Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave (Sicily, Italy)

Recent improvements in the analysis of 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. Multi-omics analysis of dental calculus showed a diet rich of animal proteins which is also reflected on the oral microbiome composition. Our results demonstrate the power of using a multi-omics approach in the study of prehistoric human populations.

Archaeometric evidence for the earliest exploitation of lignite from the bronze age Eastern Mediterranean

This paper presents the earliest evidence for the exploitation of lignite (brown coal) in Europe and sheds new light on the use of combustion fuel sources in the 2nd millennium BCE Eastern Mediterranean. We applied Thermal Desorption/Pyrolysis–Gas Chromatography-Mass Spectrometry and Polarizing Microscopy to the dental calculus of 67 individuals and we identified clear evidence for combustion markers embedded within this calculus. In contrast to the scant evidence for combustion markers within the calculus samples from Egypt, all other individuals show the inhalation of smoke from fires burning wood identified as Pinaceae, in addition to hardwood, such as oak and olive, and/or dung. Importantly, individuals from the Palatial Period at the Mycenaean citadel of Tiryns and the Cretan harbour site of Chania also show the inhalation of fire-smoke from lignite, consistent with the chemical signature of sources in the northwestern Peloponnese and Western Crete respectively. This first evidence for lignite exploitation was likely connected to and at the same time enabled Late Bronze Age Aegean metal and pottery production, significantly by both male and female individuals.

Wild cereal grain consumption among Early Holocene foragers of the Balkans predates the arrival of agriculture

Forager focus on wild cereal plants has been documented in the core zone of domestication in southwestern Asia, while evidence for forager use of wild grass grains remains sporadic elsewhere. In this paper, we present starch grain and phytolith analyses of dental calculus from 60 Mesolithic and Early Neolithic individuals from five sites in the Danube Gorges of the central Balkans. This zone was inhabited by likely complex Holocene foragers for several millennia before the appearance of the first farmers ~6200 cal BC. We also analyzed forager ground stone tools for evidence of plant processing. Our results based on the study of dental calculus show that certain species of Poaceae (species of the genus Aegilops) were used since the Early Mesolithic, while ground stone tools exhibit traces of a developed grass grain processing technology. The adoption of domesticated plants in this region after ~6500 cal BC might have been eased by the existing familiarity with wild cereals.

The Role of Cytokines Produced via the NLRP3 Inflammasome in Mouse Macrophages Stimulated with Dental Calculus in Osteoclastogenesis

Dental calculus (DC) is a common deposit in periodontitis patients. We have previously shown that DC contains both microbial components and calcium phosphate crystals that induce an osteoclastogenic cytokine IL-1β via the NLRP3 inflammasome in macrophages. In this study, we examined the effects of cytokines produced by mouse macrophages stimulated with DC on osteoclastogenesis. The culture supernatants from wild-type (WT) mouse macrophages stimulated with DC accelerated osteoclastogenesis in RANKL-primed mouse bone marrow macrophages (BMMs), but inhibited osteoclastogenesis in RANKL-primed RAW-D cells. WT, but not NLRP3-deficient, mouse macrophages stimulated with DC produced IL-1β and IL-18 in a dose-dependent manner, indicating the NLRP3 inflammasome-dependent production of IL-1β and IL-18. Both WT and NLRP3-deficient mouse macrophages stimulated with DC produced IL-10, indicating the NLRP3 inflammasome-independent production of IL-10. Recombinant IL-1β accelerated osteoclastogenesis in both RANKL-primed BMMs and RAW-D cells, whereas recombinant IL-18 and IL-10 inhibited osteoclastogenesis. These results indicate that DC induces osteoclastogenic IL-1β in an NLRP3 inflammasome-dependent manner and anti-osteogenic IL-18 and IL-10 dependently and independently of the NLRP3 inflammasome, respectively. DC may promote alveolar bone resorption via IL-1β induction in periodontitis patients, but suppress resorption via IL-18 and IL-10 induction in some circumstances.

RANGKA MANUSIA DARI BENDAHARA: SUDUT PANDANG PALEOPATOLOGI

This study discusses human remains from the Bendahara, Tamiang, which is located in Aceh. There is no information regarding the exact location and the date of this site. It can be ascertained that this skeleton originated from prehistoric periods based on the dental modifications evidences. This aims of this study is to identify the human remains from the Bendahara, Tamiang, Aceh by looking at sex, age at death, disease and the influences of cultural and environmental which recorded on the skeletons. This study used macroscopic and paleopathological analysis methods. The results of this study are this individual was female based on her skull. Her age at death between 20-30 years old. The abnormalities that these individuals have are only presents in their teeth, such as dental calculus, dental modification, and unbalanced attrition. This condition indicates that this individual predominantly chewing using one of the lateral sides of the mouth. If we connected her young age at death with the attrition, it is possible that this individual uses the right side of his teeth as a tool. Penelitian ini mendiskusikan sisa-sisa manusia dari Bendahara, Tamiang yang terletak di Aceh. Tidak terdapat keterangan mengenai lokasi pasti dan penanggalan dari situs ini. Rangka ini memiliki probabilitas yang tinggi berasal dari masa prasejarah berdasarkan bukti modifikasi pada gigi-giginya. Permasalahan penelitian ini adalah untuk mengetahui identitas biologis rangka dari Bendahara Tamiang dan kehidupannya pada masa lampau. Penelitian ini bertujuan untuk mengidentifikasi individu sisa manusia dari Bendahara, Tamiang, Aceh dengan cara melihat jenis kelamin, umur ketika mati, penyakit, bukti kultural dan lingkungan yang terekam pada rangka tersebut. Penelitian ini menggunakan metode analisis makroskopis dan paleopatologis. Hasil dari penelitian ini adalah individu berjenis kelamin wanita, dengan umur ketika mati sekitar 20-30 tahun. Kelainan yang dimiliki individu ini terdapat pada organ giginya yaitu kalkulus gigi, modifikasi gigi, dan adanya atrisi yang tidak seimbang. Kondisi tersebut menunjukkan bahwa individu ini mengunyah dengan dominan pada salah satu sisi lateral organ mulutnya. Jika dikaitkan dengan umurnya yang tergolong muda, terdapat kemungkinan bahwa individu ini menggunakan sisi kanan giginya sebagai alat bantu dalam melakukan pekerjaan.

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.

Investigating Biases Associated with Dietary Starch Incorporation and Retention with an Oral Biofilm Model

Dental calculus has proven to contain a wealth of information on the dietary habits of past populations. These insights have, to a large extent, been obtained by the extraction and identification of starch granules contained within the mineralised dental plaque from a wide range of regions and time periods. The scope of previous studies have been limited to microfossil extraction and identification to reconstruct dietary preferences from the archaeological record, and few studies have attempted to address the biases of starch retention in dental calculus. Those that have considered this problem have been limited to in vivo studies on modern humans and non-human primates. Here, we present a multispecies oral biofilm model, which allows experimental research on starch incorporation and retention to be conducted on in vitro dental calculus in a controlled laboratory setting. The biofilms were exposed to treatment solutions with known quantities of dietary starches (wheat and potato) during the 25-day growth period. After this, the starch granules were extracted from the mature biofilm (by dissolution in EDTA), and counted. We show that the granule counts extracted from the model dental calculus represented a low proportion (ranging from 0.06% to 0.16%) of the total number of granules exposed to the biofilms throughout the experiment. Additionally, we found that the ratios of granule sizes from the extracted starch granules differed from the original treatment solutions, with large granules (>20 μm) consistently being under-represented. We also found a correlation between the absolute granule counts and dry-weight of the biofilm (r = 0.66, 90%CI[0.46,0.79]), as well as between the concentration (count per mg) of granules and dry-weight (r = 0.30, 90%CI[0.06,0.51]). Our results reinforce previous in vivo studies suggesting that dental calculus presents a very small, and partly biased picture of the original dietary intake of starches, with an over-representation of plants producing granules smaller than 20 μm in size. The experimental model presented here is well-suited to address the need for further validation of methods and biases associated with dietary research on dental calculus.