Saturday, May 15, 2010

Archaea in the news - a growing trend

Archaea, the so-called "third" branch in the tree of life, don't get in the news much but good when they do and for some reason, they are getting in the news more and more these days.  See below for some links to news stories.

Friday, May 07, 2010

Request - information on the fraction of microbes that can be cultured

To all - I am looking for some information on the fraction of microbes that can currently be cultured from different environments. If you know of any good review papers or databases or other information on this topic, it would be very useful.

Here are examples of some information I have found:
  • From Jo Handelsman's review on metagenomics in 2004: "One of the indicators that cultured microorganisms did not represent much of the microbial world was the oft-observed "great plate count anomaly" (135)—the discrepancy between the sizes of populations estimated by dilution plating and by microscopy. This discrepancy is particularly dramatic in some aquatic environments, in which plate counts and viable cells estimated by acridine orange staining can differ by four to six orders of magnitude (66), and in soil, in which 0.1 to 1% of bacteria are readily culturable on common media under standard conditions (138, 139)."
  • From Phil Hugenholtz's review in 2002: "under aerobic conditions, at moderate temperatures. Easily isolated organisms are the ‘weeds’ of the microbial world and are estimated to constitute less than 1% of all microbial species (this figure was estimated by comparing plate counts with direct microscopic counts of microorganisms in environmental samples; it has been called the “great plate-count anomaly” [1]). " Reference 1 is Staley JT and Kanopka 1985.
But what I am looking for is some sort of review or database that has information for lots of different ecosystems.
Anyone know of anything like this?

Monday, May 03, 2010

Holy lateral transfer batman; amazing story on fungal to aphid transfer from Nancy Moran

As many know, I generally do not write a lot about papers in non open access journal because I like readers to be able to access all the papers which I write about. But this is one of the exceptions to my normal rule. An amazing paper was published a few days ago in Science by Nancy Moran and Tyler Jarvik. Lateral Transfer of Genes from Fungi Underlies Carotenoid Production in Aphids -- Moran and Jarvik 328 (5978): 624 -- Science

I first found out about this from Ed Yong's blog post here (just a note - his Not Exactly Rocket Science is such a frigging incredible blog). He really does the whole story on this so I am just posting a bit here.

Anyway Moran and Jarkiv paper focuses on genes in the aphid genome that encode enzymes for carotenoid synthesis. These enzymes are involved in red and/or green coloring seen in the pea aphids. Recently the pea aphid genome was sequenced (a paper about this was published in PLoS Biology ) and it was analysis of the genome data that helped lead Moran and Jarvik to the study reported in the recent issue of Science.

In their study they report a detailed evolutionary and phylogenetic analysis of the carotenoid synthesis genes found in the aphid genome and show quite convincingly that these genes do not appear to be of "normal" descent. That is, they seem to have an ancestry separate from many of the "normal" animal genes in the genome. Instead, these genes are related to genes from fungi. In fact, these genes are embedded in an evolutionary sense, in a group of genes which are all from fungi and thus Moran and Jarvik conclude the most likely explanation is that some time in relatively recent pea aphid evolutionary history, these genes were acquired from some fungus.

About to have some eye drops put in my eyes so gotta go for now, but just wanted to get something out there about this fascinating work. For more on this story - there is lots out there, such as the following:

Moran, N., & Jarvik, T. (2010). Lateral Transfer of Genes from Fungi Underlies Carotenoid Production in Aphids Science, 328 (5978), 624-627 DOI: 10.1126/science.1187113

. (2010). Genome Sequence of the Pea Aphid Acyrthosiphon pisum PLoS Biology, 8 (2) DOI: 10.1371/journal.pbio.1000313

Open access: getting more & more support incl. from #UCDavis

Everyone interested in science should take a look at the press release from the "Alliance for Taxpayer Access." The release discusses how "Major research institution leaders support legislation to ensure public access to publicly funded research". I am quoting much of the release here because I think it is very valuable:
The provosts and presidents of 27 major private and public research institutions have voiced their support for the Federal Research Public Access Act in an “Open Letter to the Higher Education Community,” released Friday by the Harvard University Provost. The Act, first introduced in the Senate last year, was introduced in the House of Representatives on April 15. The letter signals expanded support for public access to publicly funded research among the largest research institutions in the U.S.
The letter reads, in part:
“As scholars and university administrators, we are acutely aware that the present system of scholarly communication does not always serve the best interests of our institutions or the general public. Scholarly publishers, academic libraries, university leaders, and scholars themselves must engage in an ongoing dialogue about the means of scholarly production and distribution. This dialogue must acknowledge both our competing interests and our common goals. The passage of FRPAA will be an important step in catalyzing that dialogue, but it is not the last one that we will need to take.
For the full letter see “The Open Letter to the Higher Education Community” is available at

I am very very happy to note that UC Davis is one of the signatories (represented by Provost Enrique Lavernia).  This is a good change of pace as one of our previous vice-provosts Barbara Horwitz was an extreme anti-open access advocate.

And if you want your institution to be added to the list of supporters, talk to your administrators and get them to register their support here.  Seems to me that many should want to get on board.

Hat tip to Michael Rogawski from the UC Davis Department of Neurology for pointing this out.

Sunday, May 02, 2010

Good kids activity around Davis: Aerospace Museum of California

Good time today with my kids at the Aerospace Museum of California. Just East of Sacramento - with a nice facility, great outdoor playground, and lots of plances and satellites and rockets and other things. My kids loved it. Here are some pics:

Irresponsible reporting on "poop doping" from the Washington Post

UPDATE - see below - the author updated her article including some of my critiques. Went on a bit of a Twitter tirade last night. See mor...