Proteomic anlysis of dental calculus samples from Xiaohe
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Dental Plaque
SUBMITTER: 
Ashley Scott
LAB HEAD: Christina Warinner
PROVIDER: PXD027706 | Pride | 2021-09-09
REPOSITORIES: Pride
Similar Datasets
Project description:Archaeological and archaeogenetic evidence points to the Pontic-Caspian steppe zone between the Caucasus and the Black Sea as the crucible from which the earliest steppe pastoralist societies arose and spread, ultimately influencing populations from Europe to Inner Asia. However, little is known about their economic foundations and the factors that may have contributed to their extensive mobility. Here we investigate the dental calculus proteomes of 45 individuals spanning the Neolithic to Greco-Roman periods in the Pontic-Caspian Steppe and neighboring South Caucasus, Oka-Volga-Don, and East Urals regions.
2021-11-03 | PXD027728 | Pride
Project description:Although the key role of long-distance trade in the transformation of cuisines worldwide has been well-documented since at least the Roman era, the prehistory of the Eurasian food trade is less visible. In order to shed light on the transformation of Eastern Mediterranean cuisines during the Bronze and Early Iron Age, we analyzed microremains and proteins preserved in the dental calculus of individuals who lived during the 2nd millennium BCE in the Southern Levant. Our results provide clear evidence for the consumption of expected staple foods, such as cereals (Triticeae), sesame (Sesamum) and dates (Phoenix). We additionally report evidence for the consumption of soybean (Glycine), probable banana (Musa), and turmeric (Curcuma), which pushes back the earliest known availability of these foods in the Mediterranean by centuries (turmeric) or even millennia (soybean). We find that, from the early 2nd millennium onwards, at least some people in the Eastern Mediterranean had access to food from distant locations, including South Asia, and such trade goods likely reached the Eastern Mediterranean in the form of oils, dried fruits, and spices. These novel insights force us to rethink the complexity and intensity of Indo-Mediterranean trade during the Bronze Age and also the degree of globalization in early Eastern Mediterranean cuisine.
2020-12-22 | PXD021498 | Pride
Project description:The extreme environments of the Tibetan Plateau offer significant challenges to human survival, demanding novel adaptations. While the role of biological and agricultural adaptations in enabling early human colonization of the plateau has been widely discussed, the contribution of pastoralism is less well understood, especially the dairy pastoralism that has historically been central to Tibetan diets. Here, we analyze preserved proteins from the dental calculus of 40 ancient individuals to report the earliest direct evidence of dairy consumption on the Tibetan Plateau. Our palaeoproteomic results demonstrate that dairy pastoralism began on the higher plateau by approximately 3,500 years ago, more than 2,000 years earlier than the recording of dairying in historical sources. With less than 1% of the Tibetan Plateau dedicated to farmland, pastoralism and the milking of ruminants were essential for large-scale human expansion into agriculturally-marginal regions that make up the majority of the plateau. Dairy pastoralism allowed conversion of abundant grasslands into nutritional human food, which facilitating adaptation in the face of extreme climatic and altitudinal pressures, and maximizing the land area available for long-term human occupation of the “roof of the world”.
2023-03-15 | PXD028538 | Pride
Project description:Ancient protein analysis of human dental calculus to look for evidence of early milk consumption
2021-08-09 | PXD022300 | Pride
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
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
Project description:Food and diet were class markers in nineteenth-century Ireland, which became evident as nearly one million people, primarily the poor and destitute, died as a consequence of the notorious Great Famine of 1845–1852. Famine took hold after a blight (Phytophthora infestans) destroyed the only means of subsistence—the potato crop—for a significant proportion of the population. This study seeks to elucidate the variability of diet in mid-nineteenth-century Ireland through microparticle and proteomic analysis of human dental calculus samples (n = 42) from victims of the Famine. The sample derives from remains of people who died between August 1847 and March 1851 while receiving poor relief as inmates in the union workhouse in the city of Kilkenny (52°39’N, -7°15’W). The results corroborate the historical accounts of food provisions before and during the Famine, with evidence of corn (maize), potato and cereal starch granules from the microparticle analysis and milk proteins from the proteomic analysis. Unexpectedly, there is also evidence of egg proteins—a food source generally reserved only for export and the better-off social classes—which highlights the variability of the Famine experience for those who died. Through historical contextualisation, this study shows how the notoriously monotonous potato diet of the nineteenth-century Irish poor was supplemented by other foodstuffs on an opportunistic basis. While the Great Irish Famine was one of the worst subsistence crises in history, it was foremost a social disaster induced by the lack of access to food and not the lack of food availability.
2019-10-17 | PXD015002 | Pride
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
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:Recent improvements in the analysis ancient biomolecules from human remains and associated dental calculus have provided new insights into the prehistoric diet and past genetic diversity of our species. Here we present a “multi-omics” study, integrating genomic and proteomic analyses of two post-Last Glacial Maximum (LGM) individuals from San Teodoro cave (Italy), to reconstruct their lifestyle and the post-LGM resettlement of Europe. Our analyses show genetic homogeneity in Sicily during the Palaeolithic, representing a hitherto unknown Italian genetic lineage within the previously identified “Villabruna cluster”. We argue that this lineage took refuge in Italy during the LGM, followed by a subsequent spread to central-western Europe. Analyses of dental calculus using genomics and proteomics showed a similar oral microbiome composition as Neandertals, but distinct from later foragers and farmers, revealing also a diet based on mammals, fish and plants. Our results demonstrate the power of using a multi-omics approach in the study of prehistoric human populations.
2022-10-27 | PXD024346 | Pride