Fagernäs, Zandra, García-Collado, Maite I., Hendy, Jessica orcid.org/0000-0002-3718-1058 et al. (4 more authors) (2020) A unified protocol for simultaneous extraction of DNA and proteins from archaeological dental calculus. Journal of archaeological science. 105135. ISSN 0305-4403
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.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2020 The Authors. |
Keywords: | Ancient DNA,Dental plaque,Metagenomics,Oral microbiome,Palaeoproteomics |
Dates: |
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Institution: | The University of York |
Academic Units: | The University of York > Faculty of Arts and Humanities (York) > Archaeology (York) |
Depositing User: | Pure (York) |
Date Deposited: | 20 Jul 2020 15:20 |
Last Modified: | 13 Nov 2024 09:14 |
Published Version: | https://doi.org/10.1016/j.jas.2020.105135 |
Status: | Published |
Refereed: | Yes |
Identification Number: | 10.1016/j.jas.2020.105135 |
Related URLs: | |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:163514 |
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