Iowa City Darwin Day

Reposted with light editing from the Iowa Citizens for Science site:

Darwin Day is fast approaching, and we’ll be celebrating with two and a half days’ worth of festivities here in Iowa in February, put together by Iowa City Darwin Day Inc. along with co-sponsors.

We’ll kick off Thursday night, February 14th at 7:00 pm, with Dr. Massimo Pigliucci reading from his latest book at Live from Prairie Lights, with drinks and snacks following at a location TBA.

Friday February 15th will consist of academic talks by Dr. Pigliucci and Dr. Martha McClintock.

On Saturday February 15th there will be a series of public talks followed by an informal reception in Iowa Hall.

• University of Iowa paleontologist Dr. Christopher Brochu will kick off the afternoon, whose topic will be “The Dead Speak: What we learned from the Tyrannosaurus.” Dr. Brochu was the lead researcher on the analysis of “Sue” the tyrannosaurus at Chicago’s Field Museum.
• Dr. McClintock will follow, discussing “Social Isolation and Breast Cancer: Psychosocial Regulation of Gene Expression”.
• Dr. Pigliucci will be the last of the afternoon’s talks, speaking on “What’s science got to do with it? When scientists misspeak about religion”–a topic sure to bring about some interesting discussion.
  

A panel discussion and Q&A session with all of the speakers will wrap up the afternoon, and the reception will follow.

Please join us! It promises to be an exciting and stimulating few days–and we’re also looking for ideas (and manpower!) for Darwin Day 2009.

Evolution of Meiotic Genes: The Case of Spo11

In the vein of shameless self-promotion, it's my pleasure to announce that a recent paper from my lab has just been published as an Advance Access article in Molecular Biology & Evolution: Protist Homologs of the Meiotic Spo11 Gene and Topoisomerase VI Reveal an Evolutionary History of Gene Duplication and Lineage-Specific Loss (Shehre-Banoo Malik, Marilee A. Ramesh, Alissa M. Hulstrand & John M. Logsdon, Jr., Molecular Biology & Evolution, in press).

This paper is the first in a series of papers that is emerging from Banoo Malik's PhD thesis and is a result of a long-standing project with former postdoc Marilee Ramesh (now at Roanoke College). It's also the first of a number of meiotic "gene stories" that we have been untangling over the past few years. The image shown is a summary of the phylogenetic distribution of Spo11 homologs that we determined. The paper is not Open Access (sorry); however, if you are interested in reading it and do not have a subscription to MB&E, drop me an email.

Abstract
Spo11 is a meiotic protein of fundamental importance as it is a conserved meiosis-specific transesterase required for meiotic recombination initiation in fungi, animals and plants. Spo11 is homologous to the archaebacterial topoisomerase VIA (Top6A) gene, and its homologs are broadly distributed among eukaryotes, with some eukaryotes having more than one homolog. However, the evolutionary relationships among these genes are unclear, with some debate as to whether eukaryotic homologs originated by lateral gene transfer. We have identified and characterized protist Spo11 homologs by degenerate PCR and sequencing and by analyses of sequences from public databases. Our phylogenetic analyses show that Spo11 homologs evolved by two ancient eukaryotic gene duplication events prior to the last common ancestor of extant eukaryotes, resulting in three eukaryotic paralogs: Spo11-1, Spo11-2 and Spo11-3. Spo11-1 orthologs encode meiosis-specific proteins and are distributed broadly among eukaryotic lineages, though Spo11-1 is absent from some protists. This absence coincides with the presence of Spo11-2 orthologs, which are meiosis-specific in Arabidopsis and are found in plants, red algae and some protists, but absent in animals and fungi. Spo11-3 encodes a Top6A subunit that interacts with topoisomerase VIB (Top6B) subunits, which together play a role in vegetative growth in Arabidopsis. We identified Spo11-3 (Top6A) and Top6B homologs in plants, red algae, and a few protists, establishing a broader distribution of these genes among eukaryotes, indicating their likely vertical descent followed by lineage-specific loss.

Why Rosie doesn't work on Sex

My friend and colleague, Rosie Redfield, has written an interesting post about the origin of eukaryotic sex, entitled "Why I don't work on sex in eukaryotes ". She sums up what we do and don't know about deep eukaryotic relationships and how this impinges on the origin of sex and meiosis. One bottom line is that we still don't know what the earliest branch on the eukaryotic tree is. The other is that it might not matter for the origin of meiosis since work in my lab has shown that homologs of meiotic genes are present in all of the major protist lineages (e.g, this paper, but stay tuned for more details...). Rosie ends her provocative post by paying me a sincere compliment:

"I'm glad that John Logsdon has been working on this, rather than me."

Thanks, Rosie!

Banning the word "prokaryote"

Here I am at the the American Society for Microbiology annual meeting which is being held in Toronto. As Larry Moran has already pointed out, there are a few of us bloggers that are getting together with him while we are here. This should be great.

My first day (actually, part day) was capped off with a really fun, but in many ways maddening, lecture from Norman Pace. Norm was on my PhD committee, and it was the first time I had seen him for 12 years. The talk was wonderfully vintage Norm—even some of the phrases were the same as I remembered. That's not to say that the talk was at all tired. Norm is so fun to see in the spotlight; in this case, he had a big and well-deserved stage on which to perform! As an historical aside, Norm's class on the biochemistry of nucleic acids at Indiana University was the only biochemistry course that I ever took that started by reference to a rRNA tree of life. Norm has been ahead of the curve for a long time...

A major—and provocative—theme of Norm's talk is that we microbiologists should strike the word "procaryote" (or prokaryote, as I prefer to spell it) from our vocabulary. This is not a trivial matter for the microbiologists in attendance, both from practical and intellectual points of view. This part of his talk followed directly from his recently published piece in Nature entitled "Time for a change." (2006) 441:289. I happen to strongly disagree with Norm on this point and am much more aligned with the views subsequently published by Martin & Koonin entitled "A positive definition of prokaryotes" in Nature (2006) 442: 868. Although I'm too short on energy to do so now, I'll try to decipher my notes and give a more clear account of what Norm said (and my reactions to it) in the coming days.