Windows into the past: recent scientific techniques in dental analysis.

Teeth are the hardest and most chemically stable tissues in the body, are well-preserved in archaeological remains and, being resistant to decomposition in the soil, survive long after their supporting structures have deteriorated. It has long been recognised that visual and radiographic examination of teeth can provide considerable information relating to the lifestyle of an individual. This paper examines the latest scientific approaches that have become available to investigate recent and ancient teeth. These techniques include DNA analysis, which can be used to determine the sex of an individual, indicate familial relationships, study population movements, provide phylogenetic information and identify the presence of disease pathogens. A stable isotopic approach can shed light on aspects of diet and mobility and even research climate change. Proteomic analysis of ancient dental calculus can reveal specific information about individual diets. Synchrotron microcomputed tomography is a non-invasive technique which can be used to visualise physiological impactful events, such as parturition, menopause and diseases in cementum microstructure - these being displayed as aberrant growth lines.

Effect of phosphoproteins on intracellular calcification of bacteria.

This study aimed to evaluate the effects of phosphoproteins on bacterial mineralization. Dental calculus formation is attributed to bacterial mineralization in the oral cavity; however, the influence of phosphoproteins (which are abundant in saliva) is not clear. The model bacterium Escherichia coli was suspended in a calcification solution containing casein as a model phosphoprotein. To evaluate mineralization independent of bacterial metabolism, bacteria killed by heat treatment at 70°C were compared with viable bacteria. After incubation at 37°C for 24 h, the mode of calcification was observed using electron microscopy and energy dispersive x-ray spectroscopy. Solutions without casein produced precipitation in solution, which was identical to that in experiments without bacteria. In contrast, calcification solutions with 200 ppm casein only produced calcium phosphate deposition intracellularly. Without heat treatment, intracellular calcification rarely occurred, even when casein was added. Thus, phosphoproteins promoted intracellular calcification of dead bacteria; this is similar to the calcification of insoluble matrices, such as collagen fibrils, promoted by acidic polymers. We concluded that intracellular calcification is caused by the collagen fibril-like behavior of dead bacteria. The promotion of intracellular calcification of dead bacteria by phosphoproteins suggested a basic principle of dental calculus formation.

Teeth record pneumonia-and racism.

Research raises standards for working with anthropological collections.

The genomic origins of the Bronze Age Tarim Basin mummies.

The identity of the earliest inhabitants of Xinjiang, in the heart of Inner Asia, and the languages that they spoke have long been debated and remain contentious1. Here we present genomic data from 5 individuals dating to around 3000-2800 BC from the Dzungarian Basin and 13 individuals dating to around 2100-1700 BC from the Tarim Basin, representing the earliest yet discovered human remains from North and South Xinjiang, respectively. We find that the Early Bronze Age Dzungarian individuals exhibit a predominantly Afanasievo ancestry with an additional local contribution, and the Early-Middle Bronze Age Tarim individuals contain only a local ancestry. The Tarim individuals from the site of Xiaohe further exhibit strong evidence of milk proteins in their dental calculus, indicating a reliance on dairy pastoralism at the site since its founding. Our results do not support previous hypotheses for the origin of the Tarim mummies, who were argued to be Proto-Tocharian-speaking pastoralists descended from the Afanasievo1,2 or to have originated among the Bactria-Margiana Archaeological Complex3 or Inner Asian Mountain Corridor cultures4. Instead, although Tocharian may have been plausibly introduced to the Dzungarian Basin by Afanasievo migrants during the Early Bronze Age, we find that the earliest Tarim Basin cultures appear to have arisen from a genetically isolated local population that adopted neighbouring pastoralist and agriculturalist practices, which allowed them to settle and thrive along the shifting riverine oases of the Taklamakan Desert.

Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus.

Archaeological dental calculus, or mineralized plaque, is a key tool to track the evolution of oral microbiota across time in response to processes that impacted our culture and biology, such as the rise of farming during the Neolithic. However, the extent to which the human oral flora changed from prehistory until present has remained elusive due to the scarcity of data on the microbiomes of prehistoric humans. Here, we present our reconstruction of oral microbiomes via shotgun metagenomics of dental calculus in 44 ancient foragers and farmers from two regions playing a pivotal role in the spread of farming across Europe-the Balkans and the Italian Peninsula. We show that the introduction of farming in Southern Europe did not alter significantly the oral microbiomes of local forager groups, and it was in particular associated with a higher abundance of the species Olsenella sp. oral taxon 807. The human oral environment in prehistory was dominated by a microbial species, Anaerolineaceae bacterium oral taxon 439, that diversified geographically. A Near Eastern lineage of this bacterial commensal dispersed with Neolithic farmers and replaced the variant present in the local foragers. Our findings also illustrate that major taxonomic shifts in human oral microbiome composition occurred after the Neolithic and that the functional profile of modern humans evolved in recent times to develop peculiar mechanisms of antibiotic resistance that were previously absent.

Characteristics of Dietary Fatty Acids Isolated from Historic Dental Calculus of the 17th- and 18th-Century Inhabitants of the Subcarpathian Region (Poland).

Dental calculus analysis can be a valuable source of archaeological knowledge, since it preserves not only microbial and host biomolecules but also dietary and environmental debris, as well as metabolic products likely originating from dietary and craft activities. Here we described GC-MS analysis of a set of historic dental calculus samples from the front teeth of the mandibles of seven individuals found in 17th- and 18th-century graves in the city of Rzeszow, located in South-eastern Poland. We have found that only saturated fatty acids, which are characteristic for fats of animal origin, were present in the tested samples. Our preliminary results indicate that the diet of modern-period inhabitants of Rzeszow was rich in animal products, such as meat and dairy products.

Environmental implications and evidence of natural products from dental calculi of a Neolithic-Chalcolithic community (central Italy).

In this contribution, we investigated the role of plants in the prehistoric community of Casale del Dolce (Anagni, FR, central Italy), through microparticles recovered from dental calculus. The finding of a great amount of pollen types, even in form of compact lumps, could indicate use of natural substances, such as honeybee products and/or conifer resins. This plant-microremain record also suggested environmental implications relative to the Neolithic and Chalcolithic period. Additionally, the stability of the tartar microenvironment had preserved starches and other microparticles, such as one epidermal trichome, a sporangium, and fragments of plant tissue, rarely detected in ancient dental calculus. The detection of secondary metabolites in the ancient matrix confirmed the familiarity of this community with plant resources. All these data supply various interesting food for thought and expand the knowledge about the potential of dental calculus in archaeological and archaeobotanical fields with a special focus on palaeoecology.

Exotic foods reveal contact between South Asia and the Near East during the second millennium BCE.

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 Age and Early Iron Age, we analyzed microremains and proteins preserved in the dental calculus of individuals who lived during the second 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 evidence of these foods in the Mediterranean by centuries (turmeric) or even millennia (soybean). We find that, from the early second millennium onwards, at least some people in the Eastern Mediterranean had access to food from distant locations, including South Asia, and such goods were likely consumed as oils, dried fruits, and spices. These insights force us to rethink the complexity and intensity of Indo-Mediterranean trade during the Bronze Age as well as the degree of globalization in early Eastern Mediterranean cuisine.

Exploring late Paleolithic and Mesolithic diet in the Eastern Alpine region of Italy through multiple proxies.

OBJECTIVES: The analysis of prehistoric human dietary habits is key for understanding the effects of paleoenvironmental changes on the evolution of cultural and social human behaviors. In this study, we compare results from zooarchaeological, stable isotope and dental calculus analyses as well as lower second molar macrowear patterns to gain a broader understanding of the diet of three individuals who lived between the end of the Late Pleistocene and the Early Holocene (ca., 17-8 ky cal BP) in the Eastern Alpine region of Italy. MATERIALS AND METHODS: We analyze individuals buried at the sites of Riparo Tagliente (Verona), Riparo Villabruna, and Mondeval de Sora (Belluno). The three burials provide a unique dataset for diachronically exploring the influence of climatic changes on human subsistence strategies. RESULTS: Isotopic results indicate that all individuals likely relied on both terrestrial and freshwater animal proteins. Even though dental calculus analysis was, in part, hindered by the amount of mineral deposit available on the teeth, tooth macrowear study suggests that the dietary habits of the individuals included plant foods. Moreover, differences in macrowear patterns of lower second molars have been documented between Neanderthals and modern humans in the present sample, due to a prevalence of Buccal wear among the former as opposed to higher values of Lingual wear in modern human teeth. DISCUSSION: Isotopic analyses have emphasized the contribution of animal proteins in the diet of the three foragers from the Eastern Alpine region. The possible intake of carbohydrate-rich plant foods, suggested by the retrieval of plant remains in dental calculus, is supported by the signal of macrowear analysis. Moreover, the latter method indicates that the distribution of macrowear in lower second molars (M2 s) allows us to discriminate between Neanderthals and modern humans within the present reference sample. Overall, our results show these three prehistoric hunter-gatherers were well adapted to the environment in which they lived exploiting many natural resources.

Entrapment of drugs in dental calculus - Detection validation based on test results from post-mortem investigations.

For prospective investigation of drugs and metabolites in archaeological and contemporary dental calculus, a sensitive, broadly applicable ultra-high-performance liquid chromatography-tandem mass spectrometry method using pneumatically assisted electrospray ionisation (UHPLC-ESI-MS/MS) was developed. The dental calculus was treated with citric acid and the dissolution extracts were cleaned using weak and strong polymeric cation-exchange sorbents. The method was validated on hydroxyapatite for the analysis of 67 drugs and metabolites. Typically, the lower limits of quantification were in the range of 0.01-0.05ng for the sample mass extracted. The general applicability of the method was tested using dental calculus material sampled from 10 corpses undergoing forensic autopsy. The calculus material was washed several times before dissolution to remove residual substances originating from saliva, gingival crevicular fluid and blood. The wash extracts and the calculus samples (cleaned calculus material) were analysed using the same instrumental conditions. The dry mass of the calculus samples ranged from 1 to 10mg. The total number of drug detections was 131 in the dental calculus samples and 117 in the whole blood samples. From the analyses of the wash extracts and calculus samples, it was proven that drug residues were trapped in the interior of the calculus material. In 82 of the drug detections, the drug concentrations were higher in the dental calculus than in the blood. Among substances detected in the dental calculus but not in the blood were cocaine, heroin, 6-MAM and THCA-A.

Dental Calculus as a Potential Biosource for Human Papillomavirus Detection in Oral Squamous Cell Carcinoma.

OBJECTIVE: The infection of human papillomaviruses (HPVs) plays a role in the development of oral squamous cell carcinoma (OSCC). A poor oral hygiene and dental calculus may cause the infection to persist. Therefore, this study aimed to assess whether this dental calculus could serve as a potential biosource in early detection of HPVs in patients with OSCC. METHODS: DNA was isolated from the dental calculus of people diagnosed with OSCC, and MY09/11 primer set was used to detect the presence of HPV. The positive samples were further sequenced and aligned using megablast NCBI BLAST tool to identify the HPV genotype. RESULTS: Electrophoresis examination showed that 4 of 14 samples collected (29%) had a clear single band, of which three had 97% to 99% similarity to a high-risk genotype HPV-58. Meanwhile, the other sample had 99% similarity to an unclassified papillomaviridae. CONCLUSION: Dental calculus is a promising source of HPV in oral cavity and could be used as a biomarker for early detection.

Ancient DNA analysis of food remains in human dental calculus from the Edo period, Japan.

Although there are many methods for reconstructing diets of the past, detailed taxon identification is still challenging, and most plants hardly remain at a site. In this study, we applied DNA metabarcoding to dental calculus of premodern Japan for the taxonomic identification of food items. DNA was extracted from 13 human dental calculi from the Unko-in site (18th-19th century) of the Edo period, Japan. Polymerase chain reaction (PCR) and sequencing were performed using a primer set specific to the genus Oryza because rice (Oryza sativa) was a staple food and this was the only member of this genus present in Japan at that time. DNA metabarcoding targeting plants, animals (meat and fish), and fungi were also carried out to investigate dietary diversity. We detected amplified products of the genus Oryza from more than half of the samples using PCR and Sanger sequencing. DNA metabarcoding enabled us to identify taxa of plants and fungi, although taxa of animals were not detected, except human. Most of the plant taxonomic groups (family/genus level) are present in Japan and include candidate species consumed as food at that time, as confirmed by historical literature. The other groups featured in the lifestyle of Edo people, such as for medicinal purposes and tobacco. The results indicate that plant DNA analysis from calculus provides information about food diversity and lifestyle habits from the past and can complement other analytical methods such as microparticle analysis and stable isotope analysis.

Exploitation and utilization of tropical rainforests indicated in dental calculus of ancient Oceanic Lapita culture colonists.

Remote Oceania, which largely consists of islands covered in tropical forests, was the last region on earth to be successfully colonized by humans, beginning 3,000 years ago. We examined human dental calculus from burials in an ancient Lapita culture cemetery to gain insight into the early settlement of this previously untouched tropical environment, specifically on the island of Efate in Vanuatu. Dental calculus is an ideal material to analyse questions of human and plant interactions due to the ingestion of plant-derived microparticles that become incorporated into the calculus as it forms throughout a person's life. Most of the microparticles identified here are from tree and shrub resources, including a ~2,900 calibrated (cal) BP example of banana in Remote Oceania, providing direct evidence for the importance of forests and arboriculture during the settlement of Remote Oceania.

Biological effects on tooth root surface topographies induced by various mechanical treatments.

The cleaning and physicochemical properties on tooth root biointerfaces are pivotal for periodontal healing. Herein, this work investigated the impact of multi-treatment on the physicochemical features of tooth root surfaces and the responsive behavior of human gingival fibroblasts (hGFs). It was found that the combination of various mechanical treatments significantly affects the topographical pattern and size as well as wettability on tooth root surfaces. Furthermore, biological experiments revealed that hGF behaviors (i.e., cell adhesion, shape, spreading, arrangement, and viability) were regulated by the topography and wettability of tooth root surfaces. Also, there was no significant difference in the protein expression of NLRP3 inflammasome and IL-1ß in hGFs among tooth root surfaces under various treatments. This study provides new insights to efficiently remove the dental calculus and to understand the interaction between the tooth root interface and cell, which could guide the clinical operation and thereby is more conducive to periodontal recovery.

Lifestyle of a Roman Imperial community: ethnobotanical evidence from dental calculus of the Ager Curensis inhabitants.

BACKGROUND: The analysis of ancient calcified dental plaque is a powerful archaeobotanical method to elucidate the key role of the plants in human history. METHODS: In this research, by applying both optic microscopy and gas chromatography mass spectrometry on this matrix, a detailed qualitative investigation for reconstructing the lifestyle of a Roman imperial community of the Ager Curensis (Sabina Tiberina, Central Italy) was performed. RESULTS: The detection of animal micro-remains and molecules (e.g., hairs, feather barbules, markers of dairy products), starch granules of several cereals and legumes, pollen (e.g., Juglans regia L., Hedera sp. L.) and other plant micro-debris (e.g., trichome of Olea sp., hemp fibers), and phytochemicals (e.g., Brassicaceae, Lamiaceae herbs, Ferula sp., Trigonella foenum-graecum L., wine, and Humulus lupulus L.) in the dental calculus sample demonstrated that plant-derived foods were regularly consumed together with animal resources. CONCLUSIONS: This nutritional plan, consistent with the information reported in ancient written texts, suggested that the studied population based its own subsistence on both agriculture and husbandry, probably also including beekeeping and hunting activities. All together, these results represent proofs for the comprehension of food habits, phytotherapeutic practices, and cultural traditions of one of the first Roman settlements in the Sabina Tiberina area.

Relief food subsistence revealed by microparticle and proteomic analyses of dental calculus from victims of the Great Irish Famine.

Food and diet were class markers in 19th-century Ireland, which became evident as nearly 1 million people, primarily the poor and destitute, died as a consequence of the notorious Great Famine of 1845 to 1852. Famine took hold after a blight (Phytophthora infestans) destroyed virtually 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-19th-century Ireland through microparticle and proteomic analysis of human dental calculus samples (n = 42) from victims of the famine. The samples derive 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 protein from the proteomic analysis. Unexpectedly, there is also evidence of egg protein-a food source generally reserved only for export and the better-off social classes-which highlights the variability of the prefamine experience for those who died. Through historical contextualization, this study shows how the notoriously monotonous potato diet of the poor was opportunistically supplemented by other foodstuffs. 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.

Micro-Raman Spectroscopy Reveals the Presence of Octacalcium Phosphate and Whitlockite in Association with Bacteria-Free Zones Within the Mineralized Dental Biofilm.

Through a correlative analytical approach encompassing backscattered electron scanning electron microscopy (BSE-SEM), energy dispersive X-ray spectroscopy (EDX), and micro-Raman spectroscopy, the composition of the mineralized biofilm around a dental implant, retrieved due to peri-implantitis, was investigated. The mineralized biofilm contains two morphologically distinct regions: (i) bacteria-containing zones (Bact+), characterized by aggregations of unmineralized and mineralized bacteria, and intermicrobial mineralization, and (ii) bacteria-free zones (Bact-), comprised mainly of randomly oriented mineral platelets. Intramicrobial mineralization, within Bact+, appears as smooth, solid mineral deposits resembling the morphologies of dental plaque bacteria. Bact- is associated with micrometer-sized Mg-rich mineral nodules. The Ca/P ratio of Bact+ is higher than Bact-. The inorganic phase of Bact+ is carbonated apatite (CHAp), while that of Bact- is predominantly octacalcium phosphate (OCP) and whitlockite (WL) inclusions. Compared with native bone, the inorganic phase of Bact+ (i.e., CHAp) exhibits higher mineral crystallinity, lower carbonate content, and lower Ca/P, C/Ca, Mg/Ca, and Mg/P ratios. The various CaPs found within the mineralized dental biofilm (CHAp, OCP, and WL) are related to the local presence/absence of bacteria. In combination with BSE-SEM and EDX, micro-Raman spectroscopy is a valuable analytical tool for nondestructive investigation of mineralized dental biofilm composition and development.

Evaluation of Cadmium Levels in Dental Calculus of Male Oral SCC Patients with Betel-Quid Chewing in Hunan Province of China.

Cadmium (Cd) is a widespread trace toxic heavy metal with long biological half-life and may induce higher risk of cancer on multiple organs of human body. Recent studies have confirmed that dental calculus has enormous potential for investigation of exposure to Cd in the human mouth by acting as a time capsule. We aimed to examine relationship between Cd levels in dental calculus due to betel-quid chewing and risk of oral cancer. This study included 85 male oral squamous cell carcinoma (SCC) cases with betel-quid chewing and smoking as observation subjects (group A) and 67 healthy people with smoking but without betel-quid chewing as control subjects (group B) in Hunan province of Mainland China. Cd levels in calcified dental calculus samples from all participants were measured by inductively coupled plasma mass spectrometry (ICP-MS). The results of this study indicated that cadmium levels in dental calculus were significantly higher in male oral SCC patients with betel-quid chewing and smoking than that in healthy individuals without habit of betel-quid chewing and with smoking (p < 0.0001). This study gives some evidence to support that there may be a positive relationship between cadmium in dental calculus due to betel-quid chewing and risk of oral SCC.

The efficacy of whole human genome capture on ancient dental calculus and dentin.

OBJECTIVES: Dental calculus is among the richest known sources of ancient DNA in the archaeological record. Although most DNA within calculus is microbial, it has been shown to contain sufficient human DNA for the targeted retrieval of whole mitochondrial genomes. Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques. MATERIALS AND METHODS: Total DNA extracted from 24 paired archaeological human dentin and calculus samples was subjected to whole human genome enrichment using in-solution hybridization capture and high-throughput sequencing. RESULTS: Total DNA from calculus exceeded that of dentin in all cases, and although the proportion of human DNA was generally lower in calculus, the absolute human DNA content of calculus and dentin was not significantly different. Whole genome enrichment resulted in up to four-fold enrichment of the human endogenous DNA content for both dentin and dental calculus libraries, albeit with some loss in complexity. Recovering more on-target reads for the same sequencing effort generally improved the quality of downstream analyses, such as sex and ancestry estimation. For nonhuman DNA, comparison of phylum-level microbial community structure revealed few differences between precapture and postcapture libraries, indicating that off-target sequences in human genome-enriched calculus libraries may still be useful for oral microbiome reconstruction. DISCUSSION: While ancient human dental calculus does contain endogenous human DNA sequences, their relative proportion is low when compared with other skeletal tissues. Whole genome enrichment can help increase the proportion of recovered human reads, but in this instance enrichment efficiency was relatively low when compared with other forms of capture. We conclude that further optimization is necessary before the method can be routinely applied to archaeological samples.

Pleistocene dental calculus: Recovering information on Paleolithic food items, medicines, paleoenvironment and microbes.

Dental calculus is now widely used to recover information on items ingested in the past. It is particularly valuable in the earlier Paleolithic, where recovered data may represent the only evidence for plant use. Several recovery methods are used and each one produces different results. Biomolecular markers and genetic material recovered from dental calculus is providing new data on identifiable dietary and medicinal items and human microbial communities. The recovery of microfossils, in particular, starch granules, has triggered a new awareness of the role of plants in the diet throughout the Paleolithic. However, the minute amount of material recovered has little relationship with food eaten during a person's life, while salivary amylase breaks down cooked starch. Therefore, broader dietary interpretations and detection of cooked food are problematic. The study of ancient dental calculus holds great potential to recover information about past lives, within realistic parameters.