Sex determination of archaeological samples using peptide analysis of amelogenin
Ontology highlight
ABSTRACT:
INSTRUMENT(S): LTQ Orbitrap
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: 
Julia Gamble
PROVIDER: MSV000085277 | MassIVE | Mon Apr 13 05:57:00 BST 2020
REPOSITORIES: MassIVE
Similar Datasets
Project description:Biological sex is a key information for archaeological and forensic studies, which can be assessed in enamel using proteomics. However, the lack of a standard approach for fast and accurate sex identification limits the reach of proteomics applications. Here, we introduce a targeted proteomics-based workflow that builds on a rapid, non-destructive, sensitive, and quantitative mass spectrometry (MS) strategy for the determination of biological sex from human dental enamel, including a R-Shiny interface for the data analysis. The method was first developed and optimised using modern teeth material and then validated on an independent set of modern deciduous teeth of known sex. The assay was then applied to archaeological material and demonstrated unprecedented specificity and scalability for molecular sex inference, with the possibility of analysing > 300 individuals in less than two days of MS measurement time, and with subsequent confident sex assignment in less than a day of data analysis.
2024-10-17 | PXD049326 | Pride
Project description:This study tests the application of an innovative new method of sex determination utilizing enamel peptides on a sample of incompletely developed deciduous teeth, including those of perinates.
2021-01-28 | PXD021683 | Pride
Project description:Sex of individuals, estimated on human remains, is important information in anthropological, archaeological and forensic researches. In forensic anthropology, this is one of the key points for identifying a person. In archeology and paleoanthropology, information about sex is important for reconstructing the social and biological structure of a group, lifestyle, and for modeling demographic and growth processes in the past. Sex estimation of adult individuals is possible according to morphological criteria when metric and descriptive features are used. In case of poor preservation of the adult skeletons, as well as on children's remains, sex estimation by morphological criteria has some limitations. Therefore regular attempts are made to attract alternative methods for sexing human remains. As one of such methods a liquid chromatography-mass spectrometry analysis of tooth enamel peptides can be used. The result of this analysis is the identification of certain fragments of amelogenins - the main structural proteins of the organic matrix of tooth enamel, which make up more than 90% of its protein content. Amelogenin genes are located on both the X- and Y-chromosomes and the products of these genes have structural differences that allow them to be differentiated from each other. In the process of maturation of tooth enamel, its protein matrix undergoes proteolytic degradation, as a result enamel already contains proteins in the form of their peptide fragments. Reliable and reproducible detection of unique peptide fragments of amelogenins encoded on the X- and Y-chromosomes in human enamel will make it possible to estimate sex of human remains. The work presents a peptidomic analysis of tooth enamel using chromatography-mass spectrometry. Experiments were carried out on a series of teeth of various archaeological data, tafonomic condition of crown and different biological generations of teeth (deciduous and permanent ones).
2020-06-24 | PXD017965 | Pride
Project description:Shotgun metaproteomic analysis of archaeological dental calculus recovered from the teeth of Scottish prisoners from the Battle of Dunbar (1650)
2019-08-29 | MSV000084258 | MassIVE
Project description:Objectives: Sex hormone receptors are reported to be present in human dental pulp (HDP) cells. The purpose of this study was to examine the biological significance of estrogen and androgen receptors (ER and AR, respectively) in HDP cells. Design: We isolated HDP cells expressing ER- and AR-mRNAs and investigated the expression status of the receptors and the response to sex hormones in the cells. Results: HDP cells expressing ER- and/or AR-mRNAs had the ability to form alizarin red S-positive nodules in which calcium and phosphorus were deposited in vitro and to differentiate into odontoblasts-like cells and dentin-like tissue in vivo. Individual clones isolated from HDP cells exhibited a different expression pattern of mRNA for ER and AR. Some clones expressed ERM-NM-1- and/or ERM-NM-2-mRNAs and the others coexpressed ER- and AR-mRNAs. Using the Ingenuity software, we found that 17M-NM-2-estradiol (E2) and dihydrotestosterone (DHT) could act directly on HDP cells through ER- or androgen signaling-mediated mechanisms. E2 or DHT stimulated the mRNA expression for genes related to odontogenesis of dentin-containing teeth and odontoblast differentiation, suggesting that ER and AR in HDP cells may be involved in dentinogenesis. Conclusions: Our findings provide new insights into the biological significance of sex hormone receptors in HDP cells. Gene expression profiles of human dental pulp cells derived from one male patient were compared between cells treated with 10^-6 M 5alpha-dihydrotestosterone and cells treated with vehicle. Each sample has one replicate. Gene expression profiles of human dental pulp cells derived from one female patient were compared between cells treated with 10^-9 M 17beta-estradiol and cells treated with vehicle. Each sample has one replicate.
2013-03-28 | E-GEOD-44677 | biostudies-arrayexpress
Project description:Sex determination in the flour moth, Ephestia kuehniella.
| PRJEB45597 | ENA
Project description:Tooth is a remarkable source of information for paleoanthropologists. Investigation of ancient dental proteomes is able to provide biomolecular data helping at understanding past life. In particular, the enamel protein amelogenin (AMEL) offers the possibility to determine the sex of the specimen. Here, we have analysed eleven 5000 year-old human teeth from a French Neolithic site using a dedicated paleoproteomics strategy for phenotypic characterization of ancient samples. We have set up a shotgun proteomics analysis based on an optimized 3-step iterative search strategy. This allowed the identification of a total number of 1496 proteins including the main proteins characteristic of dental tissues. Most of the proteins were identified by the no enzyme database search mode included in the iterative bioinformatics data analysis pipeline. This demonstrates that a number of peptides issued from randomly degraded proteins may be missed when using the conventional semi-tryptic database search mode. Based on the identification of the sex-specific peptides TALVLTPLK, IALVLTPLK and WYQSIRPPYP of amelogenin, a targeted MS approach using a parallel reaction monitoring (PRM) mode was performed to maximize the sensitivity and the reproducibility of detecting these unique peptides for sex estimation. This led to confirm the sex of individualsin all the samples.
2019-11-13 | PXD014442 | Pride
Project description:Mineralised dental plaque (calculus) has proven to be an excellent source of ancient biomolecules. In this study we present a Mycobacterium leprae genome (6.6-fold), the causative agent of leprosy, recovered via shotgun sequencing of 16th century human dental calculus from an individual from Trondheim, Norway. Moreover, ancient mycobacterial peptides were retrieved via mass spectrometry-based proteomics, further validating the presence of the pathogen. M. leprae can readily be detected in the oral cavity and associated mucosal membranes, which likely contributed to it being incorporated into this individual’s dental calculus. This individual showed some possible, but not definitive, evidence of skeletal lesions associated with early stage leprosy. This study is the first known example of successful multi-omics retrieval of M. leprae from archaeological dental calculus. Furthermore, we offer new insights into dental calculus as an alternative sample source to bones or teeth for detecting and molecularly characterizing M. leprae in individuals from the archaeological record.
2020-10-19 | PXD017836 | Pride
Project description:The identification of sex-specific peptides in human tooth enamel by nanoflow liquid chromatography-tandem mass spectrometry (nanoLC-MS/MS) represents a quantum leap for the study of childhood and social relations more generally. Determining sex-related differences in prehistoric child rearing and mortality has been hampered by the inability to determine the biological sex of juveniles. We conducted nanoLC-MS/MS to identify sex-specific peptides in the dental enamel of a child from a settlement pit of the Early Bronze Age settlement of Schleinbach, Austria (c. 1950–1850 BC). Four perimortal impression fractures on the skull of the 5–6-year-old child indicate an intentional killing, with a co-buried loom weight as possible murder weapon. Proteomic analysis, conducted for the first time on prehistoric teeth in Austria, determined the child’s sex as male. While we cannot conclusively decide whether the child became the victim of conflicts between village groups or was slain by members of his own community, we suggest that contextual evidence points to the latter. A possible trigger of violence were the follow-on effects of an uncontrolled middle ear infection revealed by the osteological analysis. The boy from Schleinbach highlights the potential for further investigation of gender-biased violence, infanticide and child murder based on the recently developed method of proteomic sex identification.
2021-06-01 | PXD018069 | Pride
Project description:Dental calculus is becoming a crucial material in the study of past populations, with increasing interest in its proteomic and genomic content. Here we suggest further development of protocol for analysis of ancient proteins and a combined approach for subsequent ancient DNA extraction. We tested the protocol on recent teeth. We then applied the optimised protocol to ancient teeth to limit the destruction of calculus, as it is a precious and irreplaceable source of dietary, microbiological, and ecological information in the archaeological context. Finally, the applicability of the protocol was proven on samples of ancient calculus.
2023-09-11 | PXD042668 | Pride