Category: Misc.
In case you didn’t hear – #openness WON – Research Works Act shelved
John Stewart takes on H1N1 on hypochondriac update
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
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
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.
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| 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:
- Pig-to-Human ‘Superbug’ May Be Due to Animal Antibiotics (US News)
- MRSA Staph Strain Developed Drug Resistance in Your Burger (US News)
- How Using Antibiotics In Animal Feed Creates Superbugs (NPR blog)
- MRSA in Livestock May Spread to Humans (ABC news)
- Staph Turns into Drug-Resistant Superbug on Farms (SciAm blog)
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






