Matching Items (13)
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Description
The portability of genetic tools from one organism to another is a cornerstone of synthetic biology. The shared biological language of DNA-to-RNA-to-protein allows for expression of polypeptide chains in phylogenetically distant organisms with little modification. The tools and contexts are diverse, ranging from catalytic RNAs in cell-free systems to bacterial proteins expressed in human cell lines, yet they exhibit an organizing principle: that genes and proteins may be treated as modular units that can be moved from their native organism to a novel one. However, protein behavior is always unpredictable; drop-in functionality is not guaranteed.
My work characterizes how two different classes of tools behave in new contexts and explores methods to improve their functionality: 1. CRISPR/Cas9 in human cells and 2. quorum sensing networks in Escherichia coli.
1. The genome-editing tool CRISPR/Cas9 has facilitated easily targeted, effective, high throughput genome editing. However, Cas9 is a bacterially derived protein and its behavior in the complex microenvironment of the eukaryotic nucleus is not well understood. Using transgenic human cell lines, I found that gene-silencing heterochromatin impacts Cas9’s ability to bind and cut DNA in a site-specific manner and I investigated ways to improve CRISPR/Cas9 function in heterochromatin.
2. Bacteria use quorum sensing to monitor population density and regulate group behaviors such as virulence, motility, and biofilm formation. Homoserine lactone (HSL) quorum sensing networks are of particular interest to synthetic biologists because they can function as “wires” to connect multiple genetic circuits. However, only four of these networks have been widely implemented in engineered systems. I selected ten quorum sensing networks based on their HSL production profiles and confirmed their functionality in E. coli, significantly expanding the quorum sensing toolset available to synthetic biologists.
My work characterizes how two different classes of tools behave in new contexts and explores methods to improve their functionality: 1. CRISPR/Cas9 in human cells and 2. quorum sensing networks in Escherichia coli.
1. The genome-editing tool CRISPR/Cas9 has facilitated easily targeted, effective, high throughput genome editing. However, Cas9 is a bacterially derived protein and its behavior in the complex microenvironment of the eukaryotic nucleus is not well understood. Using transgenic human cell lines, I found that gene-silencing heterochromatin impacts Cas9’s ability to bind and cut DNA in a site-specific manner and I investigated ways to improve CRISPR/Cas9 function in heterochromatin.
2. Bacteria use quorum sensing to monitor population density and regulate group behaviors such as virulence, motility, and biofilm formation. Homoserine lactone (HSL) quorum sensing networks are of particular interest to synthetic biologists because they can function as “wires” to connect multiple genetic circuits. However, only four of these networks have been widely implemented in engineered systems. I selected ten quorum sensing networks based on their HSL production profiles and confirmed their functionality in E. coli, significantly expanding the quorum sensing toolset available to synthetic biologists.
ContributorsDaer, René (Author) / Haynes, Karmella (Thesis advisor) / Brafman, David (Committee member) / Nielsen, David (Committee member) / Kiani, Samira (Committee member) / Arizona State University (Publisher)
Created2017
Description
In this paper, I analyze representations of nature in popular film, using the feminist / deconstructionist concept of a dualism to structure my critique. Using Val Plumwood’s analysis of the logical structure of dualism and the 5 ‘features of a dualism’ that she identifies, I critique 5 popular movies – Star Wars, Lord of the Rings, Brave, Grizzly Man, and Planet Earth – by locating within each of them one of the 5 features and explaining how the movie functions to reinforce the Nature/Culture dualism . By showing how the Nature/Culture dualism shapes and is shaped by popular cinema, I show how “Nature” is a social construct, created as part of this very dualism, and reified through popular culture. I conclude with the introduction of a number of ‘subversive’ pieces of visual art that undermine and actively deconstruct the Nature/Culture dualism and show to the viewer a more honest presentation of the non-human world.
ContributorsBarton, Christopher Joseph (Author) / Broglio, Ron (Thesis director) / Minteer, Ben (Committee member) / Barrett, The Honors College (Contributor) / School of Sustainability (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / School of Geographical Sciences and Urban Planning (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
From 2007 to 2017, the state of California experienced two major droughts that required significant governmental action to decrease urban water demand. The purpose of this project is to isolate and explore the effects of these policy changes on water use during and after these droughts, and to see how these policies interact with hydroclimatic variability. As explanatory variables in multiple linear regression (MLR) models, water use policies were found to be significant at both the zip code and city levels. Policies that specifically target behavioral changes were significant mathematical drivers of water use in city-level models. Policy data was aggregated into a timeline and coded based on categories including user type, whether the policy was voluntary or mandatory, the targeted water use type, and whether the change in question concerns active or passive conservation. The analyzed policies include but are not limited to state drought declarations, regulatory municipal ordinances, and incentive programs for household appliances. Spatial averages of available hydroclimatic data have been computed and validated using inverse distance weighting methods. The data was aggregated at the zip code level to be comparable to the available water use data for use in MLR models. Factors already known to affect water use, such as temperature, precipitation, income, and water stress, were brought into the MLR models as explanatory variables. After controlling for these factors, the timeline policies were brought into the model as coded variables to test their effect on water demand during the years 2000-2017. Clearly identifying which policy traits are effective will inform future policymaking in cities aiming to conserve water. The findings suggest that drought-related policies impact per capita urban water use. The results of the city level MLR models indicate that implementation of mandatory policies that target water use behaviors effectively reduce water use. Temperature, income, unemployment, and the WaSSI were also observed to be mathematical drivers of water use. Interaction effects between policies and the WaSSI were statistically significant at both model scales.
ContributorsHjelmstad, Annika Margaret (Author) / Garcia, Margaret (Thesis director) / Larson, Kelli (Committee member) / Civil, Environmental and Sustainable Eng Program (Contributor, Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-12
Description
As society's energy crisis continues to become more imminent many industries and niches are seeking a new, sustainable and renewable source of electricity production. Similar to solar, wind and tidal energy, kinetic energy has the potential to generate electricity as an extremely renewable source of energy generation. While stationary bicycles can generate small amounts of electricity, the idea behind this project was to expand energy generation into the more common weight lifting side of exercising. The method for solving this problem was to find the average amount of power generated per user on a Smith machine and determine how much power was available from an accompanying energy generator. The generator consists of three phases: a copper coil and magnet generator, a full wave bridge rectifying circuit and a rheostat. These three phases working together formed a fully functioning controllable generator. The resulting issue with the kinetic energy generator was that the system was too inefficient to serve as a viable system for electricity generation. The electrical production of the generator only saved about 2 cents per year based on current Arizona electricity rates. In the end it was determined that the project was not a sustainable energy generation system and did not warrant further experimentation.
ContributorsO'Halloran, Ryan James (Author) / Middleton, James (Thesis director) / Hinrichs, Richard (Committee member) / Barrett, The Honors College (Contributor) / Mechanical and Aerospace Engineering Program (Contributor) / The Design School (Contributor) / School of Mathematical and Statistical Sciences (Contributor)
Created2014-05
Description
Plastics continue to benefit society in innumerable ways, even though recent public focus on plastics has centered mostly on human health and environmental concerns, including their endocrine-disrupting properties and the long-term pollution they represent. The benefits of plastics are particularly apparent in medicine and public health. Plastics are versatile, cost-effective, require less energy to produce than alternative materials like metal or glass, and can be manufactured to have many different properties. Due to these characteristics, polymers are used in diverse health applications like disposable syringes and intravenous bags, sterile packaging for medical instruments as well as in joint replacements, tissue engineering, etc. However, not all current uses of plastics are prudent and sustainable, as illustrated by the widespread, unwanted human exposure to endocrine-disrupting bisphenol A (BPA) and di-(2-ethylhexyl) phthalate (DEHP), problems arising from the large quantities of plastic being disposed of, and depletion of non-renewable petroleum resources as a result of the ever-increasing mass production of plastic consumer articles. Using the health-care sector as example, this review concentrates on the benefits and downsides of plastics and identifies opportunities to change the composition and disposal practices of these invaluable polymers for a more sustainable future consumption. It highlights ongoing efforts to phase out DEHP and BPA in the health-care and food industry and discusses biodegradable options for plastic packaging, opportunities for reducing plastic medical waste, and recycling in medical facilities in the quest to reap a maximum of benefits from polymers without compromising human health or the environment in the process.
ContributorsNorth, Emily Jean (Co-author) / Halden, Rolf (Co-author, Thesis director) / Mikhail, Chester (Committee member) / Hurlbut, Ben (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Chemical Engineering Program (Contributor)
Created2013-05
Description
With the rise of fast fashion and its now apparent effects on climate change, there is an evident need for change in terms of how we as individuals use our clothing and footwear. Our team has created Ray Fashion Inc., a sustainable footwear company that focuses on implementing the circular economy to reduce the amount of waste generated in shoe creation. We have designed a sandal that accommodates the rapid consumption element of fast fashion with a business model that promotes sustainability through a buy-back method to upcycle and retain our materials.
ContributorsLiao, Yuxin (Co-author) / Yang, Andrea (Co-author) / Suresh Kumar, Roshni (Co-author) / Byrne, Jared (Thesis director) / Marseille, Alicia (Committee member) / Jordan, Amanda (Committee member) / Department of Finance (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
This thesis analyzed Canon GPR-30 Black Standard Yield Toner in hopes to gain better understanding of the additives and plastic used in a popular photocopier toner formulation. By analyzing the toner’s composition from the perspective of its recyclability and potential to be manufactured using recycled plastic, this thesis hoped to fill a gap in current literature regarding how toner fits into a circular economy. While the analysis of the selected toner was ultimately inconclusive, three hypotheses about the toner’s composition are put forth based upon data from differential scanning calorimetry (DSC), solubility analysis, and Fourier Transform Infrared (FTIR) spectroscopy experimentation. It is hypothesized that the toner is most likely composed of either polymethyl methacrylate (PMMA) or polyethylene terephthalate (PET). Both of these polymers have characteristic FTIR peaks that were exhibited in the toner spectra and both polymers exhibit similar solubility behavior to toner samples. However, the glass transition temperature and melting temperature of the toner sampled were 58℃ and 74.5℃ respectively, both of which are much lower than that of PMMA and PET. Thus, a third hypothesis that would better support DSC findings is that the toner is primarily composed of nylon 6,6. While DSC data best matches this polymer, FTIR data seems to rule out nylon 6,6 as an option because its characteristic peaks were not found in experimental data. Thus, the Canon GPR-30 Black Standard Yield Toner is probably made from either PMMA or PET. Both PMMA and PET are 100% recyclable plastics which are commonly repurposed at recycling facilities, however, unknowns regarding toner additives make it difficult to determine how this toner would be recycled. If the printing industry hopes to move towards a circular economy in which plastic can be recycled to use towards toner manufacturing and toner can be “unprinted” from paper to be recycled into new toner, it is likely that monetary incentives or government regulations will need to be introduced to promote the sharing of toner formulations for recycling purposes.
ContributorsChase, Jasmine (Author) / Green, Matthew (Thesis director) / Emady, Heather (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Mechanical and Aerospace Engineering Program (Contributor)
Created2023-05
ContributorsChase, Jasmine (Author) / Green, Matthew (Thesis director) / Emady, Heather (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Mechanical and Aerospace Engineering Program (Contributor)
Created2023-05
ContributorsChase, Jasmine (Author) / Green, Matthew (Thesis director) / Emady, Heather (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Mechanical and Aerospace Engineering Program (Contributor)
Created2023-05