An Automated Tabletop Continuous Culturing System with Multicolor Fluorescence Monitoring for Microbial Gene Expression and Long-Term Population Dynamics

Diya - A universal light illumination platform for multiwell plate cultures

Recent progress in protein engineering has established optogenetics as one of the leading external non-invasive stimulation strategies, with many optogenetic tools being designed for in vivo operation. Characterization and optimization of these tools require a high-throughput and versatile light delivery system targeting micro-titer culture volumes. Here, we present a universal light illumination platform - Diya, compatible with a wide range of cell culture plates and dishes. Diya hosts specially designed features ensuring active thermal management, homogeneous illumination, and minimal light bleedthrough. It offers light induction programming via a user-friendly custom-designed GUI. Through extensive characterization experiments with multiple optogenetic tools in diverse model organisms (bacteria, yeast, and human cell lines), we show that Diya maintains viable conditions for cell cultures undergoing light induction. Finally, we demonstrate an optogenetic strategy for in vivo biomolecular controller operation. With a custom-designed antithetic integral feedback circuit, we exhibit robust perfect adaptation and light-controlled set-point variation using Diya.

Platforms for Optogenetic Stimulation and Feedback Control

Harnessing the potential of optogenetics in biology requires methodologies from different disciplines ranging from biology, to mechatronics engineering, to control engineering. Light stimulation of a synthetic optogenetic construct in a given biological species can only be achieved via a suitable light stimulation platform. Emerging optogenetic applications entail a consistent, reproducible, and regulated delivery of light adapted to the application requirement. In this review, we explore the evolution of light-induction hardware-software platforms from simple illumination set-ups to sophisticated microscopy, microtiter plate and bioreactor designs, and discuss their respective advantages and disadvantages. Here, we examine design approaches followed in performing optogenetic experiments spanning different cell types and culture volumes, with induction capabilities ranging from single cell stimulation to entire cell culture illumination. The development of automated measurement and stimulation schemes on these platforms has enabled researchers to implement various in silico feedback control strategies to achieve computer-controlled living systems—a theme we briefly discuss in the last part of this review.

Reactor control system in bacterial co-culture based on fluorescent proteins using an Arduino-based home-made device

BACKGROUND

Co-culture, fermentation with more than two microbial strains, is a potential flexible method for optimizing the metabolic conversion process in bio-production. However, maintaining an ideal population throughout the fermentation process remains a challenge.

METHODS AND RESULTS

In this study, we developed a proportional control system for controlling the population ratio of Escherichia coli strains to a set value during continuous co-culture. Two E. coli strains were distinguished by expressing different fluorescent proteins, and their population ratio was determined by culture fluorescence. Furthermore, different types of amino acid auxotrophs were provided to each strain, and among these, growth was controlled by the amino acid concentrations in the feed medium. An Arduino-based device was developed using light-emitting diodes and cadmium sulfide light sensors for the in-line monitoring of culture fluorescence. Two E. coli strains of methionine auxotroph green fluorescent protein (GFP) expressing (met-GFP) strain and arginine auxotroph red fluorescent protein (RFP) expressing (arg-RFP) strain were co-cultured using a jar-fermenter. The amounts of methionine and arginine in the feed medium were altered to guide the population ratio to a set value. During the continuous culture, the population ratio between the met-GFP and arg-RFP strains was successfully maintained at approximately the setpoint values.

CONCLUSION

This study demonstrated the development of a home-made device for controlling the reactor of E. coli based on fluorescent proteins using inexpensive parts.