Single-cell control of microbial selection and evolution

Lead Research Organisation: University of Oxford
Department Name: Engineering Science

Abstract

Feedback control is a fundamental engineering principle that has been used successfully for decades to improve the robustness and performance of engineered and natural systems, and to drive their output to desirable set-points. Examples abound, ranging from Watt's fly-ball governor to medical life-support systems to fly-by-wire planes.

With advances in computation and instrumentation, as well as new theoretical frameworks, the field is now moving towards distributed, data-driven, real-time optimal feedback control solutions. The ultimate aim is to address the challenge of controlling systems with significant uncertainty - both in their modeling, as well as in the environment they need to operate. Indeed, systems of this type are becoming more and more prevalent, and autonomous systems solutions are being sought across technology and biomedicine. The development of new theory, tools, and instrumentation for these challenges creates new opportunities, and new horizons, with significant impact in areas where feedback control has not had widespread application yet.

One such area is biological evolution. Defined as the change in inherited characteristics over successive generations of a species, it is a slow optimisation process that over time (sometimes millions of years) naturally improves traits and species fitness. Directed evolution - a cyclic process of gene diversification, screening, and selection - has had significant impact on biotechnology in the past few years, but this is largely a passive, uncontrolled process. The benefits of dynamically steering evolution so as to improve single-cell designs in a predictable fashion autonomously would be hugely significant - with applications across biotechnology and beyond. However this has not been attempted in closed loop before, not least because the experimental paradigm and feedback control frameworks required to realise this vision are currently missing.

In this new horizons project we will combine advanced instrumentation with feedback control theory to develop a first-of-its-kind platform for closed-loop directed evolution. In particular, we will create a robotic microscope platform to monitor the behaviour of ~1 million bacterial cells as they grow continuously, confined in a microfluidic chip for long periods of time. Continuous imaging of the population will be used to quantify each cell's performance, with this information driving a feedback controller that will in turn decide which cells to propagate and which not, in order to achieve a target distribution of behaviours over time. Feedback control at this scale has not been attempted before, and this application area will push the development of new theory and algorithms.

Indeed, our controlled evolution platform will advance the boundaries of what is possible right now both from the standpoint of instrumentation and control, as well as in terms of understanding and manipulating evolution. The development of this robotic control approach is motivated by the need for real-time, accurate actuation for directed evolution and is facilitated by nascent microscopy and image processing technologies. Moreover, the development of the theory is challenged by the size of the system to be controlled (millions of states) as well as uncertainties involved in modeling and observing the stochastic evolutionary process. On the whole, this high-risk high-reward project will unlock a number of biotechnological applications, as well as opening new research opportunities in biological evolution and feedback control.

Publications

10 25 50
 
Description Answer is yes however we are currently being instructed by TTO not to disclose publicly due to patent considerations. The instructions above say we should not share anything that we would not want shared publicly, so we will not include details here.
Exploitation Route Fundamental new technology approach to Engineering Biology
Sectors Digital/Communication/Information Technologies (including Software)

Electronics

Manufacturing

including Industrial Biotechology

 
Description - Presented to large-scale public lectures to >3500 people. - Discussion at open fora for regarding Biotechnology and its future impact on society.
First Year Of Impact 2023
Impact Types Societal

 
Description Doctoral Training Courses + Engineering Biology Centre for Doctoral Training
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
Impact - Consulted with Bioindustry Association on national investment policy development for Synthetic Biology. - Talks to general public on biotechnology and potential for societal benefit depending on UK/EU changes in regulations. - Talk to business leaders (CEOs and Board Members) visiting Oxford about potential impact of Biotechnologies in their area.
 
Title Created new microscopy platform for single-cell selection. 
Description As described in this grant, we developed a new approach to microscopy allowing high-throughput single-cell selection of engineered bacteria. 
Type Of Material Improvements to research infrastructure 
Year Produced 2023 
Provided To Others? No  
Impact Work will be published in the coming year as we finish characterisation and demonstration of the technology. 
 
Title Hardware for Microscopy Automation 
Description Software: Created deep-learning toolbox for microscopy image segmentation and training. This has been published open-source already for others to use. Hardware: Created new DMD micromicror system and new LED drive/sync system. This has not yet been made open source as it is undergoing validation. 
Type Of Technology New/Improved Technique/Technology 
Year Produced 2024 
Open Source License? Yes  
Impact Significant reduction in time-to-data for ~5 labs worldwide that have built on this software. Our pre-trained and generative model can reduce human input on labelling data sets by ~1 month of person-time. 
 
Description Online talk to general public 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact Talk to 3500 attendants in Online Tech Seminar Series workshop.
Year(s) Of Engagement Activity 2023
 
Description Synthetic Biology UK Conference - 1 Talk and 9 Posters 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Research group building on research in these projects presented at SynBioUK 2023. THis included one oral presentation and nine poster presentations.
Year(s) Of Engagement Activity 2023
URL https://www.bristol.ac.uk/biodesign-institute/events/2023/conference---sbuk.html
 
Description Talk to Department of Biology 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Research talk on project outputs to Biology Department.
Year(s) Of Engagement Activity 2024
 
Description Talk to University of Sydney Fora (Australia) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk to VC, senior members, academics, and students at University of Sydney as part of the General Sir John Monash Symposium held in December 2023.
Year(s) Of Engagement Activity 2023
URL https://www.johnmonash.com/