Molecular clocks in ancient proteins: Do they reflect the age at death even after millennia?

The chiral proteomic analysis applied to aging collagens by LC-MS: Amino acid racemization, post-translational modifications, and sequence degradations during the aging process

Collagen is the most abundant protein in the animal and human bodies, and it is not exempt from this aging phenomenon. Some age-related changes may appear on collagen sequences, such as increased surface hydrophobicity, the appearance of post-translational modifications, and amino acids racemization. This study has shown that the protein hydrolysis under deuterium conditions is privileged to limit the natural racemization during the hydrolysis. Indeed, under the deuterium condition, the homochirality of recent collagens is preserved whose amino acids are found in their L-form. However, in aging collagen, a natural amino acid racemization was observed. These results confirmed that the % d-amino acids are progressive according to age. The collagen sequence is degraded over time, and a fifth of the sequence information is lost during aging. Post-translational modifications (PTMs) in aging collagens can be a hypothesis to explain the modification of the hydrophobicity of the protein with the decrease of hydrophilic groups and the increase of hydrophobic groups. Finally, the exact positions of d-amino acids and PTMs have been correlated and elucidated.

Molecular age estimation based on posttranslational protein modifications in bone: why the type of bone matters

Age-at-death estimation is of great relevance for the identification of unknown deceased individuals. In skeletonised corpses, teeth and bones are theoretically available for age estimation, but in many cases, only single bones or even only bone fragments are available for examination. In these cases, conventional morphological methods may not be applicable, and the application of molecular methods may be considered. Protein-based molecular methods based on the D-aspartic acid (D-Asp) or pentosidine (Pen) content have already been successfully applied to bone samples. However, the impact of the analysed type of bone has not yet been systematically investigated, and it is still unclear whether data from samples of one skeletal region (e.g. skull) can also be used for age estimation for samples of other regions (e.g. femur). To address this question, D-Asp and Pen were analysed in bone samples from three skeletal regions (skull, clavicle, and rib), each from the same individual. Differences between the bone types were tested by t-test, and correlation coefficients (ρ) were calculated according to Spearman. In all types of bone, an age-dependent accumulation of D-Asp and Pen was observed. However, both parameters (D-Asp and Pen) exhibited significant differences between bone samples from different anatomical regions. These differences can be explained by differences in structure and metabolism in the examined bone types and have to be addressed in age estimation based on D-Asp and Pen. In future studies, bone type-specific training and test data have to be collected, and bone type-specific models have to be established.

DXAGE 2.0 - adult age at death estimation using bone loss in the proximal femur and the second metacarpal

The accurate age at death assessment of unidentified adult skeletal individuals is a critical research task in forensic anthropology, being a key feature for the determination of biological profiles of individual skeletal remains. We have previously shown that the age-related decrease of bone mineral density (BMD) in the proximal femur could be used to assess age at death in women (Navega et al., J Forensic Sci 63:497-503, 2018). The present study aims to generate models for age estimation in both sexes through bone densitometry of the femur and radiogrammetry of the second metacarpal. The training sample comprised 224 adults (120 females, 104 males) from the "Coimbra Identified Skeletal Collection," and different models were generated through least squares regression and general regression neural networks (GRNN). The models were operationalized in a user-friendly online interface at https://osteomics.com/DXAGE2/ . The mean absolute difference between the known and estimated age at death ranges from 9.39 to 13.18 years among women and from 10.33 to 15.76 among men with the least squares regression models. For the GRNN models, the mean absolute difference between documented and projected age ranges from 8.44 to 12.58 years in women and from 10.56 to 16.18 years in men. DXAGE 2.0 enables age estimation in incomplete and/or fragmentary skeletal remains, using alternative skeletal regions, with reliable results.

Biochemical analyses for dental age estimation: a review

Background

For various legal and forensic scenarios, establishing an individual’s age, both living and dead, plays a crucial role. Various morphological, radiographic, and molecular methods can be used for age estimation. In children and adolescents, age estimation is based on the established developmental stages. However, in adults, where the development ceases into maturation, the degenerative changes play a role in determining the age.

Main body of the abstract

In the natural aging process, several molecular changes occur most commonly in the long-living proteins and hard tissues like the teeth and bone. These molecular changes gradually lead to alterations in several organs and organ systems, which can be quantified and correlated with age, including aspartic acid racemization, collagen crosslinks, advanced glycation-end products, and mitochondrial DNA mutations.

Short conclusion

Among the above methods, the racemization of aspartic acid can be considered as the most precise method. The main advantage of using aspartic acid racemization is that the sample can be collected from tissues (teeth) protected from various environmental and nutritional factors. If all the confounding factors are stable, the utilization of advanced glycation-end products can also be considered valuable. Environmental factors like lead accumulations may also help determine the age. However, further studies need to be conducted, focusing on providing a more standardized method. This review provides a concise summary of the biochemical techniques that can be used for estimation of age.

Age estimation in humans through the analysis of aspartic acid racemization from teeth: A scoping review of methods, outcomes, and open research questions

Teeth are considered the most resistant structures in the human body. In forensic odontology, teeth are useful for human identification, especially when dental age estimation is necessary. Despite numerous studies, there is no consensus regarding the best methods for dental age estimation. The analysis of aspartic acid racemization, however, has shown promising results. This scoping review aimed to present a descriptive synthesis of the current literature regarding dental age estimation through aspartic acid racemization. Four electronic databases were screened: PubMed, Scielo, Web of Science, and Scopus. Cross-sectional studies published before April 2021 were selected. From 206 articles found, 26 met the eligibility criteria. Several experimental protocols and laboratory settings were detected, but the different protocols did not seem to significantly reduce error rates in dental age estimation. The analysis of aspartic acid racemization in human dental tissues produced accurate and potentially reliable results for age estimation. Aspartic acid racemization stands out especially in the adulthood - age category in which other methods struggle to deliver proper performances. Studies with larger samples, independent testing, and standardized laboratory procedures are necessary. Equator-like reporting guidelines are encouraged to enable future systematic reviews and meta-analyses.

Analysis of 14C, 13C and Aspartic Acid Racemization in Teeth and Bones to Facilitate Identification of Unknown Human Remains: Outcomes of Practical Casework

The identification of unknown human remains represents an important task in forensic casework. If there are no clues as to the identity of the remains, then the age, sex, and origin are the most important factors to limit the search for a matching person. Here, we present the outcome of application of so-called bomb pulse radiocarbon (¹⁴C derived from above-ground nuclear bomb tests during 1955–1963) analysis to birthdate human remains. In nine identified cases, ¹⁴C analysis of tooth crowns provided an estimate of the true date of birth with an average absolute error of 1.2 ± 0.8 years. Analysis of ¹⁴C in tooth roots also showed a good precision with an average absolute error of 2.3 ± 2.5 years. Levels of ¹⁴C in bones can determine whether a subject has lived after 1955 or not, but more precise carbon turnover data for bones would be needed to calculate date of birth and date of death. Aspartic acid racemization analysis was performed on samples from four cases; in one of these, the year of birth could be predicted with good precision, whereas the other three cases are still unidentified. The stable isotope ¹³C was analyzed in tooth crowns to estimate provenance. Levels of ¹³C indicative of Scandinavian provenance were found in known Scandinavian subjects. Teeth from four Polish subjects all showed higher ¹³C levels than the average for Scandinavian subjects.

Nutzung von Altersinformationen aus posttranslationalen Proteinmodifikationen und DNA-Methylierung zur postmortalen Lebensaltersschätzung: Konzept und Ergebnisse einer Pilotstudie

Mit der Identifikation und Beschreibung „molekularer Uhren“ (posttranslationale Proteinmodifikationen, DNA-Methylierung) eröffnen sich neue Möglichkeiten zur Entwicklung von Verfahren zur postmortalen Lebensaltersschätzung. Bislang werden diese Ansätze aber nur unabhängig voneinander eingesetzt. Ihre Verknüpfung verspricht eine bessere Erfassung hochkomplexer Alterungsprozesse und damit die Möglichkeit zur Entwicklung optimierter Verfahren zur Altersschätzung für verschiedenste Szenarien der forensischen Praxis.

In Vorbereitung umfangreicher Untersuchungen zur Überprüfung dieser Hypothese wurden verschiedene molekulare Uhren (Akkumulation von D‑Asparaginsäure, Akkumulation von Pentosidin und DNA-Methylierungsmarker [RPA2, ZYG11A, F5, HOXC4, NKIRAS2, TRIM59, ELOVL2, DDO, KLF14 und PDE4C]) in 4 fäulnisresistenten Geweben (Knochen, Sehne, Bandscheibe, Epiglottis) von 15 Individuen untersucht.

In allen untersuchten Geweben fand sich eine starke Korrelation beider Proteinmarker sowie jeweils mehrerer DNA-Methylierungsmarker mit dem Lebensalter. Dabei zeigten die untersuchten Parameter gewebsspezifische Veränderungen mit dem Alter.

Die Ergebnisse der Pilotstudie belegen das Potenzial der Verknüpfung molekularer Verfahren für die postmortale Altersschätzung. Weitere Untersuchungen werden zeigen, wie genau postmortale Altersschätzungen sein können, wenn Altersinformationen aus posttranslationalen Proteinmodifikationen und DNA-Methylierung aus verschiedenen Geweben in multivariaten Modellen verknüpft werden.