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Description
Ethanol is a widely used biofuel in the United States that is typically produced through the fermentation of biomass feedstocks. Demand for ethanol has grown significantly from 2000 to 2015 chiefly due to a desire to increase energy independence and reduce the emissions of greenhouse gases associated with transportation. As demand grows, new ethanol plants must be developed in order for supply to meet demand. This report covers some of the major considerations in developing these new plants such as the type of biomass used, feed treatment process, and product separation and investigates their effect on the economic viability and environmental benefits of the ethanol produced. The dry grind process for producing ethanol from corn, the most common method of production, is examined in greater detail. Analysis indicates that this process currently has the highest capacity for production and profitability but limited effect on greenhouse gas emissions compared to less common alternatives.
ContributorsSchrilla, John Paul (Author) / Kashiwagi, Dean (Thesis director) / Kashiwagi, Jacob (Committee member) / Barrett, The Honors College (Contributor) / Chemical Engineering Program (Contributor)
Created2015-05
Description
Transgene expression in mammalian cells has been shown to meet resistance in the form of silencing due to chromatin buildup within the cell. Interactions of proteins with chromatin modulate gene expression profiles. Synthetic Polycomb transcription factor (PcTF) variants have the potential to reactivate these silence transgenes as shown in Haynes & Silver 2011. PcTF variants have been constructed via TypeIIS assembly to further investigate this ability to reactive transgenes. Expression in mammalian cells was confirmed via fluorescence microscopy and red fluorescent protein (RFP) expression in cell lysate. Examination of any variation in conferment of binding strength of homologous Polycomb chromodomains (PCDs) to its trimethylated lysine residue target on histone three (H3K27me3) was investigated using a thermal shift assay. Results indicate that PcTF may not be a suitable protein for surveying with SYPRO Orange, a dye that produces a detectable signal when exposed to the hydrophobic domains of the melting protein. A cell line with inducible silencing of a chemiluminescent protein was used to determine the effects PcTF variants had on gene reactivation. Results show down-regulation of the target reporter gene. We propose this may be due to PcTF not binding to its target; this would cause PcTF to deplete transcriptional machinery in the nucleus. Alternatively, the CMV promoter could be sequestering transcriptional machinery in its hyperactive transcription of PcTF leading to widespread down-regulation. Finally, the activation domain used may not be appropriate for this cell type. Future PcTF variants will address these hypotheses by including multiple Polycomb chromodomains (PCDs) to alter the binding dynamics of PcTF to its target, and by incorporating alternative promoters and activation domains.
ContributorsGardner, Cameron Lee (Author) / Haynes, Karmella (Thesis director) / Stabenfeldt, Sarah (Committee member) / Barrett, The Honors College (Contributor) / Department of Finance (Contributor) / Harrington Bioengineering Program (Contributor)
Created2015-05
Description
Calcium hydroxide carbonation processes were studied to investigate the potential for abiotic soil improvement. Different mixtures of common soil constituents such as sand, clay, and granite were mixed with a calcium hydroxide slurry and carbonated at approximately 860 psi. While the carbonation was successful and calcite formation was strong on sample exteriors, a 4 mm passivating boundary layer effect was observed, impeding the carbonation process at the center. XRD analysis was used to characterize the extent of carbonation, indicating extremely poor carbonation and therefore CO2 penetration inside the visible boundary. The depth of the passivating layer was found to be independent of both time and choice of aggregate. Less than adequate strength was developed in carbonated trials due to formation of small, weakly-connected crystals, shown with SEM analysis. Additional research, especially in situ analysis with thermogravimetric analysis would be useful to determine the causation of poor carbonation performance. This technology has great potential to substitute for certain Portland cement applications if these issues can be addressed.
ContributorsHermens, Stephen Edward (Author) / Bearat, Hamdallah (Thesis director) / Dai, Lenore (Committee member) / Mobasher, Barzin (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
Synthetic biology is an emerging engineering disciple, which designs and controls biological systems for creation of materials, biosensors, biocomputing, and much more. To better control and engineer these systems, modular genetic components which allow for highly specific and high dynamic range genetic regulation are necessary. Currently the field struggles to demonstrate reliable regulators which are programmable and specific, yet also allow for a high dynamic range of control. Inspired by the characteristics of the RNA toehold switch in E. coli, this project attempts utilize artificial introns and complementary trans-acting RNAs for gene regulation in a eukaryote host, S. cerevisiae. Following modification to an artificial intron, splicing control with RNA hairpins was demonstrated. Temperature shifts led to increased protein production likely due to increased splicing due to hairpin loosening. Progress is underway to demonstrate trans-acting RNA interaction to control splicing. With continued development, we hope to provide a programmable, specific, and effective means for translational gene regulation in S. cerevisae.
ContributorsDorr, Brandon Arthur (Author) / Wang, Xiao (Thesis director) / Green, Alexander (Committee member) / Harrington Bioengineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Currently, approximately 40% of the world’s electricity is generated from coal and coal power plants are one of the major sources of greenhouse gases accounting for a third of all CO2 emissions. The Integrated Gasification Combined Cycle (IGCC) has been shown to provide an increase in plant efficiency compared to traditional coal-based power generation processes resulting in a reduction of greenhouse gas emissions. The goal of this project was to analyze the performance of a new SNDC ceramic-carbonate dual-phase membrane for CO2 separation. The chemical formula for the SNDC-carbonate membrane was Sm0.075Nd0.075Ce0.85O1.925. This project also focused on the use of this membrane for pre-combustion CO2 capture coupled with a water gas shift (WGS) reaction for a 1000 MW power plant. The addition of this membrane to the traditional IGCC process provides a purer H2 stream for combustion in the gas turbine and results in lower operating costs and increased efficiencies for the plant. At 900 °C the CO2 flux and permeance of the SNDC-carbonate membrane were 0.65 mL/cm2•min and 1.0×10-7 mol/m2•s•Pa, respectively. Detailed in this report are the following: background regarding CO2 separation membranes and IGCC power plants, SNDC tubular membrane preparation and characterization, IGCC with membrane reactor plant design, process heat and mass balance, and plant cost estimations.
ContributorsDunteman, Nicholas Powell (Author) / Lin, Jerry (Thesis director) / Dong, Xueliang (Committee member) / Barrett, The Honors College (Contributor) / Chemical Engineering Program (Contributor) / School of Sustainability (Contributor)
Created2014-05
Description
p-Coumaric acid is used in the food, pharmaceutical, and cosmetic industries due to its versatile properties. While prevalent in nature, harvesting the compound from natural sources is inefficient, requiring large quantities of producing crops and numerous extraction and purification steps. Thus, the large-scale production of the compound is both difficult and costly. This research aims to produce p-coumarate directly from renewable and sustainable glucose using a co-culture of Yeast and E. Coli. Methods used in this study include: designing optimal media for mixed-species microbial growth, genetically engineering both strains to build the production pathway with maximum yield, and analyzing the presence of p-Coumarate and its pathway intermediates using High Performance Liquid Chromatography (HPLC). To date, the results of this project include successful integration of C4H activity into the yeast strain BY4741 ∆FDC1, yielding a strain that completely consumed trans-cinnamate (initial concentration of 50 mg/L) and produced ~56 mg/L p-coumarate, a resting cell assay of the co-culture that produced 0.23 mM p-coumarate from an initial L-Phenylalanine concentration of 1.14 mM, and toxicity tests that confirmed the toxicity of trans-cinnamate to yeast for concentrations above ~50 mg/L. The hope for this project is to create a feasible method for producing p-Coumarate sustainably.
ContributorsJohnson, Kaleigh Lynnae (Author) / Nielsen, David (Thesis director) / Thompson, Brian (Committee member) / Chemical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
In the pursuit of sustainable sources of energy that do less harm to the environment, numerous technologies have been developed to reduce carbon emissions in the atmosphere. The implementation of carbon capture and storage systems (CCS) has played a crucial role in reducing CO2 emissions, but depleting storage reserves and ever-increasing costs of sequestrating captured CO2 has prompted the idea of utilizing CO2 as soon as it is produced (i.e. carbon capture and utilization, or CCU) and storing any remaining amounts. This project analyzes the cost of implementing a delafossite CuFeO2 backed CCU system for the average US coal-burning power plant with respect to current amounts of CO2 captured. Beyond comparing annual maintenance costs of CCU and CCS systems, the project extends previous work done on direct CO2 conversion to liquid hydrocarbons by providing a protocol for determining how the presence of NO affects the products formed during pure CO2 hydrogenation. Overall, the goal is to gauge the applicability of CCU systems to power plants with a sub 10-year lifespan left, whilst observing the potential revenue that can be potentially generated from CCU implementation. Under current energy costs ($0.12 per kWh), a delafossite CuFeO2 supported CCU system would generate over $729 thousand in profit for an average sized supercritical pulverized coal power (SCPC) plants selling diesel fuel created from CO2 hydrogenation. This amount far exceeds the cost of storing captured CO2 and suggests that CCU systems can be profitable for SCPC power plants that intend to burn coal until 2025.
ContributorsShongwe, Thembelihle Wakhile (Author) / Andino, Jean (Thesis director) / Otsengue, Thonya (Committee member) / Economics Program in CLAS (Contributor) / Chemical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Polymer modified tuning fork-based sensors were fabricated to assure reproducibility. The effect of system valve switching on the modified tuning fork-based sensors was studied at the different temperature. The response to Xylene gas sample on stabilized modified tuning fork-based sensors with temperature was defined while learning about the key analytical performance for chemical sensors to be used in the real-world application.
ContributorsRohit, Riddhi S (Author) / Forzani, Erica (Thesis director) / Tsow, Francis (Committee member) / Dean, W.P. Carey School of Business (Contributor) / Chemical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05