Tuesday, January 24, 2012

Posting latex equations in blogger.

When using the mathjax javascript code found at:


One can post mathematical equations using latex as in the following example:

LaTeX Code:
When a \ne 0, there are two solutions to ax^2 + bx + c = 0 and they are
x = {-b \pm \sqrt{b^2-4ac} \over 2a}.

RENDERED Equations:
When \(a \ne 0\), there are two solutions to \(ax^2 + bx + c = 0\) and they are
$$x = {-b \pm \sqrt{b^2-4ac} \over 2a}.$$

Great, so now I can make posts with simple matrix equations if necessary.

Tuesday, January 10, 2012

Latest News from Chemical and Engineering News

To start the new year we look at the headlines related to nucleic acids in Chemical and Engineering News.
In the first week of the year two nucleic acid notes have been written in C&EN. One concerns genetic engineering modifying DNA sequences by using Zinc-finger nuclease proteins, and the other also concerns genetic engineering but this time at the expression level by suggesting a protocol to program gene expression using so-called "RNA-devices".

Targeted chromosomal duplications and inversions in the human genome using zinc finger nucleases
Hyung Joo Lee et al.
Genome Research advanced publication (2012)

Jin-Soo Kim and coworkers at Seoul National University have designed Zn-finger nucleases that target specific genomic sequences in human embryonic kidney cells and are able to induce sequence duplication and inversions.

Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression
James M. Carothers, et al.
Science334 1716-1719 (2011)

The following is just a copy and paste of the abstract from the article due to how hermetic it seems to my understanding.
"The models and simulation tools available to design functionally complex synthetic biological devices are very limited. We formulated a design-driven approach that used mechanistic modeling and kinetic RNA folding simulations to engineer RNA-regulated genetic devices that control gene expression. Ribozyme and metabolite-controlled, aptazyme-regulated expression devices with quantitatively predictable functions were assembled from components characterized in vitro, in vivo, and in silico. The models and design strategy were verified by constructing 28 Escherichia coli expression devices that gave excellent quantitative agreement between the predicted and measured gene expression levels (r = 0.94). These technologies were applied to engineer RNA-regulated controls in metabolic pathways. More broadly, we provide a framework for studying RNA functions and illustrate the potential for the use of biochemical and biophysical modeling to develop biological design methods."