Eisen Lab Blog

Email from Biomed Central pointing to ways to get #altmetrics for recent sFAMS paper

Just received from Biomed Central and thought some people might be interested in some of the ways they try to help you gather metrics about your papers.

Dear Prof Eisen,

We thought you might be interested to know how many people have read your article:

Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource
Thomas J Sharpton, Guillaume Jospin, Dongying Wu, Morgan GI Langille, Katherine S Pollard and Jonathan A Eisen
BMC Bioinformatics, 13:264   (13 Oct 2012)
http://www.biomedcentral.com/1471-2105/13/264

Continue reading “Email from Biomed Central pointing to ways to get #altmetrics for recent sFAMS paper”

SMBE Meeting on Eukaryotic -Omics: April 29-May 2 at UC Davis

I’m leading the organization of an SMBE Satellite Meeting focused on Eukaryotic -Omics at UC Davis this spring. The meeting dates have been set as April 29-May 2, 2013, and the meeting description is as follows:

The SMBE Satellite Meeting on Eukaryotic -Omics will bring together an interdisciplinary pool of researchers to discuss current efforts, challenges, and future directions for high-throughput sequencing approaches focused on microbial eukaryotes (environmental studies of non-model organisms). The meeting program will encompass investigations of eukaryote biodiversity, ecology, and evolution, using approaches such as rRNA marker genes, shotgun metagenomics, metatranscriptomics, and computational biology tools and software pipelines.

See the meeting website (http://www.smbe.org/eukaryotes/) for program announcements, registration details, and travel award information. We’re currently in talks to tack on a QIIME workshop at the end of the meeting (tentative dates May 2-4), so keep an eye our for further details. The official conference hashtag will be #SMBEeuks on Twitter.

Our call for travel award applications includes a heavy focus on diversity–encouraging early-career applicants as well as those from underrepresented groups. Please pass on this meeting announcement to anyone who might be interested in attending. Deadline for abstract submission and travel grant applications is Feburary 22, 2013.

Done with sampling!

So after a few months and 400+ samples later, we are finally done with sampling and data collection! The results look good, with several unique key points that we will be looking into once we have sequencing data. It will be interesting to see, and hopefully correlate, the appearance or growth of an organism with a change in one of the chemicals we measured.

 

On Tuesday I went in to do some DNA purifications to refamiliarize myself with the process and going back to lab overall. Hopefully the purifications and DNA isolation goes well, and we get back some interesting data from the sequencing run.

Connotea is closing

Just got this email … not sure what the full story is behind it but Connotea is closing ….

Connotea is closing

Connotea, nature.com’s social bookmarking site, is closing on March 12th, 2013. We would like to thank you for your patience with and support for the site.

To enable you to export your bookmarks to an alternative service, we are providing a tool to make the process as easy as possible. Connotea will be available until March 12th, 2013 and you are strongly encouraged to download your bookmarks before this date as your library will not be accessible afterwards.

The Connotea Export Tool will convert your bookmarks into two formats that should be compatible with most common browsers or reference management systems:

  • HTML – compatible with most browsers
  • RIS – compatible with most reference management systems.

You will be able to log in to the Connotea Export Tool by using your Connotea username and password and following the instructions on screen. Once you have downloaded your HTML and/or RIS file, please refer to the instructions for your browser and/or reference management system to import your bookmarks.

Access the Connotea Export Tool.

As Connotea stores a large amount of data, in some cases it may take over an hour for your bookmarks file to be generated. If you experience any problems with exporting your bookmarks, or have any other questions or queries, please contact Marta Rolak

Science music video of the week: Some budding yeast I used to grow

Hat tip to Gian Baucom and Susan Perkins

#UCDavis Ecology & Evolution Seminar 1/24: Dawn Sumner #Awesome

Forwarding this:

Dear Colleagues,

The Ecology and Evolution Seminar speaker this week will be our own Dawn Sumner from Geology. Her talk on Thursday January 24th is entitled

The Modern Ecology of Ice-Covered Lakes in Antarctica: A Journey Back to Precambrian Time

and takes place at 4:10pm in 1003 Giedt Hall.

Dawn is one of the principle scientists on Curiosity, NASA’s Mars Science Laboratory. You can read about this work on her blog at

http://dawnonmars.blogspot.com/

which links to some marvelous footage/photos of their Mars explorations.

Dawn has done also extensive work on the (nearly) other-wordly ecology of microbial communities in Antarctic lakes to "develop a predictive understanding of how microbial communities produce complex microbialite morphologies." You can find out more about this at

http://mygeologypage.ucdavis.edu/sumner/Dawns_Research/Antarctica.html

and her Antarctic blog http://dawninantarctica.blogspot.com/

From iSEEM project: Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities

Quick post.  Another paper is out based on the Gordon and Betty Moore Foundation funded iSEEM project I co-ran with Jessica Green and Katie Pollard.

PLOS Computational Biology: Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities.

O’Dwyer JP, Kembel SW, Green JL (2012) Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities. PLoS Comput Biol 8(12): e1002832. doi:10.1371/journal.pcbi.1002832.

It has one of my favorite paper figures ever.

Figure 1. The local community and metacommunity framework casts local biodiversity of coexisting species in terms of a sampling process from a larger reference pool, or metacommunity. 

And the paper is definitely worth checking out.

Halophiles 2013 Conference June 23-27 U Conn.

Just got this from Thane Papke

It is my pleasure to invite everyone to the tri-annual Halophiles conference on microorganisms. This year’s event will take place from June 23-27th on the Storrs Campus of the University of Connecticut.

The conference will highlight the diverse research of over 30 invited speakers on topics of biodiversity, evolution, proteins, biochemistry, physiology, genetics, applied biotechnology, astrobiology, ecology and biogeochemistry, and there will be a joint meeting of the ICSP-Subcommittees on the taxonomy of the Halobacteriaceae and Halomonadaceae.

If you are interested in participating, please go to the following website for registration, and more information. http://www.regonline.com/halophiles2013

This announcement was made from an incomplete email list and cannot reach everyone. If you are aware of any names who should receive this and future announcements, please forward this notice to them, and let me know their address and I will add them to the list. If you are on the list and wish to be removed, please let me know.

Sincerely,
Thane

http://www.papkelab.uconn.edu

Halophiles_Conference_Poster.pdf

Overselling the microbiome: University Bern press release uses slight of hand to make mouse study seem to be about people

Interesting new paper came out recently on “Sex Differences in the Gut Microbiome Drive Hormone-Dependent Regulation of Autoimmunity.”  It is alas in Science so it is not available openly.

Anyway there are some news stories about the article where you can get the gist of it.  Best one is probably the blog post by Christine Gorman: Transplanted Bacteria Turn Up Testosterone to Protect Mice against Diabetes.  The story is pretty interesting.

For those who do not know I have been a bit obsessed about the connection between diabetes and the microbiome for a while.  See my Ted talk for example where I discuss my own personal connection to this issue.

http://embed.ted.com/talks/jonathan_eisen_meet_your_microbes.html

But the science is not what I want to talk about here.  What I want to talk about is how science press releases can just be awful.  The one for this paper is like some sort of con artist’s scheme.  Here it is on Science Daily: Good bacteria in the intestine prevent diabetes, study suggests.  First, they lure you in with a headline that, well, fails to mention that the study was in mice.  And then they keep trying to lure you with some lines about humans and their microbes.  In fact, the first two and half paragraphs I think are pretty deceptive.

All humans have enormous numbers of bacteria and other micro-organisms in the lower intestine. In fact our bodies contain about ten times more bacteria than the number of our own cells and these tiny passengers are extremely important for our health. They help us digest our food and provide us with energy and vitamins. These ‘friendly’ commensal bacteria in the intestine help to stop the ‘bad guys’ such as Salmonella that cause infections, taking hold. Even the biochemical reactions that build up and maintain our bodies come from our intestinal bacteria as well as our own cells.  

Pretty important that we get along with these little bacterial friends… definitely. But as in all beautiful relationships, things can sometimes turn sour. If the bacteria in the intestine become unbalanced, inflammation and damage can occur at many different locations in the body. The best known of these is the intestine itself: the wrong intestinal bacteria can trigger Crohn’s disease and ulcerative colitis. The liver also becomes damaged when intestinal bacteria are unbalanced. 

Research groups led by Professor Jayne Danska at the Sick Children’s Hospital of the University of Toronto and Professor Andrew Macpherson in the Clinic for Visceral Surgery and Medicine at the Inselspital and the University of Bern have now shown that the influence of the intestinal bacteria extends even deeper inside the body to influence the likelihood of getting diabetes. In children and young people, diabetes is caused by the immune cells of the body damaging the special cells in the pancreas that produce the hormone insulin.

Yup – lots and lots of stuff about people.  Which is fine.  I like people.  But the thing is. The paper is about mice.  So lines like “have now shown that the influence of the intestinal bacteria extends even deeper inside the body to influence the likelihood of getting diabetes” are kind of misleading because so far there has been no mention of mice and that line is they only true for mice, not people.  And then they wrap up this section with another line about people, clearly trying to imply that the “have now shown …” part is relevant to people.

And then, finally, they turn to mice.

By chance, 30 years ago, before the development of genetic engineering techniques, Japanese investigators noticed that a strain of NOD laboratory mice tended to get diabetes. These mice (also by chance) have many of the same genes that make some humans susceptible to the disease. With the help of the special facilities of the University of Bern and in Canada, these teams have been able to show that the intestinal bacteria, especially in male mice, can produce biochemicals and hormones that stop diabetes developing.

And then they go back to people.

Diabetes in young people is becoming more and more frequent, and doctors even talk about a diabetes epidemic. This increase in diabetic disease has happened over the last 40 years as our homes and environment have become cleaner and more hygienic. At the moment, once a child has diabetes, he or she requires life-long treatment. 

“We hope that our new understanding of how intestinal bacteria may protect susceptible children from developing diabetes, will allow us to start to develop new treatments to stop children getting the disease,” says Andrew Macpherson of the University Bern.

Wow.  So in a press release about a paper that is about mice, there are three sentences about mice and the rest are about people.  The thing is, in case you don’t know – mice are not the same as people.  Just saying.  And for trying to overplay the connection of their work to humans, I am giving the writer’s of this press release my coveted Overselling the Microbiome Award.

Past posts about this award include:

Crosspost from PLOS Biologue: Working to increase diversity of PLOS Biology Academic Editors and Advisory Board members

On the PLOS Biologue (the blog for PLOS Biology) I have a post that may be of interest.  I discuss our efforts to increase the diversity of the people involved in the various Boards of PLOS Biology.  This is my first task I have taken as the Chair of the PLOS Biology Advisory Board.  See the post: Working to increase diversity of PLOS Biology Academic Editors and Advisory Board members.