Friday, July 31, 2009

Fwd: Sign-up now for Microbial Genomics & Metagenomics workshop September 14-18, 2009

Begin forwarded message:

Subject: Sign-up now for Microbial Genomics & Metagenomics workshop September 14-18, 2009

The U.S. Department of Energy Joint Genome Institute (DOE JGI) is offering a five-day workshop on Microbial Genomics and Metagenomics September 14-18, 2009 in Walnut Creek, California. The workshop will include two days of intensive seminars and three days of hands-on tutorials. Our goal is to provide you with training in microbial genomic and metagenomic analysis and demonstrate how the cutting-edge science and technology of DOE JGI can enhance your research.

For more information, see:

Thursday, July 23, 2009

Another scam pretending to be from Elsevier

Yet another scam pretending to be from elsevier

From: elsevier issues <>
Date: July 23, 2009 5:28:22 AM PDT
To: undisclosed-recipients:;
Subject: Elsevier Scholarships


European Central Bank- Elsevier Journals Initiative.

The European Central bank in collaboration with Elsevier Journals is seeking applications from students/ researchers for 10 European- Elsevier Scholarships in 2009.

The Scholarship programme was launched in 2003. It aims to promote high quality research on the structure, integration and performance of the European financial system. Each fellowship is endowed with a honorarium of €16,000 [Sixteen thousand Euros] which would be received by 10 students/ researchers on Merit.

To be amongst the fellows who can receive this honorarium:

· Send a research paper on your Major.

o The submitted paper will go through a screening process by our group of reviewers in your field. Manuscripts should be submitted in English and include a cover letter, and a comprehensive Resume.

Prospective authors should send their manuscript(s) in Microsoft Word or PDF format to and should Include a cover sheet containing corresponding Author(s) name, Paper Title, affiliation, phone, fax number, email address etc.

Kind Regards,

Gerald Rockfield.

Asst. Commercial Manager,

Elsevier- Eurobank Initiative,

United Kingdom.

Tuesday, July 21, 2009

Why endosymbionts rule - see #PLoS Genetics paper on origin of an alternative genetic code

Way way way cool new paper in PLoS Genetics from Nancy Moran's lab. The paper (Origin of an Alternative Genetic Code in the Extremely Small and GC–Rich Genome of a Bacterial Symbiont). The paper discusses the use of genome sequencing and proteomics (as well as a variety of bioinformatic analyses) of a bacterial symbiont (Hodgkinia) of cicadas.

And for those not in the know, this is an Open Access paper using a broad Creative Commons license (since it is in a PLoS journal) so anyone can reuse material from it as long as the source is cited. This image to the left is from their paper so I am citing the source here: McCutcheon JP, McDonald BR, Moran NA (2009) Origin of an Alternative Genetic Code in the Extremely Small and GC–Rich Genome of a Bacterial Symbiont. PLoS Genet 5(7): e1000565. doi:10.1371/journal.pgen.1000565

The study has some interesting things including:
  • the genome of the symbiont has a much higher GC content than other small bacterial genomes for which the sequence is available
  • the symbiont is member of the alpha proteobacterial group, which is somewhat unusual since most other insect endosymbionts that have been studied are from the gamma proteobacterial group and/or the bacteroidetes clade
  • the UGA codon in this species is used to encode tryptophan and not as a stop codon
Taken together these things are very interesting since other species that have been found to have the UGA codon reassigned to code for an amino acid all have low genomic GC content. This correlation led people to conclude that the codon reassignment was directly related to the low GC content. However, the authors suggest here that the UGA reassignment in many species might be due to the genome reduction (loss of genes) seen in endosymbionts and not to low GC content.

Anyway the paper is worth a read ...

McCutcheon, J., McDonald, B., & Moran, N. (2009). Origin of an Alternative Genetic Code in the Extremely Small and GC–Rich Genome of a Bacterial Symbiont PLoS Genetics, 5 (7) DOI: 10.1371/journal.pgen.1000565

Monday, July 20, 2009

Ego Blogging of the Month: Thanks @SciAm for following selecting me as one of your "recommended" folks you follow on twitter

Another ego blog here. I am very honored that Scientific American listed me as one of the folks they follow on twitter (see Recommended: Science Folks We Follow on Twitter: Scientific American).

The tweeterers they list are:
Of course, I agree with them about me. I do follow Zimmer and Skloot already and will check out the others.

If you know nothing about twitter, I recommend checking it out. I think it has enormous potential as a tool in science communication (e.g., see this Bioscience article on science and twitter)

Thursday, July 16, 2009

Worst new omics word award: diseasome (thx @steinsky @noahwilliamgray @mocost )

And the winner of the "worst new omics word award" is "diseasome."

Credit for pointing this one out goes to Noah Gray and MoCost on Twitter. See Mos first post here: Twitter / Mo: Diseasome project visualiz ...

And some follow up:
Amazingly, I missed this when the New York Times used it in a headline: "Mapping the Human 'Diseasome' - Interactive Graphic -" and in many other reports (see Google search here).

What does diseasome actually mean? I do not know. And it does seem really unnecessary to me. And since I got blasted (justifiably) a bit by one of the people I gave my previous award to here is a clarification. I am not commenting here on the science behind the "diseasome" work. Just the word. And the word, I do not like.

Previous awards I have given:

On Friendfeed:

Tuesday, July 14, 2009

Deep subseafloor microbiology talk at #UCDavis raises questions about the definition of life

Wildly interesting talk here at Davis yesterday by Bo Barker Jorgensen Prof. Dr. Bo Barker Jørgensen

He talked about deep subseafloor microbiology and how many/most of the microbes there grow VERY VERY slowly or not at all.

His talk was part of a series here on "Major Issues in Modern Biology Seminar Series" funded by the Tracy and Ruth Storer Lectureship in the Life Sciences endowment

He did a great job of presenting the evidence for and possibly against whether these organisms that live in the deep subseafloor are alive and whether or not they grow really slowly (with doubling times of hundreds of years). He refers to these organisms as the "starving majority" because their main challenge appears to be getting energy.

The way they do much of their work is to take cores (from ships) of the deep subseafloor and to then characterize the microbes in the cores. They have found, for example, high #s of microbes (mostly bacteria and archaea) as far as 1000m down in the cores.

Among the things he discussed were
  • Paper by Whitman on estimating the number of prokaryotes (his word, not mine) in different places on the planet. This paper suggested most of the prokaryotes are in the subsurface (terrestrial and seafloor)
  • Paper by him in Science reviewing the starving majority.
  • Paper by Biddle et al on rRNA surveys of sedimentary subsurface that suggested that most of the microbes were archaea
  • Paper by Schippers et al (on which Jorgensen is the sr. author) that used qPCR and suggested that most of the microbes were bacteria
  • Paper by Biddle et al on metagenomics of subsurface microbes
  • Paper by Lipp et al in 2008 that looked at membrane lipids to estimate the amount of cellular carbon in the deep subsurface.
  • Various papers that suggest that radioactivity could be the indirect energy source fo these communities (note they are not proposing these are radiation-utilizaing microbes but rather that radiation can lead to the production of H2 which in turn is an energy source).
  • Various papers that suggest that the archaea found in these environments are phylgoenetically very novel
  • He did not mention it but he was a cuauthor on a cool PLOS Biology paper on giant bacteria.
  • At the dinner he discussed briefly one of my favorite topics - nano wires and mentioned one of my favorite scientists - Yury Gorby who is studying these nanowires. Nanowires appear to be mechanisms by which microbes can move electrons around and scanege for electrons
Anyway - the talk gave me lots to think about in terms of slowly growing organisms and how to determine if something was living or not.

Saturday, July 11, 2009

Strong Letter of Support for Katehi from group of UC Davis faculty

There was a strong letter of support for UC Davis' incoming chancellor Linda Katehi published in the Davis Enterprise yesterday. Alas, the enterprise is not available free online so unless you have a subscription you may not be able to read the whole thing. The letter is written by some big shot faculty on campus:

J. Clark Lagarias, professor of cellular and molecular biology
Walter S. Leal, professor and former chair of the department of entomology
Alan Hastings, professor of environmental science and policy
James R. Carey, professor of entomology
Judith S. Stern, professor of nutrition and internal medicine
Robert Rucker, emeritus professor of nutrition
Tilahun Yilma, professor of pathology, microbiology and immunology
Gabrielle Nevitt, professor of neurobiology, physiology and behavior
Chris Calvert, professor of animal science
Carl Keen, professor of nutrition and internal medicine
Charles H. Langley, professor of genetics
Bruce D. Hammock, distinguished professor of entomology

And in it they say "Katehi’s selection and appointment electrified us"

I agree.

And they also discuss the overblown reports that she may have been involved in some impropriety in admission of students at U. Illinois. I have already written about this here and I agree too. Now I am not saying the news should not report on these stories but I do wish the reports were clearer about how little evidence there is that she did anything untoward. In contrast, there is abundant evidence that she has enormous potential to help out UC Davis in trying times. So I too would like to welcome Katehi as they do.

Friday, July 10, 2009

Help request - how does one block some DNA from being PCR amplified?

Dear world:

We need help.  

We would like to use PCR amplification of rRNA genes to characterize rare bacteria in a sample where there are some very very dominant bacteria.  

The problem is that we do not know what those rare bacteria are and would like to use "universal" rRNA PCR primers to amplify the rRNA genes from these organisms. Such universal primers will also amplify the rRNA genes from the dominant organisms.  

If the rare organisms are, like, really rare, almost all the PCR products will be from the dominant organisms.  We would like to obtain sequence data for the rRNA genes from the rare organisms without sequencing 1000s of the known rRNA genes from the dominant organism.  How can we do this?  

I know of attempts to block PCR amplification of specific DNAs and also attempts to digest away PCR products or bind ones to a column to get rid of them.  But I do not know if any of these methods really work.  

Anyone out there know methods that work to do this?

Added - here are the responses on FriendFeed

Wednesday, July 08, 2009

The White House - Press Office - President Obama Announces Intent to Nominate Francis Collins as NIH Director

The White House - Press Office - President Obama Announces Intent to Nominate Francis Collins as NIH Director

Not much else to say here. Collins is being nominated to run NIH. I personally think Collins will be perfectly capable of running NIH. I have mixed fellings however about whether he is the best pick for the job. What do others think?

Sunday, July 05, 2009

Much ado about nothing - sniffing around for scandal with new UC Davis chancellor and not finding any

Well, it seems that despite the attempts of California State Senator Leland Yee nobody has found anything of any interest in the background of the incoming chancellor of UC Davis Linda Katehi. The worst that has been dug up so far is an email that she forwarded while provost at U. Illinois that could be interpreted as applying subtle pressure to get a child of a well connected person admitted to the school (see New UC Davis leader denies wrongdoing in inquiries about student in previous job - Sacramento News - Local and Breaking Sacramento News | Sacramento Bee). I guess we will just have to wait and see but I personally really hate corruption and abuse of power and would not want anyone to be the UCD chancellor if they seemed to be part of something untoward. But so far, all I can see if Sen. Yee trying to get publicity for himself by throwing mud and really very little if any of the mud seems to stick. This crusade of his is starting to sound like some of the right wing "holier than thou" crusades of recent times. A bit to vocal when nothing much seems to be there

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