Saturday, May 16, 2009

pushing the limit on DNA Origami : Nanoscale capped-box of DNA

Foreword :

A recent paper (May, 2009) in Nature talks about the most recent addition to the art and science of DNA-Origami.


Introduction to the work:

A multidisciplinary team of 15 researchers have created a DNA 'strong-box' adorned with a lid. This is the newest addition to the spectacular 'art-science' of "DNA origami" - in which oligonucleotides (short strands of nucleic acid) are used to fold longer strands of DNA into complex structures.

The allure to make 3-D DNA nanostructures had been there for quite some time, and the paper successfully attempts just that.

Methodology :

Initially the researchers wrote a computer program that would determine the genetic sequences needed to make their nanoscale 3-D box. The program begins with a digital model of a very long strand of DNA. Then, in accordance with the desired shape, it selects some 250 oligonucleotides that will attach to the DNA and aid its assembly into the desired form.

The team could also make compatible locks to their strong-boxes. A short sequence attached to one side of the box would cause it to unstitch and open in the presence of another short DNA 'key' sequence.

Promising applications :

These could be potentially used as 'cages' to deliver drugs or act as nano-biosensors.

Reference citations :

1. Andersen, E. S. et al. Nature 459, 73–76 (2009).

2. Douglas, S.M., Chou, J. J. & Shih, W. M. Proc. Natl Acad. Sci. USA 104, 6644–6648 (2007).

3. Rothemund, P. W. K. Nature 440, 297–302 (2006).


Thursday, May 14, 2009

"Selfish-Sperm" : Perfect Nemesis of Embryo Development.

.....Got hold of few papers that talk about Sperms which accumulate mutations as men age. Such mutations accumulate over time and offer a survival advantage to the sperm (hence, 'Selfish-Sperm'), but ultimately harm the offspring.

Most studies focus on the female germ line (oocytes), and very few studies have been able to examine directly mutations affecting the male germ line. Using techniques developed over the last seven years, Dr.Wilkie has attempted to answer just that.


Reference / Source citations :

Science 1 August 2003:
Vol. 301. no. 5633, pp. 643 - 646
Evidence for Selective Advantage of Pathogenic FGFR2 Mutations in the Male Germ Line
Anne Goriely, Gilean A. T. McVean, Maria Röjmyr, Björn Ingemarsson, Andrew O. M. Wilkie*

Science 2003 301: 606–7
There's something curious about paternal-age effects.
Crow JF.


The listed paper and several reports thereon point out that sperms accumulate mutations over time in several genes, but in some of them, notably, RET, FGFR2 and FGFR3, the rate at which errors are picked up is many times the normal rate of mutation in sperm.

The mutation in FGFR-2, on which the study focusses, causes several severe genetic disorders, including Apert-syndrome, which causes premature fusion of the skull bones and webbing of the fingers and toes. It occurs in around one in every 70,000 live births.

Sayf Dr. Wilkie "In around 80 cases of Apert syndrome and two related disorders, without exception the faulty gene has come from the healthy father."

On the basis of the data, the researchers conclude that the genetic mutation leading to Apert syndrome occurs rarely, but offers cells carrying it some growth advantage. One speculation is that the mutation affects the cell division cycle of the stem cells that give rise to sperm. Instead of producing equal numbers of sperms and stem cells to produce future sperm, they produce excess stem cells. These mutant cells, generating mutant sperm, gradually increase in number relative to its non-mutated, wild-type counterparts.

Largely since the mutation has no ill-effects in the testes, as men age the sperm-cells carrying the mutation become disproportionately common, increasing the likelihood that one will successfully fertilise an egg.

This is where the actual problem lies, as the paternally-contributed mutation severely impairs the ability of FGFR2 to function (which is absolutely critical) during development of the embryo.


Google adds options to help searchers get to the point

Reference citation :

The Scientific American website.

By Larry Greenemeier in 60-Second Science Blog

( )


Google has come up with a better idea to customize ones search by adding a feature called "Search Options" in an upgrade its uber-popular search engine.
Now searchers can reorganize the result of a key word search to emphasize particular kinds of links, such as video, audio etc.

"To meet the increasing demand of mobile users, Google also introduced a novelty application called Sky Map for mobile phones running the company's Android operating system that creates a map of the night sky that changes depending upon the user's location.

Google today also introduced something called Rich Snippets, which improves upon the blurbs provided under each link. When searching for a particular restaurant, for example, Rich Snippets will pull up a restaurant review while identifying who wrote it and when it was written."

Wednesday, May 13, 2009

An Essay in 'Nature' : "Is Free Will an illusion ?"

Reference citation :

Is free will an illusion?
NATURE|Vol 459|14 May 2009, 164-165

Foreword :

The essay has an interesting debate as to what constitutes Free Will and what doesnt.........and attempts to explain a very long and intriguing philosophical conundrum scientifically...... (?)


The author Martin Heisenberg is professor emeritus in the department of biology at the University of Würzburg, Germany, and works with fruit-flies.

He initiates the debate emphasising on the dictum that response is independant of stimulus, and unicellular animals move/locomote in ways which are different from that of multicellular organisms where synchrony between parts is needed to maintian a whole, but which could be completely independant of external stimulus, a fact corroborated by the earlier appearance of motor functions as compared to sensory system during developemnt.

On the basis of his experiments on fruit-flies where they (the flies) generate 'new' actions (never known to have been performed earlier by other flies), in the face of clear adversity......the author decides to explore and explain Freedom in scientific terms.

He first defines Freedom in the words of the great German philosopher, Emmanuel Kant, as when "a person acts freely if he does of his own accord what must be done" which implies a non-deterministic, stochastic behaviour, and then goes on to argue on the basis of his belief that "we need not be conscious of our decision-making to be free" as opposed to "freedom as the ability to consciously decide how to act"......

The essay though interesting, leaves quite a bit more explaining before a point could be fully made, especially when a scientific explanation is extended for a largely metaphysical question. Maybe more intuitive experiments on fruit-flies as well as more complex beings ('higher animals') should address this philosophical conundrum clearly.