Matching Items (22)
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- All Subjects: Membranes
- All Subjects: Synthetic Biology
- Creators: Chemical Engineering Program
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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
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
Advances in chemical synthesis have enabled new lines of research with unnatural genetic polymers whose modified bases or sugar-phosphate backbones have potential therapeutic and biotechnological applications. Maximizing the potential of these synthetic genetic systems requires inventing new molecular biology tools that can both generate and faithfully replicate unnatural polymers of significant length. Threose nucleic acid (TNA) has received significant attention as a complete replication system has been developed by engineering natural polymerases to broaden their substrate specificity. The system, however, suffers from a high mutational load reducing its utility. This thesis will cover the development of two new polymerases capable of transcribing and reverse transcribing TNA polymers with high efficiency and fidelity. The polymerases are identified using a new strategy wherein gain-of-function mutations are sampled in homologous protein architectures leading to subtle optimization of protein function. The new replication system has a fidelity that supports the propagation of genetic information enabling in vitro selection of functional TNA molecules. TNA aptamers to human alpha-thrombin are identified and demonstrated to have superior stability compared to DNA and RNA in biologically relevant conditions. This is the first demonstration that functional TNA molecules have potential in biotechnology and molecular medicine.
ContributorsDunn, Matthew Ryan (Author) / Chaput, John C (Thesis advisor) / LaBaer, Joshua (Committee member) / Lake, Douglas (Committee member) / Mangone, Marco (Committee member) / Arizona State University (Publisher)
Created2015
Description
Within recent years, metal-organic frameworks, or MOF’s, have gained a lot of attention in the materials research community. These micro-porous materials are constructed of a metal oxide core and organic linkers, and have a wide-variety of applications due to their extensive material characteristic possibilities. The focus of this study is the MOF-5 material, specifically its chemical stability in air. The MOF-5 material has a large pore size of 8 Å, and aperture sizes of 15 and 12 Å. The pore size, pore functionality, and physically stable structure makes MOF-5 a desirable material. MOF-5 holds applications in gas/liquid separation, catalysis, and gas storage. The main problem with the MOF-5 material, however, is its instability in atmospheric air. This inherent instability is due to the water in air binding to the zinc-oxide core, effectively changing the material and its structure. Because of this material weakness, the MOF-5 material is difficult to be utilized in industrial applications. Through the research efforts proposed by this study, the stability of the MOF-5 powder and membrane were studied. MOF-5 powder and a MOF-5 membrane were synthesized and characterized using XRD analysis. In an attempt to improve the stability of MOF-5 in air, methyl groups were added to the organic linker in order to hinder the interaction of water with the Zn4O core. This was done by replacing the terepthalic acid organic linker with 2,5-dimethyl terephthalic acid in the powder and membrane synthesis steps. The methyl-modified MOF-5 powder was found to be stable after several days of exposure to air while the MOF-5 powder exhibited significant crystalline change. The methyl-modified membrane was found to be unstable when synthesized using the same procedure as the MOF-5 membrane.
ContributorsAnderson, Anthony David (Author) / Lin, Jerry Y.S. (Thesis director) / Ibrahim, Amr (Committee member) / Chemical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Due to the environmental problems caused by global warming, it has become necessary to reduce greenhouse gas emissions across the planet. Biofuels, such as ethanol, have proven to release cleaner emissions when combusted. However, large scale production of these alcohols is uneconomical and inefficient due to limitations in standard separation processes, the most common being distillation. Pervaporation is a novel separation technique that utilizes a specialized membrane to separate multicomponent solutions. In this research project, pervaporation utilizing ZIF-71/PDMS mixed matrix membranes are investigated to see their ability to recover ethanol from an ethanol/aqueous separation. Membranes with varying nanoparticle concentrations were created and their performances were analyzed. While the final results indicate that no correlation exists between nanoparticle weight percentage and selectivity, this technology is still a promising avenue for biofuel production. Future work will be conducted to improve this existing process and enhance membrane selectivity.
ContributorsHoward, Chelsea Elizabeth (Author) / Lind, Mary Laura (Thesis director) / Nielsen, David (Committee member) / Greenlee, Lauren (Committee member) / Barrett, The Honors College (Contributor) / Chemical Engineering Program (Contributor) / Materials Science and Engineering Program (Contributor)
Created2015-05
Description
The goal of this research project is to create a mixed matrix membrane that can withstand very acidic environments but still be used to purify water. The ultimate goal of this membrane is to be used to purify urine both here on Earth and in space. The membrane would be able to withstand these harsh conditions due the incorporation of a resilient impermeable polymer layer that will be cast above the lower hydrophilic layer. Nanoparticles called zeolites will act as a water selective pathway through this impermeable layer and allow water to flow through the membrane. This membrane will be made using a variety of methods and polymers to determine both the cheapest and most effective way of creating this chemical resistant membrane. If this research is successful, many more water sources can be tapped since the membranes will be able to withstand hard conditions. This document is primarily focused on our progress on the development of a highly permeable polymer-zeolite film that makes up the bottom layer of the membrane. Multiple types of casting methods were investigated and it was determined that spin coating at 4000 rpm was the most effective. Based on a literature review, we selected silicalite-1 zeolites as the water-selective nanoparticle component dispersed in a casting solution of polyacrylonitrile in N-methylpyrrolidinone to comprise this hydrophilic layer. We varied the casting conditions of several simple solution-casting methods to produce thin films on the porous substrate with optimal film properties for our membrane design. We then cast this solution on other types of support materials that are more flexible and inexpensive to determine which combination resulted in the thinnest and most permeable film.
ContributorsHerrera, Sofia Carolina (Author) / Lind, Mary Laura (Thesis director) / Khosravi, Afsaneh (Committee member) / Hestekin, Jamie (Committee member) / Barrett, The Honors College (Contributor) / Chemical Engineering Program (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
One of the primary bottlenecks to chemical production in biological organisms is the toxicity of the chemical. Overexpression of efflux pumps has been shown to increase tolerance to aromatic compounds such as styrene and styrene oxide. Tight control of pump expression is necessary to maximize titers and prevent excessive strain on the cells. This study aimed to identify aromatic-sensitive native promoters and heterologous biosensors for construction of closed-loop control of efflux pump expression in E. coli. Using a promoter library constructed by Zaslaver et al., activation was measured through GFP output. Promoters were evaluated for their sensitivity to the addition of one of four aromatic compounds, their "leaking" of signal, and their induction threshold. Out of 43 targeted promoters, 4 promoters (cmr, mdtG, yahN, yajR) for styrene oxide, 2 promoters (mdtG, yahN) for styrene, 0 promoters for 2-phenylethanol, and 1 promoter for phenol (pheP) were identified as ideal control elements in aromatic bioproduction. In addition, a series of three biosensors (NahR, XylS, DmpR) known to be inducible by other aromatics were screened against styrene oxide, 2-phenylethanol, and phenol. The targeted application of these biosensors is aromatic-induced activation of linked efflux pumps. All three biosensors responded strongly in the presence of styrene oxide and 2-phenylethanol, with minor activation in the presence of phenol. Bioproduction of aromatics continues to gain traction in the biotechnology industry, and the continued discovery of aromatic-inducible elements will be essential to effective pathway control.
ContributorsXu, Jimmy (Author) / Nielsen, David (Thesis director) / Wang, Xuan (Committee member) / School of Life Sciences (Contributor) / Chemical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
The recovery of biofuels permits renewable alternatives to present day fossil fuels that cause devastating effects on the planet. Pervaporation is a separation process that shows promise for the separation of ethanol from biologically fermentation broths. The performance of thin film composite membranes of polydimethylsiloxane (PDMS) and zeolite imidazolate frameworks (ZIF-71) dip coated onto a porous substrate are analyzed. Pervaporation performance factors of flux, separation factor and selectivity are measured for varying ZIF-71 loadings of pure PDMS, 5 wt%, 12.5 wt% and 25 wt% at 60 oC with a 2 wt% ethanol/water feed. The increase in ZIF-71 loadings increased the performance of PDMS to produce higher flux, higher separation factor and high selectivity than pure polymeric films.
ContributorsLau, Ching Yan (Author) / Lind, Mary Laura (Thesis director) / Durgun, Pinar Cay (Committee member) / Lively, Ryan (Committee member) / Barrett, The Honors College (Contributor) / School of International Letters and Cultures (Contributor) / Chemical Engineering Program (Contributor)
Created2014-05
Description
In this research, construction of a model membrane system using Polyvinylidene Chloride-Co Acrylonitrile and Linde Type A zeolites is described. The systems aims to separate out flow through zeolite pores and flow through interfaces between zeolites and polymers through the use of pore filled and pore open zeolites. Permeation tests and salt rejection tests were performed, and the data analyzed to yield approximation of separated flow through zeolites and interfaces. This work concludes the more work is required to bring the model system into a functioning state. New polymer selections and new techniques to produce the membrane system are described for future work.
ContributorsShabilla, Andrew Daniel (Author) / Lind, Mary Laura (Thesis director) / Lin, Jerry (Committee member) / Barrett, The Honors College (Contributor) / Chemical Engineering Program (Contributor)
Created2014-05