Developing Continuum and Multi-Scale Models to Capture Pseudomonas Aeruginosa Spatiotemporal Expansion and Pyocyanin Production in Different Gel Environments 3 views

Pseudomonas aeruginosa is a pervasive opportunistic pathogen capable of establishing severe infections in hosts. Through its diverse arsenal of antibiotic resistance mechanisms and secondary metabolic pathways, P. aeruginosa can develop into persistent, virulent communities in its host environment. Individuals with muco-obstructive lung diseases, such as cystic fibrosis and chronic obstructive pulmonary disease, are especially vulnerable to these opportunistic infections as impaired lung mucus clearance allow P. aeruginosa to form high-cell density microbial communities in mucus layers. Antibiotic treatment efficacy against these communities is further diminished due to the heterogenous physiological states that emerge within the population as P. aeruginosa propagates through the mucus layer, this treatment obstacle consequently increases the risk of chronic respiratory infections. Understanding the mechanisms that influence population heterogeneity in these physical environments is crucial for informing treatment strategies to mitigate infection persistence and virulence. One mechanism that can impact how P. aeruginosa populations spread in the mucus layer is active bacterial motility driven by its polar flagella. Although motility has been recognized as a pathogenic trait that supports infection virulence, there are gaps in understanding how motility interacts with gel environments like the mucus layer to shape the growth and development of the bacterial community. In this work, we leverage the swim plate motility assay to explore the effect of motility in agar gels on the spatiotemporal development of P. aeruginosa population and production of pyocyanin, a virulence-promoting cytotoxin. To facilitate quantitative analysis, we developed continuum and multi-scale model frameworks that characterize P. aeruginosa propagation in the swim plate assay agar gel. In Chapter 2, a timelapse microscopy workflow and a continuum model were designed to quantify the changes in P. aeruginosa biomass density profiles across the gel and then characterize these fluctuations to model motility and growth parameters. Through simulation-experiment density profile comparison, we determined that the addition of MUC5AC mucin reduced P. aeruginosa PA14 motility through the gel which led to smaller macrocolony communities and faster biomass density accumulation within the macrocolony. However, addition of viscous methylcellulose solution did not reduce PA14 motility compared to the agar-only gel. Macrocolonies in these gel environments also produced significantly more pyocyanin (PCN) than batch liquid culture samples. To understand the swim plate in vitro conditions promoting PCN synthesis, we constructed a multi-scale model in Chapter 3 that could simulate a PA14 population while being guided by cellular metabolism predictions from a genome-scale metabolic network (GEM). The GEM-informed continuum model was evaluated for its biomass growth and PCN predictions of PA14 populations in different agar gel environments as well as its predictions for PA14 mutant behavior. While components of the GEM-informed continuum model were able to successfully predict some mutant results, the underlying PA14 growth behavior, elucidated by prediction shortcomings, encouraged continuing work to improve how the GEM is adjusted to reflect experimental measurements. Together, these thesis chapters provide an experimental and modeling framework to study microbial populations and their pathogenic behavior in gel environments. Chapter 4 of this thesis focuses on the scholarship of teaching and learning study carried out during my graduate co-instructor term. In this study, we explored a classroom token economy as a strategy to produce more conceptual practice opportunities for students without delegating time away from lecture or adding more out-of-class assignments. We adapted and implemented token economy interactions that extrinsically rewarded students to reattempt quiz or homework problems that they previously had conceptual difficulty with. Through this motivated exercise, we aimed for students to reinforce their understanding throughout the semester.

PHD (Doctor of Philosophy)

Pseudomonas aeruginosa; genome-scale metabolic model; continuum modeling; respiratory infection; pyocyanin; classroom token economy; bacterial motility; scholarship of teaching and learning

English

2026-04-14