Scientific Method / Science & Exploration

Neanderthal DNA sequenced

Combine DNA recovered from a well-preserved skeleton with an advanced new …

It's a fairly commonly-held view that genetic material like DNA is fragile stuff.   Recoverable from a week-old body floating in the river, but not the sort of thing that stands up to being fossilized slowly over 100,000 years.  But with a bit of hard work in the form of advances in the DNA technology, and a little luck discovering a particularly well preserved specimen, extinct individuals can still give up their genetic secrets.

And that's just what one 47,000 year old Neanderthal has done.  A team of scientists at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, recovered small amounts of DNA from a male Neanderthal skeleton, and using a novel method of sequencing have sequenced around 1 million base pairs of its genome.

Early analysis has so far shown that the Neanderthal Y chromosome is quite different to ours, suggesting that there wasn't much breeding between H. sapiens and H. neaderthalensis.  It is estimated that H. neaderthalensis last shared a common ancestor with us around 315,000 years ago.

This is quite exciting news, but if anything I'm more bowled over by the method they used to sequence the DNA.  Developed by 454 Life Sciences, a biotech company in Connecticut, the DNA is broken into small fragments and attached to beads.  Once one end is immobilized and converted into a single strand template, the beads are then dispensed into an assay plate, where each well is just large enough for a single bead. 

Surrounding this DNA bead are lots of much smaller beads that contain a number of enzymes, including luciferase.  This is the enzyme that fireflies use to glow.  DNA bases (A, C, G, T) are then washed over the plate, one at a time.  DNA polymerases use these bases to create a complimentary strand to the template, and when a base gets incorporated, the release of pyrophosphate activates the enzyme beads, which produce a photoluminescent signal.  If multiple bases are incorporated, in a AAAAA repeat, for example, the flash is brighter.  The reaction plate sits on top of a CCD, and each flash, plus its intensity, is measured.  The whole process is repeated to account for the length of the template DNA, and a DNA sequence can be created for each well by comparing the light emissions to the flow of nucleotide bases.

If that seems like so much gibberish to you, there's a movie you can watch that might clear it up, but rest assured, it's pretty cool stuff.  As each reaction plate contains 200,000 wells, huge amounts of DNA can be sequenced  in a rapid time, ready to be stitched together.  As a method to use in a study, this has almost everything.  Expensive equipment, very expensive reagents, the ability to generate more data than one would think feasible - the only thing it's missing is a laser! Not only that, but all this from tiny amounts of sample DNA. Microbeads seem to be cropping up in lots of assays now.  You can attach different antibodies to different color beads and use them to look for diffferent cytokines, hormones or other substances in the same small volume of a sample - a great selling point when you're trying to analyse lots of different variables and there's only so much to go round.  

I only have to think back not very far to my PhD and compare the techniques I had access to compared to those I take for granted now to see how fast things are moving. 

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