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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

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
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Description
This thesis focused on the development of a system that can sense light intensity and then control a smart film to provide the optimal light intensity for cyanobacteria. The overarching goal of this project is to further the study of biofuels as an alternative energy source by increasing growth rates.

This thesis focused on the development of a system that can sense light intensity and then control a smart film to provide the optimal light intensity for cyanobacteria. The overarching goal of this project is to further the study of biofuels as an alternative energy source by increasing growth rates. If more algae or cyanobacteria can be grown per day, then the cost to produce the biofuel will decrease. To achieve this goal, PDLC (polymer dispersed liquid crystal) film was selected to be controlled due to its unique properties. It can be controlled with electricity and has variable states, in other words, not restricted to simply on or off. It also blocks 80% ultraviolet light and reduces thermal heat gain by 40% which is an important consideration for outdoor growing situations. To control the film, a simple control system was created using an Arduino Uno, SainSmart 8 channel relay board, an inverter, and a power supply. A relay board was utilized to manage the 40 volts required by the PDLC film and protected the electronics on the Arduino Uno. To sense the light intensity, the Arduino Uno was connected to a photoresistor, which changes resistance with light intensity. A 15 day test of two flasks of Cyanobacteria Synechocycstis sp. 6803, one shaded by the PDLC film, and the other unshaded, yielded 65% difference in optical densities. Overall, the experiment showed promise for controlling light intensity for photobioreactors. Ideally, this research will help to optimize light intensities when growing cyanobacteria or algae outdoors or it will help to discover what an ideal light intensity is by allowing a researcher unprecedented control.
ContributorsRoney, Kitt Alicia (Author) / Nielsen, David (Thesis director) / Middleton, James (Committee member) / Barrett, The Honors College (Contributor) / Mechanical and Aerospace Engineering Program (Contributor)
Created2015-05
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Description
In our modern world the source of for many chemicals is to acquire and refine oil. This process is becoming an expensive to the environment and to human health. Alternative processes for acquiring the final product have been developed but still need work. One product that is valuable is butanol.

In our modern world the source of for many chemicals is to acquire and refine oil. This process is becoming an expensive to the environment and to human health. Alternative processes for acquiring the final product have been developed but still need work. One product that is valuable is butanol. The normal process for butanol production is very intensive but there is a method to produce butanol from bacteria. This process is better because it is more environmentally safe than using oil. One problem however is that when the bacteria produce too much butanol it reaches the toxicity limit and stops the production of butanol. In order to keep butanol from reaching the toxicity limit an adsorbent is used to remove the butanol without harming the bacteria. The adsorbent is a mesoporous carbon powder that allows the butanol to be adsorbed on it. This thesis explores different designs for a magnetic separation process to extract the carbon powder from the culture.
ContributorsChabra, Rohin (Author) / Nielsen, David (Thesis director) / Torres, Cesar (Committee member) / Barrett, The Honors College (Contributor) / Chemical Engineering Program (Contributor)
Created2015-05
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Description

Measuring changes in concentration within a dynamic system can be accomplished with a simple Arduino powered system. Currently, the system is utilized in cyanobacteria CO2 fixation experiments, where the fixation rates of multiple cultures can be measured simultaneously. The system employs solenoids in parallel and can be applied for n

Measuring changes in concentration within a dynamic system can be accomplished with a simple Arduino powered system. Currently, the system is utilized in cyanobacteria CO2 fixation experiments, where the fixation rates of multiple cultures can be measured simultaneously. The system employs solenoids in parallel and can be applied for n number of outlet streams, all are connected to one large manifold which feeds to a CO2 concentration probe. In the future, the system can be modified to fit other simple dynamic gas systems.

ContributorsInnes, Sean (Author) / Nielsen, David (Thesis director) / Jones, Christopher (Committee member) / Barrett, The Honors College (Contributor)
Created2021-12
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Description
The world today needs novel solutions to address current challenges in areas spanning areas from sustainable manufacturing to healthcare, and biotechnology offers the potential to help address some of these issues. One tool that offers opportunities across multiple industries is the use of nonribosomal peptide synthases (NRPSs). These are modular

The world today needs novel solutions to address current challenges in areas spanning areas from sustainable manufacturing to healthcare, and biotechnology offers the potential to help address some of these issues. One tool that offers opportunities across multiple industries is the use of nonribosomal peptide synthases (NRPSs). These are modular biological factories with individualized subunits that function in concert to create novel peptides.One element at the heart of environmental health debates today is plastics. Biodegradable alternatives for petroleum-based plastics is a necessity. One NRPS, cyanophycin synthetase (CphA), can produce cyanophycin grana protein (CGP), a polymer composed of a poly-aspartic acid backbone with arginine side chains. The aspartic backbone has the potential to replace synthetic polyacrylate, although current production costs are prohibitive. In Chapter 2, a CphA variant from Tatumella morbirosei is characterized, that produces up to 3x more CGP than other known variants, and shows high iCGP specificity in both flask and bioreactor trials. Another CphA variant, this one from Acinetobacter baylyi, underwent rational protein design to create novel mutants. One, G217K, is 34% more productive than the wild type, while G163K produces a CGP with shorter chain lengths. The current structure refined from 4.4Å to 3.5Å. Another exciting application of NRPSs is in healthcare. They can be used to generate novel peptides such as complex antibiotics. A recently discovered iterative polyketide synthase (IPTK), dubbed AlnB, produces an antibiotic called allenomycin. One of the modular subunits, a dehydratase named AlnB_DH, was crystallized to 2.45Å. Several mutations were created in multiple active site residues to help understand the functional mechanism of AlnB_DH. A preliminary holoenzyme AlnB structure at 3.8Å was generated although the large disorganized regions demonstrated an incomplete structure. It was found that chain length is the primary factor in driving dehydratase action within AlnB_DH, which helps lend understanding to this module.
ContributorsSwain, Kyle (Author) / Nannenga, Brent (Thesis advisor) / Nielsen, David (Committee member) / Mills, Jeremy (Committee member) / Seo, Eileen (Committee member) / Acharya, Abhinav (Committee member) / Arizona State University (Publisher)
Created2022
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Description
The current use of non-renewable fossil fuels for industry poses a threat for future generations. Thus, a pivot to renewable sources of energy must be made to secure a sustainable future. One potential option is the utilization of metabolically engineered bacteria to produce value-added chemicals during fermentation. Currently, numerous strains

The current use of non-renewable fossil fuels for industry poses a threat for future generations. Thus, a pivot to renewable sources of energy must be made to secure a sustainable future. One potential option is the utilization of metabolically engineered bacteria to produce value-added chemicals during fermentation. Currently, numerous strains of metabolically engineered Escherichia coli have shown great capacity to specialize in the production of high titers of a desired chemical. These metabolic systems, however, are constrained by the biological limits of E. coli itself. During fermentation, E. coli grows to less than one twentieth of the density that aerobically growing cultures can reach. I hypothesized that this decrease in growth during fermentation is due to cellular stress associated with fermentative growth, likely caused by stress related genes. These genes, including toxin-antitoxin (TA) systems and the rpoS mediated general stress response, may have an impact on fermentative growth constraints. Through transcriptional analysis, I identified that the genes pspC and relE are highly expressed in fermenting strains of both wild type and metabolically engineered E. coli. Fermentation of toxin gene knockouts of E. coli BW25113 revealed their potential impacts on E. coli fermentation. The inactivation of ydcB, lar, relE, hipA, yjfE, chpA, ygiU, ygjN, ygfX, yeeV, yjdO, yjgK and ydcX did not lead to significant changes in cell growth when tested using sealed tubes under microaerobic conditions. In contrast, inactivation of pspC, yafQ, yhaV, yfjG and yoeB increased cell growth after 12 hours while inactivation yncN significantly arrested cell growth in both tube and fermentation tests, thus proving these toxins’ roles in fermentative growth. Moreover, inactivation of rpoS also significantly hindered the ability of E. coli to ferment, suggesting its important role in E. coli fermentation
ContributorsHernandez, Michaella (Author) / Wang, Xuan (Thesis advisor) / Nielsen, David (Committee member) / Varman, Arul (Committee member) / Arizona State University (Publisher)
Created2022
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Description
Cyanobacteria have the potential to efficiently produce L-serine, an industrially important amino acid, directly from CO2 and sunlight, which is a more sustainable and inexpensive source of energy as compared to current methods. The research aims to engineer a strain of Cyanobacterium Synechococcus sp. PCC 7002 that increases L-serine production

Cyanobacteria have the potential to efficiently produce L-serine, an industrially important amino acid, directly from CO2 and sunlight, which is a more sustainable and inexpensive source of energy as compared to current methods. The research aims to engineer a strain of Cyanobacterium Synechococcus sp. PCC 7002 that increases L-serine production by mutating regulatory mechanisms that natively inhibit its production and encoding an exporter. While an excess of L-serine was not found in the supernatant of the cell cultures, with further fine tuning of the metabolic pathway and culture conditions, high titers of L-serine can be found. With the base strain engineered, the work can be extended and optimized by deleting degradation pathways, tuning gene expression levels, optimizing growth conditions, and investigating the effects of nitrogen supplementation for the strain.
ContributorsAbed, Omar (Author) / Nielsen, David (Thesis director) / Jones, Christopher (Committee member) / Chemical Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
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Description
Predatory bacteria are a guild of heterotrophs that feed directly on other living bacteria. They belong to several bacterial lineages that evolved this mode of life independently and occur in many microbiomes and environments. Current knowledge of predatory bacteria is based on culture studies and simple detection in natural systems.

Predatory bacteria are a guild of heterotrophs that feed directly on other living bacteria. They belong to several bacterial lineages that evolved this mode of life independently and occur in many microbiomes and environments. Current knowledge of predatory bacteria is based on culture studies and simple detection in natural systems. The ecological consequences of their activity, unlike those of other populational loss factors like viral infection or grazing by protists, are yet to be assessed. During large-scale cultivation of biological soil crusts intended for arid soil rehabilitation, episodes of catastrophic failure were observed in cyanobacterial growth that could be ascribed to the action of an unknown predatory bacterium using bioassays. This predatory bacterium was also present in natural biocrust communities, where it formed clearings (plaques) up to 9 cm in diameter that were visible to the naked eye. Enrichment cultivation and purification by cell-sorting were used to obtain co-cultures of the predator with its cyanobacterial prey, as well as to identify and characterize it genomically, physiologically and ultrastructurally. A Bacteroidetes bacterium, unrelated to any known isolate at the family level, it is endobiotic, non-motile, obligately predatory, displays a complex life cycle and very unusual ultrastructure. Extracellular propagules are small (0.8-1.0 µm) Gram-negative cocci with internal two-membrane-bound compartmentalization. These gain entry to the prey likely using a suite of hydrolytic enzymes, localizing to the cyanobacterial cytoplasm, where growth begins into non-compartmentalized pseudofilaments that undergo secretion of vesicles and simultaneous multiple division to yield new propagules. I formally describe it as Candidatus Cyanoraptor togatus, hereafter Cyanoraptor. Its prey range is restricted to biocrust-forming, filamentous, non-heterocystous, gliding, bundle-making cyanobacteria. Molecular meta-analyses showed its worldwide distribution in biocrusts. Biogeochemical analyses of Cyanoraptor plaques revealed that it causes a complete loss of primary productivity, and significant decreases in other biocrusts properties such as water-retention and dust-trapping capacity. Extensive field surveys in the US Southwest revealed its ubiquity and its dispersal-limited, aggregated spatial distribution and incidence. Overall, its activity reduces biocrust productivity by 10% at the ecosystem scale. My research points to predatory bacteria as a significant, but overlooked, ecological force in shaping soil microbiomes.
ContributorsBethany Rakes, Julie Ann (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Gile, Gillian (Committee member) / Cao, Huansheng (Committee member) / Jacobs, Bertram (Committee member) / Arizona State University (Publisher)
Created2022
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Description

Esters are important solvents in multiple industries including adhesives, food, and pharmaceuticals. Although esters are biodegradable solvents, the conventional process of producing them is not eco-friendly because they are largely derived from petrochemicals. This has led scientists to consider implementing biological routes in their production process by incorporating heterologous or

Esters are important solvents in multiple industries including adhesives, food, and pharmaceuticals. Although esters are biodegradable solvents, the conventional process of producing them is not eco-friendly because they are largely derived from petrochemicals. This has led scientists to consider implementing biological routes in their production process by incorporating heterologous or improving inherent esterification pathways. However, due to inequality in the biosynthesis of esters and their precursors (organic acid and alcohol), a significant amount of precursors are left unconverted, thereby lowering overall esterification efficiency. Therefore, the primary goal of the current research is to improve the ester titers by incorporating one more step of in vitro esterification with the culture broth, thereby esterifying the unconverted precursors using high efficiency commercial enzymes in the presence of compatible organic solvent. In principle, the medium containing the precursors will be treated with the enzyme in presence of organic solvent, where the precursors will be distributed in both the phases, aqueous and organic, based on their polarity, and the enzymatic esterification will happen at the interface. Hence, as a first step, efforts were made to optimize the reaction conditions, beginning with choosing the most efficient organic solvent and corresponding enzyme candidate. Our results showed that, for production of ethyl acetate through this reactive extraction approach, Novozyme435 exhibited significant esterification with chloroform, with almost 85% conversion efficiency. Further optimizations with phase ratios, pH and incubation time showed that the pH 6.0 (3.1 g/L) was the most optimum where ethyl acetate titer was found to improve 10 times than that at pH 7.0 (0.164 g/L) with the phase ratio of 1:1. The kinetic studies further added that the incubation at 37oC gives the maximum ethyl acetate production within 8h. After initial optimization studies, cell broth from E. coli cells transformed to overproduce an esterase was also tested with the reactive extraction method. It was found that there was a ~7.5X decrease in ethyl acetate production in the cell media versus synthetic samples with the same concentration of reactants. Such a large decrease indicates that enzymatic promiscuity or inhibition currently prevent the cell samples from reaching the same conversion as synthetic studies. To characterize the maximum reaction rate (Vmax) and affinity constants of the substrates to Novozym 435, further kinetic studies were performed with one minute of reaction. The mathematical model employed assumes that enzyme kinetics rather than diffusion was the rate limiting step, that the concentrations of reactants at the interface are equivalent to the initial concentration of reactants, and that neither substrate is an inhibitor. Vmax was found to be 18.5 Mmol min-1g-1 (of catalyst used), and the affinity constants were 0.957 M and 0.00557 M for acetic acid and ethanol respectively. Vmax was similar to literature values with Novozym 435, and the affinity constants indicate a much higher binding efficiency of ethanol in comparison to acetic acid, indicating that a cocktail of esters are likely produced from Novozym 435 in cell broth. Overall, moving away from fossil-fuel dependence is necessary to promote sustainable industry standards, and microbial cell factories combined with reactive extraction, if optimized for industrial applications, can replace harmful environmental procedures. By optimizing the reactive extraction process for ester production, biorefineries could become more competitive and economically feasible for numerous applications.

ContributorsKartchner, Danika (Author) / Varman, Arul Mozhy (Thesis director) / Nielsen, David (Committee member) / Soundappan, Thiagarajan (Committee member) / Barrett, The Honors College (Contributor) / Chemical Engineering Program (Contributor) / Watts College of Public Service & Community Solut (Contributor)
Created2022-05
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Description
Biocrusts are microbial communities that inhabit arid soil surfaces, providing essential services to dryland ecosystems. A paradoxical filamentous cyanobacterium, Microcoleus vaginatus, resides within the biocrust. While is often pioneers the colonization of bare, nutrient-poor desert soils worldwide, it cannot fix dinitrogen. In nature, M. vaginatus coexists with a unique microbial

Biocrusts are microbial communities that inhabit arid soil surfaces, providing essential services to dryland ecosystems. A paradoxical filamentous cyanobacterium, Microcoleus vaginatus, resides within the biocrust. While is often pioneers the colonization of bare, nutrient-poor desert soils worldwide, it cannot fix dinitrogen. In nature, M. vaginatus coexists with a unique microbial community, a “cyanosphere”, that is characterized by a high abundance of diazotrophic heterotrophs. This suggests mutualistic relationships wherein nutrients are traded between phototrophs and heterotrophs. To explore these relationships, I performed targeted, pedigreed isolation of cyanosphere members and used co-cultivation to recreate the mutualism in culture. Results showed that, in the absence of fixed nitrogen, M. vaginatus grew well when co-cultured with cyanosphere diazotrophs, but only poorly or not at all when alone or with non-cyanosphere diazotrophs. In agreement with this, the experimental provision of nitrogen to natural populations resulted in a loss of diazotrophs from the cyanosphere compared to controls, but the addition of phosphorus did not. Additionally, the convergence of M. vaginatus trichomes into large bundles held by a common sheath was elicited in culture by the addition of cyanosphere diazotrophs, pointing to a role of cyanobacterial motility responses in the development of mutualistic interactions. I then demonstrated that the tendency of M. vaginatus to stay within bundles and close to the sheath-dwelling cyanosphere was dependent on the cyanosphere population size. This effect was likely mediated by glutamate that acted as a signaling molecule rather than as a N source and impacted the gliding speed and negative chemophobic responses on the cyanobacterium. Glutamate seems to be used as a cue to spatially optimize cyanobacterium-cyanosphere mutualistic exchanges. My findings have potential practical applications in restoration ecology, which I further pursued experimentally. Co-inoculation of soil with cyanosphere diazotrophs resulted in swifter development of biocrusts over inoculation with the cyanobacterium only. Further, their addition to disturbed native soils containing traces of cyanobacteria sufficed for the formation of cohesive biocrusts without cyanobacterial inoculation. The inclusion of such “biocrust probiotics” in biocrust restoration is recommended. Overall, this body of work elucidates the hitherto unknown role of beneficial heterotrophic bacteria in the initial formation and development of biocrusts.
ContributorsNelson, Corey (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Penton, C. Ryan (Committee member) / Gile, Gillian (Committee member) / Bean, Heather (Committee member) / Arizona State University (Publisher)
Created2021