Evaluating differential nuclear DNA yield rates and osteocyte numbers among human bone tissue types: A synchrotron radiation micro-CT approach

DNA preservation in compact and trabecular bone

Significant variation exists in the molecular structure of compact and trabecular bone. In compact bone full dissolution of the bone powder is required to efficiently release the DNA from hydroxyapatite. In trabecular bone where soft tissues are preserved, we assume that full dissolution of the bone powder is not required to release the DNA from collagen. To investigate this issue, research was performed on 45 Second World War diaphysis (compact bone)-epiphysis (trabecular bone) femur pairs, each processed with a full dissolution (FD) and partial dissolution (PD) extraction method. DNA quality and quantity were assessed using qPCR PowerQuant analyses, and autosomal STRs were typed to confirm the authenticity of isolated DNA. Our results support different mechanisms of DNA preservation in compact and trabecular bone because FD method was more efficient than PD method only in compact bone, and no difference in DNA yield was observed in trabecular bone, showing no need for full dissolution of the bone powder when trabecular bone tissue is processed. In addition, a significant difference in DNA yield was observed between compact and trabecular bone when PD was applied, with more DNA extracted from trabecular bone than compact bone. High suitability of trabecular bone processed with PD method is also supported by the similar quantities of DNA isolated by FD method when applied to both compact and trabecular bone. Additionally similar quantities of DNA were isolated when compact bone was extracted with FD method and trabecular bone was extracted with PD method. Processing trabecular bone with PD method in routine identification of skeletonized human remains shortens the extraction procedure and simplifies the grinding process.

An optimal skeletal element for DNA testing: Evaluation of DNA quantity and quality from various bone types in routine forensic practice

For human identification, the quality and quantity of DNA must be sufficient for amplification and analysis. When DNA extraction from bone tissues and teeth is required, the optimal skeletal elements should be selected as samples for DNA extraction because DNA yield differs among elements. Recently, some studies have reported that a high quantity of high-quality DNA can be extracted from the small cancellous bones of the hands and feet. In this study, we evaluated the effectiveness of small cancellous bones in the human identification of skeletal remains in routine forensic genetic casework. Cancellous bones [phalanges, (meta)carpal bones, and (meta)tarsal bones)] and the cortical bones (femur and petrous bones) and teeth, which have generally been recommended as samples, were collected from the same individuals that needed identifying using DNA analysis in our laboratory. The quantity of DNA from small cancellous bones tended to be higher than that from cortical bones, and the quality from the former was as high as that from the latter. This study showed that in routine forensic casework, the small cancellous bones of the hands and feet should be actively selected as samples for DNA testing.

Assessing the usefulness of Raman spectroscopy and lipid analysis of decomposed human bones in forensic genetics and molecular taphonomy

Bones are among the structures most likely to be recovered after death. However, the low quantity of preserved DNA and complex processing from sample to DNA profile make forensic DNA analysis of bones a challenging task. Raman spectroscopy and gas chromatography-mass spectrometry (GC/MS), have the potential to be useful as screening tools for DNA analysis and in decomposition studies. The objective of this research was to assess the usefulness of such molecular investigations. Femur samples collected from 50 decomposing human bodies were subjected to Raman spectroscopy and GC/MS. Assessment of nuclear DNA quantity and short tandem repeat (STR) genotyping efficiency were also performed. Raman parameters (crystallinity, carbonate-to-phosphate ratio, mineral-to-matrix ratio) and detected lipids were recorded. Background fluorescence proved problematic for Raman analysis of forensic bones. Regardless, it was not associated with less preserved DNA or less detected STR alleles. Fatty acids, hydrocarbons, and five types of fatty acid methyl esters (FAMEs) were detected. The main phosphate peak position in Raman spectra was significantly correlated with preserved DNA (p = 0.03713), while significantly more STR alleles were detected in bones containing methyl hexadecenoate (p = 0.04236). Detection of FAMEs in the bone matrix suggests a reaction between methanol produced by bacteria and free fatty acids, which are not associated with the level of preservation of endogenous DNA. The techniques assessed have shown to be useful in molecular taphonomy studies and forensic genetics.

The 3D organization of the mineralized scales of the sturgeon has structures reminiscent of dentin and bone: A FIB-SEM study

Scales are structures composed of mineralized collagen fibrils embedded in the skin of fish. Here we investigate structures contributing to the bulk of the scale material of the sturgeon (Acipencer guldenstatii) at the millimeter, micrometer and nanometer length scales. Polished and fracture surfaces were prepared in each of the three anatomic planes for imaging with light and electron microscopy, as well as focused ion beam - scanning electron microscopy (FIB-SEM). The scale is composed of three layers, upper and lower layers forming the bulk of the scale, as well as a thin surface layer. FTIR shows that the scale is composed mainly of collagen and carbonated hydroxyapatite. Lacunae are present throughout the structure. Fracture surfaces of all three layers are characterized by large diameter collagen fibril bundles (CFBs) emanating from a plane comprising smaller diameter CFBs orientated in different directions. Fine lineations seen in polished surfaces of both major layers are used to define planes called here the striation planes. FIB-SEM image stacks of the upper and lower layers acquired in planes aligned with the striation planes, show that CFBs are oriented in various directions within the striation plane, with larger CFBs emanating from the striation plane. Fibril bundles oriented in different directions in the same plane is reminiscent of a similar organization in orthodentin. The large collagen fibril bundles emanating out of this plane are analogous to von Korff fibrils found in developing dentin with respect to size and orientation. Scales of the sturgeon are unusual in that their mineralized collagen fibril organization contains structural elements of both dentin and bone. The sturgeon scale may be an example of an early evolved mineralized material which is neither bone nor dentin but contains characteristics of both materials, however, the fossil data required to confirm this is missing.

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.

A multimodal 3D imaging approach of pore networks in the human femur to assess age-associated vascular expansion and Lacuno-Canalicular reduction

Cellular communication in the mechanosensory osteocyte Lacuno-Canalicular Network (LCN) regulates bone tissue remodeling throughout life. Age-associated declines in LCN size and connectivity dysregulate mechanosensitivity to localized remodeling needs of aging or damaged tissue, compromising bone quality. Synchrotron radiation-based micro-Computed Tomography (SRμCT) and Confocal Laser Scanning Microscopy (CLSM) were employed to visualize LCN and vascular canal morphometry in an age series of the anterior femur (males n = 14, females n = 11, age range = 19-101, mean age = 55). Age-associated increases in vascular porosity were driven by pore coalescence, including a significant expansion in pore diameter and a significant decline in pore density. In contrast, the LCN showed significant age-associated reductions in lacunar volume fraction, mean diameter, and density, and in canalicular volume fraction and connectivity density. Lacunar density was significantly lower in females across the lifespan, exacerbating their age-associated decline. Canalicular connectivity density was also significantly lower in females but approached comparable declining male values in older age. Our data illuminate the trajectory and potential morphometric sources of age-associated bone loss. Increased vascular porosity contributes to bone fragility with aging, while an increasingly reduced and disconnected LCN undermines the mechanosensitivity required to repair and reinforce bone. Understanding why and how this degradation occurs is essential for improving the diagnosis and treatment of age-related changes in bone quality and fragility.

The petrous bone contains high concentrations of osteocytes: One possible reason why ancient DNA is better preserved in this bone

The characterization of ancient DNA in fossil bones is providing invaluable information on the genetics of past human and other animal populations. These studies have been aided enormously by the discovery that ancient DNA is relatively well preserved in the petrous bone compared to most other bones. The reasons for this better preservation are however not well understood. Here we examine the hypothesis that one reason for better DNA preservation in the petrous bone is that fresh petrous bone contains more DNA than other bones. We therefore determined the concentrations of osteocyte cells occluded inside lacunae within the petrous bone and compared these concentrations to other bones from the domestic pig using high resolution microCT. We show that the concentrations of osteocyte lacunae in the inner layer of the pig petrous bone adjacent to the otic chamber are about three times higher (around 95,000 lacunae per mm3) than in the mastoid of the temporal bone (around 28,000 lacunae per mm3), as well as the cortical bone of the femur (around 27,000 lacunae per mm3). The sizes and shapes of the lacuna in the inner layer of the petrous bone are similar to those in the femur. We also show that the pig petrous bone lacunae do contain osteocytes using a histological stain for DNA. We therefore confirm and significantly expand upon previous observations of osteocytic lacuna concentrations in the petrous bone, supporting the notion that one possible reason for better preservation of ancient DNA in the petrous bone is that this bone initially contains at least three times more DNA than other bones. Thus during diagenesis more DNA is likely to be preserved in the petrous bone compared to other bones.

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.

Forensic DNA Typing From Femurs and Bones of the Foot: A Study of 3 Cases

ABSTRACT

Evidence has been accumulating in the sense that femur may not always be the best option for DNA typing of skeletal remains. Recent studies have shown that bones of the hands and feet appear to be a superior source of preserved DNA. The current study reanalyzed DNA quantitation, degradation, and short tandem repeat typing in femurs, lateral cuneiforms, and distal foot phalanges. Data from 3 human identification cases involving corpses in an advanced decomposition state were collected. We found that in the studied cases, the femur provided equal or inferior results, recovering 84.9% of true alleles. Lateral cuneiforms (99.2%) and distal foot phalanges (96.8%) yielded higher percentages. In addition, more drop-ins and drop-outs were detected in femurs than cuneiforms and phalanges. This study adds to current findings that advocate for further investigation into bone selection for use in forensic practice. The impacts of our findings are limited by the small number of individuals studied and may not apply to old and degraded bones.

Forensic applications of micro-computed tomography: a systematic review

Purpose

The aim of this systematic review was to provide a comprehensive overview of micro-CT current applications in forensic pathology, anthropology, odontology, and neonatology.

Methods

A bibliographic research on the electronic databases Pubmed and Scopus was conducted in the time frame 01/01/2001–31/12/2021 without any language restrictions and applying the following free-text search strategy: “(micro-computed tomography OR micro-CT) AND (forensic OR legal)”. The following inclusion criteria were used: (A) English language; (B) Application of micro-CT to biological and/or non-biological materials to address at least one forensic issue (e.g., age estimation, identification of post-mortem interval). The papers selected by three independent investigators have been then classified according to the investigated materials.

Results

The bibliographic search provided 651 records, duplicates excluded. After screening for title and/or abstracts, according to criteria A and B, 157 full-text papers were evaluated for eligibility. Ninety-three papers, mostly (64) published between 2017 and 2021, were included; considering that two papers investigated several materials, an overall amount of 99 classifiable items was counted when referring to the materials investigated. It emerged that bones and cartilages (54.55%), followed by teeth (13.13%), were the most frequently analyzed materials. Moreover, micro-CT allowed the collection of structural, qualitative and/or quantitative information also for soft tissues, fetuses, insects, and foreign materials.

Conclusion

Forensic applications of micro-CT progressively increased in the last 5 years with very promising results. According to this evidence, we might expect in the near future a shift of its use from research purposes to clinical forensic cases.

Direct STR typing from human bones

Identification by STR analysis of bones is time-consuming, mainly due to the lengthy decalcification required and complex DNA extraction process. To streamline this process, we developed a direct STR typing protocol from bone samples. We optimized bone sample amounts using femur and tibia and two commercial PCR kits (Identifiler™ Plus and IDplex Plus kits). Optimally, 100 mg of bone powder in 300 µL PBS buffer was heated at 98 °C for three minutes to produce a supernatant for DNA amplification. IDplex Plus performed better than Identifiler™ Plus in terms of allele recovery and peak height. Fifteen samples of each of seven bone elements (1st distal phalange of hand, capitate, femur, metacarpal 4, patella, talus, and tibia; N = 105) were then subjected to direct STR typing with the optimized protocol, and 94.3% were high partial to full profiles. The performance of the developed protocol was similar for all bone elements. Median peak heights were significantly better in profiles of cancellous bone than compact bone (p = 0.033) and significantly different across the bone elements (p < 0.001). Ten casework samples from various conditions and up to 7-year-PMI were subjected to both direct STR and conventional STR typing. No significant difference in the number of alleles was seen (95% HDI of -13.5 to 5.15). As well as being rapid, convenient, and safe, the protocol could help improve STR typing from bones.

Intra-bone nuclear DNA variability and STR typing success in Second World War 12th thoracic vertebrae

Bones are an important source of DNA for identification in forensic medicine, especially when the remains are skeletonized, which is the case when dealing with victims of the Second World War. Often the amount of bone available for sampling is limited, and therefore it is crucial to sample the bone segment with the highest adequate DNA quantity for identification. Studies performed on all representative skeletal element types of the human body showed that the amount of DNA obtained from different skeletal elements of different body regions varies greatly. When bones from torso were analyzed, thoracic vertebrae outperformed other vertebrae (cervical and lumbar) and, alongside the first ribs, were among the most appropriate bone elements for identification purposes. It was also shown that the quantity of DNA varies significantly within a single bone type. This study focused on exploring intra-bone DNA variability between five parts of 12th thoracic vertebrae (laminae + spinous process, pedicles + transverse processes, and corpus right, left, and middle). The research was based on the theory that the distribution of body weight and consequently bone remodeling, as well as the ratio between cancellous and cortical bone, contribute to different quantities of DNA in different parts of vertebra sampled. The vertebrae were cleaned and cut into five parts, and each part was completely ground to obtain homogenous bone powder. Half a gram of powder from each part was decalcified using a full demineralization extraction method. The DNA was purified in a Biorobot EZ1 machine (Qiagen). DNA quantity and quality were determined using the PowerQuant System (Promega) and autosomal STR typing success using the GlobalFiler Amplification Kit (Applied Biosystems). Thirty-five 12th thoracic vertebrae were sampled from a single Second World War mass grave. The best results with the highest DNA quantity were found in laminae and the spinous process, and among them all vertebrae analyzed yielded full STR profiles except three, where only a few dropouts occurred. The second-ranked bone part was the pedicles and transverse processes. The comparison of DNA degradation in the vertebral segments analyzed does not show statistically significant differences. Considering our research, when only the torso is available for identification, the 12th thoracic vertebra should be collected and the vertebral arch should be sampled for genetic analyses.

Comparison of nuclear DNA yield and STR typing success in Second World War petrous bones and metacarpals III

DNA yield and STR typing success differ among skeletal element types and within individual bones. Consequently, it is necessary to identify the skeletal elements and their intra-skeletal parts that will most likely yield utilizable and informative endogenous DNA for human identification of skeletal remains. The petrous portion of the temporal bone has been shown to be the most suitable skeletal part for sampling archaeological skeletons, and it has also been used successfully in some forensic cases. When all representative bone types were analyzed for three complete Second World War skeletons, metatarsals and metacarpals yielded more DNA than petrous bones (which generated full profiles even if the DNA yield was lower) and, among almost 200 Second World War metatarsals and metacarpals analyzed, metacarpals III were found to be the highest-yielding bones. To further improve the sampling strategy in DNA analysis of aged skeletal remains, a comparison between 26 petrous bones and 30 metacarpals III from Second World War skeletons was made considering intra-bone DNA yield variability. In metacarpals III only epiphyses were sampled, and in petrous bones only the dense part within the otic capsule was used. To exclude the influence of taphonomic issues as much as possible, petrous bones and metacarpals III from a single Second World War mass grave were examined. The difference between petrous bones and metacarpals III was explored by measuring nuclear DNA yield and success of STR typing. After cleaning the samples, full demineralization extraction was used to decalcify 0.5 g of powdered bone. PowerQuant (Promega) was used to determine DNA content and DNA degradation rates, and STR typing was performed using the PowerPlex ESI 17 Fast System (Promega). Metacarpals III produced the same DNA yields and STR typing success as petrous bones with no intra-individual difference observed in concentration of DNA, degradation rate, percentage of successfully amplified alleles, and intensity of electrophoretic signals. Sampling and processing of metacarpal III epiphyses is consequently recommended for genetic identification of highly degraded skeletal remains in routine forensic casework and in buried non-commingled aged skeletal remains whenever metacarpals III are preserved. Metacarpals III are easy to sample and less prone to contamination with modern DNA because no saw is needed for sampling in comparison to the petrous portion of the temporal bone. The data obtained in this study further improve the sampling strategy for genetic identification of Second World War skeletal remains in Slovenia.

Intra-bone nuclear DNA variability and STR typing success in Second World War first ribs

DNA sampling and typing are used for identifying missing persons or war victims. In recent forensic studies, little focus has been placed on determining intra-bone variability within a single skeletal element. When dealing with aged human bones, complete skeletal remains are rarely present. In cases in which only the torso is available, studies have shown that ribs are one of the most appropriate samples, but intra-bone variability has not yet been studied. A higher degree of remodeling was found to contribute to higher DNA yield in the parts of the skeletal element where the most strain is concentrated. This study explores intra-bone variability in proximal, middle, and distal parts of the first human rib by determining the quantity and quality of DNA using the PowerQuant System (Promega) and autosomal STR typing success using the PowerPlex ESI 17 Fast System (Promega). Thirty first ribs from a single Second World War mass grave were sampled. No variation in DNA degradation was observed across the individual rib. The highest quantity of DNA was measured in the proximal part of the first rib, and in all ribs except three, full or almost full genetic profiles were obtained. Thus, when only the torso is present in archaeological or medico-legal cases, first ribs are recommended to be collected if possible, and the proximal or vertebral ends should be sampled for genetic analysis.

Intra-bone nuclear DNA variability in Second World War metatarsal and metacarpal bones

DNA analysis of Second World War skeletal remains is challenging because of the limited yield of DNA that is usually recovered. Recent forensic research has focused on determining which skeletal elements are superior in their preservation of DNA, and little focus has been placed on measuring intra-bone variability. Metatarsals and metacarpals outperformed all the other bones in DNA yield when analyzing all representative skeletal elements of three Second World War victims, and intra-bone variability was not studied. Soft-tissue remnants were found to contribute to higher DNA yield in trabecular bone tissue. Because metatarsals and metacarpals are composed of trabecular epiphyses and a dense diaphysis, the goal of this study was to explore intra-bone variability in DNA content by measuring nuclear DNA quantity and quality using the PowerQuant System (Promega). A total of 193 bones from a single Second World War mass grave were examined. From each bone, DNA was extracted from the compact diaphysis and from both spongy epiphyses combined. This study confirms higher DNA quantity in epiphyses than diaphyses among all the bones analyzed, and more DNA was obtained from metacarpal epiphyses than from metatarsal epiphyses. Therefore, whenever the possibility for sampling both metacarpals and metatarsals from skeletal remains exists, collecting metacarpals is recommended. In cases in which the hands are missing, metatarsals should be sampled. In any case, epiphyses are a richer source of DNA than diaphyses.

Large fragment demineralization: an alternative pretreatment for forensic DNA typing of bones

In forensic genetics, the analysis of postmortem bones is one of the most challenging due to the low quantity of degraded endogenous DNA. The most widely used approach for sample preparation, in those cases, is pulverizing the bone. However, processing pulverized bone is extremely delicate, requiring strict laboratory conditions and operating procedures. In fact, several recent publications have focused on non-powder approaches. The objectives of this study were, thus, to validate a non-powder protocol for DNA extraction from forensic bones and an alternative pretreatment, large fragment demineralization (LFD). Thirty human femurs and tibiae received by the Legal Medicine Institute of Brescia, Italy, were included in the study. Bone powder and one transversal section of the diaphysis were sampled from each bone. DNA extraction from the powder was carried out using PrepFiler BTA (BTA), while the transversal section was submitted to the alternative demineralizing pretreatment (LFD) followed by DNA extraction using the QIAamp DNA Investigator. DNA extracts were assessed for human DNA quantity and degradation by means of a validated in-house qPCR assay and amplified with commercial kits. Inhibition assessment was carried out through Quality Sensor analysis using 24plex QS Kit. The differences in quantity, quality of human DNA, and number of alleles detected between both methods were comparable and not statistically significant. We propose the use of the LFD protocol as a complementary approach capable of confirming the genotypes or detect alleles not observed using BTA, without the need for pulverization.

High DNA yield from metatarsal and metacarpal bones from Slovenian Second World War skeletal remains

DNA yield varies by anatomical region, and the selection of bone types that yield maximum recovery of DNA is important to maximize the success of human identification of skeletal remains. The goal of our study was to explore inter- and intra-individual variation in DNA content by measuring nuclear DNA quantity and quality and autosomal STR typing success to determine the most promising skeletal elements for bone sampling. To exclude the influence of taphonomic issues as much as possible, three complete male skeletons from a single Second World War mass grave were examined and all representative skeletal element types of the human body were analyzed. Forty-eight different types of bones from the head, torso, arm, leg, hand, and foot were sampled from each skeleton, 144 bones altogether. The samples were cleaned, and half a gram of bone powder was decalcified using a full demineralization extraction method. The DNA was purified in a Biorobot EZ1 (Qiagen). DNA content and rates of DNA degradation were determined with the PowerQuant (Promega), and the Investigator ESSplex SE QS (Qiagen) was used for STR typing. The highest-yielding bones mostly produced the most complete STR profiles. Among the skeletal elements containing on average the most DNA and producing the most complete profiles in all three skeletons examined were metacarpals, metatarsals, and the petrous portion of the temporal bone. Metatarsals and metacarpals can easily be sampled without using a saw, thus reducing potential DNA contamination. Skeletons from the Second World War can be used as a model for poorly preserved skeletal remains, and the results of the investigation can be applied for genetic identification of highly degraded skeletal remains in routine forensic casework. Although the research was limited to only three skeletons found in a unique mass grave, the data obtained could contribute to sampling strategies for identifying old skeletal remains. More Second World War skeletons will be analyzed in the future to investigate inter-bone variation in the preservation of DNA.

Quantification of the bone lacunocanalicular network from 3D X-ray phase nanotomography images

There is a growing interest in developing 3D microscopy for the exploration of thick biological tissues. Recently, 3D X-ray nanocomputerised tomography has proven to be a suitable technique for imaging the bone lacunocanalicular network. This interconnected structure is hosting the osteocytes which play a major role in maintaining bone quality through remodelling processes. 3D images have the potential to reveal the architecture of cellular networks, but their quantitative analysis remains a challenge due to the density and complexity of nanometre sized structures and the need to handle and process large datasets, for example, 2048³ voxels corresponding to 32 GB per individual image in our case. In this work, we propose an efficient image processing approach for the segmentation of the network and the extraction of characteristic parameters describing the 3D structure. These parameters include the density of lacunae, the porosity of lacunae and canaliculi, and morphological features of lacunae (volume, surface area, lengths, anisotropy etc.). We also introduce additional parameters describing the local environment of each lacuna and its canaliculi. The method is applied to analyse eight human femoral cortical bone samples imaged by magnified X-ray phase nanotomography with a voxel size of 120 nm, which was found to be a good compromise to resolve canaliculi while keeping a sufficiently large field of view of 246 μm in 3D. The analysis was performed on a total of 2077 lacunae showing an average length, width and depth of 17.1 μm × 9.2 μm × 4.4 μm, with an average number of 58.2 canaliculi per lacuna and a total lacuno-canalicular porosity of 1.12%. The reported descriptive parameters provide information on the 3D organisation of the lacuno-canalicular network in human bones.

Characterizing the postmortem human bone microbiome from surface-decomposed remains

Microbial colonization of bone is an important mechanism of postmortem skeletal degradation. However, the types and distributions of bone and tooth colonizing microbes are not well characterized. It is unknown if microbial communities vary in abundance or composition between bone element types, which could help explain differences in human DNA preservation. The goals of the present study were to (1) identify the types of microbes capable of colonizing different human bone types and (2) relate microbial abundances, diversity, and community composition to bone type and human DNA preservation. DNA extracts from 165 bone and tooth samples from three skeletonized individuals were assessed for bacterial loading and microbial community composition and structure. Random forest models were applied to predict operational taxonomic units (OTUs) associated with human DNA concentration. Dominant bacterial bone colonizers were from the phyla Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Planctomycetes. Eukaryotic bone colonizers were from Ascomycota, Apicomplexa, Annelida, Basidiomycota, and Ciliophora. Bacterial loading was not a significant predictor of human DNA concentration in two out of three individuals. Random forest models were minimally successful in identifying microbes related to human DNA concentration, which were complicated by high variability in community structure between individuals and body regions. This work expands on our understanding of the types of microbes capable of colonizing the postmortem human skeleton and potentially contributing to human skeletal DNA degradation.

Assessment of the human bone lacuno-canalicular network at the nanoscale and impact of spatial resolution

Recently, increasing attention has been given to the study of osteocytes, the cells that are thought to play an important role in bone remodeling and in the mechanisms of bone fragility. The interconnected osteocyte system is deeply embedded inside the mineralized bone matrix and lies within a closely fitted porosity known as the lacuno-canalicular network. However, quantitative data on human samples remain scarce, mostly measured in 2D, and there are gaps to be filled in terms of spatial resolution. In this work, we present data on femoral samples from female donors imaged with isotropic 3D spatial resolution by magnified X-ray phase nano computerized-tomography. We report quantitative results on the 3D structure of canaliculi in human femoral bone imaged with a voxel size of 30 nm. We found that the lacuno-canalicular porosity occupies on average 1.45% of the total tissue volume, the ratio of the canalicular versus lacunar porosity is about 37.7%, and the primary number of canaliculi stemming from each lacuna is 79 on average. The examination of this number at different distances from the surface of the lacunae demonstrates branching in the canaliculi network. We analyzed the impact of spatial resolution on quantification by comparing parameters extracted from the same samples imaged with 120 nm and 30 nm voxel sizes. To avoid any bias related to the analysis region, the volumes at 120 nm and 30 nm were registered and cropped to the same field of view. Our results show that the measurements at 120 and 30 nm are strongly correlated in our data set but that the highest spatial resolution provides more accurate information on the canaliculi network and its branching properties.

A Powder-free DNA Extraction Workflow for Skeletal Samples

The processing of skeletal material poses several challenges for forensic laboratories. Current methods can be laborious, time-consuming, require dedicated equipment, and are vulnerable to contamination. In this study, various sample mass (1 × 50 mg, 3 × 50 mg, and 1 × 150 mg chip(s)) and incubation times (2, 4, and 16 h) were tested using the PrepFiler^® BTA™ Forensic DNA Extraction Kit to digest whole bone chips in lieu of powdering. The most effective method was then applied to bones and tooth fragments collected from contemporary human cadavers exposed to various environmental conditions using an automated platform. Over a third of the samples tested generated full DNA profiles without having to powder the bone/tooth fragment or further alter the manufacturer's protocol. However, for most samples resulting in incomplete STR profiles due to low amounts of DNA, slightly better results were achieved with powdered tissue. Overall, this work demonstrates the potential use of a faster, nonpowdering DNA extraction method for processing skeletal samples as an effective first-pass screening tool.

Extraction of DNA from Skeletonized Postcranial Remains: A Discussion of Protocols and Testing Modalities

This paper provides a retrospective of the DNA analysis performed by the Armed Forces Medical Examiner-Armed Forces DNA Identification Laboratory between 1990 and 2018. Over 13,000 postcranial osseous materials, comprised of wartime losses from World War II, the Korean War, and South-East Asia, were examined by the following: mitochondrial DNA sequencing, a modified AmpFlSTR® Yfiler™, AmpFlSTR® MiniFiler™, PowerPlex® Fusion, or NGS. Four different DNA extraction protocols were used: incomplete demineralization coupled with an organic purification; complete demineralization with an organic purification; complete demineralization with an inorganic purification using QIAquick PCR Purification Kit; and a protocol designed specifically for use with next-generation sequencing. In general, complete demineralization coupled with an organic purification was the optimal extraction protocol for sequencing of mitochondrial DNA, regardless of the osseous element tested. For STR testing, demineralization paired with an inorganic purification provided optimum results, regardless of kit used or osseous element tested.

Recent advancements in the analysis of bone microstructure: New dimensions in forensic anthropology

Bone is a mechanically active, three-dimensionally (3D) complex, and dynamic tissue that changes in structure over the human lifespan. Bone tissue exists and remodels in 3D and changes over time, introducing a fourth dimension. The products of the remodelling process, secondary and fragmentary osteons, have been studied substantially using traditional two-dimensional (2D) techniques. As a result, much has been learned regarding the biological information encrypted in the histomorphology of bone, yielding a wealth of information relating to skeletal structure and function. Three-dimensional imaging modalities, however, hold the potential to provide a much more comprehensive understanding of bone microarchitecture. The visualization and analysis of bone using high-resolution 3D imaging will improve current understandings of bone biology and have numerous applications in both biological anthropology and biomedicine. Through recent technological advancements, we can hone current anthropological applications of the analysis of bone microstructure and accelerate research into the third and fourth dimensional realms. This review will explore the methodological approaches used historically by anthropologists to assess cortical bone microstructure, spanning from histology to current ex vivo imaging modalities, discuss the growing capabilities of in vivo imaging, and conclude with an introduction of novel non-histological modalities for investigating bone quality.

Intra- and Inter-Element Variability in Mitochondrial and Nuclear DNA from Fresh and Environmentally Exposed Skeletal Remains

Successful identification of skeletonized remains often relies upon DNA analyses, frequently focusing on the mid-diaphysis of weight-bearing long bones. This study explored intra-bone DNA variability using bovine and porcine femora, along with calcanei and tali. DNA from fresh and short-term environmentally exposed bone was extracted utilizing demineralization and standard lysis buffer protocols, and DNA quantity and quality were measured. Overall, femoral epiphyses, metaphyses, and the tarsals had more nuclear and mitochondrial DNA than did the femoral diaphyses. DNA loss was much more rapid in buried bones than in surface exposed bones, while DNA quality differed based on environment, but not bone region/element. The demineralization protocol generated more DNA in some bone regions, while the standard lysis was more effective in others, and neither significantly affected DNA quality. Taken together, these findings reinforce the importance of considering inter- and intra-bone heterogeneity when sampling skeletal material for forensic DNA-based identifications.