Functional genomic approaches generate large datasets; the challenge is how to interpret them...

Jay Hinton, Institute of Food Research, Norwich

Complete genome sequences of the key bacterial food-borne pathogens have been completed over the past 5 years. The IFR has been using functional genomic approaches to exploit this new information to improve our understanding of Salmonella gene regulation (http://www.ifr.ac.uk/safety/microarrays/). Our laboratory made an important breakthrough in 2003, when we discovered how to isolate bacterial RNA from infected mammalian cells. We published the first description of the 919 Salmonella typhimurium genes that are regulated during infection of human and animal cells (http://www.ifr.bbsrc.ac.uk/Safety/molmicro/pubs/Eriksson_Unravelling.pdf).

We are now generating expression profiles for S.Typhimurium grown under different environmental conditions in vitro, and are making new deductions about the intracellular environment that is experienced by Salmonella. This approach promises to become a useful tool for unravelling the biology of infection by Salmonella and other bacteria. Now we have generated data from several hundred microarrays, we are facing a complex dataset that contains information concerning the regulatory networks of Salmonella genes, and the profiles associated with different environmental stresses.

In new collaborations that we are currently establishing with computational biologists, we are beginning to apply systems approaches to mine these data and gain new insights into the co-regulation of Salmonella genes during infection.


Vincent Moulton
© 2005, CBL
Computational Biology Laboratory,
School of Computing Sciences,
University of East Anglia,
Norwich, NR4 7TJ, UK.