Project description:Polar bears are an arctic, marine adapted species that is closely related to brown bears. Genome analyses have shown that polar bears are distinct and genetically homogeneous in comparison to brown bears. However, these analyses have also revealed a remarkable episode of polar bear gene flow into the population of brown bears that colonized the Admiralty, Baranof and Chichagof islands (ABC islands) of Alaska. Here, we present an analysis of data from a large panel of polar bear and brown bear genomes that includes brown bears from the ABC islands, the Alaskan mainland and Europe. Our results provide clear evidence that gene flow between the two species had a geographically wide impact, with polar bear DNA found within the genomes of brown bears living both on the ABC islands and in the Alaskan mainland. Intriguingly, while brown bear genomes contain up to 8.8% polar bear ancestry, polar bear genomes appear to be devoid of brown bear ancestry, suggesting the presence of a barrier to gene flow in that direction.
Project description:Male and female 2- and 3-years old brown bear from the region of Tackasen (Sweden) were captured in summer and winter. Muscle biopsies from vastus lateralis were collected in february (hibernation state) and june (active period). Total RNA were extracted from muscle tissue and full transcriptome analysis (RNA Seq) were performed. Statistical analysis were performed to winter versus summer comparison from matched paired samples
Project description:Recent studies have reported discordant gene trees in the evolution of brown bears and polar bears. Genealogical histories are different among independent nuclear loci and between biparentally inherited autosomal DNA (aDNA) and matrilineal mitochondrial DNA (mtDNA). Based on multi-locus genomic sequences from aDNA and mtDNA, we inferred the population demography of brown and polar bears and found that brown bears have 6 times (aDNA) or more than 14 times (mtDNA) larger population sizes than polar bears and that polar bear lineage is derived from within brown bear diversity. In brown bears, the effective population size ratio of mtDNA to aDNA was at least 0.62, which deviated from the expected value of 0.25, suggesting matriarchal population due to female philopatry and male-biased migration. These results emphasize that ancestral polymorphisms and sex-biased migration may have contributed to conflicting branching patterns in brown and polar bears across aDNA genes and mtDNA.
Project description:Here we provide mass-spectrometry based plasma proteomics data of hibernating and active wild Scandinavian brown bears (Ursus arctos arctos). The brown bear hibernates for half the year. Despite obesity and the prolonged period of inactivity, bears show no signs of the harmful effects associated with these conditions in humans. Thus, the hibernating bear is a protentional translational model for addressing these complications in humans. We analyzed plasma samples from 14 subadult 2- to 3-year-old (y/o) bears (6 males and 8 females) collected both during hibernation and active state, and for some for the bears during two seasons, resulting in a total of 38 analyzed plasma samples. In triplicates, the proteins in the plasma samples were unfolded and reduced. To increase depth of the analysis and the chance to detect low molecular weight proteins and peptides, we filtered samples with a 50K MWCO filter with the aim to deplete larger proteins. The proteins in the permeate were then tryptically digested, desalted, and analyzed with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Protein identification and quantification was performed with the MaxQuant software searching against an Ursus arctos horribilis protein database.
Project description:This SuperSeries is composed of the following subset Series: GSE29854: Daphnia magna exposed to narcotics and polar narcotics - aniline GSE29856: Daphnia magna exposed to narcotics and polar narcotics - 4-chloroaniline GSE29857: Daphnia magna exposed to narcotics and polar narcotics - 3,5-dichloroaniline GSE29858: Daphnia magna exposed to narcotics and polar narcotics - 2,3,4-trichloroaniline GSE29862: Daphnia magna exposed to narcotics and polar narcotics - ethanol GSE29864: Daphnia magna exposed to narcotics and polar narcotics - isopropanol GSE29867: Daphnia magna exposed to narcotics and polar narcotics - methanol Refer to individual Series
Project description:Clinicians need additional metrics for predicting quality of human oocytes for IVF procedures. Human polar bodies reflect the oocyte transcript profile. Quantitation of polar body mRNAs could allow for both oocyte ranking and embryo preferences in IVF applications. The transcriptome of a polar body has never been reported, in any organism. Eight total samples. There are 2 biological replicates of the following four conditions: pooled oocytes and their sister polar bodies and a single oocyte and its sister polar body.
Project description:Clinicians need additional metrics for predicting quality of human oocytes for IVF procedures. Human polar bodies reflect the oocyte transcript profile. Quantitation of polar body mRNAs could allow for both oocyte ranking and embryo preferences in IVF applications. The transcriptome of a polar body has never been reported, in any organism.
Project description:Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the directionality and relative timing of gene flow. We find that segments of cave bear DNA still persist in the genomes of living brown bears, with cave bears contributing 0.9 to 2.4% of the genomes of all brown bears investigated. Our results show that even though extinction is typically considered as absolute, following admixture, fragments of the gene pool of extinct species can survive for tens of thousands of years in the genomes of extant recipient species.