Ontology highlight
ABSTRACT:
PROVIDER: PRJNA988160 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25041000_1.fastq.gz | Fastqsanger.gz | |||
| SRR25041000_2.fastq.gz | Fastqsanger.gz | |||
| SRR25041001_1.fastq.gz | Fastqsanger.gz | |||
| SRR25041001_2.fastq.gz | Fastqsanger.gz | |||
| SRR25041002_1.fastq.gz | Fastqsanger.gz |
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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.
2009-03-09 | E-GEOD-15099 | biostudies-arrayexpress
Project description:Hibernating American black bears have significantly different clotting parameters than their active summer counterparts, affording them innate protection against venous thromboembolism (VTE) despite prolonged periods of immobility. Physiologic changes that occur during hibernation are thought to result from differential gene expression, rather than novel genes, and there is increasing evidence miRNAs may play an important role this regulation. We propose that significant differences exist in miRNA expression in the plasma of hibernating black bears compared to their active counter parts (summer), which lead to critical gene regulation responsible for auto-anticoagulation during hibernation. Methods: Blood was collected from 21 American black bears in the Northern Michigan Peninsula in summer 2017 and winter 2018 (11 active, 10 hibernating). Plasma was extracted Results: Fifteen miRNAs were differentially expressed in the plasma of hibernating black bears. Nine miRNAs were significantly downregulated (miR10b-3p, miR-136-3p, miR-181c-5p , miR-200a-3p, miR-200b-5p, miR-200c-3p, miR-320b, miR-320c and miR-320d) and six miRNAs were significantly upregulated (miR-15a-5p, miR-15b-3p, miR-15b-5p, miR-16-5p, miR-92a-3p, miR-150-5p) during hibernation. Twelve miRNAs had no identifiable targets, but miR-200a-3p, miR-200b-5p and miR-200c-3p found to be targets of SERPINC1, the gene responsible for the production of antithrombin (AT). Conclusions: Several miRNAs were differentially expressed in hibernating bears (12). Most importantly miR-200a-3p, miR-200b-5p and miR-200c-3p were all downregulated in hibernation and associated with increased expression of SERPINC1 and production of AT. AT is a powerful anticoagulant and this finding may explain the hibernating black bears ability to achieve auto-anticoagulation and protection from VTE.
2020-09-01 | GSE124398 | 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.
2016-09-27 | PXD003946 | Pride
Project description:Physical inactivity reduces mechanical load on the skeleton, which leads to losses of bone mass and strength in non hibernating mammalian species. Although bears are largely inactive during hibernation, they show no loss in bone mass and strength. To obtain insight into molecular mechanisms preventing disuse bone loss, we conducted a large-scale screen of transcriptional changes in trabecular bone comparing winter hibernating and summer non hibernating black bears using a custom 12,800 probe cDNA microarray. A total of 241 genes were differentially expressed (P < 0.01 and fold change > 0.5) in the ilium bone of bears between winter and summer. The Gene Ontology and Gene Set Enrichment analysis showed an elevated proportion in hibernating bears of over-expressed genes in six functional sets of genes involved in anabolic processes of tissue morphogenesis and development including skeletal development, cartilage development and bone biosynthesis. Apoptosis genes demonstrated a tendency for down regulation during hibernation. No coordinated directional changes were detected for genes involved in bone resorption, although some genes responsible for osteoclast formation and differentiation (Ostf1, Rab9a, c- Fos) were significantly under expressed in bone of hibernating bears. Elevated expression of multiple anabolic genes without induction of bone resorption genes, and the down regulation of apoptosis related genes, likely contribute to the adaptive mechanism that preserves bone mass and structure through prolonged periods of immobility during hibernation. Black bears sampled during winter hibernation were compared with the animals sampled during summer. Bone RNA were hybridized on a custom 12,800 cDNA probe nylon membrane microarray platform . Six hibernating and six summer active bears were studied in this experiments.
2012-02-15 | E-GEOD-35796 | biostudies-arrayexpress
Project description:Hibernation is energy saving adaptation involving suppression of activity to survive in highly seasonal environments. Immobility and disuse generate muscle loss in most mammalian species. In contrast to other mammals, bears and ground squirrels demonstrate limited muscle atrophy over the physical inactivity of winter hibernation. This suggests that hibernating mammals have adaptive mechanisms to prevent disuse muscle atrophy. To identify common transcriptional program underlying molecular mechanisms preventing muscle loss, we conducted a large-scale gene expression screening in hind limb muscles comparing hibernating and summer active black bears and arctic ground squirrels by the use of custom 9,600 probe cDNA microarrays. The molecular pathway analysis showed an elevated proportion of overexpressed genes involved in all stages of protein biosynthesis and ribosome biogenesis in muscle of both species during hibernation that implies induction of translation at different hibernation states. The induction of protein biosynthesis likely contributes to attenuation of disuse muscle atrophy through prolonged periods of immobility and starvation. This adaptive mechanism allows hibernating mammals to maintain full musculoskeletal function and preserve mobility during and immediately after hibernation, thus promoting survival. The lack of directional changes in genes of protein catabolic pathways does not support the importance of metabolic suppression for preserving muscle mass during winter. Coordinated reduction of multiply genes involved in oxidation reduction and glucose metabolism detected in both species is consistent with metabolic suppression and lower energy demand in skeletal muscle during inactivity of hibernation. Black bears sampled during winter hibernation were compared with the animals sampled during summer. Muscle tissue were hybridized on a custom 12,800 cDNA probe nylon membrane microarray platform . Six hibernating and six summer active bears were studied in the experiment.
2014-10-16 | E-GEOD-62220 | biostudies-arrayexpress
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.
2011-05-10 | E-GEOD-27875 | biostudies-arrayexpress
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.
2009-03-10 | GSE15099 | GEO
Project description:Physical inactivity reduces mechanical load on the skeleton, which leads to losses of bone mass and strength in non hibernating mammalian species. Although bears are largely inactive during hibernation, they show no loss in bone mass and strength. To obtain insight into molecular mechanisms preventing disuse bone loss, we conducted a large-scale screen of transcriptional changes in trabecular bone comparing winter hibernating and summer non hibernating black bears using a custom 12,800 probe cDNA microarray. A total of 241 genes were differentially expressed (P < 0.01 and fold change > 0.5) in the ilium bone of bears between winter and summer. The Gene Ontology and Gene Set Enrichment analysis showed an elevated proportion in hibernating bears of over-expressed genes in six functional sets of genes involved in anabolic processes of tissue morphogenesis and development including skeletal development, cartilage development and bone biosynthesis. Apoptosis genes demonstrated a tendency for down regulation during hibernation. No coordinated directional changes were detected for genes involved in bone resorption, although some genes responsible for osteoclast formation and differentiation (Ostf1, Rab9a, c- Fos) were significantly under expressed in bone of hibernating bears. Elevated expression of multiple anabolic genes without induction of bone resorption genes, and the down regulation of apoptosis related genes, likely contribute to the adaptive mechanism that preserves bone mass and structure through prolonged periods of immobility during hibernation.
2012-02-15 | GSE35796 | GEO
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.
2021-12-21 | PXD030482 | Pride
Project description:In mammals, loss of food intake and reduced mechanical loading/activity of skeletal muscles leads to a very rapid loss in mass and function. However, during hibernation in bears, despite spending months without feeding and with very modest muscle activity, only moderate muscle wasting is observed. Part of this tissue sparing is due to a highly reduced metabolic activity in almost all tissues, including skeletal muscle. Interestingly, myosin, one of the most abundant proteins in skeletal muscle, can have different metabolic activities in inactive muscle. Therefore, to evaluate the functional and metabolic alterations in hibernating muscles, we performed an analysis on a single muscle fiber level. Individual fibers were taken from biopsies of the same bears either during hibernation or during the active phase in the summer. We confirm that muscle fibers from hibernating bears show no loss of fiber size and a mild reduction in force generating capacity. However, ATPase activity of single muscle fibers taken from hibernating bears show a significant reduction in ATPase activity, which is due to a reduced ATP turnover by myosin. By performing a single fiber proteomics analysis, we could determine in a fiber type specific manner that muscle fibers undergo a major remodeling of their proteome. Both type 2A and type 1/2A mixed fibers show a marked reduction in mitochondrial proteins during hibernation, with a decrease in proteins linked to the TCA cycle and mitochondrial translation.
2024-12-06 | PXD050980 | Pride