Wednesday, December 9, 2009

More large RNA's in the horizon.

Nature 462, 656-659, 2009.
From Ronald Breaker's lab at Yale.

In a recent visit of Dr. Anna Pyle (from Yale) to Rutgers I informally asked about the possible existence of new large RNA structures. She definitely was well informed of new studies which show evidence for this, and I was a bit puzzled why I hadn't come across them. Now my guess is that this is because she knew of Breaker's lab results before publication, actually, perhaps she mentioned that there was going to be such a publication coming out..., my feeble memory!.
Our studies are completely dependent on large structural datasets for developing structure-knowledge based statistical models. I am very happily surprised to see evidence for the existence of such data so soon.

One post-doc at our lab who knows that I'm interested in RNA pointed out a paper of possible interest in Nature. Initially I thought that the paper would be related to some other area of RNA research of perhaps immediate medical relevance which I wouldn't be directly interested in from the structural point of view, well... I was clearly wrong.

The paper says that using sequence covariation they have found large ncRNA's in BACTERIA. This came as a surprise since I was believing the statement by Sebastian Doniach in Physics Today November issue, stating that only 1% of DNA in bacteria is non-coding. It seems from what I understand of the Nature article, that there is more than 1% of this DNA that makes up "exceptionally structured noncoding RNA's".
It's also important to note that what they call large ncRNA's are RNA's with a content greater than a 100 bases.

Wednesday, December 2, 2009

Chemical Graph Theory

Volume 51 of the Advances in Quantum Chemistry has an interesting chapter by Ivan Gutman (From Kragujevac University in Serbia) about the influence of Mathematical Chemistry in Mathematics.
He argues that the cases of:

1) Graph Energy.
2) Connectivity (Randic) Index.
3) Graph Spectral Theory from HMO Theory. -- hard to tell --
4) Wiener Index and Graph Distance.
5) Kekule Structures.

Can all be connected in one way or the other to mathematical developments, and in some cases, precede them.

I guess the most puzzling and interesting conclusion that can be drawn from this 2006 article is that chemistry based on graphs and graph theory mathematics can arrive at the same conclusions using quite different frameworks of thought. I believe the same could be argued for areas of Physics and Biology, and therefore this is yet another positive justification for highly interdisciplinary work in the exact physical and natural sciences and a weak argument against absolute rationalism.