Quantitative Biosciences Thesis Proposal
School of Physics
Advisor: Dr. Peter Yunker (School of Physics)
Open to the Community
The biophysics of biofilm surfaces
Monday, September 20, 2021, at 12:00 pm
BlueJeans Link: https://bluejeans.com/978733561
Dr. Sam Brown (School of Biological Sciences)
Dr. Jennifer Curtis (School of Physics)
Dr. Brian Hammer (School of Biological Sciences)
Bacterial colonies are a main area of focus in biomedical and ecological research, being sources of infection and accounting for a big percentage of biomass on Earth. Given their three-dimensional structure, complex material properties and social behavior, fast and accurate measurements remain elusive. Akin to how geologists study mountains and Earth’s topography to learn about the history of Earth, we postulate that the same methodology can be applied to bacterial colonies. Their topographies are rarely quantitatively characterized; these topographies reflect not only the current configuration of the colony but may also reflect some of its history.
We explore how interferometry, a measurement technique capable of measuring the surface topography of an unprepared sample, with ultra-high resolution, can allow us to understand the development of surface attached microbial colonies. We aim to link the theory developed for inert crystal surfaces with the complex self-assembling interface of biofilms. Previous work has already shown the utility of measuring topographies to identify bacterial warfare and antibiotic heteroresistance. Using time lapse interferometry, we can get large datasets of developing samples from single cells to large ~1mm tall colonies.
To establish interferometry as a tool for microbiology, we need to develop a framework that not only allows a streamlined analysis of the samples, but to be able to learn biologically relevant quantities, such as growth and death rates, species identification and age of the sample. For this purpose, we propose an approach of experimental measurements complimented by simple biophysical models and spatial computational simulations.