Sample extraction from archaeological bone

Another major problem associated with the extraction of DNA from archaeological specimens is that the procedure often co-extracts impurities that can later complicate, or prevent, the study of the extracted DNA by inhibiting PCR amplification (reviewed by 5). Commonly encountered inhibitory substances found in aDNA extracted from teeth, bones, mummified tissue, and coprolites include humic acids, ftilvic acids, tannins, porphyrin products, phenolic compounds, hematin, and collagen type I (37—42). The formation of Maillard products, commonly encountered in coprolite samples, can also prevent PCR amplification by causing DNA to become inaccessibly trapped in these sugar-derived condensation products (12). As the negative results in many aDNA studies are attributed to the presence of PCR inhibitors, our extraction method outlined below pays particular attention to the problem and offers a simple test for the presence of PCR inhibitors in DNA extracts. 

In the following description and discussion of our results, various criteria derived from the literature are used to determine whether or not each sample is of adequate preservation to allow it to be confidently included in a stable isotope study. The values applied in the various criteria have been found to be associated with archaeological bone collagen that retained an isotopic composition that was reflective of its diet, while the majority of samples that had values outside of the criteria did not retain an isotopic composition that reflected diet. The values for these criteria may vary slightly depending upon the collagen extraction methodology used, and such criteria are not exact. In this study samples that fall within the criteria values are deemed acceptable, and those that do not are deemed unacceptable. ... 

Noncollagenous proteins also show variable preservation between samples from a single archaeological site. Gel electrophoresis (Fig. 2) of human bone extracts from the 7000-year-old Windover site exhibited a... 

Figure 9.4. Non-proteinogenetic amino acids in NCP s from all archaeological human bones. The values are the averages of all archaeological human bone samples taken together (cf Table 9.1). Dark columns mineral-bound NCP light columns serum proteins. Most non-proteinogenic amino acids are extracted with the serum proteins.

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