Harness optogenetic control and real-time analysis of chemicals production in bioreactors

The UK chemical industry is vitally important to the UK economy, with annual sales over £50bn, employing 158,000 people and is one of the UK's largest exporting industries with a positive trade balance. Since around 8% of fossil fuel consumption is used to produce chemicals (including pharmaceuticals), society needs new technologies to manufacture the pharmaceuticals, chemicals and materials essential to modern life, in ways that are decoupled from fossil fuels. Alternative biomanufacturing routes will allow virtually any carbon containing material to be converted into these modern-day essentials. Building this 'High Value Bioeconomy' is at the core of research programmes in the Manchester Institute of Biotechnology. This PhD studentship contributes to this vision by developing innovative fermentation platforms for the bio-based production of fine and speciality chemicals using engineered microbial strains and optogenetic feedback control. The project is set in the Manchester Centre for Synthetic Biology SYNBIOCHEM which has set up fully integrated and automated platforms for microbial strain engineering for the production of fine and speciality chemicals.1

This is an exciting project that seeks to harness optogenetic control and real-time analysis of chemicals production in bioreactors by setting up feedback control of metabolic pathway flux through light-dependent transcriptional control during fermentation. The student will get experience of state-of-the-art synthetic biology methods in microbial strain engineering, biological parts engineering and characterisation, chemicals production through laboratory fermentations, the use of innovative mass spectrometry methods to sample product build up in the headspace of fermentations and control of the outcome of these fermentations through optogenetic feedback control with AI/machine learning components.

The PhD student based in Manchester Institute of Biotechnology (MIB) and the SYNBIOCHEM Synthetic Biology Research Centre in the MIB will be co-supervised by Professor Nigel Scrutton, Prof Eriko Takano and Dr Sam Hay, with expert scientific/technical support from Senior Experimental Officers Dr Derren Heyes and Dr Kat Hollywood. The student will be trained in broad aspects of 'wet' biotechnology, including synthetic biology, microbial strain bioengineering, molecular biology, innovative mass spectrometry and analytics, and also 'dry' science including AI/machine learning and broader aspects of computational coding for bioreactor feedback control. This project would suit individuals interested in future careers in bioengineering, chemicals production, and industrial biotechnology.

This PhD project will exploit new ways of working by providing training in a variety of approaches relevant to the Bioenergy and Industrial Biotechnology theme. This will include lab-based skills in strain bioengineering, design, build and testing of optogenetic protein components, data processing and statistical analysis, HTP analytical methods, bioreactor design and engineering, and control loop engineering. This will provide the PhD student with the ability to use and apply quantitative data-driven approaches to more fully understand biological questions and apply these to scale up/production challenges. In addition to the training the research project goals/outputs in themselves will exploit new ways of working, as they will provide innovative tools and technological approaches for the production of high-value fine chemicals and materials