Ontology highlight
ABSTRACT:
PROVIDER: PRJNA880433 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21594500.fastq.gz | Fastqsanger.gz | |||
| SRR21594501.fastq.gz | Fastqsanger.gz | |||
| SRR21594502.fastq.gz | Fastqsanger.gz | |||
| SRR21594503.fastq.gz | Fastqsanger.gz | |||
| SRR21594504.fastq.gz | Fastqsanger.gz |
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Project description:Characterisation of eggshell proteomes from the extinct Madagascar elephant bird
2023-01-20 | PXD035725 | Pride
Project description:Here we show the potential of proteins preserved in Pleistocene eggshell for addressing a longstanding controversy in human and evolution: the identity of the extinct bird that laid the eggs which were exploited by Australia’s first inhabitants. The eggs had been originally attributed to the iconic extinct flightless Genyornis newtoni, and subsequently dated to before 50 ±5 ka by Miller et al. (2016). This was taken to represent the extinction date for this endemic megafaunal species and thus implied a role of humans in its demise. A contrasting hypothesis, according to which the eggshell was laid by a large megapode (mound-builder), would therefore acquit humans of their responsibility in the extinction of Genyornis. Ancient protein sequences were reconstructed and used to assess the evolutionary proximity of the undetermined eggshell to extant birds, rejecting the megapode hypothesis. Ancient DNA could not be retrieved from these highly degraded samples, but morphometric data supported the attribution of the eggshell to Genyornis. When used in triangulation to address well-defined hypotheses, palaeoproteomics is a precious tool for reconstructing the evolutionary history of extinct and extant species. Here we show that the identification of Genyornis eggshell implies a more nuanced understanding of the modes of interactions between humans and their environment.
2022-07-19 | PXD027713 | Pride
Project description:Ancient DNA (aDNA) sequencing has enabled reconstruction of speciation, migration, and admixture events for extinct taxa. Outside the permafrost, however, irreversible aDNA post-mortem degradation has so far limited aDNA recovery to the past ~0.5 million years (Ma). Contrarily, multiple analyses suggested the presence of protein residues in Cretaceous fossil remains. Similarly, tandem mass spectrometry (MS) allowed sequencing ~1.5 million year (Ma) old collagen type I (COL1), though with limited phylogenetic use. In the absence of molecular evidence, the speciation of several Early and Middle Pleistocene extinct species remain contentious. In this study, we address the phylogenetic relationships of the Eurasian Pleistocene Rhinocerotidae using a ~1.77 Ma old dental enamel proteome of a Stephanorhinus specimen from the Dmanisi archaeological site in Georgia (South Caucasus). Molecular phylogenetic analyses place the Dmanisi Stephanorhinus as a sister group to the woolly (Coelodonta antiquitatis) and Merck’s rhinoceros (S. kirchbergensis) clade. We show that Coelodonta evolved from an early Stephanorhinus lineage and that the latter includes at least two distinct evolutionary lines. As such, the genus Stephanorhinus is currently paraphyletic and requires systematic revision. We demonstrate that Early Pleistocene dental enamel proteome sequencing overcomes the limits of ancient collagen- and aDNA-based phylogenetic inference. It also provides additional information about the sex and taxonomic assignment of the specimens analysed. Dental enamel, the hardest tissue in vertebrates, is highly abundant in the fossil record. Our findings reveal that palaeoproteomic investigation of this material can push biomolecular investigation further back into the Early Pleistocene.
2019-09-11 | PXD011008 | Pride
Project description:Claims for exceptional preservation of biomolecules in the fossil record are contested. Here we demonstrate the role of surface stabilisation in significantly prolonging protein sequence survival to ~3.8 million years. The intracrystalline environment of calcite ostrich (Struthionidae) eggshell encapsulates uterine proteins and molecular dynamics simulations of struthiocalcin-1 & -2, the dominant proteins within the eggshell, reveal that they bind to the mineral surface in distinct domains. By ~3.8 million years the struthiocalcin-1 domain with the lowest calculated binding energy is selectively preserved in eggshell samples from equatorial Africa. Sequence survival is explained by entropy loss of the peptide and water, lowering the effective temperature of the local environment at the peptide mineral interface.
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Project description:Ancient DNA from a 2,500-year-old Caribbean fossil places an extinct bird (Caracara creightoni) in a phylogenetic context
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Project description:Gene expression analysis of yw follicles at S9/10a, S10B, S12, and S14; Gene expression analysis of pxt mutant follicles (f01000 and EY03052) at S10B, S12, S14 Drosophila ovarian follicles complete development using a spatially and temporally controlled maturation process in which they resume meiosis and secrete a multi-layered, protective eggshell before undergoing arrest and/or ovulation. Microarray analysis revealed more than 150 genes that are expressed in a stage-specific manner during the last 24 hours of follicle development. These include all 30 previously known eggshell genes, as well as 19 new candidate chorion genes and 100 other genes likely to participate in maturation. Mutations in pxt, encoding a putative Drosophila cyclooxygenase, cause many transcripts to begin expression prematurely, and are associated with eggshell defects. Somatic activity of Pxt is required, as RNAi knockdown of pxt in the follicle cells recapitulates both the temporal expression and eggshell defects. One of the temporally regulated genes, cyp18a1, which encodes a cytochromome P450 protein mediating ecdysone turnover, is downregulated in pxt mutant follicles, and cyp18a1 mutation itself alters eggshell gene expression. These studies further define the molecular program of Drosophila follicle maturation and support the idea that it is coordinated by lipid and steroid hormonal signals.
2011-06-09 | GSE29815 | GEO
Project description:Gene expression analysis of yw follicles at S9/10a, S10B, S12, and S14; Gene expression analysis of pxt mutant follicles (f01000 and EY03052) at S10B, S12, S14 Drosophila ovarian follicles complete development using a spatially and temporally controlled maturation process in which they resume meiosis and secrete a multi-layered, protective eggshell before undergoing arrest and/or ovulation. Microarray analysis revealed more than 150 genes that are expressed in a stage-specific manner during the last 24 hours of follicle development. These include all 30 previously known eggshell genes, as well as 19 new candidate chorion genes and 100 other genes likely to participate in maturation. Mutations in pxt, encoding a putative Drosophila cyclooxygenase, cause many transcripts to begin expression prematurely, and are associated with eggshell defects. Somatic activity of Pxt is required, as RNAi knockdown of pxt in the follicle cells recapitulates both the temporal expression and eggshell defects. One of the temporally regulated genes, cyp18a1, which encodes a cytochromome P450 protein mediating ecdysone turnover, is downregulated in pxt mutant follicles, and cyp18a1 mutation itself alters eggshell gene expression. These studies further define the molecular program of Drosophila follicle maturation and support the idea that it is coordinated by lipid and steroid hormonal signals. minimum of 2 replicates per stage and genotype. yw=control follicles. pxt=mutant follicles.
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