Minimally Destructive DNA Extraction from Ancient Teeth
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB32750 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4896440.fastq.gz | Fastqsanger.gz | |||
| ERR4896450.fastq.gz | Fastqsanger.gz | |||
| ERR4896460.fastq.gz | Fastqsanger.gz | |||
| ERR4896470.fastq.gz | Fastqsanger.gz | |||
| ERR4896480.fastq.gz | Fastqsanger.gz |
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Project description:Ancient DNA sampling methods-although optimized for efficient DNA extraction-are destructive, relying on drilling or cutting and powdering (parts of) bones and teeth. As the field of ancient DNA has grown, so have concerns about the impact of destructive sampling of the skeletal remains from which ancient DNA is obtained. Due to a particularly high concentration of endogenous DNA, the cementum of tooth roots is often targeted for ancient DNA sampling, but destructive sampling methods of the cementum often result in the loss of at least one entire root. Here, we present a minimally destructive method for extracting ancient DNA from dental cementum present on the surface of tooth roots. This method does not require destructive drilling or grinding, and, following extraction, the tooth remains safe to handle and suitable for most morphological studies, as well as other biochemical studies, such as radiocarbon dating. We extracted and sequenced ancient DNA from 30 teeth (and nine corresponding petrous bones) using this minimally destructive extraction method in addition to a typical tooth sampling method. We find that the minimally destructive method can provide ancient DNA that is of comparable quality to extracts produced from teeth that have undergone destructive sampling processes. Further, we find that a rigorous cleaning of the tooth surface combining diluted bleach and UV light irradiation seems sufficient to minimize external contaminants usually removed through the physical removal of a superficial layer when sampling through regular powdering methods.
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Project description:Dental calculus is becoming a crucial material in the study of past populations, with increasing interest in its proteomic and genomic content. Here we suggest further development of protocol for analysis of ancient proteins and a combined approach for subsequent ancient DNA extraction. We tested the protocol on recent teeth. We then applied the optimised protocol to ancient teeth to limit the destruction of calculus, as it is a precious and irreplaceable source of dietary, microbiological, and ecological information in the archaeological context. Finally, the applicability of the protocol was proven on samples of ancient calculus.
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Project description:The combination of multi-omic techniques, e.g. genomics, transcriptomics, proteomics, metabolomics and epigenomics has revolutionised studies in medical research. These are employed to support biomarker discovery, better understand molecular pathways and identify novel drug targets. Despite concerted efforts in integrating omic datasets, there is an absence for the integration of all four biomolecules in a single extraction protocol. Here, we demonstrate for the first time a novel, minimally destructive integrated protocol for the simultaneous extraction of artificially degraded DNA, proteins, lipids and metabolites from pig brain samples. We used an MTBE-based approach to separate lipids and metabolites, followed by subsequent isolation of DNA and proteins. We have validated this protocol against standalone extraction protocols and show comparable or higher yield of all four biomolecules. This integrated protocol is key towards facilitating preservation of irreplaceable samples while promoting downstream analyses and successful data integration by removing bias from univariate dataset noise and varied distribution characteristics. Keywords: deg
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Project description:Teeth are a well-known source of information for paleoanthropologists. Here, we established the ancient dental metaproteomes in several samples from historic sites. The shotgun metaproteomics analysis relies on a iterative search strategy for the identification of the proteins and their origins.
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Project description: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 lines of evidence, 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 archaeological dental calculus. We evaluate the protocol on dental calculus from a range of ages and estimated preservation states, and compare it against standard DNA-only and protein-only protocols. We find that most aspects of downstream analyses are unaffected by the unified protocol, although minor shifts in the recovered proteome can be detected. Protein recovery depends on both the amount of starting material and choice of extraction protocol, whereas DNA recovery is significantly lowered through the unified protocol. However, DNA recovery from dental calculus is generally very high, and we found no differences in DNA fragment characteristics or taxonomic profile. In conclusion, the unified protocol allows for simultaneous extraction of two complementary lines of evidence from archaeological dental calculus without compromising downstream analyses, thereby minimizing the need for destructive analysis of this finite resource.
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