Project description:Characterization of Middle Pleistocene rhinoceros proteins and the phylogenetic relationships between extinct and extanct rhinoceros was investigated by obtaining ancient protein data for two extinct rhinoceros genera (Coelodonta antiquitatis and Stephanorhinus sp.).
2017-02-02 | PXD005534 | Pride
Project description:Whole genome sequencing of Galapagos giant tortoises
Project description:The living tree sloths Choloepus and Bradypus are the only remaining members of Folivora, a major xenarthran radiation that occupied a wide range of habitats in many parts of the western hemisphere during the Cenozoic, including both continents and the West Indies (Antilles). To date, molecular evidence has played only a minor role in folivoran systematics, as most recently-extinct species lived in places not conducive to DNA preservation. Here we utilize collagen sequence information to assess the relationships of tree sloths to a large sample (13 species) of extinct Quaternary folivorans.
Project description:Root-knot nematodes (RKNs; Meloidogyne spp.) are destructive agricultural parasites, but although giant cell formation is required for establishing parasitism, the mechanism of action has not been fully elucidated. Spatial transcriptomics enables precise spatiotemporal analyses of gene expression, facilitating studies of cell heterogeneity. We performed spatial transcriptomic sequencing on Moneymaker tomato root galls caused by M. incognita infection at 3, 5, and 7 days post-inoculation to investigate RKN-induced giant cell formation. Five major cell types were identified; of these, giant cell clusters were localized predominantly in the xylem, stele, and meristem. Four novel giant cell-specific marker genes were confirmed through RNA in situ hybridization. Pseudotime analysis revealed genes potentially associated with giant cell formation. Virus-induced gene silencing (VIGS) of four genes encoding a cyclin-dependent kinase, two cell division cycle-associated proteins, and a MYB3R-1-like transcription factor—hypothesized to maintain the cell cycle or gene expression during mitosis—resulted in significantly fewer galls and significantly smaller giant cells. This study established the first spatiotemporal atlas of RKN-infected tomato roots and identified genes associated with giant cell formation, laying a foundation for further research on the establishment of RKN feeding sites, providing novel insights into RKN pathogenic mechanisms, and potentially guiding novel control strategies.
Project description:Studies of ancient DNA have revolutionized our understanding of extinct organisms, but thus far the maximum estimated age of sequenced DNA is two million years. However, evidence for endogenous biomolecules, including proteins, lipids, and pigments have been found in much older fossils, dating to up to 195 million years. Amino acid sequence data consistent with ancient, endogenous biomolecules have been derived from specimens of the theropod Tyrannosaurus rex (MOR 1125) and the hadrosaur Brachylophosaurus canadensis (MOR 2598). Histochemical and immunological studies also identified a molecule consistent with DNA in these two ancient specimens, localized to a single point within preserved osteocytes. Here we report the sequencing and analysis of DNA extracted from osteocytes and blood vessels of T. rex and B. canadensis, liberated after demineralization of dense cortical bone. Usable sequence reads were obtained at a low recovery rate. After the removal of high-quality reads that mapped to the human genome, the remaining reads were highly fragmented, with similarities to multiple animal species including reptilian and avian genomes. Our findings support the hypothesis that DNA and histone signal from imaging, mass spectrometry, and DNA sequencing of dinosaur osteocytes are endogenously preserved biomolecules.
Project description:High resolution Mass Spectrometry and Peptides identification uncovered ancestral giant insect viruses motifs within Histone-4 peptides in human liver cells. These peptides did not match any human sequence. This finding consolidates the dogma that molecular patterns are universal and suggests that metazoan cellular structures possibly share an evolutionary link with ancient giant viruses.
