Yuchen Jin

Date of Award


Degree Type


Degree Name

Doctor of Philosophy (PhD)




Luk, Yan Yeung

Subject Categories



Biofilms formed by microbes on surfaces are the sources for persistent infectious diseases and environmental problems. The mechanism and details of how antibiotics promote biofilm formation is largely unknown. For instance, it not clear what stages of biofilm growth are promoted to proceed faster than without antibiotics, what phenotypes of bacteria form in an antibiotic-promoted biofilm, and what different biofilm compositions and structures are caused by the presence of antibiotics. Among other effects, antibiotics can cause bacteria to form filaments of living bacteria. Here, we conduct a real-time study of the adherence of bacteria and antibiotic-induced filamentous bacteria on surfaces and characterize the kinetics of surface adherence of these two forms of bacteria. Studying the effect of different surfaces on promoting filamentous bacteria’s adherence on surfaces, we characterize an unexpected correlation between the stage of bacterial growth and the formation and growth of filamentous bacteria on surfaces. Based on these results, we outline the lifestyle of filamentous bacteria and a mechanism by which antibiotics promote biofilm formation. The drug resistance of bacteria is becoming more severe since antibiotics are first discovered. The development of drug-resistance among bacteria involves spreading and drug-resistant gene “horizontally” between bacteria. These horizontal gene transfers impact the gene composition and evolution of the bacteria, and facilitate the transfer of antibiotic resistance genes. At the molecular level, all three major mechanisms of HGTs, transformation, conjugation and transduction, involve type IV pili appendages on bacterial surfaces. Here, the three mechanisms of horizontal gene transfer are studied. Saturated farnesol derivatives show inhibition effect on tetracycline-enhanced plasmid transformation, ciprofloxacin-enhances PAPI-1 transduction, and PAPI-1 conjugation. Further study of ciprofloxacin-resistance development in P. aeruginosa is conducted by using serial passage assay. The inhibited development of MIC of ciprofloxacin suggest that saturated farnesol derivative inhibits the development of resistance to ciprofloxacin in P. aeruginosa. This thesis also describes the mechanism of pili inhibition by saturated farnesol derivatives. The pili-mediated bacteriophage adsorption is studied, and the results demonstrate that saturated farnesol derivative could cause pili retraction, leading to inhibition of bacteriophage adsorption. More evidence was obtained from other colleagues in Dr. Luk’s lab to support the small molecules binding to pili. The MALDI-MS done by Hewen Zheng suggests that saturated farnesol derivative covalently binds to pili. Hewen also performed the alkaline buffer extraction experiment to demonstrate that PAO1 culturing with saturated farnesol derivative resulted in decrease in pili protein expression. Together with the bacteriophage adsorption results, we conclude that saturated farnesol derivative binding to pili cause pili retraction.


Open Access

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Biochemistry Commons