Project Projects Available for Self-funding Students:
Synthetic Biology: Biosensors for Biomass Degradation and Bio-remediation
The development of enzymatic and whole cell process for the depolymerisation of both plant biomass and plastics is to a key challenge for society. Firstly valorization of biomass to create sustainable bio-synthetic routes to chemicals, plastics, monomers, waxes, fuel and energy is a central tenet of the move towards a circular bio-economy. Secondly the ability to detect the break down of plastics by biological process would enable bioremediation optimization with huge environmental benefits .
This PhD project will look to develop and apply enabling biotechnologies to support the adoption of sustainable production processes and bioremediation. We recently developed a bacterial based biosensor for the detection of plant biomass (lignin) derived monomers (ferulic acid) . However, the most well characterized enzymes for lignin degradation have been identified from fungal sources . The aim is transfer the biosensor into a fungal host to enable the direct detection of fungal mediated degradation of natural and man-made polymeric materials.
 S. Yoshida et alA bacterium that degrades and assimilates poly(ethylene terephthalate). Science 2016
 L. F. M. Machado and N. Dixon Development and substrate specificity screening of an in vivo biosensor for the detection of biomass derived aromatic chemical building blocks Submitted 2016
 T. D. H. Bugg et al Pathways for degradation of lignin in bacteria and fungi. Natural Product Reports 2011
Dynamic Ribo-regulator Tools for Expression Control in Mammalian Cells
The development of novel SynBio gene expression tools offers the potential to refine expression and co-expression of both native host and recombinant proteins . Ribo-regulation offers an attractive alternative means of control gene expression by control translation, stability and/or processing of mRNA . The ability to finely regulate expression in mammalian has many biotechnological application and huge potential biological and biomedical impact. These range from producing recombinant therapeutic proteins to engineering cellular safety switches for cell therapy applications . However such tools to permit fine tuned regulation in mammalian cells are currently limited. The series of inducible systems used in mammalian cell systems are restricted to transcriptional control sites and are relatively coarse in their control parameters . For example, as post-transcriptional events are known to restrict the expression and processing of commercially-valuable secreted biopharmaceuticals , the ability to develop fine tuned control of post-transcriptional events offers wide scope for more efficient production processes. Uniquely, a combination of transcriptional and Ribo-regulation offers the opportunity to develop combinatorial, multiplexed regulation of cellular events (e.g. mRNA production, specific mRNA ribosomal engagement, secretory vesicular transit, precursor availability – and multiples thereof) to maximise the effectiveness of the host cell platform as a “factory” for desired protein manufacture.
This PhD project will seek to enhance the production of protein-based biotherapeutics, to lower manufacturing costs of these important medicines and reduce the burden upon the NHS and other national healthcare providers. This will entail the use of ribo-regulators and synthetic biology methods (Dixon), and mammalian cell (Chinese Hamster Ovary, CHO, and HEK) culture and bioprocess optimisation (Dickson). The driver of this applied research is to provide enhanced production processes and training to support the knowledge-based bio economy (KBBE). This PhD project will provide training in state of the art synthetic/molecular biology techniques, advanced analytical methods, and bioprocess performance analysis.
 Neil Dixon, et al. Orthogonal Riboswitches for Tuneable Co-expression in Bacteria. Angewandte Chemie International Edition (2012)
 Rosa Morra, Jayendra Shankar, Neil Dixon et alDual transcriptional-translational cascade permits cellular level tuneable expression control. Nucleic Acids Research (2016)
 Di Stasi A, et al. Inducible apoptosis as a safety switch for adoptive cell therapy N Engl J Med. (2011)
 Misaghi, S, et al (2014) It’s time to regulate: Coping with product-induced non-genetic clonal instability in CHO cell lines via regulated protein expression. Biotechnol. Prog. 30: 1432-1440.
 Hussain, H et al (2014) The endoplasmic reticulum and unfolded protein response in the control of mammalian recombinant protein expression Biotechnol. Lett. 36: 1581-1593.
Previously, I have re-engineered naturally occurring riboswitches to provide novel orthogonal tools for genetic regulation [Dixon et al PNAS 2010]. These regulatory elements have been coupled to a range of reporter proteins and other functional proteins (e.g. T7 RNAP). Currently I am involved in the development and demonstration of this novel gene expression technology for use in the bio-manufacture of human therapeutic proteins (biopharmaceuticals). I am interested in expanding this first generation riboswitch-based expression technology to provide a) higher order synthetic biology systems and devices, b) tuneable periplasmic secretion systems and, c) platform co-expression technologies - building on earlier proof-of-concept work [Dixon et al Angew. Chem. 2012].
My research interests span chemical biology, molecular detection/recognition and synthetic biology. We are currently exploring a number of research areas including i) the application of novel riboswitch-based gene expression tools, the development of tuneable recombinant protein production systems, ii) optimisation of cellular protein expression and secretion processes, iii) the fundamentals of small molecule-RNA-protein interactions, and iv) the development and application of in vivo biosensors to detection small molecules of bio-medical and biotechnological interest.
The driver of these applied research areas is the development of new chemical and synthetic biology tools to both i) help understand fundamental biological processes, ii) permit more efficient protein production process, and iii) optimise whole-cell bio-catalytic processes supporting the bio-based economy.