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."
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: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.
2015-07-17 | PXD001827 | Pride
Project description:Genotyping-by-sequencing for Arctic char in arctic Alaska
Project description:Hibernation is an energy-saving strategy adopted by a wide range of mammals to survive highly seasonal or unpredictable environments. Arctic ground squirrels living in Alaska provide an extreme example, with 6-9 months long hibernation seasons when body temperature alternates between levels near 0 C during torpor and 37 C during arousal episodes. Heat production during hibernation is provided, in part, by non-shivering thermogenesis that occurs in large deposits of brown adipose tissue (BAT). BAT is active at tissue temperatures from 0 to 37 C during rewarming and continuously at near 0 C during torpor in subfreezing conditions. Despite its crucial role in hibernation, the global gene expression patterns in BAT during hibernation compared to the non-hibernation season remain largely unknown. We report a large-scale study of differential gene expression in BAT between winter hibernating and summer active arctic ground squirrels using mouse microarrays. Selected differentially expressed genes identified on the arrays were validated by quantitative real-time PCR using ground squirrel specific primers. Our results show that the mRNA levels of the genes involved in nearly every step of the biochemical pathway leading to non-shivering thermogenesis are significantly increased in BAT during hibernation, whereas those of genes involved in protein biosynthesis are significantly decreased compared to the summer active animals in August. The differentially expressed genes also include those involved in adipose differentiation, substrate transport, and structure remodeling, which may enhance thermogenesis at low tissue temperatures in BAT. Keywords: hibernating animals vs. summer active animals