Biology subjects

Godinho, R. M.

Publications and source records attributed to Godinho, R. M..

3 recordsLinked to original sources

bioRxiv2026

Beyond dairy: Identification of dental enamel proteins in ancient human dental calculus

Ancient human dental calculus is one of the richest archives of archaeological biomolecular information, providing direct evidence of diet, oral health, and the oral microbiome. Proteomic analyses of this biological matrix have so far focused mainly on oral microbes and dietary proteins, with milk proteins such as beta-lactoglobulin (BLG) providing the largest corpus of proteomic evidence. Despite the close relation between the various stages of dental calculus formation and mineralization with the dental enamel surface, proteins from the dental enamel matrix have not previously been reported outside of dental enamel tissue. Here we reanalysed 498 ancient dental calculus proteomes from 14 published studies (n=434 individuals) reporting the presence of BLG, spanning from the Neolithic to the Victorian Era and applying different protein extraction protocols (FASP, GASP, SP3 and in-solution digestion). Dental enamel matrix proteins were identified in ten studies (n=37 individuals), with amelogenin being the most frequently detected. Enamel peptides occurred more often in studies that applied SP3, although amelogenin was successfully identified through both SP3 and FASP. Structural proteins, including enamelin, ameloblastin, and MMP20, were also identified. The detection of AMELX and AMELY peptide sequences provided new insights into cases where the sex was previously undetermined. These findings establish dental enamel proteins as a new category of biomolecules detected in dental calculus, broadening its application beyond diet and microbiome studies to possible sex estimation. HighlightsO_LIDental calculus entraps oral microbes along with endogenous and exogenous particles during formation and mineralization C_LIO_LIWe conduct reanalysis of 14 published ancient dental calculus studies (n = 434 individuals) spanning the Neolithic to Victorian Era C_LIO_LIDental enamel proteins AMELX, AMELY, AMBN, COL17A1, ENAM and MMP20 are identified in ancient human dental calculus C_LIO_LIAmelogenin was the most frequently detected enamel protein C_LIO_LIWe expand dental calculus palaeoproteomics beyond diet and oral microbiome to potentially include sex estimation C_LI

evolutionary biology↗

bioRxiv2026

Early development of Neanderthals revealed through virtual microanatomy

The ontogeny of Neanderthal (Homo neanderthalensis) perinates is poorly understood due to the paucity of juvenile skeletal remains. Here we reconstruct fetal bone growth, and explore deciduous tooth structures, in three Neanderthal juveniles (Sesselfelsgrotte, 1, 2 and 3) (90,000-50,000 years ago) from southeastern Germany using non-destructive microcomputed tomography. Sesselfelsgrotte 1 exhibited bone tissue consistent with modern human perinatal plexiform-like structures and primary osteons. Long bones showed regions of advanced growth compared to the mandible and frontal bone, which can be explained through different processes of ossification and potentially localized faster development in Neanderthals compared to modern humans. Bone microstructure resembles that of the late third trimester of modern humans, agreeing with previous estimates based on macroscopic data. Sesselfelsgrotte 2 and 3 deciduous teeth retain hypodensities deep within the crown dentine consistent with interglobular dentine. We conclude that the fetal bone patterning is similar to modern humans with areas of advanced growth, indicating that the growth trajectory for this Neanderthal perinate was broadly equivalent to that of modern humans. The abnormal dentine mineralization points toward a possible systemic disorder.

evolutionary biology↗

bioRxiv2021

SPIN - Species by Proteome INvestigation

Genetic species determination has become an indispensable tool in forensics, archaeology, ecology, and food authentication. The available methods are either suited for detecting a single taxon across many samples or for screening a wide range of species across a few samples. Here, we introduce "Species by Proteome INvestigation" (SPIN), a proteomics workflow capable of querying over 150 mammalian species in 7.2 minutes of mass spectrometry (MS) analysis. Streamlined and automated sample preparation by protein aggregation capture, high-speed chromatography and data-independent acquisition, and a confident species inference algorithm facilitate processing hundreds of samples per day. We demonstrate the correct classification of known references, reproducible species identification in degraded Iron-Age material from Scandinavia, and test the limits of our methods with Middle and Upper Palaeolithic bones from Southern European sites with late Neanderthal occupation. While this initial study is focused on modern and archaeological mammalian bone, SPIN will be open and expandable with other biological tissues and taxa.

biochemistry↗