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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

Project description:Shotgun sequencing of archaeological bone points from Droulers, Quebec.

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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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Deep palaeoproteomic profiling of archaeological human brains

Project description:Palaeoproteomics leverages the persistence, diversity, and biological import of ancient proteins to explore the past, and answer fundamental questions about phylogeny, environment, diet, and disease. These insights are largely gleaned from hard tissues like bone and teeth, as well-established protocols exist for extracting ancient proteins from mineralised tissues. No such method, however, exists for the soft tissues, which are underexplored in palaeoproteomics given permission for destructive analysis routinely depends on a proven methodology. Considering less than one-tenth of all human proteins are expressed in bone, compared to three-quarters in the internal organs, the amount of biological information presently inaccessible is substantial. We address this omission with an optimised LC-FAIMS-MS/MS workflow yielding the largest, most diverse palaeoproteome yet described. Using archaeological human brains, we test ten protocols with varied chemistries and find that urea lysis effectively disrupts preserved membrane regions to expose low-abundant, intracellular analytes. Further, we show that ion mobility spectrometry improves unique protein identification by as much as 40%, and represents a means of “pre-cleaning” dirty archaeological samples. Our methodology will be useful for improving protein recovery from a range of ancient tissues and depositional environments.

2025-04-02 | PXD062254 | Pride

Bone collagen from Pacific salmonid species contains differences allowing for peptide mass fingerprinting for easy identification

Project description:MS/MS spectra of archaeological (Oncorhynchus) and modern (Salmo salar) bone collagen.

2019-04-15 | MSV000083687 | MassIVE