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Design Principles of Biological Oscillators through Optimization: Forward and Reverse Analysis.
Irene Otero-Muras1, Julio R Banga1
1BioProcess Engineering Group, IIM-CSIC, Spanish National Research Council, Vigo, Spain.
Plos One
|December 16, 2016
Summary
This study introduces a novel tool for designing biological oscillators by optimizing trade-offs between performance goals. It enables automated design and reveals underlying design principles for synthetic biology applications.
Area of Science:
- Systems Biology
- Synthetic Biology
- Computational Biology
Background:
- Biological oscillators, crucial for functions from cyanobacteria to humans, have complex molecular mechanisms.
- Understanding the design principles linking oscillator structure and function remains a challenge.
Purpose of the Study:
- To explore biological oscillator design principles using multiobjective optimization.
- To develop a tool for automated oscillator design and inference of design principles.
Main Methods:
- Utilized multicriteria global optimization for a multiobjective perspective.
- Developed a tool with two modes: automatic design (forward) and design principle inference (reverse analysis).
- Applied Pareto optimality concepts for systematic exploration of the design space.
Main Results:
- Demonstrated automated design of synthetic oscillators mimicking natural properties.
- Facilitated exploration of design principles in 3-gene oscillatory systems.
- Provided a framework for understanding structure-function relationships in biological oscillators.
Conclusions:
- The developed tool offers a powerful approach for synthetic biology design problems.
- Multiobjective optimization provides insights into the trade-offs governing biological oscillator design.
- This work advances the understanding and engineering of biological oscillators.
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