Decomposition in an extreme cold environment and associated microbiome-prediction model implications for the postmortem interval estimation.

Introduction: The accurate estimation of postmortem interval (PMI), the time between death and discovery of the body, is crucial in forensic science investigations as it impacts legal outcomes. PMI estimation in extremely cold environments becomes susceptible to errors and misinterpretations, especially with prolonged PMIs. This study addresses the lack of data on decomposition in extreme cold by providing the first overview of decomposition in such settings. Moreover, it proposes the first postmortem microbiome prediction model for PMI estimation in cold environments, applicable even when the visual decomposition is halted. Methods: The experiment was conducted on animal models in the second-coldest region in the United States, Grand Forks, North Dakota, and covered 23 weeks, including the winter months with temperatures as low as -39°C. Random Forest analysis models were developed to estimate the PMI based either uniquely on 16s rRNA gene microbial data derived from nasal swabs or based on both microbial data and measurable environmental parameters such as snow depth and outdoor temperatures, on a total of 393 samples. Results: Among the six developed models, the best performing one was the complex model based on both internal and external swabs. It achieved a Mean Absolute Error (MAE) of 1.36 weeks and an R2 value of 0.91. On the other hand, the worst performing model was the minimal one that relied solely on external swabs. It had an MAE of 2.89 weeks and an R2 of 0.73. Furthermore, among the six developed models, the commonly identified predictors across at least five out of six models included the following genera: Psychrobacter (ASV1925 and ASV1929), Carnobacterium (ASV2872) and Pseudomonas (ASV1863). Discussion: The outcome of this research provides the first microbial model able to predict PMI with an accuracy of 9.52 days over a six-month period of extreme winter conditions.

From flesh to bones: Multi-omics approaches in forensic science.

Recent advancements in omics techniques have revolutionised the study of biological systems, enabling the generation of high-throughput biomolecular data. These innovations have found diverse applications, ranging from personalised medicine to forensic sciences. While the investigation of multiple aspects of cells, tissues or entire organisms through the integration of various omics approaches (such as genomics, epigenomics, metagenomics, transcriptomics, proteomics and metabolomics) has already been established in fields like biomedicine and cancer biology, its full potential in forensic sciences remains only partially explored. In this review, we have presented a comprehensive overview of state-of-the-art analytical platforms employed in omics research, with specific emphasis on their application in the forensic field for the identification of the cadaver and the cause of death. Moreover, we have conducted a critical analysis of the computational integration of omics approaches, and highlighted the latest advancements in employing multi-omics techniques for forensic investigations.

Bone Proteomics Method Optimization for Forensic Investigations.

The application of proteomic analysis to forensic skeletal remains has gained significant interest in improving biological and chronological estimations in medico-legal investigations. To enhance the applicability of these analyses to forensic casework, it is crucial to maximize throughput and proteome recovery while minimizing interoperator variability and laboratory-induced post-translational protein modifications (PTMs). This work compared different workflows for extracting, purifying, and analyzing bone proteins using liquid chromatography with tandem mass spectrometry (LC-MS)/MS including an in-StageTip protocol previously optimized for forensic applications and two protocols using novel suspension-trap technology (S-Trap) and different lysis solutions. This study also compared data-dependent acquisition (DDA) with data-independent acquisition (DIA). By testing all of the workflows on 30 human cortical tibiae samples, S-Trap workflows resulted in increased proteome recovery with both lysis solutions tested and in decreased levels of induced deamidations, and the DIA mode resulted in greater sensitivity and window of identification for the identification of lower-abundance proteins, especially when open-source software was utilized for data processing in both modes. The newly developed S-Trap protocol is, therefore, suitable for forensic bone proteomic workflows and, particularly when paired with DIA mode, can offer improved proteomic outcomes and increased reproducibility, showcasing its potential in forensic proteomics and contributing to achieving standardization in bone proteomic analyses for forensic applications.

Transferability of Human and Environmental Microbiome on Clothes as a Tool for Forensic Investigations.

Considering the growing importance of microbiome analyses in forensics for identifying individuals, this study explores the transfer of the skin microbiome onto clothing, its persistence on fabrics over time, and its transferability from the environment and between different garments. Furthermore, this project compares three specific QIAGEN microbiome extraction kits to test their extraction efficiency on fabric samples. Additionally, this study aims to check if these extracts contain human DNA, providing a chance to obtain more information from the same evidence for personal identification. The results obtained show: (1) variations in the skin microbiome between the volunteers, potentially due to their different sex; (2) differences in microbial composition between worn and unworn clothing; (3) the influence of the environment on the microbial signature of unworn clothing; (4) the potential use of certain phyla as biomarkers to differentiate between worn and unworn garments, even over extended periods; (5) a tendency towards extraction biases in the QIAampMP® DNA microbiome kit among the three tested ones; and (6) none of the extraction kits allow for the typing of human genetic profiles suitable for comparison. In conclusion, our study offers supplementary insights into the potential utility of time-transferred microbiome analysis on garments for forensic applications.

Association between nanoscale strains and tissue level nanoindentation properties in age-related hip-fractures.

Measurement of the properties of bone as a material can happen in various length scales in its hierarchical and composite structure. The aim of this study was to test the tissue level properties of clinically-relevant human bone samples which were collected from donors belonging to three groups: ageing donors who suffered no fractures (Control); untreated fracture patients (Fx-Untreated) and patient who experienced hip fracture despite being treated with bisphosphonates (Fx-BisTreated). Tissue level properties were assessed by (a) nanoindentation and (b) synchrotron tensile tests (STT) where strains were measured at the 'tissue', 'fibril' and 'mineral' levels by using simultaneous Wide-angle - (WAXD) and Small angle- X-ray diffraction (SAXD). The composition was analysed by thermogravimetric analysis and material level endo- and exo-thermic reactions by differential scanning calorimetry (TGA/DSC3+). Irrespective of treatment fracture donors exhibited significantly lower tissue, fibril and mineral strain at the micro and nanoscale respectively and had a higher mineral content than controls. In nanoindentation only nanohardness was significantly greater for Controls and Fx-BisTreated versus Fx-Untreated. The other nanoindentation parameters did not vary significantly across the three groups. There was a highly significant positive correlation (p < 0.001) between organic content and tissue level strain behaviour. Overall hip-fractures were associated with lower STT nanostrains and it was behaviour measured by STT which proved to be a more effective approach for predicting fracture risk because evidently it was able to demonstrate the mechanical deficit for the bone tissue of the donors who had experienced fractures.

The 'ForensOMICS' approach for postmortem interval estimation from human bone by integrating metabolomics, lipidomics, and proteomics.

The combined use of multiple omics allows to study complex interrelated biological processes in their entirety. We applied a combination of metabolomics, lipidomics and proteomics to human bones to investigate their combined potential to estimate time elapsed since death (i.e., the postmortem interval [PMI]). This 'ForensOMICS' approach has the potential to improve accuracy and precision of PMI estimation of skeletonized human remains, thereby helping forensic investigators to establish the timeline of events surrounding death. Anterior midshaft tibial bone was collected from four female body donors before their placement at the Forensic Anthropology Research Facility owned by the Forensic Anthropological Center at Texas State (FACTS). Bone samples were again collected at selected PMIs (219-790-834-872days). Liquid chromatography mass spectrometry (LC-MS) was used to obtain untargeted metabolomic, lipidomic, and proteomic profiles from the pre- and post-placement bone samples. The three omics blocks were investigated independently by univariate and multivariate analyses, followed by Data Integration Analysis for Biomarker discovery using Latent variable approaches for Omics studies (DIABLO), to identify the reduced number of markers describing postmortem changes and discriminating the individuals based on their PMI. The resulting model showed that pre-placement metabolome, lipidome and proteome profiles were clearly distinguishable from post-placement ones. Metabolites in the pre-placement samples suggested an extinction of the energetic metabolism and a switch towards another source of fuelling (e.g., structural proteins). We were able to identify certain biomolecules with an excellent potential for PMI estimation, predominantly the biomolecules from the metabolomics block. Our findings suggest that, by targeting a combination of compounds with different postmortem stability, in the future we could be able to estimate both short PMIs, by using metabolites and lipids, and longer PMIs, by using proteins.

Preliminary Investigation of the Effect of Maceration Procedures on Bone Metabolome and Lipidome.

The study of post-mortem changes is a crucial component of forensic investigation. Human forensic taphonomic facilities (HFTFs) are the only institutions allowing the design and execution of controlled human decomposition experiments. When bodies are skeletonized, bones are normally stored in skeletal collections and used for anthropological studies. However, HFTFs apply chemical and/or thermal treatments to the remains prior bone long-term storage. These treatments are believed to alter heavily the original biochemical and molecular signature of bone material. The present study aims to evaluate the effect of these procedures on the bone metabolome and lipidome by using an animal bone model. Three intact bovine tibiae were processed using three protocols routinely applied at HFTFs, and their three counterparts were used as non-treated controls. Bone powder samples were subjected to biphasic extraction and both metabolites and lipids were analysed via liquid chromatography tandem mass-spectrometry. Results showed severe reductions in the abundances of both metabolites and lipids, and the presence of contamination introduced by cleaning agents. Despite the preliminary nature of the study, we demonstrated that the biochemical profile of bone is heavily affected by the maceration procedures. Ideally, these treatments should be avoided, or replaced by minimally invasive procedures agreed across HFTFs.

Estimation of Age-at-Death Using Cortical Bone Histomorphometry of the Rib and Femur: A Validation Study on a British Population.

Histomorphometry constitutes a valuable tool for age estimation. Histological interpopulation variability has been shown to affect the accuracy of age estimation techniques and therefore validation studies are required to test the accuracy of the pre-existing methodologies. The present research constitutes a validation study of widely known histological methods on the sixth rib and the femoral midshaft of a 19th century British population originating from Blackburn, England. An evaluation of the histomorphometric features of eleven ribs and five femora was performed and used to test the accuracy of selected methods. Results indicated that osteon area and circularity were the only histomorphometric variables that presented significant interpopulation variability. Cho et al.'s method for the ribs and the average value produced using Kerley and Ubelaker's method for intact osteon and percentage of lamellar bone equations for femur were considered the only reliable markers for estimating the age on the Blackburn sample. In the case of old individuals, Goliath et al.'s method provided more satisfactory results. Overall, the present study provides evidence on the applicability of the aging histomorphometric methods on a British sample and highlights the limitations of applying histomorphometric methods developed on different reference populations than the one under investigation.

Age estimation for two Mediterranean populations: rib histomorphometry applied to forensic identification and bone remodelling research.

Numerous intrinsic and extrinsic factors influence bone remodelling rates and have shown to affect the accuracy of histological aging methods. The present study investigates the rib cortex from two Mediterranean skeletal collections exploring the development of population-specific standards for histomorphometric age-at-death estimation. Eighty-eight standard ribs from two samples, Cretans and Greek-Cypriots, were processed histologically. Thirteen raw and composite histomorphometric parameters were assessed and observer error tested. The correlation between age and the parameters and the differences between sex and population subsamples were explored through group comparisons and analysis of covariance. General linear models assessed through data fit indicators and cross-validation were generated from the total dataset, and by sex and population subsamples. Most of the histological variables showed a statistically significant correlation with age with some differences observed by sex and by sample. From the twelve models generated, the optimal model for the whole sample included osteon population density (OPD), osteon perimeter, and osteon circularity producing an error of 10.71 years. When sex and samples were separated, the best model selected included OPD and osteon perimeter producing an error of 8.07 years for Greek-Cypriots. This research demonstrates the feasibility of quantitative bone histology to estimate age, obtaining errors rates in accordance with macroscopic ageing techniques. Sex and sample population differences need further investigation and inter-population variation in remodelling rates is suggested. Moreover, this study contributes to the creation of population-specific standards for Cretans and Greek-Cypriots.

Insights into the Differential Preservation of Bone Proteomes in Inhumed and Entombed Cadavers from Italian Forensic Caseworks.

Bone is a hard biological tissue and a precious reservoir of information in forensic investigations as it retains key biomolecules commonly used for identification purposes. Bone proteins have recently attracted significant interest for their potential in estimating post-mortem interval (PMI) and age at death (AAD). However, the preservation of such proteins is highly dependent on intrinsic and extrinsic factors that can hinder the potential application of molecular techniques to forensic sciences. The present study aims at investigating the effects that two commonly used types of burial practices (entombment and inhumation) have on bone protein survival. The sample consists of 14 exhumed individuals from cemeteries in Southern Italy with different AADs (29-85 years) and PMIs (1-37 years). LC-MS/MS analyses show that 16 proteins are better preserved under the entombed conditions and 4 proteins are better preserved under the inhumed conditions, whereas no clear differences are detected for post-translational protein modifications. Furthermore, several potential "stable" protein markers (i.e., proteins not affected by the burial environment) are identified for PMI and AAD estimation. Overall, these results show that the two burial environments play a role in the differential preservation of noncollagenous proteins, confirming the potential of LC-MS/MS-based proteomics in forensic sciences.

Assessing bone maturity: Compositional and mechanical properties of rib cortical bone at different ages.

Understanding what maturity entails for bone, when it arrives, and its pre- and post-maturity traits and properties are very important for understanding its evolution and physiology. There is a clear but fine distinction between the chronological age of bone (the age of its donor) and the tissue age of the bone packets it comprises at the microscopic level. Whole bone fragility changes with age due to mass and architecture effects, but so do the properties of bone at the tissue level. Tissue age and tissue-level properties are therefore increasingly attracting a great deal of attention recently. The present study investigated compositional and material changes in the hydroxyapatite crystals, the collagenous phase, changes in bone matrix composition and its nanoindentation properties and their decline with chronological age in later life. The aim was to track the age threshold at which cortical bone arrives at maturity and what happens following that threshold. To do so FTIR, DSC/TGA, XRD, nanoindentation and microindentation were used to investigate rib cortical bone material across a cohort of 86 individuals from one ethnic group with age spanning between 17 and 82 years. Results of this cross-sectional study showed a clear increase in mineral content relative to the organic and water contents across all ages. Furthermore, an increase in crystal size and consequent decrease in strain (coherence length) was detected associated with secondary mineralisation and an increase in carbonate substitution. Overall, we observe a number of modifications which contribute to a typical functional behaviour of bone showing an increase in both indentation modulus and hardness until the age of about 35 after which both of these properties decline gradually and concomitantly to other physicochemical changes and seemingly until the end of one's life.

Bone Diagenesis in Short Timescales: Insights from an Exploratory Proteomic Analysis.

The evaluation of bone diagenetic phenomena in archaeological timescales has a long history; however, little is known about the origins of the microbes driving bone diagenesis, nor about the extent of bone diagenesis in short timeframes-such as in forensic contexts. Previously, the analysis of non-collagenous proteins (NCPs) through bottom-up proteomics revealed the presence of potential biomarkers useful in estimating the post-mortem interval (PMI). However, there is still a great need for enhancing the understanding of the diagenetic processes taking place in forensic timeframes, and to clarify whether proteomic analyses can help to develop better models for estimating PMI reliably. To address these knowledge gaps, we designed an experiment based on whole rat carcasses, defleshed long rat bones, and excised but still-fleshed rat limbs, which were either buried in soil or exposed on a clean plastic surface, left to decompose for 28 weeks, and retrieved at different time intervals. This study aimed to assess differences in bone protein relative abundances for the various deposition modalities and intervals. We further evaluated the effects that extrinsic factors, autolysis, and gut and soil bacteria had on bone diagenesis via bottom-up proteomics. Results showed six proteins whose abundance was significantly different between samples subjected to either microbial decomposition (gut or soil bacteria) or to environmental factors. In particular, muscle- and calcium-binding proteins were found to be more prone to degradation by bacterial attack, whereas plasma and bone marrow proteins were more susceptible to exposure to extrinsic agents. Our results suggest that both gut and soil bacteria play key roles in bone diagenesis and protein decay in relatively short timescales, and that bone proteomics is a proficient resource with which to identify microbially-driven versus extrinsically-driven diagenesis.

Human Bone Proteomes before and after Decomposition: Investigating the Effects of Biological Variation and Taphonomic Alteration on Bone Protein Profiles and the Implications for Forensic Proteomics.

Bone proteomic studies using animal proxies and skeletonized human remains have delivered encouraging results in the search for potential biomarkers for precise and accurate post-mortem interval (PMI) and the age-at-death (AAD) estimation in medico-legal investigations. The development of forensic proteomics for PMI and AAD estimation is in critical need of research on human remains throughout decomposition, as currently the effects of both inter-individual biological differences and taphonomic alteration on the survival of human bone protein profiles are unclear. This study investigated the human bone proteome in four human body donors studied throughout decomposition outdoors. The effects of ageing phenomena (in vivo and post-mortem) and intrinsic and extrinsic variables on the variety and abundancy of the bone proteome were assessed. Results indicate that taphonomic and biological variables play a significant role in the survival of proteins in bone. Our findings suggest that inter-individual and inter-skeletal differences in bone mineral density (BMD) are important variables affecting the survival of proteins. Specific proteins survive better within the mineral matrix due to their mineral-binding properties. The mineral matrix likely also protects these proteins by restricting the movement of decomposer microbes. New potential biomarkers for PMI estimation and AAD estimation were identified. Future development of forensic bone proteomics should include standard measurement of BMD and target a combination of different biomarkers.

Age related changes of rib cortical bone matrix and the application to forensic age-at-death estimation.

Forensic anthropology includes, amongst other applications, the positive identification of unknown human skeletal remains. The first step in this process is an assessment of the biological profile, that is: sex, age, stature and ancestry. In forensic contexts, age estimation is one of the main challenges in the process of identification. Recently established admissibility criteria are driving researchers towards standardisation of methodological procedures. Despite these changes, experience still plays a central role in anthropological examinations. In order to avoid this issue, age estimation procedures (i) must be presented to the scientific community and published in peer reviewed journals, (ii) accurately explained in terms of procedure and (iii) present clear information about the accuracy of the estimation and possible error rates. In order to fulfil all these requirements, a number of methods based on physiological processes which result in biochemical changes in various tissue structures at the molecular level, such as modifications in DNA-methylation and telomere shortening, racemization of proteins and stable isotopes analysis, have been developed. The current work proposes a new systematic approach in age estimation based on tracing physicochemical and mechanical degeneration of the rib cortical bone matrix. This study used autopsy material from 113 rib specimens. A set of 33 parameters were measured by standard bio-mechanical (nanoindentation and microindentation), physical (TGA/DSC, XRD and FTIR) and histomorphometry (porosity-ImageJ) methods. Stepwise regressions were used to create equations that would produce the best 'estimates of age at death' vs real age of the cadavers. Five equations were produced; in the best of cases an equation counting 7 parameters had an R2 = 0.863 and mean absolute error of 4.64 years. The present method meets all the admissibility criteria previously described. Furthermore, the method is experience-independent and as such can be performed without previous expert knowledge of forensic anthropology and human anatomy.

Rib histomorphometry: A reliability and validation study with a critical review of histological techniques for forensic age estimation.

Fragmented human remains present a challenge for forensic experts as they attempt to identify individuals using standard forensic methods. Several histological age estimation techniques have been developed during the last fifty years to aid in this process. However, very few validation studies have been conducted in order to test their accuracy and bias, and thus, validation assessment is required as we employ them while testifying in court. Histological variables are assessed from rib thin sections from two Mediterranean samples; Cretans (N = 41) and Greek-Cypriots (N = 47). Intra and inter-observer errors are assessed through TEM analysis and Intra-class Correlation Coefficient by testing observers with different levels of experience as they collected data on osteon counts and area measurements. The relation between the variables and age is determined using correlation coefficients. Histomorphometric data are applied to four widely used age estimation formulas assessing the performance of the methods for the entire sample. Inaccuracy and bias are calculated with age estimations and known age tested for significance and proportional bias assessed. Overall, histological parameters presented acceptable intra- and inter-observer errors. All variables exhibited statistically significant correlation with age (P < 0.01). For three of the techniques, data showed a systematic underestimation of age with an increase in inaccuracy in older individuals. One of the age estimation formulas produced overestimation of young individuals yet, it more accurately estimated the age of older individuals. This validation study explores inter-population variation in bone remodeling dynamics and presents a critical evaluation on methodological issues that can affect the performance of existing histological techniques.

Bone histomorphometry of the clavicle in a forensic sample from Albania.

Forensic assessment of skeletal material includes age estimation of unknown individuals. When dealing with extremely fragmented human remains that lack macro-features used in age estimation, histological assessment of the skeletal elements can be employed. Historically, microscopic methods for age assessment used by forensic anthropologists have been available since 1965. Several skeletal elements have been used for this purpose. Among them, the clavicle has garnered very little attention. The purpose of this study is to explore the validity of clavicular histomorphometry as an age marker in a modern Balkan sample. This study examined a modern clavicular autopsy sample from Albania. The sample consisted of 33 individuals of known age and cause of death. Data were collected for micro-anatomical features including osteon population density (OPD) and cortical area. Intra- and inter-observer errors were assessed through technical error of measurement (TEM) and R coefficient. A validation study was performed in order to test the accuracy of existing histological formulae. Regression analysis was run to developed age prediction models with the best models tested through cross-validation and the comparison between OPD for the Albanian sample and a European-American sample examined. Intra- and inter-observer error TEM results demonstrated values falling within the limits of acceptance. The existing histological methods did not perform accurately on the sample under study. Regression equations for Albanians produced age estimations deviating 8 and 11 years from known age. Cross-validation on the most accurate regression formula which includes OPD as a single variable demonstrated similar mean errors. Statistically significant differences were observed between the Albanian and the European-American population when the two samples were compared. The research presented is the fifth article published and the fifth population explored on clavicular microstructure. The potential of histology to estimate age on the Albanian population is shown here; however, population effect, diet and health status might be considered. Further inclusion of individuals will corroborate our preliminary findings.

The posterior portion of the ilium as a sex indicator: A validation study.

Establishing a biological profile of skeletal remains is a key task of forensic anthropologists. Sex estimation is essential in forensic examination, as other elements of the biological profile, such as age at death or stature, are sex dependent. Visual assessment is considered low-cost and quick, therefore it is a commonly applied method of sex estimation. The most reliable results can be obtained with the analysis of the anterior part of the pelvis, however, these skeletal elements are fragile and prone to destruction. In contrary, the more robust posterior portion of the pelvis is often recovered. Several features of the posterior pelvis have been explored in the context of sexual dimorphism. The aim of the present study was to test three previously published methods of sex assessment based on the analysis of the inferior shape of the auricular surface (Novotný, 1975), the greater sciatic notch shape (Walker, 2005 (revised)) and overall morphology, apex morphology and inflection of the auricular surface (Luna et al., 2017). The sample consisted of 194 individuals of Greek origin from a documented modern collection. Four features of the auricular surface and shape of the greater sciatic notch were examined. Logistic regression analysis was applied to produce a sex discriminatory formula. The method proposed by Luna et al. (2017) failed to produce satisfactory results with overall accuracies of 36%, 50% and 53% for overall morphology, apex morphology and inflection respectively. Slightly better results (64%) were obtained with the inferior shape morphology (Novotný, 1975). However, the highest accuracy rate of 81% was noted for the greater sciatic notch shape (Walker, 2005 (revised)). The formula produced in this study allowed correct classification of 83.2% of the sample. This study illustrates that in spite of the presence of sexual dimorphism in the posterior portion of ilium, features of the auricular surface proposed as sex indicators by Novotný (1975) and Luna et al. (2017) should not be used for sex estimation purposes in the Greek population. The formula produced in this study and the greater sciatic notch shape should only be used as additional methods in cases where neither the cranium nor the anterior portion of the pelvis is present.

Rib biomechanical properties exhibit diagnostic potential for accurate ageing in forensic investigations.

Age estimation remains one of the most challenging tasks in forensic practice when establishing a biological profile of unknown skeletonised remains. Morphological methods based on developmental markers of bones can provide accurate age estimates at a young age, but become highly unreliable for ages over 35 when all developmental markers disappear. This study explores the changes in the biomechanical properties of bone tissue and matrix, which continue to change with age even after skeletal maturity, and their potential value for age estimation. As a proof of concept we investigated the relationship of 28 variables at the macroscopic and microscopic level in rib autopsy samples from 24 individuals. Stepwise regression analysis produced a number of equations one of which with seven variables showed an R2 = 0.949; a mean residual error of 2.13 yrs ±0.4 (SD) and a maximum residual error value of 2.88 yrs. For forensic purposes, by using only bench top machines in tests which can be carried out within 36 hrs, a set of just 3 variables produced an equation with an R2 = 0.902 a mean residual error of 3.38 yrs ±2.6 (SD) and a maximum observed residual error 9.26yrs. This method outstrips all existing age-at-death methods based on ribs, thus providing a novel lab based accurate tool in the forensic investigation of human remains. The present application is optimised for fresh (uncompromised by taphonomic conditions) remains, but the potential of the principle and method is vast once the trends of the biomechanical variables are established for other environmental conditions and circumstances.