Matching Items (9)
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- All Subjects: E. coli
- Creators: Nielsen, David
Description
Post-combustion carbon capture is a viable option for reducing CO2 greenhouse gas emissions, and one potentially promising technology for this route is adsorption using chemically and physically based sorbents. A number of exceptional CO2 sorbents materials have been prepared including metal organic frameworks, zeolites, and carbon based materials. One particular group of capable materials are amine based solid sorbents that has shown to possess high adsorption capacities and favorable adsorption kinetics. A key variable in the synthesis of an amine based sorbent is the support which acts as the platform for the amine modification. Aerogels, due to their high porosities and surface areas, appear to be a promising support for an amine modified CO2 sorbent. Therefore, in order to develop a commercially viable CO2 sorbent, particulate aerogels manufactured by Cabot Corporation through an economical and proprietary ambient drying process were modified with amines using a variety of functionalization methods. Two methods of physical impregnation of the amino polymer TEPA were performed in order to observe the performance as well as understand the effects of how the TEPA distribution is affected by the method of introduction. Both samples showed excellent adsorption capacities but poor cyclic stability for lack of any covalent attachment. Furthermore the method of TEPA impregnation seems to be independent on how the polymer will be distributed in the pore space of aerogel. The last two methods utilized involved covalently attaching amino silanes to the surface silanols of the aerogel. One method was performed in the liquid phase under anhydrous and hydrous conditions. The materials developed through the hydrous method have much greater adsorption capacities relative to the anhydrous sample as a result of the greater amine content present in the hydrous sample. Water is another source of silylation where additional silanes can attach and polymerize. These samples also possessed stable cyclic stability after 100 adsorption/regeneration cycles. The other method of grafting was performed in the gas phase through ALD. These samples possessed exceptionally high amine efficiencies and levels of N content without damaging the microstructure of the aerogel in contrast to the liquid phase grafted sorbents.
ContributorsLinneen, Nick (Author) / Lin, Jerry (Thesis advisor) / Pfeffer, Robert (Thesis advisor) / Lind, Mary (Committee member) / Rege, Kaushal (Committee member) / Nielsen, David (Committee member) / Anderson, James (Committee member) / Arizona State University (Publisher)
Created2014
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
Depletion of fossil fuel resources has led to the investigation of alternate feedstocks for and methods of chemical synthesis, in particular the use of E. coli biocatalysts to produce fine commodity chemicals from renewable glucose sources. Production of phenol, 2-phenylethanol, and styrene was investigated, in particular the limitation in yield and accumulation that results from high product toxicity. This paper examines two methods of product toxicity mitigation: the use of efflux pumps and the separation of pathways which produce less toxic intermediates. A library of 43 efflux pumps from various organisms were screened for their potential to confer resistance to phenol, 2-phenylethanol, and styrene on an E. coli host. A pump sourced from P. putida was found to allow for increased host growth in the presence of styrene as compared to a cell with no efflux pump. The separation of styrene producing pathway was also investigated. Cells capable of performing the first and latter halves of the synthesis were allowed to grow separately and later combined in order to capitalize on the relatively lower toxicity of the intermediate, trans-cinnamate. The styrene production and yield from this separated set of cultures was compared to that resulting from the growth of cells containing the full set of styrene synthesis genes. Results from this experiment were inconclusive.
ContributorsLallmamode, Noor Atiya Jabeen (Author) / Nielsen, David (Thesis director) / Cadillo-Quiroz, Hinsby (Committee member) / Barrett, The Honors College (Contributor) / Chemical Engineering Program (Contributor) / School of Life 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
The goals of the styrene oxide adsorption experiments were to develop reliable isotherms of styrene oxide onto Dowex Optipore L-493 resin and onto mesoporous carbon adsorbents, in addition to determining the ideal conditions for styrene oxide production from E. coli. Adsorption is an effective means of separation used in industry to separate compounds, often organics from air and water. Styrene oxide adsorption runs without E. coli were conducted at concentrations ranging from 0.15 to 3.00 g/L with resin masses ranging from 0.1 to 0.5 g of Dowex Optipore L-493 and 0.5 to 0.75 g of mesoporous carbon adsorbent. Runs were conducted on a shake plate operating at 80 rpm for 24 hours at ambient temperature. Isotherms were developed from the results and then adsorption experiments with E. coli and L-493 were performed. Runs were conducted at glucose concentrations ranging from 20-40 g/L and resin masses of 0.100 g to 0.800 g. Samples were incubated for 72 hours and styrene oxide production was measured using an HPLC device. Specific loading values reached up to 0.356 g/g for runs without E. coli and nearly 0.003 g of styrene oxide was adsorbed by L-493 during runs with E. coli. Styrene oxide production was most effective at low resin masses and medium glucose concentrations when produced by E. coli.
ContributorsHsu, Joshua (Co-author) / Oremland, Zachary (Co-author) / Nielsen, David (Thesis director) / Staggs, Kyle (Committee member) / Barrett, The Honors College (Contributor) / Chemical Engineering Program (Contributor) / School of Sustainability (Contributor)
Created2014-05
Description
The inability of a single strain of bacteria to simultaneously and completely consume multiple sugars, such as glucose and xylose, hinder industrial microbial processes for ethanol and lactate production. To overcome this limitation, I am engineering an E. coli co-culture system consisting of two ‘specialists'. One has the ability to only consume xylose and the other only glucose. This allows for co-utilization of lignocellulose-derived sugars so both sugars are completely consumed, residence time is reduced and lactate and ethanol titers are maximized.
ContributorsAyla, Zeynep Ece (Author) / Nielsen, David (Thesis director) / Flores, Andrew (Committee member) / Chemical Engineering Program (Contributor) / School of Sustainability (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
Escherichia coli is a bacterium that is used widely in metabolic engineering due to its ability to grow at a fast rate and to be cultured easily. E. coli can be engineered to produce many valuable chemicals, including biofuels and L-Phenylalanine—a precursor to many pharmaceuticals. Significant cell growth occurs in parallel to the biosynthesis of the desired biofuel or biochemical product, and limits product concentrations and yields. Stopping cell growth can improve chemical production since more resources will go toward chemical production than toward biomass. The goal of the project is to test different methods of controlling microbial uptake of nutrients, specifically phosphate, to dynamically limit cell growth and improve biochemical production of E. coli, and the research has the potential to promote public health, sustainability, and environment. This can be achieved by targeting phosphate transporter genes using CRISPRi and CRISPR, and they will limit the uptake of phosphate by targeting the phosphate transporter genes in DNA, which will stop transcriptions of the genes. In the experiment, NST74∆crr∆pykAF, a L-Phe overproducer, was used as the base strain, and the pitA phosphate transporter gene was targeted in the CRISPRi and CRISPR systems with the strain with other phosphate transporters knocked out. The tested CRISPRi and CRISPR mechanisms did not stop cell growth or improved L-Phe production. Further research will be conducted to determine the problem of the system. In addition, the CRISPRi and CRISPR systems that target multiple phosphate transporter genes will be tested in the future as well as the other method of stopping transcriptions of the phosphate transporter genes, which is called a tunable toggle switch mechanism.
ContributorsPark, Min Su (Author) / Nielsen, David (Thesis director) / Machas, Michael (Committee member) / Chemical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Amine-modified solid sorbents and membrane separation are promising technologies for separation and capture of carbon dioxide (CO2) from combustion flue gas. Amine absorption processes are mature, but still have room for improvement. This work focused on the synthesis of amine-modified aerogels and metal-organic framework-5 (MOF-5) membranes for CO2 separation. A series of solid sorbents were synthesized by functionalizing amines on the surface of silica aerogels. This was done by three coating methods: physical adsorption, magnetically assisted impact coating (MAIC) and atomic layer deposition (ALD). CO2 adsorption capacity of the sorbents was measured at room temperature in a Cahn microbalance. The sorbents synthesized by physical adsorption show the largest CO2 adsorption capacity (1.43-1.63 mmol CO2/g). An additional sorbent synthesized by ALD on hydrophilic aerogels at atmospheric pressures shows an adsorption capacity of 1.23 mmol CO2/g. Studies on one amine-modified sorbent show that the powder is of agglomerate bubbling fluidization (ABF) type. The powder is difficult to fluidize and has limited bed expansion. The ultimate goal is to configure the amine-modified sorbents in a micro-jet assisted gas fluidized bed to conduct adsorption studies. MOF-5 membranes were synthesized on α-alumina supports by two methods: in situ synthesis and secondary growth synthesis. Characterization by scanning electron microscope (SEM) imaging and X-ray diffraction (XRD) show that the membranes prepared by both methods have a thickness of 14-16 μm, and a MOF-5 crystal size of 15-25 μm with no apparent orientation. Single gas permeation results indicate that the gas transport through both membranes is determined by a combination of Knudsen diffusion and viscous flow. The contribution of viscous flow indicates that the membranes have defects.
ContributorsRosa, Teresa M (Author) / Lin, Jerry (Thesis advisor) / Pfeffer, Robert (Thesis advisor) / Dai, Lenore (Committee member) / Nielsen, David (Committee member) / Arizona State University (Publisher)
Created2010
Description
Four enzymes, ATF1, ATF2, ATF, and CAT, were screened to determine which would be most effective at catalyzing the formation of aromatic esters. The CAT enzyme successfully catalyzed the reaction to produce 2-phenethyl acetate using 20x more lysate to improve the probability of enzyme presence in the lysate. The CAT enzyme was able to catalyze the reaction producing concentrations that increased by 62% every 12 hours. Enzymatic activity resulted in the production of 2.15 mg/L of 2-phenethyl acetate at 12 hours, 5.62 mg/L of 2-phenethyl acetate at 24 hours, and 15.12 mg/L of 2-phenethyl acetate at 48 hours.
ContributorsBrown, Kristen Ashley (Author) / Nielsen, David (Thesis director) / Thompson, Brian (Committee member) / Chemical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05