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We investigated correlated photon-pair generation via spontaneous four-wave mixing in an integrated chalcogenide Ge11.5As24Se64.5 photonic nanowire. The coincidence to accidental ratio, a key measurement for the quality of correlated photon-pair sources, was measured to be only 0.4 when the photon pairs were generated at 1.9 THz detuning from the pump frequency due to high spontaneous Raman noise in this regime. However, the existence of a characteristic low-Raman window at around 5.1 THz in this material's Raman spectrum and dispersion engineering of the nanowire allowed us to generate photon pairs with a coincidence to accidental ratio of 4.5, more than 10 times higher than the 1.9 THz case. Through comparing the results with those achieved in chalcogenide As2S3 waveguides which also exhibit a low Raman-window but at a larger detuning of 7.4 THz, we find that the position of the characteristic low-Raman window plays an important role on reducing spontaneous Raman noise because the phonon population is h...

We present a method of directly measuring the spontaneous Raman scattering in optical waveguides in an alignment-free setup. Using a pulsed laser, liquid-crystal-on-silicon spatial light modulator and single-photon detector, we create a broadband photon-counting Raman spectrometer. The temperature and polarization dependence are characterized in an As2S3 amorphous glass fiber for a Stokes detuning range of 1 to 9 THz from the pump frequency. We fit our experimental data with a theoretical model and extract the Raman-gain spectrum and compare to free-space measurements of bulk As2S3. The sensitivity of the method in principle allows direct characterization of chip-scale nanophotonic devices.

In this paper we investigate uncorrelated noise from spontaneous Raman scattering (SpRS) and its effect on photon-pair generation in chalcogenide (As2S3). We measure a coincidence-to-accidental ratio (CAR) of 4.2 in a 7 cm As2S3 single-mode fiber, with enhancements from our previous result attributed to pulsed pumping and cooling. Using an analytical model we characterize the magnitude of the SpRS at different temperatures. Our analysis shows that even after cooling to liquid nitrogen temperature (77 K), SpRS is still significant. For large detunings from the pump, the dependence on temperature for the Stokes SpRS intensity becomes negligible, so cooling is not a complete solution to improve the quality of the photon source.

Proteins have long been known to persist in Quaternary bone fossils and are often targeted as a source of carbon used in radiocarbon dating and stable isotope analyses for determining provenance and obtaining dietary information. We have previously reported a technique using the dominant structural protein collagen (type I) as a source of genetic information for species identification in modern and relatively young (Holocene) archaeological samples. We report a systematic investigation of amino acid composition and collagen peptide mass fingerprints (PMF), for a range of samples dating back approximately 1.5 million years. Extrapolation from high temperature experimental decomposition rates predict that at a constant 10°C (the approximate mean annual air temperature in Britain today) it will take between 0.2 and 0.7 Ma for levels of collagen to fall to 1% of their original concentration in an optimal burial environment. Even when the glacial intervals of the British Quaternary are factored into the temperature calculations, the more conservative of these two estimates extends the range for collagen sequencing to the Lower Pleistocene as confirmed by the presence of collagen peptides in bones from the Weybourne Crag (~1.5 Ma). Collagen fingerprinting can extend the range of identifiable taxa present at sites with large assemblages of fragmentary bone material such as that encountered at the ~900 Ka site at Happisburgh (Norfolk, UK) recently identified as showing signs of the earliest humans in Britain.

The successful retrieval of ancient DNA from two geographically dispersed Neanderthal skeletons1,2 has fuelled a demand for more Neanderthal DNA sequences for analysis. However, these exceptionally well-preserved specimens were geologically young and the mean annual temperature of their cave sites low, so the survival of this ancient DNA could have been due to unusually favourable conditions. Here we calculate the thermal history of a range of Holocene and Pleistocene bones whose DNA quality has been tested and find that in only very few sites with Neanderthal remains is the preservation of DNA likely to match the quality of that from the skeleton found at Mezmaiskaya Cave2. We recommend that any additional Neanderthal destined for destructive analysis should be carefully selected, taking into account its integrated thermal history.

We used authentication tests developed for ancient DNA to evaluate claims by Asara et al . (Reports, 13 April 2007, p. 280) of collagen peptide sequences recovered from mastodon and Tyrannosaurus rex fossils. Although the mastodon samples pass these tests, absence of amino acid composition data, lack of evidence for peptide deamidation, and association of α1(I) collagen sequences with amphibians rather than birds suggest that T. rex does not.

Nature 438, 1151–1156 (2005) There are two errors in the author listings for this Letter: the surname of Anne Lafon was misspelt as 'Lafton' and the affiliation of Hiroyuki Horiuchi should have been number 16 (and not 15, as was published).

Christina M. Nielsen-Marsh, Peggy H. Ostrom, Hasand Gandhi, Beth Shapiro, Alan Cooper, Peter V. Hauschka, and Matthew J. Collins

Deciding whether to farm cattle for milk or beef was just as complex in the past as it is today. Compared with meat production, dairying is a high-input, high-output, high-risk operation indicative of an intensive, sophisticated economy, but this practice is notoriously difficult to demonstrate in the archaeological record1. Here we provide evidence for the presence of milk proteins preserved in prehistoric vessels, which to our knowledge have not been detected before. This finding resolves the controversy that has surrounded dairying on the Scottish Atlantic coast during the Iron Age2,3,4,5 and indicates that farming by the early inhabitants of this harsh, marginal environment was surprisingly well developed.

Our claim, published in this journal, for successful immunodetection of the protein osteocalcin in dinosaur bone has been challenged on the grounds that the findings are inconsistent with the kinetics of decomposition. Here we show that the close association of osteocalcin to the bone mineral vastly enhances its preservation potential relative to the same protein in aqueous solution. We conducted heating experiments (75–95 °C) of modern bone powder and monitored the survival of three different regions of osteocalcin (N-terminal, His 4 -Hyp 9 ; C-terminal, Phe 45 -Val 49 ; and the mid-region, Pro 15 -Glu 31 ) with monoclonal antibodies. Extrapolation of our data to 10 °C ambient burial temperatures indicates that preservation of the γ-carboxylated mid-region in fossil bone cannot be excluded on kinetic grounds. Clearly, in situ sequence analysis will be the only method by which the preservation of fossil macromolecules will be unequivocally established. Nevertheless, our findings demonstrate the importance of mineral association to protein survival, as was borne out by an investigation of Holocene (ca. 6 ka) bones. Only in those samples with little recrystallization was the γ-carboxylated mid-region well preserved. These results imply that the future success of ancient biomolecule research largely depends on our understanding the interaction between these materials and their environment throughout diagenesis.

Commentary on Ohtani S, Matsushima Y, Kobayashi Y, Kishi K. Evaluation of aspartic acid racemization ratios in the human femur for age estimation. J Forensic Sci 1998;43(5):949–953.

Two different immunological assays were used to identify the remains of a bone matrix protein, osteocalcin (OC), in the bones of dinosaurs and other fossil vertebrates. Antibodies raised against OC from modern vertebrates showed strong immunological cross-reactivity with modern and relatively young fossil samples and significant reactions with some of the dinosaur bone extracts. The presence of OC was confirmed by the detection of a peptide-bound, uniquely vertebrate amino acid, γcarboxyglutamic acid (Gla). Preservation of OC in fossil bones appears to be strongly dependent on the burial history and not simply on age. These results extend the range of protein preservation in the geologic record and provide a first step toward a molecular phylogeny of the dinosaurs.

Surveys of Kuwait sand and mudflats reveal two species of fiddler crabs, Uca lactea annulipes and U. inversa sindensis. It is proposed primarily on the grounds of male pleopod morphology that the latter subspecies be accorded specific status as U. sindensis. Observed ecological separation between the two species appears to be due to differences in feeding morphology and related to sediments of differing particle size and organic content.

Antibodies prepared against macromolecules isolated from the shells of three living brachiopod genera have proved to be of considerable taxonomic significance, in that the pattern of cross‐reactivity of all three antisera consistently points to a new interpretation for the evolution of the largest extant brachiopod order, the Terebratulida. This new molecular evidence actually complements rather than contradicts the existing morphology‐based taxonomy, since detailed systematic investigation of the taxa in question has already demonstrated subtle but significant morphological differences in the major taxonomic characters which appear to reflect this new interpretation. As fragments of skeletal macromolecules, including antigenic determinants, are known to survive for many millions of years within the protected micro‐environments provided by enclosing biominerals, these results suggest that such molecular fossils could well provide important insights on at least the high‐level taxonomic relationships of fos...

Over 500 Free Amino Acid (FAA) and corresponding Total Hydrolysed Amino Acid (THAA) analyses were completed from eight independently-dated, multi-century coral cores of massive Porites sp. colonies. This dataset allows us to re-evaluate the application of amino acid racemization (AAR) for dating late Holocene coral material, 20years after Goodfriend et al. (GCA 56 (1992), 3847) first showed AAR had promise for developing chronologies in coral cores. This re-assessment incorporates recent method improvements, including measurement by RP-HPLC, new quality control approaches (e.g. sampling and sub-sampling protocols, statistically-based data screening criteria), and cleaning steps to isolate the intra-crystalline skeletal protein. We show that the removal of the extra-crystalline contaminants and matrix protein is the most critical step for reproducible results and recommend a protocol of bleaching samples in NaOCl for 48h to maximise removal of open system proteins while minimising the induced racemization. We demonstrate that AAR follows closed system behaviour in the intra-crystalline fraction of the coral skeletal proteins. Our study is the first to assess the natural variability in intra-crystalline AAR between colonies, and we use coral cores taken from the Great Barrier Reef, Australia, and Jarvis Island in the equatorial Pacific to explore variability associated with different environmental conditions and thermal histories. Chronologies were developed from THAA Asx D/L, Ala D/L, Glx D/L and FAA Asx D/L for each core and least squares Monte Carlo modelling applied in order to quantify uncertainty of AAR age determinations and assess the level of dating resolution possible over the last 5 centuries. AAR within colonies follow consistent stratigraphic aging. However, there are systematic differences in rates between the colonies, which would preclude direct comparison from one colony to another for accurate age estimation. When AAR age models are developed from a combined dataset to include this natural inter-colony variability THAA Asx D/L, Glx D/L and Ala D/L give a 2σ age uncertainty of ±19, ±38 and ±29year, for the 20th C respectively; in comparison 2σ age uncertainties from a single colony are ±12, ±12 and ±14year. This is the first demonstration of FAA D/L for dating coral and following strict protocols 2σ precisions of ±24years can be achieved across different colonies in samples from the last 150years, and can be ±10years within a core from a single colony. Despite these relatively large error estimates, AAR would be a valuable tool in situations where a large number of samples need to be screened rapidly and cheaply (e.g. identifying material from mixed populations in beach or uplift deposits), prior to and complementing the more time-consuming geochronological tools of U/Th or seasonal isotopic timeseries.

An understanding of the structural complexity of mineralised tissues is fundamental for exploration into the field of diagenesis. Here we review aspects of current and past research on bone and tooth diagenesis using the most comprehensive collection of literature on diagenesis to date. Environmental factors such as soil pH, soil hydrology and ambient temperature, which influence the preservation of skeletal tissues are assessed, while the different diagenetic pathways such as microbial degradation, loss of organics, mineral changes, and DNA degradation are surveyed. Fluctuating water levels in and around the bone is the most harmful for preservation and lead to rapid skeletal destruction. Diagenetic mechanisms are found to work in conjunction with each other, altering the biogenic composition of skeletal material. This illustrates that researchers must examine multiple diagenetic pathways to fully understand the post-mortem interactions of archaeological skeletal material and the burial environment.

Until recently few studies of amino acid racemization of fossil bivalves and gastropods collected from river terrace deposits in Europe were based on the analysis of the intra-crystalline fraction. Instead they were based on the epimerization (racemization) of a single amino acid, isoleucine, and its inter-conversion to alloisoleucine. This paper presents data from the analysis of the intra-crystalline fraction of the shells, using a preparation technique of sample bleaching to remove the leachable matrix, thus leaving a component that exhibits closed-system behaviour. Reverse-phase HPLC separation with fluorescence detection allows the interpretation of four amino acids in detail: aspartic acid, glutamic acid, alanine and valine. The intra-crystalline fraction offers greater potential for improved resolution, especially when combined with the analysis of multiple amino acid d/l values, which racemize at different rates. This is explored using three species of freshwater gastropods (Bithynia tentaculata and troschelii, Valvata piscinalis) and the bivalve Corbicula. Sites of different ages within the Lower Thames river terrace sequence are used as a stratigraphical framework, with samples from other southern UK sites providing supplementary evidence. The results indicate better resolution using the intra-crystalline fraction over that obtained using unbleached shells, with differentiation possible at sites of up to MIS 7 age. However, for older sites, although values are always higher, the separation is less successful. A species effect has been identified between the gastropod shells. Despite the analysis of intra-crystalline protein, amino acid data from Corbicula remain problematical. Preliminary data on the opercula from Bithynia indicate that better resolution is possible, particularly at older sites.

The use of ancient DNA has increased during the past two decades in several scientific disciplines. However, the underlying mechanism of DNA degradation in bone tissue are poorly understood. Here w ...

Cooking is perhaps the most common pre–burial taphonomic transformation that occurs to bone, yet it is still one of the least understood. Little progress has been made in determining a method of identifying cooked bone in the archaeological record, despite its import for various branches of archaeology. This paper attempts to describe boiling in terms of its physico–chemical effects on bone, and uses a suite of diagenetic indicators to do this. It is shown that cooking for brief periods of time has little distinguishable effect on bone in the short term, but that increased boiling times can mirror diagenetic effects observed in archaeological bone. The relationship between the loss of collagen and alterations to the bone mineral is explored through heating experiments, and the results compared with archaeological data.The possibility of boiling being used as an analogue for bone diagenesis in future studies is raised, and the key relationship between protein and mineral is once again highlighted as vital to our understanding of bone diagenesis.

The yellow ligaments of the spine are characterized by an exceptionally high content of elastin, a protein with a proved longevity in several human tissues. This unique biochemical composition suggested a suitability of yellow ligaments for age estimation based on aspartic acid racemization (AAR), which was tested by determination of AAR in total tissue specimens and in purified elastin from yellow ligaments of individuals of known age. AAR was found to increase with age in both sample sets. The purified elastin samples exhibited a much faster kinetics than the total tissue, with ca. 3.7–4.6-fold higher apparent rates. The relationship between AAR and age was much closer in the purified elastin samples ( r =0.96–0.99) and it can therefore be used as a basis for biochemical age estimation. The analysis of total tissue samples cannot be recommended since the AAR values can be strongly influenced even by slight, histologically non-detectable variations in the collagen content. Age estimation based on AAR in purified elastin from yellow ligaments may be a valuable additional tool in the identification of unidentified cadavers, especially in cases where other methods cannot be applied (e.g. no available teeth, body parts).

The preservation of the osteological material at the medieval site of Apigliano, in southern Italy, is characterized by bones with highly crystalline, and altered, mineral phases. In addition to this, some material retains perfect histological preservation, with the exception of small microfissures present throughout this structure. Diagenetic porosity is indicative of collagen loss via chemical degradation. The levels of residual collagen in these bones are much lower than is predicted from simple models of gelatinization, and thus a more complex explanation for the state of preservation must be sought. Possible explanations for the rapid loss of bone collagen are considered, including a high-temperature event, the acceleration of hydrolysis due to liming and extreme wetting and drying cycles.

The recording and analysis of a burnt mound and adjacent palaeochannel deposits on the floodplain of the River Soar in Leicestershire revealed that the burnt mound was in use, possibly for a number of different purposes, at the transition from the Neolithic to the Bronze Age. An extensive radiocarbon dating programme indicated that the site was revisited. Human remains from the palaeochannel comprised the remains of three individuals, two of whom pre-dated the burnt mound by several centuries while the partial remains of a third, dating from the Late Bronze Age, provided evidence that this individual had met a violent death. These finds, along with animal bones dating to the Iron Age, and the remains of a bridge from the early medieval period, suggest that people were drawn to this location over a long period of time.

Ancient Egyptians are thought to have been the only people in the Old World who were practising mummification in the Bronze Age (c. 2200-700 BC). But now a remarkable series of finds from a remote Scottish island indicates that Ancient Britons were performing similar, if less elaborate, practices of bodily preservation. Evidence of mummification is usually limited to a narrow range of arid or frozen environments which are conducive to soft tissue preservation. Mike Parker Pearson and his team show that a combination of microstructural, contextual and AMS 14C analysis of bone allows the identification of mummification in more temperate and wetter climates where soft tissues and fabrics do not normally survive. Skeletons from Cladh Hallan on South Uist, Western Isles, Scotland were buried several hundred years after death, and the skeletons provide evidence of post mortem manipulation of body parts. Perhaps these practices were widespread in mainland Britain during the Bronze Age.

Although the origins of domestic animals have been well-documented, it is unclear when livestock were first exploited for secondary products, such as milk. The analysis of remnant fats preserved in ceramic vessels from two agricultural sites in central and eastern Europe dating to the Early Neolithic (5900-5500 cal BC) are best explained by the presence of milk residues. On this basis, the authors suggest that dairying featured in early European farming economies. The evidence is evaluated in the light of analysis of faunal remains from this region to determine the scale of dairying. It is suggested that dairying—perhaps of sheep or goats—was initially practised on a small scale and was part of a broad mixed economy.

Immunological assays are highly favoured for their ability to readily discriminate subtle structural differences in complex biopolymers, such as proteins and polysaccharides. Immunological reactions previously reported with extracts from biominerals at least 70 Myr old have fuelled hopes that such biopolymeric structures can survive the process of fossilization. We have raised antibodies against biopolymers from a range of Recent brachiopod shells to reconstruct a fine-grained pattern of phylogenetic relationships. Using the same antibodies, the phylogenetic affinities of fossil relatives were tested. Immunological reaction patterns for Plio-Pleistocene shells were essentially identical to the patterns of modern shells (although the breadth of reactivity was narrowed) and entirely consistent with current systematic interpretations. Older samples (>4–21 Myr) were immunologically reactive, but failed to satisfy the criterion of systematic specificity. Our results provide an unequivocal demonstration that original macromolecular structures capable of yielding systematic information are preserved and accessible for immunological analysis for at least two million years. Non-specific reactions observed with the older material may relate in part to formation of mineral-induced diagenetic determinants (MIDDs).

We report the recovery of short fragments of PCR amplifiable ancient DNA from exoskeletal fragments of the grain weevil Sitophilus granarius (L.) extracted from Roman and medieval deposits in Northern England. If DNA preservation in archaeological insect remains is widespread then many applications in the spheres of evolutionary studies and archaeology can be conceived, some of which are outlined.

We demonstrate degenerate correlated photon-pair generation in a 96 μm long silicon photonic crystal waveguide via slow-light enhanced spontaneous four-wave mixing. This provides an ultra-compact platform for generating indistinguishable photons for future quantum technologies.