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Screening Archaeological Bone

ABSTRACT: Screening archaeological bone for palaeogenetic and palaeoproteomic studies

PROVIDER: PRJEB37812 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR4029120.fastq.gz	Fastqsanger.gz
	ERR4029130.fastq.gz	Fastqsanger.gz
	ERR4029140.fastq.gz	Fastqsanger.gz
	ERR4029150.fastq.gz	Fastqsanger.gz
	ERR4029160.fastq.gz	Fastqsanger.gz

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Poor preservation of antibodies in archaeological human bone and dentine

Project description:The growth of proteomics-based methods in archaeology prompted an investigation of the survival of non-collagenous proteins, specifically immunoglobulin G (IgG), in archaeological human bone and dentine. Over a decade ago reports were published on extracted, immunoreactive archaeological IgG, and the variable yields of IgG molecules detected by Western blots of 1D and 2D SDS-PAGE gels. If IgG can indeed be recovered from archaeological skeletal material, it offers remarkable opportunities for exploring the history of disease - for example in applying functional anti-malarial IgGs to study past patterns of malaria. More recently, the field has seen a move away from immunological approaches and towards the use of shotgun proteomics via mass spectrometry. Using previously published techniques, this study attempted to extract and characterize archaeological IgG proteins. In only one extraction method were immunoglobulin derived peptides identified, and these displayed extensive evidence of degradation. The failure to extract immunoglobulins by all but one method, along with observed patterns of protein degradation, suggests that IgG may be an unsuitable target for detecting disease-associated antigens. This research highlights the importance of revisiting previously ‘successful’ biomolecular methodologies using emerging technologies.

2016-02-08 | PXD002295 | Pride

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Screening archaeological bone for palaeogenetic and palaeoproteomic studies.

Project description:The recovery and analysis of ancient DNA and protein from archaeological bone is time-consuming and expensive to carry out, while it involves the partial or complete destruction of valuable or rare specimens. The fields of palaeogenetic and palaeoproteomic research would benefit greatly from techniques that can assess the molecular quality prior to sampling. To be relevant, such screening methods should be effective, minimally-destructive, and rapid. This study reports results based on spectroscopic (Fourier-transform infrared spectroscopy in attenuated total reflectance [FTIR-ATR]; n = 266), palaeoproteomic (collagen content; n = 226), and palaeogenetic (endogenous DNA content; n = 88) techniques. We establish thresholds for three different FTIR indices, a) the infrared splitting factor [IRSF] that assesses relative changes in bioapatite crystals' size and homogeneity; b) the carbonate-to-phosphate [C/P] ratio as a relative measure of carbonate content in bioapatite crystals; and c) the amide-to-phosphate ratio [Am/P] for assessing the relative organic content preserved in bone. These thresholds are both extremely reliable and easy to apply for the successful and rapid distinction between well- and poorly-preserved specimens. This is a milestone for choosing appropriate samples prior to genomic and collagen analyses, with important implications for biomolecular archaeology and palaeontology.

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Droulers bone points

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Low-invasive sampling method for taxonomic for the identification of archaeological and paleontological bone by proteomics of their collagens

Project description:Bone collagen is an important organic material for isotopic measurement, radiocarbon and paleoproteomic analyzes, to provide information on diet, dating, taxonomic identification. Current paleoproteomics methods are destructive and require from a few milligrams to several tenths of milligrams of bone for analysis. In many cultures, bones are raw materials for artefact which are conserved in museum which hampers to damage these precious objects during sampling. Here, we describe a minimal sampling method that identifies collagen, taxonomy and post-translational modifications from Holocene and Upper Pleistocene bones dated to 130,000 and 5,000 years ago using dermatological skin tape-discs for sampling. The sampled bone micro-powder were digested following our highly optimized eFASP protocol, then analyzed by MALDI FTICR MS and LC-MS/MS for identifying the genus taxa of the bones. We show that this low-invasive sampling does not deteriorate the bones and achieves results similar to those obtained by destructive sampling. Moreover, this sampling method can be performed at archaeological sites or in museums.

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Project description:Control bone extractions completed using an SP3 based extraction and used to confirm the sharred masses in collagen peptide mass fingerprints. See associated publications: Bleasdale et al. 2000 for more information about the sample and the extraction and Wang et al 2000 for information on it's use to identify shared mammal MALDI peptides.

2020-08-09 | MSV000085935 | MassIVE

Assessment of seven minimally sampling protocols of archaeological skeletal proteomes

Project description:Archaeological bone material is increasingly being sampled for various molecular analyses. Minimally invasive sampling protocols should therefore be utilised whenever possible. We compare the proteomic output of 10 Early Neolithic Bos sp. humeri, from two different preservation contexts, of seven sampling protocols, namely retrieving bone chips (with and without demineralisation), acid etching (FASP and chemical neutralisation), eraser, membrane box, and polishing film. We note that minimally invasive sampling methods can extract a substantial amount of protein groups and provide sufficient taxonomic identifications if preservation conditions are favorable. However, if preservation conditions are poorer more invasive sampling techniques should be considered.

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