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- All Subjects: chemical engineering
- All Subjects: Biology
- Genre: Masters Thesis
- Creators: Wang, Xuan
- Creators: Mu, Bin
- Resource Type: Text
Description
Single and double deletion strains of Escherichia coli were grown in paired co-cultures with an intent to identify examples of metabolite exchange and cooperative interactions between strains. The essential genes pheA, argA, tyrA, and trpC, as well as the non- essential genes pykF, pykA, mdh, ppc, and nuoN were deleted from Escherichia coli strains Bw25113 and ATCC 9637. Cultures were paired at three different initial ratios and grown at plate and flask scale. Optical density measurements were used to observe the performance of tested co-cultures, with changes in maximum optical density and growth rate used as indicators of interaction or lack thereof between tested pairs. Auxotrophic strains unable to produce essential amino acids were observed to grow in co-culture but not in monoculture, indicative of metabolite exchange facilitating growth. An increase in optical density for non-essential pairs when compared to the prototrophic parent and precursor monocultures was indicative of metabolite exchange. The initial frequency of paired mutants with non-essential deletions appeared to have an impact on growth performance, but whether this was indicative of any beneficial exchange was not able to be determined from data.
ContributorsFenner, Alexander James (Author) / Nielsen, David (Thesis advisor) / Wang, Xuan (Committee member) / Varman, Arul (Committee member) / Arizona State University (Publisher)
Created2022
Description
Reactive oxygen species (ROS) including superoxide, hydrogen peroxide, and hydroxyl radicals occur naturally as a byproduct of aerobic respiration. To mitigate damages caused by ROS, Escherichia coli employs defenses including two cytosolic superoxide dismutases (SODs), which convert superoxide to hydrogen peroxide. Deletion of both sodA and sodB, the genes coding for the cytosolic SOD enzymes, results in a strain that is unable to grow on minimal medium without amino acid supplementation. Additionally, deletion of both cytosolic SOD enzymes in a background containing the relA1 allele, an inactive version of the relA gene that contributes to activation of stringent response by amino acid starvation, results in a strain that is unable to grow aerobically, even on rich medium. These observations point to a relationship between the stringent response and oxidative stress. To gain insight into this relationship, suppressors were isolated by growing the ∆sodAB relA1 cells aerobically on rich medium, and seven suppressors were further examined to characterize distinct colony sizes and temperature sensitivity phenotypes. In three of these suppressor-containing strains, the relA1 allele was successfully replaced by the wild type relA allele to allow further study in aerobic conditions. None of those three suppressors were found to increase tolerance to exogenous superoxides produced by paraquat, which shows that these mutations only overcome the superoxide buildup that naturally occurs from deletion of SODs. Because each of these suppressors had unique phenotypes, it is likely that they confer tolerance to SOD-dependent superoxide buildup by different mechanisms. Two of these three suppressors have been sent for whole-genome sequencing to identify the location of the suppressor mutation and determine the mechanism by which they confer superoxide tolerance.
ContributorsFlake, Melissa (Author) / Misra, Rajeev (Thesis advisor) / Shah, Dhara (Committee member) / Wang, Xuan (Committee member) / Arizona State University (Publisher)
Created2024
Description
The large-scale anthropogenic emission of carbon dioxide into the atmosphere leads to many unintended consequences, from rising sea levels to ocean acidification. While a clean energy infrastructure is growing, mid-term strategies that are compatible with the current infrastructure should be developed. Carbon capture and storage in fossil-fuel power plants is one way to avoid our current gigaton-scale emission of carbon dioxide into the atmosphere. However, for this to be possible, separation techniques are necessary to remove the nitrogen from air before combustion or from the flue gas after combustion. Metal-organic frameworks (MOFs) are a relatively new class of porous material that show great promise for adsorptive separation processes. Here, potential mechanisms of O2/N2 separation and CO2/N2 separation are explored.
First, a logical categorization of potential adsorptive separation mechanisms in MOFs is outlined by comparing existing data with previously studied materials. Size-selective adsorptive separation is investigated for both gas systems using molecular simulations. A correlation between size-selective equilibrium adsorptive separation capabilities and pore diameter is established in materials with complex pore distributions. A method of generating mobile extra-framework cations which drastically increase adsorptive selectivity toward nitrogen over oxygen via electrostatic interactions is explored through experiments and simulations. Finally, deposition of redox-active ferrocene molecules into systematically generated defects is shown to be an effective method of increasing selectivity towards oxygen.
First, a logical categorization of potential adsorptive separation mechanisms in MOFs is outlined by comparing existing data with previously studied materials. Size-selective adsorptive separation is investigated for both gas systems using molecular simulations. A correlation between size-selective equilibrium adsorptive separation capabilities and pore diameter is established in materials with complex pore distributions. A method of generating mobile extra-framework cations which drastically increase adsorptive selectivity toward nitrogen over oxygen via electrostatic interactions is explored through experiments and simulations. Finally, deposition of redox-active ferrocene molecules into systematically generated defects is shown to be an effective method of increasing selectivity towards oxygen.
ContributorsMcIntyre, Sean (Author) / Mu, Bin (Thesis advisor) / Green, Matthew (Committee member) / Lind, Marylaura (Committee member) / Arizona State University (Publisher)
Created2019
Description
In the past, the photovoltaic (PV) modules were typically constructed with glass superstrate containing cerium oxide and EVA (ethylene vinyl acetate) encapsulant containing UV absorbing additives. However, in the current industry, the PV modules are generally constructed without cerium oxide in the glass and UV absorbing additives in EVA to increase quantum efficiency of crystalline silicon solar cells in the UV regions. This new approach is expected to boost the initial power output of the modules and reduce the long-term encapsulant browning issues. However, this new approach could lead to other durability and reliability issues such as delamination of encapsulant by damaging interfacial bonds, destruction of antireflection coating on solar cells and even breakage of polymeric backbone of EVA. This work compares the durability and reliability issues of PV modules having glass without cerium oxide and EVA with (aka, UVcut or UVC) and without (aka, UVpass or UVP) UV absorbing additives. In addition, modules with UVP front and UVC back EVA have also been investigated (aka, UVhybrid or UVH). The mini-modules with nine split cells used in this work were fabricated at ASU’s Photovoltaic Reliability Laboratory. The durability and reliability caused by three stress variables have been investigated and the three variables are temperature, humidity/oxygen and UV dosage. The influence of up to 800 kWh/m2 UV dosage has been investigated at various dosage levels. Many material and device characterizations have been performed to ascertain the degradation modes and effects. The UVC modules showed encapsulant discoloration at the cell centers as expected but the UVH modules showed a ring-shaped encapsulant discoloration close to the cell edges as evidenced in the UV fluorescence (UVF) imaging study. The PV modules containing UVP on both sides of cells with limited access to humidity or oxygen through backsheet (covered backsheet with adhesive aluminum tape) seem to experience encapsulant delamination as evidenced in the UVF images. Plausible explanations for these observations have been presented.
ContributorsArularasu, Pooja (Author) / Tamizhmani, Govindasamy (Thesis advisor) / Mu, Bin (Thesis advisor) / Varman, Arul M (Committee member) / Arizona State University (Publisher)
Created2019
Description
Ethylene vinyl acetate (EVA) is the most commonly used encapsulant in photovoltaic modules. However, EVA degrades over time and causes performance losses in PV system. Therefore, EVA degradation is a matter of concern from a durability point of view.
This work compares EVA encapsulant degradation in glass/backsheet and glass/glass field-aged PV modules. EVA was extracted from three field-aged modules (two glass/backsheet and one glass/glass modules) from three different manufacturers from various regions (cell edges, cell centers, and non-cell region) from each module based on their visual and UV Fluorescence images. Characterization techniques such as I-V measurements, Colorimetry, Different Scanning Calorimetry, Thermogravimetric Analysis, Raman spectroscopy, and Fourier Transform Infrared Spectroscopy were performed on EVA samples.
The intensity of EVA discoloration was quantified using colorimetric measurements. Module performance parameters like Isc and Pmax degradation rates were calculated from I-V measurements. Properties such as degree of crystallinity, vinyl acetate content and degree of crosslinking were calculated from DSC, TGA, and Raman measurements, respectively. Polyenes responsible for EVA browning were identified in FTIR spectra.
The results from the characterization techniques confirmed that when EVA undergoes degradation, crosslinking in EVA increases beyond 90% causing a decrease in the degree of crystallinity and an increase in vinyl acetate content of EVA. Presence of polyenes in FTIR spectra of degraded EVA confirmed the occurrence of Norrish II reaction. However, photobleaching occurred in glass/backsheet modules due to the breathable backsheet whereas no photobleaching occurred in glass/glass modules because they were hermetically sealed. Hence, the yellowness index along with the Isc and Pmax degradation rates of EVA in glass/glass module is higher than that in glass/backsheet modules.
The results implied that more acetic acid was produced in the non-cell region due to its double layer of EVA compared to the front EVA from cell region. But, since glass/glass module is hermetically sealed, acetic acid gets entrapped inside the module further accelerating EVA degradation whereas it diffuses out through backsheet in glass/backsheet modules. Hence, it can be said that EVA might be a good encapsulant for glass/backsheet modules, but the same cannot be said for glass/glass modules.
This work compares EVA encapsulant degradation in glass/backsheet and glass/glass field-aged PV modules. EVA was extracted from three field-aged modules (two glass/backsheet and one glass/glass modules) from three different manufacturers from various regions (cell edges, cell centers, and non-cell region) from each module based on their visual and UV Fluorescence images. Characterization techniques such as I-V measurements, Colorimetry, Different Scanning Calorimetry, Thermogravimetric Analysis, Raman spectroscopy, and Fourier Transform Infrared Spectroscopy were performed on EVA samples.
The intensity of EVA discoloration was quantified using colorimetric measurements. Module performance parameters like Isc and Pmax degradation rates were calculated from I-V measurements. Properties such as degree of crystallinity, vinyl acetate content and degree of crosslinking were calculated from DSC, TGA, and Raman measurements, respectively. Polyenes responsible for EVA browning were identified in FTIR spectra.
The results from the characterization techniques confirmed that when EVA undergoes degradation, crosslinking in EVA increases beyond 90% causing a decrease in the degree of crystallinity and an increase in vinyl acetate content of EVA. Presence of polyenes in FTIR spectra of degraded EVA confirmed the occurrence of Norrish II reaction. However, photobleaching occurred in glass/backsheet modules due to the breathable backsheet whereas no photobleaching occurred in glass/glass modules because they were hermetically sealed. Hence, the yellowness index along with the Isc and Pmax degradation rates of EVA in glass/glass module is higher than that in glass/backsheet modules.
The results implied that more acetic acid was produced in the non-cell region due to its double layer of EVA compared to the front EVA from cell region. But, since glass/glass module is hermetically sealed, acetic acid gets entrapped inside the module further accelerating EVA degradation whereas it diffuses out through backsheet in glass/backsheet modules. Hence, it can be said that EVA might be a good encapsulant for glass/backsheet modules, but the same cannot be said for glass/glass modules.
ContributorsPatel, Aesha Parimalbhai (Author) / Tamizhmani, Govindasamy (Thesis advisor) / Green, Matthew (Committee member) / Mu, Bin (Committee member) / Arizona State University (Publisher)
Created2018
Description
Emergence of multidrug resistant (MDR) bacteria is a major concern to global health. One of the major MDR mechanisms bacteria employ is efflux pumps for the expulsion of drugs from the cell. In Escherichia coli, AcrAB-TolC proteins constitute the major chromosomally-encoded drug efflux system. AcrB, a trimeric membrane protein is well-known for its substrate promiscuity. It has the ability to efflux a broad spectrum of substrates alongside compounds such as dyes, detergent, bile salts and metabolites. Newly identified AcrB residues were shown to be functionally relevant in the drug binding and translocation pathway using a positive genetic selection strategy. These residues—Y49, V127, D153, G288, F453, and L486—were identified as the sites of suppressors of an alteration, F610A, that confers a drug hypersensitivity phenotype. Using site-directed mutagenesis (SDM) along with the real-time efflux and the classical minimum inhibitory concentration (MIC) assays, I was able to characterize the mechanism of suppression.
Three approaches were used for the characterization of these suppressors. The first approach focused on side chain specificity. The results showed that certain suppressor sites prefer a particular side chain property, such as size, to overcome the F610A defect. The second approach focused on the effects of efflux pump inhibitors. The results showed that though the suppressor residues were able to overcome the intrinsic defect of F610A, they were unable to overcome the extrinsic defect caused by the efflux pump inhibitors. This showed that the mechanism by which F610A imposes its effect on AcrB function is different than that of the efflux pump inhibitors. The final approach was to determine whether suppressors mapping in the periplasmic and trans-membrane domains act by the same or different mechanisms. The results showed both overlapping and distinct mechanisms of suppression.
To conclude, these approaches have provided a deeper understanding of the mechanisms by which novel suppressor residues of AcrB overcome the functional defect of the drug binding domain alteration, F610A.
Three approaches were used for the characterization of these suppressors. The first approach focused on side chain specificity. The results showed that certain suppressor sites prefer a particular side chain property, such as size, to overcome the F610A defect. The second approach focused on the effects of efflux pump inhibitors. The results showed that though the suppressor residues were able to overcome the intrinsic defect of F610A, they were unable to overcome the extrinsic defect caused by the efflux pump inhibitors. This showed that the mechanism by which F610A imposes its effect on AcrB function is different than that of the efflux pump inhibitors. The final approach was to determine whether suppressors mapping in the periplasmic and trans-membrane domains act by the same or different mechanisms. The results showed both overlapping and distinct mechanisms of suppression.
To conclude, these approaches have provided a deeper understanding of the mechanisms by which novel suppressor residues of AcrB overcome the functional defect of the drug binding domain alteration, F610A.
ContributorsBlake, Mellecha (Author) / Misra, Rajeev (Thesis advisor) / Stout, Valerie (Committee member) / Wang, Xuan (Committee member) / Arizona State University (Publisher)
Created2016
Description
While the solution diffusion model and pore flow model dominate pervaporation transport mechanism modeling, a new model combining the solution diffusion and viscous flow models is validated using membranes with large scale defects exceeding 2 nm in diameter. A range of membranes was characterized using scanning electron microscopy and x-ray diffraction (XRD) to determine quality and phase characteristics. MFI zeolite membranes of He/SF6 pure gas permeation ideal selectivities of 25, 15, and 3 for good, medium, and poor quality membranes were subjected to liquid pervaporations with a 5% ethanol in water feed, by weight. Feed pressure was increased from 1 to 5 atm, to validate existence of viscous flow in the defects. Component molar flux is modeled using the solution diffusion model and the viscous flow model, via J_i=F_i (γ_i x_i P_i^sat )+(ρ )/M_W ∅/μ_ij x_i P_h. A negative coefficient of thermal expansion is observed as permeances drop as a function of temperature in all three membranes, where ϕ=((ϵr_p^2)/τ∆x). Experimental parameter ϕ increased as a function of temperature, and increased with decreasing membrane quality. This further proves that zeolitic pores are shrinking in one direction, and pulling intercrystalline voids larger, increasing the (ϵ/τ) ratio. Permiabilities of the bad, medium, and good quality membrane also decreased over time for both ethanol and water, meaning that fundamental membrane characteristics changed as a function of temperature. To conclude, the model reasonably fits empirical data reasonably well.
ContributorsWilliams, Suzanne Jean (Author) / Lin, Jerry Y.S. (Thesis advisor) / Emady, Heather (Committee member) / Mu, Bin (Committee member) / Arizona State University (Publisher)
Created2016
Description
Biomass synthesis is a competing factor in biological systems geared towards generation of commodity and specialty chemicals, ultimately limiting maximum titer and yield; in this thesis, a widely generalizable, modular approach focused on decoupling biomass synthesis from the production of the phenylalanine in a genetically modified strain of E. coli BW25113 was explored with the use of synthetic trans-encoded small RNA (sRNA) to achieve greater efficiency. The naturally occurring sRNA MicC was used as a scaffold, and combined on a plasmid with a promoter for anhydrous tetracycline (aTc) and a T1/TE terminator. The coding sequence corresponding to the target binding site for fourteen potentially growth-essential gene targets as well as non-essential lacZ was placed in the seed region of the of the sRNA scaffold and transformed into BW25113, effectively generating a unique strain for each gene target. The BW25113 strain corresponding to each gene target was screened in M9 minimal media; decreased optical density and elongated cell morphology changes were observed and quantified in all induced sRNA cases where growth-essential genes were targeted. Six of the strains targeting different aspects of cell division that effectively suppressed growth and resulted in increased cell size were then screened for viability and metabolic activity in a scaled-up shaker flask experiment; all six strains were shown to be viable during stationary phase, and a metabolite analysis showed increased specific glucose consumption rates in induced strains, with unaffected specific glucose consumption rates in uninduced strains. The growth suppression, morphology and metabolic activity of the induced strains in BW25113 was compared to the bacteriostatic additives chloramphenicol, tetracycline, and streptomycin. At this same scale, the sRNA plasmid targeting the gene murA was transformed into BW25113 pINT-GA, a phenylalanine overproducer with the feedback resistant genes aroG and pheA overexpressed. Two induction times were explored during exponential phase, and while the optimal induction time was found to increase titer and yield amongst the BW25113 pINT-GA murA sRNA variant, overall this did not have as great a titer or yield as the BW25113 pINT-GA strain without the sRNA plasmid; this may be a result of the cell filamentation.
ContributorsHerschel, Daniel Jordan (Author) / Nielsen, David R (Thesis advisor) / Torres, César I (Committee member) / Wang, Xuan (Committee member) / Arizona State University (Publisher)
Created2016
Description
Synthetic biology and metabolic engineering has aided the production of chemicals using renewable resources, thus offering a solution to our dependence on the dwindling petroleum resources. While a major portion of petroleum resources go towards production of fuels, a significant fraction also goes towards production of specialty chemicals. There has been a growing interest in recent years in commercializing bio-based production of such high value compounds. In this thesis the biosynthesis of aromatic esters has been explored, which have typical application as flavor and fragrance additive to food, drinks and cosmetics. Recent progress in pathway engineering has led to the construction of several aromatic alcohol producing pathways, the likes of which can be utilized to engineer aromatic ester biosynthesis by addition of a suitable enzyme from the acyltransferase class. Enzyme selection and screening done in this work has identified chloramphenicol O-acetyltransferase enzyme(CAT) as a potential candidate to complete the biosynthetic pathways for each of 2-phenethyl acetate, benzyl acetate, phenyl acetate and acetyl salicylate. In the end, E. coli strains capable of producing up to 60 mg/L 2-phenethyl acetate directly from glucose were successfully constructed by co-expressing CAT in a previously engineered 2-phenylethanol producing host.
ContributorsMadathil Soman Pillai, Karthika (Author) / Nielsen, David (Thesis advisor) / Wang, Xuan (Committee member) / Torres, Cesar (Committee member) / Arizona State University (Publisher)
Created2016
Description
We report the synthesis of novel boronic acid-containing metal-organic frameworks (MOFs), which was synthesized via solvothermal synthesis of cobalt nitride with 3,5-Dicarboxyphenylboronic acid (3,5-DCPBC). Powder X-ray diffraction and BET surface area analysis have been used to verify the successful synthesis of this microporous material.
We have also made the attempts of using zinc nitride and copper nitride as metal sources to synthesize the boronic acid-containing MOFs. However, the attempts were not successful. The possible reason is the existence of copper and zinc ions catalyzed the decomposition of 3,5-Dicarboxyphenylboronic acid, forming isophthalic acid. The ended product has been proved to be isophthalic acid crystals by the single crystal X-ray diffraction. The effects of solvents, reaction temperature, and added bases were investigated. The addition of triethylamine has been shown to tremendously improve the sample crystallinity by facilitating ligand deprotonation
We have also made the attempts of using zinc nitride and copper nitride as metal sources to synthesize the boronic acid-containing MOFs. However, the attempts were not successful. The possible reason is the existence of copper and zinc ions catalyzed the decomposition of 3,5-Dicarboxyphenylboronic acid, forming isophthalic acid. The ended product has been proved to be isophthalic acid crystals by the single crystal X-ray diffraction. The effects of solvents, reaction temperature, and added bases were investigated. The addition of triethylamine has been shown to tremendously improve the sample crystallinity by facilitating ligand deprotonation
ContributorsYu, Jiuhao (Author) / Mu, Bin (Thesis advisor) / Forzani, Erica (Committee member) / Nielsen, David (Committee member) / Arizona State University (Publisher)
Created2014