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Current PhD projects

1. Natural product discovery from rare microorganism using genome mining approach

Project description:

Huge progress in our understanding of the molecular mechanisms of natural product biosynthesis has been made in the last two and a half decades. This has underpinned the development, of genome mining as a tool for the discovery of novel bioactive natural products, leading to renewed industrial interest in such compounds as leads for the development of novel drugs and agrochemicals. Over the past decade, microbial genome sequencing projects have uncovered hundreds of so-called “cryptic” natural product biosynthetic pathways, for which the metabolic products are unknown. Marine actinobacteria have been shown to be a particularly prolific resource of cryptic biosynthetic pathways and, given the provenance of this group of microorganisms, it seems highly likely that many of the metabolic products of such pathways will be novel antimicrobials with the potential to tackle the emerging health threat posed by AMR. Advances in both DNA sequencing technology has made it possible to obtain complete bacterial genome sequences using Pacific Biosciences SMRT sequencing in a matter of weeks. The long sequence reads generated by Pacific Biosciences SMRT sequencing facilitates the correct assembly of natural product biosynthetic gene clusters (BGCs), especially those encoding modular polyketide synthase (PKS) or nonribosomal peptide synthetase (NRPS) multienzymes, which are frequently involved in antibiotic biosynthesis.

In collaboration with the Ocean University of China, the candidate will carry out initial LC-ESI-TOF-MS survey of the metabolites produced by marine microorganism strain selected for genome sequencing. This will facilitate rapid de-replication to avoid rediscovery of known compounds. Molecular formulae and UV-Vis spectra generated by these analyses will be compared with databases to ascertain whether they correspond to known natural products. Subsequently, the candidate will analyse metabolite profiles of both wild type and non-producing mutant strains generated by collaborators, purify novel compounds for structure elucidation and investigate activity against the ESKAPE panel of pathogens. The purified material will be used for further anti-microbial property investigation.

During this project, you will learn advanced analytical chemistry techniques, including bacterial fermentation optimisation and natural product extraction, normal phase and reverse phase liquid chromatography, dereplication, modern high resolution and high accuracy mass spectrometry and NMR for structural elucidation.

Project Aims:

1. Optimizing fermentation conditions, manipulating regulatory factors to activate silent gene cluster or enhance gene expression and improve titer of bioactive compounds.

2. De-replication with high resolution LC-MS/MS to identify potential novel compounds.

3. Purify novel antibiotics, structure elucidation using a combination of 1D, 2D NMR and high resolution MS, MS/MS techniques.

4. Purified bioactive compounds will be evaluated for their antimicrobial activity against a range of Gram-positive and Gram-negative bacteria, including representative members of the ESKAPE panel of pathogens.

2. Investigation of the effect of agrochemicals on the enviroment and their connection with antimicrobial resisitance

Project description:

The discovery and usage of antibiotics have made enormous contribution to human and animal health worldwide. However, the overuse of antibiotics, particularly in agricultural applications have significantly accelerated the emergency of multidrug resistant pathogenic microorganisms, which pose serious threat to both human and animal health. Most of the antibiotics used either in human or animal are eventually ended up in the environment in its active form. It is widely reported that many clinically used antibiotics have been detected from polluted soil and waters samples, often at concentration high enough to put microorganisms in the environment under elevated and persistent selective pressure and promote resistance to evolve. It is foreseeable that resistance genes developed in non-pathogenic environmental microorganism can eventually reach pathogens through the exchange of genetic material, such as horizontal gene transfer. To understand the fate of antibiotics in the environment, we first need to determine their distribution and then to accurately quantify their level and monitor their degradation. Combining with molecular microbiological detection of resistant genes, a complete picture of environmental impact of antibiotic usage can be established.

During this project, you will use advanced analytical tools, including high performance liquid chromatography, high resolution mass spectrometry and nuclear magnetic resonance spectroscopy to establish methodology to identify, characterise and quantify agrochemicals, including veterinary antibiotics, insectcides, herbcides and their degradation products. In collaboration with colleagues in the School of Life Sciences at Warwick, you will also receive training in advanced microbiology techniques and experimental design.

Project Aims:

1. Environmental sample collection and processing

2. Metabolite profiling and identification of known and novel compounds.

3. MRM based quantitation method development on triple quadrupole mass spectrometer.

4. Quantify target compounds.

5. Analysis the connection with agrochemical usage and antimicrobial resistance through collaboration with SLS.