RP2

In silico mining of metagenomics data and in vitro tests to identify new MAMPS

For this research project, Mrs Dragana DOBRIJEVIC has been recruited.

Main Supervision

INRA (E. Maguin & M. van de Guchte)

Co-supervisor

University of Aberdeen (D. Kelly)

Duration : 36 months 

Start date : end of 2008/beginning of 2009

Objective : Identify bacterial surface-exposed proteins implicated in bacteria-host interactions in the gastro-intestinal tract.

Approach. in silico analysis of (meta)genomic sequences from GI microbiota to predict surface-exposed proteins. High throughput cloning and expression of selected genes which will be then tested on in-vitro models to evaluate their effect on the expression of cytokines and defensins. For positive clones, the eukaryotic signalling pathways involved will be identified. The reacting bacterial proteins will be analyzed in silico to identify putative MAMPS which will then be validated.

Deliverables.

  • Month-8, list of proteins of interest and high throughput vector
  • M-15, library of selected genes
  • M-23, clones affecting pathways
  • M-30, validation of MAMPS
  • M-36, publications & PhD viva

Techniques that will be used : Bioinformatic mining; molecular microbiology; measures of the epithelial response ; analysis of immune function; use of germ-free and gnotobiotic mice; transcriptomics; cytokine & chemokine profiling; cell biology and in-vitro screens; immunohistochemistry