Monday, September 12, 2005

An Interesting Inovation On DNA Extraction from Fossil Bones

According to New Scientist an new technique has been developed to extract DNA from bones. Before going further a little background information is in order.

Above is a picture of the structure of bone. Bones are made up of two components. One component is the cellular component - which are called osteocytes. The other component is the matrix component. The matrix component is composed of collagen fibers with hydoxyapatite crystals, which form in the holes between fibers. The fibers are lined in arrays

and the orientation of the array determines the type of bone (more or less).

The bone matrix is formed by cells called osteoblasts which lie on the surface of the bone and secrete a substance - mainly collagen - that is then mineralized. Occasionally the osteoblast becomes embedded in the matrix (as hydroxyapatite crystals stick to the collagen fibers) and is then referred to as an osteocyte. With this, somewhat simplistic, overview of bone microstructure in mind we can now look at the new DNA extraction technique.

Most attempts to extract DNA from bone involve:

"...grinding up bone, decalcifying it, and converting the collagen matrix to gelatin. "

The DNA is then subjected to the PCR technique (a subject for another post) which multipies the amount of DNA present. Their are two problems however. First, DNA degrades quickly and burial in soil leads to contamination with foriegn DNA. Second, fossil bones can contain substences that inhibit the PCR reation.

The new technique seems to provide a way around this. This is the way New Scientist describes the new technique:

Bones form as cells mineralise, depositing tiny crystals of hydroxyapatite in a matrix of collagen fibres. Some DNA remains in the structure, and earlier studies extracted it by grinding up bone, decalcifying it, and converting the collagen matrix to gelatin. However, much of the DNA had been damaged, and samples were vulnerable to contamination.

Looking for alternatives, the team turned to crystal aggregates inside bone. They extracted the clumps by soaking bone powder in a solution containing sodium hypochlorite, the active agent in chlorine bleaches and disinfectants. Further processing showed the clumps contained strings of DNA.

More of the DNA sequences from the clumped crystals can be reproduced than DNA sequences taken from ground-up whole-bone samples, team member Noreen Tuross of Harvard University in Cambridge, Massachusetts, US, told New Scientist. The crystals also contain longer strings of better-preserved DNA, with fewer contaminants than DNA from whole bone.

Essentially, then, they are looking at extracting material trapped between clumps of the hydroxyapatite crystals that mineralize the collagen fibers, rather than trying to grind up a slice of the bone.

Added 9/20/05: The BBC has a story on this here a fact I learned from Abnormal Interests. The BBC also mentions the impact this will have on the neanderthal/homo issue quoting Stringer:

"The mitochondrial DNA on its own can't tell us if we're a distinct species," he explains.

"It depends what mammal you take. There are some species where the difference in mitochondrial DNA between us and Neanderthals would say they were a different species.

"Whereas in chimpanzees, our closest relative, you could contain the variation between us and Neanderthals in a single species alive today in Africa."

Scientists need to recover better DNA from our fossils, especially the nuclear DNA.

"Each gene has a separate evolution so to understand Neanderthals properly we will need different bits of their DNA to see if they're all telling us the same story," he adds.