The TNH2 hominin enamel proteome
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive HF-X
ORGANISM(S): Homo
TISSUE(S): Tooth Enamel
SUBMITTER: 
Frido Welker
LAB HEAD: Enrico Cappellini
PROVIDER: PXD018721 | Pride | 2022-04-06
REPOSITORIES: Pride
Similar Datasets
Project description:Here we analyse two enamel protein extractions from a single Late Pleistocene dental fragment from Nam Lot (Laos). The proteome is analyzed for potential phylogenetic information, from which we concude the specimen represents an individual belonging to the genus Pongo, and characterized in terms of its molecular damage (deamidation, peptide lengths).
2021-11-30 | PXD027426 | Pride
Project description:Hominin relationships and their dispersal throughout Eurasia during the Early and Middle Pleistocene are highly debated. The relationships between Early and Middle Pleistocene hominins, like Homo antecessor and Homo erectus, and hominin species that dominate the Late Pleistocene fossil record, like Homo sapiens, Neanderthals and Denisovans, are unclear. Here, we obtain enamel proteomes from Homo antecessor (Atapuerca, Spain) and Homo erectus (Dmanisi, Georgia), two key fossil assemblages that have a central role in models of Pleistocene hominin morphology, dispersal, and divergence. We recover endogenous ancient proteomes from the Atapuerca and Dmanisi hominins. In addition, our proteomic data indicates that the sampled Homo antecessor molar derives from a male hominin through amelogenin protein sexing. Our data includes preserved in vivo phosphorylation and enamel proteome proteolytic digestion.
2020-04-02 | PXD014342 | Pride
Project description:Gigantopithecus blacki was a giant hominid that inhabited Southeast Asia during the Pleistocene. Its evolutionary relationship to other great ape species, and their divergence during the Middle and Late Miocene (16-5.3 Mya), remains disputed. In part, this is due to the absence of cranial and postcranial remains and size-induced allometry. Proposed hypothesis on the phylogenetic positions of Gigantopithecus have therefore been wide-ranging among hominoids, but none has received independent validation based on molecular evidence. To clarify the phylogenetic placement of Gigantopithecus blacki, we retrieved enamel proteome sequences from a 1.9 million years (Mya) old molar found in Chuifeng Cave, China. We demonstrate that Gigantopithecus is most closely related to orangutans (genus Pongo). We also estimate the Gigantopithecus-Pongo divergence to about 10-12 Mya, implying its speciation is part of the Miocene radiation of great apes. These sequences are approximately 6 times older, in a normalized thermal context, than any previously published mammalian proteome or genome. The survival of an Early Pleistocene dental enamel proteome in the subtropics further expands the scope of palaeoproteomic analysis into geographic areas and time periods previously considered incompatible with biomolecular preservation.
2019-11-12 | PXD013838 | Pride
Project description:Pleistocene Pongo teeth show substantial variation in size and morphology, fueling taxonomic debates about the paleodiversity of the genus. We investigated prominent features of the enamel-dentine-junction junction (EDJ) – phylogenetically informative internal structures – of 71 fossil Pongo lower molars from various sites by applying geometric morphometrics and conducted paleoproteomic analyses from enamel proteins to attempt to identify extinct orangutan species. Forty-three orangutan lower molars representing Pongo pygmaeus and Pongo abelii were included for comparison. The shape of the EDJ was analyzed by placing five landmarks on the tip of the main dentine horns, and 142 semilandmarks along the marginal ridges connecting the dentine horns. Paleoproteomic analyses were conducted on 15 teeth of Late Pleistocene Pongo using high-resolution tandem mass spectrometry. The geometric morphometric results show variations in EDJ shape regarding aspects of the height and position of the dentine horns and connecting ridges. Despite the issue of molar position and sample size, modern molars are distinguished from fossil counterparts by their elongated tooth outline and narrowly positioned dentine horns. Proteomic results show that neither a distinction of P. pygmaeus and P. abelii, nor a consistent allocation of fossil specimens to extant species is feasible. Based on the EDJ shape, the (late) Middle to Late Pleistocene Pongo samples from Vietnam share the same morphospace, supporting the previous allocation to P. devosi, although substantial overlap with Chinese fossils could also indicate close affinities with P. weidenreichi. The hypothesis that both species represent one chronospecies cannot be ruled out. Two fossil specimens, one from Tam Hay Marklot (Laos, Late Pleistocene), and another from Sangiran (Java, Early to Middle Pleistocene), along with some specimens within the Punung sample (Java), exhibit affinities with Pongo abelii. The Punung fossils might represent a mix of early Late Pleistocene and later specimens (terminal Pleistocene to Holocene) related to modern Pongo. The taxonomy and phylogeny of the complete Punung sample needs to be further investigated.
2023-09-06 | PXD040213 | Pride
Project description:Palaeoproteomics of skeletal tissues has the potential to provide new insights into the evolutionary relationships between globally distributed hominin fossils across the Pleistocene. The use of alternative or additional proteases has the potential to increase both proteome size and protein. However, the potential of alternative proteases beside trypsin remains unexplored systematically in palaeoproteomic studies. Here, we present a comparison of the bone proteome size and protein sequence recovery of six different proteases from four Pleistocene bone specimens. We observe that the majority of the preserved bone proteome is inaccessible to trypsin. We also note that for proteins recovered consistently across several proteases, protein sequence coverage can be increased significantly by combining peptide identifications from two or more proteases. Our results thereby demonstrate that the proteolysis of Pleistocene proteomes by several proteases has clear advantages when addressing evolutionary questions in palaeoproteomics.
2020-10-13 | PXD018264 | Pride
Project description:To study the genomic RNA sequence of SARS CoV from different patients and cultured virus.
2007-04-25 | E-MEXP-510 | biostudies-arrayexpress
Project description:Understanding the effect of glycation on the function of transferrin, the systemic iron transporter, is fundamental to fully grasp the mechanisms leading to the loss of iron homeostasis observed in diabetes mellitus (DM). The spontaneous reaction with protein amino groups is one of the main causes of glucose toxicity, but the site specificity of this reaction is still poorly understood. Unbalance of iron metabolism has long been described in DM patients, and one of the main features is the occurrence of non-transferrin-bound iron in the blood serum. The presence of these toxic iron species is observed, despite low transferrin saturation levels. Here in, an in vitro approach was used to study human holo-transferrin glycation in detail. Holo-transferrin was incubated with increasing concentration of glucose (10; 20; 100 and 500 mM) and glycation sites were identified using nano-reverse phase – liquid chromatography coupled to high resolution mass spectrometry (nLC-MS). Overall 21 glycation hotspots were identified with lysine residues 103, 312 and 380 proving to be the most reactive sites. Glycation specificity was found to be remarkably different from that described for apo-transferrin.
2018-05-30 | PXD009345 | Pride
Project description:A dentine sample from a previously unknown hominin specimen deriving from the Tibetan Plateau was analyzed using LC-MS/MS in order to characterize its proteome, protein damage characteristics, and phylogenetic affinities to known Late Pleistocene hominin clades (humans, Neanderthals, Denisovans).
2019-05-08 | PXD011377 | Pride
Project description:To study the genomic RNA sequence of SARS CoV from different patients, cultured virus, and clones
2007-10-30 | E-MEXP-511 | biostudies-arrayexpress
Project description:Genetic changes causing brain size expansion in human evolution have remained elusive. Notch signaling is essential for radial glia stem cell proliferation and a determinant of neuronal number in the mammalian cortex. We find three paralogs of human-specific NOTCH2NL are highly expressed in radial glia. Functional analysis reveals different alleles of NOTCH2NL have varying potencies to enhance Notch signaling by interacting directly with NOTCH receptors. Consistent with a role in Notch signaling, NOTCH2NL ectopic expression delays differentiation of neuronal progenitors, while deletion accelerates differentiation. Furthermore, NOTCH2NL genes provide the breakpoints in typical cases of 1q21.1 distal deletion/duplication syndrome, where duplications are associated with macrocephaly and autism, and deletions with microcephaly and schizophrenia. Thus, the emergence of hominin-specific NOTCH2NL genes may have contributed to the rapid evolution of the larger hominin neocortex accompanied by loss of genomic stability at the 1q21.1 locus and a resulting recurrent neurodevelopmental disorder.
2018-02-26 | GSE111082 | GEO