Monday, October 31, 2011

Pumpkin hunting in #davisCA

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

Sunday, October 30, 2011

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

Saturday, October 29, 2011

Team Helicobacter referees - red card for anyone who doesn't love microbes


(me and Miriam Martin)

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.

Andres as a lion - note - I love Halloween


Thursday, October 27, 2011

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

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

Irresponsible reporting on "poop doping" from the Washington Post

UPDATE - see below - the author updated her article including some of my critiques. Went on a bit of a Twitter tirade last night. See mor...