Leighton Pritchard

• Computational biology and bioinformatics.
• Oomycete and bacterial plant pathogens.
• Systems biology of plant-pathogen interactions.
• Comparative genomics of plant pathogens.

Research interests

My research centres around plant-pathogen interactions. Primarily, I aim to understand what it is about microbial plant pathogens that enables them to infect plants, and what it is is about plants that allows microbes to cause disease on them. As a computational biologist, most of my work involves the computational and mathematical analysis of biological data such as genome sequences, microarray gene expression profiles, and networks of metabolic and regulatory processes.

Systems biology

• Plant cells contain complex systems of signalling, regulatory and metabolic networks (Pritchard and Birch, 2011). These are perturbed by invading microbes, which introduce effector proteins and other molecular species into the plants they infect. Invaded plants detect molecular components of the invading pathogen and changes to their cellular networks, usually responding with effective resistance. I am interested in the implications of the dynamics and structure of these cellular networks, for the development of plant disease caused by microbial pathogens.

Genomics and comparative genomics of plant pathogens

• Genome sequencing has changed the face of biology, and revolutionised our understanding of the molecular biology of microbes. Sequenced genomes provide an opportunity for comparative genomics to determine which features might confer particular functions and behaviours on an organism. Sequence annotation also remains a challenge, even for well-studied organisms. I use computational and machine-learning approaches to aid classification of genome features and identify features that may be associated with the ability of a microbe to cause disease.
  Phytophthora infestans (Haas et al. 2009) and Pectobacterium atrosepticum (Bell et al. 2004) genome projects. Comparative genomics of plant pathogens (Toth et al. 2006), including microarray comparative genomic hybridisation (Pritchard et al. 2009). Identification and classification of pathogen effectors (McNally et al. 2012, Whisson et al. 2007, Haas et al. 2009) and other genomic features (Jupe et al. 2012, Avrova et al. 2007, Kikuchi et al. 2007, Whisson et al. 2005, Bell et al. 2004). Diagnostic assays from rough draft genome sequences (Pritchard et al. in preparation).

Oomycete and bacterial plant pathogens

• Much of my work is directed towards providing insight into and understanding of plant-pathogen interactions. This is in support of the practical goal of reducing the impact of severe and financially significant crop diseases caused by oomycete and bacterial plant pathogens, such as Phytophthora infestans and Dickeya species. In order to understand the relationship between our models and the outcome of infection, we need to appreciate both the biological and the mathematical details of the problem. Oomycete effector proteins (Birch et al. 2009, Birch et al. 2006, Armstrong et al. 2005), and interactions with plant defences (Gilroy et al. 2007). Microarray design and analysis of gene expression profiles in bacterial plant pathogens (McNally et al. 2012, Antunez-Lamas et al. 2009, Ravirala et al. 2007). Persistence of human pathogenic bacteria on plants (Holden et al. 2008).

Computational Biology and Bioinformatics

• Bioinformatics and mathematics are the tools that I use to study and make sense of biological sequences and other data. I am interested in visualisation tools for large datasets, and a collaboration in this area with Ian Toth, Michel Perombelon, and Prof. Elaine Shemilt of the Duncan of Jordanstone College of Art and Design resulted in exhibitions in Dundee and Singapore. I have also contributed code to open source bioinformatics projects, including Biopython. Visualisation of comparative genomic data (Pritchard et al. 2006). Directed evolution and error-prone PCR (Pritchard et al. 2005). Protein sequence-structure-function analysis, including covariation analysis (Pritchard et al. 2003, Pritchard et al. 2001, Pritchard and Dufton 2000, Pritchard and Dufton, 1999)

Collaborations

• Plant pathogen research is a multidisciplinary effort, and I collaborate with a number of researchers in a range of fields, in the UK and internationally.