My favorite new thing/site on the web: Download The Universe

I am completely fascinated by this new site: Download The Universe. It is a group effort from (so far) some 16 science writers. The main goal of the site is summarized in a post from Carl Zimmer who appears to be the instigator in chief of this effort:
“… It is still tough for readers to discover new science ebooks. Traditional book reviews limit themselves to works on paper. Some ebooks may appear in computer magazines, but buried in reviews of laptops and printers. In between, we need a community.
Download the Universe is a step towards that community. It is the work of a group of writers and scientists who are deeply intrigued by the future of science books. (You can find our names and links to our web sites on the right.) Here we review science ebooks–broadly defined, except for ebooks that are just spin-offs of print books. We hope to build up a library of titles that curious readers can browse. Some reviews will be positive, others negative. We welcome your own judgments, and we look forward to vibrant (but civilized) discussions in the comment threads. We will also write essays from time to time about the changes that publishing is undergoing.
As we continue to build Download the Universe, we may change our minds about the scope of its mission. We can’t say what those changes will be. We can only be sure they will be here before too long.”
I confess – I have never read an ebook of any kind – science or not. And I really really love “real” books – I have collected them for years and years. But I think I am going to start on the ebooks thing. And this site is giving me some ideas for what to start with … This site is definitely worth checking out, and keeping an eye on …

In case you didn’t hear – #openness WON – Research Works Act shelved

See this story from infojustice.org: Research Works Act Shelved by Sponsors
This is just awesome news. The act was completely inane.
Hooray for Open Access and Open Science and Openness in general.

John Stewart takes on H1N1 on hypochondriac update

The Daily Show with Jon Stewart Mon – Thurs 11p / 10c
Hypochondriac Update
www.thedailyshow.com
http://media.mtvnservices.com/mgid:cms:item:comedycentral.com:408965
Daily Show Full Episodes Political Humor & Satire Blog The Daily Show on Facebook

PCR amplification and pyrosequencing of rpoB as complement to rRNA

Figure 1. Number of OTUs as
 a function of fractional sequence difference
 (OTU cut-off) for the 16S rRNA marker
 gene (A) and the rpoB marker gene (B).

Interesting new paper in PLoS One: PLoS ONE: A Comparison of rpoB and 16S rRNA as Markers in Pyrosequencing Studies of Bacterial Diversity

In the paper they test and use PCR amplification and pyrosequencing of the rpoB gene for studies of the diversity of bacteria. Due to the lower level of conservation of rpoB than rRNA genes at the DNA level they focused on proteobacteria. It seems that with a little perseverance once can get PCR for protein coding genes to work reasonably well for even reasonably broad taxonomic groups (not totally new here but I am not aware of too many papers doing this with pyrosequencing). Anyway, the paper is worth a look.

Citation:
 Vos M, Quince C, Pijl AS, de Hollander M, Kowalchuk GA (2012) A Comparison of rpoB and 16S rRNA as Markers in Pyrosequencing Studies of Bacterial Diversity. PLoS ONE 7(2): e30600. doi:10.1371/journal.pone.0030600 ResearchBlogging.org Vos, M., Quince, C., Pijl, A., de Hollander, M., & Kowalchuk, G. (2012). A Comparison of rpoB and 16S rRNA as Markers in Pyrosequencing Studies of Bacterial Diversity PLoS ONE, 7 (2) DOI: 10.1371/journal.pone.0030600

Second video of the week: Mackenzie Smith on Open Licenses

Interesting piece by John Rennie at Smartplanet: What comes after antibiotics?

Interesting piece by John Rennie at Smartplanet: What comes after antibiotics? | SmartPlanet. It discusses a variety of topics including antiomicrobial peptides, nanotechnology, Kary Mullis, Michael Zasloff, DARPA, Maryn McKenna, and more. Definitely worth checking out.

Notes for talk by Mackenzie Smith – candidate for #UCDavis University Librarian position

Here are some notes I took using my iPAD for a talk by Mackenzie Smith about libraries: Note Feb 21, 2012
She is a candidate for the UC Davis University Librarian position for which I am on the committee.  This is the first time I have taken and posted notes from a talk using my iPAD – so please bear with me – it is an experiment of sorts. Note to do this I used an iPAD2, a Bamboo Stylus and the Notability App. I then exported to PDF and posted it (the Note above).  For the images below I then had to export single pages to JPGs.  If anyone knows an easy way to export a multipage PDF as a single JPG I would appreciate information … Inspiration provided by Kosta.

http://storify.com/phylogenomics/mackenzie-smith-talk-at-ucdavis.js?template=slideshow[<a href=”http://storify.com/phylogenomics/mackenzie-smith-talk-at-ucdavis” target=”_blank”>View the story “Mackenzie Smith talk at #UCDavis” on Storify</a>]

Antibiotic use in animals (may) lead to superbugs in people #mBIO

New paper in mBIO of potential interest from Lance Price et al.:  Staphylococcus aureus CC398: Host Adaptation and Emergence of Methicillin Resistance in Livestock.  For those not in the know, mBIO is a relatively new Open Access journal from the American Society for Microbiology.  The paper discusses genomic studies of MRSA which has led the authors to conclude that antibiotic use in animals may contribute to the rise and spread of superbugs in people.

From here. Maximum-parsimony tree of the 89 CC398 isolates (including ST398SO385) based on 4,238 total SNPs, including 1,102 parsimony-informative SNPs with a CI of 0.9591. Clades and groups of importance are labeled in a hierarchical fashion to facilitate description in the text. The tree was rooted with clade I based on an iterative selection process that identified this group as the most ancestral (see Materials and Methods). COO, country of origin; AT, Austria; BE, Belgium; CA, Canada; CH, Switzerland; CN, China; DE, Germany; DK, Denmark; ES, Spain; FI, Finland; FR, France; GF, French Guiana; HU, Hungary; IT, Italy; NL, The Netherlands; PE, Peru; PL, Poland; PT, Portugal; SI, Slovenia; US, United States; P, pig; H, human; R, horse; T, turkey; B, bovine; MET, methicillin susceptibility; R, resistant; S, susceptible.

The figure above is the only figure in the main text of the paper.  There are others in supplemental information which seems a bit strange to me – why put anything in supplemental information when the paper is only released online?  Or at least have thumbnail images for all figures in the main text …

Anyway, the paper and press release got picked up by many newsy places.  See for example:

I note – the Press Release is MUCH better than the last one that was about a paper by Price that I wrote about here: The Tree of Life: #PLoSOne paper keywords revealing: (#Penis #Microbiome #Circumcision #HIV); press release misleading …  Lance was awesomally quick to respond to my complaints about that PR.  The PR for this paper is not so bad — a bit over the top in some of the quotes – but no need for comments I think. 
Citation:
Price LB, et al. 2012. Staphylococcus aureus CC398: host adaptation and emergence of methicillin resistance in livestock. mBio 3(1):e00305-11. doi:10.1128/mBio.00305-11.

UPDATE 2/21 5:30 PM: an alternative (and much more pleasing) press release from ASM is here.

Slideshow w/ audio of my talk on "A Field Guide to the Microbes" from the AAAS Meeting #AAASMtg

I recorded the audio of my talk on “Towards a field guide to the microbes” from the AAAS meeting on Saturday AM. Here is a slideshow of the talk with audio synched to the slides (I did this using Keynote on a Mac with the “record Slideshow” function).

My slides from the talk are available at Slideshare.

Results of #UCDavis Faculty Resolutions released re: Katehi, Pepper Spray, #OccupyUCDavis

Just received the three emails below regarding results of three UC Davis Faculty Senate Resolutions regarding the pepper spray incident from November and thought they might be of some interest.  See this post for a little background.  

REPORT OF THE DAVIS DIVISION OF THE ACADEMIC SENATE COMMITTEE ON ELECTIONS, RULES AND JURISDICTION

On December 20, 2011, a petition bearing the signatures of at least 50 members of the Davis Division of the Academic Senate of the University of California was submitted asking that the following Motion Concerning Police Actions be voted on by the membership of the Davis Division (tenure/tenure-track faculty of the UC Davis Campus):


Motion:


Be it resolved that that the Davis Division of the Senate of the University of California hereby (1) condemns both the dispatch of police and use of excessive force in response to non-violent protests on November 18, 2011;
(2) opposes violent police response to non-violent protests on campus;
(3) demands that police deployment against protestors be considered only after all reasonable efforts have been exhausted and with direct consultation with Academic Senate leadership.


The Davis Division membership was notified on February 3, 2012 that on-line balloting was open and would be closed on February 17, 2012, at 5:00 PM.  The on-line ballot results were reviewed by the Committee on Elections, Rules and Jurisdiction on February 17, 2012 after 5:00 PM and are reported as follows:


Total eligible voters:                               2,693


Required to pass:                               Majority


Vote received:
      Yes:                                                     635
      No:                                                      343


Invalid Ballots:                                             0


The Motion was therefore declared approved and the University of California, Davis Division of the Academic Senate does support the Motion Concerning Police Actions.


Respectfully submitted,


Committee on Elections, Rules and Jurisdiction
G.J. Mattey, Chair
James Fadel
Mark Grismer

REPORT OF THE DAVIS DIVISION OF THE ACADEMIC SENATE
COMMITTEE ON ELECTIONS, RULES AND JURISDICTION




On December 15, 2011, a petition bearing the signatures of at least 50 members of the Davis Division of the Academic Senate of the University of California was submitted asking that the following Five-Resolution Vote of Confidence be voted on by the membership of the Davis Division (tenure/tenure-track faculty of the UC Davis Campus):


Resolution:


Be it therefore resolved that the Davis Division of the Academic Senate:


1)     Condemns both the dispatch of police in response to non-violent protests and the use of excessive force that led to the deplorable pepper-spraying events of November 18, 2011.
2)     Opposes all violent police responses to non-violent protests on campus.
3)     Demands that police deployment against protesters be considered only after all reasonable administrative efforts to bridge differences have been exhausted, including direct consultation with the leadership of the Davis Division of the Academic Senate.
4)     Accepts Chancellor Linda Katehi’s good faith apology.
5)     Expresses confidence in Chancellor Linda Katehi’s leadership and efforts to place UC Davis among the top 5 public universities in the nation.


The Davis Division membership was notified on February 3, 2012 that on-line balloting was open and would be closed on February 17, 2012, at 5:00 PM.  The on-line ballot results were reviewed by the Committee on Elections, Rules and Jurisdiction on February 17, 2012 after 5:00 PM and are reported as follows:


Total eligible voters:                               2,693


Required to pass:                               Majority


Vote received:
      Yes:                                                     586
      No:                                                      408


Invalid Ballots:                                             0


The Motion was therefore declared approved and the University of California, Davis Division of the Academic Senate does support the Five-Resolution Vote of Confidence.


Respectfully submitted,


Committee on Elections, Rules and Jurisdiction
G.J. Mattey, Chair
James Fadel
Mark Grismer

REPORT OF THE DAVIS DIVISION OF THE ACADEMIC SENATE
COMMITTEE ON ELECTIONS, RULES AND JURISDICTION




On December 6, 2011, a petition bearing the signatures of at least 50 members of the Davis Division of the Academic Senate of the University of California was submitted asking that the following Motion Concerning the Chancellor’s Judgment be voted on by the membership of the Davis Division (tenure/tenure-track faculty of the UC Davis Campus):


Motion:  In light of the events on the quadrangle of the UC Davis campus on the afternoon of Friday November 18, 2011, in light of Chancellor Linda Katehi’s email to faculty of November 18 in which she admitted that she had ordered the police to take action against the students who were demonstrating on the quadrangle and said that she had had “no option” but to proceed in this way, and in light of the failure of Chancellor Katehi to act effectively to resolve the resulting crisis in the intervening days,


Be it therefore resolved that the Davis Division of the Senate of the University of California lacks confidence in the leadership of Chancellor Katehi, and


Be it also resolved that the result of the vote on this motion be communicated to the Board of Regents and the President of the University of California.


The Davis Division membership was notified on February 3, 2012 that on-line balloting was open and would be closed on February 17, 2012, at 5:00 PM.  The on-line ballot results were reviewed by the Committee on Elections, Rules and Jurisdiction on February 17, 2012 after 5:00 PM and are reported as follows:


Total eligible voters:                               2,693


Required to pass:                               Majority


Vote received:
      Yes:                                                     312
      No:                                                      697


Invalid Ballots:                                             0


The Motion was therefore declared defeated and the University of California, Davis Division of the Academic Senate does not support the Motion Concerning the Chancellor’s Judgment.


Respectfully submitted,


Committee on Elections, Rules and Jurisdiction
G.J. Mattey, Chair
James Fadel
Mark Grismer