Tardigrada
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR083827_1.fastq.gz | Fastqsanger.gz | |||
| DRR083827_2.fastq.gz | Fastqsanger.gz | |||
| DRR083828_1.fastq.gz | Fastqsanger.gz | |||
| DRR083828_2.fastq.gz | Fastqsanger.gz | |||
| DRR083829_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 168 |
Similar Datasets
Project description:Limno-terrestrial tardigrades enter a state called anhydrobiosis when exposed to desiccation, and acquire tolerance against various extreme environments. The anhydrobiotic tardigrade Hypsibius dujardini, is a non-pigmented tardigrade easy to culture and RNAi method have been established, therefore making it a model tardigrade for tardigrade molecular research. Previous genome assemblies of this tardigrade had increased size due to heterozygosity. Here, we have sequenced the genome of H. dujardini using single individual Illumina DNA-Seq data and PacBio long read data, and employed a heterozygosity aware assembly method to assemble a near-complete high quality genome. In order to annotate the genome with gene predictions, we conducted RNA-Sequencing of various stages of developmental, juvenile, adult, and anhydrobiotic stage H. dujardini and Ramazzottius varieornatus, a tardigrade capable of rapid anhydrobiosis entry, and used these data for gene prediction with BRAKER v1.9 or differential gene expression analysis of the active and anhydrobiotic stages.
2017-02-28 | GSE94295 | GEO
Project description:Tardigrades can survive remarkable doses of ionizing radiation, up to about 1000 times the lethal dose for humans. How they do so is incompletely understood. We found that the tardigrade Hypsibius exemplaris suffers DNA damage upon gamma irradiation, but damage is repaired. We show that this tardigrade has a specific and robust response to ionizing radiation: irradiation induces a rapid upregulation of many DNA repair genes. This upregulation is unexpectedly extreme, making some DNA repair transcripts among the most abundant transcripts in the animal. By expressing tardigrade genes in bacteria, we validate that increased expression of some repair genes can suffice to increase radiation tolerance. We show that at least one such gene is important for tardigrade radiation tolerance. We hypothesize that tardigrades’ ability to sense ionizing radiation and massively upregulate specific DNA repair pathway genes may represent an evolved solution for maintaining DNA integrity.
2024-04-12 | GSE240501 | GEO
Project description:Tardigrades can survive remarkable doses of ionizing radiation, up to about 1000 times the lethal dose for humans. How they do so is incompletely understood. We found that the tardigrade Hypsibius exemplaris suffers DNA damage upon gamma irradiation, but damage is repaired. We show that tardigrades have a specific and robust response to ionizing radiation: irradiation induces a rapid and dramatic upregulation of many DNA repair genes. By expressing tardigrade genes in bacteria, we validate that increased expression of some repair genes can suffice to increase radiation tolerance. We show that at least one such gene is necessary for tardigrade radiation tolerance. Tardigrades’ ability to sense ionizing radiation and massively upregulate specific DNA repair pathway genes may represent an evolved solution for maintaining DNA integrity.
2024-04-12 | GSE253470 | GEO
Project description:Transcriptome analysis of the extremophile tardigrade Hypsibius exemplaris exposed to the DNA-damaging agent bleomycin
2024-05-07 | GSE168917 | GEO
Project description:We explore whether a low-energy diet intervention for Metabolic dysfunction-associated steatohepatitis (MASH) improves liver disease by means of modulating the gut microbiome. 16 individuals were given a low-energy diet (880 kcal, consisting of bars, soups, and shakes) for 12 weeks, followed by a stepped re-introduction to whole for an additional 12 weeks. Stool samples were obtained at 0, 12, and 24 weeks for microbiome analysis. Fecal microbiome were measured using 16S rRNA gene sequencing. Positive control (Zymo DNA standard D6305) and negative control (PBS extraction) were included in the sequencing. We found that low-energy diet improved MASH disease without lasting alterations to the gut microbiome.
2024-12-31 | E-MTAB-14061 | biostudies-arrayexpress
Project description:Tardigrades can survive remarkable doses of ionizing radiation, up to about 1000 times the lethal dose for humans. How they do so is incompletely understood. We found that the tardigrade Hypsibius exemplaris suffers DNA damage upon gamma irradiation, but damage is repaired. We show that tardigrades have a specific and robust response to ionizing radiation: irradiation induces a rapid, dramatic upregulation of many DNA repair genes. By expressing tardigrade genes in bacteria, we validate that increased expression of some repair genes can suffice to increase radiation tolerance. We show that at least one such gene is necessary for tardigrade radiation tolerance. Tardigrades’ ability to sense ionizing radiation and massively upregulate specific DNA repair pathway genes may represent an evolved solution for maintaining DNA integrity.
2024-12-13 | PXD047724 | Pride
Project description:Tardigrades are microscopic invertebrates renowned for their ability to survive extreme environmental stress such as radiation, extreme temperatures, and desiccation. Yet, the biochemical mechanisms they utilize to survive these extremes are poorly understood. Herein, we implement proteomics to investigate the biomolecular underpinnings of tardigrade osmobiosis – a survival state in response to osmotic pressure. Using two solutes, the non-ionic sucrose and the ionic NaCl, we reveal that de novo gene expression is not required for osmobiosis induction. While sucrose and NaCl induce slightly different proteomic effects, both solutes lead to an increased abundance or oxidation of proteins involved in ER or mitochondrial activity. Further, we investigate the role of mitochondria in tardigrade osmobiosis and demonstrate that inhibition of the alternative oxidase (AOX) within the mitochondrial respiratory chain (MRC) increases the rate of osmobiosis formation across both sucrose and NaCl. Subsequent electron paramagnetic resonance (EPR) spectroscopy reveals an increased rate of reactive oxygen species (ROS) formation in osmobiotes with AOX inhibited, suggesting a regulation of osmobiosis through MRC-derived ROS. In sum, this work suggests mitochondrial-ROS signaling is necessary for tardigrade osmobiosis and further clarifies the biochemical mechanisms contributing to tardigrade extremotolerance.
2025-07-14 | PXD058865 | Pride
Project description:Tardigrades contain characteristic free-floating body cavity cells that are also called storage cells. To investigate the cell-specific expression patterns of tardigrade-unique genes, the expression levels of dissected storage cells are compared to those of the whole body.
2023-01-04 | GSE212632 | GEO
Project description:Pancreatic cancer is the 3rd most prevalent cause of cancer related deaths in United states alone, with over 55000 patients being diagnosed in 2019 alone and nearly as many succumbing to it. Late detection, lack of effective therapy and poor understanding of pancreatic cancer systemically contributes to its poor survival statistics. Obesity and high caloric intake linked co-morbidities like type 2 diabetes (T2D) have been attributed as being risk factors for a number of cancers including pancreatic cancer. Studies on gut microbiome has shown that lifestyle factors as well as diet has a huge effect on the microbial flora of the gut. Further, modulation of gut microbiome has been seen to contribute to effects of intensive insulin therapy in mice on high fat diet. In another study, abnormal gut microbiota was reported to contribute to development of diabetes in Db/Db mice. Recent studies indicate that microbiome and microbial dysbiosis plays a role in not only the onset of disease but also in its outcome. In colorectal cancer, Fusobacterium has been reported to promote therapy resistance. Certain intra-tumoral bacteria have also been shown to elicit chemo-resistance by metabolizing anti-cancerous agents. In pancreatic cancer, studies on altered gut microbiome have been relatively recent. Microbial dysbiosis has been observed to be associated with pancreatic tumor progression. Modulation of microbiome has been shown to affect response to anti-PD1 therapy in this disease as well. However, most of the studies in pancreatic cancer and microbiome have remained focused om immune modulation. In the current study, we observed that in a T2D mouse model, the microbiome changed significantly as the hyperglycemia developed in these animals. Our results further showed that, tumors implanted in the T2D mice responded poorly to Gemcitabine/Paclitaxel (Gem/Pac) standard of care compared to those in the control group. A metabolomic reconstruction of the WGS of the gut microbiota further revealed that an enrichment of bacterial population involved in drug metabolism in the T2D group.
2020-11-30 | E-MTAB-8739 | biostudies-arrayexpress