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[Closes 29 Jan 2018] PhD in synthetic bioremediation at Newcastle University

Climate change due to anthropogenic deterioration of the environment is a major threat to the biosphere. One way to address this problem comes from bioremediation through synthetic biology. This project aims to abstract ecosystems into sets of compounds, reactions and connections. Such ecological templates will then be mathematically formalised, and experimentally reproduced, to allow their integration into the rational design of genetic circuits

Further information from the Lead Supervisor, Dr Angel Goni-Moreno:

"Climate change due to anthropogenic deterioration of the environment is a major threat to the biosphere. Environmental pollution puts ecosystems at risk of irreversible collapse. An encouraging, yet challenging, way to address this problem comes from bioremediation through synthetic biology. Synthetic biology applies rational engineering principles to the design and build of novel biological systems. The visionary application to bioremediation involves releasing such engineered organisms into the environment to counterbalance its otherwise inevitable decline. This project addresses the UN Sustainable Development Goals (SDG) by taking action to combat climate change through restoration of ecosystems – a challenge with increasing presence in scientific and political agendas.

Inside the laboratory, synthetic biology has effectively outplaced the virtually abandoned filed of genetic engineering. This was done by introducing genuine engineering notions such as design, modularity, standardisation and orthogonality. Compatible DNA components are assembled in a Lego-like fashion to build biomolecular networks à la carte – the so-called ‘genetic circuits’. Outside the laboratory, however, most efforts in bioremediation lac of a synthetic biology perspective. There are no compatible components to assemble. As a result, current bioremediation strategies do not seem powerful enough to cope with the challenges that climate change confront us with. The project aims at reversing this state of affairs.

A major problem of engineering biology for ecological use is that environmental conditions are way too different from pristine laboratory setups. We will formalise and standardise the connections between DNA components and the chemicals of specific ecological environments. We will develop registries of biological parts (sequences of DNA with specific biological function) which performance is optimised for a given environmental scenario. This will allow, for the first time, to select components to build complex synthetic circuits that will function reliably in ecological domains. What we refer to as ‘synthetic eco-registries’ will constitute fundamental starting points for bioremediation strategies based on synthetic biology.

The key to the success of the project is to abstract ecosystems into sets of compounds, reactions and connections. Such ecological templates will then be mathematically formalised, and experimentally reproduced, to allow their integration into the rational design of genetic circuits. This highly novel approach has been unattained to date. Its realization involves the application of methods at the interface of Computer Sciences, Engineering and Biology, for which our interdisciplinary group has world-leading expertise. Conveniently, ecosystem abstraction will allow the project to run indoors (i.e. inside the laboratory) without in situ testing. Nevertheless, we will collaborate with the Policy, Ethics and Life Sciences (PEALS) research centre to discuss further research on the topic that involves the release of engineered organisms.

The outcome of this project will be instrumental in follow-up research on bioremediation aiming at addressing the SDG challenges by 2030. The interdisciplinary nature of the supervisory team, along with an extensive network of academic and industrial experts, ensures the smooth flow of the project. Our laboratory comprises of all equipment needed for the PhD candidate to conduct theoretical and experimental research on bacterial-based synthetic biology."

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The Synthetic Biology Strategic Research Initiative provides a hub for anyone interested in Synthetic Biology at the University of Cambridge, including researchers, commercial partners and external collaborators.