Fun with a $1300 3D printer - featuring @ryneches in my lab

Just a quick one here.  I am posting some links to videos and blog posts about efforts by a student in my lab - Russell Neches - to use 3D printing to help with carrying out high throughput studies of microbial diversity. Basically the idea is that we can use new very cheap 3D printer technologies to help with normalizing sample volumes by printing in essence micro titer dishes with variable well depth. For more on this see some of the links/videos/etc below:  

From Russell's blog:
Some of Russell's videos

Aggie TV news story about Russell's work on this:


Further proof of the ascendancy of microbes: 2011 NSF "biodiversity" grants mostly focused on microbes

As if the readers of this blog needing any more proof of the ascendancy of microbes and microbiology. Well, regardless, here is more. The NSF Announced recipients of the 2011 grants on "Dimensions of Biodiversity" - see The National Science Foundation (NSF) News Diversity of Life on Earth: NSF Awards Grants for Study of Dimensions of Biodiversity

And the recipients are strongly biased towards microbes relative to the general past patterns at many funding agencies.

Microbial focused awards:

Title: Pattern and process in marine bacterial, archaeal, and protistan biodiversity, and effects of human impacts
PI (Principal investigator): Jed Fuhrman, University of Southern California
Summary: Very little about marine microbial systems is understood, despite the fact that these diverse groups dominate cycling of elements in the oceans. Fuhrman and colleagues will compare heavily affected harbor regions with relatively pristine ocean habitat in the Los Angeles basin to understand patterns and relationships in marine microbial communities.

Title: Diversity and symbiosis: Examining the taxonomic, genetic, and functional diversity of amphibian skin microbiota
PI: Lisa Belden, Virginia Polytechnic Institute & State University
Summary: All animals host internal and external symbiotic microbes; most cause no harm and many are beneficial. This study seeks to understand the regulation of microbial communities on the skin of amphibian species, and how they may limit infection by a chytrid fungus that has decimated many amphibian populations around the globe.

Title: Lake Baikal responses to global change: The role of genetic, functional and taxonomic diversity in the planktonPI: Elena Litchman, Michigan State University
Summary: Microscopic plant- and animal-like plankton are the first links in aquatic food chains. This project will study the planktonic food web of the world's largest, oldest, and most biologically diverse lake--Lake Baikal in Siberia--to predict how native vs. non-native plankton in this ecosystem will respond to accelerating environmental change

Single cell genomics even has its own software: SmashCell

Somehow I was not aware of this software called SmashCell even though it came out a while ago.  But it is worth checking out if you are interested in single-cell genomics.  There is an open access paper describing the software: SmashCell: a software framework for the analysis of single-cell amplified genome sequences.

Single cell genomics is becoming more and more important in studies of environmental microbiology as well as other fields like cancer biology.  One of the challenges with single cell genomics is that the amplification processes used to make copies of the genome from single cells are not completely accurate or efficient so you frequently end up with partial, somewhat messed up samples of genomes.  If you then sequence these amplified genomes it can be hard to make sense out of the data.  Hopefully this software may be of use to some doing this type of work.

Note - for those interested in more see this PLoS One paper I am a coauthor on:

Assembling the Marine Metagenome, One Cell at a Time

Wish I had access? Umm ... no ... and I will definitely not be recommending to my librarian.

Well, I got this email.  I do not view it as a valuable message.  But I thought I would share with others.  I guess the tone annoys me "Wish you had access?"  Well, not exactly.  I wish EVERYONE had access.  Therefore I wish that statisticians would publish in open access journals and that these journals would make more of their material freely available.  See below.

Some microbe papers from the Royal Society archives

As many be aware, the Royal Society has made their entire archive of papers available for free.  This has included some classics and has attracted a lot of attention (e.g., papers by Darwin and Franklin and others).  Well, here are some of microbial interest

First I did a search for the term bacteria and searched by date (with oldest first): and found a few of interest.

Uh oh - we are so lost we ended up in a sorghum maze

The ascendancy of microbiology: #UCDavis and the Institute of Medicine as examples

Just another few lines of evidence of the ascendancy of microbiology to report.

#1 - At UC Davis Microbiology is very big and getting bigger.

Consider this. The Dean of the School of Medicine, Claire Pomeroy is an infectious disease expect and microbiologist.

The new Dean of the College of Biological Sciences, James Hildreth research focuses on HIV.

The new Dean of the School of Veterinary Medicine Michael Lairmore specializes in HTLVs (human T-lymphotropic viruses).

Microbes seem to be literally taking over the place here ...

#2 The Institute of Medicine (IOM) has been picking more and more microbiologists.

Already there are many microbiologists in the Institute of Medicine. Not surprising of course as microbiology is a major area of medical research. (I note, two of the three people I listed above - Hildreth and Larimore and in the IOM).

And now today the IOM announced newly elected members. IOM Elects 65 New Members, Five Foreign Associates - Institute of Medicine. And a quick glance IDs many many microbiologists - I think the fraction is going up. Among the new members:

Claire Pomeroy, from UC Davis (see above).

Claire Fraser-Liggett, of U. of Maryland. I note I used to work at a place, TIGR, some of you may have heard of back in the day. This place was run by Claire F-L. Now I work at a place where some parts (I have a 50% appointment in the medical school) are run by Claire P. Seems I have a thing for working at places with microbiologists name Claire in positions of power.

David Relman, microbiomologist from Stanford.

Martin Blaser, another microbiomologist.

Patricia Conrad, parasitologist/microbiologist at UC Davis.

Paul Offit, immunologist.

And others. I know - I am of course biased. But everywhere I look, from the science section(s) of the New York Times, to articles and news and stories all around, microbes seem to be creeping in more and more. And that is a good thing.

The story behind Pseudomonas syringae comparative genomics / pathogenicity paper; guest post by David Baltrus (@surt_lab)

More fun from the community.  Today I am very happy to have another guest post in my "Story behind the paper" series.  This one comes to us from David Baltrus, an Assistant Professor at University of Arizona.  For more on David see his lab page here and his twitter feed here.  David has a very nice post here about a paper on the "Dynamic evolution of pathogenicity revealed by sequencing and comparative genomics of 19 Pseudomonas syringae isolates" which was published in PLoS Pathogens in July.  There is some fun/interesting stuff in the paper, including analysis of the "core" and "pan" genome of this species.  Anyway - David saw my request for posts and I am very happy that he responded.  Without further ado - here is his story (I note - I added a few links and Italics but otherwise he wrote the whole thing ...).

I first want to than Jonathan for giving me this opportunity. I am a big fan of “behind the science” stories, a habit I fed in grad school by reading every Perspectives (from the journal Genetics) article that I could get a hold of. Science can be rough, but I remember finding solace in stories about the false starts and triumphs of other researchers and how randomness and luck manage to figure into any discovery. If anything I hope to use this space to document this as it is fresh in my mind so that (inevitably) when the bad science days roll around I can have something to look back on. In the very least, I'm looking forward to mining this space in the future for quotes to prove just how little I truly understood about my research topics in 2011. It took a village to get this paper published, so apologies in advance to those that I fail to mention. Also want to mention this upfront, Marc Nishimura is my co-author and had a hand in every single aspect of this paper.

Something smells off with this - grant to fund travel to meeting, if you use Roche technologies

Just got this email from Roche announcing a grant program to pay registration and travel fees for the AGBT meeting if you are using Roche-454 sequencing or Roche-Nimblegen arrays as part of your work (see below).  Seems like this would have some of the same conflict of interest issues as a pharma company paying someone to give a talk.  I note - I participated in a session supported by 454 at a meeting but paid my own way to avoid this type of conflict of interest issue.  Anyone have opinions on this?  Is this a common pharma method creeping its way more and more into genomics?

Guest post from Katherine Scott of the Journal of Visualized Experiments on #OpenAccess challenges

Today we have another guest post here. This one is from Katherine Scott from JOVE - the Journal of Visualized Experiments. I really like the concept behind JOVE - high quality videos of experimental protocols. Publications in JOVE were initially freely available to all (see my 2008 post about JOVE here). Alas, a few years ago, things changed with the introduction of a subscription model. This saddened many out there, myself included, since JOVE was a wonderful addition to the collection of freely available scientific resources.  I wish they had been able to avoid this, but it seems that they could not.  Katherine Scott from JOVE explains their side of the story below:

Guest post by Katherine Scott "Open Access from the Perspective of an Academic Journal"

Open access from the perspective of an academic journal. I work for the first and only peer-reviewed science video journal indexed in PubMed and MEDLINE, the Journal of Visualized Experiments (JoVE). We started as an open access resource in 2006, but that model wasn’t sustainable for us. The cost of producing high-quality video simply too high.

So how do we remain profitable without losing our open access roots? Balance.

We started offering subscriptions in 2009, but still try to open up access wherever we can. We recently partnered with Health InterNetwork Access to Research Initiative (HINARI), to give free subscriptions to developing countries in South America, Asia and Africa.

Wikileaks obtains internal Nobel Prize committee communications revealing 2011 winners

Stockholm. October 3, 2011. 

Well, Wikileaks has done it again. Though this time they have cracked one of the most secret organizations in the world - the Nobel Prize Committee, Julian Assange announced in a press conference today. Assange said
"We have obtained the entire database of email communications for all Nobel Prize decisions for the last ten years. To say the least, these provide a fascinating look at the secret decision making process."
The cables have not yet been released to the public. Assange said
"We are working with journalists to go through all the documents and redact out names in order to protect the innocent. There is some potentially damaging material in there and though we are inclined to release it immediately, we also understand there are risks. For example, there are many discussions disparaging the work of many famous scientists as being "obvious" or "inane." In addition, we have obtained all the nominations submitted from around the world, which includes a remarkable number of self-nominations by people who have done relatively trivial work."
Assange proceeded to show highly redacted examples of email communications from inside some of the committees, discussing things such as who would look good next to the King of Sweden or the King of Norway and thgat the peace prize award to Obama was given simply "for not being George Bush."

Assange also stated that the communications reveal the winners of the 2011 prizes which he was not going to reveal "in order to make a little bit of money on the side" to support Wikileaks activities. Although Assange did state that "I can conclusively state that Obama will not win the Medicine prize for his healthcare system" as some have suggested.

PLoS picture of the day: Simon Chan from #UCDavis sports #PLoSOne shirt when presenting to @BillGates

Good to see here that Simon Chan, from UC Davis, knows what is the best outfit to wear to present his work to Bill Gates.  
Thanks to Simon for sending me the photo and to the Bill and Melinda Gates Foundation for approving it'sits use here.

Burgess Sale vs. Shale

Every time I see this ad I clipped out twenty years ago, I think of Stephen Jay Gould and the Burgess Shale.  I sent it to him when I was a grad. student and would see this ad in the SF Chronicle for Burgess Honda.