Tag: Misc.

LinkedIn unlinked from Twitter Sharing

Of possible interest: Annual Notification of “How to File Whistleblower Reports” at #UCDavis

Just received this:

From: Office of the Provost and Executive Vice Chancellor <whistleblower>
Date: Fri, Jun 29, 2012 at 9:01 AM
Subject: Annual Notification: How to File Whistleblower Reports
To: UC Davis Employees

Greetings:

In accordance with the California Government Code, UC Davis must annually provide all employees with the attached information from the State Auditor’s office on how to file whistleblower reports of improper activities. Please review the attached poster, which contains information on how and where employees may file reports of improper activities at both the Davis campus and the Health System. Departments are encouraged to print the updated 2012 poster for posting to unit bulletin boards.

Thank you,

Wendi Delmendo

Chief Compliance Officer, General Campus

Office of the Provost and Executive Vice Chancellor

WB_Poster_legal_UCD_2012.pdf

National Research Council awards for graduate, postdoctoral & senior researchers at participating federal laboratories & affiliated institutions.

Just got this …

Dear Department Head:

We are asking your assistance in forwarding this message to inform students and faculty in your department of these outstanding fellowship opportunities. More detailed information and an online application can be found at www.nationalacademies.org/rap.

The National Research Council of the National Academies sponsors a number of awards for graduate, postdoctoral and senior researchers at participating federal laboratories and affiliated institutions. These awards include generous stipends ranging from $42,000 – $75,000 per year for recent Ph.D. recipients, and higher for additional experience.Graduate entry level stipends begin at $30,000. These awards provide the opportunity for recipients to do independent research in some of the best-equipped and staffed laboratories in the U.S. Research opportunities are open to U.S. citizens, permanent residents, and for some of the laboratories, foreign nationals.

Detailed program information, including online applications, instructions on how to applyand a list of participating laboratories, is available on the NRC Research AssociateshipPrograms Website (see link above).

Questions should be directed to the NRC at 202-334-2760 (phone) or rap@nas.edu.

There are four annual review cycles.

Review Cycle: November; Opens September 1; Closes November 1
Review Cycle: February; Opens December 1; Closes February 1
Review Cycle: May; Opens March 1; Closes May 1
Review Cycle: August; Opens June 1; Closes August 1

Applicants should contact prospective Adviser(s) at the lab(s) prior to the application deadline to discuss their research interests and funding opportunities.

Thank you for your assistance.

Sincerely yours,
H. Ray Gamble
Director of the Fellowship Programs
National Research Council
The National Academies
500 5th Street NW, Keck 568
Washington, DC 20001

Nice review on HiSeq/MiSeq rRNA sequencing from Caporaso et al #microbes

Quick post — nice review worth checking out: The ISME Journal – Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

from Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R.

A key part of the paper, with highlighting from me:-

These observations, in agreement with studies that have addressed this question directly (Kuczynski et al., 2010), suggest that increasing the sequencing depth is not likely to provide additional insight into questions of beta diversity, and we therefore argue that (for questions of beta diversity in particular) the decreased cost of sequencing should be applied to study microbial systems using many more samples, for example, in dense temporal or spatial analyses, rather than with many more sequences per sample.  Of course, if the objective is to identify taxa that are very rare in communities, deeper sequencing will be advantageous. Additionally we note that while as few as 10 sequences per sample may be useful for differentiating very different environment types (for example, soil and feces), as environments become more similar (for example, two soil samples of different pH) more sequences will be required to differentiate them.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Most unusual use of #microbes of the week: fermented fashion

Fermented clothing on mannequin from
http://bioalloy.org/o/projects/micro-be.html

Well, this is certainly unusual: The Genteel | Fermented Fashion.  I found out about this from a Tweet from Irene Kim

Anyway the article describes the “Micro’be'” project for which more details are available here.  Some interesting details at that site include a description

Imagine a fabric that grows…a garment that forms itself without a single stitch!
The fashion that starts with a bottle of wine…
Micro’be’ fermented fashion investigates the practical and cultural biosynthesis of clothing – to explore the possible forms and cultural implications of futuristic dress-making and textile technologies.
Instead of lifeless weaving machines producing the textile, living microbes will ferment a garment.
A fermented garment will not only rupture the meaning of traditional interactions with body and clothing; but also raise questions around the contentious nature of the living materials themselves.
This project redefines the production of woven materials.
By combining art and science knowledge and with a little inventiveness, the ultimate goal will be to produce a bacterial fermented seamless garment that forms without a single stitch. 

So – in essence they are trying to grow clothing as a side product of wine fermentation.  Not sure what it is like to wear such clothing – or to be around someone wearing it – but it is a fun idea.

//platform.twitter.com/widgets.js

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Video, slides & storify of my talk on "#Phylogeny-driven approaches to #genomics and #metagenomics" from #CSMUBC2012

Just got back from the Canadian Society for Microbiology meeting where I gave the keynote talk on the last day of the meeting (Saturday).  Was a very short, but good trip.  Got to see some key collaborators and colleagues and Vancouver was very nice for the few days I was there.

I recorded my talk on my laptop using the Keynote “Record Slideshow” function.  I then exported it to Slideshare (just the slides – no audio) and to Youtube (video of slides with audio).  They are posted below.  I also did a mini storification of my talk which is also below.

“Phylogeny-driven studies in genomics and metagenomics” talk by Jonathan Eisen at #CSMUBC2012

http://storify.com/phylogenomics/my-talk-at-csmubc2012.js[&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;a href=”http://storify.com/phylogenomics/my-talk-at-csmubc2012&#8243; target=”_blank”&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;View the story “My talk at CSMUBC2012” on Storify&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;/a&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;]

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

For those who missed it: "Science as an open enterprise" from Royal Society

This will be of interest to many I think: Science as an open enterprise – Report | Royal Society

It is a comprehensive report from the Royal Society with links to videos, text, previous meetings, references, EPUBs, and more relating to a report that was released a few days ago.  From the web site:

Six key areas for action are highlighted in the report:

  • Scientists need to be more open among themselves and with the public and media
  • Greater recognition needs to be given to the value of data gathering, analysis and communication
  • Common standards for sharing information are required to make it widely usable
  • Publishing data in a reusable form to support findings must be mandatory
  • More experts in managing and supporting the use of digital data are required
  • New software tools need to be developed to analyse the growing amount of data being gathered

Definitely worth a serious browsing/reading.

For more on this see …

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Science Magazine Special Issue on H5N1 #Links #Microbes

"As a service to the community, AAAS is also making these articles free to the public. "

Would be nice to make ALL of Science available to the public but AAAS is a dinosaur of sorts. Anyway — at least these are available. (Thanks to Eileen Choffnes for the links).

H5N1: Bruce Alberts

Science 22 June 2012: 1521

http://www.sciencemag.org/content/336/6088/1521.full.pdf

Benefits and Risks of Influenza Research: Lessons Learned: Anthony S. Fauci and Francis S. Collins

http://www.sciencemag.org/content/336/6088/1522.full.pdf

Implementing the New U.S. Dual-Use Policy:Carrie D. Wolinetz

http://www.sciencemag.org/content/336/6088/1525.full.pdf

Evolution, Safety, and Highly Pathogenic Influenza Viruses:Marc Lipsitch, Joshua B. Plotkin, Lone Simonsen, and Barry Bloom

http://www.sciencemag.org/content/336/6088/1529.full.pdf

Influenza: Options to Improve Pandemic Preparation : Rino Rappuoli and Philip R. Dormitzer

http://www.sciencemag.org/content/336/6088/1531.full.pdf

Perspectives

Regulating the Boundaries of Dual-Use Research – Mark Frankel http://www.sciencemag.org/content/336/6088/1523.full.pdf

Securing Medical Research: A Cybersecurity Point of View : Bruce Schneier http://www.sciencemag.org/content/336/6088/1527.full.pdf

Airborne Transmission of Influenza A/H5N1 Virus Between Ferrets (2012). Sander Herfst et al. http://www.sciencemag.org/content/336/6088/1534.full.pdf

· Materials/Methods, Supporting Text, Tables, Figures, and/or References Download Supplement

The Potential for Respiratory Droplet–Transmissible A/H5N1 Influenza Virus to Evolve in a Mammalian Host. Colin A. Russell et al. (2012). http://www.sciencemag.org/content/336/6088/1541.full.pdf

· Materials/Methods, Supporting Text, Tables, Figures, and/or References Download Supplement

Quick summary of session at #ASM2012 on “The Great Indoors” #microBEnet

 The session at the ASM 2012 meeting on “The Great Indoors” seems to have gone well. I will be writing up a more detailed report but here is a quick summary done via “Storify”.

http://storify.com/phylogenomics/asm2012-microbenet.js[&amp;lt;a href=”http://storify.com/phylogenomics/asm2012-microbenet&#8221; target=”_blank”&amp;gt;View the story “Session at #ASM2012 on The Great Indoors: Recent Advances in the Ecology of Built Environments ” on Storify&amp;lt;/a&amp;gt;]

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Some notes from GSC13 session on microbiology of the built environment #microBEnet

At the GSC13 meeting a few months ago there was a session on microbiology of the built environment which was sponsored by my microBEnet project.

Posting some details from the meeting here.

Meeting notes and reports

Talk videos:

Paula Olsiewski

  http://www.scivee.tv/flash/embedCast.swf

The Indoor Standards – What Parameters Do We Need to Record? Jeffrey Siegel (University of Texas at Austin, USA)

http://www.scivee.tv/flash/embedCast.swf

Minimal Metadata for the Built Environment: A MIxS Extension Lynn Schriml (University of Maryland, USA)

http://www.scivee.tv/flash/embedCast.swf

The Home Microbiome Project: Unraveling the Relationship Between Human-associated and Home-associated Microbial Signatures. Jack Gilbert (University of Chicago/Argonne National Laboratory, USA)

http://www.scivee.tv/flash/embedCast.swf

The Indoor Virome! Scott Kelley (San Diego State University, USA)

http://www.scivee.tv/flash/embedCast.swf

The Role of VAMPs in the MoBEDAC Initiative Mitchell Sogin (Marine Biological Laboratory, Woods Hole, USA)

http://www.scivee.tv/flash/embedCast.swf

MoBEDAC – Handling Fungal Data From MicroBE Jason Stajich (University of California, Riverside, USA)

http://www.scivee.tv/flash/embedCast.swf

MoBeDAC – Integrated data and analysis for the indoor and built environment Folker Meyer (Argonne National Laboratory, USA)

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–