Of mice and men: Traces of life in the death registries of the 1630 plague in Milano

Fungal and bacterial species richness in biodeteriorated seventeenth century Venetian manuscripts

Historical paper documents are susceptible to complex degradation processes, including biodeterioration, which can progressively compromise their aesthetic and structural integrity. This study analyses seventeenth century handwritten historical letters stored at the Correr Museum Library in Venice, Italy, exhibiting pronounced signs of biodeterioration. The techniques used encompassed traditional colony isolation on agar plates and proteomics analyses, employing nanoscale liquid chromatography coupled with high-resolution mass spectrometry (nano-LC-MS). Fluorescence microscopy was used for the first time in the historical paper biodeterioration context to supplement the conventional stereoscopic, optical, and scanning electron microscopic imaging techniques. This method enables the visualisation of microorganisms beyond and beneath the paper's surface through their natural intrinsic autofluorescence in a non-invasive and non-destructive way. The results demonstrate a diverse, complex, and abundant microbiota composed of coexisting fungal and bacterial species (Ascomycota, Mucoromycota, Basidiomycota, Proteobacteria, and Actinobacteria), along with mite carcasses, insects, parasites, and possibly protists. Furthermore, this study reveals certain species that were not previously documented in the biodeterioration of historical paper, including human pathogens, such as Histoplasma capsulatum, Brucella, Candida albicans, and species of Aspergillus (A. flavus, A. fumigatus, A. oryzae, A. terreus, A. niger) known to cause infections or produce mycotoxins, posing substantial risk to both artefacts and humans.

Count Dracula Resurrected: Proteomic Analysis of Vlad III the Impaler's Documents by EVA Technology and Mass Spectrometry

The interest of scientists in analyzing items of World Cultural Heritage has been exponentially increasing since the beginning of the new millennium. These studies have grown considerably in tandem with the development and use of sophisticated and sensitive technologies such as high-resolution mass spectrometry (MS) and the non-invasive and non-damaging technique, known under the acronym EVA (ethylene-vinyl acetate). Here, we report the results of the MS characterization of the peptides and proteins harvested by the EVA technology applied to three letters written in 1457 and 1475 by the voivode of Wallachia, Vlad III, also known as Vlad the Impaler, or Vlad Dracula. The discrimination of the "original" endogenous peptides from contaminant ones was obtained by monitoring their different levels of deamidation and of other diagenetic chemical modifications. The characterization of the ancient proteins extracted from these documents allowed us to explore the environmental conditions, in the second half of the 15th century, of the Wallachia, a region considered as a meeting point for soldiers, migrants, and travelers that probably carried not only trade goods and cultural traditions but also diseases and epidemics. In addition, the identification of many human peptides and proteins harvested from the letters allowed us to uncover more about Vlad Dracula the Impaler. Particularly, the experimental data show that he probably suffered from inflammatory processes of the respiratory tract and/or of the skin. In addition, proteomics data, although not exhaustive, suggest that, according to some stories, he might also have suffered from a pathological condition called hemolacria, that is, he could shed tears admixed with blood. It is worth noting that more medieval people may have touched these documents, which cannot be denied, but it is also presumable that the most prominent ancient proteins should be related to Prince Vlad the Impaler, who wrote and signed these letters. The data have been deposited to the ProteomeXchange with the identifier ⟨PXD041350⟩.

Artefact Profiling: Panomics Approaches for Understanding the Materiality of Written Artefacts

This review explains the strategies behind genomics, proteomics, metabolomics, metallomics and isotopolomics approaches and their applicability to written artefacts. The respective sub-chapters give an insight into the analytical procedure and the conclusions drawn from such analyses. A distinction is made between information that can be obtained from the materials used in the respective manuscript and meta-information that cannot be obtained from the manuscript itself, but from residues of organisms such as bacteria or the authors and readers. In addition, various sampling techniques are discussed in particular, which pose a special challenge in manuscripts. The focus is on high-resolution, non-targeted strategies that can be used to extract the maximum amount of information about ancient objects. The combination of the various omics disciplines (panomics) especially offers potential added value in terms of the best possible interpretations of the data received. The information obtained can be used to understand the production of ancient artefacts, to gain impressions of former living conditions, to prove their authenticity, to assess whether there is a toxic hazard in handling the manuscripts, and to be able to determine appropriate measures for their conservation and restoration.

Review of recent advances on the use of mass spectrometry techniques for the study of organic materials in painted artworks

The study of painted artworks using scientific methods is fundamental for understanding the techniques used in their creation and their appropriate conservation. The ethical constraints involved in the handling of, and sampling from, these objects has steered recent developments in the field of Heritage science towards a range of new non-invasive/non-destructive spectroscopic techniques capable of providing important insights into their elemental or bulk chemical compositions. Due to the inherent complexities of heritage artefacts, however, their organic components are especially difficult to study in this way and their identification and degradation pathways are thus often best investigated using mass spectrometric (MS) techniques. The versatility, sensitivity and specificity of MS techniques are constantly increasing, with technological advances pushing the boundaries of their use in this field. The progress in the past ten years in the use of MS techniques for the analysis of paint media are described in the present review. While some historical context is included, the body of the review is structured around the five most widely used or emerging capabilities offered by MS. The first pertains to the use of spatially resolved MS to obtain chemical maps of components in cross-sections, which may yield information on both inorganic and organic materials, while the second area describes the development of novel sample preparation approaches for gas chromatography (GC)-MS to allow simultaneous analysis of a variety of components. The third focuses on thermally assisted analysis (either with direct MS or coupled with GC-MS), a powerful tool for studying macromolecules requiring zero (or minimal) sample pre-treatment. Subsequently, the use of soft ionisation techniques often combined with high-resolution MS for the study of peptides (proteomics) and other macromolecules (such as oligosaccharides and triglycerides) is outlined. The fifth area covers the advances in radiocarbon dating of painting components with accelerator MS (AMS). Lastly, future applications of other MS techniques to the study of paintings are mentioned; such as direct analysis in real time MS (DART-MS) and stable isotope ratio MS (IRMS). The latter, having proven its efficiency for the study of lipids in archaeological artefacts, is envisioned to become a valuable tool for this area, whereas DART-MS is already being utilised to study the surface composition of various museum objects. Rapid technological advances, resulting in increased sensitivity and selectivity of MS techniques, are opening up new approaches for paintings analysis, overcoming the fundamental hurdle of sample size available for destructive analysis. Importantly, while the last decade has seen proteomics applications come to the fore, this review aims to emphasise the wider potential of advanced MS techniques for the study of painting materials and their conservation.

Paleoproteomics

Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.

Meta-proteomic analysis of two mammoth's trunks by EVA technology and high-resolution mass spectrometry for an indirect picture of their habitat and the characterization of the collagen type I, alpha-1 and alpha-2 sequence

The recent paleoproteomic studies, including paleo-metaproteomic analyses, improved our understanding of the dietary of ancient populations, the characterization of past human diseases, the reconstruction of the habitat of ancient species, but also provided new insights into the phylogenetic relationships between extant and extinct species. In this respect, the present work reports the results of the metaproteomic analysis performed on the middle part of a trunk, and on the portion of a trunk tip tissue of two different woolly mammoths some 30,000 years old. In particular, proteins were extracted by applying EVA (Ethylene-Vinyl Acetate studded with hydrophilic and hydrophobic resins) films to the surface of these tissues belonging to two Mammuthus primigenus specimens, discovered in two regions located in the Russian Far East, and then investigated via a shotgun MS-based approach. This approach allowed to obtain two interesting results: (i) an indirect description of the habitat of these two mammoths, and (ii) an improved characterization of the collagen type I, alpha-1 and alpha-2 chains (col1a1 and col1a2). Sequence characterization of the col1a1 and col1a2 highlighted some differences between M. primigenius and other Proboscidea together with the identification of three (two for col1a1, and one for col1a2) potentially diagnostic amino acidic mutations that could be used to reliably distinguish the Mammuthus primigenius with respect to the other two genera of elephantids (i.e., Elephas and Loxodonta), and the extinct American mastodon (i.e., Mammut americanum). The results were validated through the level of deamidation and other diagenetic chemical modifications of the sample peptides, which were used to discriminate the "original" endogenous peptides from contaminant ones. The data have been deposited to the ProteomeXchange with identifier < PXD029558 > .

Proteomics and metabolomics composition of the ink of a letter in a fragment of a Dead Sea Scroll from Cave 11 (P1032-Fr0)

It is well established that the ink pigment used for writing the Dead Sea Scrolls (DSS) is mainly composed of carbon soot. The ink's binder however has yet to be securely identified. By applying EVA (ethylene vinyl acetate containing strong anion and cation exchangers admixed with C₈ and C₁₈) diskettes on one fragment and analyzing the captured material, the following study was able to determine the composition of the binder. Proteins admixed of plant proteins (ribulose biphosphate carboxylase, rhamnogalacturonate lyase, α-galactosidase A, calmodulin, among those identified) as well as of a few glycoproteins with different combinations of pentosyl and hexosyl units with plant acids (stearic, palmitic, oleic, linoleic and linolenic acids) and terpenes (triacontanol, catechin, lupeol) are mixed attributes of acacia trees which suggests the use of gum Arabic as the ink's binder. SIGNIFICANCE: Whereas a huge body of reports has explored any possible aspect of the Dead Sea Scrolls, including the dating and the animal origin of the parchment, one aspect had not been investigated so far, namely which kind of ligand had been adopted to ensure a firm binding of the ink (in reality carbon soot) to the supporting parchment. In the present investigation it has been demonstrated that this "glue" is a mixture of plant proteins, as well as a few glycoproteins, together with plant acids and terpenes. These proteins and metabolites belong to two species of trees, Vachellia nilotica and Acacia Albida, widespread in this Middle East region. The EVA methodology here adopted has shown that it is possible to explore any item pertaining to the world Cultural Heritage in the absence of damage or contamination thus permititng to analyze any possible precious document stored in museum, public libraries and private collections.

The books are alive with biological data: an introduction to the field of biocodicology and its implications for historical health sciences collections

Recent global events have underscored the need for broad access to digitized library special collections. At the same time, a burgeoning field of scientific and historical inquiry is finding a goldmine of data in the physical old books and manuscripts stored for centuries on library shelves. This article gives an overview of some of the interesting studies employing library materials in the new field of biocodicology, which expands the field of codicology (learning about book history through studying a copy's physical attributes, sometimes referred to as “archaeology of the book”) to interrogate physical books with proteomic, genomic, and microbiomic tools. Historical health sciences collections provide rich, new research avenues for budding biocodicologists, and biocodicology and other interdisciplinary fields focused on material culture present an unforeseen justification for institutions' continued preservation and access to individual physical copies.

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.

Paleoproteomic profiling of organic residues on prehistoric pottery from Malta

Mass spectrometry-based approaches have been successfully applied for identifying ancient proteins in bones and other tissues. On the contrary, there are relatively few examples of the successful recovery and identification of archeological protein residues from ceramic artifacts; this is because ceramics contain much lower levels of proteins which are extensively degraded by diagenetic effects. In this paper, we report the results of the characterization of proteins extracted from pottery of the Maltese site of Baħrija, the guide-site for the Baħrija period (half of 9th-second half of eighth century BCE), recently identified as the final part of the Borġ in-Nadur culture. Proteomic data here reported confirm that one of the major issue of these kind of studies is represented by contamination of animal and human agents that may complicate endogenous protein identification and authentication. The samples tested included a small group of ceramic forms, namely three tableware and six coarse ware thought to have been used in food preparation and/or storage. In this context, the limited availability of paleobotanical and archeozoological analyses may be compensated by the outcomes of the first proteomics profiling which, even if obtained on a limited selection of vessels, revealed the centrality of wheat in the diet of the ancient community of Baħrija. The data have been deposited to the ProteomeXchange with identifier < PXD022848 > .

New baits for fishing in cultural heritage's Mare Magnum

We describe here a modern tool for exploring documents pertaining to the world Cultural Heritage while avoiding their contamination or damage. Known under the acronym EVA, it consists of a plastic foil of Ethylene Vinyl Acetate studded with strong cation and anion resins admixed with C₈ and C₁₈ hydrophobic beads. When applied to any surface such foils can harvest any type of surface material, which is then eluted and analyzed via standard means, such as GS/MS (typically for metabolites), MS/MS (for peptide and protein analysis), X-ray (for elemental analysis). We briefly review here a number of past data, such as screening of original documents by Bulgakov, Chekov, Casanova, Kepler, while dealing in extenso with very recent data, pertaining to Orwell and Stalin and analysis of the skin of an Egyptian mummy. The technique was also successfully applied to paintings, such as the Donna Nuda at the Hermitage in St. Petersburg, attributed to Leonardo and his school. This novel methodology represents a formidable tool for exploring the past life of famous authors, scientist and literates in that it can detect traces of their pathologies and even drug consumption left by saliva and sweat traces on their original hand-written documents.

Stalin's "black dog": a postmortem diagnosis

Undoubtedly, the two leaders who were under enormous pressure during World War II (WWII) were Winston Churchill and Joseph Stalin' since their respective countries had to sustain most of the war weight, at least in Europe. Lord Moran recounted in his memoir Winston Churchill: The Struggle for Survival that he had diagnosed a middle-aged Churchill with bipolar disorder. Churchill himself often referred to his periods of intense and prolonged depression as his "black dog." On the contrary, not much is known about Stalin's mental conditions, although in 1927 the neurologist V. M. Bekhterev, the day prior to his sudden death, upon a long examination of the leader's mental status, declared that he had found him affected by paranoia. No chemical evidence via clinical chemistry analyses was provided for the two leaders, though. We have had access to the collection of books (stored in the Russian Government Archive of Social and Political History, RGASPI, of the former Institute of Marxism and Leninism under the Central Committee of the USSR Communist Party) that Stalin was reading during WWII, with pages containing personal annotations on the margins. Upon harvesting surface material via EVA disks (ethylene-vinyl acetate studded with strong cation and anion exchangers and C₈-C₁₈ resins) and instrumental analysis via X-ray photoelectron spectroscopy, we detected lithium levels (~ 100 ± 8 ng/cm²) compatible with those present in the sweat and/or saliva of patients treated with lithium salts for curing bipolarity and paranoia or probably gout. These data are the first clear indication that Stalin was under cure for this pathology.Graphical abstract.

EVA Technology and Proteomics: A Two-Pronged Attack on Cultural Heritage

A novel way for exploring the world's cultural heritage in the absence of damage or contamination (such as removing pigments in paintings or chipping away pieces of bones) of the items under investigation is here reported, called the EVA technique. It is based on films of ethylene vinyl acetate (EVA) impregnated with strong anion and cation exchangers, admixed with hydrophobic resins, C₈ and C₁₈. When in contact with any surface these films can harvest nanomoles of macromolecules (proteins and DNA) as well as metabolites, which can then be identified by standard instrumentation. Some important applications are reported, such as the findings of the renal pathology and assumption of morphine in the original manuscript of Master I Margarita by Bulgakov, the presence of TBC bacterium in Chekhov's shirt and in a letter by Orwell, the Y. pestis and anthrax bacteria in the death registries of Milan's lazaretto in the 1630 plague bout, as well as ample traces of five metals in Kepler's manuscripts, suggesting his potential practice of alchemy. Also, in the pages of the Memoirs of Casanova, although the gonorrhea bacterium could not be found, spots of HgS could be measured, suggesting its use for curing the disease. A family of EVA films is described, enlarging its use to dedicated applications, such as the capture of drugs of abuse in the pages of famous writers and even in the paintings of fauvists. It is hoped that the present methodology could open the doors of museums, state archives, and private collections for detecting biological traces left by artists, literates, and men of culture in their masterpieces.

"1984": What Orwell could not predict. Proteomic analysis of his scripts

George Orwell, fighter for the Republican Army during the Spanish Civil War, was shot through the throat by a sniper on 20th May 1937 and nearly killed. After receiving only a summary external treatment, on the 29th, he was cured in a Barcelona hospital where he was infected by the Koch bacillus. After fleeing from Spain on 23rd June 1937, he repaired to his cottage in Wallington, Hertfordshire, wherefrom he wrote a letter to Sergey Dynamov, Editor of Soviet journal "Foreign Literature." This typewritten letter was analyzed by application of five EVA strips (ethylene vinyl acetate studded with strong cation and anion and with C₈ and C₁₈ resins; four on the corners and one over his signature), searching for biological traces. Upon elution of the captured biologicals, trypsin digestion and Orbitrap Fusion trihybrid mass spectrometer analyses, three of the five strips yielded clear traces of six unique proteins (via proteotypic peptides) of the tuberculosis bacterium. Additionally, MALDI TOF analysis of saliva of a tuberculosis patient and the EVA strip eluates gave a spectrum of 14 peptide bands (Mr 2700 to 6700 Da range) coincident between the two samples, thus, fully confirming Orwell's pathology. These results are attributed to saliva traces on Orwell's fingertips and to the fact that the letter was written on 2nd July 1937, when Orwell's pathology was at its peak.