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Proteomic Analysis of Dental Calculus from an Elite Mongol Cemetery

ABSTRACT: This project explores dietary proteins in human dental calculus through shotgun proteomics

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Shevan Wilkin

LAB HEAD: Nicole Boivin

PROVIDER: PXD024510 | Pride | 2023-05-10

REPOSITORIES: Pride

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Permafrost preservation reveals proteomic evidence for yak milk consumption in the 13<sup>th</sup> century.

Ventresca Miller Alicia R AR Wilkin Shevan S Bayarsaikhan Jamsranjav J Ramsøe Abigail A Clark Julia J Byambadorj Batsuren B Vanderwarf Sandra S Vanwezer Nils N Haruda Ashleigh A Fernandes Ricardo R Miller Bryan B Boivin Nicole N

Communications biology 20230331 1

Domesticated yaks endure as iconic symbols of high-altitude frozen landscapes, where herding communities depend on their high-fat milk, transport, dung, and natural fibers. While there is established proteomic evidence for ancient consumption of ruminant and horse milk in the mountains and steppes of northern Eurasia, yak dairy products have yet to be detected. Yak domestication and the species' dispersal from Tibet into the mountainous zones to the north are also poorly resolved due to a paucit ...[more]

PMID: 37002413

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The spread of herds and horses into the Altai

Project description:This project explores dietary proteins in human dental calculus through shotgun proteomics

2022-04-06 | PXD029267 | Pride

Proteomic Evidence of Dietary Sources in Ancient Dental Calculus

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

Proteomic anlysis of dental calculus samples from Xiaohe

Project description:This analysis is a part of a larger study of the genomic origins of the Tarim Basin mummies. The dental calculus of seven individuals from Xiaohe contained ruminant dairy proteins, confirming milk consumption by the earliest inhabitants of Xiaohe.

2021-09-09 | PXD027706 | Pride

Protein Extraction from Ancient Teeth and Dental Calculus Compatible with Subsequent DNA Extraction

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.

2023-09-11 | PXD042668 | Pride

Proteomic Evidence of Ancient Mongolian Dietary Dairy Sources in Ancient Dental Calculus

Project description:To investigate dairy consumption in ancient Mongolia, we analysed dental calculus samples from four Late Bronze Age (LBA, 1500-1000 BCE) individuals for proteomic evidence of milk proteins. As many archaeological sites before Mongolia's Iron Age suffer from a dearth of occupational materials, looking to biomolecular markers of dietary intake can open new investigational avenues into ancient economies. In this case, we use a previously established method of extracting proteins from calculus to explore the consumption of dairy products at LBA Khirigsuur sites in northern Mongolia's Hovsgol Aimag. Seven of nine individual's calculus contained peptides from the whey protein Beta-lactoglobulin from Ovis, Capra hircus, Bos, and general Bovidae species. Aside from proteomics, these and 16 other individuals from the site were analysed for aDNA. We found that 18 of the 20 were primarily from one genetic ancestral group, and Ancient North Eurasian (ANE). One of the outliers represents a combination of ANE and Western Steppe Herder (WSH), with the other a combination of ANE and Eastern Asian (EE). This finding, while important in its own right, evidences the earliest known dairy consumption in Mongolia, and supports a widely held assumption that pastoralism was a primary subsistence strategy in the ancient Eastern Steppes. The combined proteomic and DNA evidence suggest that Western Steppe dairy animals and technology entered Mongolia before genetic admixture.

2018-10-19 | PXD008217 | Pride

Palmer et al: Dental Method Comparison

Project description:The dental calculus proteome from human remains is a considered a valuable archaeological resource for studying the diet, oral microbiome, health/disease of individuals and occupation activities individuals within past societies/civilisations. The combination of advancements in LC/MS instrument sensitivity and sample prepartion methods enables the analysis of these well preserved proteomes otherwise invisible to other biomolecular approaches. Maximizing proteome recovery from this minute and finite resource is paramount to our understanding of these past societies and civilisations in terms of diet and disease. Here we compare the more traditional ultrafiltration-based and acetone precipitation approaches with the newer paramagnetic bead approach (SP3) in a step towards achieving this aim. We specifically evaluate different acids (EDTA and HCl) and proteome extraction methodologies (Ultrafiltration, Acetone Precipitation and SP3)to test the influence of demineralization acid and method of extraction on the recovered proteome complexity (including numbers of peptides recovered) and sequence coverageand observed for these ancient dental calculus specimens.

2021-02-19 | PXD023399 | Pride

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

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.

2020-04-27 | PXD015817 | Pride

Human Dental Calculus_Neolithic_Southern Italy

Project description:Characterisation of the metaproteome of a dental calculus sample extracted from a Neolithic burial, San Lorenzo Bellizzi, Italy (CS).

2023-10-24 | PXD039654 | Pride

Dairying enabled Early Bronze Age Yamnaya steppe expansions - additional files

Project description:This project explores dietary proteins in human dental calculus through shotgun proteomics. These files are in addition to those accidentally not included in the original publication, Dairying enabled Early Bronze Age Yamnaya steppe expansions . DOI https://doi.org/10.1038/s41586-021-03798-4. Files include raw, mgf, and mzid files from the two Botai individuals: DA092 (Botai 2A), DA089 (CII(3) 30-40), and additional files from Russian sites: DA431, DA431 (Lebyazhinka 5, LEB N-0), Z333 (Khvalynsk 2, KHA2 N-12), and Z444 (Murziha 2, MUR2 N-128) as well as the blanks used in the experiments. It also inlcludes the corresponding files for DA436, as in the previous upload an under-injected sample was included as the MDF.

2022-05-16 | PXD033607 | Pride

Dairying enabled Early Bronze Age Yamnaya steppe expansions

Project description:Ancient protein analysis of human dental calculus to look for evidence of early milk consumption

2021-08-09 | PXD022300 | Pride