Sunday, 5 June 2011

This Week in Science (June 5, 2011)

Just a pair of papers for this week's TWIS. I haven't had much time to dedicate to reading new research this week, but I'll have more next week!

To start off, I'll point you in the direction of the infamous "arsenic bacteria" paper, which has finally been published in Science after languishing on Science's pre-print server for months. This paper, if you're unfamiliar with it, claimed to show the discovery of a new species of bacteria that utilized arsenic in its DNA rather than phosphorus. It was torn to shreds by critics due to problems in the authors' methodology and doubts about the results - and for good reason. Science's response to all the negative criticism that the paper has recieved has been to publish a list of criticisms (and the authors' responses) along with the paper. Jerry Coyne has a good rundown of the paper's publication on his blog.

Continuing on:

  • DNA computing and square roots  - Published this week in Science is a paper by L. Qian and E. Winfree detailing an interesting advancement in DNA computing. The authors were able to design and string together DNA logic gates to create a simple molecular computer able to calculate square roots. Creating a DNA logic gate is actually quite simple, and there are multiple ways it can be done. The authors did it by using a "seesaw gate"design: the gate consists of a short stretch of DNA that can pair with multiple different sequences. One such sequence is added as an "input", which competes and replaces a second sequence that is already bound to the gate. This replaced sequence becomes the "output", which is then free to act as an input for a second gate. Gates can be strung together to create more complicated systems. The authors devised a way to string such gates together to create a system that could calculate square roots. As cool as this is, though, this early biological calculator takes a while to complete calculations - up to eight hours. Nevertheless, this is a big step towards creating bigger and more powerful DNA computers. A more detailed summary of the paper has been posted on Wired, which I highly recommend, as they do a better job explaining logic gates than me!
(L. Qian and E. Winfree . "Scaling up digital circuit computation with DNA strand displacement cascades" . Science . 2011 . 332(6034): 1196-1201, doi: 10.1126/science.1200520)

  • Proteins successfully extracted from mammoth bones - A paper published this week1 in the journal Geochimica et Cosmochimica Acta describes the successful extraction of collagen protein from 600,000 year old mammoth bones. The authors were investigating the idea that peptide mass spec. could be used to identify fossils; that is, if you could determine the sequence of proteins in the fossil, you could compare the sequences to a database of known proteins. Finding proteins which are a close match would narrow down the identity of the fossils in question. To test this idea, the authors used bones from two mammoth fossils and one mastodon fossil. After grinding samples of the fossils into powder, they performed a series of chemical extractions and washes, then prepared them for mass spec. This allowed them to sequence the extracted protein, which was confirmed as collagen. The sequence data was good enough that the collagen - and consequently, the fossils - were correctly identified as being related to elephants. The authors were even able to use this data to distinguish the samples as elephantid (mammoth) or mammutid (mastodon). These findings are important for two reasons: first, they show that proteins can successfully be recovered from fossils as old as 600,000 years; and secondly, they demonstrate that protein mass spec. can be used to correctly identify ancient fossils (or at the very least, identify the closest living relative). Exciting indeed!
(M. Buckley, N. Larkin, and M. Collins . "Mammoth and Mastodon collagen sequences; survival and utility" . Geochemica et Cosmochimica Acta . 2011 . 75(7): 2007-2016

1. This paper actually wasn't published this week, it was published in April. For whatever reason, it looks like it only made the news now.

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