Collagen Peptide Mass Fingerprinting Research Articles

Combined osteomorphological, isotopic, aDNA, and ZooMS analyses of sheep and goat remains from Neolithic Ulucak, Turkey

The site of Ulucak is pivotal in exploring the Neolithic of the eastern Aegean and western Anatolia. It has an impressive stratigraphic sequence stretching from the first half of the seventh millennium BC to the first half of the sixth millennium BC. Recent zooarchaeological analyses have provided insight into the importance of animal husbandry practices and dairying at the site throughout the Neolithic but also raised questions about the changing nature of herd management strategies and whether these differed for sheep and goat. The faunal data, coupled with the significance of the site and condition of the assemblage, prompted the application of a number of methodological techniques to assess differences between sheep and goat. In this paper, we combine traditional osteomorphological analysis, ancient DNA, collagen peptide mass fingerprinting (zooarchaeology by mass spectrometry, or ZooMS), and stable isotope analysis of δ18O and δ13C from tooth enamel carbonate as well as δ13C and δ15N from bone collagen. As such, this is the first study of its kind. We evaluate the juxtaposition of these four approaches and their application in this important case, with relevance for future studies in the region.

Species identification and decay assessment of Late Pleistocene fragmentary vertebrate remains from Pin Hole Cave (Creswell Crags, UK) using collagen fingerprinting

Ancient bone remains are widely utilized when investigating vertebrate biodiversity of past animal populations but are often so highly fragmented that the majority of specimens cannot be identified to any meaningful taxonomic level. Recently, high‐throughput methods for objective species identification using collagen peptide mass fingerprinting have been created to overcome this with the added indication that they could also offer a means of relative ageing through decay measurement. Here we explore both species identification and decay measurements for the Pin Hole Cave ‘microfaunal’ assemblage, the site that has been designated as a representative for Marine Oxygen Isotope Stage 3 in Britain in terms of its suite of mammalian fauna. We explore the technique's potential to corroborate the faunal diversity established previously by macroscopic studies and evaluate the decay measurements across the species boundary. The results support that the analysis of fragmentary remains by collagen fingerprinting can yield a more diverse set of fauna, and offer additional information relating to taphonomy, than the analysis of morphologically intact bones on their own. However, although useful for identifying likely contaminations of an assemblage, there was an unexpected decrease in the decay measurements observed for some megafauna compared with much younger microfauna, indicating that other factors need to be carefully monitored before it could be used as a relative ageing technique in Quaternary deposits.

Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans.

Over the last few centuries, many cetacean species have witnessed dramatic global declines due to industrial overharvesting and other anthropogenic influences, and thus are key targets for conservation. Whale bones recovered from archaeological and palaeontological contexts can provide essential baseline information on the past geographical distribution and abundance of species required for developing informed conservation policies. Here we review the challenges with identifying whale bones through traditional anatomical methods, as well as the opportunities provided by new molecular analyses. Through a case study focused on the North Sea, we demonstrate how the utility of this (pre)historic data is currently limited by a lack of accurate taxonomic information for the majority of ancient cetacean remains. We then discuss current opportunities presented by molecular identification methods such as DNA barcoding and collagen peptide mass fingerprinting (zooarchaeology by mass spectrometry), and highlight the importance of molecular identifications in assessing ancient species’ distributions through a case study focused on the Mediterranean. We conclude by considering high-throughput molecular approaches such as hybridization capture followed by next-generation sequencing as cost-effective approaches for enhancing the ecological informativeness of these ancient sample sets.This article is part of the themed issue ‘From DNA barcodes to biomes’.

Using combined biomolecular methods to explore whale exploitation and social aggregation in hunter–gatherer–fisher society in Tierra del Fuego

Cetaceans were an important food and raw material resource for the South American hunter–gatherer–fisher (HGF) communities of Tierra del Fuego. Historic ethnographic evidence suggests that relatively mobile HGF groups came together in large numbers to exploit carcasses from individual cetacean stranding events. Substantial accumulations of whale bones within shell middens in the Lanashuaia locality of the Beagle Channel suggests that these social aggregation events may also have occurred in pre-historic periods. The difficulty in assigning taxonomic identifications to the fragmentary whale remains, however, made it difficult to explicitly test this hypothesis. Here, we applied two different biomolecular techniques, collagen peptide mass fingerprinting (ZooMS) and ancient mitochondrial DNA analysis to 42 archeological bone fragments from the Lanashuaia locality to provide accurate species identifications. There was a clear correspondence between ZooMS and DNA results, identifying five different cetacean species (Southern bottlenose, blue, humpback, right, and sei whale) as well as human and sea lion remains. The biomolecular results were not conclusively consistent with HGF social aggregation, revealing an unexpectedly diverse range of cetaceans within the Lanashuaia middens. However, the results could not fully refute the hypothesis that cetacean remains can be used as anthropic markers of aggregation events, as the observed species and haplotypes revealed potential shared exploitation of some whale resources between midden sites.

Searching for Scandinavians in pre-Viking Scotland: molecular fingerprinting of Early Medieval combs

The character and chronology of Norse colonisation in Early Medieval northern Scotland (8th–10th centuries AD) is hotly debated. The presence of reindeer antler raw material in ‘native’ or ‘Pictish’ type combs from the Orkney Isles, northern Scotland has been put forward as evidence for a long and largely peaceful initial period of cultural contact, as opposed to a shorter, more polarised period probably in the late ninth century. Here this hypothesis is tested using a minimally-destructive collagen peptide mass fingerprinting method (ZooMS) to speciate the raw material of 20 combs. Eleven were identified as red deer, four as reindeer and one as whale. The accuracy and gentleness of this method was tested by the subsequent application of ancient DNA (aDNA) methods to fourteen of the same samples: in ten, amplification was successful and all supported the preliminary ZooMS identification. All ‘native’-type combs in the sample are identified as red deer, and all Norse types as reindeer. These results challenge previous species identifications for these combs' raw materials. The balance of evidence no longer supports the existence of a long period of cultural contact between Atlantic Scotland and Scandinavian settlers before the late 9th century. ZooMS is shown to have considerable potential for identification of worked bone and antler artefacts, with applications in archaeology and wildlife/art-history forensics.

Identification of Bilirubin Binding Site in Type I Collagen

The interaction of bilirubin with collagen in the significance of jaundice incidence have been previously reported and investigated. The novel peptide sequences containing bilirubin binding domain was identified and located to develop a basis for further studies investigating the interactions of collagen with bilirubin in the present study. In this study an intricate interaction between bilirubin and collagen was characterized and their binding domain has been established using in-gel digestion and LC–MS/MS analysis based on the collagen sequencing and peptide mass fingerprinting. The biotinylated bilirubin derivatives bind to α1(I) chain but not to α2(I) chains which clearly designates that bilirubin shows greater affinity to α1 chains of collagen. The intact proteins collected after analyzing the resulting complex mixture of peptides was used for peptide mapping. Using the electrospray method, among the other peptide sequence information obtained, the molecular weight of collagen alpha-2(I) chain was obtained by locating a 130 kDa weight peptide sequences with greater pi value (9.14) with 1,364 amino acid residues and collagen alpha-1(I) chain with 1,463 amino acid residues with 138.9 kDa molecular weight. This information leads to locate the exact sequence of these helices focussing on the domain identification. The total charge of the peptide domain sequences infers that the bilirubin participates in the electrostatic mode of interaction with collagen peptide. Moreover, other modes of interactions such as hydrogen bonding, covalent interactions and hydrophobic interactions are possible.

Collagen fingerprinting of archaeological bone and teeth remains from Domuztepe, South Eastern Turkey

We applied a recently developed method of collagen peptide mass fingerprinting for taxonomic identification in faunal remains to 111 specimens from the Neolithic site of Domuztepe in southeastern Turkey. Advances on the published technique allow us to move beyond the key domesticated fauna (sheep, goat, pig and cattle) to include non-domesticates (deer and gazelle, as well as humans). As the animal economy of Domuztepe was dominated by domestic sheep and goats, a large number of the samples tested were morphologically indistinguishable sheep/goat remains. A number of samples represented elements that provide information on age (i.e., mandibles) or sex (pelvis); thus, this represents the first major study to attempt to improve kill-off profiles using collagen fingerprinting. We also show that the collagen extracted from dentine is equally amenable to the proposed methodology as bone collagen.