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- Creators: Barrett, The Honors College
Description
Synthetic biology is constantly evolving as new ideas are incorporated into this increasingly flexible field. It incorporates the engineering of life with standard genetic parts and methods; new organisms with new genomes; expansion of life to include new components, capabilities, and chemistries; and even completely synthetic organisms that mimic life while being composed of non-living matter. We have introduced a new paradigm of synthetic biology that melds the methods of in vitro evolution with the goals and philosophy of synthetic biology. The Family B proteins represent the first de novo evolved natively folded proteins to be developed with increasingly powerful tools of molecular evolution. These proteins are folded and functional, composed of the 20 canonical amino acids, and in many ways resemble natural proteins. However, their evolutionary history is quite different from natural proteins, as it did not involve a cellular environment. In this study, we examine the properties of DX, one of the Family B proteins that have been evolutionarily optimized for folding stability. Described in chapter 2 is an investigation into the primitive catalytic properties of DX, which seems to have evolved a serendipitous ATPase activity in addition to its selected ATP binding activity. In chapters 3 and 4 we express the DX gene in E. coli cells and observe massive changes in cell morphology, biochemistry, and life cycle. Exposure to DX activates several defense systems in E. coli, including filamentation, cytoplasmic segregation, and reversion to a viable but non-culturable state. We examined these phenotypes in detail and present a model that accounts for how DX causes such a rearrangement of the cell.
ContributorsStomel, Joshua (Author) / Chaput, John C (Thesis advisor) / Korch, Shaleen (Committee member) / Roberson, Robert (Committee member) / Ghirlanda, Gionvanna (Committee member) / Arizona State University (Publisher)
Created2011
Description
Developed a business product with a team of CS students.
ContributorsPerri, Cole Thomas (Co-author) / Hernandez, Maximilliano (Co-author) / Schneider, Kaitlin (Co-author) / Call, Andy (Thesis director) / Hunt, Neil (Committee member) / School of Accountancy (Contributor) / Watts College of Public Service & Community Solut (Contributor) / WPC Graduate Programs (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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
This project explores how modern mobile technology can be used to provide support for domestic violence victims. The goal of the project is to create a proof-of-concept iOS mobile application that maintains a discreet safety front and provides domestic violence victims with resources and safety planning. The design and implementation are disguised as a hair salon app to maintain a low profile on the user’s phone. The HairHelp app features quick exit navigation, a secure database to store a user’s private and personal documents in case of emergency, and a checklist of safety planning measures. The steps taken in this project serve as the foundation for a larger project in the long term.
ContributorsShovkovy, Sophia (Author) / Balasooriya, Janaka (Thesis director) / Wilkey, Douglas (Committee member) / Computer Science and Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
HackerHero is an educational game designed to teach children, especially those from marginalized backgrounds, computation thinking skills needed for STEAM fields. It also teaches children about social injustice. This project was focused on creating an audio visualization for an AI character within the HackerHero game. The audio visualization consisted of a static silhouette of a face and a wave-like form to represent the mouth. Audio content analysis was performed on audio sampled from the character’s voice lines. Pitch and amplitude derived from the analysis was used to animate the character’s visual features such as it’s brightness, color, and mouth movement. The mouth’s movement and color was manipulated with the audio’s pitch. The lights of Wave were controlled by the amplitude of the audio. Design considerations were made to accommodate those with visual disabilities such as color blindness and epilepsy. Overall the final audio visualization satisfied the project sponsor and built upon existing audio visualization work. User feedback will be a necessity for improving the audio visualization in the future.
ContributorsNguyen, Joshep D (Author) / Chavez-Echaegaray, Helen (Thesis director) / Waggoner, Trae (Committee member) / Department of Psychology (Contributor) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
The increased shift towards environmentalism has brought notable attention to a universal excessive plastic consumption and subsequent plastic overload in landfills. Among these plastics, polyethylene terephthalate, more commonly known as PET, constitutes a large percentage of the waste that ends up in landfills. Material and chemical/thermal methods for recycling are both costly, and inefficient, which necessitates a more sustainable and cheaper alternative. The current study aims at fulfilling that role through genetic engineering of Bacillus subtilis with integration of genes from LCC, Ideonella sakaiensis, and Bacillus subtilis. The plasmid construction was done through restriction cloning. A recombinant plasmid for the expression of LCC was constructed, and transformed into Escherichia coli. Future experiments for this study should include redesigning of primers, with possible combination of signal peptides with genes during construct design, and more advanced assays for effective outcomes.
ContributorsKalscheur, Bethany Ann (Author) / Varman, Arul (Thesis director) / Andino, Jean (Committee member) / Chemical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
Nucleic acids encode the information required to create life, and polymerases are the gatekeepers charged with maintaining the storage and flow of this genetic information. Synthetic biologists utilize this universal property to modify organisms and other systems to create unique traits or improve the function of others. One of the many realms in synthetic biology involves the study of biopolymers that do not exist naturally, which is known as xenobiology. Although life depends on two biopolymers for genetic storage, it may be possible that alternative molecules (xenonucleic acids – XNAs), could be used in their place in either a living or non-living system. However, implementation of an XNA based system requires the development of polymerases that can encode and decode information stored in these artificial polymers. A strategy called directed evolution is used to modify or alter the function of a protein of interest, but identifying mutations that can modify polymerase function is made problematic by their size and overall complexity. To reduce the amount of sequence space that needs to be samples when attempting to identify polymerase variants, we can try to make informed decisions about which amino acid residues may have functional roles in catalysis. An analysis of Family B polymerases has shown that residues which are involved in substrate specificity are often highly conserved both at the sequence and structure level. In order to validate the hypothesis that a strong correlation exists between structural conservation and catalytic activity, we have selected and mutated residues in the 9°N polymerase using a loss of function mutagenesis strategy based on a computational analysis of several homologues from a diverse range of taxa. Improvement of these models will hopefully lead to quicker identification of loci which are ideal engineering targets.
ContributorsHaeberle, Tyler Matthew (Author) / Chaput, John (Thesis director) / Chen, Julian (Committee member) / Larsen, Andrew (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
A primary goal in computer science is to develop autonomous systems. Usually, we provide computers with tasks and rules for completing those tasks, but what if we could extend this type of system to physical technology as well? In the field of programmable matter, researchers are tasked with developing synthetic materials that can change their physical properties \u2014 such as color, density, and even shape \u2014 based on predefined rules or continuous, autonomous collection of input. In this research, we are most interested in particles that can perform computations, bond with other particles, and move. In this paper, we provide a theoretical particle model that can be used to simulate the performance of such physical particle systems, as well as an algorithm to perform expansion, wherein these particles can be used to enclose spaces or even objects.
ContributorsLaff, Miles (Author) / Richa, Andrea (Thesis director) / Bazzi, Rida (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor)
Created2015-05
Description
Currently in synthetic biology only the Las, Lux, and Rhl quorum sensing pathways have been adapted for broad engineering use. Quorum sensing allows a means of cell to cell communication in which a designated sender cell produces quorum sensing molecules that modify gene expression of a designated receiver cell. While useful, these three quorum sensing pathways exhibit a nontrivial level of crosstalk, hindering robust engineering and leading to unexpected effects in a given design. To address the lack of orthogonality among these three quorum sensing pathways, previous scientists have attempted to perform directed evolution on components of the quorum sensing pathway. While a powerful tool, directed evolution is limited by the subspace that is defined by the protein. For this reason, we take an evolutionary biology approach to identify new orthogonal quorum sensing networks and test these networks for cross-talk with currently-used networks. By charting characteristics of acyl homoserine lactone (AHL) molecules used across quorum sensing pathways in nature, we have identified favorable candidate pathways likely to display orthogonality. These include Aub, Bja, Bra, Cer, Esa, Las, Lux, Rhl, Rpa, and Sin, which we have begun constructing and testing. Our synthetic circuits express GFP in response to a quorum sensing molecule, allowing quantitative measurement of orthogonality between pairs. By determining orthogonal quorum sensing pairs, we hope to identify and adapt novel quorum sensing pathways for robust use in higher-order genetic circuits.
ContributorsMuller, Ryan (Author) / Haynes, Karmella (Thesis director) / Wang, Xiao (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
Investment real estate is unique among similar financial instruments by nature of each property's internal complexities and interaction with the external economy. Where a majority of tradable assets are static goods within a dynamic market, real estate investments are dynamic goods within a dynamic market. Furthermore, investment real estate, particularly commercial properties, not only interacts with the surrounding economy, it reflects it. Alive with tenancy, each and every commercial investment property provides a microeconomic view of businesses that make up the local economy. Management of commercial investment real estate captures this economic snapshot in a unique abundance of untapped statistical data. While analysis of such data is undeniably valuable, the efforts involved with this process are time consuming. Given this unutilized potential our team has develop proprietary software to analyze this data and communicate the results automatically though and easy to use interface. We have worked with a local real estate property management and ownership firm, Reliance Management, to develop this system through the use of their current, historical, and future data. Our team has also built a relationship with the executives of Reliance Management to review functionality and pertinence of the system we have dubbed, Reliance Dashboard.
ContributorsBurton, Daryl (Co-author) / Workman, Jack (Co-author) / LePine, Marcie (Thesis director) / Atkinson, Robert (Committee member) / Barrett, The Honors College (Contributor) / Department of Finance (Contributor) / Department of Management (Contributor) / Computer Science and Engineering Program (Contributor)
Created2015-05