How to get your goat: automated identification of species from MALDI-ToF spectra.

MOTIVATION: Classification of archaeological animal samples is commonly achieved via manual examination of matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) spectra. This is a time-consuming process which requires significant training and which does not produce a measure of confidence in the classification. We present a new, automated method for arriving at a classification of a MALDI-ToF sample, provided the collagen sequences for each candidate species are available. The approach derives a set of peptide masses from the sequence data for comparison with the sample data, which is carried out by cross-correlation. A novel way of combining evidence from multiple marker peptides is used to interpret the raw alignments and arrive at a classification with an associated confidence measure. RESULTS: To illustrate the efficacy of the approach, we tested the new method with a previously published classification of parchment folia from a copy of the Gospel of Luke, produced around 1120 C.E. by scribes at St Augustine's Abbey in Canterbury, UK. In total, 80 of the 81 samples were given identical classifications by both methods. In addition, the new method gives a quantifiable level of confidence in each classification. AVAILABILITY AND IMPLEMENTATION: The software can be found at https://github.com/bioarch-sjh/bacollite, and can be installed in R using devtools. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Proteomic evidence of dietary sources in ancient dental calculus.

Archaeological dental calculus has emerged as a rich source of ancient biomolecules, including proteins. Previous analyses of proteins extracted from ancient dental calculus revealed the presence of the dietary milk protein ß-lactoglobulin, providing direct evidence of dairy consumption in the archaeological record. However, the potential for calculus to preserve other food-related proteins has not yet been systematically explored. Here we analyse shotgun metaproteomic data from 100 archaeological dental calculus samples ranging from the Iron Age to the post-medieval period (eighth century BC to nineteenth century AD) in England, as well as 14 dental calculus samples from contemporary dental patients and recently deceased individuals, to characterize the range and extent of dietary proteins preserved in dental calculus. In addition to milk proteins, we detect proteomic evidence of foodstuffs such as cereals and plant products, as well as the digestive enzyme salivary amylase. We discuss the importance of optimized protein extraction methods, data analysis approaches and authentication strategies in the identification of dietary proteins from archaeological dental calculus. This study demonstrates that proteomic approaches can robustly identify foodstuffs in the archaeological record that are typically under-represented due to their poor macroscopic preservation.

Animal origin of 13th-century uterine vellum revealed using noninvasive peptide fingerprinting.

Tissue-thin parchment made it possible to produce the first pocket Bibles: Thousands were made in the 13th century. The source of this parchment, often called "uterine vellum," has been a long-standing controversy in codicology. Use of the Latin term abortivum in many sources has led some scholars to suggest that the skin of fetal calves or sheep was used. Others have argued that it would not be possible to sustain herds if so many pocket Bibles were produced from fetal skins, arguing instead for unexpected alternatives, such as rabbit. Here, we report a simple and objective technique using standard conservation treatments to identify the animal origin of parchment. The noninvasive method is a variant on zooarchaeology by mass spectrometry (ZooMS) peptide mass fingerprinting but extracts protein from the parchment surface by using an electrostatic charge generated by gentle rubbing of a PVC eraser on the membrane surface. Using this method, we analyzed 72 pocket Bibles originating in France, England, and Italy and 293 additional parchment samples that bracket this period. We found no evidence for the use of unexpected animals; however, we did identify the use of more than one mammal species in a single manuscript, consistent with the local availability of hides. These results suggest that ultrafine vellum does not necessarily derive from the use of abortive or newborn animals with ultrathin hides, but could equally well reflect a production process that allowed the skins of maturing animals of several species to be rendered into vellum of equal quality and fineness.

A biological reading of a palimpsest.

In the Middle Ages, texts were recorded and preserved on parchment, an animal-derived material. When this resource was scarce, older manuscripts were sometimes recycled to write new manuscripts. In the process, the ancient text was erased, creating what is known as a palimpsest. Here, we explore the potential of peptide mass fingerprinting (PMF), widely applied to identify species, to help reconnect the dispersed leaves of a manuscript and reveal differences in parchment manufacturing. In combination with visual methods, we analyzed a whole palimpsest, the codex AM 795 4to from the Arnamagnæan Collection (Copenhagen, Denmark). We find that both sheep and goat skins were used in this manuscript, and that parchment differed in quality. Notably, the PMF analysis distinguished five groups of folios which match the visual groupings. We conclude that this detailed interrogation of a single mass spectrum can be a promising tool to understand how palimpsest manuscripts were constructed.

Beneficial effects of omega-3 fatty acids in the proteome of high-density lipoprotein proteome.

BACKGROUND: Omega-3 poly-unsaturated fatty acids (ω-3 PUFAs) have demonstrated to be beneficial in the prevention of cardiovascular disease, however, the mechanisms by which they perform their cardiovascular protection have not been clarified. Intriguingly, some of these protective effects have also been linked to HDL. The hypothesis of this study was that ω-3 PUFAs could modify the protein cargo of HDL particle in a triglyceride non-dependent mode. The objective of the study was to compare the proteome of HDL before and after ω-3 PUFAs supplemented diet. METHODS: A comparative proteomic analysis in 6 smoker subjects HDL before and after a 5 weeks ω-3 PUFAs enriched diet has been performed. RESULTS: Among the altered proteins, clusterin, paraoxonase, and apoAI were found to increase, while fibronectin, α-1-antitrypsin, complement C1r subcomponent and complement factor H decreased after diet supplementation with ω-3 PUFAs. Immunodetection assays confirmed these results. The up-regulated proteins are related to anti-oxidant, anti-inflammatory and anti-atherosclerotic properties of HDL, while the down-regulated proteins are related to regulation of complement activation and acute phase response. CONCLUSIONS: Despite the low number of subjects included in the study, our findings demonstrate that ω-3 PUFAs supplementation modifies lipoprotein containing apoAI (LpAI) proteome and suggest that these protein changes improve the functionality of the particle.

The Vienna Genesis: An Example of Late Antique Purple Parchment.

The investigation and conservation of the Vienna Genesis, a Late Antique manuscript on purple parchment, included the study of parchment production and purple dyeing in the sixth century. The process of parchment making and of purple dyeing was recreated and compared with the Vienna Genesis and other manuscripts from the sixth and eighth centuries. Parchment made from the hides of young lambs and dyed with orchil resembled the folios of the Vienna Genesis. The results of material analysis and the study of parchment technology influenced decisions for the conservation and storage of the manuscript. Fragile areas of ink and parchment were stabilised with strips of adhesive coated Japanese tissue paper. The single folios are stored in folders of Japanese paper and museum matboard within a sink mat.

Expression and purification of recombinant apolipoprotein A-I Zaragoza (L144R) and formation of reconstituted HDL particles.

Apolipoprotein A-I Zaragoza (L144R) (apo A-I Z), has been associated with severe hypoalphalipoproteinemia and an enhanced effect of high density lipoprotein (HDL) reverse cholesterol transport. In order to perform further studies with this protein we have optimized an expression and purification method of recombinant wild-type apo A-I and apo A-I Z and produced mimetic HDL particles with each protein. An pET-45 expression system was used to produce N-terminal His-tagged apo A-I, wild-type or mutant, in Escherichia coli BL21 (DE3) which was subsequently purified by affinity chromatography in non-denaturing conditions. HDL particles were generated via a modified sodium cholate method. Expression and purification of both proteins was verified by SDS-PAGE, MALDI-TOF MS and immunochemical procedures. Yield was 30mg of purified protein (94% purity) per liter of culture. The reconstituted HDL particles checked via non-denaturing PAGE showed high homogeneity in their size when reconstituted both with wild-type apo A-I and apo A-I Z. An optimized system for the expression and purification of wild-type apo A-I and apo A-I Z with high yield and purity grade has been achieved, in addition to their use in reconstituted HDL particles, as a basis for further studies.

Scratching the surface: the use of sheepskin parchment to deter textual erasure in early modern legal deeds.

Historic legal deeds are one of the most abundant resources in British archives, but also one of the most neglected. Despite the millions that survive, we know remarkably little about their manufacture, including the species of animal on which they were written. Here we present the species identification of 645 sixteenth-twentieth century skins via peptide mass fingerprinting (ZooMS), demonstrating the preferential use of sheepskin parchment. We argue that alongside their abundance and low cost, the use of sheepskins over those of other species was motivated by the increased visibility of fraudulent text erasure and modification afforded by the unique structure of their skin. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40494-021-00503-6.

Girding the loins? Direct evidence of the use of a medieval English parchment birthing girdle from biomolecular analysis.

In this paper, we describe palaeoproteomic evidence obtained from a stained medieval birth girdle using a previously developed dry non-invasive sampling technique. The parchment birth girdle studied (Wellcome Collection Western MS. 632) was made in England in the late fifteenth century and was thought to be used by pregnant women while giving birth. We were able to extract both human and non-human peptides from the manuscript, including evidence for the use of honey, cereals, ovicaprine milk and legumes. In addition, a large number of human peptides were detected on the birth roll, many of which are found in cervico-vaginal fluid. This suggests that the birth roll was actively used during childbirth. This study is, to our knowledge, the first to extract and analyse non-collagenous peptides from a birth girdle using this sampling method and demonstrates the potential of this type of analysis for stained manuscripts, providing direct biomolecular evidence for active use.

The York Gospels: a 1000-year biological palimpsest.

Medieval manuscripts, carefully curated and conserved, represent not only an irreplaceable documentary record but also a remarkable reservoir of biological information. Palaeographic and codicological investigation can often locate and date these documents with remarkable precision. The York Gospels (York Minster Ms. Add. 1) is one such codex, one of only a small collection of pre-conquest Gospel books to have survived the Reformation. By extending the non-invasive triboelectric (eraser-based) sampling technique eZooMS, to include the analysis of DNA, we report a cost-effective and simple-to-use biomolecular sampling technique for parchment. We apply this combined methodology to document for the first time a rich palimpsest of biological information contained within the York Gospels, which has accumulated over the 1000-year lifespan of this cherished object that remains an active participant in the life of York Minster. These biological data provide insights into the decisions made in the selection of materials, the construction of the codex and the use history of the object.

Pathogens and host immunity in the ancient human oral cavity.

Calcified dental plaque (dental calculus) preserves for millennia and entraps biomolecules from all domains of life and viruses. We report the first, to our knowledge, high-resolution taxonomic and protein functional characterization of the ancient oral microbiome and demonstrate that the oral cavity has long served as a reservoir for bacteria implicated in both local and systemic disease. We characterize (i) the ancient oral microbiome in a diseased state, (ii) 40 opportunistic pathogens, (iii) ancient human-associated putative antibiotic resistance genes, (iv) a genome reconstruction of the periodontal pathogen Tannerella forsythia, (v) 239 bacterial and 43 human proteins, allowing confirmation of a long-term association between host immune factors, 'red complex' pathogens and periodontal disease, and (vi) DNA sequences matching dietary sources. Directly datable and nearly ubiquitous, dental calculus permits the simultaneous investigation of pathogen activity, host immunity and diet, thereby extending direct investigation of common diseases into the human evolutionary past.

High-density lipoprotein cholesterol increase and non-cardiovascular mortality: a meta-analysis.

CONTEXT: Many observational prospective studies have confirmed the inverse relationship between high-density lipoprotein (HDL) cholesterol and coronary heart disease. However, the potential benefit of the pharmacological increase in HDL cholesterol has not been clearly demonstrated. Moreover, in some interventions an increase in total mortality has been reported. OBJECTIVE: The objective of this meta-analysis was to determine the relationship between HDL cholesterol increase and non-cardiovascular mortality in randomised trials. DATA SOURCES: Authors searched Medline up to December 2008. STUDY SELECTION: Four reviewers identified randomised trials in which, through different types of interventions, HDL cholesterol increase in the treatment group was >4% compared to control group, both groups reported separately non-cardiovascular mortality and the duration of the study was, at least, one year. DATA EXTRACTION: Data of HDL cholesterol concentrations and deaths were collected as they appeared in the original studies. If necessary, reviewers calculated data by using trial information. RESULTS: Meta-regression analysis included 44 articles corresponding to 107 773 participants. Analysis showed an association between HDL cholesterol increase and non-cardiovascular mortality (p=0.023), however, the correlation disappeared when we excluded the ILLUMINATE (Investigation of Lipid Level Management to Understand its Impact in Atherosclerosis Events) trial from the analysis (p=0.972). CONCLUSIONS: Meta-regression analysis results suggest that increases in HDL cholesterol up to 40% are not associated with higher non-cardiovascular death. The increase in adverse events observed in some trials where HDL cholesterol was raised in large amounts could be related with the drug mechanisms more than the HDL cholesterol increase itself.

Proteomic study of macrophages exposed to oxLDL identifies a CAPG polymorphism associated with carotid atherosclerosis.

OBJECTIVE: Macrophages play a key role in the development of atherosclerosis. The objective of this observational study was to characterize the proteome of macrophages to identify proteins implicated in atherosclerosis. METHODS: The proteome of macrophage exposed to oxidized low-density lipoprotein (LDL) was studied in a sample of 12 subjects with autosomal dominant hypercholesterolemia and analyzed according to carotid atherosclerosis. Carotid intima-media thickness (IMT), genotyping of the polymorphisms responsible for the amino acid change present in the identified proteins, and an association study was performed in a sample of 320 subjects with autosomal dominant hypercholesterolemia and 145 normolipemic controls. RESULTS: Mass spectroscopy identified two proteins, gelsolin like capping protein (CapG) and glutathione-S-transferase omega 1 (GSTO1), with large variability among subjects which corresponded with two common genetic variants. The rs6886 polymorphism in CAPG was significantly associated with carotid IMT. Carriers of the minor allele in CAPG polymorphism presented less carotid IMT than noncarriers in the hypercholesterolemia group (mean and maximum internal carotid IMT p=0.016 and p=0.032, respectively). This effect was more important in subjects below 50 years old (mean and maximum internal carotid IMT p<0.001). CONCLUSIONS: Association analysis revealed rs6886 polymorphism in CAPG to be associated with carotid IMT, suggesting that this polymorphism could modulate macrophages' response to oxidized LDL in subjects with hypercholesterolemia.