Tuesday, July 31, 2012

My Tree of Life doodle on our food container from dinner at Seasons in #DavisCa


William Shatner, Mars, Curiosity, Rover ... fun fun fun

William Shatner narrates video detailing how Curiosity will land on Mars next week Hat tip to Dawn Sumner, UC Davis Geology professor working on Curiosity mission, for pointing me to this. Don't like that? Well, here is a narration by Wil Wheaton

Posts from #microBEnet that may be of interest

Quick post here - posting links to recent blog posts on the microBEnet blog that may be of interest here.  The microBEnet blog is part of the microBEnet project that I run on microbiology of the built environment.

Sunday, July 29, 2012

Saturday, July 28, 2012

Not a #badomics word but - "Evolutionary Systems Biology" is - well - pretty complex

Just saw the title of this article Evolutionary Systems Biology: Historical and Philosophical Perspectives on an Emerging Synthesis by Maureen A. O’Malley in Advances in Experimental Medicine and Biology, 2012, Volume 751, 1-28, DOI: 10.1007/978-1-4614-3567-9_1.  And my first thought was "Hmmm - WTF is Evolutionary Systems Biology".  Given that I am still unsure what Systems Biology is exactly I figured - this could be a doozy.  Thus I perused the abstract:

According to the abstract
Systems biology (SB) is at least a decade old now and maturing rapidly. A more recent field, evolutionary systems biology (ESB), is in the process of further developing system-level approaches through the expansion of their explanatory and potentially predictive scope. This chapter will outline the varieties of ESB existing today by tracing the diverse roots and fusions that make up this integrative project. My approach is philosophical and historical. As well as examining the recent origins of ESB, I will reflect on its central features and the different clusters of research it comprises. In its broadest interpretation, ESB consists of five overlapping approaches: comparative and correlational ESB; network architecture ESB; network property ESB; population genetics ESB; and finally, standard evolutionary questions answered with SB methods. After outlining each approach with examples, I will examine some strong general claims about ESB, particularly that it can be viewed as the next step toward a fuller modern synthesis of evolutionary biology (EB), and that it is also the way forward for evolutionary and systems medicine. I will conclude with a discussion of whether the emerging field of ESB has the capacity to combine an even broader scope of research aims and efforts than it presently does.
I am not sure what to say here.  The author has published some interesting work previously on philosophical issues in biology.   But from the abstract - well - I am pretty lost.  It seems that ESB covers a lot of ground.  First - systems biology - whatever it means -  itself is pretty broad.  And then on top of that, ESB apparently covers even more than SB.  Still not sure what ESB is --- I am torn about whether it could be interesting or completely flaky.  I am (as many know) a big fan of adding evolutionary approaches to just about any area of biology.  So that alone makes me think about reading the paper to see whether there is any there there.  But alas, I do not have access, so I am going to have to move on to something else.

Some comments from the web on this paper

Future of the human microbiome project (HMP) at NIH?

Just got this question by email
"Dear Professor Eisen, I wonder if you can shed any light on the question whether the Human Microbiome Project will be renewed or if it is being discontinued at NIH. I happened to thumb through (on a Kindle) the 2013 proposed budget for the NIH Common Fund to find to my astonishment that the HMP -- which had been lionized in June and July in issues of Nature and Science and PLoS --- has been apparently zeroed out. The Budget narrative states bleakly: "The FY 2013 President’s Budget request of $1.207 million for HMP represents a decrease of $22.531 million, or 94.92 percent less than the FY 2012 level. The estimated decrease in funding reflects the planned FY 2012 conclusion of all but one of the awards. This award had a late start, and therefore will continue into FY 2013. There is a possibility of supporting a second phase of the HMP program, pending an analysis of current needs." If you go on the HMP website, you will see that all the program RFPs have been archived under the statement "There are no funding opportunities at this time." (See http://commonfund.nih.gov/hmp/grants.aspx). I am an avid follower of your Tree of life Blog. Thank you for running it. I imagine other readers might also be interested in what is going on with respect to the HMP budget. "
Interesting question.  Here is what I know which is very limited.

  • The NIH Human Microbiome Project was funded as a "Roadmap" initiative.  
    • "The Human Microbiome Project is part of the NIH Roadmap for Medical Research. The Roadmap is a series of initiatives designed to pursue major opportunities and gaps in biomedical research that no single NIH institute could tackle alone, but which the agency as a whole can address to make the biggest impact possible on the progress of medical research. Additional information about the NIH Roadmap can be found at www.nihroadmap.nih.gov."
    • It was a five year program, starting in 2007 and ending in 2012. 
  • The full details of the 2013 NIH budget request are here
  • In 2013 testimony by NIH at congress the HMP is discussed
    • "One fascinating area of basic research is the Human Microbiome Project, an initiative supported through the NIH Common Fund. This project is giving us wonderful insights into the sweeping range of bacteria that live on and in each of us, and is expanding our knowledge about the role of these microbial communities in health and disease. Recent scientific evidence suggests that changes in the composition and activity of the human microbiome may contribute to obesity, which may provide us with new ways of addressing this serious threat to our nation’s health."
I have heard discussions about how NIH might try to do another round of funding for the HMP but I do not know where this stands.  If anyone out there knows anything else -- please post.

Best #human #microbiome item of week: #MinaBissellToo #Cancer #TED

From Science Friday.
My wife just told me about a fascinating Science Friday episode that I missed today: Building Organs, On One Microchip At A Time : NPR.  The discussion was with Dr. Donald Ingber from Harvard who has been designing mock organ systems with microchips.

Of particular relevance to microbiome studies are the following sections
"One example was that we put human intestinal cells that have been studied and cultured for years, and the pharmaceutical companies actually use them for looking at absorption in dishes, but everybody knows they're not very good. They don't really mimic gut function. When we put them in our chip and when we give them peristaltic-like undulating stretching rhythmically and we trickle flow over them like in your gut, they start forming villi, which are like the finger-like projections that increase surface area for absorption in your intestine. 
And what really surprised me is that the proliferative cells, the cells that are dividing rapidly, are in the crypt, the bottom - like between your fingers, at the bottom of these fingers, which is exactly like in your intestine. Plus, they put out mucus on the top of it, which protects it, and now we can put microbes on top. If you put microbes - if you put bacteria on cells in a dish, we call it contamination, and you have to throw it out and sterilize it. But we put microbes on the top and they're perfectly happy. They're symbiotic. And this is important because - and I don't know if your show highlighted it, but over the last few months there's been a lot of news that the microbiome - the microorganisms that live in our body can be very important for various diseases. And so we now have ways to study that. And the microbiome in the human is different than the mouse. And so this is very exciting for new opportunities."

And then later
And I think other groups are looking at, you know, viral infections, for example. With our gut-on-a-chip, we're hoping to study Crohn's disease. Where it's known in Crohn's disease, there are three major contributors. One is inflammation, and we could add white blood cells, for example. The other is the microbiome, the microbes living in the gut. The other is peristaltic-like motions - again, mechanics. And so we can control all three of those.
Now I am sure there is some excessive enthusiasm for the power of their chip system here.  But it is fascinating and certainly will have many uses for testing models of function of host-microbe interacting systems.

The part I find most fascinating has nothing per se to do with the gut - what is most interesting is the concept that mechanical forces are fundamentally important to cell and organ function, development and regulation.  Here is one portion of what Ingber said:
We, you know, we actually - I've worked for 35 years in a strange - from a strange perspective in biology in that I've been - I was convinced that mechanical forces, that the forces due to breathing-like motions and stretching, you know, your muscles and the pulsations of blood through your vessels, that the stretching and the relaxing, the mechanical stresses are as important for regulating cell and tissue function as chemicals in genes. This is now getting more accepted in biology, but because of that, I felt that we had to create microenvironments that could mimic that - we had to develop microchips that can mimic that microenvironment. And what we 're finding consistently is that cells that people used before that they didn't think were very good are now recapitulating organ-like functions. 
And as I said at a meeting yesterday, you know, there are no bad cells, just like there are no bad kids. There are bad families. There are bad neighborhoods and so forth. But - and so you have to give it the right microenvironment. We've also - I guess another surprising thing in the lung - and this was surprising - is that not only did we mimic complex functions such as the entire inflammatory response if we put a bacteria in the airspace in our little breathing lung on a chip, we saw in human, white blood cells stick to the vessel migrate across and engulf them. And that is something we hope for. 
But when we started to do things like we looked at toxicities of airborne particulates like in smog, we found that they were absorbed across the airspace to the vessel, which was great, but we found that breathing motions, physiological breathing motions increase the efficiency of that by tenfold. Now that no one's even thought of before, nor have I. And so that was a prediction. And then we went back to animal models where we could control ventilation and we found exactly the same thing.

I have been thinking a lot about mechanical focuses and biology recently - especially since Mina Bissell came to visit UC Davis last year.  I wrote about her visit here: Mina Bissell, another of my science heroes, returns to #UCDavis (and also about her last visit before that here --- The Tree of Life: A eureka moment - but not of the good kind).  Mina has been focused on how mechanical forces are critical to cancer development.  The best way to learn about Mina's obsession is to watch one of her talks such as one that was recently posted at TED.

In the era of genomics and other ones the importance of mechanical forces and local environment has been ignored by many.  But it shouldn't be.  When I was a graduate student at Stanford, one professor there - Paul Green - was completely obsessed by mechanical forces and their effects of biological systems.  Sadly - Paul - who was an amazing teacher and person - died of pancreatic cancer just as I was finishing my PhD.  But every time I see something about mechanical forces I think of him and I think he would have really enjoyed this Science Friday as well as Bissell's work.

Thursday, July 26, 2012

Good morning to my Twitter SPAM followers - is Twitter even trying to stop this?

Here are some of my SPAM followers from this morning ... again ... all pointing to blog.livedoor.jp addresses.  Twitter still does not seem willing or able to do anything about this.  Annoying.

I and others have written about this extensively and still no response or action from Twitter.

Sunday, July 22, 2012

MoreCite Feed from my Google Citations Page

Just got an email from someone at MoreCite.com describing a simple widget they have made to display information from one's Google Citation page. So I took the bait .. and two minutes later I have a feed: This is not an endorsement of MoreCite.Com. I know very little of what they are about. But I like the little widget ...

For those interested ... storification of twitter discussion criticizing NY Times article on Venter cell model

Storification is here and below.

#UCDavis neurosurgeons conducted experimental surgery w/o IRB approval

Not really sure what to say about this other than that this story should be read by many/all who are interested in medical research and/or UC Davis: 2 UC Davis neurosurgeons accused of experimental surgery are banned from human research - Investigations - The Sacramento Bee.

UPDATE 7/23.  Added a summary: Two UC Davis neurosurgeons were treating terminally ill brain cancer patients with an unapproved, experimental treatment that is referred to as "Probiotic Intracranial Therapy for Malignant Glioma".  The treatment involved purposefully infecting patients brains with a bacterium Enterobacter aerogenes apparently because of prior anecdotes and case reports that suggested that patients with these brain cancers who also had brain infections might live longer than those with the cancer but without the infection.  According to the article, there was an investigation at UC Davis into the practices of the surgeons.  It was determined by UC Davis that they did not have IRB approval to carry out the treatments and that there were some other issues with the practice going on.  At the conclusion of the investigation UC Davis wrote a letter to the FDA detailing the case and has banned the two neurosurgeons from performing medical research on humans.  Read the article for much more detail and see the link below.

Many interconnected issues in here involving IRB approval, human experimental treatments and informed consent, UC Davis, and even "probiotics".  Still taking it all in ...  Uggh ...

Other stories posted in the SacBee at the same time:
See also

Saturday, July 21, 2012

"Life on Man" - amazing book on human associated microbes

Just got this book by Theodor Rosebury in the mail: The Tree of Life Store - Life on Man.

I ordered it a few days ago after someone named Richard Montgomery posted a comment about it in relation to my "Human microbiome" talk that is posted at TED.

Just starting the book but it is awesome so far.  Definitely worth trying to get a copy.  Though it is out of print, I found many copies online ...

Friday, July 20, 2012

Twitter seems to have lost complete control of some spam

Aaarrrrggg ... this is driving me crazy.  For over a month now I have been seeing 10-20-30 or more new followers a day on Twitter that are some sort of SPAM.

For example, a few minutes ago I looked at my most recent followers:

And when I look at them in more detail I see many of them are simply posting links to some SPAMMY sites at the domain "blog.livedoor.jp".  For example


and many many many many more.  They are all like this with links to some spammy site at blog.livedoor.jp.  It is so easy to identify these ... but it is a pain.  Why can't Twitter get a handle on this?   I mark them as SPAM - day after day after day.  And more come. Uggh.

Monday, July 16, 2012

My "human associated microbes" talk now available on TED site (w/ transcripts too).

My TedMed talk is now on Ted.Com. See below. Some interesting comments too - have been trying to respond to most -- even the unusual ones.

Plus there is now a transcript available in English and German. And the transcripts are hot linked to the portions of the video ...

Thanks to Tedmed for allowing this and to TED to posting the talk.  Plus the folks at TED re-edited the talk and added some more camera angles for the part where I tossed giant stuffed microbes into the crowd ...

Sunday, July 15, 2012

Three talks, 1.5 days at #ISMB ... phylogeny, phylogenomics, open science and more

Gave three talks in 1.5 days here in Long Beach as part of the satellite meetings associated with the "Intelligent Systems for Molecular Biology" (ISMB) 2012 Conference. I will write more about the meeting and the craziness of giving three very different talks in 1.5 days. But for now I wanted to at least get my talks posted here since I posted the slides to slideshare and recorded the audio in synch with the slides and posted these "slideshows" to YouTube. Here are the talks below:

Talk 1 for the "Bioinformatics Open Source Conference" BOSC2012.  Was asked to talk about Open Science ... so ... I did ...

Slideshow with audio:

Talk 2 for the Student Council Symposium SCS2012. Sort of supposed to be a career guidance discussion so I geared my talk on the lines of "lessons learned" ...

Slideshow with audio:

Talk 3 for the "Automated function prediction" AFP2012 satellite meeting.  I decided to talk about phylogenetic and phylogenomics approaches to functional prediction ...

Slideshow with audio:

Friday, July 13, 2012

My new paper in #Gigascience: #Badomics words and the power and peril of the ome-meme

I have a new paper in the new Open Access journal Gigascience:  GigaScience | Full text | Badomics words and the power and peril of the ome-meme.  It is basically a text version of my obsession with #badomics words.

It was inspired by a paper also in this first issue of Gigascience The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome by Daniel McDonald, Jose C Clemente, Justin Kuczynski, Jai Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle, Folker Meyer, Rob Knight, and J Caporaso.

For more on my obsession with badomics words see some of these earlier posts:

Thursday, July 12, 2012

Posted to Twitter, FB, etc but had to post to blog too: best genomics Venn Diagram ever

Words do not do this justice.  This is just stunning.
From here.

Ref: "The banana (Musa acuminata) genome and the evolution of monocotyledonous plants" Nature 2012 doi:10.1038/nature11241

Also see this Storify.

Wednesday, July 11, 2012

Lake Arrowhead Microbial Genomes 2012 #Genomes #Microbes #Mountains #Lake #Fun #Wine #MustGo

Helping the organizers plan the Lake Arrowhead Microbial Genomes meeting this year (see Microbial Genomics - ARROWHEAD 2012).  In particular I organized a session on Microbiology of the Built Environment relating to the http://microbe.net project.

This session should be good

  • Session Chair: Jonathan Eisen – University of California, Davis, CA “Alfred P. Sloan Foundation Workshop”
  • Anne M. Womack – University of Oregon, Eugene, OR “Microbial Ecology of the Built Environment”
  • Jason E. Stajich – University of California, Riverside, CA “Fungi in the Built Environment”
  • Laura Sauder – University of Waterloo, Waterloo, Ontario “Archaea in the Built Environment”
  • Scott Kelley – San Diego State University, San Diego, CA “The Indoor Microbiome: Bacterial and Metagenomic Approaches for Studying the Built Environment”
  • Susanna Remold – University of Louisville, Louisville, KY “Pseudomonas as a Model for Studies of Microbes in the Home”
And the other sessions that the meeting also look good (see program here).  But whatever you think of the speaker list, the best part of the Lake Arrowhead meetings is the venue and the interactions among people.  I have been going to this meeting for many years and here are some posts of mine about previous meetings

Monday, July 09, 2012

Can food safety be fun? Not sure, but this video is OK. #microbes

Continuing with my running theme of microbe-related music videos here is another one. It has good and bad parts. But then again, don't we all ...

Google/ Blogger "Dynamic Views" - Fancy but limited

So - I keep switching back and forth between the current view on my blog and Google's "Dynamic Views" system.  Right now I am annoyed with the Dynamic Views so switched it off.

To see Dynamic Views check out

Each has its benefits but the whole Dynamic Views system is incompatible with many things I would like to do with my blog - examples include embedding Storify stories (the embeds don't work in dynamic views); jump breaks (to show only the beginning of a story with a species transition point); and much more. 

So - anyway - apologies for switching back and forth.  Still playing with what to have as a default ...

Visit to Capitol Public Radio HQ & appearance on "Insight" w/ @CapRadioRuyak

Just got back from a brief visit to Sacramento (which is 15 minutes or so my where I live in Davis, CA). I had a mini 10 minute or so appearance on "Insight" a radio show on Capitol Public Radio.

My visit all started maybe a few weeks ago when I bumped into Lin Weaver in Davis.  Lin was showing some friends of hers around Davis and we chatted for a while on the sidewalk.  One of the topics was my recent fun giving a Tedmed talk.

Anyway - we chatted for 15-20 minutes or so and then I headed home.  And a few days later I got an email from Lin inviting me to be a guest on Insight.  Cool.  I love the show - and listen to it whenever I can.  So I said I had to check some details and then got back to her later and said "yes."

Lin and the folks at Capitol Public Radio then sent me some additional details and asked for some links to use for their website.

And this AM I headed on in to town.  I was asked to get to their studio at 9:45 AM.  Their studio is on the campus of Sacramento State and I headed on in early and got their at about 9:30.  Of course - I took some pics and posted some stuff to twitter ...

Sunday, July 08, 2012

Extra fruit in your trees? Don't let it rot - donate it #DavisCA #VillageHarvest

Today, one of our neighbor came over and told us that the "Village Harvest" group was at their house to collect fruit from their trees and she wanted to know if they could come into our yard as part of the collection.  I said "please ... and tell them they can collect from our tree too."  You see, we have a pluot tree that produces more fruit than I can keep up with (and I note - we get a lot of the pluots from our neighbors tree too since it leans over our yard).  I have made 40+ jars of jam, 40+ fruit rolls, froze a bunch of pulp for later projects and still there was more fruit.  So I invited people over to collect some of the pluots and still there was more fruit.  So I was very happy to see the Village Harvest folks next door.  

Village Harvest is a " a nonprofit volunteer organization in the greater San Francisco Bay Area which harvests fruit from backyards and small orchards, then passes it along to local food agencies to feed the hungry."

And they have a Davis chapter: http://www.villageharvest.org/davis/

And so they came over and started collecting some of the pluots and I took some pictures and video of the event ...


Definitely going to sign up for this for all cases when we can't use all of our fruit ...

Possibly new (not sure) connection between colic and Helicobacter pylori infections

Interesting article: JAMA Network | Archives of Pediatrics & Adolescent Medicine | Helicobacter pylori and Infantile Colic.  The study basically suggests that infants with colic have a much higher incidence of Helicobacter pylori infections than do a control group of infants.  No causal relationship was established - just a correlation.

The article has been picked up by a few bloggers/news sources such as:
I was surprised that this was suggested to be a completely new connection - between HP and colic.  Given the amount of work on HP this just seemed odd.  So of course I decided to snoop around the web.  And I found a few things that were related especially:
So it seems that others have noticed a possible connection between HP and colic previously.  But in the end there is not a lot of literature out there on the topic.   If anyone out there knows anything else on this topic, please post ...

Saturday, July 07, 2012

Fungal parasite of caterpillars is source of "Himalayan viagra"

Photo by Nicolas Merky

Wow - never heard of this fungus before reading this CNN piece: 'Himalayan Viagra' taking its toll on Nepal - CNN.com. The fungus infects caterpillars (larva of a ghost moth) in the Himalayas and kills them. And the fungal coated dead caterpillars are, alas, considered to have multiple uses in various traditional Chinese medicine practices. One of the uses is as an aphrodisiac and thus these have become known as "Himalayan viagra".

The fungus that does this is Ophiocordyceps sinensis - (it is an Ascomycota).  Not a huge literature out there if you search just for this species name but thanks to Wikipedia I found out there are some synonyms so if you search Pubmed for all the names one gets 328 papers and 56 of these have free full text including a few that seem quite useful:
So - seems that what happens here is the fungus infects larva and then kills them and then a fruiting body grows out of the caterpillars head ... fun.

Snooping around led to some other news stories about this system including many that came out recently
Anyway - seems like this would be a fun organism for genome sequencing ... 

Microbial music: Christine Lavin and the Amoeba Hop

Always searching for science-art-music combinations.  Especially ones that focus on some aspect of science I work on, like microbes. And, well, though this recording is less than ideal, and you need to wait a minute and a half or so, once you get to the song it is worth it.

The song is "The Amoeba Hop" and the singer is the brilliant Christine Lavin.

I have had this song in my head on and off for years and wanted to post about it for a while.  I finally remembered to Google it tonight after reading a tweet about combining music and biology.  I used to listen to Lavin all the time in college and even went to a show of hers in 1989 in Ft. Collins, CO with my brother and my friend Saul Jacobson.  As a side note - we saw Lavin at some music hall type of place the the night after seeing Killdozer at a VFW post.  As a second side note - the Killdozer show was crazy (and I even found someone else who wrote about it here).

Anyway - not only did I find the video posted above but I discovered she wrote a book in 2002 based on the song - and the book even got a review in the New York Times.   Gonna probably have to get that book at some point ...

Thursday, July 05, 2012

A #microbe by any other name would smell as sweat?

Love the them of this post and what may be a series of posts on smells of microbes: Which Bacteria Smell Like Tortillas, Flowers, or Delicious Browned Butter? | Discoblog | Discover Magazine

Looking forward to smelling/reading more from Veronica Greenwood on this topic.  For other stuff on smells of microbes see:
and much more ...

Oh - and yes, the "sweat" not "sweet" in the title is on purpose ...

If the International Whaling Commission really wanted to improve cetacean-science it could require openness rather than allowing whaling

There is a bit of a kerfuffle going on over South Korea announcing plans to increase whaling for "scientific reasons."

See for example: Grist: South Korea may start hunting whales again, for ‘science’ and CNN: South Korea says it may resume whaling, angering environment groups' and WSJ South Korea Whaling Plan Sparks Outcry

This seems to me to be pretty cut and dry.  The Korean's do not seem to be truly interested in the science here.  And I note - nor does the "International Whaling Commission": Commission information.  If they really wanted to expand the scientific study of whales they would do things like foster sharing of samples, collaboration across groups, open access to data and resources, and such.  But as far as I can tell they do no such things.

The whole operation here smells fishy - or whaly.  Sounds like this is pretty much all about hunting and making money and giving in to pressure to find something other than people to blame for mismanagement of fish stocks.

Microbe humor of the week: Jon Stewart from 1999 on Giant Bacterium

Jon Stewart from 1999 on Giant Bacterium

The Daily Show with Jon StewartMon - Thurs 11p / 10c
Other News - Baby's Got Bacteria
Daily Show Full EpisodesPolitical Humor & Satire BlogThe Daily Show on Facebook

Wednesday, July 04, 2012

Huffington Post picks me & two members of lab as top biologists/chemists to follow on Twitter

From here.
Good press for my lab here: Scientists On Twitter: 30 Biologists And Chemists To Follow

The list (which started out at 30 and expanded to 47) included three people from my lab: me (@phylogenomics), post doc Holly Bik (@dr_bik) and PhD student Russell Neches (@ryneches).

I like that I am the first one shown on the slideshow (though not sure if this means I am #1 on their list or just random ...).

Making such lists is always a challenge and also rife with issues.  There are many many great tweeters of chemistry and biology not on the list, for example. But I think they did a pretty good job covering diverse types of people here.  Lots of women too, which was good to see.

Anyway - thanks to Rebecca Searles and her advisor Jason Goldman for compiling the list and making my lab look pretty good ...

Full list:

  1. @phylogenomics
  2. @NerdyChristie
  3. @nparmalee
  4. @biochembelle
  5. @kejames
  6. @DrBondar
  7. @kzelnio
  8. @girlscientist
  9. @MiriamGoldste
  10. @modernscientist
  11. @PolymerPhD
  12. @toraks
  13. @RichardDawkins
  14. @nuin
  15. @DrRubidium
  16. @mitpostdoc
  17. @Evolutionistrue
  18. @ChemicalBiology
  19. @WhySharksMatter
  20. @Aur_ora
  21. @ChemistPD
  22. @dgmacarthur
  23. @DNLee5
  24. @aetiology
  25. @Myrmecos
  26. @thisischristina
  27. @deborahblum
  28. @SeeArrOh
  29. @carmendrahl
  30. @Dr_Bik
  31. @TCNoel
  32. @nssampson
  33. @sciencegeist
  34. @SFriedScientist
  35. @kg_science
  36. @JATetro
  37. @JacquelynGill
  38. @Katie_PhD
  39. @D_Aldridge
  40. @JohnFBruno
  41. @ScientistMags
  42. @jtotheizzoe
  43. @MayaPlass
  44. @scimomof2
  45. @DrTwittenheimer
  46. @leonidkruglyak
  47. @ryneches

Nice feature on the human microbiome in the SF Chron w/ a little Toxoplasma error

Nice article in the SF Chronicle by Erin Allday on human microbiome related topics.  It features some Bay Area scientists working on the issue - David Relman, Janet Jansson, Les Dethlefsen, and Michael Fischbach.  See:100 trillion good bacteria call human body home - SFGate.

It has some nice pictures of Relman in the lab (though I think he could use some new lighting in there ...).  There is one microbial error in there
At least one bacterium - toxoplasmosis gondii - has been shown to affect behavior. The bacterium reproduces only in cats, and studies have shown that when mice or rats are infected with it, the bacterium makes them less afraid of cats, and they are, therefore, more likely to be eaten by them.
Alas toxoplasmosis is caused by a microbial eukaryote known as Toxoplasma gondii (it is a relative of the causative agent of malaria Plasmodium falciparum).  But otherwise the article is a good read.  I like the end

Fischbach at UCSF is perhaps facing the most difficult challenge: caring for his days-old daughter and nurturing her infant microbiome. He's in the tough position of having both too much and not nearly enough information. 
"My wife and I have tried to pledge to each other that this is going to be our baby, not our experimental subject," Fischbach said with a laugh. "At the same time, my thinking is influenced by the things going on around me. The cast of characters in her is changing dramatically week to week, day to day. I do wonder, where are most of the bacteria that she's got in the gut coming from?"
And as a bonus there is an interview with Relman too:  Sequencing of human microbiome fills knowledge gap

Sunday, July 01, 2012

Is Illumina the "duct tape" of sequencing?

Photo from Wikipedia.  Photo by Evan-Amos

For the last year or so I have become a big fan of Illumina sequencing.  We are using it for everything in the lab.  And many others are using it quite a lot too.  All sorts of interesting applications.  But of course -there are other sequencing systems that each have some advantages relative to Illumina.  And one of the key limitations of Illumina sequencing has been the read length (though that limitation gets less and less as read lengths get longer and longer from Illumina machines).

The UC Davis Genome Center has had Illumina sequencing systems for many years now and we use them extensively.  However, we felt for some time that we and others around town could benefit from complementary methods, especially those that could get longer reads.  So we sought funding to buy other systems.  And fortunately we got an NSF MRI grant to do just that -which we used to buy a Roche 454 Jr machine and contribute to the purchase of a Pacific Biosciences machine.  These are good to have around because they open up new windows into sequencing - not just long reads but other areas as well.  For example, the PacBio system also has the ability to use it to detect modifications to bases like methylation.

Alas, both the 454 and PacBio systems have higher error rates than the Illumina systems.  And this makes some analyses challenging and limits the benefits that come from the longer reads.  So what to do?  For a while people have been using Illumina sequencing to "correct" the errors make by 454 and PacBio sequencing.  And today Matt Herper at Forbes (For A New DNA Sequencer, A Technical Fix May Have Come Too Late - Forbes) discusses a new further improvement in the ability to do this error correction (a paper just came out on the topic from Adam Phillippy, Sergey Koren, Michael Schatz, and others).

I find this whole concept a bit funny / interesting.  Not only does Illumina sequencing have many uses but one of its uses in essence helps keep aloft the potential of some of it's competitors.  In this way - Illumina can be considered the duct tape of sequencing systems.  1001 uses.  Not sure the Illumina folks will be overly thrilled with this use but that is the way it goes ...

(As an aside - any high throughput highly accurate sequencing method could be used in the same way as Illumina in most cases - ABI solid for example.  But alas for ABI Illumina has kind of taken over this part of the market).

(An another aside - we will have to wait and see how/if the Ion Torrent systems take off in the sequencing ecosystem)

(As another aside - still waiting to see some more detail from the Oxford Nanopores folks ... I would be happy to be a beta tester if anyone from Oxford is reading this).