Diagenesis, not biogenesis: Two late Roman skeletal examples

Using portable X-ray fluorescence elemental analysis to explore porous skeletal lesions: Interplay of sex, age at death, and cause of death

OBJECTIVES

Search for possible associations between bone elemental concentration and the presence of porous skeletal lesions (PSLs), considering the sex, age, and cause of death (COD) of the individuals.

MATERIALS AND METHODS

The sample comprised 107 non-adult individuals (56 females, 51 males) aged 0-20 (x̄ = 13.2, SD = 5.8) from the Coimbra and Lisbon Identified Skeletal Collections. Cribra cranii, orbitalia, humeralis, and femoralis were recorded as present/absent, and elemental concentrations were assessed by portable x-ray fluorescence (pXRF). A multivariate statistical approach was applied.

RESULTS

Well-preserved skeletons with minimal diagenesis showed no sex-related elemental variations or PSL associations. In contrast, age-at-death correlated with elevated Ca, P, Sr, and Pb levels. Cribra cranii increased with age while other cribra declined post-adolescence. Higher concentrations of Fe and lower of S were linked to cribra cranii. Respiratory infections as COD increased the odds of expressing cribra femoralis (OR = 5.25, CI = 1.25-15.14), cribra cranii (OR = 2.91, CI = 0.97-8.69), and cribra orbitalia (OR = 2.76, CI = 1.06-7.24).

DISCUSSION

Feasible pXRF results and low cribra intraobserver error assure replicability. Elevated Ca, P, and Sr in older individuals may relate to skeletal growth, while increased Pb suggests bioaccumulation. Cribra's increase with age reflects different rates of marrow conversion and bone remodeling. Higher Fe and lower S in individuals with cribra cranii possibly reflects poor nutrition, early alcohol use, and sideroblastic anemia, aligning with 19th-20th-century Portugal's living conditions. Respiratory infections increased cribra expression, revealing intricate interplays among inflammation, anemia(s), marrow expansion, and diet. This research highlights a complex scenario and blazes a new path for cribra interpretation.

The mysteries of DNA preservation in bone: A comparative study of petrous bones and metacarpal epiphyses using ATR-FTIR spectroscopy

A comparative analysis of 26 petrous bones and epiphyses of metacarpals from the Second World War era revealed no significant differences in DNA yield or success in STR typing. This unexpected parity in DNA preservation between the petrous bone, a renowned source of endogenous DNA in skeletal remains, and the epiphyses of metacarpals, which are porous and susceptible to taphonomic changes, is surprising. In this study, we introduced ATR-FTIR spectroscopy as an approach to unravel the correlation between bone molecular structure and DNA preservation. Metacarpals and petrous bones with same taphonomic history were sampled and prepared for DNA analyses. While one portion of the sample was used for DNA analysis, the other underwent ATR-FTIR spectroscopic examination. The normalized spectra and FTIR indices between the epiphyses of metacarpals and petrous bones were compared. Because the taphonomic history of the remains used is relatively short and stable, the ATR-FTIR spectroscopy unveiled subtle structural differences between the two bone types. Petrous bones exhibited higher mineralization, whereas epiphyses contained more organic matter. The unexpected preservation of DNA in the epiphyses of metacarpals can likely be attributed to the presence of soft tissue remnants within the trabeculae. Here observed differences in the molecular structure of bones indicate there are different mechanisms enabling DNA preservation in skeletal tissues.

The Role of Fe, S, P, Ca, and Sr in Porous Skeletal Lesions: A Study on Non-adult Individuals Using pXRF

Portable X-ray fluorescence is a new tool in the study of human bone. This research aims to investigate if variations in bone elemental concentrations are related with porous skeletal lesions (PSLs). One hundred well-preserved non-adult skeletons aged 0-11 years were selected from the archaeological site Convent of São Domingos, Lisbon (18th-19th century). Measuring a standard reference material and calculating the technical error of measurement assured elemental data reliability. Moreover, measuring soil samples excluded possible contamination of bones with elements from the soil, except for Pb. Additionally, the Ca/P ratio indicates maintenance of bone integrity. Cribra cranii, orbitalia, humeralis, and femoralis were recorded as present/absent, and the estimated intra-/inter-observer errors were low. The multivariate analysis found higher odds of having cribra orbitalia (OR = 1.76; CI = 0.97-3.20) and cribra femoralis (OR = 1.42; CI = 0.73-2.74) in individuals with lower Fe and higher S. Furthermore, higher levels of P, Ca, and Sr increased the odds of individuals developing cribra femoralis (OR = 2.30; CI = 1.23-4.29). Age also correlated with increased odds of exhibiting cribra orbitalia (OR = 1.86; CI = 0.94-3.68), cribra femoralis (OR = 6.97; CI = 2.78-17.45), and cribra humeralis (OR = 8.32; CI = 2.71-25.60). These findings suggest a shared etiology for these three cribras, contrasting with the higher Fe levels in individuals with cribra cranii. Lower Fe and higher S levels in individuals with cribra suggest a complex etiology, possibly involving conditions like megaloblastic or chronic disease anemia(s). Age-related elemental changes support the hypothesis that age influences cribra frequencies. This study highlights PSL complexity and opens new avenues for research.

Elemental analysis using portable X-ray fluorescence: Guidelines for the study of dry human bone

OBJECTIVE

X-ray fluorescence (XRF) is a non-destructive technique that measures the elemental concentration of different materials, including human bone. Recently, it began to be applied to paleopathological studies due to the development of portable devices and their relative ease of use. However, the lack of uniform procedures hampers comparability and reproducibility. This paper aims to provide guidelines for an efficient and standardized evaluation of bone elemental composition with a portable XRF (pXRF) device.

MATERIALS

This technical note is based on the application of the Thermo Scientific Niton XL3t 900 GOLDD+.

METHODS

This work includes suggestions for the choice and preparation of human bone samples, both from archaeological context and documented collections, and methodological procedures in pXRF setup, such as choice of calibration, assessment of accuracy, and analysis run time. Additionally, recommendations for data validation and statistical analysis are also included.

CONCLUSIONS

This technique has great potential in paleopathology since bone chemical variations may be associated with different pathological conditions, environmental contamination (e.g., lead), and/or administered treatments, such as mercury. Following an expected increase in the number of studies, it is essential to establish good practices that allow results from different researchers to be comparable.

SIGNIFICANCE

X-ray fluorescence is a non-destructive technique that measures small concentrations (ppm) of elements from magnesium (12Mg) through bismuth (83Bi).

LIMITATIONS

pXRF does not detect elements lighter than Mg, and its lower energy excitation penetrates less than other techniques.

SUGGESTIONS FOR FURTHER RESEARCH

Other research groups should test these guidelines and comment on their usefulness and replicability.

Recognition of the Presence of Bone Fractures Through Physicochemical Changes in Diagenetic Bone

Much research has focused on attempting to understand the drivers of bone diagenesis. However, this sensitive process is easily influenced by various factors, particularly the condition of the remains (i.e., whether they have been subjected to trauma). Previous research demonstrates that trauma can influence soft tissue decomposition, yet to date, no studies have looked at how bone fractures could affect bone diagenesis. To address this gap, two short timescale studies were conducted to investigate the influence of bone fractures on the physicochemical composition of disarticulated, partially fleshed animal remains. Disarticulated porcine bones were either fractured using blunt force or sharp force whilst fresh (producing perimortem damage), at 60 days producing postmortem damage (postmortem interval (PMI)), or left intact and left outside for up to 180 days post-fracture/240 days PMI. Retrieved bone sections were then analyzed for physicochemical differences using non-destructive methods, i.e., scanning electron microscopy energy dispersive spectroscopy and Fourier transform infrared spectroscopy with attenuated total reflectance. It was hypothesized that differences would be found in the physicochemical composition between the bones with fractures and those without after undergoing diagenetic change. The bone fractures significantly affected the elemental composition of bone over time, but structural composition initially remained stable. It was also possible to distinguish between perimortem and postmortem fractures using these two analytical techniques due to physicochemical differences. This research shows bone fractures can significantly alter the physicochemical composition of the bone during the postmortem period and have the potential to facilitate more accurate PMI estimations in forensic contexts.

Genetic sexing of subadult skeletal remains

When subadult skeletons need to be identified, biological sex diagnosis is one of the first steps in the identification process. Sex assessment of subadults using morphological features is unreliable, and molecular genetic methods were applied in this study. Eighty-three ancient skeletons were used as models for poorly preserved DNA. Three sex-informative markers on the Y and X chromosome were used for sex identification: a qPCR test using the PowerQuant Y target included in PowerQuant System (Promega), the amelogenin test included in ESI 17 Fast STR kit (Promega), and a Y-STR amplification test using the PowerPlex Y-23 kit (Promega). Sex was successfully determined in all but five skeletons. Successful PowerQuant Y-target, Y-amelogenin, and Y-chromosomal STR amplifications proved the presence of male DNA in 35 skeletons, and in 43 subadults female sex was established. No match was found between the genetic profiles of subadult skeletons, and the elimination database and negative control samples produced no profiles, indicating no contamination issue. Our study shows that genetic sex identification is a very successful approach for biological sexing of subadult skeletons whose sex cannot be assessed by anthropological methods. The results of this study are applicable for badly preserved subadult skeletons from routine forensic casework.

Comparison of DNA preservation and ATR-FTIR spectroscopy indices of cortical and trabecular bone of metacarpals and metatarsals

Shape, size, composition, and function of the bones in the human body vary on the macro, micro and nanoscale. This can influence changes caused by taphonomy and post-mortem preservation, including DNA. Highly mineralised compact bone is less susceptible to taphonomic factors than porous trabecular bone. Some studies imply that DNA can be better preserved in trabecular bone, due to remnants of the soft tissue or bacteria better digesting organic matter while not digesting DNA. The aim of this study was to understand the differences between compact (diaphyses) and trabecular (epiphyses) bone on a molecular level and thus the reasons for the better preservation of the DNA in the trabecular bone. The powder obtained from epiphyses and diaphyses of metacarpals and metatarsals was analysed using ATR-FTIR spectroscopy and compared. Samples with poorest DNA preservation originated from diaphyses, predominantly of metatarsals. They were characterised by higher concentrations of phosphates and crystallinity, while lower collagen quality in comparison to samples with the best DNA preservation. Epiphyses presented higher concentrations of better-preserved collagen while diaphyses had higher concentrations of carbonates and phosphates and higher crystallinity. Due to better-preserved collagen in the epiphyses, the soft tissue remnants hypothesis seems more likely than the bacteria hypothesis.

Eye and hair color prediction of an early medieval adult and subadult skeleton using massive parallel sequencing technology

Phenotypic trait prediction in ancient DNA analysis can provide information about the external appearance of individuals from past human populations. Some studies predicting eye and hair color in ancient adult skeletons have been published, but not for ancient subadult skeletons, which are more prone to decay. In this study, eye and hair color were predicted for an early medieval adult skeleton and a subadult skeleton that was anthropologically characterized as a middle-aged man and a subadult of unknown sex about 6 years old. When processing the petrous bones, precautions were taken to prevent contamination with modern DNA. The MillMix tissue homogenizer was used for grinding, 0.5 g of bone powder was decalcified, and DNA was purified in Biorobot EZ1. The PowerQuant System was used for quantification and a customized version of the HIrisPlex panel for massive parallel sequencing (MPS) analysis. Library preparation and templating were performed on the HID Ion Chef Instrument and sequencing on the Ion GeneStudio S5 System. Up to 21 ng DNA/g of powder was obtained from ancient petrous bones. Clean negative controls and no matches with elimination database profiles confirmed no contamination issue. Brown eyes and dark brown or black hair were predicted for the adult skeleton and blue eyes and brown or dark brown hair for the subadult skeleton. The MPS analysis results obtained proved that it is possible to predict hair and eye color not only for an adult from the Early Middle Ages, but also for a subadult skeleton dating to this period.

Comparison of DNA preservation between adult and non-adult ancient skeletons

Studies evaluating DNA preservation in non-adults, or comparing preservation in adults and non-adults, are very rare. This study compares the preservation of DNA in the skeletal remains of adults and non-adults. It compares the quality and quantity of DNA recovered from different skeletal elements of adults and non-adults, and from non-adults of different age classes. In addition, the preservation of DNA in males and females is compared. Bone DNA preservation was estimated by measuring nuclear DNA concentration and its degradation, and through STR typing success. The study analyzed 29 adult skeletons and 23 non-adult skeletons from the Ljubljana-Polje archeological site, dating from the seventeenth to nineteenth century, and up to four skeletal elements (petrous bone, femur, calcaneus, and talus) were included. After full demineralization extraction, the PowerQuant System and the PowerPlex ESI 17 Fast System (Promega) were used for qPCR and STR typing, respectively. The results showed that, among the four bone types analyzed, only the petrous bone proved to be a suitable source of DNA for STR typing of non-adult skeletal remains, and DNA yield is even higher than in the adult petrous bone, which can be attributed to the higher DNA degradation observed in the adult petrous bone. In adult skeletons, petrous bones and tali produced high STR amplification success and low DNA yield was observed in adult femurs. The results of this study are applicable for the sampling strategy in routine forensic genetics cases for solving identification cases, including badly preserved non-adult and also adult skeletons.

Differential diagnosis of a diffuse sclerosis in an identified male skull (early 20th century Coimbra, Portugal): A multimethodological approach for the identification of osteosclerotic dysplasias in skeletonized individuals

OBJECTIVE

This work aims to discuss the difficulties in diagnosing osteosclerotic changes in skeletonized individuals and to raise awareness of osteosclerotic dysplasias as a group of rare ancient diseases.

MATERIALS

The skull of a 62-year-old male individual from the International Exchange Skull Collection, curated by the University of Coimbra, who died in 1928 presenting albuminous nephritis (Bright disease)/uraemia as the registered cause of death.

METHODS

The skull was macroscopically and radiologically examined and bone elemental analysis was investigated. The genealogy and medical records of the individual were also searched.

RESULTS

The lesions are in accordance with an osteosclerotic process possibly pointing to osteosclerosis, osteosclerotic metaphyseal dysplasia, or dysosteosclerosis, but osteoclasia with hyperphosphatasia, endosteal hyperostosis, sclerosteosis, or osteopathia striata with cranial sclerosis cannot be ruled out.

CONCLUSIONS

Representativeness of the skeleton is a crucial feature in diagnosing rare diseases and, to avoid a misdiagnosis, the final diagnosis should include a group of diseases rather than a definite disease.

SIGNIFICANCE

Difficulties in diagnosing rare diseases are discussed and best approaches in the study osteosclerotic dysplasias in skeletonized individuals are offered in the light of current clinical knowledge.

LIMITATIONS

The absence of the postcranial skeleton and of pathognomonic lesions associated with osteosclerotic dysplasias limits diagnosis. Although rare diseases often have a genetic basis, specific genetic testing for the diagnosis of rare diseases in paleopathological cases are not yet available.

SUGGESTIONS FOR FURTHER RESEARCH

Future genetic studies might help narrow down the diagnosis.

Metals in bones of the middle-aged inhabitants of Sardinia island (Italy) to assess nutrition and environmental exposure

Metals in bones of 72 subjects lived between the twelfth and eighteenth century AC and collected in four Sardinian (Italian insular region) burial sites (Alghero, Bisarcio, Geridu, and Sassari) were determined and used as biomarkers to evaluate diet and potential social-environmental differences. Concentrations of Ba, Ca, Cd, Cu, Hg, Pb, Sr, and Zn were quantified in different types of compact bone (femur, fibula, humerus, radius, tibia, ulna) by sector field inductively coupled plasma mass spectrometry previous acidic digestion and differences among the various burial sites, centuries, types of bone, gender, and age were explored by univariate and multivariate analyses. Results indicated differences between sites in terms of diet: Bisarcio (inland village) had increased ratios of Ba/Ca and Zn/Ca due to higher incidence of vegetables, cereals, and animal foods in the diet; Geridu (coastal village) showed increased Sr/Ca ratio indicating foods of plant and marine origin that were predominant; Alghero (coastal site) and Sassari (inland site) displayed prevalently a mixed diet reflecting a higher economy and food imports. In addition, these latter sites showed increased levels of Hg/Ca (fish, drugs, cosmetics) and Pb/Ca (coins, utensils, pipeline for water). In conclusion, the elemental Ba/Ca, Sr/Ca, and Zn/Ca ratios were indicative of provenance and diet, while Hg/Ca and Pb/Ca ratios were associated to various forms of environmental exposure.

Reconstructing Ancient Egyptian Diet through Bone Elemental Analysis Using LIBS (Qubbet el Hawa Cemetery)

One of the most important advantages of LIBS that make it suitable for the analysis of archeological materials is that it is a quasi-nondestructive technique. Archeological mandibles excavated from Qubbet el Hawa Cemetery, Aswan, were subjected to elemental analysis in order to reconstruct the dietary patterns of the middle class of the Aswan population throughout three successive eras: the First Intermediate Period (FIP), the Middle Kingdom (MK), and the Second Intermediate Period (SIP). The bone Sr/Ca and Ba/Ca ratios were significantly correlated, so the Sr/Ca ratios are considered to represent the ante-mortem values. It was suggested that the significantly low FIP Sr/Ca compared to that of both the MK and the SIP was attributed to the consumption of unusual sorts of food and imported cereals during years of famine, while the MK Sr/Ca was considered to represent the amelioration of climatic, social, economic, and political conditions in this era of state socialism. The SIP Sr/Ca, which is nearly the same as that of the MK, was considered to be the reflection of the continuity of the individualism respect and state socialism and a reflection of agriculture conditions amelioration under the reign of the 17th Dynasty in Upper Egypt.

Human brains found in a fire-affected 4000-years old Bronze Age tumulus layer rich in soil alkalines and boron in Kutahya, Western Anatolia

Undecomposed human bodies and organs always attracted interest in terms of understanding biological tissue stability and immortality. Amongst these, cases of natural mummification found in glaciers, bog sediments and deserts caused even more attention. In 2010, an archeological excavation of a Bronze Age layer in a tumulus near the Western Anatolia city Kütahya revealed fire affected regions with burnt human skeletons and charred wooden objects. Inside of the cracked skulls, undecomposed brains were discernible. To analyze the burial taphonomy of the rare phenomenon of brain preservation, we analyzed brains, bone, teeth and surrounding soils elements using Inductively Coupled Plasma-Mass Spectrometer (ICP-MS). Adipocere formation or saponification of postmortem tissue fat requires high levels of alkalinity and especially potassium. Indeed, ICP-MS analysis of the brain, teeth and bone and also of the surrounding soil revealed high levels of potassium, magnesium, aluminum and boron, which are compatible with the famous role of Kütahya in tile production with its soil containing high level of alkalines and tile-glazing boron. Fatty acid chromatography revealed simultaneous saturation of fats and protection of fragile unsaturated fatty acids consistent with soil-presence of both pro-oxidant and anti-oxidant trace metals. Computerized tomography revealed protection of diencephalic, metencephalic and occipital tissue in one of the best-preserved specimens. Boron was previously found as an intentional preservative of Tutankhamen and Deir el Bahari mummies. Here, in natural soil with its insect-repellant, anti-bacterial and fire-resistance qualities it may be a factor to preserve heat-affected brains as almost bioporcellain specimens.

Dating human skeletal remains using a radiometric method: biogenic versus diagenetic 90Sr and 210Pb in vertebrae

In forensic science, there is a strong interest in determining the post-mortem interval (PMI) of human skeletal remains up to 50 years after death. Currently, there are no reliable methods to resolve PMI, the determination of which relies almost exclusively on the experience of the investigating expert. Here we measured (90)Sr and (210)Pb ((210)Po) incorporated into bones through a biogenic process as indicators of the time elapsed since death. We hypothesised that the activity of radionuclides incorporated into trabecular bone will more accurately match the activity in the environment and the food chain at the time of death than the activity in cortical bone because of a higher remodelling rate. We found that determining (90)Sr can yield reliable PMI estimates as long as a calibration curve exists for (90)Sr covering the studied area and the last 50 years. We also found that adding the activity of (210)Po, a proxy for naturally occurring (210)Pb incorporated through ingestion, to the (90)Sr dating increases the reliability of the PMI value. Our results also show that trabecular bone is subject to both (90)Sr and (210)Po diagenesis. Accordingly, we used a solubility profile method to determine the biogenic radionuclide only, and we are proposing a new method of bone decontamination to be used prior to (90)Sr and (210)Pb dating.

An assessment of natural concentrations of selected metals in the bone tissues of the femur head

The study was aimed at assessing the natural concentrations of copper, iron, potassium, lead and cadmium in the femur head using regression analysis. The material was collected during the operation of total hip arthroplasty from patients of southern and central Poland suffering from diagnosed coxarthrosis. In total, 197 samples were collected, including 68 samples of spongious bone, 59 samples of cortical bone and 70 samples of cartilage surface. After wet microwave digestion, the metal content in the samples was measured by atomic absorption spectrophotometry. The average concentrations of metals in the femur head were 67.30 microgFe/g, 760.58 microgK/g, 0.07 microgCd/g, 0.81 microgCu/g and 2.76 microgPb/g. A comparison of metal concentrations in bone tissues assessed by regression analysis to the findings of other authors revealed that the technique can be used to assess the natural concentration of elements in tissues and the results may provide a basis for the evaluation of metal concentrations in the human organism.