You know about adenine, thymine, guanine, cytosine. Now get used to SICS and MMO2.

In this JACS article published this month, researchers at the Scripps Institute reported the identification of these two artificial bases. They are efficiently incorporated during in vivo DNA synthesis by the Klenow fragment of E.coli DNA polymerase and pair together with high fidelity.

At the moment the applications for these new bases are are limited mainly to providing new building blocks for the in vivo synthesis of DNA-based nanostructures. However, work is ongoing to incorporate them into living cells and make them code for specific amino acids. Although it is far from clear whether this can be done, if achieved it will lead to some new, very powerful tools for protein engineering.

In the old days, restriction digests were a great excuse for long lunch breaks. Come back 1-2 hours later and it’s done.

But, just to ruin our fun, Fermentas then NEB started to offer ranges of restriction enzymes that do their job in 5 minutes. Nothing changed with these enzymes - someone just figured out that 60-120 minutes was just a number selected at random, probably by someone who wanted a longer lunch break.

But what about this? Read more »

One of the several popular views regarding the origin of life stems from thermodynamics. Harold Morowitz refers to it as “Metabolism recapitulates biogenesis”.

In PLoS Biology there’s an interesting essay that was submitted posthumously by the chemist Leslie Orgel on this subject - The Implausibility of Metabolic Cycles on the Prebiotic Earth. Orgel takes a hearty dose of skepticism to contemporary hypotheses presented by Wächtershäuser and Morowitz^3,4, including the reverse citric acid cycle in particular. For clarification: the reverse citric acid cycle has been proposed to have operated nonenzymatically, not only fixing carbon but (in a chaotic soup-like mixture of inorganic catalysts) also producing metabolic intermediates for many of the amino acids, nucleotides, etc., required for the later RNA world.
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Form follows physics in the fly eye, say Sascha Hilgenfeldt, Sinem Erisken, and Richard Carthew

Simple forces, complex shapes: While most biological features appear complex in their geometries and varieties of components, appearances can be deceiving. That finding is supported by a recent modeling study by Hilgenfeldt, et al., looking at the arrangement of cone cells in the Drosophilia eye. They found that cell elasticity and adhesion strength alone can explain the cell arrangement, into the image shown (source: Hilgenfeldt/NAS).
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Reports, grant applications, theses, manuscripts, essays, patent applications, your Nobel Prize acceptance speech.

As a scientist, there are so many things you have to write. And writing them well is important. Writing clearly and with structure allows you to get your message across and avoiding grammatical errors stops you looking stupid in front of your audience in Stockholm.

But writing is just one of the many transferrable skills you have to master to get on in science - how will you ever get the time to work on it? Read more »

Continuing with the recent theme on model organisms, there is the nematode (roundworm) Caenorhabditis elegans. This organisms is particularly useful owing to the fact that it has very defined development patterns involving fixed numbers of cells, and it can be rapidly assayed for abnormalities. Further, strains are cheap to breed and can be frozen. When subsequently thawed they remain viable, allowing long-term storage. Because the complete cell lineage of the species has been determined, C. elegans has proven especially useful for studying cellular differentiation.
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Please read and pass this life-saving information on to your friends.

A chemical that all of us use in the lab has turned out to be highly dangerous. It is an asphyxiant, can cause severe burns and is a contributor to the greenhouse effect. Medical organizations all over the world confirm it to be responsible for killing thousand of people, of all ages, every year.

Although there is no confirmed causative effect, there is also evidence to suggest that it is involved in the formation of cancer and has been found in excised tumors of EVERY kind. Read more »

There were some great posts in the science blogosphere this week… here are my favorites! Read more »

The big biotech news of the week has been the successful construction of an artificial bacterial genome by J. Craig Venter et al., chemically assembled from scratch. While the genome is little more than a watermarked version of the wild bacterium Mycoplasma genitalium, it is now technologically feasible to construct custom genomes for bacteria of our choosing. Jorge Cham of PHD Comics has the appropriate levity for the situation:

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Another popular model organism is the African Clawed Frog, Xenopus laevis, which is extremely useful for studying development and cellular physiology, owing to its particularly large and easy manipulable oocytes and embryo.
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