Browse
Submit Data
Databases
API
Help

Dataset Information

162 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Palaeoproteomics species identification of Toteng remains

ABSTRACT: This project has two main objectives: 1. Identify the best suited decalcification protocol for bones and teeth from African archaeological sites; 2. Provide species identification of the remains based on UHPLC-MS/MS data.

INSTRUMENT(S): maXis

ORGANISM(S): Suidae Ovis Aries Equidae

TISSUE(S): Tooth, Long Bone

SUBMITTER: Severine Zirah

LAB HEAD: Severine Zirah

PROVIDER: PXD010725 | Pride | 2018-09-14

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20170221_07_Tot15_0-6_RB2_01_218.d.zip	Other
	20170221_13_Tot15_1_RB1_01_224.d.zip	Other
	Louise_Tot09_06_GD6_01_626.d.zip	Other
	Louise_Tot09_1_BA8_01_647.d.zip	Other
	Louise_Tot09_EDTA_GB5_01_600.d.zip	Other

Items per page:

1 - 5 of 57

Similar Datasets

Palaeoproteomics gives new insight into southern african early pastoralism

Project description:The advent of domestication is a major step that transformed the subsistence strategies of past human societies. In Africa, domestic caprines (sheep and goat) were introduced in the north-eastern part of the continent from the Near East more than 9000 years ago. However, their diffusion southwards was slow. They were thought to have made their first appearance in the southern part of the continent ca. 2000 years ago, at a few Later Stone Age sites, including Leopard Cave (Erongo region, Namibia), which provided the oldest directly dated remains assigned to sheep or goat on the basis of morphology of bones and teeth. However, similarities in morphology between these two domesticated caprine species and between them and small wild antelopes, as well as the high fragmentation of the sites osteological remains which alter their initial morphology, raised questions about the species attribution. In this paper, we report species identification of the Leopard Cave remains using palaeoproteomics, a method that uses protein markers in bone and tooth collagen to achieve taxonomic identification of archaeological remains. We also report new direct radiocarbon dates. Wild antelope remains from museum collections were used to enrich the available protein record and propose de novo type I collagen sequences. Our results demonstrate that the remains morphologically described as domesticates actually belong to a wild antelope species and that domestic caprines first appeared at Leopard Cave 1500 years later than previously thought. This study illustrates that the use of palaeoproteomics coupled to direct radiocarbon dates is particularly suited to complement classic zooarchaeological studies, in this case concerning the arrival of the first herding practices in arid environments.

2020-09-08 | PXD017519 | Pride

The name of the game: palaeoproteomics and radiocarbon dates further refine the presence and dispersal of caprines in eastern and southern Africa

Project description:Genetic, linguistic, and archaeological studies have demonstrated the existence of strong links between eastern and southern Africa over the past millennia, including the diffusion of the first domesticated sheep and goats. However, the proportions at which they were introduced into past human subsistence strategies in Africa is difficult to assess archaeologically, as caprines share skeletal features with a number of wild bovids. Palaeoproteomics has proven effective at retrieving biological information from archaeological remains in African arid contexts. Using published collagen sequences and generated de novo ones of wild bovids, we present the molecular (re-)attribution of remains morphologically identified as sheep/goat or unidentifiable bovids from seventeen archaeological sites distributed between eastern and southern Africa and spanning seven millennia. More than 70% of the remains were identified and the direct radiocarbon dating of domesticates specimens allowed the chronological refinement of the arrival of caprines in both African regions. Our results further substantiate a predominance of sheep in the assemblages along with a similar arrival chronology. Beyond adding substantial biological data to the field of (palaeo-)proteomics, it is the first large-scale palaeoproteomics investigation to include both eastern and southern African sites, opening promising future applications of the method on the continent.

2023-11-08 | PXD045452 | Pride

Successive protein extraction using hydroxylamine to increase the depth of proteome coverage in fresh, forensic and archaeological bones

Project description:Proteomics is continually being applied to a wider range of applications, now including the analysis of archaeological samples and anatomical specimens, in particular, collagen-containing tissues such as bones and teeth. Here we present the application of a chemi-cal digestion-based proteomics sample preparation protocol to the analysis of fresh, anatomical and archaeological samples. We are describing and discussing two protocols, one using hydroxylamine as an additional step of the proteomic workflow, applied to the insoluble fraction, and another focusing directly on demineralized bones and teeth. We demonstrate the additional information that can be extracted using both protocols, including increasing the sequence coverage and number of peptides detected in modern and archaeological samples, and increasing the number of proteins identified in archaeological samples. Targeting research related to collagens or extracellular matrix proteins, the use of this protocol will open new insights considering both fresh and ancient mineral-ized samples.

2024-03-28 | PXD046969 | Pride

Pilot study: Basal gene expression in bone

Project description:Pilot study Analysis of basal gene expression of the protective bones of the skull (parietals), weight-bearing bones of the limb (ulnae) and mandibular bone and teeth

2008-11-15 | GSE13563 | GEO

Transcription profiling of mouse protective bones of the skull (parietals), weight-bearing bones of the limb (ulnae), mandibular bone and teeth to obtain basal gene expression levels

Project description:Pilot study; Analysis of basal gene expression of the protective bones of the skull (parietals), weight-bearing bones of the limb (ulnae) and mandibular bone and teeth Experiment Overall Design: RNA extraction from normal bone

2008-11-22 | E-GEOD-13563 | biostudies-arrayexpress

Palaeoproteomic identification of breast milk protein residues from the archaeological skeletal remains of a neonatal dog

Project description:Accurate postmortem estimation of breastfeeding status for archaeological or forensic neonatal remains is difficult. Confident identification of milk-specific proteins associated with these remains, would provide direct evidence of breastmilk consumption. We used liquid chromatography coupled to tandem mass spectrometry (MS) to confidently identify beta-lactoglobulin-1 (LGB1) and whey acidic protein (WAP), major whey proteins associated with a neonatal dog (Canis lupus familiaris) skeleton (430–960 cal AD), from an archaeological site in Hokkaido, Japan. The age at death of the individual was estimated to be approximately two weeks after birth. Protein residues extracted from rib and vertebra fragments were analyzed and identified by matching tandem MS spectra against the dog reference proteome. A total of 200 dog protein groups were detected and at least 1 peptide from canine LGB1 and two peptides from canine WAP were confidently identified. These milk proteins most probably originated from the mother’s breastmilk, ingested by the neonate just before it died. We suggest the milk diffused outside the digestive apparatus during decomposition, and by being absorbed into the bones, it partially preserved. The result of this study suggests that proteomic analysis can be used for postmortem reconstruction of the breastfeeding status at the time of death of neonatal mammalian, by analyzing their skeletal archaeological remains. This method is also applicable to forensic and wildlife studies.

2019-09-09 | PXD014657 | Pride

Sex Determination of Infant Remains

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

Sex estimation of human remains using the results of tooth enamel peptidomic analyses, LC-MSMS

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

No ancient pathogen DNA in petrous bones

Project description:Ancient pathogen DNA in human teeth and petrous bones

| PRJEB24937 | ENA

PALEOPROTEOMICS APPLIED TO THE WAZIERS SITE

Project description:The ancient preserved molecules in bones offer the opportunity to gain a better knowledge on the biological past. In recent years, bones proteomics has become an attractive method to study extinct species and phylogenetic evolution as an alternative to DNA analysis which is limited by DNA amplification present in ancient samples and its contamination. The analysis of fossils must consume a low quantity of material to avoid damaging the samples. Another difficulty is the absence of genomic data for most of the extinct species. This study applied a proteomic methodology to mammalian bones of 130,000 / 120,000 years old from the last Chibanian and the earlier Upper Pleistocene site of Waziers (France). The presence of lithic artefacts and the traces of butchery observed on the bones indicate the presence of Neanderthal Man on this site. Starting from 5 milligram samples, our results show that most detected peptides match collagen I alpha 1 and alpha 2 proteins with a sequence coverage up to 60 %. Using sequence homology with modern sequences, a biological classification was successfully achieved. Each bone taxonomic rank by proteomics was consistent with the existing osteomorphological studies and palaeoenvironmental and palaeodietary data.

2023-04-20 | PXD039657 | Pride