Friday, October 08, 2010

Gary Olsen's Talk on Lateral Gene Transfer at SDSU

Today Gary Olsen, who was my Ph.D advisor at the University of Illinois, gave a talk here in town at SDSU. The listed title was "Lateral Gene Transfer in Prokaryotes", which I was going to kid him about as Gary is a former postdoc of Norm Pace (who famously objects to the term "prokaryote"). But it turns out that the title was actually supplied by his host, so no dice there.

The talk dealt with further work in the Olsen lab on the topic of codon bias in relation to lateral gene transfer -- a topic which dates back to my time in the lab in the 1990s -- in fact Gary presented a figure from my dissertation near the beginning of the talk -- a PCA projection of E. coli codon usage showing the "rabbit head" pattern initially proposed by Médigue. In this projection, codon usage is shown to form three clusters, a cluster of "normal" genes (the "head"), an "ear" of known highly expressed genes, and an "ear" of genes of unusual codon usage containing many genes (such as integrases) thought to be recently transferred into the genome. The idea is that over time, transferred genes will assimilate into the codon usage of the host, much as immigrants lose their accents, making them impossible to detect through codon usage.

The obvious question is whether we can we use the codon usage of recent arrivals to determine their origin. In my day, the answer was no, we couldn't -- but we only had about 20 genomes available and so it was plausible that nothing close to the source organism had been sequenced. Now with over 1,000 genomes at our disposal, can we finally answer this question? Not exactly, but Gary and colleagues have discovered an interesting property -- the presumed transferred genes in E. coli and relatives seem to have a closer codon usage to *each other* regardless of host rather than being similar to any known organism, suggesting that they form a collection of genes that hop around from genome to genome, never staying around long enough to assimilate into the host -- it isn't a case of being transferred from the core of genome X to the fringe of genome Y as we supposed. They have found similar collections for other phylogenetic groups as well. This is really quite a different way to think about horizontally transferred genes.

Wednesday, October 06, 2010

Under the Spreading Chestnut Tree

In George Orwell's novel 1984, he mentions that the drink favored by patrons of the Chestnut Tree Cafe (frequented by dissidents after serving their jail sentence) is gin with "saccharine flavored by cloves". I actually tried that recently, although using Equal (aspartame) rather than saccharine). It was actually quite good. In fact, I don't really see the point of sweetener at all. Just gin and cloves is actually quite good. I don't understand why I never really understood cloves. Except for Christmas mincemeat pie, I'm not sure if I ever really tasted cloves. What an awesome flavor.

Saturday, September 25, 2010

"Bubbly" Pauline & the $1000 genome

I'm currently reading Kevin Davies' new book, "The $1000 Genome", which is an account of the various players trying to bring down the cost of human genome sequencing to commodity levels that would make having your own genome sequenced a practical reality. Although I know some of the technologies described in the book from my work, Davies' book focuses not only on the technical side but on the business/economic side as well and is written for the general reader. It's quite well written and interesting, and I recommend it. But what made me burst out laughing was encountering the following line:

"An important next step was to compare the data from Venter and Watson, which was first done by Pauline Ng, a bubbly Venter Institute researcher."

Pauline is a colleague and friend of mine who now leads a group at the Genome Institute of Singapore. We wrote a review chapter together on the human microbiome in a book that should be coming out soon. I suppose if you had to sum her up in a single adjective, "bubbly" works. But I guess I find the idea of someone I know being reduced to a journalistic cliché kind of amusing.

Saturday, May 08, 2010

Zoologist with awesome name new President of Nigeria

On May 6th, former Vice President Goodluck Jonathan became President of Nigeria following the death of his predecessor, Umaru Yar'Adua. It remains to be seen what this will mean for Nigeria for good or ill. However, while I was initially intrigued by his unusual name, I discovered that there is another thing about Jonathan that is unusual for a politician -- he has a Ph.D. in Zoology, and has published on issues dealing with the environment in relation to fishing. He apparently published an article as recently as last year (unfortunately not as Open Access however):

Breeding seasonality and population dynamics of the catfish Schilbe mystus (Schilbeidae) in the Cross River, Nigeria

P.E Lebo, R.P King, L Etim, B.E Akpan, G.E Jonathan


Twelve consecutive months length frequency data (N = 6999) and FiSAT software were used in the study of the dynamics of exploited population the catfish Schilbe mystus in the Cross River Nigeria. Variation in monthly mean gonadosmtic index showed two peaks, March and September and this indicates that the species spawned twice in a year. Fitting the seasonalized von Bertalantffy growth function to our length frequency data gave the following growth parameters: L∞ = 38 cm, k = 0.33 y-1, C = 0.42 and WP = 0.96. The seasonalized length converted catch curve procedure gave the instantaneous total mortality coefficient Z = 2.97 y-1, the instantaneous natural mortality coefficient M = 0.81 Y-1, the instantaneous fishing mortality coefficient F = 2.16 y-1 and the current exploitation rate E = 0.73. This high value of E points to the high fishing pressure on the stock. The analysis of probability of capture of each length class showed that the length at first capture Lc 28.67cm. The predicted maximum exploitation rate of Emax = 0.59. This stock was deemed overexploited because E>Emax. Relative yield isopleths were used to demonstrate the response of relative yield per recruit of the fish to variation Lc and E. Suitable management procedure must be instituted to avoid the collapse of the fishery.