New technologies for modelling, monitoring and predicting agrochemical transport in plants[PhD project, NexGenAgriChem].This project measures the ability of agrochemicals to cross artificial membranes constructed to resemble those found in agriculturally relevant species. This involves developing new microfluidic technologies for manufacturing inter-connected 2-D and 3-D membranes as well as exploiting cutting edge imaging tools to measure agrochemical transport through these barriers. This will lead to general or class-specific design principles for agrochemical membrane translocation with these results directly feeding into industrial research programmes. This project also examines the role of membrane-bound proteins in the active transport of chemicals.
A novel two dimensional infrared spectroscopic tool to study herbicide interaction in plants[PhD project, NexGenAgriChem]. This project investigates the application of a novel form of 2D Infra-red (2D-IR) electron vibration vibration (EVV) spectroscopy to study herbicide interaction. This form of spectroscopy, which can be considered as an optical analogue of 2D NMR, is able to probe interactions in protein systems. The project therefore facilitates rational herbicide design, and will directly feed into the industrial agrochemical pipeline.
Novel chemical probes to investigate the metabolism and mode of action of insecticides[PhD project, NexGenAgriChem].This project develops a generic approach for the rapid identification and characterisation of the metabolising enzymes responsible for detoxification of specific insecticides. Insecticides will be immobilised and the resulting conjugates will be employed as pull-down probes; proteomic analysis of the interactome protein fractions will ensue. Covalent cross-linking ‘warheads’ will also be generated and attached to the insecticides in order to target the interactome, and will be monitored using fluorescence microscopy in insect cells and/ or plant cell. Overall, the project involves the integration of synthetic chemistry, chemical biology and biochemistry to create a bespoke solution to identify the key P450 enzymes involved in insecticide metabolism in specific plants and to track their spatio-temporal distribution in cells.
Novel chemical probes to probe the metabolism and mode of action of fungicides [PhD project, NexGenAgriChem]. This project develops and applies novel chemical methods for the identification of the specific enzymes responsible for detoxification of a given fungicide. It probes the site and mode of chemical reaction of these enzymes to aid our understanding of fungal detoxification pathways to allow for the design of more effective fungicides in the future. The plan has been to immobilise fungicidal compounds onto various support matrices via linkers/spacers co-functionalised with cross-linking ‘warhead’ functionality and employ these as pull-down probes. Overall, the project involves the integration of synthetic chemistry, chemical biology and biochemistry to create tailored protocols for the rapid mapping of fungicide-protein interactomes.
Chemical dissection of the targets of insecticides with a novel mode of action [PhD project, NexGenAgriChem]. Recent developments around tools for target ID in the Tate lab have presented a unique opportunity to profile the targets of pyridalyl (PAL), a potent and selective insecticide of substantial commercial importance. Understanding the targets of this molecule is a high priority for Syngenta and would open up new classes of insecticide target for future exploitation. Addition of a 'clickable' tag to selected inhibitors will facilitate ligation of combinations of biotin and fluorescent dye labels and will enable imaging and pull-down based assays.
Lipidated proteomics: Chemical validation of protein lipidation pathways as antifungal targets[PhD project, NexGenAgriChem].This project profiles the substrates of protein lipidation of plant pathogentic fungi, more specifically N-myristoyltransferase (NMT). The Tate lab has developed powerful tools for analysis of this enzyme in living systems, and the project exploits these capabilities to establish in vivo mode of action for known and novel NMT inhibitors as anti-fungal agents. The technology features a strong emphasis on exploiting synthetic chemistry to understand agrochemical mode of action and enables facile incorporation into target proteins without disturbing the system of interest, whilst permitting imaging and pull-down based on a highly optimized 'chemical proteomic' workflow.
Multiscale analysis of protein and DNA structures: from atomic structures to large-scale conformational substructures[PhD project, NexGenAgriChem]. This project employs the multiscale analysis of protein and DNA structures to examine potential fungicide and allergen targets. Particular focus is on histidine kinases (HKKS) (HOG pathway) by interrogating the role of particular domains over different timescales, which combined with a mutational analysis will lead to the identification of hotspots for agrochemical binding sites. Initial testing will employ bacterial systems to validate the method which will then be ported to investigate fungal as well as allergen systems. In the latter the correct identification of epitopes with minimal false positives is of great relevance.
Biochemical imaging of compounds in plants[PhD project, NexGenAgriChem]. This project develops a novel validated analytical method to detect and analyse compounds (such as agrochemical) in biological matrices and try to solve the issues related to existing methodologies. These issues involve long and complex labelling procedures coupled with the fact that there is only a limited set of pesticides that are detectable with the existing methods.