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A quantum computer attains computational advantage when outperforming the best classical computers running the best-known algorithms on well-defined tasks. No photonic machine offering programmability over all its quantum gates has demonstrated quantum computational advantage: previous machines1,2 were largely restricted to static gate sequences. Earlier photonic demonstrations were also vulnerable to spoofing3, in which classical heuristics produce samples, without direct simulation, lying closer to the ideal distribution than do samples from the quantum hardware. Here we report quantum computational advantage using Borealis, a photonic processor offering dynamic programmability on all gates implemented. We carry out Gaussian boson sampling4 (GBS) on 216 squeezed modes entangled with three-dimensional connectivity5, using a time-multiplexed and photon-number-resolving architecture. On average, it would take more than 9,000 years for the best available algorithms and supercomputers to produce, using exact methods, a single sample from the programmed distribution, whereas Borealis requires only 36 μs. This runtime advantage is over 50 million times as extreme as that reported from earlier photonic machines. Ours constitutes a very large GBS experiment, registering events with up to 219 photons and a mean photon number of 125. This work is a critical milestone on the path to a practical quantum computer, validating key technological features of photonics as a platform for this goal.

Between the sixteenth and nineteenth century, British agriculture underwent a ‘revolutionary’ transformation. Yet despite over a century of research and the recognised centrality of agricultural developments to industrialisation and population growth, the character or chronology of any ‘revolution’ during this period remains contentious. Enquiry has been hampered by the fragmented and locally specific nature of historic accounts and the broad dating of early-modern zooarchaeological assemblages. To address this, we conducted stable isotope analysis on 658 legal documents written on sheepskin parchment; a unique biological resource that records the day, month and year of use (AD 1499 to 1969). We find these provide a high temporal resolution analysis of changing agricultural practices and episodes of disease. Most significantly, they suggest that if an ‘Agricultural Revolution’ occurred in livestock management, it did so from the mid-nineteenth century, in the aftermath of the Napoleonic Wars.

Gigantopithecus blacki was a giant hominid that inhabited densely forested environments of Southeast Asia during the Pleistocene epoch1. Its evolutionary relationships to other great ape species, and the divergence of these species during the Middle and Late Miocene epoch (16-5.3 million years ago), remain unclear2,3. Hypotheses regarding the relationships between Gigantopithecus and extinct and extant hominids are wide ranging but difficult to substantiate because of its highly derived dentognathic morphology, the absence of cranial and post-cranial remains1,3-6, and the lack of independent molecular validation. We retrieved dental enamel proteome sequences from a 1.9-million-year-old G. blacki molar found in Chuifeng Cave, China7,8. The thermal age of these protein sequences is approximately five times greater than that of any previously published mammalian proteome or genome. We demonstrate that Gigantopithecus is a sister clade to orangutans (genus Pongo) with a common ancestor about 12-10 million years ago, implying that the divergence of Gigantopithecus from Pongo forms part of the Miocene radiation of great apes. In addition, we hypothesize that the expression of alpha-2-HS-glycoprotein, which has not been previously observed in enamel proteomes, had a role in the biomineralization of the thick enamel crowns that characterize the large molars in Gigantopithecus9,10. The survival of an Early Pleistocene dental enamel proteome in the subtropics further expands the scope of palaeoproteomic analysis into geographical areas and time periods previously considered incompatible with the preservation of substantial amounts of genetic information. E.C. and F.W. are supported by VILLUM FONDEN (17649) and by the European Commission through a Marie Skłodowska-Curie (MSCA) Individual Fellowship (795569). T.M.-B. is supported by BFU2017-86471-P (MINECO/FEDER, UE), NIHM grant U01 MH106874, Howard Hughes International Early Career grant, Obra Social ‘La Caixa’ and Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880). E.C., J.C., J.V.O., D.S. and P.G. are supported by the Marie Skłodowska-Curie European Training Network (ETN) TEMPERA, a project funded by the European Union’s EU Framework Program for Research and Innovation Horizon 2020 under grant agreement no. 722606. M.J.C. and M.M. are supported by the Danish National Research Foundation award PROTEIOS (DNRF128). Work at the Novo Nordisk Foundation Center for Protein Research is funded in part by a donation from the Novo Nordisk Foundation (NNF14CC0001). Research at Chuifeng Cave is made possible by support from the National Natural Science Foundation of China (41572023) and by a grant from the Bagui Scholar of Guangxi. M.K. was supported by a Deutsche Forschungsgemeinschaft (DFG) fellowship (KU 3467/1-1) and the Postdoctoral Junior Leader Fellowship Programme from ‘la Caixa’ Banking Foundation (LCF/BQ/PR19/11700002). M.E.A. is supported by the Independent Research Fund Denmark (7027-00147B). We thank E. Willerslev for critical reading of the manuscript, scientific support and guidance.

Brain tissue is ubiquitous in the archaeological record. Multiple, independent studies report the finding of black, resinous or shiny brain tissue, and Petrone et al. [2020 “Heat-induced Brain Vitrification from the Vesuvius Eruption in C.E. 79.” N Engl J Med. 382: 383–384; doi:10.1056/NEJMc1909867] raise the intriguing prospect of a role for vitrification in the preservation of ancient biomolecules. However, Petrone et al. (2020) have not made their raw data available, and no detailed laboratory or analytical methodology is offered. Issues of contamination and misinterpretation hampered a decade of research in biomolecular archaeology, such that addressing these sources of bias and facilitating validation of specious findings has become both routine and of paramount importance in the discipline. We argue that the evidence they present does not support their conclusion of heat-induced vitrification of human brain tissue, and that future studies should share palaeoproteomic data in an open access repository to facilitate comparative analysis of the recovery of ancient proteins and patterns of their degradation.

Growing interest in quantum computing for practical applications has led to a surge in the availability of programmable machines for executing quantum algorithms1,2. Present-day photonic quantum computers3–7 have been limited either to non-deterministic operation, low photon numbers and rates, or fixed random gate sequences. Here we introduce a full-stack hardware−software system for executing many-photon quantum circuit operations using integrated nanophotonics: a programmable chip, operating at room temperature and interfaced with a fully automated control system. The system enables remote users to execute quantum algorithms that require up to eight modes of strongly squeezed vacuum initialized as two-mode squeezed states in single temporal modes, a fully general and programmable four-mode interferometer, and photon number-resolving readout on all outputs. Detection of multi-photon events with photon numbers and rates exceeding any previous programmable quantum optical demonstration is made possible by strong squeezing and high sampling rates. We verify the non-classicality of the device output, and use the platform to carry out proof-of-principle demonstrations of three quantum algorithms: Gaussian boson sampling, molecular vibronic spectra and graph similarity8. These demonstrations validate the platform as a launchpad for scaling photonic technologies for quantum information processing. A system for realizing many-photon quantum circuits is presented, comprising a programmable nanophotonic chip operating at room temperature, interfaced with a fully automated control system.

UNLABELLED: Historic legal deeds are one of the most abundant resources in British archives, but also one of the most neglected. Despite the millions that survive, we know remarkably little about their manufacture, including the species of animal on which they were written. Here we present the species identification of 645 sixteenth-twentieth century skins via peptide mass fingerprinting (ZooMS), demonstrating the preferential use of sheepskin parchment. We argue that alongside their abundance and low cost, the use of sheepskins over those of other species was motivated by the increased visibility of fraudulent text erasure and modification afforded by the unique structure of their skin. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40494-021-00503-6.

The rate at which endogenous DNA from differently prepared (butchered, boiled and baked) compact pig bones degrades in five different Danish terrestrial and marine environments over 12 months was investigated. Although > 70% of the estimated endogenous mtDNA is lost after just four weeks of exposure, no cytosine deamination of DNA was recognised. A correlation between the presence of oxygen and the amount of preserved DNA was observed. The results provide valuable information on the interaction between the endogenous DNA and the depositional environment in the early stages of bone diagenesis, which can be a support in the interpretation of the initial diagenetic pathways of archaeological bone.

We present the isotopic discrimination between paired skin and bone collagen from animals of known life history, providing a modern baseline for the interpretation of archaeological isotopic data. At present, the interpretation of inter-tissue variation (Δ (skin–bone) ) in mummified remains is based on comparisons with other archaeological material, which have attributed divergence to their contrasting turnover rates, with rapidly remodelling skin collagen incorporating alterations in environmental, cultural and physiological conditions in the months prior to death. While plausible, the lack of baseline data from individuals with known life histories has hindered evaluation of the explanations presented. Our analysis of a range of animals raised under a variety of management practices showed a population-wide trend for skin collagen to be depleted in 13 C by –0.7‰ and enriched in 15 N by +1.0‰ relative to bone collagen, even in stillborn animals. These results are intriguing and difficult to explain using current knowledge; however, on the basis of the findings reported here, we caution any results which interpret simply on differing turnover rates. We hypothesize that there may be a consistent difference in the routing of dietary protein and lipids between skin and bone, with potentially on-site synthesis of non-essential amino acids using carbon and nitrogen that have been sourced via different biochemical pathways.

Funder: Greek Archaeological Committee UK (GACUK), Funder: Leventis Foundation; Id: http://dx.doi.org/10.13039/501100004117, This study compares histological preservation in archeological bones from different burial types to unravel the histotaphonomy‐to‐funerary practices relationship. Αn intraskeletal approach is also adopted to explore intraindividual (inner ear part of the petrous bone vs. upper/lower limb long bones) and intrabone (proximal vs. distal diaphysis) variability in bone collagen preservation, δ13C, and δ15N. The aim is to (a) target bones that likely retain higher amounts of collagen, (b) better understand the inner ear bone collagen isotopic signature and remodeling, and (c) assess intrabone isotopic and histological homogeneity. For the histological analysis, the data have been collected from 61 specimens (20 individuals) from the medieval/postmedieval cemetery of St. Rombout, Belgium. Thin sections have been studied using optical and scanning electron microscopy. For the collagen and isotopic data, 101 samples have been collected from 21 individuals. Distinct histological patterns are observed only in bones from single coffin burials; however, bone histology can display intraindividual and intrabone variability, which are important to account for interpretations. Collagen wt.%, δ13C, and δ15N show significant intraindividual differences but insignificant intrabone variability. This study also confirms the extraordinary nature of the petrous bone, as the inner ear bone collagen δ13C and δ15N values reflect the dietary input of the first approximately 2–3 years of life.

Next Generation Lab turns large and hitherto unstudied urban assemblages of archaeological leather and bone into a laboratory learning experience for high school students. The students, in turn, provide species identifications and thus increase knowledge on medieval and Renaissance livestock exploitation and material selection by craftsmen.

One of the greatest successes of the application of Palaeoproteomics to Archaeology is its use by a number of authors to track evidence of dairying practice, both in terms of its origin and the selection of animal species. To this end, the whey protein β-lactoglobulin entrapped in pottery and dental calculus is widely studied because it is so frequently recovered but why is it differentially preserved? Hydrolysis plays a big part in the breakdown of proteins. Therefore, it is essential to explore the role of water in degradation to uncover some of the patterns linked to protein survival. One approach to understand the hydrolytic process is to examine the molecular behaviour of this protein and in particular of the peptide most commonly recovered: T125PEVDXEALEK135. In this study, we use Molecular Dynamics, with the Amber14SB forcefield and the SPC/E water model in Gromacs 2020, to first explore the dynamics of this peptide in bulk water. Despite the difficulties in describing reactive processes with classical methods, we were able to identify geometric arrangements between water and protein residues which are similar to the ones described in the literature for protein hydrolysis. These arrangements helped to identify potential sites for hydrolysis along the bovine β-lactoglobulin T125PEVDDEALEK135 amino acid chain.

Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.

Mollusc shells represent excellent systems for the preservation and retrieval of genuine biomolecules from archaeological or palaeontological samples. As a consequence, the post-mortem breakdown of intracrystalline mollusc shell proteins has been extensively investigated, particularly with regard to its potential use as a "molecular clock" for geochronological applications. But despite seventy years of ancient protein research, the fundamental aspects of diagenesis-induced changes to protein structures and sequences remain elusive. In this study we investigate the degradation of intracrystalline proteins by performing artificial degradation experiments on the shell of the thorny oyster, Spondylus gaederopus, which is particularly important for archaeological research. We used immunochemistry and tandem mass tag (TMT) quantitative proteomics, a novel analytical approach that allowed us to simultaneously track patterns of structural loss and of peptide bond hydrolysis. Powdered and bleached shell samples were heated in water at four different temperatures (80, 95, 110, 140 °C) for different time durations. The structural loss of carbohydrate and protein groups was investigated by immunochemical techniques (ELLA and ELISA) and peptide bond hydrolysis was studied by tracking the changes in protein/peptide relative abundances over time using TMT quantitative proteomics. We find that heating does not induce instant organic matrix decay, but first facilitates the uncoiling of cross-linked structures, thus improving matrix detection. We calculated apparent activation energies of structural loss: Ea (carbohydrate groups) = 104.7 kJ/mol, Ea (protein epitopes) = 104.4 kJ/mol, which suggests that secondary matrix structure degradation may proceed simultaneously with protein hydrolysis. While prolonged heating at 110 °C (10 days) results in complete loss of the structural signal, surviving peptide sequences were still observed. Eight hydrolysis-prone peptide bonds were identified in the top scoring shell sequence, the uncharacterised protein LOC117318053 from Pecten maximus. Interestingly, these were not the expected "weak" bonds based on published theoretical stabilities calculated for peptides in solution. This further confirms that intracrystalline protein degradation patterns are complex and that the overall microchemical environment plays an active role in protein stability. Our TMT approach represents a major stepping stone towards developing a model for studying protein diagenesis in biomineralised systems.

Biocodicological analysis of parchments from manuscript books and archives offers unprecedented insight into the materiality of medieval literacy. Using ZooMS for animal species identification, we explored almost the entire library and all the preserved single leaf charters of a single medieval Cistercian monastery (Orval Abbey, Belgium). Systematic non-invasive sampling of parchment collagen was performed on every charter and on the first bifolium from every quire of the 118 codicological units composing the books (1490 samples in total). Within the genuine production of the Orval scriptorium (26 units), a balanced use of calfskin (47.1%) and sheepskin (48.5%) was observed, whereas calfskin was less frequent (24.3%) in externally produced units acquired by the monastery (92 units). Calfskin was preferably used for higher quality manuscripts while sheepskin tends to be the standard choice for ‘ordinary’ manuscript book production. This finding is consistent with thirteenth-century parchment accounts from Beaulieu Abbey (England) where calfskin supply was more limited and its price higher. Our study reveals that the making of archival documents does not follow the same pattern as the production of library books. Although the five earliest preserved charters are made of calfskin, from the 1230s onwards, all charters from Orval are written on sheepskin.

The cellular cytoplasm is crowded with macromolecules and other species that occupy up to 40% of the available volume. Previous studies have reported that for high crowder molecule concentrations, colloidal tracer particles have a dampened diffusion due to the higher solution viscosity. However, these studies employed uniform distributions of crowder molecules. We report a scenario, previously unexplored experimentally, of increased tracer transport driven by a nonuniform concentration of crowder macromolecules. In gradients of a polymeric crowder, tracer particles undergo transport several times higher than that of their bulk diffusion rate. The direction of the transport is toward regions of lower crowder concentration. Mechanistically, hard-sphere interactions and the resulting volume exclusion between the tracer and crowder increase the effective diffusion by inducing a convective motion of tracers, which we explain through modeling. Strikingly, soft deformable particles show even greater enhancement in transport in crowder gradients compared to similarly sized hard particles. Overall, this demonstration of enhanced transport in nonuniform distributions of crowders is anticipated to clarify aspects of multicomponent intracellular transport.

Entangled multiphoton states lie at the heart of quantum information, computing, and communications. In recent years, topology has risen as a new avenue to robustly transport quantum states in the presence of fabrication defects, disorder and other noise sources. Whereas topological protection of single photons and correlated photons has been recently demonstrated experimentally, the observation of topologically protected entangled states has thus far remained elusive. Here, we experimentally demonstrate the topological protection of spatially-entangled biphoton states. We observe robustness in crucial features of the topological biphoton correlation map in the presence of deliberately introduced disorder in the silicon nanophotonic structure, in contrast with the lack of robustness in nontopological structures. The topological protection is shown to ensure the coherent propagation of the entangled topological modes, which may lead to robust propagation of quantum information in disordered systems., Comment: 17 pages, 5 figures

Rationale Although mass spectrometry (MS) is routinely used to determine deamination in peptide mixtures, the effects of the choice of ionisation source have not yet been investigated. In particular, matrix-assisted laser desorption/ionisation (MALDI) has become a popular tool with which to measure levels of glutamine deamidation in ancient proteins. Here we use model synthetic peptides to rigorously compare MALDI and electrospray ionisation (ESI). Methods We used two synthetic peptides, with glutamine (Q) in one substituted for glutamic acid (E) in the other, to investigate the suitability of MALDI and ESI sources for the assessment of deamidation in peptides using MS. We also compared measurements of the same Q- and E-containing peptide mixtures using two different mass analysers (time-of-flight (TOF) and Fourier transform ion cyclotron resonance (FT-ICR)). Results When standard mixtures of the Q- and E-containing peptides were analysed using MALDI, under-representation of the E-containing peptide was observed. This observation was consistent between analyses carried out using either TOF or FT-ICR-MS. When the same mixtures were analysed using ESI FT-ICR-MS, no ionisation bias was observed. Conclusions MALDI may not be a suitable ionisation method for the determination of deamidation in peptide mixtures. However, ESI was successfully used to determine the ratio in known mixtures of Q- and E-containing peptides. These preliminary observations warrant further investigation into ionisation bias when measuring deamidation in other peptide sequences.

Ancient protein analysis is a rapidly developing field of research. Proteins ranging in age from the Quaternary to Jurassic are being used to answer questions about phylogeny, evolution, and extinction. However, these analyses are sometimes contentious, and focus primarily on large vertebrates in sedimentary fossilisation environments; there are few studies of protein preservation in fossils in amber. Here we show exceptionally slow racemisation rates during thermal degradation experiments of resin enclosed feathers, relative to previous thermal degradation experiments of ostrich eggshell, coral skeleton, and limpet shell. We also recover amino acids from two specimens of fossil feathers in amber. The amino acid compositions are broadly similar to those of degraded feathers, but concentrations are very low, suggesting that much of the original protein has been degraded and lost. High levels of racemisation in more apolar, slowly racemising amino acids suggest that some of the amino acids were ancient and therefore original. Our findings indicate that the unique fossilisation environment inside amber shows potential for the recovery of ancient amino acids and proteins.

We used palaeoproteomics and peptide mass fingerprinting to obtain secure species identifications of key specimens of early domesticated fauna from South Africa, dating to ca. 2000 BP. It can be difficult to distinguish fragmentary remains of early domesticates (sheep) from similar-sized local wild bovids (grey duiker, grey rhebok, springbok—southern Africa lacks wild sheep) based on morphology alone. Our analysis revealed a Zooarchaeology by Mass Spectrometry (ZooMS) marker (m/z 1532) present in wild bovids and we demonstrate through LC–MS/MS that it is capable of discriminating between wild bovids and caprine domesticates. We confirm that the Spoegrivier specimen dated to 2105 ± 65 BP is indeed a sheep. This is the earliest directly dated evidence of domesticated animals in southern Africa. As well as the traditional method of analysing bone fragments, we show the utility of minimally destructive sampling methods such as PVC eraser and polishing films for successful ZooMS identification. We also show that collagen extracted more than 25 years ago for the purpose of radiocarbon dating can yield successful ZooMS identification. Our study demonstrates the importance of developing appropriate regional frameworks of comparison for future research using ZooMS as a method of biomolecular species identification.

The dodo Raphus cucullatus Linnaeus, 1758, an extinct and flightless, giant pigeon endemic to Mauritius, hasfascinated people since its discovery, yet has remained surprisingly poorly known. Until the mid-19th century, almost all thatwas known about the dodo was based on illustrations and written accounts by 17th century mariners, often of questionableaccuracy. Furthermore, only a few fragmentary remains of dodos collected prior to the bird’s extinction exist. Ourunderstanding of the dodo’s anatomy was substantially enhanced by the discovery in 1865 of subfossil bones in a marsh calledthe Mare aux Songes, situated in southeastern Mauritius. However, no contextual information was recorded during earlyexcavation efforts, and the majority of excavated material comprised larger dodo bones, almost all of which wereunassociated. Here we present a modern interdisciplinary analysis of the Mare aux Songes, a 4200-year-old multitaxicvertebrate concentration Lagerst€atte. Our analysis of the deposits at this site provides the first detailed overview of theecosystem inhabited by the dodo. The interplay of climatic and geological conditions led to the exceptional preservation ofthe animal and associated plant remains at the Mare aux Songes and provides a window into the past ecosystem of Mauritius.This interdisciplinary research approach provides an ecological framework for the dodo, complementing insights on itsanatomy derived from the only associated dodo skeletons known, both of which were collected by Etienne Thirioux and arethe primary subject of this memoir.

The degradation of archaeological bones is influenced by many variables. The bone material itself is a composite of both organic and inorganic components, and their degradation depends on processes occurring both before and after burial, and on both intrinsic bone characteristics as well as extrinsic environmental parameters. In this study we attempt to quantify the effect of some of the variables using a novel approach that includes detailed monitoring of the burial environment combined with respirometry studies of bone material from five archaeological sites in West Greenland. First, we compare the state of preservation of excavated bone material with the current burial environment including the soil pH, thawing degree days, soil porosity and soil moisture. Secondly, we investigate oxic degradation of collected bone samples through respirometry and quantify the effects of temperature and moisture on the oxidation rate of individual bones. Finally, we discuss how the oxidation rate is influenced by intrinsic bone parameters. Some of the main conclusions are:1) There is a significant correlation between the current burial environment and the current state of preservation of the bones.2) The oxidation rate measured by respirometry increases on average fourfold as temperature increases by 10 degrees C, and more than hundred-fold when dry bones are soaked in water.3) The oxidation rate of different bones varies over two orders of magnitude due to intrinsic variables such as organic content and state of preservation of the bones.4) The median oxidation rate of wet bone at 15 degrees C corresponds to a yearly loss of 3.8% of their mean organic content, while the median yearly loss for dry bones at 75% RH is 0.02%.5) Respirometry is a promising tool for quantitative degradation studies of bone, but more studies are needed in order to obtain a better understanding of the oxidation processes involved.

The domestic dog has inhabited the anthropogenic niche for at least 15 000 years, but despite their impact on human strategies, the lives of dogs and their interactions with humans have only recently become a subject of interest to archaeologists. In the Arctic, dogs rely exclusively on humans for food during the winter, and while stable isotope analyses have revealed dietary similarities at some sites, deciphering the details of provisioning strategies have been challenging. In this study, we apply zooarchaeology by mass spectrometry (ZooMS) and liquid chromatography tandem mass spectrometry to dog palaeofaeces to investigate protein preservation in this highly degradable material and obtain information about the diet of domestic dogs at the Nunalleq site, Alaska. We identify a suite of digestive and metabolic proteins from the host species, demonstrating the utility of this material as a novel and viable substrate for the recovery of gastrointestinal proteomes. The recovered proteins revealed that the Nunalleq dogs consumed a range of Pacific salmon species (coho, chum, chinook and sockeye) and that the consumed tissues derived from muscle and bone tissues as well as roe and guts. Overall, the study demonstrated the viability of permafrost-preserved palaeofaeces as a unique source of host and dietary proteomes. 1. Introduction 2. Material and methods (a) Samples (b) Palaeoproteomics (c) Zooarchaeology by mass spectrometry 3. Results and discussion (a) Metaproteomics (b) Host proteins (c) Dietary proteins (d) Challenges and future directions 4. Conclusion

Unidad de excelencia María de Maeztu CEX2019-000940-M The origins, prevalence and nature of dairying have been long debated by archaeologists. Within the last decade, new advances in high-resolution mass spectrometry have allowed for the direct detection of milk proteins from archaeological remains, including ceramic residues, dental calculus, and preserved dairy products. Proteins recovered from archaeological remains are susceptible to post-excavation and laboratory contamination, a particular concern for ancient dairying studies as milk proteins such as beta-lactoglobulin (BLG) and caseins are potential laboratory contaminants. Here, we examine how site-specific rates of deamidation (i.e., deamidation occurring in specific positions in the protein chain) can be used to elucidate patterns of peptide degradation, and authenticate ancient milk proteins. First, we characterize site-specific deamidation patterns in modern milk products and experimental samples, confirming that deamidation occurs primarily at low half-time sites. We then compare this to previously published palaeoproteomic data from six studies reporting ancient milk peptides. We confirm that site-specific deamidation rates, on average, are more advanced in BLG recovered from ancient dental calculus and pottery residues. Nevertheless, deamidation rates displayed a high degree of variability, making it challenging to authenticate samples with relatively few milk peptides. We demonstrate that site-specific deamidation is a useful tool for identifying modern contamination but highlight the need for multiple lines of evidence to authenticate ancient protein data.

In this paper, we describe palaeoproteomic evidence obtained from a stained medieval birth girdle using a previously developed dry non-invasive sampling technique. The parchment birth girdle studied (Wellcome Collection Western MS. 632) was made in England in the late fifteenth century and was thought to be used by pregnant women while giving birth. We were able to extract both human and non-human peptides from the manuscript, including evidence for the use of honey, cereals, ovicaprine milk and legumes. In addition, a large number of human peptides were detected on the birth roll, many of which are found in cervico-vaginal fluid. This suggests that the birth roll was actively used during childbirth. This study is, to our knowledge, the first to extract and analyse non-collagenous peptides from a birth girdle using this sampling method and demonstrates the potential of this type of analysis for stained manuscripts, providing direct biomolecular evidence for active use.

We report a simple histological study on skin biopsies from young domestic sheep following each step in transformation from skin to parchment production. During the recreation of historical parchment manufacture, histological analyses were conducted; before and after lime treatment, hair removal, and stretching. Sections were fixed and stained using a variety of histological stains to identify the presence of different molecular classes and the fibrous proteins, collagen and elastin. The results reveal surprisingly few histological changes in most steps in the production process. However, very visible changes in the supramolecular ordering of skin macromolecules (elastin, collagen) occur during the final stage of parchment production when stretched on the frame. Collagen fibres and hair follicles were all strongly re-oriented in the direction of strain. Surprisingly despite the thinness of the lambskin and the exhaustive treatment in lime, not all fats were saponified and even in the final product Oil Red O stained fat bodies were detectable on the hair side of the skin. We believe this study will help compensate for the lack of sources on microscopic changes in parchment during the recreation of its historical manufacture.

In this paper we describe a dry non-invasive extraction method to detect palaeoproteomic evidence from stained manuscripts. The manuscript analysed in this study is a medieval parchment birth girdle (Wellcome Collection Western MS. 632) made in England and thought to be used by pregnant women while giving birth. Using a dry non-invasive sampling method we were able to extract both human and non-human peptides from the stains, including evidence for the use of honey, cereals, ovicaprine milk and legumes. In addition, a large number of human peptides were detected on the birth roll, many of which are found in cervico-vaginal fluid. This suggests that the birth roll was actively used during childbirth. This study is the first to extract and analyse non-collagenous peptides from a parchment document using a dry non-invasive sampling method and demonstrates the potential of this type of analysis for stained manuscripts, providing direct biomolecular evidence for active use.

The extensive peat bogs of Southern Scandinavia have yielded rich Mesolithic archaeological assemblages, with one of the most iconic artefacts being the bone point. Although great in number they remain understudied. Here we present a combined investigation of the typology, protein-based species composition, and absolute chronology of Maglemosian bone points. The majority of the bone points are made from cervids and bovines. However, changes both in species composition and barb morphology can be directly linked to a paucity of finds lasting nearly 600 years in Southern Scandinavia around 10,300 cal BP. We hypothesize that this hiatus was climate-driven and forced hunter-gatherers to abandon the lakes. Furthermore, the marked change in bone points coincides with a change in lithic technology. We, therefore, propose that the Maglemose culture in Southern Scandinavia is fundamentally divided into an Early Complex and a Late Complex. Results - Bone points - Radiocarbon dating - Protein analysis Discussion Methods - Materials - Radiocarbon dating - Proteomics

We report demonstrations of both quadrature squeezed vacuum and photon number difference squeezing generated in an integrated nanophotonic device. Squeezed light is generated via strongly driven spontaneous four-wave mixing below threshold in silicon nitride microring resonators. The generated light is characterized with both homodyne detection and direct measurements of photon statistics using photon number-resolving transition edge sensors. We measure $1.0(1)$~dB of broadband quadrature squeezing (${\sim}4$~dB inferred on-chip) and $1.5(3)$~dB of photon number difference squeezing (${\sim}7$~dB inferred on-chip). Nearly-single temporal mode operation is achieved, with measured raw unheralded second-order correlations $g^{(2)}$ as high as $1.95(1)$. Multi-photon events of over 10 photons are directly detected with rates exceeding any previous quantum optical demonstration using integrated nanophotonics. These results will have an enabling impact on scaling continuous variable quantum technology., Comment: Minor revisions, and Fig. 5 corrected; Now published in Science Advances

Rates of peptide bond hydrolysis and other diagenetic reactions are not favourable for Mesozoic protein survival. Proteins hydrolyse into peptide fragments and free amino acids that, in open systems such as bone, can leach from the specimen and be further degraded. However, closed systems are more likely to retain degradation products derived from endogenous proteins. Amino acid racemisation data in experimental and subfossil material suggests that mollusc shell and avian eggshell calcite crystals can demonstrate closed system behaviour, retaining endogenous amino acids. Here, high-performance liquid chromatography reveals that the intra-crystalline fraction of Late Cretaceous (estimated ~80 Ma) titanosaur sauropod eggshell is enriched in some of the most stable amino acids (Glx, Gly, Ala, and possibly Val) and those that racemise are fully racemic, despite being some of the slowest racemising amino acids. These results are consistent with degradation trends deduced from modern, thermally matured, sub-fossil, and ~3.8 Ma avian eggshell, as well as ~30 Ma calcitic mollusc opercula. Selective preservation of certain fully racemic amino acids, which do not racemise in-chain, along with similar concentrations of free versus total hydrolysable amino acids, likely suggests complete hydrolysis of original peptides. Liquid chromatography-tandem mass spectrometry supports this hypothesis by failing to detect any non-contamination peptide sequences from the Mesozoic eggshell. Pyrolysis-gas chromatography-mass spectrometry reveals pyrolysates consistent with amino acids as well as aliphatic hydrocarbon homologues that are not present in modern eggshell, suggestive of kerogen formation deriving from eggshell lipids. Raman spectroscopy yields bands consistent with various organic molecules, possibly including N-bearing molecules or geopolymers. These closed-system amino acids are possibly the most thoroughly supported non-avian dinosaur endogenous protein-derived constituents, at least those that have not undergone oxidative condensation with other classes of biomolecules. Biocrystal matrices can help preserve mobile organic molecules by trapping them (perhaps with the assistance of resistant organic polymers), but trapped organics are nevertheless prone to diagenetic degradation even if such reactions might be slowed in exceptional circumstances. The evidence for complete hydrolysis and degradation of most amino acids in the eggshell raises concern about the validity of reported polypeptide sequences from open-system non-avian dinosaur bone and other Mesozoic fossils.

We report a simple histological study on skin biopsies from young domestic sheep following each step in transformation from skin to parchment production. Histological analyses were conducted; before and after lime treatment, hair removal, and stretching. Sections were fixed and stained using a variety of histological stains to identify the presence of different molecular classes and the fibrous proteins, collagen and elastin. The results reveal surprisingly few histological changes in most steps in the production process. However, very visible changes in the supramolecular ordering of skin macromolecules (elastin, collagen) occur during the final stage of parchment production when stretched on the frame. Collagen fibres and hair follicles were all strongly re-oriented in the direction of strain. Surprisingly, despite the thinness of the lambskin and the exhaustive treatment in lime, not all fats were saponified and even in the final product Oil Red O stained fat bodies were detectable on the hair side of the skin.