:) Ion Torrent Server up!

Using the Acropora digitifera genome to understand coral responses to environmental change.

Using the Acropora digitifera genome to understand coral responses to environmental change.

Shinzato C, Shoguchi E, Kawashima T, Hamada M, Hisata K, Tanaka M, Fujie M, Fujiwara M, Koyanagi R, Ikuta T, Fujiyama A, Miller DJ, Satoh N.

Nature. 2011 Jul 24. doi: 10.1038/nature10249. [Epub ahead of print]

Despite the enormous ecological and economic importance of coral reefs, the keystone organisms in their establishment, the scleractinian corals, increasingly face a range of anthropogenic challenges including ocean acidification and seawater temperature rise. To understand better the molecular mechanisms underlying coral biology, here we decoded the approximately 420-megabase genome of Acropora digitifera using next-generation sequencing technology. This genome contains approximately 23,700 gene models. Molecular phylogenetics indicate that the coral and the sea anemone Nematostella vectensis diverged approximately 500 million years ago, considerably earlier than the time over which modern corals are represented in the fossil record (∼240 million years ago). Despite the long evolutionary history of the endosymbiosis, no evidence was found for horizontal transfer of genes from symbiont to host. However, unlike several other corals, Acropora seems to lack an enzyme essential for cysteine biosynthesis, implying dependency of this coral on its symbionts for this amino acid. Corals inhabit environments where they are frequently exposed to high levels of solar radiation, and analysis of the Acropora genome data indicates that the coral host can independently carry out de novo synthesis of mycosporine-like amino acids, which are potent ultraviolet-protective compounds. In addition, the coral innate immunity repertoire is notably more complex than that of the sea anemone, indicating that some of these genes may have roles in symbiosis or coloniality. A number of genes with putative roles in calcification were identified, and several of these are restricted to corals. The coral genome provides a platform for understanding the molecular basis of symbiosis and responses to environmental changes.

PMID:

21785439

[PubMed - as supplied by publisher]

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Build an app that makes science more open

Build an app that makes science more open
Wow just after I blogged about Web 2.0 failing to make scientists more productive .. here comes an app challenge!

Hmmm fresh outta ideas at 2 am .. will sleep on this ..

PLoS and Mendeley, the popular reference manager and academic social network, have teamed up to create a Binary Battle contest to build the best apps that make science more open using PLoS and/or Mendeley’s APIs (Application Programming Interface). There’s $16,000 in prize money to be won plus other cool gifts and the opportunity to get your entries in front of a panel of influential judges from technology, media and science that include:

Tim O’Reilly - Founder and CEO of O’Reilly Media which is changing the world by spreading the knowledge of innovators. Tim also co-hosts the annual Science Foo Camp with Google and Nature.

Dr. Werner Vogels - CTO of Amazon.com and former research scientist at Cornell University. Werner is one of world’s top experts on cloud computing and ultra-scalable systems.

Juan Enriquez – Managing Director of Excel Venture Management and CEO of Biotechonomy. Juan is recognized as one of the world’s leading authorities on the economic and political impacts of life sciences.

John Wilbanks - VP for Science at Creative Commons. Seed Magazine named John a “Game Changer” among their Revolutionary Minds of 2008.

James Powell - CTO of Thomson Reuters, the world’s leading information services company. Still a nerd at heart, James is particularly interested in how technology gets applied to solve problems.

We have two APIs for you to mine in this competition. The PLoS Search API allows anyone to build their own applications for the web, desktop or mobile devices using PLoS content. The Mendeley API opens up a database of over 80 million research papers, usage statistics, reader demographics, social tags, and related research recommendations. Since Mendeley got this competition up and running before PLoS joined the party, you can see what some people have already made using their API. It’s also worth knowing that Mendeley are organizing two simultaneous Hackathons at their NY and London offices on Saturday June 11-Sunday June 12, 2011.

Here’s the lowdown on the amazing prizes:

• Grand prize: $10001 + $1000 Amazon Web Services Credits
• Second prize: $5000 + $500 Amazon Web Services Credits – an extra $1000 plus a Parrott AR Drone Quadricopter is available to the best combined PLoS/Mendeley app.
• Last day to submit your app: September 30^th 2011
• Winner announced on: November 30^th 2011

Entries will be judged on criteria such as: activity; popularity/usefulness; whether it increases collaboration and/or transparency and how cool is it (does it make our jaws drop!). Please note, we can not accept entries from PLoS or Mendeley staff or their immediate families, their investors or board members. To get started, developers need to get a key from PLoS, Mendeley or both. Don’t forget, the last day to submit your app is September 30^th 2011.

Web 2.0 will revolutionize science!

nsaunders  laments on the sad fact that web 2.0 hasn't really influenced fellow scientists in improving productivity !


I’ve given up trying to educate colleagues in best practices. Clearly, I’m the one with the problem, since this is completely normal, acceptable behaviour for practically everyone that I’ve ever worked with. Instead, I’m just waiting for them to retire (or die). I reckon most senior scientists (and they’re the ones running the show) are currently aged 45-55. So it’s going to be 10-20 years before things improve.
Until then, I’ll just have to keep deleting your emails. Sorry.

All 57 stackexchange sites

Oh wow didn't know the full site list included so many of my interests!
http://stackexchange.com/sites

Genomics of Emerging Infectious Disease: A PLoS Collection

Genomics of Emerging Infectious Disease: A PLoS Collection 
This collection of essays, perspectives, and reviews from six PLoS Journals provides insights into how genomics can revolutionize our understanding of emerging infectious disease

International Crowdsourcing Initiative to Combat the E. Coli Breakout in Germany

Guest Post: International Crowdsourcing Initiative to Combat the E. Coli Breakout in Germany

 Permanent link

June 8, 2011 

Editor’s Note: In light of the recent E coli outbreak in Germany, NGS Leaders invited Joyce Peng from BGI to comment on the organization’s efforts to understand the culprit. Below Joyce describes BGI’s efforts to rally the international community in combating the outbreak. – Eric Glazer
In response to the recent E. coli outbreak in Germany, BGI and its collaborators at the University Medical Centre Hamburg-Eppendorf have released their third version of the assembled genome, which includes new data from this E. coli O104 (ftp://ftp.genomics.org.cn/pub/Ecoli_TY-2482/Escherichia_coli_TY-2482.contig.20110606.fa.gz ). The FTP site contains a file that provides the PCR primer sequences which researchers have used to create diagnostic kits for rapid identification of this highly infectious bacterium.