OEX_高_2404202217
Ontology highlight
ABSTRACT:
SUBMITTER: 高 壮
PROVIDER: OEX00027756 | NODE | 2024-06-19
REPOSITORIES: NODE
Similar Datasets
Project description:Regulator of Telomere Elongation Helicase 1 (RTEL1) plays a critical role in telomere replication by disassembling DNA secondary structures such as G-quadruplexes and telomeric loops (T-loops). However, its precise mechanism remains unclear. Previously, we generated HeLa cells homozygous for ATPase-dead RTEL1. Here, we found that these cells have a 50-60% reduction in the synthesis of both telomere strands, indicating that RTEL1 ATPase activity is essential for replicating both leading and lagging telomeric DNA. Surprisingly, these cells also showed a substantial reduction in Telomerase Reverse Transcriptase (TERT) mRNA levels and a 60-80% reduction in telomerase activity, without activating alternative lengthening of telomeres (ALT). Forced TERT overexpression suppressed proliferation and caused late S/G2 accumulation, implying that the natural TERT reduction provides adaptive resistance. Expressing wild-type (WT) RTEL1 at levels close to physiological levels failed to rescue growth defects, suggesting a dominant-negative effect. These results reveal unexpected interactions between RTEL1 and telomerase and show how cancer cells compensate for RTEL1 dysfunction by decreasing TERT expression.
2026-07-24 | GSE338949 | GEO
Project description:During the application of thermal treatment, cell survival depends on biological factors (such as growth stage, culture conditions, and the composition of the stress medium) as well as physical factors inherent to the thermal process (including amplitude, duration at the stress temperature, and the rate of temperature increase). In this study, the yeast Saccharomyces cerevisiae BY4742 was exposed to two different thermal treatment kinetics in a nutrient medium after being cultivated in YPD medium at 25 °C for 48 hours (to reach the stationary growth phase). The thermal treatments were applied between 25 °C and 50 °C, followed by a 30-minute hold at 50 °C before returning to 25 °C. The yeast cells were exposed either to a heat shock (heating kinetics: 50 °C/min) or to a gradual temperature increase (heating kinetics: 0.5 °C/min). Generally, it is known that heat shock induces lower survival (30%) compared to the gradual increase (80%). In this study, we demonstrate that despite the small difference in survival rate (less than one logarithmic reduction in both cases), the transcriptomes vary significantly. The use of bioinformatics tools such as WGCNA revealed a correlation between differentially expressed gene clusters and phenotypic traits (measured by spectroscopy, fluorescence microscopy, flow cytometry, among others). Here, we focused on both mRNA and ncRNA (non coding RNA).
2024-09-04 | GSE276309 | GEO
Project description:CK 30-20 30-50 30-100 60-50 Transcriptome
| PRJNA1390318 | ENA
Project description:Colon polyposis (the presence of multiple colon polyps) is very common with Cowden syndrome, as over 60% of patients have 50 or more polyps. In a previous clinical trial, some participants had reduction in the number of colon polyps with the use of the medication sirolimus for a very short time period. This study is investigating sirolimus and its effect on the number of colon polyps in patients with Cowden syndrome and polyposis over a 1 year period.
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Project description:Simulating predicted future climate conditions, stress response and stress-related memory after one week of recovery were transcriptionally characterised in young and old leaves, phloem-bark, developing xylem and roots of 3-month-old Grey poplar plants that had undergone three weeks of stress or were kept under control conditions. The control conditions include ambient or elevated CO2 levels (380 μL L-1 and 500 μL L-1, respectively) with a daily maximum temperature of 27 °C. The stress conditions include a periodic and a chronic drought-heat scenario at elevated CO2 levels (500 μL L-1) with a daily maximum temperature of 33 °C. The periodic stress treatment included three cycles of reduced irrigation (50%, 60% and 70% reduction compared with the controls), each one lasting for six days; between the cycles, there were recovery periods with a duration of two days and a daily maximum temperature of 27 °C. In the chronic stress treatment, irrigation was gradually reduced for 22 days, down to 70% reduction compared with the controls. Three biological replicates were examined per group defined by a specific environmental condition (droughtPER: periodic stress, droughtCHR: chronic stress, control500: elevated CO2 control, control380: ambient CO2 control), a specific harvesting time (S: stress phase, R: recovery phase) and a specific tissue (LE1: young leaves, LE2: old leaves, PHL: phloem-bark, XYL: developing xylem, ROO: roots). For stress phase ambient CO2 control in old leaves, one replicate failed quality control.
2019-01-11 | E-MTAB-6121 | biostudies-arrayexpress
Project description:Primary objectives: The main objective of this trial is to evaluate the efficacy and safety of the medicinal product TachoSil to reduce the degree of stenosis of the ureteres in patients undergoing radical cystectomy for bladder cancer and non-malignant conditions. As TachoSil is not registered for this use, a pilot study is chosen as an initial evaluation of the use in urological surgery.
The primary measurement will be assessment of kidney function at follow up relative to kidney function at inclusion. Kidney function will be evaluated by means of intravenous renography and GFR (glomerular filtration rate). A reduction in kidney function of 10% in one side measured by renography will be regarded as indicative of ureteral stenosis and a reduction of GFR 25% will indicate bilateral reduction/stenosis. . The kidney function will be assessed by intravenous renography and Glomerular Filtration Rate (GRF) at follow up after 2-3 months and 1 year after discharge.
Primary endpoints: The primary measurement will be assessment of kidney function at follow up relative to kidney function at inclusion. Kidney function will be evaluated by means of intravenous renography and GFR (glomerular filtration rate). A reduction in kidney function of 10% in one side measured by renography will be regarded as indicative of ureteral stenosis and a reduction of GFR 25% will indicate bilateral reduction/stenosis. . The kidney function will be assessed by intravenous renography and Glomerular Filtration Rate (GRF) at follow up after 2-3 months and 1 year after discharge. These two tests are chosen for evaluation of kidney function as they are the tests with a high level of evidence. All patients with reduced kidney function shown in one or both tests will be evaluated whether the reduction is caused by stenosis or other reasons (infections etc.).
| 2522613 | ecrin-mdr-crc
Project description:protein extraction was performed from kernels collected at fifteen and thirty days post self-pollination of the ubp5 mutant heterozygous (smd/+) and wild-type specimens using phenol. For quantifying protein expression levels, 500μg of dissolved protein underwent reduction by 50 mM DTT (3483-12-3, Sigma-Aldrich) at 37°C for 1 hour. Subsequently, 150 mM iodoacetamide (144-48-9, Sigma-Aldrich) was added to modify the reduced sulfhydryl groups. Following a 30-minute incubation period in darkness at room temperature, the protein sample underwent buffer exchange to 50 mM ammonium bicarbonate (A6141, Sigma-Aldrich) through an ultrafiltration column (UFC501096, Millipore). Enzymatic digestion was carried out using trypsin (V5111, Promega), and the resulting digest underwent purification using C18 Spin Tips (84850, Thermo) followed by elution with 60% acetonitrile and rapid drying under vacuum conditions.
2023-12-17 | PXD047889 |
Project description:microarray experiment to test the gene expression in long term lines of mutator and non-mutator yeast. Here we use an experimental evolution approach to investigate the conditions required for evolution of a reduction in mutation rate and the mechanisms by which populations tolerate the accumulation of deleterious mutations. We find that after ~6700 generations four out of eight experimental mutator lines had evolved a decreased mutation rate.
2012-02-02 | GSE35440 | GEO
Project description:Cell growth rate is regulated in response to resource availability including the abundance, and molecular form, of essential nutrients. In the model eukaryotic cell, Saccharomyces cerevisiae (budding yeast), the molecular form of environmental nitrogen impacts both cell growth rate and mRNA expression. Disentangling causal relationships between nitrogen availability, cell growth rate and differential gene expression poses a considerable challenge. Using experimental control of cell growth rate using chemostats, we studied the effect of variation in environmental nitrogen on differential gene expression. We find that the primary determinant of nitrogen-regulated gene expression is nitrogen abundance whereas variation in nitrogen source affects the expression of only a small number of transcripts with highly specialized functions. To study the dynamics of nitrogen-responsive gene expression we perturbed steady-state nitrogen-limited chemostat cultures by addition of either proline or glutamine. Addition of either proline or glutamine to cells growing in nitrogen-limited chemostats results in repression of the nitrogen catabolite repression (NCR) regulon consistent with nitrogen abundance, and not nitrogen source, being the primary determinant of nitrogen-regulated gene expression. We find that a transition from nitrogen-limited to nitrogen-replete conditions is accompanied by rapid induction of transcripts required for protein translation. We identified a reciprocal relationship between specific regulons required for protein translation (RP and RiBi) and the NCR regulon. Using mathematical modeling we find evidence that cells adopt a metabolically inefficient growth mode during this transition. By means of high resolution time series analysis we find evidence that rapid, and potentially accelerated, mRNA degradation plays an important role in remodeling gene expression programs in response to change in environmental nitrogen. We propose that the evolutionarily conserved TORC1 signaling pathway orchestrates the balance between protein translation and assimilation of nitrogen sources at the transcriptional level to optimize rates of cell proliferation. A total of of 102 samples were analyzed in different nitrogen-limited conditions using chemostats in both steady-state and dynamic conditions. A common reference obtained from an ammonium-limited chemostat growing at a dilution rate of 0.12/hr was used for all two color hybridization experiments.
2014-05-05 | E-GEOD-57293 | biostudies-arrayexpress
Project description:The plant pathogen Agrobacterium tumefaciens attaches to and forms biofilms on both biotic and abiotic surfaces. The transition between free-living, planktonic A. tumefaciens and multicellular biofilms is regulated by several well-defined environmental and nutritional inputs, including pH, oxygen tension, and phosphate concentration. In many bacterial species limiting iron levels inhibit attachment and biofilm formation. We demonstrate that A. tumefaciens biofilm formation is reduced under limiting iron conditions. Treatment of A. tumefaciens cultures with EDDHA, an iron-specific extracellular chelator, inhibited both planktonic growth rate and adherent biomass. These effects were reversed upon addition of exogenous ferrous iron. This reduced biofilm formation effect is independent of the known iron-responsive regulators Irr and RirA. Transcriptome analysis comparing gene expression under iron-replete versus iron-deficient conditions identified hundreds of genes that are differentially regulated. Downregulated genes suggest an iron sparing response. Four biological replicates, independent RNA preparations, one dye swap.
2015-07-22 | E-GEOD-71138 | biostudies-arrayexpress