Tuesday, September 30, 2008

Congrats to Gary Andersen, Developer of the Phylochip, for Getting a WSJ Technology Award

The Phylochip, developed by Gary Andersen, of Lawrence Berkeley National Lab, and colleagues, has won a Wall Street Journal, Technology Innovation Award. For more see the Wall Street Journal here. Their phylochip is a microarray which can be used to rapidly survey rRNAs from different organisms and get a measure of the types and abundances of organisms present in a sample. It is similar in concept although different in design from a rRNA chip that was used by David Relman, Pat Brown, Chana Palmer and others. Not sure why the chip from Brown et al did not also win the award (it probably was not nominated, or something like that), but still, always good to see cool things in microbiology win awards like this.

Joe Derisi and Open Science featured on Voice of America

Well, I already gave him one of my awards, so what else could he do?  Anyway, always good to see Open Science getting promoted and nice to see Voice of America running a story on Joe Derisi after his Heinz Award and featuring this openness (listen to an MP3 of the radio story here).  And they even interviewed me because of my blog about him.  Blogs and the "real" news merge closer and closer every day.

Monday, September 29, 2008

Humorous sciency signs #2: Squirrel liberation front

Here is another funny science related sign. I think this was from the Grand Canyon or somewhere near there, taken by my mother, many years ago.

Like I needed any more justification to not trust organisms bigger than a large protist.

Wanted - Evolutionary Genomicist at UCSB

Todd Oakley, of UCSB and more importantly, the Evolutionary Novelty Blog, forwarded this to me.  UCSB is looking for an Asst. Prof. in Evolutionary Genomics.  If only they had said "Phylogneomics" then I would have written a longer posting ...

See here for more detail. Also see the ad on Oakley's blog.

Science Faux Pas #4: Nature wishes their dog ate this advertisement

I know others have written about this already but I had to add this to my collection of Science Faux Pas because it is pretty good.  Nature had a recent issue that was covering the US election.  And look at the front and back cover ... they claim it was an accident but hard to imagine given the posing/color matching.  I note I first heard about this from Bora on FriendFeed. And now the Times Online has a whole story on it.

Saturday, September 27, 2008

$ 700 billion will buy a lot of taq, LB, submarines, and other things

I know, my research tends to be expensive as I work on deep sea organisms and do genomics and such. But for $700 billion, a lot could get done in my work areas. Here are some things one could get for that amount of money that directly relate to my work (this was inspired by a conversation with Drew Endy Friday)
  • 1,400,000 Roche 454 Sequencing Machines (for $500,000 each). If you had money for reagents, that would get you a lot of sequencing.
  • 70 million bacterial genomes (at $10,000 each for the shotgun sequencing)
  • 280,000 liters (yes that is right, liters) of Taq polymerase (at 100$/40 ul)
  • 29.16 billion liters of sterilized LB broth (from Sigma at 12$/500 ml). That is one big vat of LB. It is also about 11,666 olympic swimmings pools worth of LB.
  • 7 billion copies of my Evolution textbook
  • 7 million people years of computational biologists to analyze data (at $100,000 per person year)
  • 538 million open access fees for publishing in PLoS One (at $1300 each)
  • 116.67 years of the National Science Foundation's Budget (at current costs of $6 billion per year)
  • A fleet of 32,407 Alvin submarine replacements (at 21.6 million a pop). Think of all of the deep sea work that could be done
  • Registration fees for 350 million people to go to the AGBT meeting in Marco Island
  • 28 million special guest appearances by Craig Venter (assuming he charges a 25,000 speaking fee, which is probably a bit high)
So it goes. I was always thinking of writing this type of blog about the money spent on the Iraq War. But this "bailout" $$$ got me thinking again.

And please post your own lists of what else this $$$ could buy.

Humorous sciency signs #1: Please do not molest the spawning salmon

I am starting yet another thread here --- my favorite humorous science related signs.  This one is from Alaska.  Not sure what Sarah Palin would think of this one, but that is another topic.

Davis Outdoor Art

I am planning to keep posting pics of Davis outdoor art whenever I can. Here are some pictures from the UC Davis Vet Hospital in an art display in honor of companion animals

Thursday, September 25, 2008

Drew Endy talking at Davis tomorrow ....

For those from UC Davis or the area who read the blog and have an interest in genetic engineering or synthetic biology or open science, you should come to this talk.

Genome Center Colloquium
Storer Life Sciences Endowment Presents

Drew Endy, PhD
Stanford University

"Post-Synthesis Genetics & Engineering Biological Simplicity"

Friday, September 26, 2008

10:00 a.m., 1005 GBSF Auditorium

For more on Drew Endy, well, use google of course or go here:

Science Faux Pas #3: Editirs in Chief

The pictire seys it all.  Note - we think this was the restaurant's fault.

Funny Davis Signs #1

Going to start a new section here ... posting pictures of funny Davis
signs. This is one of my favorites.

MapMyRun for Davis is a nice way to find new places to explore in town

I meant to post this a while ago but was in over my head with other things.  I found this cool site while googling for Davis MAPS and thought I would share --MapMyRun.com | Find Runs and Running Routes in Davis, CA

It has a diversity of routes for biking, walking and running in and around town.

Wednesday, September 24, 2008

Lance Armstrong Coming to Davis for the Tour of California

Get ready Davis.  Not only will Davis host a stage of the Tour of California this year, but new reports are today confirming the rumors - Lance Armstrong will apparently race in the Tour of California for the Astana team.  See for example

Tuesday, September 23, 2008

Much ado about plants and blogs in PLoS Biology

Some good new articles in PLoS Biology in the last few weeks worth checking out.  There is definitely a theme there if you want to look for it.  So here are some of the papers connected to that theme and even one that covers both.

What does privacy mean to you? Please complete this survey

ThePrivacyPlace.Org Privacy Survey is Underway!

Researchers at ThePrivacyPlace.Org are conducting an online survey about privacy policies and user values. The survey is supported by an NSF ITR grant (National Science Foundation Information Technology Research) and was first offered in 2002. We are offering the survey again in 2008 to reveal how user values have changed over the intervening years. The survey results will help organizations ensure their website privacy practices are aligned with current consumer values.

The URL is: http://theprivacyplace.org/currentsurvey

We need to attract several thousand respondents, and would be most appreciative if you would consider helping us get the word out about the survey, which takes about 5 to 10 minutes to complete. The results will be made available via our project website (http://www.theprivacyplace.org/).

Prizes include
$100 Amazon.com gift certificates sponsored by Intel Co.
IBM gifts

On behalf of the research staff at ThePrivacyPlace.Org, thank you!

Friday, September 19, 2008

Fwd: MG-RAST User Newsletter No.2 -- MG-RAST paper available // NEW version released // 2nd User Workshop planned

Out sick so email updates will have to do
Got this by email

Subject: MG-RAST User Newsletter No.2 -- MG-RAST paper available // NEW version released // 2nd User Workshop planned

Dear MG-RAST users,

The MG-RAST team has some news we would like to share:

1) MG-RAST manuscript published

The manuscript for MG-RAST has been accepted in BMC Bioinformatics and is available under the following URL:


Please cite:
The metagenomics RAST server F. Meyer, et al
BMC Bioinformatics 2008, 9:386

2) New version of the server software available

After a lot of testing (Thanks again to all beta testers), we have released a new version of our MG-RAST server software. You will notice improvements in nearly all aspects of the MG-RAST platform and user experience.

Here is a  summary of changes and additions:
- added overview page with statistical summary
- ability to download arbitrary subsets of fragments as fasta
- user can change parameters for metabolic reconstruction and phylogenetic reconstruction on the fly
- ditto comparison/heatmaps
- recruitment plot
- metabolic comparison tool using KEGG pathway maps
- updated databases in background (NR no longer from 2006, Silva RNA database included)
- detailed sequence information and alignments
- support for groups and inviting friends to look at data
- much faster user interface
- ability to see/download fragments and see blast alignments
- added Silva rRNA database (from: http://www.arb-silva.de/)
- many small detailed fixes

3) MG-RAST workshop planned for winter 2008/2009
In addition to the tutorial at Metagenomics 2008 in San Diego (see: http://metagenomics.calit2.net/) we are inviting participant registration for our second MG-RAST workshop. Please send an email to mg-rast@mcs.anl.gov if you are interested in participating.

-- from the MG-RAST team

Wednesday, September 17, 2008

Amy Harmon, New York Times, on Open Access publishing

Amy Harmon, who writes for the New York Times and has written some excellent recent pieces on evolution and genomics is answering some questions on the New York Times website

And one of them was about communicating science and Amy responded (with other comments):
Of course, the one way scientists do, theoretically, communicate with the public is by publishing their results. Since these papers are written for other scientists, they can be hard to understand. But even for people game to wade through them, they are often hard to obtain. The two leading scientific journals, Science and Nature, and many others, require people to pay for access to papers whose authors have been financed by taxpayers. “Open access” publishers like the Public Library of Science do not, so it would be nice to see scientists choosing — or being required — to publish in journals that are open to the public.
Nothing more for me to add.

Tuesday, September 16, 2008

Congratulations to Stanley Falkow, Microbiologist Extraordinaire and Lasker Winner

Short one here as I am at a conference. Very happy to see Stan Falkow get a Lasker Award.
"The breadth and depth of Falkow’s career is being recognized with the 2008 Lasker-Koshland Award for Special Achievement in Medical Science."
He is a great scientist but more importantly to me, he has an infectious (no pun intended) enthusiasm for science, microbiology, and life. For more detail, there is a really nice article in the Stanford Report about him and his career. Every time I interact with him (e.g., when I was a student at Stanford) I feel like I got a microbiology passion boost that lasted for years. And clearly he has had this effect on many many others. Congratulations to him for a well deserved award.

Caution - Maverick Scientist Ahead

Interesting article on David Goldstein (a co-author of my Evolution textbook) in the New York Times Mostly, it is kind of portraying him as a "maverick" in genomics (Note - Nick Wade seems to specialize a bit in portraying scientists as mavericks -- think of Craig Venter). Maverick of course is a term that is being overused in the election in the US these days and Wade does not use it to describe Goldstein, but that is the gist. Even the title "A Dissenting Voice as the Genome Is Sifted to Fight Disease."

The key quote is
“There is absolutely no question,” he said, “that for the whole hope of personalized medicine, the news has been just about as bleak as it could be.
He also sort of disses the HapMap project and related activities. Goldstein, who I went to grad. school with, certainly can be contrary. And I do not work on human genomics so I do not know how close to home his claims about the lack of utility of the HapMap. But I think his general feeling here is probably right. Human genomics, as with many other genomicy things, has been oversold by many of the practitioners. That does not mean it is not useful --- and Goldstein makes this point. It is just that we need to be careful (I think and it seems so does Goldstein) in making claims about what the benefits of something in genomics will be before we see the actual benefits.

Lake arrowhead notes - UPDATED

Well I gave my talk

Seemed to go ok except getting cutoff early because the chair ignored
that the session started late but that is ok

George Weinstock is now speaking using my laptop so I am trying to
post from my phone

He said one key thing I left out ... Big scale microbial sequencing
projects are now possible thanks to next gen sequencing in particular
454-Roche tools

More later
Sent from my iPhone


More now

George Weinstock gave a good overview of the "Human Microbiome Project" which is a NIH Roadmap initiative to catalogue the genomic content of the microbes associated with humans. He described some of the big picture of why do the project, of the different fundingin initiatives being done through NIH and he gave some detail on the "jumpstart" project going on at the big genome centers right now. He outlined how the current plan is to select a few hundred people and to survey their mcirobiomes from multiple sites using rRNA PCR and possibly metagenomics. In addition, he described how there is also an effort to sequence 100s if not a 1000 genomes of cultured organisms that have been isolated from human environments. He did say one thing I disagreed with which is that he thinks it is somewhat reasonable to treat the environment that microbes live in in essence as a big bag of genes. In other words, if you sequence from a community, he implied that one can focus just on the genes and their functions and not the organisms that they come from. On this I disagree (and pointed this out after the next talk). But overall George gave anice overview of the project and its goals.

Eric Wommack gave a good talk about viral metagenomics work he has been doing. He pointed out that a lot of the viral world is "unknown" but that does not mean it is unimportant. And this is consistent with what I and George Weinstock said which is that we need more genome data from viral isolates. Eric presented some very useful results on the challenges of using short read sequence data in metagenomics and he referenced a few papers on this. He also referred to a cool viral genome survey project that I was not aware of by Hatfull which involved undergraduates in sequencing and analyzing the genomes of phage that infect Mycobacterium smegmatis.

Jim Bristow on Biofuels. He is now giving a summary of some of the JGI work on the genomics of cellulolytic organisms and processes. He is focusing on the termite gut community and had some good one liners about this (e.g., he said many people want to kill termites but not JGI. They are our friends; he also said "it takes a village to sequence a termite gut").

Not sure exactly how to say this, but here goes. There was one talk in the AM I was not overly fond of. This was a talk by Bernard Palsson. Now I confess, I am not overly familiar with much of his work but what I know of it suggests he does some really solid, interesting and important work on metabolic network modeling and analysis. But his talk at this meeting was disappointing. His talk was about his use of genome sequencing to characterize "adaptive evolution" in E. coli. And the results he presented seemed solid enough. The problem I had was that it was a prime example of "overselling genomics". Why? Here is what they did. They took E. coli mutants. And the then took them through cycles of growth and then dilution. And then they looked at the populations after a certain number of generations and did a variety of analyses. Included in this was some whole genome sequencing that helped identify mutations arising in the cultures. And then they did some characterization of these mutations/mutants including some competition experiments and some pretty interesting gene expression studies of some RNA polymerase mutants. And he made some conclusions based on their results like that E. coli in the lab can find new adaptive peaks and that mutations differ in different replicates, and that different mutations confer different fitness, that they can monitor the appearance of mutations over time, and so on.

So what is the problem -- the problem is that he (1) presented this as though the serial cycling of E. coli was novel when in fact it is not and that (2) he presented the conclusions as though they were novel when they also are not. People have been doing this type of experiment for many decades (in fact, one person, Rich Lenski, has been doing an experiment like this for decades). And they get these exact results. But they have not sequenced genomes as part of their experiment. And thus, at least for this talk, they were not mentioned, and the rediscovery of many truisms in population genetics was presented as novel because it involved genome sequencing.

Trent Northen created a serious buzz during and after his talk with his presentation of some of the things one can do with Nanostructure Initiated Mass Spectrometry (NIMS). I confess - I want his toys.

Lynn Silver is now talking about the challenges in the development of new antibiotics. She argues that the focus by some on trying to find new targets for antibiotics has been a bit misguided.

Julian Parkhill gave a good talk about population genomics of Salmonella. He pointed out a few things people still ignore. For example, if you want to identify polymorphisms in a species to use for population genetics/genomics studies, you really need to do a survey to identify polymoprhisms from diverse members of the population. If you do not, and then you use a biased set of polymorphisms, your population inferences will be wrong. He also said, in response to a quesiton of mine, that at least for this species, they see very little variation in copy number in genes which is different than what people seem to see in humans.

Tiffany Williams from Baylor gave a talk about using high throughput sequencing in collaborations with developing countries. She outlined some of the challenges as well as the benefits from such collaborations.

Kim Lewis gave a very interesting talk on microbial biofilms and persister cells, of which I know vanishingly little. He showed some very cool experiments trying to "complement" unculturable organisms and get them to grow.

Jeffrey F. Miller gave a talk focusing on diversity generating retroelements in bacteria which appear to be a means by which bacteria can target particular regions of the genome for mutagenesis in a comparable way to VDJ mutagenesis in humans. This was perhaps my favorite talk so far at the meeting as it combined microbial genomics, evolvability, mutation processes and other things I tend to focus on.

Steven Benner gave a talk which I had to skip out on early because I was doing a radio interview. Benner said one thing that annoyed me at the beginning - he made a comment that was complaining about prior talks that referred to "Rosetta Stone" methods of predicting function (I was one of the people who mentioned this) because he thought that we were referring to blast searches. He clearly was not paying any attention as the Rosetta Stone method is a method to predict function for genes by finding connections between non homologous proteins based upon having other proteins that have domains found in both of the original proteins of interest. Oh well, glad I had to leave early because I was itching to jump up and correct him.

Heather Allen, from Jo Handelsman's gave a very good talk about doing functional metagenomic screens for antibiotic resistance encoding genes. She has been using DNA from multiple soil sites, including a pristine site in Alaska, and screening the DNA for antibiotic resistance genes in E. coli. These screens identify a wide diversity of genes, including some novel forms. This work helps highlight the need to not just sequence the snot out of the world but to also do some functional assays at the same time. In addition she mentioned that she was able to come to the meeting because Jo Handelsman set up a fund for mothers to pay for babysitters to come to a meeting with them. All I can say is Jo Handelsman was already one of my favorite people in science and this is just another brilliant and wonderful thing that she does.

David Relman gave a talk about two studies of the human microbiome that his lab has been doing: (1) studies of marine mammals to compare the microbial diversity in their surfaces with the diversity in the water and the diversity on their insides and (2) study the response of the human gut microbial community to antibiotic treatment. I am particularly fond of the antibitotic treatment study because they are treating it as an "ecological disturbance" study and analyzing it much like ecologists would analyze recovery of a forest after fires. I think we definitely need more ecologists to bring their techniques and skills to human microbiome studies and so this was exciting to see.

Ashlee Earl gave a talk about biofilm formation in Bacillus subtilis. Much like Kim Lamb's talk earlier, this talk was in an area I know little about and I guess you could say it kind of blew my mind. It seems that in B. subtilis and I guess in many other microbes biofilms are in essence analogous to multicellular organisms. Within a biofilm there are different types of cells that have different roles and the patterns are highly reproducible and organized. It seems to me that the boundary between multicellular and single-celled organisms is getting blurrier and blurrier. Ashlee reported on some cool experiments where she collected strains from around the world and then dod comparative genetics and genomics of their biofilm formation patterns.

Alas I missed Mary Lidstrom's talk which based upon prior experiences I am sure was fascinating. She has been working in studying processes inside single bacterial cells and has been developing a suite of techniques and tools to carry out such studies. Maybe someone else from the meeting can post details about her talk.

Unfortunately, I had a conference call during some of the next talks that I had to do so I do not have details for the blog. Then I returned and served as chair for a session. I did take some notes so here goes.

Byung-Kwan Cho gave a tour de force talk about reconstructing the transcriptional regulatory network in E. coli. He presented results from a dazzling and dizzying array of genome-scale methods (e.g., ChipChip, tiled arrays, sequencing, etc etc) to characterize transcription regulation. In addition he did some complex and big scale computational work to combine all of the data together to characterize networks. It was quite impressive stuff.

Ginger Armbrust talked about her favorite critters - diatoms and focused on how they used the genome data to characterize silicon deposition processes. She was convincing as to the importance of diatoms and to the value of having the genome sequences from some species. She did discuss some of the challenges of using the genome data including the challenges in gene prediction for microbial eukaryotes. She also discussed her dream of utilizing some of the new genomic information as part of real time sensors in the oceans.

Anthanasios Typas discussed work to build tools for carrying out genome-scale analyses of genetic and chemical-genetic interactions. For example they are working on taking two comprehensive gene KO libraries from E. coli and using them to create all possible double mutants and to then screen those mutants for whether they have the same or different phenotypes than the single mutants. This allows them to look for gene-gene interactions. They also are doing this type of analysis with chemical-gene interactions.

Devaki Bhaya gave a brief talk on what I think is the single most interesting thing in all of microbiology right now - CRISPRs. These are clustered regularly interspaced short palindromic repeats. She is studying them in cyanobacteria from Yellowstone hot springs

Good quotes from the meeting:

  • So we simply sequenced the genome of the different variants
  • Antibitoics do not kill things, they corrupt them
  • Dormancy is the default mode of most bacterial life
  • Who knows what a yoctomole is?
  • I am going to defend genomics
  • There comes a point in life when you have to bring chemists into the picture
  • Gosh, was that today or yesterday
  • The rectal swabs are here in tan color
  • I'll try to let the pictures do the talking and I will get out of the way
  • Our model system de jour
  • And there's Jeffrey Dahmer
  • And this is my cheesy analogy here
  • He could not be here so I am here. His loss. My gain. Hopefully not your loss.
  • We are the environment. We live the phenotype.
  • If I have time I will tell you about a dream
  • Every fifth breath - thank a diatom
  • While we still have poles
  • A paper came out next year

Monday, September 15, 2008

Oh brother there art though (Uh oh, my brother has a blog)

Well, just in case people out there did not have enough trouble distinguishing my brother, Michael Eisen,  from me (me - UCD - him UCB, me microbial genome evolution, him drosophila and yeast genome evolution, me - OA fanatic PLoS Biology AEIC, him PLoS founder and board member, and so on), here comes a new thing to deal with.

Seems worth checking out.  First posts are 

Sunday, September 14, 2008

It's Miller Time - Lake Arrowhead Microbial Genomes Conference -- about to begin

Well, I am back.  Every two years I come back to this small meeting about small genomes.  The meeting is officially the "16th Annual International Meeting on Microbial Genomics at Lake Arrowhead, CA" but in reality, every two years it is at Lake Arrowhead and every other two years it is elsewhere.  And I rarely go to the other one -- but I keep coming back to Lake Arrowhead.

Why?  Well, you might guess it is because it is at UCLA's conference center up in the mountains.  But you would be wrong.  You might guess it is because I generally hate big meetings and this one is nice and small/medium.  But you would be wrong again.  For there are lots of meetings in pretty places.  And there are lots of medium sized meetings an omnivore like me could go to.  I go back every two years because of Jeffrey H. Miller, the organizer.  He invites me.  I can never say no.  

Why? Well, many reasons.  Sure one is that I like him.  Another is that he does meetings in the right way (not too many talks in one day --- some time to relax and talk with other people and to interact, etc).  But the truth is, I say yes because he is one of the few people I know who is interested in both DNA repair processes and microbial genomes.  And his meetings reflect this interest.  So I guess even though I do not spend enough time working on DNA repair any more, I did do my PhD on it, and I did basically try and copy some classic Jeffrey Miller mutator experiments.  So I just have to go to this meeting.  And here I am (see my 2006 meeting notes here) - despite having been very sick this summer and getting ready to teach a new class in the fall with 400+ students.

Anyway - More on the meeting coming.Here are the talks for those interested

James C. Liao
University of California, Los Angeles, CA
“Non-fermentative Pathways for Synthesis of Branched-Chain Higher Alcohols as Biofuels”

Jonathan Eisen
University of California, Davis, CA
“A Genomic Encyclopedia of Bacteria and Archaea”

Bernhard Palsson
University of California, San Diego, CA
“The Genetic Basis for Adaptive Evolution in E. coli”

George Weinstock
Baylor College of Medicine, Cambridge, MA
“The Human Microbiome: Progress and Challenges”

Gary Siuzdak
The Scripps Research Institute, La Jolla, CA
“Metabolomics Reveals Large Effect of Gut Microflora on Biochemistry and Activation of a Host Response”

Jim Bristow
DOE Joint Genomme Institute, Walnut Creek, CA
"Microbial Sequencing for Biofuels Applications"

 Eric Wommack
University of Delaware, Newark, DE
“Making sense of the chaff: What will metagenomic approaches tell us about viral ecology?

Valérie de Crécy-Lagard
University of Florida, Gainesville, FL
“Making Sense of Genomes: Linking Gene and Function by Comparative Genomics”

Trent Northen
The Scripps Research Institute, La Jolla, CA
“High Throughput Mass Spectrometry Based Metabolomic and Enzymatic Assays for Functional Genomics”

Matteo Pellegrini
University of California, Los Angeles, CA
“New Methods for Processing High-throughput Sequencing Data: Improving the Solexa/Illumina Data Analysis Pipeline”

Sabeeha S. Merchant
University of California, Los Angeles, CA
“Transcriptomics of Nutritional Copper Homeostasis in Chlamydomonas”

Lynn L. Silver
LL Silver Consulting, LLC, Springfield, NJ
“The State of Antibacterial Discovery in 15 minutes”

Julian Parkhill
Welcome Trust Sanger Institute, Cambridge, UK
“Discovering Variation in Genetically Monomorphic Bacteria: SNPs and the Evolution of Salmonella Typhi”

Tiffany Williams
Baylor College of Medicine, Houston, TX
“Global Health and Next Generation Sequencing Technologies: Streptococcus pneumoniae sertoype 1 in Africa”

Kim Lewis
Northeastern University, Boston, MA
“Persister Cells and Biofilm Resistance”

Jeffery F. Miller
University of California, Los Angeles, CA
“Diversity-Generating Retroelements”

Steven A. Benner
Foundation for Applied Molecular Evolution, Gainesville, FL
“Molecular Paleoscience”

Joe Zhou
University of Oklahoma, Norman, OK
“Metagenomics Insights of the Feedback Responses of a Grassland Ecosystem to Elevated Atmospheric CO2”
Heather Allen
University of Wisconsin-Madison, WI
“Using Functional Metagenomics to Discover Antibiotic Resistance Genes in Natural Environments”

David A. Relman
Stanford University School of Medicine, Stanford, CA
“Response of the Human Distal Gut Mircobiota to Disturbance: The Effect of Antibiotics”

Ashlee Earl
Harvard Medical School, Boston, MA
“Bacillus subtilis Biofilm Diversity”

Mary E. Lidstrom
University of Washington, Seattle, WA
“Coupling Function to Phylogeny via Single-Cell Phenotyping”

John Dueber
University of California, Berkeley, CA
“Use of Synthetic Protein Scaffolds to Balance Pathway Flux of Engineered Metabolic Pathways”

Maria L. Ghirardi
National Renewable Energy Laboratory, Golden, CO
“Hydrogen Fuel Production by Microalgae: Issues and Future Directions“

Caroline S. Harwood
University of Washington, Seattle, WA
“Redirection of Metabolism of Hydrogen Production”

Byung-Kwan Cho
University of California, San Diego, CA
“The Reconstruction of the Transcriptional Regulatory Network in E. coli ”

E. Virginia Armbrust
University of Washington, Seattle, WA
“Molecular Insights into Silicon Bioprocesses in Marine Diatoms”

Athanasios Typas
University of California, San Francisco
“High-throughput Quantitative Analysis of Genetic and Chemical-Genetic Interactions in E. coli”

Devaki Bhaya
Carnegie Institution for Science, Stanford, CA
“Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes.”

Erin Sanders-Lorenz
University of California, Los Angeles, CA
“Integrating Discovery-based Undergraduate Research Experiences into UCLA Courses Using a Collaborative Curriculum Model”

Cheryl Kerfeld
DOE Joint Genome Institute, Walnut Creek, CA
“The JGI Microbial Genome Annotation Program”

Fredrick Blattner
University of Wisconsin, Madison, Wisconsin
“Insights from the Genomes of Commonly Used Lab Strains”

Colin J. Ingham
Wageningen University, Wageningen, The Netherlands
“Reinventing the Petri Dish: Miniaturized Tools for High Throughput Microbial Culture”

Maureen Hillenmeyer
Stanford University, Stanford, CA
“The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes”

Simon Prochnik
DOE – Joint Genome Institute, Walnut Creek, CA
“The Genome Sequence of the Deep-Branching Amoeboflagellate Naegleria gruberi Reveals Ancestral Eukarotic Functions”

Elizabeth Fozo
National Institute of Allergy and Infectious Diseases, Bethesda,MD
“Regulating Bacterial Expression of Short Hydrophobic Toxic Proteins with Small RNAs”

Mariusz Nowacki
Princeton University, Princeton, NJ
“RNA-mediated Epigenetic Programming of a Genome-Rearrangement Pathway”

Barry L. Wanner
Purdue University, West Lafayette, IN
“Development of the www.EcoliHub.org Information Resource”

Hirotada Mori
Nara Institute of Science and Technology, Nara, Japan
“Systematic Analysis of Genetic Interaction of Esccherichia coli”

Thursday, September 11, 2008

Open Science Required Reading: MSNBC on "Era of scientific secrecy nears its end"

There is a must read out there about Open Science. Robin Lloyd has a excellent article on Open Science (Era of scientific secrecy nears its end) posted at MSNBC. I am not sure whether this was originally written for MSNBC or not nor the whole history of the piece. But the article discusses some of the issues associated with Open Science.

It has some good sections like:
The openness at the technological and cultural heart of the Internet is fast becoming an irreplaceable tool for many scientists, especially biologists, chemists and physicists — allowing them to forgo the long wait to publish in a print journal and instead to blog about early findings and even post their data and lab notes online. The result: Science is moving way faster and more people are part of the dialogue
It also lists some of the aspects of Open Science including
  • Blogs where "scientists can correspond casually about their work long before it is published in a journal";
  • Social networks "that are scientist friendly such as Laboratree and Ologeez"
  • Sharable sites like "GoogleDocs and wikis which make it easy for people to collaborate via the Web on single documents"
  • Citation sharing sites like "Connotea that allows scientists to share bookmarks for research papers"
  • Preprint servers "such as Arxiv, where physicists post their "pre-print" research papers before they are published in a print journal"
  • OpenWetWare "which allows scientists to post and share new innovations in lab techniques"
  • Video sharing sites like "The Journal of Visualized Experiments, an open-access site where you can see videos of how research teams do their work"
  • Sequence databases like "GenBank, an online searchable database for DNA sequences"
  • "Science Commons, a non-profit project at MIT to make research more efficient via the Web, such as enabling easy online ordering of lab materials referenced in journal articles";
  • "Online open-access (and free) journals like Public Library of Science"
  • "Open-source software that can often be downloaded free off Web sites"
Sure the article gets a few things a little mixed up. For example, software can be free even if it is not open source. And not all open access journals are the same. But the article is overall very good and has some of my favorite Open Science advocates in it like Cameron Neylon and Jean-Claude Bradley.

Wednesday, September 10, 2008

Follow up to Amy Harmon's NY Times Story on Evolution

The NY Times published a few letters that are follow ups on Amy Harmon's excellent story on evolution teaching in Florida.  

Also check out my blog posting about her story which has links to the story and some other information.

Tuesday, September 09, 2008

Open Access Pioneer Award #3: Joe Derisi

So I was reading the web page of WTOP radio, which I used to listen to all the time in DC and somehow still have their page near the top of my bookmarks. And there was a headline I could not resist. It said: "Malaria Researcher Wins Heinz Award." As I know a few people studying malaria here and there I had to check it out. And indeed, one of the winners of the award is Joe Derisi, from UCSF, who I know reasonably well and like very much. I am very pleased to see him win one of these Heinz Awards

The Heinz Site says "Joseph DeRisi receives the Heinz Award in Technology, the Economy and Employment for his extraordinary breakthroughs in detecting both new and existing viruses."

In addition to his science they say

"Joseph DeRisi has made breakthrough discoveries in the laboratory that have provided clarity and insight into the detection of some of the world's most threatening viruses as well as distinguished himself as a generous and tireless advocate for the free and open sharing of scientific research. With a brilliant mind and expansive heart, he has ennobled the field of science."

Here here. Derisi is one of the true pioneers of Open Science, not only promoting Open Access publishing but also promoting open sharing of methods, equipment, data, and everything. And, not that he needs another award (to go with his Heinz, his HHMI position, and his Macarthur among many things), but I am giving him my Open Access Pioneer Award #3 for his firm commitment to open science.

Blogs getting a bit more respect at UC Davis

Well, to go along with the FreindFeed discussions I have been having recently here is a tidbit of interest. Blogs keep getting a bit more respect at UC Davis. First, there was Egghead, a blog about research at Davis sponsored by University Communications the College of Biological Sciences and edited by Andy Fell of the UC Davis News Service. And now there is "UC Davis Blogs" a web site with details about blogs by UC Davis people also maintained by University Communications. And here is their current list:

Behind the Lens by Karin Higgins

Arts and humanities

Business and law

Science and agriculture

Social science

They have left out a few including one of my favorites: "Mario's Entangled Bank" by Mario Pineda-Krch but the listing by UC Davis is a good thing.

Darwin on the Wall

Lots of other bloggers posting about this but I got to put it out there too.  Check out the remarkable story of the Darwin Shaped Wall Stain and how it is galvanizing the evolution community - See Evolutionists Flock To Darwin-Shaped Wall Stain.  It is from the Onion.  One of my favorite "news" sources.  Hat tip to many many people for pointing this out.

Predicting the future (for molluscs)

As many of you know, I spend a decent amount of my blogging time trying to come up with funny evolution or genomics related posts. Well, if you like that type of thing, you really have to check out this new site:

The Molluskan Zodiac

The site states
"While most people are familiar with western astrology and with the Chinese zodiac, much less is known about the ‘molluskan zodiac’ (sometimes known as the mariners zodiac). But ask any fisherman, and they will tell you instantly which of the ten signs of the molluskan zodiac they were born under."
It is very very funny. And real of course. Kudos to Keith Bradnam, who happens to be from the UC Davis Genome Center (where I work) for revealing the inner secrets of these wonderful invertebrates. And while you are checking out the Zodiac, check out Bradnam's new PLoS One paper on intron length which he authored with Ian Korf. Science humor, invertebrates, and Open Access publishing. Now what could be better than that?

Saturday, September 06, 2008

Tracing the evolutionary history of Sarah Palin: links to a parasitic nematode and the pathogenic fungus Botryotinia fuckeliana

You see, as a total sequence analysis dork, when I see names, I frequently ask whether the letters in the name include only letters which are used as amino acid abbreviations. I started this game when the brilliant notes/letters came out in Science in the early 90s about whether ELVIS was overrepresented in protein sequences. Of course, despite being 20 years old, Science still keeps these under wraps requiring registration to see them (see for example the Stevens letter).

Anyway, alas, three of the major candidates for the US election have names that do not use traditional amino acid abbreviations so I am stuck with analyzing Sarah Palin. But that is OK because of her professed aversion to evolution and support to Creationism (and since sequence analysis is inherently an evolutionary study).

So - I took here name and went to the NCBI Blast page and did some searches. And what came up? Well, here are some of the top hits from the blastp searches (which I used to compare the pretend peptide "SARAHPALIN" with all the peptides in the non redundant collection at Genbank).

>ref|XP_001545292.1| Gene info hypothetical protein BC1G_16161 [Botryotinia fuckeliana B05.10]
gb|EDN25226.1| Gene info predicted protein [Botryotinia fuckeliana B05.10]

GENE ID: 5425746 BC1G_16161 | hypothetical protein
[Botryotinia fuckeliana B05.10]

Score = 26.9 bits (56), Expect = 189
Identities = 8/9 (88%), Positives = 8/9 (88%), Gaps = 0/9 (0%)

Sbjct 209 SARAQPALI 217

>ref|YP_061725.1| Gene info homoserine dehydrogenase [Leifsonia xyli subsp. xyli str. CTCB07]
gb|AAT88620.1| Gene info homoserine dehydrogenase [Leifsonia xyli subsp. xyli str. CTCB07]

GENE ID: 2939000 thrA | homoserine dehydrogenase
[Leifsonia xyli subsp. xyli str. CTCB07] (10 or fewer PubMed links)

Score = 26.9 bits (56), Expect = 189
Identities = 8/9 (88%), Positives = 8/9 (88%), Gaps = 0/9 (0%)

Sbjct 267 SARVHPALI 275

>ref|ZP_02031476.1| hypothetical protein PARMER_01474 [Parabacteroides merdae ATCC
gb|EDN87136.1| hypothetical protein PARMER_01474 [Parabacteroides merdae ATCC

Score = 26.1 bits (54), Expect = 340
Identities = 7/8 (87%), Positives = 8/8 (100%), Gaps = 0/8 (0%)

Query 3 RAHPALIN 10

Sbjct 170 RAHPALVN 177

>ref|XP_567332.1| Gene info hypothetical protein CNJ01520 [Cryptococcus neoformans var. neoformans
ref|XP_773201.1| Gene info hypothetical protein CNBJ1950 [Cryptococcus neoformans var. neoformans
gb|EAL18554.1| Gene info hypothetical protein CNBJ1950 [Cryptococcus neoformans var. neoformans
gb|AAW45815.1| Gene info hypothetical protein CNJ01520 [Cryptococcus neoformans var. neoformans

GENE ID: 3254188 CNJ01520 | hypothetical protein
[Cryptococcus neoformans var. neoformans JEC21] (10 or fewer PubMed links)

Score = 26.1 bits (54), Expect = 340
Identities = 8/9 (88%), Positives = 8/9 (88%), Gaps = 0/9 (0%)

Sbjct 415 SARQHPALI 423

>ref|YP_001626035.1| Gene info citrate synthase [Renibacterium salmoninarum ATCC 33209]
gb|ABY24621.1| Gene info citrate synthase [Renibacterium salmoninarum ATCC 33209]

GENE ID: 5822379 RSal33209_2898 | citrate synthase
[Renibacterium salmoninarum ATCC 33209]

Score = 25.7 bits (53), Expect = 456
Identities = 9/11 (81%), Positives = 9/11 (81%), Gaps = 2/11 (18%)

Query 1 SARAHP--ALI 9
Sbjct 218 SARAHPYAALI 228

>ref|YP_001817256.1| Gene info integral membrane sensor hybrid histidine kinase [Opitutus terrae
gb|ACB73656.1| Gene info integral membrane sensor hybrid histidine kinase [Opitutus terrae

GENE ID: 6208547 Oter_0366 | integral membrane sensor hybrid histidine kinase
[Opitutus terrae PB90-1]

Score = 25.2 bits (52), Expect = 611
Identities = 7/7 (100%), Positives = 7/7 (100%), Gaps = 0/7 (0%)

Query 3 RAHPALI 9
Sbjct 256 RAHPALI 262

>ref|YP_001757871.1| Gene info putative anti-sigma regulatory factor, serine/threonine protein
kinase [Methylobacterium radiotolerans JCM 2831]
gb|ACB27188.1| Gene info putative anti-sigma regulatory factor, serine/threonine protein
kinase [Methylobacterium radiotolerans JCM 2831]

GENE ID: 6141303 Mrad2831_5232 | putative anti-sigma regulatory factor,
serine/threonine protein kinase [Methylobacterium radiotolerans JCM 2831]

Score = 25.2 bits (52), Expect = 611
Identities = 7/8 (87%), Positives = 8/8 (100%), Gaps = 0/8 (0%)

Query 2 ARAHPALI 9
Sbjct 299 ARAHPALV 306

>ref|ZP_01466013.1| hydrolase, TatD family [Stigmatella aurantiaca DW4/3-1]
gb|EAU63211.1| hydrolase, TatD family [Stigmatella aurantiaca DW4/3-1]

Score = 25.2 bits (52), Expect = 611
Identities = 7/7 (100%), Positives = 7/7 (100%), Gaps = 0/7 (0%)

Query 3 RAHPALI 9
Sbjct 79 RAHPALI 85

>ref|YP_001558323.1| Gene info glycosyl transferase group 1 [Clostridium phytofermentans ISDg]
gb|ABX41584.1| Gene info glycosyl transferase group 1 [Clostridium phytofermentans ISDg]

GENE ID: 5743305 Cphy_1206 | glycosyl transferase group 1
[Clostridium phytofermentans ISDg]

Score = 25.2 bits (52), Expect = 611
Identities = 8/10 (80%), Positives = 8/10 (80%), Gaps = 0/10 (0%)


Sbjct 113 SERAHPLLIN 122

There does not appear to be a perfect match in the NCBI NR protein database. But take a close look at the #1 scoring hit. That is right, it is from and organism called Botryotinia fuckeliana. No comment on the appropriateness of this name, but it does contain a term I will probably use a lot if she gets elected.

Of course, anybody who has heard me blather on and on about evolution knows that I am always talking about how blast top hits are not a good measure of relatedness per se (see my NAR paper where I first talked about this in 1995). So - I decided to build a tree of Sarah Palin. I used the NCBI Distance Tree option which you can do from blast searches.

Since most likely you cannot see that in enough detail - here is a zoom in.

That one did not come through on the Blog so well either so I decided to output the tree in Newick format and then I searched for a program that could draw a better figure on the web (we have tools in my lab to do this but I am trying to do this all on the web as an exercise). And I found a web site that makes drawtree available. And I plugged in the Newick format and it made a nicer one.

Though making trees from really short sequences is not ideal, in this tree, Sarah Palin is shown to be at the root of a branch including a protein from the parasitic nematode Brugia malayi. So if we take an evolutionary interpretation it seems that this causative agent of filariasis (well, a protein from this agent) is descended from SarahPalin. In other words, she seems to be ancestral to this parasite.

So in conclusion - by similarity - SarahPalin is closest to a plant pathogen with an unusual name. And by phylogeny SarahPalin is ancestral to a parasitic nematode. Sounds about right.

Friday, September 05, 2008

Science Faux Pas Example #2: V = MA

OK.  This is far and away my favorite Science Faux Pas I have seen.  I cut this out of some magazine many years ago and posted it on my door in college, grad. school and in my previous job, so it is a little beat up.  But you got to hand it to Mathey-Tissot - promoting a precision watch with "Velocity equals mass x acceleration (V = MA)." Must be one heck of an interesting mechanism inside that watch. 

Thursday, September 04, 2008

Science Faux Pas Example #1: 97% of internet users have internet access

I am starting a new series here on Science Faux Pas.  Here is one of my favorites from Nature a while back.  They report in this promotion that 97% of Nature's readers have internet access.  How did they determine this? By an online readers survey.  The real question is - who are the 3% that completed the survey but said they did not have internet access?

I am going to try and make a collection of these over time so if you have any or can point to some out there please let me know.  It may not be as fun as Carl Zimmer's tattoo series, but there are some doozies out there.

Help save the world and get $100,000 seed grant to do it

Just got this email and thought I would share since it does relate to some of the themes of my blog. I note that the Gates Foundation is VERY supportive of Open Access publishing as one of their previous grants helped support the journal "PLoS Neglected Tropical Diseases." I am hoping that at some point the Gatges Foundation will require OA publishing for all of the projects they fund.
The Bill & Melinda Gates Foundation is now accepting grant proposals for Round 2 of Grand Challenges Explorations, a US$100 million initiative to encourage unconventional global health solutions.

Based on your feedback, we have made changes for Round 2 of Grand Challenges Explorations. We modified the topics from Round 1 and added two additional topics. We will no longer require applicants to register for a topic in advance of submitting their proposals. We also updated the application form in response to feedback from the initial round.

Grant proposals are being accepted online at http://www.gcgh.org/explorations until November 2, 2008, on the following topics:

New! -- Create new vaccines for diarrhea, HIV, malaria, pneumonia, and tuberculosis
New! -- Create new tools to accelerate the eradication of malaria
-- Create new ways to protect against infectious diseases
-- Create drugs or delivery systems that limit the emergence of resistance
-- Create new ways to prevent or cure HIV infection
-- Explore the basis for latency in tuberculosis

Initial grants will be $100,000 each, and projects showing promise will have the opportunity to receive additional funding of $1 million or more. Full descriptions of the new topics and application instructions are available at http://www.gcgh.org/explorations.

We are looking forward to receiving innovative ideas from scientists around the world and from all scientific disciplines. Anyone can apply, regardless of education or experience level. If you don't submit a proposal yourself, we hope you will forward this message to someone else who might be interested.

Thank you for your commitment to solving the world's greatest health challenges.

Wednesday, September 03, 2008

Monday, September 01, 2008

Cool Plant Comparative Genomics Resource: Phytozome

I spent the last few days at a "retreat" for the Joint Genome Institute and heard about a few things there worth sharing with everyone. I will try and post about some of them in the next few days. Here is one. The JGI and the Center for Integrative Genomics have made a pretty cool tool for comparative analyses of plant genomes. It is called Phytozome and has a variety of simple and nice features. JGI is doing more and more work on plant genomes as part of their energy research and I think Phytozome could turn into a good place to go to get the latest plant genome information. Go to http://www.phytozome.net to see the real thing.

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