Ancient human dental calculus
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ABSTRACT:
PROVIDER: PRJNA608541 | ENA |
REPOSITORIES: ENA
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Project description:Metagenomic analysis of ancient human dental calculus from Italy and the Balkans
| PRJEB44313 | ENA
Project description:Metagenomic analysis of dental calculus of ancient baboons
| PRJEB34875 | ENA
Project description:Archaeological dental calculus has emerged as a rich source of ancient biomolecules, including proteins. Previous analyses of proteins extracted from ancient dental calculus revealed the presence of the dietary milk protein β-lactoglobulin, providing direct evidence of dairy consumption in the archaeological record. However, the potential for calculus to preserve other food-related proteins has not yet been systematically explored. Here we analyse shotgun metaproteomic data from 100 archaeological dental calculus samples ranging from the Iron Age to the post-medieval period (8thC BC - 19thC AD) in Britain, as well as dental calculus from contemporary dental patients and recently deceased individuals, to characterise the range and extent of dietary proteins preserved in dental calculus. In addition to milk proteins, we detected proteomic evidence of foodstuffs such as cereals and plant products, as well as the digestive enzyme salivary amylase. We discuss the importance of optimized protein extraction methods, data analysis approaches, and authentication strategies in the identification of dietary proteins from archaeological dental calculus. Our ability to detect dietary proteins, although limited, demonstrates the potential of these methods to robustly identify foodstuffs in the archaeological record that are under-represented due to their poor preservation.
2018-07-18 | PXD009603 | Pride
Project description:The purpose of this study was to investigate oral microbiome and host proteins in archaeological human dental tissues using a shotgun proteomics approach. The research focuses on dental calculus (mineralized plaque), dentine, a carious lesion, and an alveolar bone abscess from the medieval site of Dalheim, Germany (ca. AD 950-1200). For comparison, proteins were also analyzed from archaeological faunal dental tissues and human dental calculus samples from modern Swiss dental patient controls. Protein extraction and generation of tryptic peptides from tooth and dental calculus specimens was performed using a filter-aided sample preparation (FASP) protocol, modified for mineralized and degraded samples. Total protein extraction was performed on a total of fourteen samples: four ancient human calculus samples (indicated as: G12, B71, B61, and B78), four ancient human tooth root samples (indicated as: G12, B17, B61, and B78), one carious lesion (indicated as: B17), one alveolar bone abscess (indicated as: B17), two ancient fauna crown cementum/calculus samples (indicated as: F1 [sheep] and F5 [cattle]), and two modern dental calculus samples from clinical patients (indicated as: P1 and P2). All samples were extracted at the Centre for Evolutionary Medicine (ZEM) at the University of Zürich with the exception of dental calculus from G12, P1, and P2, which were extracted at the Center for GeoGenetics (CGG) at the University of Copenhagen. Two samples (G12 and B61 calculus) were extracted a second time in an independent laboratory at the University of York (YORK) for comparison. Sample extracts were then sequenced (LC-MS/MS) at the Functional Genomics Center Zürich (FGCZ) using an LTQ-Orbitrap Velos, at the Novo Nordisk Foundation Center for Protein Research (CPR) using a Q-Exactive Hybrid Quadrupole Orbitrap, and at the University of York’s Proteomics and Analytical Biochemistry Laboratories (PABL) using a MaXis UHR-Qq-TOF.
2014-01-29 | PXD000412 | Pride
Project description:This study investigated the consumption of milk products in the archaeological record, utilizing human dental calculus as a reservoir of dietary proteins from archaeological samples from across Eurasia. Protein extraction and generation of tryptic peptides from dental calculus was performed using a filter-aided sample preparation (FASP) protocol, modified for ancient samples, on 92 samples of archaeological dental calculus. Samples were extracted at three laboratories; the Functional Genomics Centre Zürich (FGCZ), the Centre for GeoGenetics at the National History Museum of Denmark, and BioArCh at the University of York. Sample extracts were sequenced (LC-MS/MS) using an LTQ-Orbitrap Velos (FGCZ), a Q-Exactive Hybrid Quadrupole Orbitrap and an LTQ-Orbitrap Elite (Central Proteomics Facility, Target Discovery Institute, Oxford).
2015-02-26 | PXD001362 | Pride
Project description:Detailed investigation of extremely severe pathological conditions present in ancient human skeletons is important because they can illuminate the breadth of potential interactions between humans and disease etiologies in the past. Here, we applied palaeoproteomics to investigate the bacterial pathogenic factors and host defense response to an ancient human skeletal individual with severe oral pathology. This female skeleton, from the Okhotsk period (i.e., 5th–13th century) of northern Japan, poses abnormal deposition of large amounts of dental calculus and oral dysfunction due to severe periodontal disease. A shotgun mass-spectrometry analysis identified 81 human proteins and 15 bacterial proteins from her calculus. Two pathogenic or bio-invasive proteins originating from two of the three “red complex” bacteria, the core species associated with severe periodontal disease in modern humans, as well as additional two bio-invasive proteins of periodont-associated bacteria were identified. Human proteins associated with the defense response system were identified, but their proportion was mostly similar to that reported in ancient and modern human individuals with lower calculus deposition. These results suggest that the bacterial etiology was similar and the host defense response was not necessarily higher in ancient individuals with abnormal deposition of large amounts of dental calculus.
2024-04-01 | PXD044070 | Pride
Project description:This study investigated the consumption of milk products in the archaeological record, utilizing human dental calculus as a reservoir of dietary proteins from archaeological samples from across Eurasia. Protein extraction and generation of tryptic peptides from dental calculus was performed using a filter-aided sample preparation (FASP) protocol, modified for ancient samples, on 92 samples of archaeological dental calculus. Samples were extracted at three laboratories; the Functional Genomics Centre Zürich (FGCZ), the Centre for GeoGenetics at the National History Museum of Denmark, and BioArCh at the University of York. Sample extracts were sequenced (LC-MS/MS) using an LTQ-Orbitrap Velos (FGCZ), a Q-Exactive Hybrid Quadrupole Orbitrap and an LTQ-Orbitrap Elite (Central Proteomics Facility, Target Discovery Institute, Oxford).
2015-02-25 | PXD001361 | Pride
Project description:This study investigated the consumption of milk products in the archaeological record, utilizing human dental calculus as a reservoir of dietary proteins from archaeological samples from across Eurasia. Protein extraction and generation of tryptic peptides from dental calculus was performed using a filter-aided sample preparation (FASP) protocol, modified for ancient samples, on 92 samples of archaeological dental calculus. Samples were extracted at three laboratories; the Functional Genomics Centre Zürich (FGCZ), the Centre for GeoGenetics at the National History Museum of Denmark, and BioArCh at the University of York. Sample extracts were sequenced (LC-MS/MS) using an LTQ-Orbitrap Velos (FGCZ), a Q-Exactive Hybrid Quadrupole Orbitrap and an LTQ-Orbitrap Elite (Central Proteomics Facility, Target Discovery Institute, Oxford).
2015-02-25 | PXD001357 | Pride
Project description:This study investigated the consumption of milk products in the archaeological record, utilizing human dental calculus as a reservoir of dietary proteins from archaeological samples from across Eurasia. Protein extraction and generation of tryptic peptides from dental calculus was performed using a filter-aided sample preparation (FASP) protocol, modified for ancient samples, on 92 samples of archaeological dental calculus. Samples were extracted at three laboratories; the Functional Genomics Centre Zürich (FGCZ), the Centre for GeoGenetics at the National History Museum of Denmark, and BioArCh at the University of York. Sample extracts were sequenced (LC-MS/MS) using an LTQ-Orbitrap Velos (FGCZ), a Q-Exactive Hybrid Quadrupole Orbitrap and an LTQ-Orbitrap Elite (Central Proteomics Facility, Target Discovery Institute, Oxford).
2015-02-25 | PXD001360 | Pride
Project description:This study investigated the consumption of milk products in the archaeological record, utilizing human dental calculus as a reservoir of dietary proteins from archaeological samples from across Eurasia. Protein extraction and generation of tryptic peptides from dental calculus was performed using a filter-aided sample preparation (FASP) protocol, modified for ancient samples, on 92 samples of archaeological dental calculus. Samples were extracted at three laboratories; the Functional Genomics Centre Zürich (FGCZ), the Centre for GeoGenetics at the National History Museum of Denmark, and BioArCh at the University of York. Sample extracts were sequenced (LC-MS/MS) using an LTQ-Orbitrap Velos (FGCZ), a Q-Exactive Hybrid Quadrupole Orbitrap and an LTQ-Orbitrap Elite (Central Proteomics Facility, Target Discovery Institute, Oxford).
2015-02-26 | PXD001359 | Pride