Periodic Reporting for period 2 - COSY-BIO (Control Engineering of Biological Systems for Reliable Synthetic Biology Applications)
Período documentado: 2018-10-01 hasta 2021-03-31
The overarching aim of the COSY-BIO consortium is to develop a theoretical and methodological framework together with innovative technological tools to reliably engineer biological systems that are robust despite their individual components being not, by translating principles of control engineering to molecular and cell biology. Attempts to apply engineering principles to biological processes to understand and build new functions in cells have led to the growing interdisciplinary community of Synthetic Biology. Currently synthetic circuits can perform only very basic functions thus having a limited impact in biotechnology and biomedicine. Application and adaption of established theories and techniques from conventional control engineering have been hampered by the peculiarities of biological systems, such as cell-to-cell variability, metabolic load, cross-talking and practical realizability. COSY-BIO aims to build the theoretical and methodological foundations of biomolecular control engineering. COSY-BIO focuses on three major control strategies to impose a desired dynamical behaviour to a biological process of interest, with increasing levels of sophistication and with complementary practical applications: external controllers, embedded controllers and multicellular controllers. This is fundamental to make a major leap in current synthetic biology research, especially in the direction of high-impact applications.
The main results of achieved in COSY-BIO are listed below:
• Theoretical/Methodological:
o General methods for realizing classes of nonlinear dynamical systems using mass-action or michaelis-menten-type kinetics.
o Biomolecular PID control architectures that take into consideration the biological implementation aspect.
o Analytical means to compute the average vector field of a toggle switch subjected to periodic stimulations enabling the design of external and embedded controllers for this kind of systems.
o Multicellular feedback control strategies to regulate gene expression using controller and target cells.
o Introduced and solved the “ratiometric control problem”of keeping two bacterial populations at the desired ratio.
o An optimal control strategy for the microbial differentiation of cells.
o Designed an embedded controller to achieve self-synchronisation of the cell cycle across the yeast population
• Experimental:
o A platform combining video-microscopy and microfluidics to perform closed loop system identification
o External controller enabling synchronisation of the cell cycle in a yeast cell population by means of microfluidics and optogenetics.
o External control of the concentrations of two cellular populations growing in continuous culture.
o The first embedded Integral controller in bacterial cells.
o Embedded control of burden exerted by synthetic circuits in the cell in terms of competition for resources and induction of cell stress.
o Engineered bacterial strain to act as ‘Controller’, capable of monitoring and controlling the output of another strain acting as ‘Target’.
• Software tools:
o ReacSight, a generic and flexible software strategy to enhance multi-bioreactor platforms for automated measurements and reactive experiment control
o MicroMator, is a software solution for reactive microscopy.
o ODEComposer software tool to enable composition of ODE models from a library of right-hand side terms to identify a suitable model structure from experimental data.
The consortium as a whole has published 28 manuscripts in peer-reviewed journals, 10 manuscripts in conference proceedings, 1 book chapter and 5 in preprint servers. We also organised two Image Analysis Workshops, and six between special sessions and workshops on Cybergenetics at the European Control Conference and the Control and Decision Conference (CDC). Consortium members gave over 78 presentations at scientific events including seminars, invited lectures and international conferences.
• Theoretical/Methodological:
o General methods for realizing classes of nonlinear dynamical systems using mass-action or michaelis-menten-type kinetics.
o Biomolecular PID control architectures that take into consideration the biological implementation aspect.
o Analytical means to compute the average vector field of a toggle switch subjected to periodic stimulations enabling the design of external and embedded controllers for this kind of systems.
o Multicellular feedback control strategies to regulate gene expression using controller and target cells.
o Introduced and solved the “ratiometric control problem”of keeping two bacterial populations at the desired ratio.
o An optimal control strategy for the microbial differentiation of cells.
o Designed an embedded controller to achieve self-synchronisation of the cell cycle across the yeast population
• Experimental:
o A platform combining video-microscopy and microfluidics to perform closed loop system identification
o External controller enabling synchronisation of the cell cycle in a yeast cell population by means of microfluidics and optogenetics.
o External control of the concentrations of two cellular populations growing in continuous culture.
o The first embedded Integral controller in bacterial cells.
o Embedded control of burden exerted by synthetic circuits in the cell in terms of competition for resources and induction of cell stress.
o Engineered bacterial strain to act as ‘Controller’, capable of monitoring and controlling the output of another strain acting as ‘Target’.
• Software tools:
o ReacSight, a generic and flexible software strategy to enhance multi-bioreactor platforms for automated measurements and reactive experiment control
o MicroMator, is a software solution for reactive microscopy.
o ODEComposer software tool to enable composition of ODE models from a library of right-hand side terms to identify a suitable model structure from experimental data.
The consortium as a whole has published 28 manuscripts in peer-reviewed journals, 10 manuscripts in conference proceedings, 1 book chapter and 5 in preprint servers. We also organised two Image Analysis Workshops, and six between special sessions and workshops on Cybergenetics at the European Control Conference and the Control and Decision Conference (CDC). Consortium members gave over 78 presentations at scientific events including seminars, invited lectures and international conferences.
Control Engineering is a scientific discipline devoted to engineer complex systems and make sure they behave reliably and robustly. For example, airplanes and self-driving cars are equipped with “controllers” that make sure they track the the correct route at the correct speed, in spite of external disturbances such as wind, rain, traffic, etc. The basic idea driving the COSY-BIO project is to translate Control Engineering principles to living cells to engineer molecular circuits endowing cells with new functions with applications to biotechnology and biomedicine. Attempts to apply engineering principles to biological processes to understand and build new functions in cells have led to the growing research interdisciplinary community of Synthetic Biology. However, application and adaption of established theories and techniques from conventional control engineering have been hampered by the peculiarities of biological systems.
COSYBIO research has considerably advanced the state of the art both at the theoretical/methodological level in designing biocontrollers and in their experimental implemenation.
At the methodological level, we have found a set of guiding principles that allow us to design external, embedded and multicellular biological controllers that work reliably and robustly in the cell. At the experimental level, we have implemented external, embedded and multicellular controllers in bacteria and yeast, thus experimentally validating the theoretical and methodological results we obtained. We also developed technologies and software to help advance and streamline biocontrol engineering, by building an automated platform able to autonomously perform experiments in bacterial and yeast cells and to build a mathematical model of the biological process of interest, based on the experiment results. We also developed open-source software tools to ease image analysis, automated microscopy and model building.
The benefits to society of the technology developed in COSYBIO are many: in the short-term biocontrol engineering can make an impact in biotechnology where engineered microbial cells are used to convert biomass and other feedstock into desired products such as fuels, food and antibiotics. These processes can be made much more efficient and environmentally sustainable by engineering external, embedded or multicellular controllers that ensure the cells behave as desired in the bioreactors to maximise production. In the long-term, we foresee a major impact in biomedicine where biocontrol engineering will lead to major inroads into bacterial and human cell engineering for therapeutic purposes and regenerative medicine (e.g. bacteria able to deliver a therapeutic payload to cancer cells, or metabolise toxic products to treat metabolic disease; or engineered human T cells to fight cancer).
COSYBIO research has considerably advanced the state of the art both at the theoretical/methodological level in designing biocontrollers and in their experimental implemenation.
At the methodological level, we have found a set of guiding principles that allow us to design external, embedded and multicellular biological controllers that work reliably and robustly in the cell. At the experimental level, we have implemented external, embedded and multicellular controllers in bacteria and yeast, thus experimentally validating the theoretical and methodological results we obtained. We also developed technologies and software to help advance and streamline biocontrol engineering, by building an automated platform able to autonomously perform experiments in bacterial and yeast cells and to build a mathematical model of the biological process of interest, based on the experiment results. We also developed open-source software tools to ease image analysis, automated microscopy and model building.
The benefits to society of the technology developed in COSYBIO are many: in the short-term biocontrol engineering can make an impact in biotechnology where engineered microbial cells are used to convert biomass and other feedstock into desired products such as fuels, food and antibiotics. These processes can be made much more efficient and environmentally sustainable by engineering external, embedded or multicellular controllers that ensure the cells behave as desired in the bioreactors to maximise production. In the long-term, we foresee a major impact in biomedicine where biocontrol engineering will lead to major inroads into bacterial and human cell engineering for therapeutic purposes and regenerative medicine (e.g. bacteria able to deliver a therapeutic payload to cancer cells, or metabolise toxic products to treat metabolic disease; or engineered human T cells to fight cancer).