Monday, April 11, 2005

Arabidopsis minisymposium

The sixth Arabidopsis minisymposium, joined this year with the spring Mid-Atlantic section ASPB meeting, was a big success. It's great to be at the center of something, and helping to host a regional meeting of such high quality definitely makes me feel that I am at the center of Arabidopsis research, even though my colleagues are entirely responsible for the excellent selection of speakers and I still have to pause and mentally review whenever anyone relies on my knowledge of photosynthesis, parts of the flower or plant hormones. Caren gets credit for putting the two meetings together and for inviting Susan Lolle to tell us about the work that put Arabidopsis on the front page of the New York Times. Heven, Zhongchi, June and their students all deserve credit for making this happen.

My own talk was well received, even though it was the last and delayed by an unplanned break when the projector overheated after about eight hours of nearly continuous use. I am happy to have made the case before this audience that RNA processing, including alternative splicing, is important in plants. I was aided in this by talks that presented roles for RNA binding proteins in crosstalk between ethylene and auxin (Jose Alonso), pollen tube growth (Mark Johnson) and leaf polarity (Randy Kerstetter); RNA binding proteins are getting hot! The question I most appreciate came from Ken Birnbaum, who challenged me to think of an example in which a forward genetic screen identified regulated alternative splicing. Of course, there is the regulation of flowering time through FLC (Simpson and Dean) but that appears to be regulated by polyadenylation, not alternative splicing.

Tuesday, April 05, 2005

What you can do with a dozen genomes

I really enjoyed the ISR Distinguished Lecture by Eric Green a few weeks ago. It reinforced my excitement about the idea that having a dozen genomes will allow us to obtain qualitatively different information than we’ve been able to obtain from a single genome. In addition to the alignment-based methods he described, there is the (rather amazing) possibility of reconstructing the ancestral sequence (see Blanchette et al. 2004, a very nice paper by an all-star cast) and methods of assigning gene function based on patterns of duplication and loss (e.g. the recent paper by Li, Pellegrini and Eisenberg in Nature Biotechnology). A talk by Najib El-Sayed on Friday about three trypanosomic genomes (Trypanosoma brucei, Trypanosoma cruzi and Leishmania) underscored the prospect of understanding the responses of genomes to selection. It strikes me that with 20-30 appropriately related genomes one could deduce whether individual nucleotides within a conserved block are under selection, an incredibly powerful tool (of course, I’m thinking about ESEs). Like many new methods, comparative genomics will yield insights in ways that will not be fully appreciated until the data are at hand. It is exciting, and it reminds me of the excitement we all felt during the late 70s, when the first sequences were being obtained.

This was originally posted on Steve's View a few weeks ago, soon after the talk from Eric Green.