Microbiology PhD research projects

Supervisor: Bruce, Professor Neil C

Mining composting communities for new lignocellulose mobilising enzymes (2015-16)

From both a fundamental and industrial biotech viewpoint understanding the deconstruction of lignocellulose in soil and compost is of central importance. In the natural environments microbial communities can efficiently degrade or modify lignin to enable the effective enzymatic hydrolysis of the polysaccharides present in plant cell walls. Globally, this is important for cycling carbon in the environment and as potential sources of biocatalysts for efforts at converting plant biomass into biofuels and commodity chemicals. The objectives of this project are to use metatranscriptomics and proteomics to determine gene- and protein-centred details to determine new mechanisms and improved methods of lignocellulose deconstruction in mixed microbial communities from composting cereal straw. The project will use proteomics analysis to interrogate the secretome of microbial communities in composting cereal straw and metatranscriptomics will be used to explore the expression of genes associated with lignocellulose digestion. To identify new linocellulose degrading enzymes, the peptide sequences from the proteomics analysis will be used to probe the metatranscriptomic library for full and partial coding sequences. These coding sequences will be cloned, expressed and the recombinant proteins characterised.

Co-directors:Simon McQueen-Mason

Supervisor: Chong, Dr James

Please email to discuss potential projects

Supervisor: Jeffares, Dr Daniel

Self-funded PhD applications are welcome.

 

Supervisor: Ferrari, Dr Julia

Multiple beneficial symbionts – too much of a good thing? (2015-16)

All organisms face a multitude of environmental threats and have to adapt to overcome these challenges.  Many insects get help from an unexpected source – bacterial symbionts that live in their bodies.  These endosymbionts affect their host’s biology, from allowing the host insect to feed on unbalanced diets to protecting from extreme temperatures or natural enemies.  A newly acquired symbiont can rapidly spread through a population and alter the insects’ interactions with other species and the environment under suitable conditions. This can have undesirable consequences if the host insect is an agricultural pest.

Endosymbionts that confer ecologically important benefits are particularly well studied in aphids, where phenotypic effects are fairly well understood.  However, often multiple species of symbionts occur in the same aphid individual.  It is likely that these species compete for resources and the host might be overexploited as a consequence.  This project will elucidate how single and multiple infections of beneficial symbionts differ in their effect on the host’s ecology.  The student will have the opportunity to develop this project according to his/her interests; this might include investigating the competitive interactions within the aphid, assessing the effects on the wider ecological community, or a mechanistic understanding of the interactions.

Supervisor: Moir, Dr James W B

Antibacterial activity of Carbon Monoxide releasing molecules (2015-16)

Carbon monoxide is a well-known toxic gas. However, it is also a normal part of human physiology, being generated during the normal turnover of haem. In previous work we have found that CO release from metal carbonyl compounds known as CO releasing molecules (CORMs) has specifically antibacterial properties. In this project, we intend to extend this work by exploring more deeply the mechanism of action of CORMs against specific bacterial pathogens in order to (i) identify the target sites of action, (ii) determine the influence of environmental conditions on the cytotoxicity of CORMs, and (iii) determine whether CORMs can be used as suitable drugs against bacterial infections in in vitro disease models and tissue culture. 

The project will be based in the Biology department where the focus will be on using microbiological and biochemical methods to analyse CORM function. Additionally, there will be the opportunity to carry out design and synthesis of CORMs in Chemistry. This project is an interdisciplinary project, in which you will be trained to work with both the chemical and biological aspects essential to success in the project.

Co directors: Ian Fairlamb and Jason Lynam (Chemistry)