with the intent of metroidvania-style progression
and an interconnected world map.
The current version of Helix is a turn based role-playing game, with the intent of roguelike
gameplay and a dark fantasy theme. We will first be exploring the challenges that came
with programming my own game - not quite from scratch, but also without a prebuilt
engine - then transition into game design and how Helix has evolved from its original form
to what we see today.
for my thesis, is an action-platformer, with the intent of metroidvania-style progression
and an interconnected world map.
The current version of Helix is a turn based role-playing game, with the intent of roguelike
gameplay and a dark fantasy theme. We will first be exploring the challenges that came
with programming my own game - not quite from scratch, but also without a prebuilt
engine - then transition into game design and how Helix has evolved from its original form
to what we see today.
ContributorsDiscipulo, Isaiah K (Author) / Meuth, Ryan (Thesis director) / Kobayashi, Yoshihiro (Committee member) / School of Mathematical and Statistical Sciences (Contributor) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
RecyclePlus is an iOS mobile application that allows users to be knowledgeable in the realms of sustainability. It gives encourages users to be environmental responsible by providing them access to recycling information. In particular, it allows users to search up certain materials and learn about its recyclability and how to properly dispose of the material. Some searches will show locations of facilities near users that collect certain materials and dispose of the materials properly. This is a full stack software project that explores open source software and APIs, UI/UX design, and iOS development.
ContributorsTran, Nikki (Author) / Ganesh, Tirupalavanam (Thesis director) / Meuth, Ryan (Committee member) / Watts College of Public Service & Community Solut (Contributor) / Department of Information Systems (Contributor) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
This paper details the specification and implementation of a single-machine blockchain simulator. It also includes a brief introduction on the history & underlying concepts of blockchain, with explanations on features such as decentralization, openness, trustlessness, and consensus. The introduction features a brief overview of public interest and current implementations of blockchain before stating potential use cases for blockchain simulation software. The paper then gives a brief literature review of blockchain's role, both as a disruptive technology and a foundational technology. The literature review also addresses the potential and difficulties regarding the use of blockchain in Internet of Things (IoT) networks, and also describes the limitations of blockchain in general regarding computational intensity, storage capacity, and network architecture. Next, the paper gives the specification for a generic blockchain structure, with summaries on the behaviors and purposes of transactions, blocks, nodes, miners, public & private key cryptography, signature validation, and hashing. Finally, the author gives an overview of their specific implementation of the blockchain using C/C++ and OpenSSL. The overview includes a brief description of all the classes and data structures involved in the implementation, including their function and behavior. While the implementation meets the requirements set forward in the specification, the results are more qualitative and intuitive, as time constraints did not allow for quantitative measurements of the network simulation. The paper concludes by discussing potential applications for the simulator, and the possibility for future hardware implementations of blockchain.
ContributorsRauschenbach, Timothy Rex (Author) / Vrudhula, Sarma (Thesis director) / Nakamura, Mutsumi (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
Description
Many researchers aspire to create robotics systems that assist humans in common office tasks, especially by taking over delivery and messaging tasks. For meaningful interactions to take place, a mobile robot must be able to identify the humans it interacts with and communicate successfully with them. It must also be able to successfully navigate the office environment. While mobile robots are well suited for navigating and interacting with elements inside a deterministic office environment, attempting to interact with human beings in an office environment remains a challenge due to the limits on the amount of cost-efficient compute power onboard the robot. In this work, I propose the use of remote cloud services to offload intensive interaction tasks. I detail the interactions required in an office environment and discuss the challenges faced when implementing a human-robot interaction platform in a stochastic office environment. I also experiment with cloud services for facial recognition, speech recognition, and environment navigation and discuss my results. As part of my thesis, I have implemented a human-robot interaction system utilizing cloud APIs into a mobile robot, enabling it to navigate the office environment, identify humans within the environment, and communicate with these humans.
ContributorsDSouza, Daniel Anand (Author) / Kambhampati, Subbarao (Thesis director) / Zhang, Yu (Committee member) / Computer Science and Engineering Program (Contributor) / School of Computing, Informatics, and Decision Systems Engineering (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
Lie detection is used prominently in contemporary society for many purposes such as for pre-employment screenings, granting security clearances, and determining if criminals or potential subjects may or may not be lying, but by no means is not limited to that scope. However, lie detection has been criticized for being subjective, unreliable, inaccurate, and susceptible to deliberate manipulation. Furthermore, critics also believe that the administrator of the test also influences the outcome as well. As a result, the polygraph machine, the contemporary device used for lie detection, has come under scrutiny when used as evidence in the courts. The purpose of this study is to use three entirely different tools and concepts to determine whether eye tracking systems, electroencephalogram (EEG), and Facial Expression Emotion Analysis (FACET) are reliable tools for lie detection. This study found that certain constructs such as where the left eye is looking at in regard to its usual position and engagement levels in eye tracking and EEG respectively could distinguish between truths and lies. However, the FACET proved the most reliable tool out of the three by providing not just one distinguishing variable but seven, all related to emotions derived from movements in the facial muscles during the present study. The emotions associated with the FACET that were documented to possess the ability to distinguish between truthful and lying responses were joy, anger, fear, confusion, and frustration. In addition, an overall measure of the subject's neutral and positive emotional expression were found to be distinctive factors. The implications of this study and future directions are discussed.
ContributorsSeto, Raymond Hua (Author) / Atkinson, Robert (Thesis director) / Runger, George (Committee member) / W. P. Carey School of Business (Contributor) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
Global violent conflict has become an increasing problem in recent decades, especially in the African continent. Civil wars, terrorism, riots, and political violence has wrought havoc not only on civilian lives, but also on economic foundations. Trade networks are a way to measure these economic foundations. To summarize trade networks clustering coefficient as well as trade quantity/value summation measures are used. To understand effects of global trade on violent conflict, Pearson product-moment correlations are utilized. This work details a comparison of African national economies and violent conflict events using clustering coefficient, trade summation measures and Pearson correlation coefficient.
ContributorsKadambi, Sagarika Sanjay (Author) / Maciejewski, Ross (Thesis director) / Shutters, Shade (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05