Muscle transcriptome from active and hibernating brown bears (Ursus arctos)
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA605162 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11034900.fastq.gz | Fastqsanger.gz | |||
| SRR11034901.fastq.gz | Fastqsanger.gz | |||
| SRR11034902.fastq.gz | Fastqsanger.gz | |||
| SRR11034903.fastq.gz | Fastqsanger.gz | |||
| SRR11034904.fastq.gz | Fastqsanger.gz |
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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.
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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
2021-09-01 | GSE144856 | GEO
Project description:Brown bears (Ursus arctos) hibernate for 5-7 months without eating, drinking, urinating and defecating at a metabolic rate of only 25% of the summer activity rate. Nonetheless, they emerge healthy and alert in spring. We analyzed the physiological adaptations for hibernation by comparing the proteome, metabolome, and hematologic features of blood from hibernating and active free-ranging sub-adult brown bears with a focus on conservation of health and energy. We found that the concentrations of most plasma proteins and white blood cell types decreased during hibernation. Strikingly, antimicrobial defense proteins increased in concentration. Central functions in hibernation involving the coagulation response and protease inhibition, as well as lipid transport and metabolism, were upheld by increased levels of very few key or broad-specificity proteins. A dramatic 45-fold increase in sex-hormone-binding-globulin SHBG levels during hibernation draws, for the first time, attention to its significant but unknown role in maintaining hibernation physiology. We propose that energy for the costly protein synthesis is reduced by three mechanisms, (i) dehydration, which increases protein concentration without de novo synthesis; (ii) reduced protein degradation rates due to a 6°C reduction in body temperature, decreased protease activity, and increased plasma viscosity; and (iii) a marked redistribution of energy resources only increasing de novo synthesis of few key proteins. This comprehensive global data identified novel biochemical strategies for bear adaptations to the extreme condition of hibernation, and have implications for our understanding of physiology in general.
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Project description:We conducted a large-scale gene expression screen using the 3,200 cDNA probe microarray developed specifically for Ursus americanus to detect expression differences in liver and skeletal muscle that occur during winter hibernation in comparison to animals sampled during summer. The expression of 12 genes, including RNA binding protein motif 3 (Rbm3), that are mostly involved in protein biosynthesis, was induced during hibernation in both liver and muscle. The Gene Ontology and Gene Set Enrichment analysis consistently showed a highly significant enrichment of the protein biosynthesis category by over-expressed genes in both liver and skeletal muscle during hibernation. Coordinated induction in transcriptional level of genes involved in protein biosynthesis is a distinctive feature of the transcriptome in hibernating black bears. This finding implies induction of translation and suggests an adaptive mechanism that contributes to a unique ability to reduce muscle atrophy over prolonged periods of immobility during hibernation. Comparing expression profiles in bears to small mammalian hibernators shows a general trend during hibernation of transcriptional changes that include induction of genes involved in lipid metabolism and carbohydrate synthesis as well as depression of genes involved in the urea cycle and detoxification function in liver. Black bears sampled during winter hibernation were compared with the animals sampled during summer. Two tissue types, liver and muscle, were hybridized on a custom 3,200-gene nylon membrane microarray platform with three replicates for each gene (9.600 spots in total). Six hibernating and five summer active bears were studied in experiments with liver tissue, five hibernating and five summer active animals were tested with muscle tissue.
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Project description:We analyzed gene expression in the American black bear, Ursus americanus, using a custom 12,800 cDNA probe (BA02) microarray to detect differences in expression that occur in heart and liver during winter hibernation in comparison to summer active animals. We identified 245 genes in heart and 319 genes in liver that were differentially expressed between winter and summer. The expression of 24 genes was significantly elevated during hibernation in both heart and liver. These genes are mostly involved in lipid catabolism and protein biosynthesis and include RNA binding protein motif 3 (Rbm3), which enhances protein synthesis at mildly hypothermic temperatures. Elevated expression of protein biosynthesis genes suggests induction of translation that may be related to adaptive mechanisms reducing cardiac and muscle atrophies over extended periods of low metabolism and immobility during hibernation in bears. Coordinated reduction of transcription of genes involved in amino acid catabolism suggests redirection of amino acids from catabolic pathways to protein biosynthesis. We identify common for black bears and small mammalian hibernators transcriptional changes in the liver that include induction of genes responsible for fatty acid β oxidation and carbohydrate synthesis and depression of genes involved in lipid biosynthesis, carbohydrate catabolism, cellular respiration and detoxification pathways. Our findings show that modulation of gene expression during winter hibernation represents molecular mechanism of adaptation to extreme environments. Black bears sampled during winter hibernation were compared with the animals sampled during summer. Two tissue types, liver and heart, were hybridized on a custom 12,800 cDNA probe nylon membrane microarray platform . Six hibernating and five summer active bears were studied in experiments with liver tissue, six hibernating and five summer active animals were tested with heart tissue.
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