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

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 types of biomolecules or microparticles, 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 a single sample of archaeological dental calculus. We evaluate the protocol on dental calculus from six individuals from a range of time periods and estimated preservation states, and compare it against previously published DNA-only and protein-only protocols. We find that most aspects of downstream analyses are unaltered by the unified protocol, although minor shifts in the recovered proteome can be detected, such as a slight loss of hydrophilic proteins. Total protein recovery depends on both the amount of starting material and choice of extraction protocol, whereas total DNA recovery is significantly reduced using the unified protocol (mean 43%). Nevertheless, total DNA recovery from dental calculus is generally very high, and we found no differences in DNA fragment characteristics or taxonomic profile between the protocols. In conclusion, the unified protocol allows for simultaneous extraction of two complementary lines of biomolecular evidence from archaeological dental calculus without compromising downstream results, thereby minimizing the need for destructive analysis of this finite resource

Ancient dental calculus preserves signatures of biofilm succession and interindividual variation independent of dental pathology

Dental calculus preserves oral microbes, enabling comparative studies of the oral microbiome and health through time. However, small sample sizes and limited dental health metadata have hindered health-focused investigations to date. Here, we investigate the relationship between tobacco pipe smoking and dental calculus microbiomes. Dental calculus from 75 individuals fromthe 19th century Middenbeemster skeletal collection (Netherlands) were analyzed by metagenomics. Demographic and dental health parameters were systematically recorded, including the presence/number of pipe notches. Comparative data sets fromEuropean populations before and after the introduction of tobaccowere also analyzed. Calculus species profileswere comparedwith oral pathology to examine associations between microbiome community, smoking behavior, and oral health status. The Middenbeemster individuals exhibited relatively poor oral health,with a high prevalence of periodontal disease, caries, heavy calculus deposits, and antemortem tooth loss. No associations between pipe notches and dental pathologies, or microbial species composition,were found. Calculus samples before and after the introduction of tobacco showed highly similar species profiles. Observed interindividual microbiome differences were consistent with previously described variation in human populations from the Upper Paleolithic to the present. Dental calculus may not preserve microbial indicators of health and disease status as distinctly as dental plaque

Orphan crops of archaeology-based crop history research

Agrobiodiversity is central to sustainable farming worldwide. Cultivation, conservation and reintroduction of diverse plant species, including ‘forgotten’ and ‘underutilized’ crops, contribute to global agrobiodiversity, living ecosystems and sustainable food production. Such efforts benefit from traditional and historical knowledge of crop plants' evolutionary and cultural trajectories. This review is a first attempt at systematically gauging species representativeness in studies of archaeological plant remains. Results indicate that, in addition to discipline-specific methodological sources of bias, modern agricultural biases may replicate themselves in crop history research and influence understandings of ‘forgotten crops’. Recognizing these biases is an initial stride towards rectifying them and promoting agrobiodiversity in both research and practical applications. Summary: So-called ‘forgotten’ or ‘orphan’ crops are an important component of strategies aimed at preserving and promoting biodiversity. Knowledge of historical cultivation, usage, and geographic and evolutionary trajectories of plants, that is, crop history research, is important for the long-term success of such efforts. However, research biases in the crops chosen for study may present hurdles. This review attempts to systematically identify patterns in crop species representativeness within archaeology-based crop history research. A meta-analysis and synthesis of archaeobotanical evidence (and lack thereof) is presented for 268 species known to have been cultivated for food prior to 1492 CE from the Mediterranean region to South Asia. We identified 39 genera with known crop plants in this geographical and historical context that are currently absent from its archaeobotanical record, constituting ‘orphan’ crops of archaeobotany. In addition, a worldwide synthesis of crop species studied using geometric morphometric, archaeogenetic and stable isotope analyses of archaeological plant remains is presented, and biases in the species represented in these disciplines are discussed. Both disciplinary methodological biases and economic agenda-based biases affecting species representativeness in crop history research are apparent. This study also highlights the limited geographic diffusion of most crops and the potential for deeper historical perspectives on how crops become marginalized and ‘forgotten’

Time to Switch to Second-line Antiretroviral Therapy in Children With Human Immunodeficiency Virus in Europe and Thailand.

Background: Data on durability of first-line antiretroviral therapy (ART) in children with human immunodeficiency virus (HIV) are limited. We assessed time to switch to second-line therapy in 16 European countries and Thailand. Methods: Children aged <18 years initiating combination ART (≥2 nucleoside reverse transcriptase inhibitors [NRTIs] plus nonnucleoside reverse transcriptase inhibitor [NNRTI] or boosted protease inhibitor [PI]) were included. Switch to second-line was defined as (i) change across drug class (PI to NNRTI or vice versa) or within PI class plus change of ≥1 NRTI; (ii) change from single to dual PI; or (iii) addition of a new drug class. Cumulative incidence of switch was calculated with death and loss to follow-up as competing risks. Results: Of 3668 children included, median age at ART initiation was 6.1 (interquartile range (IQR), 1.7-10.5) years. Initial regimens were 32% PI based, 34% nevirapine (NVP) based, and 33% efavirenz based. Median duration of follow-up was 5.4 (IQR, 2.9-8.3) years. Cumulative incidence of switch at 5 years was 21% (95% confidence interval, 20%-23%), with significant regional variations. Median time to switch was 30 (IQR, 16-58) months; two-thirds of switches were related to treatment failure. In multivariable analysis, older age, severe immunosuppression and higher viral load (VL) at ART start, and NVP-based initial regimens were associated with increased risk of switch. Conclusions: One in 5 children switched to a second-line regimen by 5 years of ART, with two-thirds failure related. Advanced HIV, older age, and NVP-based regimens were associated with increased risk of switch

Life on the frontier: exploring economy and subsistence in transitional multi-faith societies of medieval Spain

International audienceWe present the results of interdisciplinary bioarchaeological research on the multicultural frontier context of the (Re)conquest of Islamic Iberia, focusing on human and animal subsistence as a proxy of political, social and economic changes from multiple sites in the province of Guadalajara between 10th and 15th c. CE.Guadalajara, located in central Spain was defined by opposing Christian and Muslim frontier societies in the 11th and 12th centuries. We study sites dating to either side of the (Re)conquest to explore this frontier in transition, including the castle of Molina de Aragón, Prao de los Judíos, the Cathedral of Sigüenza, Alcázar Real de Guadalajara, Palacio de los Guzmán, castle of Zorita de los Canes, the cemetery of Guadalajara and the Campus de las Cristinas cemetery. These are mainly urban and military settlements which played a role as central places in the region and represent differing religious communities, including Muslim, Christian and Jewish contexts.Biomolecular techniques were applied to these contexts in order to obtain a deeper understanding of animal husbandry strategies and food consumption patterns by both livestock and humans. Bulk carbon (δ13C), nitrogen (δ15N) and sulphur (δ34S) stable isotope analyses were performed on the bone collagen of >300 samples, including humans, domestic mammals, birds and fish. A subsample of these were also analysed for oxygen (δ16O) and strontium (87/86Sr) isotopes to investigate mobility. Research questions to be addressed through these data include exploring differences in production strategies through time and between religious communities, differences between food supply networks to cities and castles and the consequences of changes in political rulership in animal husbandry management. Particular themes emerge, such as the use of C4 plants as fodder or the supply and consumption of fish at these inland settlements

Isotopic adventures in Medieval Guadalajara: animal and human subsistence on the frontier

International audienc

Life on the frontier: exploring economy and subsistence in transitional multi-faith societies of medieval Spain

International audienceWe present the results of interdisciplinary bioarchaeological research on the multicultural frontier context of the (Re)conquest of Islamic Iberia, focusing on human and animal subsistence as a proxy of political, social and economic changes from multiple sites in the province of Guadalajara between 10th and 15th c. CE.Guadalajara, located in central Spain was defined by opposing Christian and Muslim frontier societies in the 11th and 12th centuries. We study sites dating to either side of the (Re)conquest to explore this frontier in transition, including the castle of Molina de Aragón, Prao de los Judíos, the Cathedral of Sigüenza, Alcázar Real de Guadalajara, Palacio de los Guzmán, castle of Zorita de los Canes, the cemetery of Guadalajara and the Campus de las Cristinas cemetery. These are mainly urban and military settlements which played a role as central places in the region and represent differing religious communities, including Muslim, Christian and Jewish contexts.Biomolecular techniques were applied to these contexts in order to obtain a deeper understanding of animal husbandry strategies and food consumption patterns by both livestock and humans. Bulk carbon (δ13C), nitrogen (δ15N) and sulphur (δ34S) stable isotope analyses were performed on the bone collagen of >300 samples, including humans, domestic mammals, birds and fish. A subsample of these were also analysed for oxygen (δ16O) and strontium (87/86Sr) isotopes to investigate mobility. Research questions to be addressed through these data include exploring differences in production strategies through time and between religious communities, differences between food supply networks to cities and castles and the consequences of changes in political rulership in animal husbandry management. Particular themes emerge, such as the use of C4 plants as fodder or the supply and consumption of fish at these inland settlements

Ethno-religious identities and subsistence practices in multicultural frontier societies of Medieval Iberia

International audienc

Orphan crops of archaeology‐based crop history research

Publication status: PublishedFunder: Social Sciences and Humanities Research Council of Canada; doi: http://dx.doi.org/10.13039/501100000155Funder: University of Cambridge; doi: http://dx.doi.org/10.13039/501100000735Societal Impact Statement: Agrobiodiversity is central to sustainable farming worldwide. Cultivation, conservation and reintroduction of diverse plant species, including ‘forgotten’ and ‘underutilized’ crops, contribute to global agrobiodiversity, living ecosystems and sustainable food production. Such efforts benefit from traditional and historical knowledge of crop plants' evolutionary and cultural trajectories. This review is a first attempt at systematically gauging species representativeness in studies of archaeological plant remains. Results indicate that, in addition to discipline‐specific methodological sources of bias, modern agricultural biases may replicate themselves in crop history research and influence understandings of ‘forgotten crops’. Recognizing these biases is an initial stride towards rectifying them and promoting agrobiodiversity in both research and practical applications. Summary: So‐called ‘forgotten’ or ‘orphan’ crops are an important component of strategies aimed at preserving and promoting biodiversity. Knowledge of historical cultivation, usage, and geographic and evolutionary trajectories of plants, that is, crop history research, is important for the long‐term success of such efforts. However, research biases in the crops chosen for study may present hurdles. This review attempts to systematically identify patterns in crop species representativeness within archaeology‐based crop history research. A meta‐analysis and synthesis of archaeobotanical evidence (and lack thereof) is presented for 268 species known to have been cultivated for food prior to 1492 CE from the Mediterranean region to South Asia. We identified 39 genera with known crop plants in this geographical and historical context that are currently absent from its archaeobotanical record, constituting ‘orphan’ crops of archaeobotany. In addition, a worldwide synthesis of crop species studied using geometric morphometric, archaeogenetic and stable isotope analyses of archaeological plant remains is presented, and biases in the species represented in these disciplines are discussed. Both disciplinary methodological biases and economic agenda‐based biases affecting species representativeness in crop history research are apparent. This study also highlights the limited geographic diffusion of most crops and the potential for deeper historical perspectives on how crops become marginalized and ‘forgotten’