Novel contribution on the diagenetic physicochemical features of bone and teeth minerals, as substrates for ancient DNA typing

Historic and Prehistoric Epidemics: An Overview of Sources Available for the Study of Ancient Pathogens

Since life on earth developed, parasitic microbes have thrived. Increases in host numbers, or the conquest of a new species, provide an opportunity for such a pathogen to enjoy, before host defense systems kick in, a similar upsurge in reproduction. Outbreaks, caused by "endemic" pathogens, and epidemics, caused by "novel" pathogens, have thus been creating chaos and destruction since prehistorical times. To study such (pre)historic epidemics, recent advances in the ancient DNA field, applied to both archeological and historical remains, have helped tremendously to elucidate the evolutionary trajectory of pathogens. These studies have offered new and unexpected insights into the evolution of, for instance, smallpox virus, hepatitis B virus, and the plague-causing bacterium Yersinia pestis. Furthermore, burial patterns and historical publications can help in tracking down ancient pathogens. Another source of information is our genome, where selective sweeps in immune-related genes relate to past pathogen attacks, while multiple viruses have left their genomes behind for us to study. This review will discuss the sources available to investigate (pre)historic diseases, as molecular knowledge of historic and prehistoric pathogens may help us understand the past and the present, and prepare us for future epidemics.

Raman Spectra and Ancient Life: Vibrational ID Profiles of Fossilized (Bone) Tissues

Raman micro-spectroscopy is a non-destructive and non-contact analytical technique that combines microscopy and spectroscopy, thus providing a potential for non-invasive and in situ molecular identification, even over heterogeneous and rare samples such as fossilized tissues. Recently, chemical imaging techniques have become an increasingly popular tool for characterizing trace elements, isotopic information, and organic markers in fossils. Raman spectroscopy also shows a growing potential in understanding bone microstructure, chemical composition, and mineral assemblance affected by diagenetic processes. In our lab, we have investigated a wide range of different fossil tissues, mainly of Mesozoic vertebrates (from Jurassic through Cretaceous). Besides standard spectra of sedimentary rocks, including pigment contamination, our Raman spectra also exhibit interesting spectral features in the 1200–1800 cm⁻¹ spectral range, where Raman bands of proteins, nucleic acids, and other organic molecules can be identified. In the present study, we discuss both a possible origin of the observed bands of ancient organic residues and difficulties with definition of the specific spectral markers in fossilized soft and hard tissues.

Technical Note: Post-burial alteration of bones: Quantitative characterization with solid-state 1H MAS NMR

The identification of markers of the modifications occurring in human bones after death and of the sedimentary and post-sedimentary processes affecting their state of preservation, is of interest for several scientific disciplines. A new index, obtained from spectral deconvolution of the 1H MAS NMR spectra of bones, relating the number of organic protons to the amount of hydrogen nuclei in the OH- groups of bioapatite, is proposed as indicator of the state of preservation of the organic fraction. In the osteological material from three different archaeological sites, this index resulted positively correlated with the extent of collagen loss derived from infrared spectroscopy. Its sensitivity to changes in the physical and chemical characteristics of bone allows to identify distinct diagenetic pathways specific to each site and to distinguish different trajectories within the same site.

Application of ATR-FTIR spectroscopy and chemometrics for the discrimination of human bone remains from different archaeological sites in Turkey

Examining diagenetic parameters such as the organic carbonate contents and the crystallinity of bone apatite quantify the post-mortem alteration of bone. Burial conditions are one of the factors that can influence the diagenesis process. We studied the changes to the organic and mineral components and crystallinity of human bone remains from five Medieval sites in Turkey: Hakemi Use, Komana, İznik, Oluz Höyük and Tasmasor using Attenuated Total Reflectance Fourier Transform Infrared spectroscopy (ATR-FTIR) and principal component analysis (PCA). Analysis of spectral band ratios related to organic and mineral components of bone demonstrated differences in the molecular content in the skeletal remains from the five sites. In order to examine the degree of carbonation of a phosphate matrix, curve-fitting procedures were applied to the carbonate band. We found that the infrared crystallinity index appears to not be sensitive to carbonate content at room temperature for the bone remains studied here. The recrystallization process in bone remains behaved differently among the archaeological sites. The results demonstrate that the burial environments differently affect the organic and mineral components of archaeological bone remains.

A protocol for using attenuated total reflection Fourier-transform infrared spectroscopy for pre-screening ancient bone collagen prior to radiocarbon dating

RATIONALE

Pre-screening of bone collagen quality is important to reduce the cost for analyses such as radiocarbon (¹⁴ C) dating with accelerator mass spectrometry in archaeological studies. We developed a pre-screening protocol based on attenuated total reflection (ATR) Fourier-transform infrared spectroscopy (FTIR) for assessing the chemical composition and mineralogy of ancient bone samples.

METHODS

ATR-FTIR measurements were performed on bulk bones of diverse origin and age before collagen extraction. The percentage nitrogen of bulk bones, as well as the weight percentage, and the percentage carbon and nitrogen of extracted organic matter were noted. Several machine learning algorithms were applied to the spectral data and compared for their efficacy in screening for well preserved collagen.

RESULTS

The results showed that (a) the first derivative of the spectral data was better suited to screening than the raw FTIR data, especially for a wider spectral range and (b) certain classification algorithms [e.g. gradient boosting machine (GBM)] were able to efficiently predict the degree of preservation in bone samples.

CONCLUSIONS

This pre-screening protocol can serve as a fast, concise and inexpensive pre-screening tool for determining relative degrees of preservation before collagen extraction and subsequent ¹⁴ C dating. The screening power based on the machine learning techniques can be further improved by accumulating the FTIR spectral data of bones.

The petrous bone: Ideal substrate in legal medicine?

Over the last few years, palaeogenomic studies of the petrous bone (the densest part of the temporal bone) have shown that it is a source of DNA in both larger quantities and of better quality than other bones. This dense bone around the otic capsule has therefore been called the choice substrate in palaeogenomics. Because the practice of forensic genetics responds to different imperatives, we implemented a study aimed at (i) understanding how and why the petrous bone is an advantageous substrate in ancient DNA studies and (ii) establishing whether it is advantageous in forensic STR typing. We selected 50 individual skeletal remains and extracted DNA from one tooth and one petrous bone from each. We then amplified 24 STR markers commonly used in forensic identification and compared the quality of that amplification using the RFU intensities of the signal as read on the STR profiles. We also performed histological analyses to compare (i) the microscopic structure of a petrous bone and of a tooth and (ii) the microscopic structure of fresh petrous bone and of an archaeological or forensic sample. We show that the RFU intensities read on STR profiles are systematically higher in experiments using DNA extracted from petrous bones rather than teeth. For this reason, we were more likely to obtain a complete STR profile from petrous bone material, increasing the chance of identification in a forensic setting. Histological analyses revealed peculiar microstructural characteristics (tissue organization), unique to the petrous bone, that might explain the good preservation of DNA in that substrate. Therefore, it appears that despite the necessity of analysing longer fragments in forensic STR typing compared to NGS palaeogenomics, the use of petrous bones in forensic genetics could prove valuable, especially in cases involving infants, toothless individuals or very degraded skeletal remains.

First successful stabilization of consolidated amorphous calcium phosphate (ACP) by cold sintering: toward highly-resorbable reactive bioceramics

An adequate tuning of amorphous calcium phosphates ionic composition and cold sintering conditions allowed the first successful stabilization of these bioactive compounds. These results show promise for the setup of highly-resorbable bone substitutes.

A soft environmental control effect of apatite doped with mineral traces in the fowl droppings

Fowl-dropping apatite (Ca10-z[PO4]6-z[OH]2-z) synthesized from carbonized, incinerated fowl droppings contains PO4 and OH groups that are partially substituted by CO32- ions. It shows stronger ion conductivity than commercially available hydroxyapatite in a wide range of temperatures from 23°C to 800°C. Fowl-dropping apatite readily adsorbs NO2 and SO2 gases and, without re-releasing these gases, slowly decomposes them at room temperature under sunlight via ultraviolet-visible (UV-Vis) irradiation. A limited amount of minerals and organics contained in fowl droppings causes light-induced activities in fowl-dropping apatite with a crystal structure that has a developed c face; this initiates excitation-induced atomic transfer on the solid surface derived from PO4 exposed on the c face, which then advances the decomposition reaction.

Sources of Materials for Paleomicrobiology

The Paleomicrobiology establishes the diagnosis of ancient infectious diseases by studying ancient pathogens. This recent science also analyzes the evolution of these pathogens, virulence, and their adaptation to their habitat and their vectors. The DNA persists a long time after the death of an organism despite the chemical and enzymatic degradation. The possibility of sequencing bacterial, viral, parasitic and archaeal DNA molecules persists over time.Various sources are used for these studies: frozen tissue and particularly human tissue are a exceptional source for the analysis because at very low temperatures, all biological activity is suspended. The coprolites are a source of choice for studying the human microbiome. Other sources, the ancient bones are the most abundant, however, they may contain only small amounts of DNA due to natural leaching. When the use of the tooth is possible, is a particularly interesting source because of its highly mineralized structure, which gives greater persistence than bone. The calcified tartar deposited on teeth is a source of interest for the study of oral microbiome.All these sources are subject to precautions (gloves and masks hat) at the time of sampling to avoid cross contamination and also be listed in the most precise way because they are precious and rare.

Nail Damage (Severe Onychodystrophy) Induced by Acrylate Glue: Scanning Electron Microscopy and Energy Dispersive X-Ray Investigations

BACKGROUND

Scanning electron microscopy (SEM) and energy dispersive X-ray (EDX) techniques have been used in various fields of medical research, including different pathologies of the nails; however, no studies have focused on obtaining high-resolution microscopic images and elemental analysis of disorders caused by synthetic nails and acrylic adhesives.

METHODS

Damaged/injured fingernails caused by the use of acrylate glue and synthetic nails were investigated using SEM and EDX methods.

RESULTS

SEM and EDX proved that synthetic nails, acrylic glue, and nails damaged by contact with acrylate glue have a different morphology and different composition compared to healthy human nails.

CONCLUSIONS

SEM and EDX analysis can give useful information about the aspects of topography (surface sample), morphology (shape and size), hardness or reflectivity, and the elemental composition of nails.

Adsorption of nucleotides on biomimetic apatite: The case of cytidine 5' monophosphate (CMP)

The chemical interaction between DNA macromolecules and hard tissues in vertebrate is of foremost importance in paleogenetics, as bones and teeth represent a major substrate for the genetic material after cell death. Recently, the empirical hypothesis of DNA "protection" over time thanks to its adsorption on hard tissues was revisited from a physico-chemical viewpoint. In particular, the existence of a strong interaction between phosphate groups of DNA backbone and the surface of apatite nanocrystals (mimicking bone/dentin mineral) was evidenced on an experimental basis. In the field of nanomedicine, DNA or RNA can be used for gene transport into cells, and apatite nanocarriers then appear promising. In order to shed some more light on interactions between DNA molecules and apatite, the present study focuses on the adsorption of a "model" nucleotide, cytidine 5' monophosphate (CMP), on a carbonated biomimetic apatite sample. The follow-up of CMP kinetics of adsorption pointed out the rapidity of interaction with stabilization reached within few minutes. The adsorption isotherm could be realistically fitted to the Sips model (Langmuir-Freundlich) suggesting the influence of surface heterogeneities and adsorption cooperativity in the adsorption process. The desorption study pointed out the reversible character of CMP adsorption on biomimetic apatite. This contribution is intended to prove helpful in view of better apprehending the molecular interaction of DNA fragments and apatite compounds, independently of the application domain, such as bone diagenesis or nanomedicine. This study may also appear informative for researchers interested in the origins of life on Earth and the occurrence and behavior of primitive biomolecules.