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  A unified protocol for simultaneous extraction of DNA and proteins from archaeological dental calculus

Fagernäs, Z., García-Collado, M. I., Hendy, J., Hofman, C. A., Speller, C., Velsko, I. M., et al. (2020). A unified protocol for simultaneous extraction of DNA and proteins from archaeological dental calculus. Journal of Archaeological Science, 118: 105135. doi:10.1016/j.jas.2020.105135.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0006-4ECA-0 Version Permalink: http://hdl.handle.net/21.11116/0000-0006-4ECB-F
Genre: Journal Article

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 Creators:
Fagernäs, Zandra1, Author              
García-Collado, Maite I., Author
Hendy, Jessica2, Author              
Hofman, Courtney A., Author
Speller, Camilla3, Author              
Velsko, Irina Marie1, Author              
Warinner, Christina2, Author              
Affiliations:
1Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2074310              
2Kostbare Kulturen, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2591692              
3Archaeology, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2074312              

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Free keywords: Ancient DNA, Palaeoproteomics, Oral microbiome, Dental plaque, Metagenomics
 Abstract: Archaeological materials are a finite resource, and efforts should be made to minimize destructive analyses. This can be achieved by using protocols combining extraction of several types of biomolecules or microparticles, which decreases the material needed for analyses while maximizing the information yield. Archaeological dental calculus is a source of several different types of biomolecules, as well as microfossils, and can tell us about the human host, microbiome, diet, and even occupational activities. Here, we present a unified protocol allowing for simultaneous extraction of DNA and proteins from a single sample of archaeological dental calculus. We evaluate the protocol on dental calculus from six individuals from a range of time periods and estimated preservation states, and compare it against previously published DNA-only and protein-only protocols. We find that most aspects of downstream analyses are unaltered by the unified protocol, although minor shifts in the recovered proteome can be detected, such as a slight loss of hydrophilic proteins. Total protein recovery depends on both the amount of starting material and choice of extraction protocol, whereas total DNA recovery is significantly reduced using the unified protocol (mean 43%). Nevertheless, total DNA recovery from dental calculus is generally very high, and we found no differences in DNA fragment characteristics or taxonomic profile between the protocols. In conclusion, the unified protocol allows for simultaneous extraction of two complementary lines of biomolecular evidence from archaeological dental calculus without compromising downstream results, thereby minimizing the need for destructive analysis of this finite resource.

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Language(s): eng - English
 Dates: 2020-04-242020-06
 Publication Status: Published in print
 Pages: 11
 Publishing info: -
 Table of Contents: -
 Rev. Method: Peer
 Identifiers: DOI: 10.1016/j.jas.2020.105135
Other: shh2580
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Title: Journal of Archaeological Science
Source Genre: Journal
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Publ. Info: London : Academic Press
Pages: - Volume / Issue: 118 Sequence Number: 105135 Start / End Page: - Identifier: ISSN: 0305-4403
CoNE: https://pure.mpg.de/cone/journals/resource/954922648108