Project description:Here we provide proteomic datasets of pairs of cortical and trabecular bone from six Early Holocene Caprinae rib fragments from the site of La Draga, Spain, using shotgun proteomics. Our observations on proteome size and protein, peptide, and amino acid degradation have implications for the sampling of archaeological skeletal remains in highly degraded proteomic contexts, where preference should be given to the sampling of cortical bone in order to maximise the retrieval of larger and better-preserved skeletal proteomes.
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.
Project description:The extensive peat bogs of Southern Scandinavia have yielded rich Mesolithic archaeological assemblages, which has informed prehistoric studies for more than a century. Central to this has been the first recognizably Mesolithic culture, the Maglemose (c. 11,000 - 8,000 BP), first described in 1903 which has become a yardstick against which all other Early Mesolithic cultures have been compared. Despite the excellent preservation of organic material, we have for the first time conducted a combined investigation of the typology, species composition and absolute chronology of Maglemose bone points. A demonstrable and significant change in barb morphology can be directly linked to a significant paucity of finds in Southern Scandinavia around 10,300 cal BP, potentially linked to climate change. Peptide mass fingerprinting (ZooMS) reveals that the majority of bone points are made from cervids and bovines. The ribs of bovines; for instance, are more frequently utilized following the hiatus. Furthermore, the marked change in barbed bone point morphology coincides with a change in lithic technology. This change in material culture has been shown to arrive archaeologically with eastern pioneers and colonisations through Fennoscandinavia. We, therefore, propose that the Maglemose culture in Southern Scandinavia is fundamentally divided into an Early Complex (c. 11,600 - 10,300 cal BP) and a Late Complex (c. 10,300 - 8,600 cal BP): the former characterized by percussion blade production and “fine-barbed bone points” and the latter characterized by the innovations of pressure-blade production and “larger barbed bone points”. Finally, through these integrated analyses we are able to show that a single artifact type can be used as a proxy for human populations as well as inferences on potential climate changes.
Project description:Protocols for bone protein extraction adapted for radiocarbon dating were compared for their capability of being used also for paleoproteomics applications. Eight extraction protocols were tested on modern and archaeological bones. Molecular characterization of the extracts was performed by shot-gun proteomics. The effect of each extraction protocol on species identification through database searchnig was evaluated.
Project description:We report the gene expression of human chronic myelomonocytic leukemia by performing whole transcriptome shotgun sequencing of bone marrow mononuclear cells of patients with chronic myelomonocytic leukemia.
