Nobel Prize in Technology

The 2012 Millennium Technology Prize (Technology Academy Finland) will be awarded to Linus Torvalds and Dr Shinya Yamanaka.

Linus Torvalds initiated LINUX about 20 years ago (as mentioned previously, see here).

Dr. Yamanaka pioneered work on induced pluripotent stem cells (iPS cells or iPSCs), using a combination of c-Myc, Klf4, Oct-3/4, and Sox2.

As a bioinformatician, I cannot help but point out that ComputerScience and stem-cell research are sharing such a prestigious award. Somewhat a confirmation of the idea that combining the two in a fruitful way is a very good idea, indeed. And in this context I’d like to mention Hans Schöler, whom I had the pleasure to listen to recently. In his excellent work he demonstrated that Oct4 plays a key-role in reprogramming. The structural underpinnings he presented were simply brilliant – see the PDB molecule-of-the-month article on “Oct and Sox Transcription Factors” as a substitute.

(found via heise.de and zdnet.com)

Happy Holidays!

OMG (OhMightyGraph)! This year is almost over, so I’d like to thank you, my dear reader, for your kind interest. WordPress reports well over 3200 clicks for “cistronic”, which has now been up here for about a year. The rendering of the nucleosome (PDB:1KX5) in the style of a bubbly xmas candle wrapped in green DNA is meant as a virtual seasons greeting card from yours truly, courtesy of the organisation in the core of your cells.

I’ll be travelling a couple of days and hence updates and new posts will probably occur quite infrequently until January. But with more than 120 posts in total now there is plenty to dig through! In the meantime, if you’d like to make my day, take a couple of minutes for a brief comment or email: What’s your (most/least) favourite post, which topics deserve more depth and coverage, what’s missing? Any hints, criticism, praise, questions and interesting additions are very much welcome.

I wish you a happy and healthy 2012, stay curious and tuned for more to come. Cheers!

A Multiverse of Exploration

The Institute for the Future  explored at a recent Technology Horizons Program conference the “Future of Science.”

As a result, they identified 6 main areas and visualized them on this map. Most fascinating and closely related to my own interests are the topics on the right side of it:

• data intensive science spawns new disciplines
• science becomes gameified (i.e. fold.it)
• scientific papers are executable as code
• massively linked data becomes a public utility
• wikipedia of science models is created
• human microbiome is mapped
• organisms become programmable
• epigenetics informs real-time genome tweaking
• new lifeforms created from scratch (synthetic biology?!)
• engineered evolution

I am not an expert on the rest of the pack, “space-time cloaks” and “teleportation” still sound far too much like science fiction to me to bet on it. However, for the above-mentioned items, I can see they get realized (and have a major impact) during the next decade – some aspects of the list have already been covered in previous posts. Some of these “scientific projects” are already almost there, considering for example the advances in directed evolution, crowd-sourcing and open linked data. As any strange map, it conveys a certain set of ideas and contains some build-in bias – but going through them and discovering where it (mis-)matches with ones own views of the multiverse I always find illuminating.

Found via this article on boingboing.

DREAM – RECOMB

The 6th Annual DREAM on Reverse Engineering Challenges, the 7th Annual RECOMB Satellite on Systems Biology, and the 8th Annual RECOMB Satellite on Regulatory Genomics will be held jointly at the IDIBELL institute (Barcelona) on October 14-19, 2011. The meeting will start at 9am on Friday October 14, 2011, and run till 6pm on Wednesday October 19, 2011 (October 14: DREAM; October 16-17: Systems Biology; October 18-19: Regulatory Genomics).

Histone Modification Patterns …

play a predictive role in embryonic cell differentiation – this paper published this week in Science reveals a “functional “prepattern” of chromatin states within multipotent progenitors and potential targets to modulate cell fate induction“. An additional discussion is in this article on genomeweb/proteomonitor by Adam Bonislawski.

It fits the picture that not only gene-regulation, cancer- and pluri-potent stem-cells rely on the state-switching machinery revolving around nucleosome/chromatin. Also Frank Holstege’s lab has a recent paper in this field (in MolecularCell – congrats!).

Hence I dug up this visualisation of the nucleosome and its lateral surface I did some time ago and put it up here. Enjoy!

Nucleosome from Michael Lappe on Vimeo.

P.S.: There is a nice expert review on the topic by M.S. Cosgrove “Histone proteomics and the epigenetic regulation of nucleosome mobility“. (PMID:17705705) (Hinted to by Robert Schneider)