Saturday, October 27, 2007

Biologists are happier than Computer Scientists

A recent survey conducted by the National Survey on Drug Use and Health (NSDUH) compared the percentage of US workers reporting an MDE (Major Depressive Episode) in the past year across occupation, gender, and age. Some of the results were fairly predictable, such as food and service workers having a greater than average occurrence of MDEs, and I had read before that women and older people tend to be more depressed on average, but some of the other results were quite surprising, at least to me. For example, "Mathematical and Computer Scientists" had a considerably higher rate (6.2%) of MDEs than did "Life, Physical, and Social Scientists" (4.4%). Not sure where that leaves bioinformaticians....

Wednesday, October 17, 2007

GME 2007 Highlights

Well, I haven't blogged much lately, but there hasn't been much coverage of last week's GME 2007 (no, not this GME 2007!), other than Jonathan Eisen's brief live comments, so I figured it might be of interest to talk about some of the talks I attended there.

GME (Genomes, Medicine, and the Environment) is the meeting that was once called GSAC (Genome Sequencing and Analysis Conference), with the name change reflecting that the focus is now more on the use of genomics to understand medicine and the environment rather than on genome sequencing per se (although there was still a session on sequencing technology). It was held in San Diego, which allowed me to visit the La Jolla branch of the JCVI and to see former colleagues who have transplanted to the “left coast”.

Colleen Cavanaugh and Nancy Moran gave interesting back-to-back talks on bacterial symbionts of plants and animals and brought up many of the same issues in their evolution – namely that the genome size of symbionts seems to be correlated with the estimated age of their relationship with their host – that is that large bacterial symbiont genomes seem to shrink over time. Not that this is surprising, given that mitochondria and plastids are thought to be remnants of symbionts with larger genomes, but it is nice to see evidence of the process in progress today. The isolated environment of symbionts also seems to result in other oddities, such as increase levels of drift and chance fixation. As I am currently involved in a genome project of an endosymbiont of a cellulose-degrading shipworm, both Nancy's and Colleen's talks gave me many ideas for interesting things to look for.

JCVI's own Nobel laureate, Ham Smith, gave a pleasantly low-key talk on the status of his synthetic life project (no, bad scientific reporting to the contrary, he hasn't succeeded yet). Basically, now that his group has successfully transferred a genome from one bacterium to another, they are building an entire synthetic genome of Mycoplasma genitalium from scratch. Of course, even when they successfully transfer this they won't really have “synthetic life”, but it is clearly a step that needs to be done along the way. Again, I really liked it how Ham basically just said what he was doing without any hype – but then, when you have the Nobel, I guess you don't need hype.

A younger JCVI researcher, Yuri Gorby, presented his work on “nanowires” -- basically, structures produced by some bacteria that conduct electricity. The theory is that these allow the bacteria to disseminate electrons in a biofilm, thus freeing the bacteria from having to have direct contact with an electron acceptor. Really cool stuff, although not universally accepted yet.

Edward Bayer gave a talk about the “cellulosome”, which I hadn't heard of before, but given that I'm working on a cellulose degrading bacterium, I suppose I should have. Basically, not all cellulases are free in the cytoplasm – basically many form a complex (the aforementioned “cellulosome”) which is far more efficient than free cellulases. As Jonathan Eisen mentioned, Edward's paraphrase of Genesis at the start of the talk did seem rather off-putting, but hopefully it's just a cultural thing – perhaps in Israel such talk is just a manner of speaking and not a sign of creationism. He did mention evolution at one point, which was somewhat reassuring.

My former TIGR colleague John Heidelberg gave a talk on his work on metagenomics of cyanobacterial mats in Yellowstone Park hot-springs. Besides the interesting results, he brought up the important (if somewhat scary) observation that it is possible to assemble a genome from metagenomic data that doesn't actually exist in nature (much like nobody has the average 2.2 children).

Gene Tyson and Mary Ann Moran both talked about “metatranscriptomics”, which despite being a new “omics” (another one? geez!), is actually a really good idea – don't just sequence genomes from the environment – sequence the mRNAs to get an idea of what genes are turned on in a population in a given condition. Tyson was using microbial data from the Hawaii Ocean Time-series station ALOHA, and Moran was looking at her coastal Roseobacters.

Jonathan Eisen talked about his “Genomic Encyclopedia” which he plans to do with the JGI. Basically he plans to sequence (in a high throughput manner) hundreds of bacteria and archaea He aims to start with a pilot of 200 organisms (100 of which he'll close), but there's talk of maybe doing everything in Bergey's manual. From Jonathan's perspective, the point is to make a “happy tree of life” in which we have data to make truly representative phylogenetic analyses. As a genomicist, I find this both awesome and scary. Obviously, I'd love to have the data, but it looks like the time of “genome projects” as such is becoming as quaint as cloning and sequencing a single gene. Well, times move on, I suppose. Jonathan also talked about our Hyphomonas work as an example of how genomics helps resolve phylogenetic questions.

Shannon Williamson (now of JCVI-La Jolla) presented a talk about phage metagenomics in deep sea environments. Basically, she found that bacteria in diffuse-flow thermal vents have more lysogenic phages than do bacteria in the surrounding cold water (presumably because lytic phages would have have a hard time finding a host in a diffuse environment). Additionally, the phages are less diverse than in the surrounding waters, This talk was especially interesting to me because I helped her with some of the bioinformatics analyses, but I hadn't seen the big picture before.