Search

Contamination is a potential problem in the study of ancient proteins, either from prior handling of the sample, laboratory consumables, or cross-sample carryover from mass spectrometers. Recently, deamidation of glutamine has been proposed as a measure for assessing the degradation of ancient proteins. Here, we present deamiDATE 1.0, a method for the authentication of ancient proteins using measure of site-specific deamidation rates. We test this approach on shotgun proteomic data derived from bone collagen from modern, archaeological and extinct taxa. We further demonstrate how this method may be used to differentiate between modern contaminants and authentic ancient proteins using a case study from Neolithic dental calculus.

We present the analysis of an osseous finger ring from a predominantly early Neolithic context in Denmark. To characterize the artefact and identify the raw material used for its manufacture, we performed micro-computed tomography scanning, zooarchaeology by mass spectrometry (ZooMS) peptide mass fingerprinting, as well as protein sequencing by liquid chromatography tandem mass spectrometry (LC-MS/MS). We conclude that the ring was made from long bone or antler due to the presence of osteons (Haversian canals). Subsequent ZooMS analysis of collagen I and II indicated that it was made fromAlces alcesorCervus elaphusmaterial. We then used LC-MS/MS analysis to refine our species identification, confirming that the ring was made fromCervus elaphus, and to examine the rest of the proteome. This study demonstrates the potential of ancient proteomics for species identification of prehistoric artefacts made from osseous material.

In the version of this Perspective originally published, in the third paragraph of the section 'Selection and sampling', the sentence beginning 'Pyrolysis-gas chromatography' should have also referred to high-performance liquid chromatography; the sentence has now been amended to read 'Pyrolysis-gas chromatography/mass spectrometry (py-GC/MS) and high-performance liquid chromatography (HPLC) can be used to detect the presence of amino acids62 in any putative proteinaceous sample.'

ZooMS (Zooarchaeology by Mass Spectrometry) is increasingly being used as a method for species identification of archaeological and historical remains. The method identifies species from the peptid...

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 (eighth century BC to nineteenth century AD) in England, as well as 14 dental calculus samples from contemporary dental patients and recently deceased individuals, to characterize the range and extent of dietary proteins preserved in dental calculus. In addition to milk proteins, we detect 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. This study demonstrates that proteomic approaches can robustly identify foodstuffs in the archaeological record that are typically under-represented due to their poor macroscopic preservation.

https://orcid.org/0000-0001-7487-2635

Rationale The oxygen (O) isotope composition of collagen proteins is a potential indicator of adult residential location, useful for provenancing in ecology, archaeology and forensics. In acidic solution, proteins can exchange O from carboxylic acid moieties with reagent O. This study investigated whether this exchange occurs during demineralisation and gelatinisation preparation of bone/ivory collagen. Methods EDTA and HCl demineralisation or gelatinisation reagents were made up in waters with different δ18O values, and were used to extract collagen from four skeletal tissue samples. Aliquots of extracted collagen were exposed to two different atmospheric waters, at 120°C and ambient temperature, and subsequently dried in a vacuum oven at 40°C or by freeze drying. Sample δ18O values were measured by HT‐EA pyrolysis/IRMS using a zero‐blank autosampler. Results Collagen samples exchanged O with both reagent waters and atmospheric water, which altered sample δ18O values. Exchange with reagent waters occurred in all extraction methods, but was greater at lower pH. Damage to the collagen samples during extraction increased O exchange. The nature of exchange of O with atmospheric water depended on the temperature of exposure: kinetic fractionation of O was identified at 120°C but not at ambient temperature. Exchange was difficult to quantify due to the high variability of δ18O values between experimental replicates. Conclusions Studies of δ18O values in collagen proteins should avoid extraction methods using acidic solutions.

How humans got their goatsLittle is known regarding the location and mode of the early domestication of animals such as goats for husbandry. To investigate the history of the goat, Dalyet al.sequenced mitochondrial and nuclear sequences from ancient specimens ranging from hundreds to thousands of years in age. Multiple wild populations contributed to the origin of modern goats during the Neolithic. Over time, one mitochondrial type spread and became dominant worldwide. However, at the whole-genome level, modern goat populations are a mix of goats from different sources and provide evidence for a multilocus process of domestication in the Near East. Furthermore, the patterns described support the idea of multiple dispersal routes out of the Fertile Crescent region by domesticated animals and their human counterparts.Science, this issue p.85

Medieval manuscripts, carefully curated and conserved, represent not only an irreplaceable documentary record but also a remarkable reservoir of biological information. Palaeographic and codicological investigation can often locate and date these documents with remarkable precision. The York Gospels (York Minster Ms. Add. 1) is one such codex, one of only a small collection of pre-conquest Gospel books to have survived the Reformation. By extending the non-invasive triboelectric (eraser-based) sampling technique eZooMS, to include the analysis of DNA, we report a cost-effective and simple-to-use biomolecular sampling technique for parchment. We apply this combined methodology to document for the first time a rich palimpsest of biological information contained within the York Gospels, which has accumulated over the 1000-year lifespan of this cherished object that remains an active participant in the life of York Minster. These biological data provide insights into the decisions made in the selection of materials, the construction of the codex and the use history of the object.

Reliable sources of photons will be required to develop many photonic quantum technologies. Current on-demand sources are lacking in brightness, compactness, and scalability. Here, we review the use of silicon photonic crystal waveguides as nonlinear photon generators in the 1550 nm band. We show that these photon sources can create strong frequency correlations, that the predictability of photon generation can be improved through the active multiplexing of many sources, and that photons from these sources can be useful for quantum communication.

Strontium isotope analysis (87Sr/86Sr) has been employed as a provenancing tool for archaeological wool textiles. To date, the effect of post-depositional (soil burial environment) contamination on keratin samples, which contain ∼ppm concentrations of Sr, has not been rigorously investigated. We compared published methods for removing exogenous Sr from keratinous textiles, using either: (1) compressed N2 gas, (2) HF(aq) solution (with and without a strong oxidising agent to remove dyestuff) or (3) organic solvents. 87Sr/86Sr ratios and Sr contents were determined in undyed and madder-dyed/alum-mordanted moieties of the same wool textile, buried for up to three years in contrasting environments (marine sediment/fenland bog), and two archaeological textiles recovered in Iceland (one typical and one atypical of local manufacture). Undyed experimental samples had low Sr contents (0.07–0.29 ppm) that were increased by both dyeing (0.14–8.92 ppm) and soil burial (0.11–15.01 ppm). The efficacy of Sr removal was: HF(aq) + oxidising agent > organic solvents > HF(aq) > compressed N2. Unburied samples showed little variation in 87Sr/86Sr ratio between cleaning methods (0.00006–0.00035); buried samples showed greater variation (0.00257–0.00713). Archaeological samples showed Sr contents greater than experimental soil burials (1–118 ppm), and 87Sr/86Sr values consistent with Icelandic groundwater (0.70357–0.70540). No cleaning methods retrieved original (unburied and undyed) 87Sr/86Sr ratios except treatment with compressed N2 in undyed samples. Exogenous Sr from the short term soil burial environment is probably mostly present as particulates. We conclude that 87Sr/86Sr ratios of archaeological wool textiles recovered from wet burial environments do not accurately reflect wool provenance even after cleaning with the methods investigated.

Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi-fold increases in both the quantity of ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 ancient genomes have been sequenced, moving from 0.7× coverage (mammoth) in 2008 to more than 50× coverage (Neanderthal) in 2014. Studies of rapid evolutionary changes, such as the evolution and spread of pathogens and the genetic responses of hosts, or the genetics of domestication and climatic adaptation, are developing swiftly and the importance of palaeogenomics for investigating evolutionary processes during the last million years is likely to increase considerably. However, these new datasets require new methods of data processing and analysis, as well as conceptual changes in interpreting the results. In this review we highlight important areas of future technical and conceptual progress and discuss research topics in the rapidly growing field of palaeogenomics.

This paper presents evidence of the discovery of a new Middle Pleistocene site in central southern England, with undisturbed evidence of hominin occupation well-dated to an interstadial towards the end of Marine Isotope Stage 8, c. 250,000 BP. The site consists of a preserved remnant of a river terrace and its alluvial floodplain overlain by chalk-rich bankside deposits, all abutting a Chalk bedrock riverbank. It preserves an area of occupation with activity focused on the riverbank, complemented by occasional activity on a palaeo-landsurface developed on the surface of the alluvial floodplain. Lithic technology at the site consists almost entirely of handaxe manufacture, allowing attribution to an Acheulian industrial tradition. Mammalian and other palaeo-environmental remains are present and associated with the occupation horizons, including large mammal bones showing signs of hominin interference. Dating was based on OSL determinations on the sediments and amino acid racemisation of molluscan remains, supported by biostratigraphic indications. Besides being a rare instance of an undisturbed Palaeolithic palaeo-landscape covering several hectares, the site contributes to wider Quaternary research concerns over the ability of Middle Pleistocene hominins to tolerate colder climatic episodes in higher latitudes, and over settlement history and changing lithic industrial traditions of northwest Europe in relation to climate change and British peninsularity. It is suggested that the Harnham evidence may represent an insular population that had persisted in southern Britain since MIS 10/9, which became locally extinct during the glacial maximum 8.2 marking the end of MIS 8.

Medieval manuscripts, carefully curated and conserved, represent not only an irreplaceable documentary record but also a remarkable reservoir of biological information. Palaeographic and codicological investigation can often locate and date these documents with remarkable precision. The York Gospels (York Minster Ms. Add. 1) is one such codex, one of only a small collection of pre-conquest Gospel books to have survived the Reformation. By extending the non-invasive triboelectric (eraser-based) sampling technique eZooMS, to include the analysis of DNA we report a cost effective and simple-to-use biomolecular sampling technique. We apply this combined methodology to document for the first time a rich palimpsest of biological information contained within the York Gospels, which has accumulated over the 1,000 year lifespan of this cherished object that remains an active participant in the life of York Minster. This biological data provides insights into the decisions made in the selection of materials, the construction of the codex and the use history of the object.

The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to a revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for environmental variables. We propose a model for ancient DNA decay wherein fragmentation rapidly reaches a threshold, then subsequently slows. The observed loss of DNA over time may be due to a bulk diffusion process in many cases, highlighting the importance of tissues and environments creating effectively closed systems for DNA preservation. This model of DNA degradation is largely based on mammal bone samples due to published genomic dataset availability. Continued refinement to the model to reflect diverse biological systems and tissue types will further improve our understanding of ancient DNA breakdown dynamics.

IntroductionDental calculus is a mineralized microbial dental plaque biofilm that forms throughout life by precipitation of salivary calcium salts. Successive cycles of dental plaque growth and calcification make it an unusually well-preserved, long-term record of host-microbial interaction in the archaeological record. Recent studies have confirmed the survival of authentic ancient DNA and proteins within historic and prehistoric dental calculus, making it a promising substrate for investigating oral microbiome evolution via direct measurement and comparison of modern and ancient specimens.ObjectiveWe present the first comprehensive characterization of the human dental calculus metabolome using a multi-platform approach.MethodsUltra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) quantified 285 metabolites in modern and historic (200 years old) dental calculus, including metabolites of drug and dietary origin. A subset of historic samples was additionally analyzed by high-resolution gas chromatography-MS (GC-MS) and UPLC- MS/MS for further characterization of polar metabolites and lipids, respectively. Metabolite profiles of modern and historic calculus were compared to identify patterns of persistence and loss.ResultsDipeptides, free amino acids, free nucleotides, and carbohydrates substantially decrease in abundance and ubiquity in archaeological samples, with some exceptions. Lipids generally persist, and saturated and mono-unsaturated medium and long chain fatty acids appear to be well-preserved, while metabolic derivatives related to oxidation and chemical degradation are found at higher levels in archaeological dental calculus than fresh samples.ConclusionsThe results of this study indicate that certain metabolite classes have higher potential for recovery over long time scales and may serve as appropriate targets for oral microbiome evolutionary studies.

Peptide mass fingerprinting of bone collagen (ZooMS) has previously been proposed as a method to calculate the extent of the non-enzymatic degradation of glutamine into glutamic acid (deamidation). Temporal and spatial variation of glutamine deamidation at a single site, however, has not been investigated. Here we apply ZooMS screening of Châtelperronian and Early Holocene bone specimens from Quinçay, France, to explore temporal and spatial variation in glutamine deamidation. Our results indicate that chronological resolution is low, while spatial variation is high. Nevertheless, our analysis allows the identification of bone specimens that have undergone diagenetic histories remarkably different (either in length or in type) from spatially related bone specimens. Therefore, ZooMS ammonium-bicarbonate screening is capable of testing bone assemblage homogeneity, which could guide subsequent analysis and interpretation.

We present an automated and stable method to measure an arbitrary portion of the joint spectral intensity of quantum photonic devices with an unprecedented resolution of 10 GHz in the telecommunication band. The method is applied to a 20 cm chalcogenide As2S3 fiber that generates correlated photons via spontaneous four-wave mixing. Good qualitative agreement between our measurements and an idealized theoretical model is obtained. The entanglement present in the system is extracted via a Schmidt decomposition where the reduction in the Schmidt number compared to that calculated via the model is attributed to the high amount of spontaneous Raman scattered noise photons present in chalcogenide fiber.

Fibre products, such as textiles and animal pelts, are often recovered in the corrosion crust of archaeological metal artefacts. Because clothed burials are an important resource for the study of past societies, accurate fibre identification is important. However, extreme mineralisation of animal fibres can render microscopic visualisation difficult for species identification. Peptide mass fingerprinting (PMF) has been successfully used to identify the species origin in both collagen and keratin-made archaeological artefacts. The approach requires little material but the state of degradation (protein hydrolysis) is a limiting factor as it might impact on the identification of key markers. In this study we analysed pelt and textile fragments found in association with copper-alloy objects with different degrees of mineralisation; samples were obtained from a Viking-Age (10th c.) grave in Britain and from a burial in Mongolia (3rd c. BC to 2nd c. AD). Species identification was possible in all but one sample, revealing PMF can be applied to corrosion products, thereby further expanding the value of these objects for textile research.

RATIONALE Archaeological keratin samples are increasingly the subject of palaeodietary, provenancing and dating studies. Keratin samples from wet archaeological contexts are microbiologically and chemically degraded, causing differential diagenesis of protein structures in hair fibres. The effects of these processes on the analytical parameters of interest are currently unknown. METHODS This study examined the impact of degradation of wool fibres on isotopic (δ13C, δ15N, un-exchangeable δ2H and δ18O values) composition. It compared two models of archaeological protein degradation in wet burial environments: (1) short term (up to 8 years) experimental burial in three contrasting soil environments; and (2) laboratory wet conditions, in which elevated temperature (80 °C, 110 °C, and 140 °C) and pressure simulated longer exposure. Elemental and amino acid (AA) composition were also measured. RESULTS In experimentally soil-buried samples, AA, elemental and isotopic composition changes were small, despite extensive macroscopic alteration. Isothermally heated samples showed preferential loss of hydrophilic AAs (Asx, Glx, Ser, Gly) from wool residues, with depletion in 2H and 18O at higher temperatures (up to −73‰ change in δ2H and −2.6‰ in δ18O values). The δ13C and δ15N values showed little change except in densely pigmented samples at low temperatures only. Samples dyed with madder/alum were better preserved than undyed samples. CONCLUSIONS Diagenesis in experimentally soil-buried wool textiles was consistent with microbiological, non-protein-selective activity, in contrast to highly AA-selective hydrolytic behaviour under laboratory wet conditions. Changes in δ2H and δ18O values were correlated with degree of AA change, but the δ13C and δ15N values were not. The results contribute to a baseline for interpreting analytical data from archaeological hair samples preserved by burial in wet environments. Copyright © 2014 John Wiley & Sons, Ltd.

Despite being widely utilized in the production of cultural objects, keratinous hard tissues, such as horn, baleen, and tortoiseshell, rarely survive in archaeological contexts unless factors combine to inhibit biodeterioration. Even when these materials do survive, working, use, and diagenetic changes combine to make identification difficult. This paper reviews the chemistry and deterioration of keratin and past approaches to the identification of keratinous archaeological remains. It describes the formation of horn, hoof, baleen, and tortoiseshell and demonstrates how identification can be achieved by combining visual observation under low-power magnification with an understanding of the structure and characteristic deterioration of these materials. It also demonstrates how peptide mass fingerprinting of the keratin can be used to identify keratinous tissues, often to species, even when recognizable structural information has not survived.

A key resource for quantum optics experiments is an on-demand source of single and multiple photon states at telecommunication wavelengths. This letter presents a heralded single photon source based on a hybrid technology approach, combining high efficiency periodically poled lithium niobate waveguides, low-loss laser inscribed circuits, and fast (>1 MHz) fibre coupled electro-optic switches. Hybrid interfacing different platforms is a promising route to exploiting the advantages of existing technology and has permitted the demonstration of the multiplexing of four identical sources of single photons to one output. Since this is an integrated technology, it provides scalability and can immediately leverage any improvements in transmission, detection and photon production efficiencies.

Clovis, with its distinctive biface, blade and osseous technologies, is the oldest widespread archaeological complex defined in North America, dating from 11,100 to 10,700 C-14 years before present (BP) (13,000 to 12,600 calendar years BP)(1,2). Nearly 50 years of archaeological research point to the Clovis complex as having developed south of the North American ice sheets from an ancestral technology(3). However, both the origins and the genetic legacy of the people who manufactured Clovis tools remain under debate. It is generally believed that these people ultimately derived from Asia and were directly related to contemporary Native Americans(2). An alternative, Solutrean, hypothesis posits that the Clovis predecessors emigrated from southwestern Europe during the Last Glacial Maximum(4). Here we report the genome sequence of a male infant (Anzick-1) recovered from the Anzick burial site in western Montana. The human bones date to 10,705 +/- 35 C-14 years BP (approximately 12,707-12,556 calendar years BP) and were directly associated with Clovis tools. We sequenced the genome to an average depth of 14.4x and show that the gene flow from the Siberian Upper Palaeolithic Mal'ta population(5) into Native American ancestors is also shared by the Anzick-1 individual and thus happened before 12,600 years BP. We also show that the Anzick-1 individual is more closely related to all indigenous American populations than to any other group. Our data are compatible with the hypothesis that Anzick-1 belonged to a population directly ancestral to many contemporary Native Americans. Finally, we find evidence of a deep divergence in Native American populations that predates the Anzick-1 individual.

Graphene and boron nitride are two-dimensional materials whose atoms are arranged in a honeycomb lattice. Their unique properties arise because their electrons behave like relativistic particles (without and with mass, respectively)---namely, they obey the Dirac equation. Here, we use a photonic analog of boron nitride to observe Dirac physics in a silicon integrated optical platform. This will allow for photonic applications of Dirac dispersions (gapped and ungapped) to be realized in an on-chip, integrated nanophotonic platform.

In Western Europe, the Middle to Upper Paleolithic transition is associated with the disappearance of Neandertals and the spread of anatomically modern humans (AMHs). Current chronological, behavioral, and biological models of this transitional period hinge on the Châtelperronian technocomplex. At the site of the Grotte du Renne, Arcy-sur-Cure, morphological Neandertal specimens are not directly dated but are contextually associated with the Châtelperronian, which contains bone points and beads. The association between Neandertals and this "transitional" assemblage has been controversial because of the lack either of a direct hominin radiocarbon date or of molecular confirmation of the Neandertal affiliation. Here we provide further evidence for a Neandertal-Châtelperronian association at the Grotte du Renne through biomolecular and chronological analysis. We identified 28 additional hominin specimens through zooarchaeology by mass spectrometry (ZooMS) screening of morphologically uninformative bone specimens from Châtelperronian layers at the Grotte du Renne. Next, we obtain an ancient hominin bone proteome through liquid chromatography-MS/MS analysis and error-tolerant amino acid sequence analysis. Analysis of this palaeoproteome allows us to provide phylogenetic and physiological information on these ancient hominin specimens. We distinguish Late Pleistocene clades within the genus Homo based on ancient protein evidence through the identification of an archaic-derived amino acid sequence for the collagen type X, alpha-1 (COL10α1) protein. We support this by obtaining ancient mtDNA sequences, which indicate a Neandertal ancestry for these specimens. Direct accelerator mass spectometry radiocarbon dating and Bayesian modeling confirm that the hominin specimens date to the Châtelperronian at the Grotte du Renne.

Eggshell is a potentially common archaeological resource, but it tends to be ignored. The recent development of ZooMS (zooarchaeology by mass spectrometry) as a rapid and robust system for taxonomic identification of preserved eggshell fragments has facilitated new insights into patterns of egg use in the past. This paper presents a case study of egg use at two sites in Anglo-Scandinavian York (Hungate and Coppergate). The results described below suggest that the relative prevalence of goose eggshell may become a useful indicator of status, consistent with other characteristics of the two sites, and also demonstrate an apparent lack of exploitation of eggs of wild birds in York during the Anglo-Scandinavian period. These results highlight the interpretative potential of eggshell, which can now begin to be more fully explored. Copyright © 2013 John Wiley & Sons, Ltd.

Deamidation of glutamine (Q) and asparagine (N) has been recognized as a marker of degradation and aging in ancient proteins. Using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) to study deamidation in wool textiles, we identified eight peptides from α-keratin proteins in sheep wool that could potentially be used to assess the level of degradation. For each chosen peptide, the extent of deamidation was determined by comparing the calculated theoretical distribution with the measured distribution using a genetic algorithm that gives the best fit to the measured distribution. Variations in the levels of deamidation were observed between peptides and in modern wool samples buried for up to 8 years in which deamidation levels were relatively low under short-term burial. In contrast, deamidation was higher in archeological textile fragments from medieval sites ranging from the 9th to 13th century in York (United Kingdom) and Newcastle (United Kingdom) and from the 13th to 16th century in Reykholt (Iceland). Major differences were observed between the British and the Icelandic samples, showing a negative correlation between age of samples and levels of deamidation, but highlighting the effect of local environment. In addition, nanoscale liquid chromatography-electrospray ionization tandem mass spectrometry (nanoLC-ESI-MS/MS) data indicated that deamidation in wool's α-keratin was influenced by primary and higher-order structures. Predominance of deamidation on glutamine rather than asparagine in the archeological samples was attributed to a higher abundance of Q in the α-helical core domain of keratins, neighboring residues and steric hindrance preventing deamidation of N.

Rationale In ancient and/or damaged artefacts containing keratinous materials, the species of origin of the materials can be difficult to identify through visual examination; therefore, a minimally destructive methodology for species identification is required. While hair fibres from some species have seen substantial characterisation, others such as horn or baleen have received little or no attention, or lack protein sequences allowing formal identification using proteomics techniques. Methods We used the PMF method (Peptide Mass Fingerprinting with matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF-MS)) to catalogue and identify diagnostic peptide markers up to the genus level. Sequences were checked using nanoflow liquid chromatography/electrospray ionisation tandem mass spectrometry (nanoLC/ESI-MS/MS) and unidentified peptides were searched against a theoretical database generated by substituting amino acids in keratin sequences. Results Specific peptides were identified by m/z and sequences characterised whenever possible for a range of species belonging to Bovidae and Camelidae, and for tissues such as baleen and horn. The theoretical database allowed an increase in the number of peptides of up to 10% in species with little genetic information. Conclusions A proteomics approach can successfully identify specific markers for the identification of materials to the genus level, and should be considered when identification by other means is not possible. Identification by PMF is fast, reliable and inexpensive.

RATIONALE: A variety of metabolic, dietary and climatic influences on isotopic variation have been established in mammalian hair. The relevance of these factors to collagen isotopic composition is unknown, but would be of great interest to zooarchaeological analyses of faunal skeletal tissue. METHODS: The relationships between carbon (δ 13 C), nitrogen (δ 15 N), non-exchangeable hydrogen (δ 2 H) and oxygen (δ 18 O) values of defatted, demineralised and gelatinised bone collagen and defatted wool keratin from two sheep flocks (n=20, 5) in the UK were investigated, including testing for the effects of nutritional plane, sex, pregnancy and season of sample collection. The sulfur composition (δ 34 S values) was also investigated for tissues from the smaller flock. RESULTS: Bulk collagen was enriched in 13 C over bulk keratin by 2.02.7‰ and in 2 Hb y 2940‰ but depleted in 18 O relative to keratin by 1.8‰. Differences in δ 15 N values were within experimental error. The collagen samples were generally more enriched in 34 S than keratin, but this was very variable. Pregnancy, sex and season, but not nutritional plane, significantly affected isotope values but did not change overall keratin-collagen relationships. CONCLUSIONS: This dataset provides a baseline measure of variability and comparability for isotopic investigations into origin and husbandry conditions in archaeological sheep tissues, both collagen and keratin. Copyright © 2013 John Wiley & Sons, Ltd.

The facile racemization of protein-bound amino acids plays an important role in the aging and pathologies of living tissues, and it can be exploited for protein geochronological studies in subfossil biominerals. However, the in-chain degradation pathways of amino acids are complex and difficult to elucidate. Serine has proven to be particularly elusive, and its ability to racemize as a peptide-bound residue (like asparagine and aspartic acid) has not been demonstrated. This study investigates the patterns of degradation of a model peptide (WNSVWAW) at elevated temperatures, quantifying the extent of racemization and peptide bond hydrolysis using reverse-phase high-performance liquid chromatography (RP-HPLC) and tracking the presence of degradation products by MALDI-MS. We provide direct evidence that, under these experimental conditions, both serine and asparagine are able to undergo racemization as internally bound residues, which shows their potential for initiating protein breakdown and provides an explanation for the presence of d-enantiomers in living mammalian tissues.

Woollen textiles recovered from archaeological excavations are usually fragile, discoloured, mineralised, or highly biodeteriorated fragmentary remains. The nature and extent of preservation is highly dependent on the site of burial and factors such as soil composition, pH, temperature, oxygen content, and contact with a wood coffin or metals. Understanding the particular biodegradation in archaeological sites is important for biomolecular studies of textiles, and to assist in the conservation of these finds. Wool fabrics dyed and buried for up to 8 yr in bog-type soils in Denmark (Lejre) and Norway (Rormyra), and in marine sediments in Sweden (Marstrand) were evaluated by proteomics analysis. Wool degradation was found to occur through a range of differing mechanisms, mainly due to the complex nature of wool itself with its many families of proteins (keratin and keratin-associated proteins) and structures. Microbial activity was a large contributory factor to the physical deterioration of the wool fabrics at Lejre and Marstrand, and might result in faster loss of keratin-associated proteins over keratins. Additional hydrolysis took place at Marstrand, influenced by the environmental conditions of the sediment, and in particular the alkaline pH, contributing to the degradation of keratins. However, cross-linking was associated with the long-term preservation of the fabrics at Rormyra, where pH, temperature, and vegetative composition of the bog prevented microbial activity, and sphagnum moss might preserve wool by binding with keratins.

It is nearly thirty years since the last inter-laboratory study was carried out for amino acid racemization (AAR) analysis using powdered fossil material ( Wehmiller 1984 ). Since then there have been major changes in sample preparation and instrumentation, and it was considered timely to coordinate a new inter-laboratory study in support of current methodologies. In 2010, two such studies were undertaken. The first of these, coordinated by Wehmiller (this edition), used homogeneous hydrolysates of Pleistocene mollusc and eggshell materials and focused on the agreement of analytical measurements between laboratories, without interference from differing sample preparation procedures. The second (this study) was designed specifically as a proficiency test. Unlike previous inter-laboratory comparisons that have focussed on precision estimates, the purpose of this study was to carry out an evaluation of measurement bias by comparing the measurement results of laboratories carrying out their routine methods, including extraction, against the consensus values. Participants were sent one dried sample of a mixed amino acid standards solution and five homogeneous powders: two Pleistocene mollusc test materials prepared from material (ILC-A) supplied and used by Wehmiller in previous inter-laboratory studies (1984; and this edition), one Pleistocene opercula test material from the terrestrial gastropod, Bithynia tentaculata , and two heat-treated modern ostrich eggshell test materials. Results from this study demonstrate that whilst individual laboratory precision may be excellent, suggesting good control of random error influences (less than 1% for replicate measurements by some individual laboratories), agreement between methods, or even between laboratories carrying out the same method, may be very different. Trueness evaluation (determined as the relative percentage bias) reveals the extent of the disagreement reflected by the inter-laboratory variability. Individual laboratory D / L value biases of 10–30% or more when compared to the consensus values are not uncommon. We demonstrate why bias contributions should also be included in AAR uncertainty estimation and recommend that the preparation of defined reference materials are seen as a priority in order to control and correct for systematic error influences in the analytical system.

Collagen peptides are analyzed using a low-cost, high-throughput method for assessing deamidation using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). For each chosen peptide, the theoretical distribution is calculated and the measured distribution for each sample compared with this to determine the extent of glutamine deamidation. The deamidation of glutamine (Q) to glutamic acid (E) results in a mass shift of +0.984 Da. Thus, from the resolution of our data, the second peak in the isotope distribution for a peptide containing one glutamine residue coincides with the first peak of the isotope distribution for the peptide in which the residue is deamidated. A genetic algorithm is used to determine the extent of deamidation that gives the best fit to the measured distribution. The method can be extended to peptides containing more than one glutamine residue. The extent of protein degradation assessed in this way could be used, for example, to assess the damage of collagen, and screen samples for radiocarbon dating and DNA analysis.

Analysis of ancient cattle husbandry is compromised by the need for conventional analysis of sex and age at death to use different elements of the skeleton, usually from different individuals. We demonstrate a technique using aDNA acquired from cattle mandibles and combined with age-at-death estimation based on dental eruption in the same specimens. Application to small sample groups from two sites in Na h-Eileanan Siar (the Scottish Western Isles) show a high success rate, and demonstrates the potential for a more nuanced interpretation of ancient cattle husbandry.

We report the characterisation of meat and bone meal (MBM) standards (Set B-EFPRA) derived from cattle, sheep, pig and chicken, each rendered at four different temperatures (133, 137, 141 and 145 °C). The standards, prepared for an EU programme STRATFEED (to develop new methodologies for the detection and quantification of illegal addition of mammalian tissues in feeding stuffs), have been widely circulated and used to assess a range of methods for identification of the species composition of MBM. The overall state of mineral alteration and protein preservation as a function of temperature was monitored using small angle X-ray diffraction (SAXS), amino acid composition and racemization analyses. Progressive increases in protein damage and mineral alteration in chicken and cattle standards was observed. In the case of sheep and pig, there was greater damage to the proteins and alteration of the minerals at the lowest treatment temperature (133 °C), suggesting that the thermal treatments must have been compromised in some way. This problem has probably impacted upon the numerous studies which tested methods against these heat treatments. We use protein mass spectrometric methods to explore if thermostable proteins could be used to identify rendered MBM. In more thermally altered samples, so-called 'thermostable' proteins such as osteocalcin which has been proposed as a ideal target to speciate MBM were no longer detectable, but the structural protein type I collagen could be used to differentiate all four species, even in the most thermally altered samples.

We employ “photonic boron nitride” — a silicon photonic crystal slab composed of a honeycomb lattice of holes — to observe Dirac physics of guided optical modes. The lattice is composed of two component triangular lattices of different hole-size Δr, which breaks the Dirac cone and opens up an observable band gap.

We experimentally demonstrate topologically protected optical waveguiding in silicon at the interface between two topologically distinct dimer chains. Further, we propose and demonstrate beating between topological and trivial defect modes.

We investigate the origin of archaeological wool textiles preserved by anoxic waterlogging from seven medieval archaeological deposits in north-western Europe (c. 700–1600 AD), using geospatial patterning in carbon (δ13C), nitrogen (δ15N) and non-exchangeable hydrogen (δ2H) composition of modern and ancient sheep proteins. δ13C, δ15N and δ2H values from archaeological wool keratin (n = 83) and bone collagen (n = 59) from four sites were interpreted with reference to the composition of modern sheep wool from the same regions. The isotopic composition of wool and bone collagen samples clustered strongly by settlement; inter-regional relationships were largely parallel in modern and ancient samples, though landscape change was also significant. Degradation in archaeological wool samples, examined by elemental and amino acid composition, was greater in samples from Iceland (Reykholt) than in samples from north-east England (York, Newcastle) or northern Germany (Hessens). A nominal assignment approach was used to classify textiles into local/non-local at each site, based on maximal estimates of isotopic variability in modern sheep wool. Light element stable isotope analysis provided new insights into the origins of wool textiles, and demonstrates that isotopic provenancing of keratin preserved in anoxic waterlogged contexts is feasible. We also demonstrate the utility of δ2H analysis to understand the location of origin of archaeological protein samples.

Scientific Reports 5: Article number: 16498;10.1038/srep16498 Published online: November132015; Updated: June022016 The Acknowledgements section in this Article is incomplete. “This work was supported by the European Research Council (FP7 ERC-Synergy Nexus1492 project grant number 319209) and the US National Institutes of Health (R01 {"type":"entrez-nucleotide","attrs":{"text":"GM089886","term_id":"221304226","term_text":"GM089886"}}GM089886), the BBVA Foundation (I Ayudas a Investigadores, Innovadores y Creadores), the Generalitat Valenciana (VALi+d APOSTD/2014/123 and GV/2015/060), the European Union (EUROTAST FP7 PEOPLE-2010 MC ITN, Braudel-IFER-FMSH; FP7/2007-2013 - MSCA-COFUND, n°245743), and the Centre for Chronic Diseases and Disorders (C2D2) Research Priming Fund grant to CFS. C2D2 is part-funded by the Wellcome Trust (ref: 097829). The authors thank Joaquin Lomba for his assistance with obtaining samples; Amanda Henry for providing helpful comments on the manuscript; Jacqueline Eng for providing osteological data for the Samdzong sample; Maria Haber and Azucena Aviles for providing osteological data for the Camino del Molino sample; Malin Holst for providing osteological data for the Tickhill samples; and also Matthias Garn & Partner, the Parish Church Council for St. Mary’s Church, Tickhill, South Yorkshire, and Wiles & Maguire, Ltd., for assistance with sample provisioning.” should read: “This work was supported by the European Research Council (FP7 ERC-Synergy Nexus1492 project grant number 319209), the US National Science Foundation (BCS-1516633) and the US National Institutes of Health (R01 {"type":"entrez-nucleotide","attrs":{"text":"GM089886","term_id":"221304226","term_text":"GM089886"}}GM089886), the BBVA Foundation (I Ayudas a Investigadores, Innovadores y Creadores), the Generalitat Valenciana (VALi+d APOSTD/2014/123 and GV/2015/060), the European Union (EUROTAST FP7 PEOPLE-2010 MC ITN, Braudel-IFER-FMSH; FP7/2007-2013 - MSCA-COFUND, n°245743), and the Centre for Chronic Diseases and Disorders (C2D2) Research Priming Fund grant to CFS. C2D2 is part-funded by the Wellcome Trust (ref: 097829). The authors thank Joaquin Lomba for his assistance with obtaining samples; Amanda Henry for providing helpful comments on the manuscript; Jacqueline Eng for providing osteological data for the Samdzong sample; Maria Haber and Azucena Aviles for providing osteological data for the Camino del Molino sample; Malin Holst for providing osteological data for the Tickhill samples; and also Matthias Garn & Partner, the Parish Church Council for St. Mary’s Church, Tickhill, South Yorkshire, and Wiles & Maguire, Ltd., for assistance with sample provisioning.”

One-dimensional models with topological band structures represent a simple and versatile platform to demonstrate novel topological concepts. Here we experimentally study topologically protected states in silicon at the interface between two dimer chains with different Zak phases. Furthermore, we propose and demonstrate that, in a system where topological and trivial defect modes coexist, we can probe them independently. Tuning the configuration of the interface, we observe the transition between a single topological defect and a compound trivial defect state. These results provide a new paradigm for topologically protected waveguiding in a complementary metal-oxide-semiconductor compatible platform and highlight the novel concept of isolating topological and trivial defect modes in the same system that can have important implications in topological physics.

It is a fundamental challenge in quantum optics to deterministically generate indistinguishable single photons through non-deterministic nonlinear optical processes, due to the intrinsic coupling of single- and multi-photon-generation probabilities in these processes. Actively multiplexing photons generated in many temporal modes can decouple these probabilities, but key issues are to minimize resource requirements to allow scalability, and to ensure indistinguishability of the generated photons. Here we demonstrate the multiplexing of photons from four temporal modes solely using fibre-integrated optics and off-the-shelf electronic components. We show a 100% enhancement to the single-photon output probability without introducing additional multi-photon noise. Photon indistinguishability is confirmed by a fourfold Hong–Ou–Mandel quantum interference with a 91±16% visibility after subtracting multi-photon noise due to high pump power. Our demonstration paves the way for scalable multiplexing of many non-deterministic photon sources to a single near-deterministic source, which will be of benefit to future quantum photonic technologies., Deterministically generated single photons are useful for quantum communications, but the processes that create such light are often non-deterministic. Here, the authors enhance the single-photon output probability by multiplexing photons from four temporal modes using fibre-integrated optics.

Proteins persist longer in the fossil record than DNA, but the longevity, survival mechanisms and substrates remain contested. Here, we demonstrate the role of mineral binding in preserving the protein sequence in ostrich (Struthionidae) eggshell, including from the palaeontological sites of Laetoli (3.8 Ma) and Olduvai Gorge (1.3 Ma) in Tanzania. By tracking protein diagenesis back in time we find consistent patterns of preservation, demonstrating authenticity of the surviving sequences. Molecular dynamics simulations of struthiocalcin-1 and -2, the dominant proteins within the eggshell, reveal that distinct domains bind to the mineral surface. It is the domain with the strongest calculated binding energy to the calcite surface that is selectively preserved. Thermal age calculations demonstrate that the Laetoli and Olduvai peptides are 50 times older than any previously authenticated sequence (equivalent to ~16 Ma at a constant 10°C). DOI: http://dx.doi.org/10.7554/eLife.17092.001, eLife digest The pattern of chemical reactions that break down the molecules that make our bodies is still fairly mysterious. Archaeologists and geologists hope that dead organisms (or artefacts made from them) might not decay entirely, leaving behind clues to their lives. We know that some molecules are more resistant than others; for example, fats are tough and survive for a long time while DNA is degraded very rapidly. Proteins, which are made of chains of smaller molecules called amino acids, are usually sturdier than DNA. Since the amino acid sequence of a protein reflects the DNA sequence that encodes it, proteins in fossils can help researchers to reconstruct how extinct organisms are related in cases where DNA cannot be retrieved. Time, temperature, burial environment and the chemistry of the fossil all influence how quickly a protein decays. However, it is not clear what mechanisms slow down decay so that full protein sequences can be preserved and identified after millions of years. As a result, it is difficult to know where to look for these ancient sequences. In the womb of ostriches, several proteins are responsible for assembling the minerals that make up the ostrich eggshell. These proteins become trapped tightly within the mineral crystals themselves. In this situation, proteins can potentially be preserved over geological time. Demarchi et al. have now studied 3.8 million-year-old eggshells found close to the equator and, despite the extent to which the samples have degraded, discovered fully preserved protein sequences. Using a computer simulation method called molecular dynamics, Demarchi et al. calculated that the protein sequences that are able to survive the longest are stabilized by strong binding to the surface of the mineral crystals. The authenticity of these sequences was tested thoroughly using a combination of several approaches that Demarchi et al. recommend using as a standard for ancient protein studies. Overall, it appears that biominerals are an excellent source of ancient protein sequences because mineral binding ensures survival. A systematic survey of fossil biominerals from different environments is now needed to assess whether these biomolecules have the potential to act as barcodes for interpreting the evolution of organisms. DOI: http://dx.doi.org/10.7554/eLife.17092.002

The purported migrations that have formed the peoples of Britain have been the focus of generations of scholarly controversy. However, this has not benefited from direct analyses of ancient genomes. Here we report nine ancient genomes (∼1 ×) of individuals from northern Britain: seven from a Roman era York cemetery, bookended by earlier Iron-Age and later Anglo-Saxon burials. Six of the Roman genomes show affinity with modern British Celtic populations, particularly Welsh, but significantly diverge from populations from Yorkshire and other eastern English samples. They also show similarity with the earlier Iron-Age genome, suggesting population continuity, but differ from the later Anglo-Saxon genome. This pattern concords with profound impact of migrations in the Anglo-Saxon period. Strikingly, one Roman skeleton shows a clear signal of exogenous origin, with affinities pointing towards the Middle East, confirming the cosmopolitan character of the Empire, even at its northernmost fringes., Here, Martiniano et al. examine the genetic structure of northern Britain in the late BC/early AD using ancient genome sequencing of 9 individuals. They uncover evidence of far-reaching Roman and later Anglo-Saxon migrations within a background of Britons similar to the earlier Iron Age.

We show topological waveguiding of single and correlated photons generated in a spatially modulated array of silicon nanowires. These are the first experiments with correlated quantum states in any topological photonic system.