Tuesday, September 30, 2008
Congrats to Gary Andersen, Developer of the Phylochip, for Getting a WSJ Technology Award
Joe Derisi and Open Science featured on Voice of America
Monday, September 29, 2008
Humorous sciency signs #2: Squirrel liberation front
Wanted - Evolutionary Genomicist at UCSB
Science Faux Pas #4: Nature wishes their dog ate this advertisement
Sunday, September 28, 2008
Saturday, September 27, 2008
$ 700 billion will buy a lot of taq, LB, submarines, and other things
- 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)
Humorous sciency signs #1: Please do not molest the spawning salmon
Davis Outdoor Art
Thursday, September 25, 2008
Drew Endy talking at Davis tomorrow ....
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:
Edge: ENGINEERING BIOLOGY: A Talk with Drew Endy
Wired 13.01: Life, Reinvented
IT Conversations | O'Reilly Media Open Source Conference | Drew Endy
YouTube - iGEM - Drew Endy Defining Synthetic Biology (video)
Synthetic Biology Debate with Drew Endy and Jim Thomas at Fort ...
MIT World » : The Implications of Synthetic Biology
Seedmagazine.com | MIND08 | Drew Endy: Synthetic Biology
Funny Davis Signs #1
signs. This is one of my favorites.
MapMyRun for Davis is a nice way to find new places to explore in town
Wednesday, September 24, 2008
Lance Armstrong Coming to Davis for the Tour of California
Tuesday, September 23, 2008
Much ado about plants and blogs in PLoS Biology
- Control of Jasmonate Biosynthesis and Senescence by miR319 Targets
- Rice XB15, a Protein Phosphatase 2C, Negatively Regulates Cell Death and XA21-Mediated Innate Immunity (note - by my friend and colleague and fellow blogger Pam Ronald)
- A Mutual Support Mechanism through Intercellular Movement of CAPRICE and GLABRA3 Can Pattern the Arabidopsis Root Epidermis
- A Morning-Specific Phytohormone Gene Expression Program underlying Rhythmic Plant Growth
- Advancing Science through Conversations: Bridging the Gap between Blogs and the Academy
What does privacy mean to you? Please complete this survey
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.
and
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
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:
http://www.biomedcentral.com/1471-2105/9/386/abstract
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
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
"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
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
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
-------------------------------------------------
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)
Sunday, September 14, 2008
It's Miller Time - Lake Arrowhead Microbial Genomes Conference -- about to begin
University of California, Los Angeles, CA
“Non-fermentative Pathways for Synthesis of Branched-Chain Higher Alcohols as Biofuels”
University of California, Davis, CA
“A Genomic Encyclopedia of Bacteria and Archaea”
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”
The Scripps Research Institute, La Jolla, CA
“Metabolomics Reveals Large Effect of Gut Microflora on Biochemistry and Activation of a Host Response”
DOE Joint Genomme Institute, Walnut Creek, CA
"Microbial Sequencing for Biofuels Applications"
University of Delaware, Newark, DE
“Making sense of the chaff: What will metagenomic approaches tell us about viral ecology?
University of Florida, Gainesville, FL
“Making Sense of Genomes: Linking Gene and Function by Comparative Genomics”
The Scripps Research Institute, La Jolla, CA
“High Throughput Mass Spectrometry Based Metabolomic and Enzymatic Assays for Functional Genomics”
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”
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”
University of California, Los Angeles, CA
“Diversity-Generating Retroelements”
Steven A. Benner
Foundation for Applied Molecular Evolution, Gainesville, FL
“Molecular Paleoscience”
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”
Harvard Medical School, Boston, MA
“Bacillus subtilis Biofilm Diversity”
University of Washington, Seattle, WA
“Coupling Function to Phylogeny via Single-Cell Phenotyping”
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“
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”
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.”
University of California, Los Angeles, CA
“Integrating Discovery-based Undergraduate Research Experiences into UCLA Courses Using a Collaborative Curriculum Model”
DOE Joint Genome Institute, Walnut Creek, CA
“The JGI Microbial Genome Annotation Program”
University of Wisconsin, Madison, Wisconsin
“Insights from the Genomes of Commonly Used Lab Strains”
Wageningen University, Wageningen, The Netherlands
“Reinventing the Petri Dish: Miniaturized Tools for High Throughput Microbial Culture”
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”
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”
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"
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 dialogueIt 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"
Wednesday, September 10, 2008
Follow up to Amy Harmon's NY Times Story on Evolution
Tuesday, September 09, 2008
Open Access Pioneer Award #3: Joe Derisi
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
Behind the Lens by Karin Higgins
Arts and humanities
- The Huffington Post — Bob Ostertag:
- Ecology Without Nature: by Timothy Morton,
- The Pull of Gravity: by Julie Wyman
Business and law
- Anupam Chander:
- Harga-Blog: by Andrew Hargadon,
- ImmigrationProf Blog: A blog edited by Kevin Johnson,
Science and agriculture
- Tomorrow's Table: by Pam Ronald,
- The Tree of Life: by Jonathan Eisen
- ANR News Blog:A agricultural news commentary from the UC Division of Agriculture and Natural Resources
- Bug Squad: by Kathy Keatley Garvey,
Social science
- Beyond Homophobia: by Gregory Herek,
- The Edge of the American West: A team blog including UC Davis history professors Ari Kelman and Eric Rauchway
- Eric Rauchway’s blog: by Eric Rauchway
Darwin on the Wall
Predicting the future (for molluscs)
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
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| hypothetical protein BC1G_16161 [Botryotinia fuckeliana B05.10]
gb|EDN25226.1| predicted protein [Botryotinia fuckeliana B05.10]
Length=383
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%)
Query 1 SARAHPALI 9
SARA PALI
Sbjct 209 SARAQPALI 217
>ref|YP_061725.1| homoserine dehydrogenase [Leifsonia xyli subsp. xyli str. CTCB07]
gb|AAT88620.1| homoserine dehydrogenase [Leifsonia xyli subsp. xyli str. CTCB07]
Length=451
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%)
Query 1 SARAHPALI 9
SAR HPALI
Sbjct 267 SARVHPALI 275
>ref|ZP_02031476.1| hypothetical protein PARMER_01474 [Parabacteroides merdae ATCC
43184]
gb|EDN87136.1| hypothetical protein PARMER_01474 [Parabacteroides merdae ATCC
43184]
Length=299
Score = 26.1 bits (54), Expect = 340
Identities = 7/8 (87%), Positives = 8/8 (100%), Gaps = 0/8 (0%)
Query 3 RAHPALIN 10
RAHPAL+N
Sbjct 170 RAHPALVN 177
>ref|XP_567332.1| hypothetical protein CNJ01520 [Cryptococcus neoformans var. neoformans
JEC21]
ref|XP_773201.1| hypothetical protein CNBJ1950 [Cryptococcus neoformans var. neoformans
B-3501A]
gb|EAL18554.1| hypothetical protein CNBJ1950 [Cryptococcus neoformans var. neoformans
B-3501A]
gb|AAW45815.1| hypothetical protein CNJ01520 [Cryptococcus neoformans var. neoformans
JEC21]
Length=437
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%)
Query 1 SARAHPALI 9
SAR HPALI
Sbjct 415 SARQHPALI 423
>ref|YP_001626035.1| citrate synthase [Renibacterium salmoninarum ATCC 33209]
gb|ABY24621.1| citrate synthase [Renibacterium salmoninarum ATCC 33209]
Length=386
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
SARAHP ALI
Sbjct 218 SARAHPYAALI 228
>ref|YP_001817256.1| integral membrane sensor hybrid histidine kinase [Opitutus terrae
PB90-1]
gb|ACB73656.1| integral membrane sensor hybrid histidine kinase [Opitutus terrae
PB90-1]
Length=936
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
RAHPALI
Sbjct 256 RAHPALI 262
>ref|YP_001757871.1| putative anti-sigma regulatory factor, serine/threonine protein
kinase [Methylobacterium radiotolerans JCM 2831]
gb|ACB27188.1| putative anti-sigma regulatory factor, serine/threonine protein
kinase [Methylobacterium radiotolerans JCM 2831]
Length=331
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
ARAHPAL+
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]
Length=209
Score = 25.2 bits (52), Expect = 611
Identities = 7/7 (100%), Positives = 7/7 (100%), Gaps = 0/7 (0%)
Query 3 RAHPALI 9
RAHPALI
Sbjct 79 RAHPALI 85
>ref|YP_001558323.1| glycosyl transferase group 1 [Clostridium phytofermentans ISDg]
gb|ABX41584.1| glycosyl transferase group 1 [Clostridium phytofermentans ISDg]
Length=357
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%)
Query 1 SARAHPALIN 10
S RAHP LIN
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
Help save the world and get $100,000 seed grant to do it
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
Quick Post - Spore Sounds Cool
Monday, September 01, 2008
Cool Plant Comparative Genomics Resource: Phytozome
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