| dc.description.abstract | In this document we describe a novel platform for the engineered evolution of microbes. Our platform consists of three major components, which we discuss in subsequent chapters. Technology: We have developed a novel continuous culture device called the Flexostat. The Flexostat is a flexible, programmable, eight chamber, turbidostat with multiplexed fluidics. The design of the Flexostat is open sourced and has accompanying detailed assembly instructions. Modularity of the design also enables users to rapidly create derivative devices without needed to adapt unrelated components of the device. Cell Chassis: While the majority of laboratory strains of S. cerevisiae do not form biofilms or flocs. Unfortunately, E. coli does form robust biofilms. To compound this, continuous culture and turbidostats in particular select strongly for biofilms as they are immune to washout. We have developed a new, MG1655 derived, strain of E. coli that does not form biofilms. The inability of our strain to form biofilms enables longterm evolution and characterization experiments in E. coli. Theory: We develop a stochastic hybrid systems model for evolution in a turbidostat. With our model we show that there exists an optimally challenging environment as well as optimal population size for single evolutionary steps. We also use insights gained from our model to develop a control strategy for accelerated evolution in parallel turbidostats and demonstrate it’s utility in a randomly generated model system. At the time of this writing, the Flexostat or derivative has been built in over a dozen labs at institutions including the Massachusetts Institute of Technology, California Institute of Technology, Rice, University of California San Diego, and three companies, DuPont, Bolt Threads, and Arzeda | |
