A generalizable experimental framework for automated cell growth and laboratory evolution

Abstract

In the post-genomics era, exploration of phenotypic adaptation is limited by our ability to experimentally control selection conditions, including multi-variable and dynamic pressure regimes. While automated cell culture systems offer real-time monitoring and fine control over liquid cultures, they are difficult to scale to high-throughput, or require cumbersome redesign to meet diverse experimental requirements. Here we describe eVOLVER, a multipurpose, scalable DIY framework that can be easily configured to conduct a wide variety of growth fitness experiments at scale and cost. We demonstrate eVOLVERs versatility by configuring it for diverse growth and selection experiments that would be otherwise challenging for other systems. We conduct high-throughput evolution of yeast across different population density niches. We perform growth selection on a yeast knockout library under temporally varying temperature regimes. Finally, inspired by large-scale integration in electronics and microfluidics, we develop novel millifluidic multiplexing modules that enable complex fluidic routines including multiplexed media routing, cleaning, vial-to-vial transfers, and automated yeast mating. We propose eVOLVER to be a versatile design framework in which to study, characterize, and evolve biological systems.