This PhD project is funded through the SynBioCDT. It aims to identify simple biochemical mechanisms in metabolic enzymatic reaction systems that can generate bistability and oscillatory dynamics. The resulting mechanisms are then analyzed against real system, where they can be identified and used to control metabolic system dynamics. The identified mechanisms can also be incorporated in vitro using cell free enzymatic systems.
This project is funded by the BBSRC, through their "Tools and Resources Development Fund". It aims to collect weekly microbiome data for over a year from several industrial-scale anaerobic digestion plants across the UK. Thus, the project will achieve an unprecedented temporal microbiome data set from these methane producing bioreactors. This data set, together with meta-data on methane production and other operational parameters, will be used to develop computational models for predicting community function, structure and failure. Timeframe: 2016-2017. See project website anaerodynamics
This project is funded by BBSRC as part of their 20m investment in synthetic biology. One of the six strategic LoLa's (longer and larger grants), this 5 year project brings together an interdisciplinary team of engineers, microbiologists, evolutionary biologists, synthetic biologists, and bioinformaticians to understand natural microbial communities and engineer synthetic ones. The communities we will focus are those that underline anaerobic digestion; breakdown of organic waste into methane in the absence of oxygen. To read more about the project and track our progress, please visit the dedicated project website. Timeframe: 2013-2018.
Engineering a synthetic community for high value chemical production. This project was part of the Warwick Integrative Centre for Synthetic Biology (WISB) that is funded by the BBSRC and EPSRC. It aimed to build a synthetic ecosystem that incorporates phototrophic and heterotrophic microorganisms. It resulted in the establishment of a cross feeding co-culture between two heterotrophs, where metabolic cycling of manganese is possible. This system can form the basis of interactions with a phototroph. Timeframe: 2015-2017. Modelling host-virus metabolic interaction. This PhD project was funded by the Defence Science and Technology Laboratory (DSTL), under their research program on pathogens posing a biothreat. This project focused on developing (stoichiometric) metabolic models of the host-virus interaction, to explore if host metabolism could be modulated in such a way so to limit virus production. It led to the identification of such modulation points in host metabolism that can now be experimentally test. Timeframe: 2014-2017. Parasite disruption points in host networks. This project was funded by the Defence Science and Technology Laboratory (DSTL) as part of the partnership program between DSTL and University of Exeter. The project concentrated on analysing epigenetic changes upon host infection. Timeframe: 2013-2016. Parasite-host interaction at the metabolic level. This project was funded by the Defence Science and Technology Laboratory (DSTL) as part of the partnership program between DSTL and University of Exeter. The project concentrated on analyzing the interaction of Burkholderia pseudomallei and Francisella tularensis with human macrophages. Timeframe: 2012-2015. Engineering a semi-biotic immune system. This project was funded by the EPSRC Flashlight Funding: Engineering Challenges in Synthetic Biology initiative, which aims to support young academics that are the leaders of the future. Timeframe: 2010-2015. EPSRC link Deciphering The Molecular Basis of Environmental Persistence in Campylobacter Using a Systems Approach (research project with Titball R, Hemsley C, and Luo J, funded by BBSRC). 2011-2014. BBSRC link Evolving controllers and controlling evolution (research project with Akman O, Bates D, Steinacher A, and Montefusco F, funded by EPSRC). 2011-2014. EPSRC link Computational capabilities and underlying mechanisms in biological signaling networks (PhD project, Varun Kothamachu, funded by a EPSRC/Microsoft Research Dorothy Hodgkin PhD Award). 2010 - 2014. Response dynamics and evolution in signalling networks regulating bacterial chemotaxis (PhD project, Munia Amin, funded by Exeter Systems Biology). 2010 - 2013.