third generation genome sequencers

I have covered the upcoming revolution in genome sequencing, i.e. the development of "third generation" sequencers that can read single molecules and/or use electronic instead of optical base detection a few times now (e.g. this feature in Education in Chemistry and this essay review in C&I), so I'm really excited that we now reach another milestone in this development.

Today, Pacific Biosciences announces the full-scale commercial release of its single molecule sequencer, the PacBio RS.

Without any attempts at false modesty, the company PR declares: "The PacBio RS is a revolutionary DNA sequencing system that incorporates novel, single molecule sequencing techniques and advanced analytics to reveal biology in real time. The system delivers unprecedented sequence readlengths - over a thousand DNA bases on average. And unlike ‘second generation’ systems on the market today that typically take over one week to deliver results, the PacBio RS allows customers to obtain results in less than a day."

Details of how the PacBio machine works are included in my EiC feature, which is openly accessible here.

I have recently written two other features about third generation sequencers (one in English and one in German), which are now in press, so watch this space.

single molecule sequencing

It is ironic and an underappreciated fact that the revolution in genome research started to happen only after "the" human genome was sequenced. While the sequencing of the generic human genome relied on the classic (but, on the genome scale astronomically expensive) Sanger method, new methods developed after 2000 have led to a rapid increase in productivity and drop in costs. Now the third generation is upon us, promising genome sequences from a single copy of the DNA, and even further price drops.

I wrote a feature about these developments for Education in Chemistry, which appears in the September issue, p 144-147 (Single molecule sequencing). Now online on the EiC website (free access).

aromatase and cancer

There is a huge family of enzymes known as the Cytochrome P450 family, which I always used to find very confusing. Man species have hundreds of them, doing apparently unrelated things, so I never managed to remember anything about these proteins because whenever I came across a bit of information, it didn't seem to fit with the previous one.

Recently I've managed to figure out what it's about (the clue is in the spare oxygen atom left over after the reaction they all share -- with that they can do all kinds of chemistry) and written a couple of pieces about this field, pegged to the crystal structure of aromatase, an enzyme that plays a key role in a large number of breast tumours, and is thus a prime target for cancer therapy. Aromatase is also interesting for the chemist as it is so far the only known enzyme that can turn an aliphatic ring (such as cyclohexene) into an aromatic one (such as benzene), hence the name.

My latest musings on CytP450s, aromatase, and cancer appear in the January issue of Education in Chemistry (but not on their website, I'm afraid):

Aromatase: a target for cancer treatment.
Education in Chemistry 47, No 1, 22-24.

This is also my first publication of 2010, hooray!

towards better biofuels

I've written a feature article on second generation biofuels (i.e. those that make use of waste materials or at least of whole plants as opposed to edible parts of food crops), which is out in the May issue of Education in Chemistry and on open access.

The story also made it onto the cover of the magazine: