Streptavidin rocks again!

Streptavidin is one of the most well understood ligand-protein binding complex. It is naturally composed of 4 separate chains arranged into 2 dimers. The attempt to make a stable single chain dimer of streptavidin for amendability to phage and chip display has long remained unsuccessful because of the streptavidin binding site is made up of portions of both dimers therefore when the tetrameric complex is disrupted, the biotin binding pocket is lost.

Charle Cantor and his group in Boston University, MA just discovered a really interesting story about the mutant streptavidin dimer in that despite significant reduction in biotin binding affinity, the mutant is able to bind B4F (biotin-4-fluorescein) at 100000-fold higher than the ability to bind biotin.

Moreover, though the B4F binding is at a very high affinity, it is reversible unlike the traditional streptavidin-biotin system that binds very tightly so that draconean condition will be required for releasing of biotin.

Reference:

1. Allison D, Nature Methods 2005 July 22;2(8):573
2. Aslan FM, Yu Y, Mohr SC, Cantor CR.,Proc Natl Acad Sci USA. 2005 Jun 14;102(24):8507-12.
   

synthetic biology

cool

some more interesting stuff

http://www.sciencemag.org/sciext/125th/
http://www.biomachina.org/
http://www.ub.rug.nl/eldoc/dis/science/
http://www.ph.tn.tudelft.nl/Courses/FIP/noframes/fip-Contents.html
http://nramm.scripps.edu/
http://nramm.scripps.edu/seminars/2003/cryoem/lectures/
http://www.yaleglobal.yale.edu/
http://www.yaleinsider.org/
http://us.expasy.org/
http://saturn.med.nyu.edu/research/sb/stokeslab/image-analysis.html
http://its.med.yale.edu/software/mac/powerpoint_files/logo_listings2.html
http://partners.adobe.com/public/developer/opentype/afdko/topic_feature_file_syntax.html#1

Cyberman

After a long period of terrible insomnia. Today I have had a damn good rest all day.

I start writing an article in Thai again about the Cyborg. Indeed, It is such a pain in the ass to do something I haven't done for at least 5 years.

Cybernetic organism is something really interesting. I never know that this technology exists in a matter of 30 years by a pioneer in the field of wearable computer and, of course, cybernetics, Steve Mann, after the term was coined by Manfred E Clynes and Nathan Kline in 1960 in the NASA human space exploration.

Mann start wearing his machine 25 years ago and he live his life with it most of the time. In 2002, he was confiscated by the airport security in Canada and was enforced to remove his cybernetic setup. By which, He was having problem with nausea and many symptoms so he had to board on the wheelchair like a handicap. It is pretty obvious that he has integrated himself to the technology far too intimately and far too long. Therefore he, ultimately, cannot endure separating from it anymore.

Mann's invention is actually really interesting. His eyetap is capable to freeze moving object like wheel of running car or rotating propeller of a plane. Moreover it can record still image of what he is looking at at his whim.Stopping object from moving gives him an opportunity to have better face and detail recognition as well as ability to see something he cannot visualize clearly with his natural eyes. His wearable computer ,in addition, augments his remembrance by giving him extra-memory where he can access it anytime he would want to when it is attached to his body.

Well! Even though some people think he is just another blasphemist who is trying to enhance his ability to against god, he is still continue doing his amazing and extraordinary works and hope that one day it might change the way of our life to the better direction.

Big picture

Discussion with Fenny is always intellectual and interesting.
Having been discussing with many people always taugh us something at least how they think.

Fenny reccommend me a book so-called "A PhD is not enough" by Peter J Feibelman.

The first chapter is about how to deal with the project and assignment and so on.

We were discussing part of this book espectially how to see the big picture of the whole project we have to do, what is the goal and what is the way to achieve that goal.

We have also finally come to the conclusion that, usually, if we ask people about the technical detail of how to conduct our work from some experts without telling them the outline or the big picture of the work itself, they are not going to be interested and, usually, they will not pay attention on whatever we are asking even though it is a total match on their expertise. This might be because of the fact that they don't see how important the work is to them or they dont really know exactly what the question is...

Anyway, I found a review of this book byDerek R. Oliver, Ph.D

" 1 - "Do you see yourself in this picture"In the preface, Feibelman describes the development of young scientists as a " ...Darwinian selection process ..." based on "benign neglect." With this assertion in mind, he describess a number of case histories that illustrate various intellectual, structural and iterpersonal "traps" that exist in the early (PhD/postdoc) stages of a science career. These examples are brief enough to so that the reader doesn't lose the overall thread of the chapter, yet contain enough details that the cases illuminate the points being developed.Emphasis is placed on the need for an aspiring scientist to find a mentor to over come the "neglect" mentioned in the preface. The choice of such a person leads into some of the aspects of the next Chapter."

Well! I think I will need to read this book myself to be able to say something more.

A Ph.D. Is Not Enough: A Guide to Survival in Science by Peter J Feibelman

Book review : http://scijobs.freeshell.org/c-derk.htm

Shaker structure revealed

my gosh! Shaker K channel is humongous, Rod Mackinnon rocks again.
According to his new duopapers with Steve Long in Science, The shaker type Kv1.2 Potassium channel structure has been solved down to 2.9 A resolution which also give us some glim of how the voltage gated potassium channel works.

The contradiction of the sensor movement is in a very big argument. I just waded through his papers a couple times without really concentrating myself reading them.

However, the structure is really beautiful and the crystal packing seems to have a lot less contraint than the KvAP. Even if Steve add back the magic mixture of lipid into the crystal trial, the final structure doesnt show any density of the lipid at all which will leave a mystery if the crystal packing still effects the transmembrane part of the protein becasue of

1. There is a tremendous space between the pore domains in the crystal which is likely to be filled with lipid However, this may not be a big issue because it is also possible that the lipid itself is too fexible to be able to resolved any structure by diffraction.
   
2. The pore domain still interact with Beta region of another Kv1.2 channel which may somehow distort the orientation of the flexible helices in the crystal but this shouldnot be a problem either.

Well! this structure indeed give us an enormous information about the eukaryotic potassium channel and provides a lot of insight into the movement of the voltage sensor of the famous Shaker channel.

All I could say is that "his work is always extremely impressive"

Gelernter & Silver Sand Beach

Originally, we planed to go canoeing. Unfortunately, we cannot find launch point so we went back to VA hospital where my friends work.

A friend of mine told me about his advisor.I found out that his PI's brother is very famous computer professor who has been contributing significantly in parallel computing (esp. in tuple space) and developing of Linda programming system.

After the glorious day, Prof Gelernter got a mailbomb by Unabomb who was identified as "Theodore Kaczynski" former mathematic Asst Prof at UC Berkeley.

Fortuitously, Prof. Gelernter is still alive. Even though he suffers from the permanent damage with his right hand and eye, Still he published a book "Drawing Life: Surviving the Unabomber" and was, subsequently, nominated to be and finally become a member of National Council on the Arts. In addition, he is now a seminal contributors of the rightist magazine (rightist are referred to the right-wing, the political right in left-right politics)

Finally, we stop by the Silver Sand Beach in Milford for unintentional sunbathing and picnic. It was fun even if I got darker by -2 according to photographic grayscale.

Anyway, after all, I then look up more about Unabomber. I found that there are many more intelligent mathematical killers other than Kaczynski.

The Zodiac (a.k.a. serial killer) is another remarkable one. He/She had continuously killed people by knife and shortgun in the full moon night and remains unidentified even if he left a bunches of clues and ciphers.

Right after I went home to rid all my carry on, I went to Starbuck to have coffee where I was impressed by a fine drawing of a local artist. We had had some chat about art and life and I was shock after realizing that he has some problem with bipolar disorder.

My goodness! Despite his psychological problem, this guy has potential in arts. That tells me one thing; you cannot judge people from their station and blah blah...

At The Beginning

Beginning my blog in english. I don't know how much time I will be spending on this but we shall see anyway

Deep in thought

I just found a really interesting paper in Nature (436, Jul 2005) saying that the

"Cybernetics thingy just jumps into psychiatry business."

Neurosurgeons in Catholic University of Leuven in Belgium and in University of Cologne, Germany have individually successfully employed the technology so-called DBS or Deep Brain Stimulation which basically is a type of implantation of a stimulator into chest or belly of the patient where they can control it remotely. The stimulator is connected to several microelectrodes which are inserted into an extremely precise neuroanotomical target in the brain to help normalizing neuronal activities of the problematic neuron in Obsessive-Compulsive Disorder (OCD) patient.

It is amazing how they actually visualize the brain (fMRI) and make a tomogram (Positron Emission Tomography) and finally pinpoint where exactly to put electrode to stimulate the brain. The team originally believe that the high frequency pulse from stimulator merely block excitatory neuron, by which, it damp down all the circuit. Low frequency does the same but by stimulating the inhibitory neuron instead.

Another cool stuff after having heard about implant of the first real cyborg guy "Matt Nagle".

Whewww !!