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- Member of: Barrett, The Honors College Thesis/Creative Project Collection
Description
With the aid of metabolic pathways engineering, microbes are finding increased use as biocatalysts to convert renewable biomass resources into fine chemicals, pharmaceuticals and other valuable compounds. These alternative, bio-based production routes offer distinct advantages over traditional synthesis methods, including lower energy requirements, rendering them as more "green" and "eco-friendly". Escherichia coli has recently been engineered to produce the aromatic chemicals (S)-styrene oxide and phenol directly from renewable glucose. Several factors, however, limit the viability of this approach, including low titers caused by product inhibition and/or low metabolic flux through the engineered pathways. This thesis focuses on addressing these concerns using magnetic mesoporous carbon powders as adsorbents for continuous, in-situ product removal as a means to alleviate such limitations. Using process engineering as a means to troubleshoot metabolic pathways by continuously removing products, increased yields are achieved from both pathways. By performing case studies in product toxicity and reaction equilibrium it was concluded that each step of a metabolic pathway can be optimized by the strategic use of in-situ adsorption as a process engineering tool.
ContributorsVasudevan, Anirudh (Author) / Nielsen, David R (Thesis advisor) / Torres, César I (Committee member) / Wang, Xuan (Committee member) / Arizona State University (Publisher)
Created2014
Description
The Multiple Antibiotic Resistance Regulator Family (MarR) are transcriptional regulators, many of which forms a dimer. Transcriptional regulation provides bacteria a stabilized responding system to ensure the bacteria is able to efficiently adapt to different environmental conditions. The main function of the MarR family is to create multiple antibiotic resistance from a mutated protein; this process occurs when the MarR regulates an operon. We hypothesized that different transcriptional regulator genes have interactions with each other. It is known that Salmonella pagC transcription is activated by three regulators, i.e., SlyA, MprA, and PhoP. Bacterial Adenylate Cyclase-based Two-Hybrid (BACTH) system was used to research the protein-protein interactions in SlyA, MprA, and PhoP as heterodimers and homodimers in vivo. Two fragments, T25 and T18, that lack endogenous adenylate cyclase activity, were used for construction of chimeric proteins and reconstruction of adenylate cyclase activity was tested. The significant adenylate cyclase activities has proved that SlyA is able to form homodimers. However, weak adenylate cyclase activities in this study has proved that MprA and PhoP are not likely to form homodimers, and no protein-protein interactions were detected in between SlyA, MprA and PhoP, which no heterodimers have formed in between three transcriptional regulators.
ContributorsTao, Zenan (Author) / Shi, Yixin (Thesis advisor) / Wang, Xuan (Committee member) / Bean, Heather (Committee member) / Arizona State University (Publisher)
Created2018
Description
Lignocellulosic biomass represents a renewable domestic feedstock that can support large-scale biochemical production processes for fuels and specialty chemicals. However, cost-effective conversion of lignocellulosic sugars into valuable chemicals by microorganisms still remains a challenge. Biomass recalcitrance to saccharification, microbial substrate utilization, bioproduct titer toxicity, and toxic chemicals associated with chemical pretreatments are at the center of the bottlenecks limiting further commercialization of lignocellulose conversion. Genetic and metabolic engineering has allowed researchers to manipulate microorganisms to overcome some of these challenges, but new innovative approaches are needed to make the process more commercially viable. Transport proteins represent an underexplored target in genetic engineering that can potentially help to control the input of lignocellulosic substrate and output of products/toxins in microbial biocatalysts. In this work, I characterize and explore the use of transport systems to increase substrate utilization, conserve energy, increase tolerance, and enhance biocatalyst performance.
ContributorsKurgan, Gavin (Author) / Wang, Xuan (Thesis advisor) / Nielsen, David (Committee member) / Misra, Rajeev (Committee member) / Nannenga, Brent (Committee member) / Arizona State University (Publisher)
Created2018
Description
Peatlands represent 3% of the earth’s surface but have been estimated to contain up to 30% of all terrestrial soil organic carbon and release an estimated 40% of global atmospheric CH4 emissions. Contributors to the production of CH4 are methanogenic Archaea through a coupled metabolic dependency of end products released by heterotrophic bacteria within the soil in the absence of O2. To better understand how neighboring bacterial communities can influence methanogenesis, the isolation and physiological characterization of two novel isolates, one Methanoarchaeal isolate and one Acidobacterium isolate identified as QU12MR and R28S, respectively, were targeted in this present study. Co-culture growth in varying temperatures of the QU12MR isolate paired with an isolated Clostridium species labeled R32Q and the R28S isolate were also investigated for possible influences in CH4 production. Phylogenetic analysis of strain QU12MR was observed as a member of genus Methanobacterium sharing 98% identity similar to M. arcticum strain M2 and 99% identity similar to M. uliginosum strain P2St. Phylogenetic analysis of strain R28S was associated with genus Acidicapsa from the phylum Acidobacteria, sharing 97% identity to A. acidisoli strain SK-11 and 96% identity similarity to Occallatibacter savannae strain A2-1c. Bacterial co-culture growth and archaeal CH4 production was present in the five temperature ranges tested. However, bacterial growth and archaeal CH4 production was less than what was observed in pure culture analysis after 21 days of incubation.
ContributorsRamirez, Zeni Elizia (Author) / Cadillo-Quiroz, Hinsby (Thesis advisor) / Roberson, Robert (Thesis advisor) / Wang, Xuan (Committee member) / Arizona State University (Publisher)
Created2018
Description
Synechocystis sp. PCC 6803 is a readily transformable cyanobacteria used to study cyanobacterial genetics, as well as production of biofuels, polyesters, and other industrial chemicals. Free fatty acids are precursors to biofuels which are used by Synechocystis cells as a means of energy storage. By genetically modifying the cyanobacteria to expel these chemicals, costs associated with retrieving the products will be reduced; concurrently, the bacteria will be able to produce the products at a higher concentration. This is achieved by adding genes encoding components of the Escherichia coli AcrAB-TolC efflux system, part of the resistance-nodulation-division (RND) transporter family, to Synechocystis sp. PCC 6803. AcrAB-TolC is a relatively promiscuous multidrug efflux pump that is noted for expelling a wide range of substrates including dyes, organic solvents, antibiotics, and free fatty acids. Adding components of the AcrAB-TolC multidrug efflux pump to a previously created high free fatty acid producing strain, SD277, allowed cells to move more free fatty acids to the extracellular environment than did the parent strain. Some of these modifications also improved tolerance to antibiotics and a dye, rhodamine 6G. To confirm the function of this exogenous efflux pump, the genes encoding components of the AcrAB-TolC efflux pump were also added to Synechocystis sp. PCC 6803 and shown to grow on a greater concentration of various antibiotics and rhodamine 6G. Various endogenous efflux systems have been elucidated, but their usefulness in expelling products currently generated in Synechocystis is limited. Most of the elucidated pumps in the cyanobacteria are part of the ATP-binding cassette superfamily. The knowledge of the resistance-nodulation-division (RND) family transporters is limited. Two genes in Synechocystis sp. PCC 6803, slr2131 and sll0180 encoding homologs to the genes that encode acrB and acrA, respectively, were removed and the modifications resulted in changes in resistance to various antibiotics and a dye and also had an impact on free fatty acid secretion. Both of these deletions were complemented independently with the homologous E. coli gene and the resulting cyanobacteria strains had some of the inherent resistance restored to chloramphenicol and free fatty acid secretion was modified when compared to the wild-type and a high free fatty acid producing strain.
ContributorsBellefleur, Matthew Paul Allen (Author) / Curtiss, III, Roy (Thesis advisor) / Nielsen, David R (Committee member) / Wang, Xuan (Committee member) / Rittmann, Bruce E. (Committee member) / Arizona State University (Publisher)
Created2018
Description
Engineering is a multidisciplinary field with a variety of applications. However, since there are so many disciplines of engineering, it is often challenging to find the discipline that best suits an individual interested in engineering. Not knowing which area of engineering most aligns to one’s interests is challenging when deciding on a major and a career. With the development of the Engineering Interest Quiz (EIQ), the goal was to help individuals find the field of engineering that is most similar to their interests. Initially, an Engineering Faculty Survey (EFS) was created to gather information from engineering faculty at Arizona State University (ASU) and to determine keywords that describe each field of engineering. With this list of keywords, the EIQ was developed. Data from the EIQ compared the engineering students’ top three results for the best engineering discipline for them with their current engineering major of study. The data analysis showed that 70% of the respondents had their major listed as one of the top three results they were given and 30% of the respondents did not have their major listed. Of that 70%, 64% had their current major listed as the highest or tied for the highest percentage and 36% had their major listed as the second or third highest percentage. Furthermore, the EIQ data was compared between genders. Only 33% of the male students had their current major listed as their highest percentage, but 55% had their major as one of their top three results. Women had higher percentages with 63% listing their current major as their highest percentage and 81% listing it in the top three of their final results.
ContributorsWagner, Avery Rose (Co-author) / Lucca, Claudia (Co-author) / Taylor, David (Thesis director) / Miller, Cindy (Committee member) / Chemical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
The impact of physical/chemical properties of gray water on microbial inactivation in gray water using chlorine was investigated through creating artificial gray water in lab, varying specific components, and then measuring microbial inactivation. Gray water was made through taking autoclaved nanopure water, and increasing the concentration of surfacants, the turbidity, the concentration of organic content, and spiking E. coli grown in tryptic soy broth (TSB); chlorine was introduced using Clorox Disinfecting Bleach2. Bacteria was detected using tryptic soy agar (TSA), and E. coli was specifically detected using the selective media, brilliance. The log inactivation of bacteria detected using TSA was shown to be inversely related to the turbidity of the solution. Complete inactivation of E. coli concentrations between 104-105 CFU/100 ml in gray water with turbidities between 10-100 NTU, 0.1-0.5 mg/L of humic acid, and 0.1 ml of Dawn Ultra, was shown to occur, as detected by brilliance, at chlorine concentrations of 1-2 mg/L within 30 seconds. These result in concentration time (CT) values between 0.5-1 mg/L·min. Under the same gray water conditions, and an E. coli concentration of 104 CFU/100 ml and a chlorine concentration of 0.01 mg/L, complete inactivation was shown to occur in all trials within two minutes. These result in CT values ranging from 0.005 to 0.02. The turbidity and humic acid concentration were shown to be inversely related to the log inactivation and directly related to the CT value. This study shows that chlorination is a valid method of treatment of gray water for certain irrigation reuses.
ContributorsGreenberg, Samuel Gabe (Author) / Abbaszadegan, Morteza (Thesis director) / Schoepf, Jared (Committee member) / Alum, Absar (Committee member) / Chemical Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Increasing energy and environmental problems describe the need to develop renewable chemicals and fuels. Global research has been targeting using microbial systems on a commercial scale for synthesis of valuable compounds. The goal of this project was to refactor and overexpress b6-f complex proteins in cyanobacteria to improve photosynthesis under dynamic light conditions. Improvement in the photosynthetic system can directly relate to higher yields of valuable compounds such as carotenoids and higher yields of biomass which can be used as energy molecules. Four engineered strains of cyanobacteria were successfully constructed and overexpressed the corresponding four large subunits in the cytochrome b6-f complex. No significant changes were found in cell growth or pigment titer in the modified strains compared to the wild type. The growth assay will be performed at higher and/or dynamic light intensities including natural light conditions for further analysis.
ContributorsNauroth, Benjamin (Author) / Varman, Arul (Thesis director) / Singharoy, Abhishek (Committee member) / Li, Han (Committee member) / Chemical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
This research investigated deionized water contact angle measurement reliability with alumina powder using the Washburn method. This method relates the capillary rise of a liquid through a column of packed powder to the contact angle of the system. A reference liquid that is assumed to be perfectly wetting, such as hexane due to the low surface energy, must be used to compare to the tested liquid. Consistency was hypothesized to be achieved with more powder structure and consistency of packing between reference and test trials. The three types of packing structures explored in this study were unstructured, visually-structured (user tapped), and machine-structured tapping. It was also hypothesized that similar contact angle results would be found for different packing methods of the same powder and liquid. However, the average contact angle for unstructured packing was found to be 32.9°, while the angle for the tapped structure was only 11.7°. This large deviation between types of packing shows that there are more inconsistencies with the use of this method than just the regulation of the packing structure. There were two similar glass chromatography columns used, but the second column experienced an unknown interference that led to a delay in the hexane uptake into the powder, which then led to invalid contact angle calculations. There was no discernible relationship between the packing structure and the standard deviation between trials, so the more structured packing does not seem to affect the consistency of results. It is recommended to perform more experiments on a single packing type with different apparatuses and a narrower particle size range.
ContributorsConvery, Brittany Alexis (Author) / Emady, Heather (Thesis director) / Vajrala, Spandana (Committee member) / Chemical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
Description
The Experimental Data Processing (EDP) software is a C++ GUI-based application to streamline the process of creating a model for structural systems based on experimental data. EDP is designed to process raw data, filter the data for noise and outliers, create a fitted model to describe that data, complete a probabilistic analysis to describe the variation between replicates of the experimental process, and analyze reliability of a structural system based on that model. In order to help design the EDP software to perform the full analysis, the probabilistic and regression modeling aspects of this analysis have been explored. The focus has been on creating and analyzing probabilistic models for the data, adding multivariate and nonparametric fits to raw data, and developing computational techniques that allow for these methods to be properly implemented within EDP. For creating a probabilistic model of replicate data, the normal, lognormal, gamma, Weibull, and generalized exponential distributions have been explored. Goodness-of-fit tests, including the chi-squared, Anderson-Darling, and Kolmogorov-Smirnoff tests, have been used in order to analyze the effectiveness of any of these probabilistic models in describing the variation of parameters between replicates of an experimental test. An example using Young's modulus data for a Kevlar-49 Swath stress-strain test was used in order to demonstrate how this analysis is performed within EDP. In order to implement the distributions, numerical solutions for the gamma, beta, and hypergeometric functions were implemented, along with an arbitrary precision library to store numbers that exceed the maximum size of double-precision floating point digits. To create a multivariate fit, the multilinear solution was created as the simplest solution to the multivariate regression problem. This solution was then extended to solve nonlinear problems that can be linearized into multiple separable terms. These problems were solved analytically with the closed-form solution for the multilinear regression, and then by using a QR decomposition to solve numerically while avoiding numerical instabilities associated with matrix inversion. For nonparametric regression, or smoothing, the loess method was developed as a robust technique for filtering noise while maintaining the general structure of the data points. The loess solution was created by addressing concerns associated with simpler smoothing methods, including the running mean, running line, and kernel smoothing techniques, and combining the ability of each of these methods to resolve those issues. The loess smoothing method involves weighting each point in a partition of the data set, and then adding either a line or a polynomial fit within that partition. Both linear and quadratic methods were applied to a carbon fiber compression test, showing that the quadratic model was more accurate but the linear model had a shape that was more effective for analyzing the experimental data. Finally, the EDP program itself was explored to consider its current functionalities for processing data, as described by shear tests on carbon fiber data, and the future functionalities to be developed. The probabilistic and raw data processing capabilities were demonstrated within EDP, and the multivariate and loess analysis was demonstrated using R. As the functionality and relevant considerations for these methods have been developed, the immediate goal is to finish implementing and integrating these additional features into a version of EDP that performs a full streamlined structural analysis on experimental data.
ContributorsMarkov, Elan Richard (Author) / Rajan, Subramaniam (Thesis director) / Khaled, Bilal (Committee member) / Chemical Engineering Program (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Ira A. Fulton School of Engineering (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05