Browsing by Author "Johnson, Timothy"

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Environment Constrains Fitness Advantages of Division of Labor in Microbial Consortia Engineered for Metabolite Push or Pull Interactions
(American Society for Microbiology, 2022-08) Beck, Ashely E.; Pintar, Kathryn; Schepens, Diana; Schrammeck, Ashely; Johnson, Timothy; Bleem, Alissa; Du, Martina; Harcombe, William R.; Bernstein, Hans C.; Heys, Jeffrey J.; Gedeon, Tomas; Carlson, Ross P.
Fitness benefits from division of labor are well documented in microbial consortia, but the dependency of the benefits on environmental context is poorly understood. Two synthetic Escherichia coli consortia were built to test the relationships between exchanged organic acid, local environment, and opportunity costs of different metabolic strategies. Opportunity costs quantify benefits not realized due to selecting one phenotype over another. The consortia catabolized glucose and exchanged either acetic or lactic acid to create producer-consumer food webs. The organic acids had different inhibitory properties and different opportunity costs associated with their positions in central metabolism. The exchanged metabolites modulated different consortial dynamics. The acetic acid-exchanging (AAE) consortium had a “push” interaction motif where acetic acid was secreted faster by the producer than the consumer imported it, while the lactic acid-exchanging (LAE) consortium had a “pull” interaction motif where the consumer imported lactic acid at a comparable rate to its production. The LAE consortium outperformed wild-type (WT) batch cultures under the environmental context of weakly buffered conditions, achieving a 55% increase in biomass titer, a 51% increase in biomass per proton yield, an 86% increase in substrate conversion, and the complete elimination of by-product accumulation all relative to the WT. However, the LAE consortium had the trade-off of a 42% lower specific growth rate. The AAE consortium did not outperform the WT in any considered performance metric. Performance advantages of the LAE consortium were sensitive to environment; increasing the medium buffering capacity negated the performance advantages compared to WT.
Gold nano rod hydrogel nanocomposite laser tissue welding
(Montana State University, 2017-04) Johnson, Timothy
The original purpose of my research was to develop mathematical models of heat transfer and cell death and combine them into a model of Laser Tissue Welding (LTW) using collagen nanocomposite materials. LTW is an alternative to surgical sutures for repairing cuts and ruptures in tissues. Our LTW model uses collagen mixed with gold nanoparticles that convert light into heat. The application of laser light leads to a temporary phase change in the collagen from a gel to a viscous liquid and back into a gel that can seal a cut in the surrounding tissue. This topic interests me because as a student in Chemical Engineering, I will likely work with heat transfer and biological systems in many future projects. To develop the model, Dr. Jeff Heys and I utilized the Python programming language along with the FEniCS software library to solve the various partial differential equations and algebraic equations in the model. I combined two previously developed mathematical models: a bio-heat transfer model and a cell death model, and adapted them to work together in a single program so that individual variables can be optimized as efficiently as possible. Thus far, we have successfully integrated the two models into a single code that can predict the temperature of the nanocomposite and the surrounding tissue as well as predict the fraction of cells that are killed by elevated temperatures at different spatial locations. It is not yet possible to optimize system parameters, but is expected to be before May, 2017.