Eisen Lab Blog

Attack of the Robo Lizards from Davis

OK – the robo lizards are not attacking. But they are used for some cool behavioral science research here at Davis. Terry Ord and Judy Stamps from UC Davis have a new paper in PNAS coming out this week where they used robo lizards to study the behavior of Anole Lizards. Check out the UCD news site here which has some videos (UC Davis News & Information :: Robo-lizards Help Prove Long-Standing Signaling Theory)

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Open Metagenomics Highlight – Metagenome Annotation using massively parallel undergrads.


Another fun metagenomics related paper in PLoS Biology. In it Pascal Hingamp et al discuss an Open Source, Open Science system for metagenome annotation (see PLoS Biology – Metagenome Annotation Using a Distributed Grid of Undergraduate Students).

They do this as part of a course on metagenome annotation. And the software for running this is all Open Source and available. They say

“Teachers wishing to use the Annotathon for their courses are invited to create new teams on the public server at http://annotathon.univ-mrs.fr/ (course logistics and team management are detailed in the instructor manual:http://annotathon.univ-mrs.fr/Metagenes/index.php/Instructor_Manual). The underlying open-source software (PHP and MySQL scripts, under a General Public License) is also available for local installation (https://launchpad.net/annotathon/). In addition, a special “Open Access” team is available for freelance students (volunteer instructors are most welcome to help oversee the Open Access team).”

IN a way this is a metagenomics version of the Undergraduate Genomics Research Initiative (UGRI) which was described in a PLoS Biology paper previously.

Well, this is really the end all be all for me combining so many things I like – genomics, metagenomics, annotation, OA publishing, open source software, etc. Nice job Pascal et al …

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Open Microbial Diversity: PLoS papers on using 454-Roche pyrosequencing for rRNA studies

ResearchBlogging.org

Two new papers that just came out in PLoS Journals are definitely worth checking out. They are

Of course I am a bit biased I suppose as I am heavily involved in PLoS and also served as Academic Editor for these papers. But with that being said, I encourage people to check them out. In the PLoS Genetics paper from the labs of Mitch Sogin and David Relman labs discusses continued development of the use of 454-Roche pyrosequencing technology to carry out deep rRNA sampling. Anybody interested in characterizing a microbial community deeply in terms of what organisms are there should consider this approach.

And in the second paper, the same two labs present an in depth study using the 454-Roche rRNA sequencing to characterize the response of microbes in the human gut to antibiotic treatment. Though there have been a few other such studies this is the one that has the deepest characterization of the microbes present.

Note – one thing I find kind of humorous is that one of the authors is listed as Susan M. Huse in one of the papers (she is the first author on the PLoS Genetics paper) and Sue Huse in the other.

Huse, S., Dethlefsen, L., Huber, J., Welch, D., Relman, D., & Sogin, M. (2008). Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing PLoS Genetics, 4 (11) DOI: 10.1371/journal.pgen.1000255

Dethlefsen, L., Huse, S., Sogin, M., & Relman, D. (2008). The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing PLoS Biology, 6 (11) DOI: 10.1371/journal.pbio.0060280

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Open Genomics: Genome Evolution Simulator

Quick post here.   Cool new paper (and the software could be cool too but have not tried it yet) on simulating genome evolution.  The paper is from Ian Holmes and others at Berkeley (see his lab page on BioWiki here) and the paper can be found here in Genome Biology. Here is the abstract:

Controlled simulations of genome evolution are useful for benchmarking tools. However, many simulators lack extensibility and cannot measure parameters directly from data. These issues are addressed by three new open-source programs: GSIMULATOR (for neutrally evolving DNA), SIMGRAM (for generic structured features) and SIMGENOME (for syntenic genome blocks). Each offers algorithms for parameter measurement and reconstruction of ancestral sequence. All three tools out-perform the leading neutral DNA simulator (DAWG) in benchmarks. The programs are available at http://biowiki.org/SimulationTools.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Genomicron on Science by press release.

Just a quick one here. Ryan Gregory is going on against science by press release – one of my biggest pet peeves. Check it out at:

Genomicron: Science by press release.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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I see PLoS in everything IV: PLoS at Metagenomics 2008 meeting

I may see PLoS even when it is not there, but in this picture, which was the group photo for the Metagenomics 2008 meeting at CalIT2, I weaseled my way to the front hoping to get my PLoS bag and PLoS shirt into the picture. And looky there – it worked.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Woodland Native Dustin Pedroia Wins AL MVP Award

As a Boston native, one of the worries I had moving out to Davis a few years ago related to being too far from the RedSox, Sure they come to Oakland and sure my brother has season tickets to the A’s mostly to get RedSox tickets, but California is really far from Fenway Park. Well, at least there are lots of RedSox fans around here, especially if I go up to Woodland. Woodland, if you do not know, is the home town of the newest RedSox superstar, Dustin Pedroia, who nearly carried the Sox into the World Series and today was awarded the American League MVP Award. Way to go Dustin and thanks Woodland for helping out my team.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Visit to the Raptor Center and Putah Creek

Just thought I would share some pics from a nice outing we had yesterday. We went to the UC Davis Raptor Center for their open house and then went for a walk along Putah Creek.

http://picasaweb.google.com/s/c/bin/slideshow.swf

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Microbiology in the news: How bleach kills germs

I am starting a new thread here – microbiology in the news. And my first posting is about bleach. Everyone probably has used it at one time or another to clean something. And some people use it to kill “germs” (aka microbes) too. Well, MSNBC is reporting (Mystery solved: How bleach kills germs – Science- msnbc.com) on a Cell article that presents evidence regarding how the active ingredient in bleach (hypochlorous acid) kills bacteria. Apparently, it works in a similar way to heat in destabilizing protein structures. Anyway, the researchers claim that this is relevant to killing of microbes inside of people because

“Hypochlorous acid is an important part of host defense,” Jakob said. “It’s not just something we use on our countertops.”

Whether this is true or not, I do not know. But what I do know is that microbes are in the news. And that is good.

For more on the bleach story see
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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ERIC, E. coli, and you

Just a little posting here. I have been playing around with a website called ERIC and thought I would post about it since it seems pretty useful. ERIC – Enteropathogen Resource Integration Center is

one of eight Bioinformatics Resource Centers (BRC) for Biodefense and Emerging/Re-Emerging Infectious Diseases. Funded by the National Institute of Allergy and Infectious Diseases (NIAID), ERIC serves as an information resource for five members of the bacterial family Enterobacteriaceae.

So if you want to learn more about E. coli and its relatives and their genomes, this is a good place to start

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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