There is no method that cannot be improved

13 May 2013 by Kerstin Hoppenhaus, posted in Ancient DNA, Genetics

Tomorrow, Marie-Theres Gansauge will start a new set of experiments.

In March, she has published a new method for library preparation together with Matthias Meyer in Nature Protocols. While the paper was in press, they already began working on improvements of their method.

Marie is a PhD student in the genetics department of Svante Pääbo. She joined the ancient DNA group as a student assistant during the Denisova project and has since then become a specialist in libraries.
Though the term ‚library’ may be a bit misleading. There are no labeled tomes lined up on sturdy shelves, no reading rooms, no catalogues, no obvious order. Her ‚books’ are neither written in ink, nor printed on paper. They aren’t even books. If anything, her libraries would look as if they had been through a shredder. If you could see them, that is. But Marie has never seen her libraries. All she sees are traces. Bars in gels, curves on screens, fluorescent marks, and numbers. Which for her is all she needs.

Library preparation is an integral part of modern high-throughput sequencing technologies. Before a sequence can be „read“, it needs to be sorted and labeled.

DNA sequencing, though much of a standard procedure these days, is never really simple. With ancient DNA it is still somewhat unlikely.

What Marie and her colleagues are after: to retrieve as much genetic information as possible from tiny amounts of really meager samples. The DNA they deal with comes from bones and teeth that have been baked and frozen, crushed and compressed, twisted and degraded for tens or even hundreds of thousands of years. The DNA they deal with is a mess.

To add to the mess, with ancient human remains, there is the constant threat of contamination. No matter how careful you handle them, how clean your cleanroom is, some modern human DNA can always sneak into your sample, distort your results, and you will never know. Over the past weeks, Marie has been testing a new method to eliminate modern human DNA from ancient samples. So far, she has been using „oligos“ , synthetic chains of nucleotides, to get the new procedure running. Tomorrow, for the first time, she will test her new ideas on ancient samples. And despite all care and preparation, there is no way of telling in advance, wether the new method will work. Only the experiments will tell.


UPDATE 07.07.2013: I followed Marie all the way through her library preparation. The collected posts can be found here.

Photo: Interior, Free Public Library, Sydney [1892]
. From the collection of the State Library of New South Wales (via flickr)

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