Developing an Automated Off-Gas Sampling System to Obtain High-Resolution CO2 Fixation Data from Cyanobacterial Cultures

171537-Thumbnail Image.png
Description
Cyanobacteria and its complex photosynthetic systems have been a prime target for synthetic biologists and their molecular engineering tools for the last couple of decades. However, characterizing meaningful carbon dioxide (CO₂) removal performance has always been a struggle within the

Cyanobacteria and its complex photosynthetic systems have been a prime target for synthetic biologists and their molecular engineering tools for the last couple of decades. However, characterizing meaningful carbon dioxide (CO₂) removal performance has always been a struggle within the field. It is proposed that measuring changes in CO₂ gas concentration within a dynamic system can be accomplished with a simple automated Arduino-powered system. The system employs solenoids in parallel (one for each outlet stream) which are then connected to one large manifold which feeds into a single IR-based CO₂ probe. Since CO₂ probes are expensive, this approach allows for sample multiplexing while remaining affordable. The development of such a system allows for high resolution growth experiments between different strains of cyanobacteria. This approach provides continuous data collection over the entire life cycle of each individual culture, allowing differences in total CO₂ fixation between strains to be readily determined. From a culture of PCC 6803, it was found that the peak mg of CO₂ fixed per day is around 92 mg CO₂/day. In the future, the system can be modified to fit other simple dynamic gas systems, as well as testing similar gas utilization/production capabilities of other organisms.
Date Created
2022
Agent

Enzymatic Reactive Extraction for the Production of Short-Chain Esters

164979-Thumbnail Image.png
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

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.

Date Created
2022-05
Agent

Plasmid construction for the overexpression of waste biomass-degrading enzymes

148490-Thumbnail Image.png
Description

Lignin is a naturally abundant source of aromatic carbon but is largely underutilized in industry because it is difficult to decompose. Under the current study we engineered Corynebacterium glutamicum for the depolymerization of lignin with the goal of using it

Lignin is a naturally abundant source of aromatic carbon but is largely underutilized in industry because it is difficult to decompose. Under the current study we engineered Corynebacterium glutamicum for the depolymerization of lignin with the goal of using it as raw feed for the sustainable production of valuable chemicals. C. glutamicum is a standout candidate for the depolymerization and assimilation of lignin because of its performance as an industrial producer of amino acids, resistance to aromatic compounds in lignin, and low extracellular protease activity. Three different foreign and native ligninolytic enzymes were tested in combination with three signal peptides to assess lignin degradation efficacy. At this stage, six of the nine plasmid constructs have been constructed.

Date Created
2021-05
Agent

Role of Metabolism in Antibiotic Resistance

131379-Thumbnail Image.png
Description
Each year, more and more multi-drug resistant bacterial strains emerge, thus complicating treatment and increasing the average stay in the intensive care unit. As antibiotics are being rendered inefficient, there is a need to look into ways of weakening the

Each year, more and more multi-drug resistant bacterial strains emerge, thus complicating treatment and increasing the average stay in the intensive care unit. As antibiotics are being rendered inefficient, there is a need to look into ways of weakening the internal state of bacterial cells to make them more susceptible to antibiotics. For this, we first need to understand what methods bacteria employ to fight against antibiotics. In this work, we have reviewed how bacteria respond to antibiotics. There is a similarity in response to antibiotic exposure and starvation (stringent stress) which changes the metabolic state. We have delineated what metabolism changes take place and how they are associated with oxidative stress. For example, there is a common change in NADH concentration that is tied to both metabolism and oxidative stress. Finally, we have compared the findings in literature with our research on an antibiotic-resistant RNA polymerase mutant that alters the gene expression profile in the general areas of metabolism and oxidative stress. Based on this thesis, we have suggested a couple of strategies to make antibiotics more efficient; however, as antibiotic-mediated killing is very complex, researchers need to delve deeper to understand and manipulate the full cellular response.
Date Created
2020-05
Agent

Glycoside Hydrolase Gene Families Of Termite Hindgut Protists

157712-Thumbnail Image.png
Description
This project was completed to understand the evolution of the ability to digest wood in termite symbiotic protists. Lower termites harbor bacterial and protist symbionts which are essential to the termite ability to use wood as a nutritional source, producing

This project was completed to understand the evolution of the ability to digest wood in termite symbiotic protists. Lower termites harbor bacterial and protist symbionts which are essential to the termite ability to use wood as a nutritional source, producing glycoside hydrolases to break down the polysaccharides found in lignocellulose. Yet, only a few molecular studies have been done to confirm the protist species responsible for particular enzymes. By mining publicly available and newly generated genomic and transcriptomic data, including three transcriptomes from isolated protist cells, I identify over 200 new glycoside hydrolase sequences and compute the phylogenies of eight glycoside hydrolase families (GHFs) reported to be expressed by termite hindgut protists.

Of those families examined, the results are broadly consistent with Todaka et al. 2010, though none of the GHFs found were expressed in both termite-associated protist and non-termite-associated protist transcriptome data. This suggests that, rather than being inherited from their free-living protist ancestors, GHF genes were acquired by termite protists while within the termite gut, potentially via lateral gene transfer (LGT). For example one family, GHF10, implies a single acquisition of a bacterial xylanase into termite protists. The phylogenies from GHF5 and GHF11 each imply two distinct acquisitions in termite protist ancestors, each from bacteria. In eukaryote-dominated GHFs, GHF7 and GHF45, there are three apparent acquisitions by termite protists. Meanwhile, it appears prior reports of GHF62 in the termite gut may have been misidentified GHF43 sequences. GHF43 was the only GHF found to contain sequences from the protists not found in the termite gut. These findings generally all support the possibility termite-associated protists adapted to a lignocellulosic diet after colonization of the termite hindgut. Nonetheless, the poor resolution of GHF phylogeny and limited termite and protist sampling constrain interpretation.
Date Created
2019
Agent

Construction of Recombinant Plasmids of Corynebacterium glutamicum for Flavonoid Production

132166-Thumbnail Image.png
Description
Due to the wide range of health properties flavonoids possess, flavonoids are sold in health supplements to the general public. Flavonoids are also utilized in research but have a high cost due to current production techniques. This project focuses on

Due to the wide range of health properties flavonoids possess, flavonoids are sold in health supplements to the general public. Flavonoids are also utilized in research but have a high cost due to current production techniques. This project focuses on engineering two DNA recombinants to develop new strains of Corynebacterium glutamicum that can produce flavonoids pinocembrin and naringenin. After culturing Escherichia coli colonies containing genes of interest, the genes were collected and purified by PCR reactions. The recombinant plasmid was assembled using CPEC and successfully transformed into Escherichia coli, with plans to transform Corynebacterium glutamicum to experiment and determine which recombinant can produce more pinocembrin and naringenin. Design work for other DNA recombinants, which were not the focus of this project, was also completed.
Date Created
2019-05
Agent