Decoding extremophile archaea with DNA microarrays

Todd Lowe, Ph.D.
University of California, Santa Cruz

Wednesday, November 12, 2003
Pacific Forum 3:00 p.m.

The Lowe Lab studies extremophile biology via a combination of computational analyses and the use of DNA microarrays. Currently, we have two full-genome spotted arrays: one for Pyrococcus furiosus, and one for Pyrobaculum aerophilum. The plan is to use "comparative expression analyses" between these distantly related archaeal species that have preserved the ability to thrive in boiling sea water. By applying diverse stresses in parallel experiments and measuring gene expression responses, we hope to start identifying genes and biological pathways unique to hyperthermophiles. We also take advantage of three closely related, sequenced Pyrococcus genomes by testing the degree of cross-hybridization between P. furiosus, P. abyssi, and P. horikoshii relative to the three-way sequence similarity of the genes they have in common. Future studies include applying the knowledge from these "calibration" hybridization experiments to genome hybridization against unsequenced species. This could aid in selection of new species for study in the lab or genome sequencing, based on inferred existence of unique pathways of interest or raw genetic relatedness as we fill in the web of life.

Next: Optical imaging with the SeaBED AUV and other underwater vehicles