Calling all phylogeneticists - we need your help with metagenomic data

I have decided to post a question here to my blog requesting help from phylogeneticists everywhere in doing phylogenetic analysis of data from metagenomic projects. Here I will try to describe the problem and then hopefully people out there can chime in on what they think we/others should do to handle this type of data.

So here is the deal. We would like to perform a variety of phylogenetic analyses of data from "environmental shotgun sequencing (ESS)" projects in which one isolates DNA from an environmental sample (e.g., soil, water) and then randomly sequences fragments of that DNA. ESS is in essence a subset of "metagenomics" which is basically the study of the genomes of organisms from environmental samples. (I wrote a brief piece on ESS in PLoS Biology last year which can be found here).

Though there are lots of things we would like to do with phylogenetic analysis of this type of data, I am going to focus here on one specific thing. We would like to take sequence reads that contain matches to specific gene/gene family (e.g., RecA, my favorite gene), build a multple sequence alignment that includes these reads as well as all members of this gene family from known organisms, and then build phylogenetic trees from these alignments. (And by we here I mean like totally lots of people, incliding in particular a Gordon and Betty Moore Foundation funded project called iSEEM I am working on with the labs of Katie Pollard and Jessica Green)

The challenge with this is really two things. First, we want to analyze just the reads themselves (i.e., we do not want to use assemblies you can make from this type of data). Second, and more importantly, we want to include in our analysis sequence reads that only cover small, not necessarily overlapping regions of the "full length" sequence alignments for the family.

The alignment would look something like

sequence 1 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
fragment 1 XXXXXXXXX-------------------------
sequence 2 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
fragment 2 ---------XXXXXXXXXXXX-------------
fragment 3 ---------------------XXXXXXXXXXXXX
fragment 4 ----XXXXXXXXXXXXXXXXXX------------
sequence 3 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
sequence 4 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
sequence 5 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
fragment 5 -----------------------XXXXXXXXXXX- 

where Xs are the regions covered by the sequences/fragments (could be DNA or amino acids)

We want to build trees from these alignments with the hope of using them to learn lots of cool things about the evolution of the fragments and the species from which they come. I can provide more information but really the key part for the phylogenetics here is the nature of the alignment.

In the past, I have decided to constrain my analyses to NOT deal with this type of alignments. I have either analyzed each fragment on its own or we have built a multiple alignment but only inlcuded fragments that cover more than 3/4 of the full length sequence and thus the matrix is much more filled out. Such an alignment would look like this

sequence 1 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
fragment 1 XXXXXXXXXXXXXXXXXXXXXXXXXXX-------
sequence 2 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
fragment 2 --XXXXXXXXXXXXXXXXXXXXXXXX--------
fragment 3 -----XXXXXXXXXXXXXXXXXXXXXXXXXXXXX
fragment 4 ----XXXXXXXXXXXXXXXXXXXXXXXXXXXX--
sequence 3 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
sequence 4 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
sequence 5 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
fragment 5 --XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX- 

But we really want to include the smaller fragments in our analysis. And we are just not certain how to best do this. We know LOTs of people out there think of similar problems in terms of sparse matrices, supermatrices, supertrees, EST data, etc. And we have ideas about how to do this and are asking around by email some phylogenetics gurus we know. But I thought it might be fun to have the discussion on a blog rather than by email.

So again, how might one best build phylogenetic trees from data that looks like this?

sequence 1 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
fragment 1 XXXXXXXXX-------------------------
sequence 2 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
fragment 2 ---------XXXXXXXXXXXX-------------
fragment 3 ---------------------XXXXXXXXXXXXX
fragment 4 ----XXXXXXXXXXXXXXXXXX------------
sequence 3 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
sequence 4 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
sequence 5 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
fragment 5 -----------------------XXXXXXXXXXX- 

And from these trees we want to place each fragment relative to (1) the full length sequences and (2) to each other if possible. We also, of course, want branch lengths to reflect some sort of amount of evolution and thus do not just want a cladogram.

Any suggestions would be appreciated. Fire away with questions too ...

Computational Biologists bring together some of the "best jobs" in the US

Check out the WSJ article on "The Best and Worst Jobs in the U.S. - WSJ.com"

The top 5 are
1. Mathematician
2. Actuary
3. Statistician
4. Biologist
5. Software Engineer

Seems like I know a fair # of people who combine #1, #3, #4 and #5 although rarely in equal amounts. I am not sure if anyone out there combines all of the top 5 but there must be some scientist/actuaries doing this computational biology right? Seems like a pretty strange list to me in some ways, but I must say, being a mathematically inclined computational biologist is pretty fun. Now if I only knew statistics ...

Hat tip to Lior Pachter for posting this to Facebook where I found it.

Acid Rock Bacteria Genome ...

Just a little plug for a new paper of which I am a co-author. This is a report on the analysis of the genome sequence of Acidithiobacillus ferrooxidans which was just published in BMC Genomics (an open access journal, by the way). This paper was a long long time coming - the genome was sequenced when I was at TIGR many years ago (Herve Tettelin coordinated most of the work). Since I was interested in the biology of this bug I volunteered to help turn the sequence into a paper, but was pretty lame about doing that. Thankfully David Holmes and Jorge Valdes in Chile helped make a paper from the data and much additional analyses. Here is the abstract:

Background
Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining). It is a chemolithoautrophic, γ-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth. It thrives at extremely low pH (pH 1–2) and fixes both carbon and nitrogen from the atmosphere. It solubilizes copper and other metals from rocks and plays an important role in nutrient and metal biogeochemical cycling in acid environments. The lack of a well-developed system for genetic manipulation has prevented thorough exploration of its physiology. Also, confusion has been caused by prior metabolic models constructed based upon the examination of multiple, and sometimes distantly related, strains of the microorganism.

Results
The genome of the type strain A. ferrooxidans ATCC 23270 was sequenced and annotated to identify general features and provide a framework for in silico metabolic reconstruction. Earlier models of iron and sulfur oxidation, biofilm formation, quorum sensing, inorganic ion uptake, and amino acid metabolism are confirmed and extended. Initial models are presented for central carbon metabolism, anaerobic metabolism (including sulfur reduction, hydrogen metabolism and nitrogen fixation), stress responses, DNA repair, and metal and toxic compound fluxes.

Conclusion
Bioinformatics analysis provides a valuable platform for gene discovery and functional prediction that helps explain the activity of A. ferrooxidans in industrial bioleaching and its role as a primary producer in acidic environments. An analysis of the genome of the type strain provides a coherent view of its gene content and metabolic potential.

Stan Falkow, only 74 and getting more famous by the day

Nice article in USA Today about Stan Falkow focusing in part on his Lasker Award. Good to see him continue to get some props as he, well, rocks. Note - I wrote about him getting a Lasker Award four months ago here but maybe I was too early?

Thanks "The Open Lab"

Very happy to get this email:

Many congratulations that your post (check http://scienceblogs.com/clock/2009/01/the_open_laboratory_2008_and_t.php for which one) was selected to be part of this year's print anthology of the best science blogging on the web.

Check out the collection at the link. There is some fun stuff there. I was selected for what else, my April Fools prank about brain doping. On the one hand, I wish something I wrote about science or policy was picked. On the other hand, I consider this April 1 joke of the best things I have done on the web ...

Ad for Genomics Faculty Position at UC Davis

Still getting back into things after being out sick ... here is an Ad for a job everyone should want ...

The UC Davis Genome Center integrates experimental and computational approaches to address key problems at the forefront of genomics. The Center is housed in a new research building with state-of-the-art computational and laboratory facilities and currently comprises 14 experimental and computational faculty. These faculty are developing an internationally recognized program in genomics and computational biology at Davis, building on and enhancing the unique strengths and unmatched breadth of the life sciences on the UC Davis campus.

The Genome Center invites applications for tenure-track faculty positions in all areas of genomics with emphasis on next-generation proteomics and statistical genomics involving animal, plant or microbial systems. Applicants interested in genomic approaches to human diseases and investigators employing large-scale, technology-driven approaches that complement existing strengths at UC Davis are particularly encouraged to apply. Candidates should be strongly motivated by the biological importance of their research and should value the opportunity to work in close collaboration with other groups and disciplines.

Candidates may be at any academic level. At the senior level, we invite applications from prominent scientists with distinguished records of research, teaching, and leadership in genomics. At the junior level, we invite applications from candidates whose accomplishments in innovative research and commitments to teaching demonstrate their potential to develop into the future leaders in these fields.

These positions require a Ph.D. or equivalent. Appointments will be at the Assistant, Associate or Full Professor level in an appropriate academic department in any of six schools, or colleges. The position will remain open until filled. For fullest consideration, applicants should submit a letter of application, a curriculum vitae, statements of research and teaching interests, and the names of at least five references to the Genome Center Web site www.genomecenter.ucdavis.edu by January 15, 2009.

The University of California is an affirmative action/equal opportunity employer

What to do when your sick? Sickblogging (and a little bit about Adm. Dennis Blair)

Well, I have had some unpleasant winter bug that on top of everything my kids seems to have or at least have something similar.  It has been fun at night here to say the least.  I was hoping to get some work done over winter break especially since I was overwhelmed with teaching in the fall quarter.  That is not happening.  But in the few moments of peace here, I have looked for something to do --- and hey there is one thing I could do with only a little time.  Blogging.  And of course I am not alone in this.  So here are some links to others on sickblogging:

• Michelle Malkin » Sickblogging
  
• The Jawa Report: Sick Blogging
  
• Last Chance Cafe: Sick Blogging
  
• Wilsonizer: Sick Blogging, Live from Home!
  
• Tuesday sick-blogging: Rock 'n Roll Reading

And what have I to say today?  Not much but here is a preview of things to come.  I have a feeling that Obama is stalking me scientifically.  Why?  Well, I am one or two steps removed from a huge number of his appointees and I plan to write about them in the next few weeks once I get better.  One things the science bloggers might not have heard about is the passion Adm. Dennis Blair has for science.  Dennis Blair is Obama's pick for DNI (Director of National Intelligence) and I know him through a program called the Defense Science Studies Group (DSSG).  I will write more about this later, but what I can say here is I think Blair is a brilliant pick by Obama.  Not only does he have a strong military and intelligence background, but more importantly to me, he believes in evidence, and is a strong supporter of science.  And below is a little pic of me getting my certificate from Adm. Blair.  

Open Evolution Highlights - the Population Genetics of dN/dS

An interesting new paper in PLoS Genetics (PLoS Genetics: The Population Genetics of dN/dS) by Sergey Kryazhimskiy and Josh Plotkin that discusses the use of the widely used parameter dN/dS (in essence a measure of the ratio of non synonymous to synonymous substitutions in protein coding genes). This parameter is commonly used to estimate the type of selection that has occurred in a protein coding gene.

Here is their summary of their article:

Since the time of Darwin, biologists have worked to identify instances of evolutionary adaptation. At the molecular scale, it is understood that adaptation should induce more genetic changes at amino acid altering sites in the genome, compared to amino acid–preserving sites. The ratio of substitution rates at such sites, denoted dN/dS, is therefore commonly used to detect proteins undergoing adaptation. This test was originally developed for application to distantly diverged genetic sequences, the differences among which represent substitutions along independent evolutionary lineages. Nonetheless, the dN/dS statistics are also frequently applied to genetic sequences sampled from a single population, the differences among which represent transient polymorphisms, not substitutions. Here, we show that the behavior of the dN/dS statistic is very different in these two cases. In particular, when applied to sequences from a single population, the dN/dS ratio is relatively insensitive to the strength of natural selection, and the anticipated signature of adaptive evolution, dN/dS>1, is violated. These results have implications for the interpretation of genetic variation sampled from a population. In particular, these results suggest that microbes may experience substantially stronger selective forces than previously thought.

The key to me is that it seems that many may have been using dN/dS ratios inappropriately when comparing samples within a species. For more, well, see the paper.

Obama indicates his clear support for science with Chu as Secretary of Energy

Well, say what you will about Steve Chu, but the fact that Obama has nominated him to be the Secretary of Energy is only a good sign for science and society as far as I am concerned.

It is a good sign for science because it shows explicitly Obama's respect and support for science. Most recent Secretaries of Energy have been non scientists (the #s depends on whether you count an engineer as a scientist - I do - but some don't) and Bush (who I want to say is out previous president but we still have him for another month) does not believe in evidence in any way, let alone science.

It is a good sign for society because it is important for the president to understand and respect science. So - some may criticize Chu for some issues - but none of the criticisms I have seen really hit home with me. Sure, I would like a Biologist in their in the Cabinet, but Chu seems to actually understand that the biological diversity of the planet is under threat from global change and he wants to do something about it. I cannot really ask for much more from a Physicist/Administrator. For full disclosure - I have an Adjunct position at LAwrence Berkeley Lab where Chu just happens to be the Director. So maybe I am not completely objective, but anyway, I think this is a good day all around.

Creative Commons- New Video and Fundraising Campaign

Everyone interested in Open Access and the open spread of information should check out the new video from the Creative Commons folks. This is being released as part of a fundraising campaign for Creative Commons  and I recommend that people consider donating to this great organization.  As a side note, the video was directed by Jesse Dylan, the director of the Emmy- award winning "Yes We Can" Barack Obama campaign video and features musical artist will.i.am from the Black Eyed Peas. 

Outdoor Art at Robbins Hall

There is some relatively outdoor art at Robbins Hall at UC Davis. The art features plants, evolution and DNA -- things I dig. Here are some pics.

Robbins Hall Outdoor Art

The only issue I have is that they did not highlight the bacteria that should be present on the bean roots (legumes fix nitrogen via nitrogen fixing bacteria that hang out in nodules in the roots). But if we take an artistic interpretation of the bean roots, some of the little black triangles there can be considered root nodules.

Anyway, just thought I would share the pics. The art is worth checking out if you are in the area.

New Dope on "Cognitive Enhancement"

Well, the world works in mysterious ways. April 1 this year, I coordinated a blogosphere hoax regarding the NIH cracking down on brain doping. See Confessions of an April Fool and the Dope on Brain Doping for more detail. And then Nature and many other publications wrote about brain doping when Nature published the results of a survey suggesting many academics take cognitive enhancing drugs. And now, perhpas most interestingly, a group has written a letter to Nature has published a commentary arguing for more research into " responsible use of cognitive-enhancing drugs by the healthy"

From their conclusion:

Like all new technologies, cognitive enhancement can be used well or poorly. We should welcome new methods of improving our brain function. In a world in which human workspans and lifespans are increasing, cognitive enhancement tools — including the pharmacological — will be increasingly useful for improved quality of life and extended work productivity, as well as to stave off normal and pathological age-related cognitive declines. Safe and effective cognitive enhancers will benefit both the individual and society.

But it would also be foolish to ignore problems that such use of drugs could create or exacerbate. With this, as with other technologies, we need to think and work hard to maximize its benefits and minimize its harms

On the one hand I agree that more work in this area is good. On the other hand, people compete all the time based upon cognitive performance. The article discusses thesae and other issues and is worth looking at. As I am on Campus right now I am not sure if the letter is Open Access or not, but I hope it is.

See also

• Smooth Pebbles: Some heavyweights vote Yes on cognitive-enhancing ...


• Mind Hacks: Mainstreaming cognitive enhancement


• Key Words: Nature Magazine Supports Cognitive Enhancing Drugs


• Brain doping: academics say yes

Hat tip to Bora for pointing this out.

Aphid-bacterial symbiosis in more detail, and in the New York Times

Nice little bit in the New York Times tomorrow about aphids and their symbionts. Henry Fountain writes (Observatory - How Tiny Insects, With a Little Help, Survive on Plant Sap - NYTimes.com) about a new article by Angela Douglas, one of the true pioneers of endosymbiont research. In her study she dissects in fine scale detail which essential amino acids are missing from the aphid sap only diet and which ones are made by the symbionts. Interestingly, the research apparently shows that the aphids may have figured out how to make methionine by themselves. I say apparently since I have been unable to track down the paper which I assume is coming out soon.

I should note, in one of the symbioses like this that I have studied with Nancy Moran we found that there were two symbionts contributing to the nutrition of the host. We found that one of the symbionts was likely making amino acids for the host (an insect called the glassy winged sharpshooter which eats only xylem sap) and the other symbiont was likley making vitamins. Nancy showed later with John McCutcheon that the symbiont that was making vitamins also was predicted to be making methionine for the host. So it seems possible there might be a missing symbiont in the aphid study? Although it would be cool if the aphid has figured out how to make an amino acid most animals are not able to make.

Hat tip to Max Lambert for pointing this out.

Tree of Life Gift Recommendation - Climate Kits

Just a quick recommendations for a gift for this holiday seasons that seems cool (metaphorically and literally). It is the climate kit. It comes from a friend of mine from college, Kathy Washienko and this is some of their text:

Kits are convenient collections of tools and tips that will help your family and friends reduce your environmental impact. By grouping what you need in one handy package, a kit makes it easy and fun to take energy-saving steps. Each kit is ultimately a gift to our environment, but will also save you money in reduced energy costs.* And every kit comes with our innovative "rebate." Check them out!

Sounds good to me. And given that I am trying here to promote trees (albeit phylogenetic ones, not real ones) I like that they are planting a tree and trying to be green.

Congrats to Pamela Ronald et al. for Award for Flood Resistant Rice

Congrats to Pam Ronald, colleague, Davis faculty member, and fellow science blogger for receiving a USDA Discovery Award for helping develop a flood resistant rice variety. For more on this see

• UC Davis Scientists Develop Flood-Resistant Rice
• USDA Discovery Award Recognizes Rice Research
• UCD researcher honored for rice breakthrough
• Waterproof rice coming soon

"Free" large scale sequencing for Department of Energy related projects ...

Interested in Department of Energy-related missions such as global carbon cycling, alternative energy production, and biogeochemistry? And want some genomes, metagenomes, or other things sequenced that are relevant to these topic areas? All you have to do is write a proposal to the Joint Genome Institute (JGI) Community Sequencing Program, get it selected by the review committee, and then the JGI will do the sequencing and some analysis for you.

Go to this web site to learn more ....JGI - CSP Overview.

UC Davis giving further props to blogs (mine that is)

Hey - thanks UC Davis.  Thanks for promoting blogs on your front page (under the Blogs, iTunes and Facebook section) and thanks for promoting my "Things Scientists should be thankful for"posting.  

What scientists should be thankful for ...

Well, it is Thanksgiving. I am up late as usual catching up on email. On this day, there is something I have been meaning to post for a few years. I think scientists should take a breath today and give thanks to those who have helped them along the way. I have some specific postings about this in terms of who I want to thanks, but I wanted to make a list here of the types of things scientists should be thankful for. So here goes.

10 things scientists should be thankful for

1. Teachers. Scientists had to learn science at some point. And most of us have had some stellar science teachers, or teachers of science-related things like math, along the way. We should give thanks to these people.
   
2. Inspirers. Similar to #1 except in many cases we have been inspired to become scientists by someone who may not have been a teacher of ours. Perhaps it was a famous scientist, or even a fictional one. Or even someone we knew. It is that inspiration that frequently gets one through the tough times.
   
3. Benefactors In general, scientists have a pretty nice life. We get paid (sometimes well, sometimes poorly) and are given research funds, to unlock the secrets of the universe. How cool is that? We should therefore be very thankful for the immediate source of our funds - such as the institutes where we work and the agencies that provide us funds.
   
4. Taxpayers. Unless one is funded by private foundations, taxpayers are the ultimate source of those funds mentioned in #3. This source of funds is frequently overlooked but should never be forgotten. Don't forget - we take money people from people that in theory they could have gotten to keep if their taxes were lower. We should thank these taxpayers..
   
5. Research personnel (including student researchers, post docs, technicians, etc). Most of the time, scientists get credit for some work that was in a large part actually done by people in our labs. They deserve our eternal gratitude.
   
6. Students we teach. Overall, for those scientists who teach, though it may be a required part of our jobs, it is also a great way to learn and to become a better scientist.
   
7. Staff at publishers. An important part of communicating science is of course publishing. And though I am a big fan of new ways to disseminate information, let us not forget that there are many many people who aid and abet this dissemination by working for publishers. These folks deserve our thanks.
   
8. Study subjects or objects. Whether one studies organisms, rocks, molecules, planets, forces, or whatever, we should all be thankful that there is interesting stuff out there to study. And for those who study living things, if one disturbs them along the way, we should
   
9. Librarians and library staff. Access to information is critical for both learning to become a scientist and being a scientist. And libraries play a key role in providing this access.
   
10. Family and friends. Late nights at the lab? Working on a grant over the weekend? Writing papers all the time? In school for years and years? All of this takes a toll on friends and family. And we owe them some props.
    

I am sure there are more categories. But these are some that came to me on this Thanksgiving. Any categories I missed?

Tackling a Hairy Beast II

For all out there who love ciliates and their relatives, you might want to check out the second paper to come out of my Tetrahymena thermophila Genome Sequencing Project for which the preprint is available in BMC Genomics.

In this project we have been sequencing, annotating and finishing the macronuclear genome of this lovely organism. Like other ciliates Tetrahymena has two nuclei and two nuclear genomes - the macronucleus (MAC) and the micronucleus (MIC). The MIC is analogous to germ cells in animals -- it is sort of a genomic repository for sexual reproduction. After sexual reproduction, the MIC genome is processed to generate the MAC genome which is then used in an analogous way to soma cells in animals (the MAC is the site for most/all gene expression in Tetrahymena). I have been the PI on this project which was supported by grants from NSF and NIH and was a collaboration involving TIGR (where I used to work), Stanford, UCSB, JCVI (which subsumed TIGR a few years ago) and the Tetrahymena research community.

Our first paper on this project was published in PLoS Biology two years ago. I have written about it previously here.

The new paper describes further work on the MAC genome including finishing many of the chromosomes (which was done spectacularly by Luke Tallon and Kristie Jones), sequencing and analyzing a larger number of ESTs, refining the annotation (coordinated by Mathangi Thiagarajan), and some other analyses. The new paper was led by Bob Coyne, who, with Barb Methé took over coordinating the work at TIGR/JCVI after I moved to UC Davis a few years back. I think they did a stellar job (ni biases here).

Note - I took the title of the posting 'Tackling a Hairy Best" from an NIH press release that was put out when we got the grants for this project.

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)

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 ...

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

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

• PLoS Genetics: Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing
• PLoS Biology - The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing

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

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.

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.

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.

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.

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.

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

• How bleach kills germs
  
• Mystery solved: How bleach kills germs
  
• Bleach Kills Germs, and Finally Scientists Know Why | 80beats ...
  
• How Bleach Kills Bacteria | LiveScience - Mixx

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

Suggestions for Obama's CTO

Want to suggest priorities for Obama's CTO? Go to http://www.obamacto.org.

Plug of the week - Extreme 2008: A Deep-Sea Adventure: University of Delaware

Just a little plug here to suggest people might want to check out the web site for a Deep Sea Research Cruise going on right now (Extreme 2008: A Deep-Sea Adventure: University of Delaware). The focus of the cruise is summarized as follows:

The scientists will focus on marine viruses and other tiny life called protists and their roles in the food chain. These organisms prey on bacteria, a primary food that sustains the vent ecosystem.

Some friends/colleagues of mine are involved in this adventure and it sounds like some cool stuff could come out of it. Also you might want to check out the blog of Lisa Z (ExtremeVirus), who is posting about the cruise.

This press release deserves some sort of award ...

Just got pointed by Ruchira Datta to a new press release from Princeton (Princeton University - Evolution's new wrinkle: Proteins with cruise control provide new perspective) that makes some interesting claims about evolution. Ruchira asked if the press release made sense to me. And alas, it does not. It has all sorts of bizarre evolution claims in it including the following

A team of Princeton University scientists has discovered that chains of proteins found in most living organisms act like adaptive machines, possessing the ability to control their own evolution.
...

"Our new theory extends Darwin's model, demonstrating how organisms can subtly direct aspects of their own evolution to create order out of randomness."

"What we have found is that certain kinds of biological structures exist that are able to steer the process of evolution toward improved fitness,"
....
Unlike Darwin, Wallace conjectured that species themselves may develop the capacity to respond optimally to evolutionary stresses. Until this work, evidence for the conjecture was lacking.
....
"In this paper, we present what is ostensibly the first quantitative experimental evidence, since Wallace's original proposal, that nature employs evolutionary control strategies to maximize the fitness of biological networks,"

It sounds like complete nonsense to me. But I am not sure. Anyone else out there know more?

Underselling Genomics Award #1: David Whitworth for "Genomes and Knowledge: A questionable relationship"

I do not normally write too much here about non Open Access publications but this one is so good I had to. Everyone with access to Trends in Microbiology should check out Julian Parkhill's rebuttal to an article written by David Whitworth in the same issue. Whitworth's article is "Genomes and knowledge – a questionable relationship? " and it is in my opinion, filled with some unsuppoerted and over the top statements. In essence, he is arguing that we should stop genome sequencing because there are a bunch of genomes out there already and after all, all that matters is work on model organisms so if you have enough genomes related to your model organism you should move on. Alas I do not have time to detail them here. But fortunately, Parkhill does a great job of responding in his article Time to remove the model organism blinkers. The end of his article reflects how I feel too:

In the end, when faced with the astonishing diversity of microorganisms, if all we manage to do is to describe a few random organisms in painstaking detail, then we will have failed to understand microbiology. To suggest we curtail the remit of microbial genomics is bad enough; to suggest it now, when we are on the brink of finally being able to truly study genomic diversity, is absurd.

So sure, sometimes we in genomics oversell the benefits of genome sequence data (and in fact, I give out a little award here for those people). But Whitworth is at the other end of the spectrum, wearing, as Parkhill states "blinkers" to the benefits of genome sequence data. As a reflection of how much I disagree with most of Whitworth's implications, I am giving him my first "Underselling Genomics Award".

Outdoor art at the Farmer's Market

Love the outdoor art in the renovated Gardens in Central Park in Davis ...

DNA Dynasty "Company" - Stealing and Lying

Well, just adding my two cents to the pissed off blogosphere regarding a company in Singapore called DNA Dynasty.  Not only are they purveying complete crap in terms of genetics/genomics (e.g., they say they have a genetic test to determine the innate abilities of your children) but they have apparently stolen the logo of the DNA Network of which I am a member.  Lovely.  I figure, if we make enough blogging noise, then when people search for them with google they will at least also see some of our postings.  So here is mine.  See also

• Nils
  
• Paulo
  
• Bill 

Metagenomics 2008 Meeting Notes

I am going to post notes here for the Metagenomics 2008 meeting.

#1 - most everyone here seems really happy about the election

#2 - mooched a ride this morning to the conference site from some of the folks who run "The Seed" and related annotation and analysis servers.  I have written about them before but people really should check them out if you are interested in microbial genome analysis. 

#3 - Alex Worden is talking now about picoeukaryotes.  Alex does some of the coolest environmental microbiology out there and just happens to focus on groups of organisms that are frequently ignored.  She just said a key quote "Physiology is not a bulk or an average property" basically saying what I say which is that an environment is not simply a bag of genes.  That is we need to remember that there are real compartments in communities.  Alex just showed an interesting figure on rRNA sampling of uncultured eukaryotes from the Sargasso See (Not et al. EM 2007).   Another key point she has made is that microbial eukaryotes are barely sampled in terms of genomics

#4 - a ridiculously short break (the organizers of this meeting really really need to change the scheduling to have more time to talk to people in breaks).  

#5 - Oded Beja is talking now.  He is really one of the key people behind the entire metagenomics revolution as he was the lead on many of the papers from the Delong Lab onthe discovery of proteorhodopsin

#6 - Shannon Williamson is showing an incredibly cool contraption that she uses to take water samples and size fractionate them in the bottom of the ocean.  It is basically a series of filter systems that works on a platform that is run by a deep sea submersible ... this allows them to sample large volumes of water in the deep sea (larger volumes than they could bring back up to the surface)

#7 - a little note --- already many talks referring to using IMG, IMG/M and MG-RAST tools to help with annotation and analysis of genomes and metagenomes.  Clearly there is enormous demand for getting ones data analyzed by some public or semi-public tools ...

#8 - Yuri Gorby --- gave a talk about nanowires which are basically little mini cables that cells use to connect to other cells and shuttle electrons around.  This stuff is beyond cool --- it is completely fascinating.

Metagenomics Meeting --- Competing with the Election

Well, I apologize but I am not going to post anything today about the metagenomics meeting in San Diego since I came late today as I wanted to be at home for the beginning of the election. But I made my way down to San Diego and made it to dinner. The dinner "entertainment" was a talk by one of the grand gurus of ocean microbiology - Steven Giovannoni. Alas, even he realized that he was competing with people wanting to know about the election and I confess I spent most of his talk hitting reload on my phone and surfing between sites. But So I have no notes to post about his talk. But I can say that I am happy about the election. And tomorrow I will try to post some notes about talks. But I may be still too happy to take notes ...

((Note added later --- in retrospect, I (and others I talked to) felt Steve G's talk had way way too much detail for an after dinner talk so I spent the next day taking out much of the detail from my talk to lighten it up. What did this get me? After my talk and later after drinks Steve G. made it clear he thought it stunk because it was too light on details of something he thought should have been in it. Oh well, I guess this goes to show you cannot make everyone happy.)).

More about How I feel - from my iPhone

How I feel - drawn on my iPhone

Charles Darwin Reiterates Endorsement of Obama

Charles Darwin has again spoken from the grave. In February I reported how Darwin endorsed Obama in the primary against Hilary Clinton (The Tree of Life: Charles Darwin Endorses Obama as the "Natural Selection") (note - his candidacy took off immediately after the 2/5 endorsement). And Darwin is getting in his own November surprise for the election tomorrow. Darwin spoke through a variety of media (I am using this term in reference to the plural of medium - people who speak to the dead .. but I am not sure whether media or mediums is the plural) and said

"This one is such a complete no brainer. Obama is so far and away the fitter candidate. Plus if Palin and McCain do not believe in my greatest work, well they can ..." (we cannot print the rest)

So there it is. Of course, most living well known scientists who have made public statements also endorse Obama, but getting Darwin's support is an extra feather in his cap.