Category Archives: Nature Magazine

I feel Chicken Gunya? Can social networks help track emerging diseases

I remember being particularly amazed at Jonathan Harris and Seepandar Kamwars  “We feel fine”  visualization based on extracted statements from blog posts around the world. Reading about the re-emergence of dengue fever , chicken-gunya , west-nile and other viruses across South Asia, I started wondering if there are ways of keeping track of emerging pathogens using the many social networks that span the Globe.

In many countries there is no paranoia associated with sharing health information like there exists in the developed world. Even if the paranoia exists like it does in the US. We are curiously caught in a world where people reading my blog are more likely to know I have contracted the flu than any two of my healthcare providers who need that information to treat me better.

While the debate on the best way to handle health information online continues, I was wondering how open I would be to sharing information about what afflicts me, if there was a societal benefit to be derived from it. It could something as simple as monitoring allergy symptoms around where I live or something fancy like tracking an emerging pathogen.

Imagine all of us updating a common channel with “de-personalized” information on what afflicts us globally.   I can imagine the system to be something like this ..I  could “submit” to this service information about what ails me ..and the machine could obfuscate my details , preserving only things like my approximate geographical area and my age and sex and add it to this health information social network.

If implemented well could  possibly then have daily visualizations along the lines of  “We feel fine” to possibly something like  “We feel chicken Gunya”


Nature precedings : A great offerring from the NPG stable

Nature just launched Nature precedings , a home for Pre-publication research and preliminary findings. Within seconds of browsing through its very intuitive interface I immediately got the purpose of this offering from Nature Publishing group.

The way it works is simple- you can upload content in the form of word documents , powerpoint files and pdf files and it gets released to the community after a preliminary check for appropriateness of content and suitability for the nature precedings audience. Signed up users can then vote on the content ( a la Digg) and it gets moves up or down its category. All of the content is also search-able and link-able and citeable.

As the help pages suggest, I hope the site serves , in the least as a repository of supplementary material and science findings related to published work anywhere, which can then be commented on and discussed.

More interestingly the FAQ page, informs us that the Nature publishing group Journals do accept material that is in the un-peer-reviewed form and that has appeared in the preprint form : So if i get together a manuscript , I can first post it on Nature precedings and then send it for consideration to Nature for review separately and nature would still consider it ( if it meets its other criteria of course).

So this site could be a great place to establish the provenance of ideas, i.e I have a great new finding , I am gutsy enough to write it up in some form , post it on Nature precedings ..and then a few months later send the finished work to a print journal like a Nature publishing group journal that would accept it.

With all of this Nature precedings has the great potential to become an online repository of pre-print findings , supplementary material and other content of use to the science community…I really cant wait for the first paper to make it from Nature Precedings to the real thing , Nature itself with a citation that first appeared online!.

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The salt lakes in the Egyptian dessert, The Sargasso sea and the cutting edge in the optical querying of neuronal circuits

I recently went to a talk given by Karl Deisseroth of Stanford University whose lab has been in the forefront of developing tools that allow neurons to be activated or de-activated using pulses of light in combination with expressed opsin transgenes. The opsins are basically photoactivated proteins ( like the rhodopsin in our retina) and they are activated by a single photon of light . Deisseroths lab had a while ago developed the use of a Channel rhodopsin- ChR2 which showed a light activated cationic (positive ion) current . Thus, when ChR2 was expressed in neurons a flash of blue light triggered a current of sodium and potassium ions which resembled the neuron firing or the action potential. The group set out looking for opsins that had the opposite effect , i.e they accelerated the suppression of the neuronal action potential ( or brought the neuron back to rest) in response to a light photon. The protein had be functional in neurons and also bring about the light activated depolarization at a time scale of the action potential .

After trolling through a few opsins the Deisseroth group in close collaboration with the Georg Nagel lab at the University of Wuerzburg in Germany zeroed in on the opsin from Naturomonas pharaonis (NpHR or Halo) an archaebacteria that lives in transient salt lakes in the Egyptian dessert in salt concentrations as high as 3.5 M NaCl and a pH of 11. The bug possibly uses the opsins to capture the energy from sunlight and uses the energy to drive the uptake of chloride which allows it to survive in the very salty lake it lives in.

This new opsin now was able to drive a chloride current on photoactivation which effectively turned the neuron off. Fortunately for the group the NpHr opsin was also activated at a wavelength entirely different from the “on switch” ChR2 opsin.

Concurrently with the publication in Nature the group released a video of a worm expressing both opsins which could be paralysed and tickled into movement by pulses of light that stimulated NpHr and CpHr respectively. In the talk Deisseroth also spoke of developments to move the experiments into a mouse model where a transgenic mouse would have a fibre optic probe inserted into its head that would then allow light to stimulate a precice area of the brain ( like a pulse of light would cause the neuron that controlled whisker movement to turn on and the mouse would twitch its whisker).

All of this clearly opens the road to other such opsins that can possibly respond to other wavelengths and drive excitatory and stimulatory currents with different properties. Interestingly way back in 2004 the metagenomics initiative by Craig Venter (the Sorcerer II expedition) published details of several novel opsins from the sargaso sea mass sequencing samples. Who knows , maybe the next such opsin may come some deep sea archaeon and have totally different spectral and kinetic properties which would allow an added level of control to the optical querying of neuronal circuits.

References and additional material

  1. Video of light stimulated supression of worm twitching upon NpHr (Halo) activation
  2. NpHr genome project page
  3. Free full text PlosBiology paper on NpHR by Xue Han and Edward Boyden
  4. Image link from an article in the MIT technology review
  5. MIT technology review article on ChR2 and NpHr ( worm video link )
  6. Request the ChR2 and NpHR (Halo) plasmids deposited by the Boyden lab at addgene
  7. The TED talks have an interesting talk by Craig Venter : around minute 3:46 he talks about the opsins
  8. Full text ( free access) PLOS Biology article on Sorcerer II data.. one of the figures contains an analysis of the spectral characteristics of proteorhodopsins from the metgagenomics dataset

Membrane Protein Crystallization Analytics

I am starting to really like analytics. I started following the developments in the “analytics movement “after reading about companies like juice analytics , swivel , gapminder and “many eyes” at the bbgm blog. Along these lines Nature magazine also recently carried a news and views piece on IBMs many-eyes and the opportunities it afforded for scientific collaboration.

As a person closely involved in membrane protein purification , characterization and crystallization , I am always on the lookout for information related to the various aspects of doing membrane protein biochemistry . The very good compilation of membrane proteins of known structure compiled by Steven white at U.C Irvine was always my go-to place for information about membrane protein structures . But talking of analytics , I recently came across the very appropriately named “Membrane protein databank” which has a lot of compiled and elegantly displayed statistics on every aspect of membrane proteins structural biology ranging from the the expression systems and source organisms used to the detergents , additives and phasing methodology used for structure solution.

The MPDB seems to be a manually curated database which relies on the efforts of its creators to keep it up-to-date and accurate. As we all get increasingly open to sharing data pre and post publication . It will be exciting to see compilations like the MPDB emerge in the empirical and trial and error world of protein expression and crystallization trials . The advantages of using web2.0 frameworks to share and store information of the kind contained in the MPDB is exciting.

I cant wait for the day that a live RSS feed on my personalized google homepage informs me of the fact that Tim Toolman from the University of Xtal has crystallized a CLC channel from Halothermotrix orenii by expression in archaeoglobus fulgidus and it simultaneously updates a live graph of the many parameters used in these experiments probably available as a desktop widget on my google toolbar.

The ABC transporter retraction

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Systems biology education : Bringing the quantitation to biology

Nature reviews Cell and Molecular Biology has an excellent freely accessible supplement called the systems biology user guide. In it are various sections that talk of the applications and challenges facing systems biology. One of them is an essay on education for systems level biologists titled “Back to the future.”

The essay talks of how the graduate level scientists are hardly trained to appreciate the interdependence of modern research on concepts across physics mathematics and biology.  Thus most undergraduate science majors regardless of their ” concentration” don’t really know much of  disciplines outside of  hwat they focus on . Consequently later at the graduate level, they are quite at a loss working on problems like systems biology which clearly require a firm grasp of concepts across all of these disciplines. The article addresses the  question of the time and format to teach these concepts to future scientists and concludes that an undergraduate introductory class in biology is probably the best time to commence such an education. Wingreen and  Botstein then relate their experiences in conducting a seminar class at Princeton which was targeted at early graduate students made up of a mix of students with biology, physics and math backgrounds.

The Seminar class used classic papers from early and relatively recent “Biology” that drew on skills across the three fields . Each paper represented a major breakthrough in Biological understanding due to a combination of keen mathematical and physical insights applied to a biological observation.

Interestingly almost all these classical papers came from the 1940s to 1990s, a time that the authors observe ” biologists’ and physical scientists’ educations were less different than they are today”.

The seminar course at Princeton  serves as an interesting model to educate future graduate students to prepare them to function and research in the systems world.  A lot of the lessons in these early papers are curiously being re-learnt by modern day practitioners of systems biology. I think it will serve anyone wishing to appreciate the systems perspective immensely  to re-read some of these classic papers.

I for one being a trained reductionist plant to go and read all of these classic papers and attempt to “re-educate” myself . Hopefully this will help me get a better grasp of the systems approach and develop a more quantitative frame of mind.

refs: Mol 515 at Princeton

Back to the future : education for systems level biologists

I wonder what went on at Foo Camp

I just heard about Foo camp ’06 which was organized by Nature Magazine and Oreilly publishing. Previous posts on the Nascent blog made the camp sound very promising.

I am curious to find out more details and I am sure only good can come from a conference which has all the google bigwigs in attendance along with the teams from Nature Magazine and Oreilly. The conference which aimed to “encourage cross-fertilization of ideas– and to have fun” I am sure was at least a lot of the latter. It also wonder who according to Nature, Oreilly and google  are considered “a fascinating crowd of world-class biologists, chemists, physicists,
earth scientists, clinicians, historians, technologists, and writers.”

All said and done , It was nice to read from the blog posts that the conference was a good mix of fundamental science and information technology. One sure would hope that these conferences were a lttle more “open” and were widely covered by webcasts and other such media…but I guess what I mean to say is I hope I get invited the next time one of these happens.