Project description:These metaproteomic datasets are from active layer soil samples collected from the area of Toolik Field Station, Arctic Alaska, USA. These datasets are described and analyzed in the forthcoming paper, "Functional partitioning and vegetational variation among Arctic soil bacteria revealed by metaproteomics."
| MSV000084386 | MassIVE
Project description:Ancient European and steppe bison mitochondrial diversity
Project description:Microbial decomposition of soil organic carbon (SOC) in Arctic permafrost is one of the most important, but poorly understood, factors in determining the greenhouse gas feedback of tundra ecosystems to climate. Here, we examine changes in the structure of microbial communities in an anoxic incubation experiment at either –2 or 8 °C for up to 122 days using both an organic and a mineral soil collected from the Barrow Environmental Observatory in northern Alaska, USA. Soils were characterized for SOC and geochemistry, and GeoChips 5.0 were used to determine microbial community structure and functional genes associated with C availability and Fe(III) reduction.
Project description:Differentiating between the genus Bos and Bison from fossil bones and teeth can be difficult and even impossible due to taphonomic deterioration, which can also muddle the identification of the sex of the animal. Both are key issues for palaeobiological and palaeoecological studies, as the two species are generally considered having quite similar spatial distributions but distinct ecological preferences, and likely similar social behaviours with males separated from female groups during most of the year. However, identifications are usually limited to “Bos/Bison” and “Sex indeterminate”, which severely limits interpretations. Here, we propose a low-invasive mass spectrometry method for simultaneous taxonomic and sex determination of Bos and Bison teeth, with successful application on a Middle Pleistocene large bovid teeth from Lazaret cave. The peptides and proteins present in the enamel were directly extracted at the surface of the teeth. The proteins were then digested with trypsin or chymotrypsin and analysed by LC-MS/MS. The results obtained show that the enamelin, COL1A3 and alpha-2-glycoprotein allow for taxonomic differentiation between Bos and Bison, while AMELX/Y sequences of the same samples allow for sex identification. Both were successfully performed on the 160-120 ky archaeological teeth, without affecting the specimen. This study highlights the potential of proteomics for simultaneous taxonomic and sex determination for others fossil samples, including rare or precious material, using low-invasive high-resolution mass spectrometry. It opens up unprecedent avenues for palaeobiological studies as well as cultural and natural heritage, and will widely participate to strengthen our knowledge of past animal and human communities. Such multi-proxy approach, shall be now developed for other mammalian species.
2025-06-16 | PXD063063 | Pride
Project description:Genotyping-by-sequencing for Arctic char in arctic Alaska
Project description:Bone samples from several vertebrates were collected from the Ziegler Reservoir fossil site, in Snowmass Village, Colorado and processed for proteomics analysis. The specimens come from Pleistocene megafauna, Bison latifrons, dating back to 110 or 120 ka. Proteomics analysis using a simplified sample preparation procedure and tandem mass spectrometry (MS) was applied to obtain protein identifications. Several bioinformatics resources were used to obtain peptide identifications based on sequence homology to extant species with annotated genomes. With the exception of soil sample controls, all samples resulted in confident peptide identifications that mapped to collagen I. In addition, we analyzed a specimen from the extinct Bison latifrons that yielded peptide identifications mapping to over 33 bovine proteins. Our analysis resulted in extensive fibrillar collagen sequence coverage, including the identification of post-translational modifications. Hydroxylysine glucosylgalactosylation, a modification thought to be involved in collagen fiber formation and bone mineralization, was identified. Meta-analyses of data from other studies indicates that this modification may be enriched in well-preserved prehistoric samples. Additional peptide sequences from extracellular matrix (ECM) and non-ECM proteins have also been identified. These data provide a framework for analyzing ancient protein signatures in well-preserved fossil specimens, while also contributing novel insights into the molecular basis of organic matter preservation.