Biology subjects

Fagernäs, Z.

Publications and source records attributed to Fagernäs, Z..

4 recordsLinked to original sources

bioRxiv2025

Identification and removal of contamination in palaeoproteomic analysis of dental enamel

Analysis of archaeological and palaeontological dental enamel allows for the study of taxonomy, phylogenetic relationships, and genetic sex of Pleistocene fauna and hominin remains. However, high-quality data is required for the study of degraded, chemically modified ancient proteomes. Protein contamination may hinder acquisition of such data, due to the abundance and better preservation of modern contaminating proteins. Here, we artificially contaminate a Pleistocene woolly rhinoceros tooth in order to investigate decontamination of archaeological dental enamel. We find that although the contaminating proteins are not identified, likely due to a lack of denaturation and digestion steps in archaeological dental enamel protein extraction protocols, contamination leads to significant loss of endogenous proteomic information. We thereafter compare five published decontamination methods, and find that a simple water or bleach wash prior to demineralization is most efficient at removing protein contamination. The water wash does not affect the endogenous proteome, while a bleach wash may lead to a loss of shorter intercrystalline peptides. We therefore conclude that decontamination is necessary in the study of ancient dental enamel, to ensure maximal retrieval of endogenous proteomic information, and can easily be achieved by incorporating a water or bleach wash step into the protein extraction protocol.

evolutionary biology↗

bioRxiv2025

New methods on the block: Taxonomic identification of archaeological bones in resin-embedded sediments through palaeoproteomics

The integration of biomolecular studies of past organisms with geoarchaeological studies can significantly improve our understanding of the relative chronology and context of archaeologically (in)visible behaviours. However, the complexity and sedimentological heterogeneity of archaeological deposits at a microscopic scale is often not taken into consideration in biomolecular studies. Here, we investigate the preservation and retrieval of palaeoproteomic data from bone fragments embedded in Pleistocene resin-impregnated sediment blocks. We show that resin impregnation has minimal effect on skeletal protein taxonomic identifications in modern skeletal material, but observe an increase in oxidation-related post-translational modifications. We then successfully retrieve proteins from resin-impregnated blocks from the Palaeolithic sites of Bacho Kiro Cave, La Ferrassie and Quincay. The taxonomic identifications of minute bones encased in resin are in line with previous analyses of the faunal communities of these sites, with a diversity of taxa (Bos sp./Bison sp., Equus sp., Ursus sp., and Caprinae) observed at a microscale in Bacho Kiro. This differs from results from La Ferrassie where most of the samples are identified as a single taxon (Bos sp./Bison sp.) across different areas of the site. The block from Quincay only provided taxonomic identification of two out of eleven bone-derived samples, likely due to diagenesis. Our work indicates that palaeoproteomes can be retrieved from bone fragments at a microstratigraphic resolution, enabling the detailed study of faunal community composition at a scale that more closely matches that of past human occupations. Significance StatementResin-embedded sediment blocks are widely used in archaeology and soil sciences to reconstruct past environments and human behavior, but their potential for biomolecular analysis is underexplored. Here, we demonstrate that ancient proteins can be successfully retrieved from bone fragments embedded in resin-impregnated sediment blocks from Pleistocene archaeological sites. Our findings show that resin impregnation has a minimal impact on protein recovery and that palaeoproteomics enables taxonomic identification of Pleistocene bone fragments at a microstratigraphic scale. This approach allows for reconstructing past faunal communities with unprecedented detail, improving our understanding of ancient ecosystems and the environmental contexts of early hominin occupations.

evolutionary biology↗

bioRxiv2024

Cleaning the Dead: Optimized decontamination enhances palaeoproteomic analyses of a Pleistocene hominin tooth from Khudji, Tajikistan

The study of ancient proteins preserved in a range of archaeological, cultural heritage, and palaeontological materials is increasingly contributing to our understanding of human evolution and archaeological research questions. Many of the specimens studied have been excavated and stored for a significant duration prior to their proteomic analysis. Human handling and storage environments therefore provide ample opportunities for protein contamination onto and into specimens of interest to palaeoproteomic studies. As such, modern protein contamination limits access to endogenous proteomes. Here, we compare five approaches of bone protein decontamination applied to a Pleistocene Equus sp. bone fragment contaminated with a modern dog salivary proteome. We find that all tested methods reduce the protein contamination, but with different efficiencies. We find that a brief bleach wash is the most effective approach in removing modern protein contamination, and that no additional damage is caused to the endogenous proteome by this treatment. Next, we apply this approach to a hominin tooth found at Khudji, a Late Pleistocene archaeological site in Tajikistan. We demonstrate that a brief bleach wash removes almost all human skin protein contamination while retaining the endogenous hominin dentine proteome. Subsequent phylogenetic analysis of the Khudji dentine proteome allowed determination that the specimen is likely not a Denisovan, but still leaves ambiguity between an assignment to either modern humans or Neanderthals.

evolutionary biology↗

bioRxiv2021

Understanding the microbial biogeography of ancient human dentitions to guide study design and interpretation

The oral cavity is a heterogeneous environment, varying in factors such as pH, oxygen levels, and salivary flow. These factors affect the microbial community composition and distribution of species in dental plaque, but it is not known how well these patterns are reflected in archaeological dental calculus. In most archaeological studies, a single sample of dental calculus is studied per individual and is assumed to represent the entire oral cavity. However, it is not known if this sampling strategy introduces biases into studies of the ancient oral microbiome. Here, we present the results of a shotgun metagenomic study of a dense sampling of dental calculus from four Chalcolithic individuals from the southeast Iberian peninsula (ca. 4500-5000 BP). Inter-individual differences in microbial composition are found to be much larger than intra-individual differences, indicating that a single sample can indeed represent an individual in most cases. However, there are minor spatial patterns in species distribution within the oral cavity that should be taken into account when designing a study or interpreting results. Finally, we show that plant DNA identified in the samples may be of environmental origin, showing the importance of including environmental controls or several lines of biomolecular evidence.

microbiology↗