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