<p>Bistable switches are commonly observed in the regulation of critical processes such as cell cycles and differentiation. The switches possess two fundamental properties: memory and bimodality. Once switched ON, the switches can remember their ON state despite a drastic drop in stimulus levels. Furthermore, at intermediate stimulus levels with cellular noise, the switches can cause a population to exhibit bimodal distribution of cell states. Till date, experimental studies have focused primarily on cellular mechanisms that generate bistable switches and their impact on cellular dynamics. </p><p>Here, I study emergent bistability due to bacterial interactions with either synthetic gene circuits or antibiotics. A synthetic gene circuit is often engineered by considering the host cell as an invariable "chassis". Circuit activation, however, may modulate host physiology, which in turn can drastically impact circuit behavior. I illustrate this point by a simple circuit consisting of mutant T7 RNA polymerase (T7 RNAP*) that activates its own expression in bacterium Escherichia coli. Although activation by the T7 RNAP* is noncooperative, the circuit caused bistable gene expression. This counterintuitive observation can be explained by growth retardation caused by circuit activation, which resulted in nonlinear dilution of T7 RNAP* in individual bacteria. Predictions made by models accounting for such effects were verified by further experimental measurements. The results reveal a novel mechanism of generating bistability and underscore the need to account for host physiology modulation when engineering gene circuits.</p><p>In the context of antibiotic treatment, I investigate bistability as the underlying mechanism of inoculum effect. The inoculum effect refers to the decreasing efficacy of an antibiotic with increasing bacterial density. Despite its implication for the design of antibiotic treatment strategies, its mechanism remains poorly understood. Here I show that, for antibiotics that target the core replication machinery, the inoculum effect can be explained by bistable bacterial growth. My results suggest that a critical requirement for this bistability is sufficiently fast turnover of the core machinery induced by the antibiotic via the heat shock response. I further show that antibiotics that exhibit the inoculum effect can cause a "band-pass" response of bacterial growth on the frequency of antibiotic treatment, whereby the treatment efficacy drastically diminishes at intermediate frequencies. The results have implications on optimal design of antibiotic treatment.</p> / Dissertation

Gene expression of porin and beta-lactamases genes during the beta-lactam antibiotic treatment and effect of inoculum size on Klebsiella pneumoniae clinical isolates ABSTRACT In recent years, Klebsiella pneumoniae has been increasingly reported to be one of the most important nosocomial pathogens, and it is usually resistant to many antibiotics. In this work, we focused on the expression of the AmpC group β- lactamase DHA-1 and its negative regulator AmpR, as well as the porins OmpK35 and OmpK36 and on effect of inoculum. We used well-characterized Klebsiella pneumoniae strains in this study. Plasmids obtained from these strains were also transformed into different wild-type Klebsiella pneumoniae strains, which were typed by pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Gene expression analysis was performed by RT-PCR using specific primers and TaqMan probes. In most strains, expression was dependent on the presence of an inducer. The highly resistant strain showed a different expression pattern, but the expression of blaDHA-1 remained inducible by cefoxitin. Different regulation was also observed in the transformants. Based on our data, we suggest that the previously described regulatory pathway for AmpC is not generally suitable, and we propose that there are more...