Biology subjects

De Groote, I.

Publications and source records attributed to De Groote, I..

5 recordsLinked to original sources

bioRxiv2025

Palaeoproteomics reveals bovine carcass processing with 6,000-year-old flint tools

Lithic tools are the most abundant cultural artefacts found at prehistoric archaeological sites. Through their study, we can understand essential activities such as hunting, processing of animal carcasses and plant materials, and working of resources such as ochre and bone, as well as broader technological and cultural practices. For the first time, proteomics was applied alongside use-wear and optical microscopy residue analyses, enabling the identification of bovine, plant, and human proteins on faceted tools from the Mesolithic-Neolithic site of Bazel-Sluis, Belgium. This retrieval of identifiable protein from an area with poor organic preservation demonstrates wide-reaching potential for archaeological research, opening a new avenue of investigation into prehistoric lifeways and adding to the growing corpus of evidence accessible through palaeoproteomics. A workflow for future analyses is suggested, based on our integrated sampling strategy requiring no additional tool manipulations.

paleontology↗

bioRxiv2024

ClassiCOL: LC-MS/MS analysis for ancient species Classification via Collagen peptide ambiguation

LC-MS/MS extends on the MALDI-TOF ZooMS approach by providing fragmentation spectra for each peptide. However, ancient bone samples generate sparse datasets containing only a few collagen proteins, rendering target-decoy strategies unusable and increasing uncertainty in peptide annotation. ClassiCOL embraces and even extends this ambiguity using a novel isoBLAST approach. The exhaustive set of potential peptide candidates created in this way is then used to retain or reject different potential paths at each taxonomic branching point down to the taxonomic level attainable with the sample information, always allowing for potential mixtures in the process. As an end point, all considered ambiguity is graphically represented with a clear prioritization of the species in the sample. Using public as well as in-house data, we demonstrate the performance of this universal postprocessing approach on different instruments and explore the possibility of identifying genetic as well as sample mixtures. Diet reconstruction from 40,000 year old cave hyena coprolites illustrates the exciting potential of this approach. TeaserClassiCOL is a postprocessing tool that allows for more accurate species classification from LC-MS/MS measurements of collagen.

bioinformatics↗

bioRxiv2019

Dental caries in human evolution: frequency of carious lesions in South African fossil hominins

Caries frequencies in South African fossil hominins were observed and compared with other hominin samples. Species studied include Paranthropus robustus, Homo naledi, Australopithecus africanus, early Homo and A. sediba. Teeth were viewed macroscopically with Micro-CT scans used to confirm lesions. Position and severity of each lesion were also noted and described. For all South African fossil hominin specimens studied, 16 have carious lesions, six of which are described for the first time in this study. These are from a minimum of six individuals, and include four P. robustus, one H. naledi, and one early Homo individual. No carious lesions were found on deciduous teeth, or any teeth assigned to A. africanus. Most are located interproximal, and only posterior teeth are affected. Caries frequency typically ranges between 1-5% of teeth in non-agricultural human samples, and this pattern seemingly holds true for at least the past two million years in the hominin lineage. Non-agricultural populations significantly above or below this threshold generally have a specialized diet, supporting other dietary evidence that A. africanus likely consumed large amounts of tough, non-cariogenic vegetation. Given the common occurrence of caries in the other hominin species, cariogenic bacteria and foods were evidently common in their collective oral environment. Along with recent research highlighting additional examples of caries in H. neanderthalensis, early Homo and Pleistocene H. sapiens, caries is clearly an ancient disease that was much more common than once maintained throughout the course of human evolution.View Full Text

paleontology↗

bioRxiv2017

Root grooves on two adjacent anterior teeth of Australopithecus africanus

Tooth root grooves and other ante-mortem dental tissue loss not associated with caries found on or near the cementoenamel junction (CEJ) are commonly termed non-carious cervical lesions. Three main processes are implicated in forming these lesions: abrasion, dental erosion, and abfraction. As yet, these lesions have not been described in non-Homo hominins. In this study South African fossil hominin collections were examined for evidence of any type of non-carious cervical lesion. Only one individual shows ante-mortem root grooves consistent with non-carious cervical lesions. Two teeth, a mandibular right permanent lateral incisor (STW 270) and canine (STW 213), belonging to the same Australopithecus africanus individual, show clear ante-mortem grooves on the labial root surface. These lesions start below the CEJ, extend over a third of the way toward the apex, and taper to a point towards the lingual side. Microscopic examination revealed no clear directional striations. The shape of these grooves is extremely similar to clinical examples of dental erosion, with the lack of striations supporting this diagnosis. These are the oldest hominin examples of non-carious cervical lesions and first described in a genus other than Homo; further, the lesions suggest that this individual regularly consumed or processed acidic food items.

paleontology↗

bioRxiv2017

Dietary and behavioral inferences from dental pathology and non-masticatory wear on dentitions from a British medieval town

Dental pathology and wear data can provide valuable insights into diet, cultural practices, and the health of populations. In this study, various dental pathologies and types of wear were recorded for 41 individuals (914 permanent teeth), excavated from the medieval cemetery of St. Owens Church in Southgate Street, Gloucester. Teeth were studied macroscopically with a 10x hand lens to confirm the presence of specific pathologies. Relatively high rates of antemortem chipping on the anterior teeth, and the presence of maxillary central incisor notches, suggested that the Gloucester population commonly used their teeth for non-masticatory activities. Abscessing and antemortem tooth loss fell within previously reported ranges for British medieval sites (2.6% and 6% respectively). However, the sample exhibits extremely high levels of carious lesions and calculus. Nearly 24% of teeth have at least one carious lesion, and the presence of calculus was recorded in 74% of teeth within the sample. Overall caries frequency is similar to sites from later time periods. This frequency may reflect Gloucesters location as a large port town. Remains from the same area, but the earlier Roman period, also shows high rates of both caries and calculus, suggesting a continuation of consuming certain cariogenic foods is likely.

pathology↗