Matthew Collins

Two alternative methods of bone preparation were examined, calcium chelation by ethylenediaminetetraacetic acid (EDTA, pH 8) and dissol!ution in strongmineral acid (HCl. The rate of EDTA demineralization of modern bone powders (< 63 um) was slow andindependent of temperature, A weak temperaturedependence (20 kJ moll) was observed for both bone shards (1-3mm) and archaeological powders which was attributed to (i) the slow rate of diffusion of EDTA through the mineral matrix of the shards, and (ii) the higher crystallinity of archaeological powders. Hydrochloric acid (HCl; 0.6 M) demineralization was rapid and could be accelerated by gentle agitation which increased the surface area of the Nernst diffusion layer. The degree of collagen degradation which occurred during HCI demineralization was contrasted with the damage caused by powdering the bone. At 4 C very little gelatinization was seen during HCI demineralization, even after prolonged incubation, but at 37 C complete gelatinization occurred after less than 100 h.However, the amount of acid soluble collagen present in the supernatant prior to .,dd demineralization was six times greater for powdered samples than for shards, equivalent to 14% of the total bone collagen. These data indicate that at low temperatures more damage is caused by grinding than by prolonged exposure to add. It is suggested that to avoid damage to proteins and other bone biopolymers, samples should be demineralized in mineral acid at a low temperature and excessive grinding of samples should be avoided.

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).

Ancient Egyptians are thought to have been the only people in the Old World who were practisingmummification in the Bronze Age (c. 2200-700 BC). But now a remarkable series of finds froma remote Scottish island indicates that Ancient Britons were performing similar, if less elaborate,practices of bodily preservation. Evidence of mummificationis usually limited to a narrow range ofarid or frozen environments which are conducive to soft tissue preservation. Mike Parker Pearsonand his team show that a combination of microstructural, contextual and AMS14C analysis ofbone allows the identification of mummification in more temperate and wetter climates wheresoft 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 provideevidence of post mortem manipulation of body parts. Perhaps these practices were widespread inmainland Britain during the Bronze Age.

Parchment represents an invaluable cultural reservoir. Retrieving an additional layer of information from these abundant, dated livestock-skins via the use of ancient DNA (aDNA) sequencing has been mooted by a number of researchers. However, prior PCR-based work has indicated that this may be challenged by cross-individual and cross-species contamination, perhaps from the bulk parchment preparation process. Here we apply next generation sequencing to two parchments of seventeenth and eighteenth century northern English provenance. Following alignment to the published sheep, goat, cow and human genomes, it is clear that the only genome displaying substantial unique homology is sheep and this species identification is confirmed by collagen peptide mass spectrometry. Only 4% of sequence reads align preferentially to a different species indicating low contamination across species. Moreover, mitochondrial DNA sequences suggest an upper bound of contamination at 5%. Over 45% of reads aligned to the sheep genome, and even this limited sequencing exercise yield 9 and 7% of each sampled sheep genome post filtering, allowing the mapping of genetic affinity to modern British sheep breeds. We conclude that parchment represents an excellent substrate for genomic analyses of historical livestock.

Avian eggshell is a common component of many archaeological deposits, but its archaeological potential remains largely unexplored. The most obvious reasons are two-fold. Firstly, despite its abundance on many sites, eggshell is often overlooked during excavation. Even when it is recovered, small fragmented remains are difficult to identify taxonomically. Here we introduce a minimally destructive qualitative analytical technique for taxonomic identification of eggshell fragments based on highly sensitive mass spectrometry and peptide mass fingerprinting (ZooMS), and illustrate its application to eggshell recovered from the Viking Age urban site at Hungate, York. We adopt a more extreme version of the method of bleach treating used to prepare ancient eggshell for DNA analysis, followed by conventional peptide mass fingerprinting using MALDI-ToF mass spectrometry. The development of this technique will allow future research to make better use of eggshell fragments recovered from archaeological sites.

Bone collagen is found throughout most of the archaeological record. Under experimental conditions, collagen is apparently preserved as an intact molecule, with amino acid compositions and isotopic profiles only changing when almost all of the protein is lost. The ubiquity of collagen in archaeological bone has lead to the development of the use of collagen peptide mass fingerprints for the identification of bone fragments—Zooarchaeology by Mass Spectrometry (ZooMS). We report a novel, but a simple method for the partial extraction of collagen for ZooMS that uses ammonium bicarbonate buffer but avoids demineralisation. We compared conventional acid demineralisation with ammonium bicarbonate buffer extraction to test ZooMS in a range of modern and archaeological bone samples. The sensitivity of the current generation of mass spectrometers is high enough for the non-destructive buffer method to extract sufficient collagen for ZooMS. We envisage that a particular advantage of this method is that it leaves worked bone artefacts effectively undamaged post-treatment, suitable for subsequent analysis or museum storage or display. Furthermore, it may have potential as a screening tool to aid curators in the selection of material for more advanced molecular analysis—such as DNA sequencing.

An analysis of chemistries known to confer high hydrothermal stability to collagen has arrived at a series of conditions that must be met. These include the formation of a stable supramolecular matrix, which must be firmly bound to the collagen triple helices. In most stabilising reactions, the chemical reactions are limited to linking elements of the collagen structure to a relatively unstable matrix. Typically, this linking step confers only moderate hydrothermal stability because the matrix is readily displaced by shrinking. In those chemical processes which result in high hydrothermal stability, the  linking step is combined with an additional step that locks the components of the matrix
together. In this way, the matrix acts like a single chemical compound, which is much  less easily displaced.

The small mineral-binding bone protein, osteocalcin, has been applied in a number of studies on ancient bone due to predictions of its long-term stability. However, the intact protein has not been shown to survive in ancient bone devoid of DNA, which is a much more phylogenetically informative biomolecule. In this investigation, the survival of osteocalcin is directly compared to the amplification of mtDNA in a set of 34 archaeological samples from four sites throughout Europe. We also present unpublished osteocalcin sequences of seven mammalian species in addition to the 19 published sequences to highlight phylogenetic limitations of this protein. The results indicate that the intact osteocalcin molecule survives less in archaeological samples than mtDNA and is more subject to the temperature of the archaeological site. Amino acid analyses show the persistence of the dominant protein collagen in samples that failed both osteocalcin and mtDNA analyses. The implications these findings present for biomolecular species identification in archaeological and palaeontological material are that, although proteins do survive beyond ancient DNA, osteocalcin does not appear to be the most ideal target.

Organic matter preserved in speleothems has considerable potential to record changes in the surrounding environment, particularly in the overlying vegetation. Here, we review three types of organic matter analysis relevant to speleothems: organic fluorescence, lipid biomarker analysis, and amino acid racemisation. Organic matter luminescence provides a useful non-destructive and rapid method for assessing dissolved organic matter quantity and quality, while biomarker analysis (amino acids and lipids) has the potential to provide a more detailed signal related to specific parts of the surrounding ecosystem such as the dominant vegetation regime and bacterial activity. Amino acid analysis has yet to prove demonstrably useful in stalagmites, due to the inability to characterise the sources of proteinaceous matter. However, the small but increasing body of work on lipid biomarker analysis in stalagmites has shown that a wide variety of recognisable biomarkers are preserved over long periods of time (>100 ka), can be recovered at temporal resolutions of <10 yr, and show meaningful changes through time. This approach is therefore of considerable potential value to Quaternary science.

There is increasing evidence that certain microbially-derived compounds may account for part of the aquatic dissolved organic nitrogen (DON) pool. Enantiomeric ratios of amino acids were used to assess the microbial input to the DON pool in the Florida Everglades, USA. Elevated levels of d-alanine, d-aspartic acid, d-glutamic acid and d-serine indicated the presence of peptidoglycan in the samples. The estimated peptidoglycan contribution to amino acid nitrogen ranged from 2.8 ± 0.1% to 6.4 ± 0.9%, increasing with salinity from freshwater to coastal waters. The distribution of individual d-amino acids in the samples suggests additional inputs to DON, possibly from archaea or from abiotic racemization of l-amino acids.

Archaeological work in advance of construction at a site on the edge of York, UK, yielded human remains of prehistoric to Romano-British date. Amongst these was a mandible and cranium, the intra-cranial space of which contained shrunken but macroscopically recognizable remains of a brain. Although the distinctive surface morphology of the organ is preserved, little recognizable brain histology survives. Though rare, the survival of brain tissue in otherwise skeletalised human remains from wet burial environments is not unique. A survey of the literature shows that similar brain masses have been previously reported in diverse circumstances. We argue for a greater awareness of these brain masses and for more attention to be paid to their detection and identification in order to improve the reporting rate and to allow a more comprehensive study of this rare archaeological survival.► Survival of a prehistoric brain in an excavated skull. ► Exceptional ceremonial deposit. ► Characterisation of the composition of the preserved brain. ► Critical review of brain survival in skeletalised human remains back to the 18th century. ► Investigation of conditions for brain preservation.

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, 20 years 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 48 h 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 ±29 year, for the 20th C respectively; in comparison 2σ age uncertainties from a single colony are ±12, ±12 and ±14 year. This is the first demonstration of FAA D/L for dating coral and following strict protocols 2σ precisions of ±24 years can be achieved across different colonies in samples from the last 150 years, and can be ±10 years 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.

ollagen 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.