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.
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.
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.
imaging with the SeaBED AUV and other underwater vehicles