Effect of periodic disturbance on assembly
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB46803 | ENA |
REPOSITORIES: ENA
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Project description:The eukaryotic cell cycle, driven by both transcriptional and post-translational mechanisms, is the central molecular oscillator underlying tissue growth throughout animals. While genome-wide studies have investigated cell cycle-associated transcription in unicellular systems, global patterns of periodic transcription in multicellular tissues remain largely unexplored. Here we define the cell cycle-associated transcriptome of the developing Drosophila wing epithelium and compare it with that of cultured Drosophila S2 cells, revealing a core set of periodic genes as well as a surprising degree of context-specificity in periodic transcription. We further employ RNAi-mediated phenotypic profiling to define functional requirements for over 300 periodic genes, with a focus on those required for cell proliferation in vivo. Finally, we investigate the role of novel genes required for interkinetic nuclear migration. Combined, these findings provide a global perspective on cell cycle control in vivo, and highlight a critical need to understand the context-specific regulation of cell proliferation.
2014-03-15 | GSE54926 | GEO
Project description:Progression through the mitotic cell cycle requires periodic regulation of gene function at the levels of transcription, translation, protein-protein interactions, post-translational modification and degradation. However, the role of alternative splicing (AS) in the temporal control of cell cycle is not well understood. By sequencing the human transcriptome through two continuous cell cycles, we identify ~1,300 genes with cell cycle-dependent AS changes. These genes are significantly enriched in functions linked to cell cycle control, yet they do not significantly overlap genes subject to periodic changes in steady-state transcript levels. Many of the periodically spliced genes are controlled by the SR protein kinase CLK1, whose level undergoes cell cycle-dependent fluctuations via an auto-inhibitory circuit. Disruption of CLK1 causes pleiotropic cell cycle defects and loss of proliferation, whereas CLK1 over-expression is associated with various cancers. These results thus reveal a large program of CLK1-regulated periodic AS intimately associated with cell cycle control.
2016-05-19 | GSE81485 | GEO
Project description:The eukaryotic cell cycle, driven by both transcriptional and post-translational mechanisms, is the central molecular oscillator underlying tissue growth throughout animals. While genome-wide studies have investigated cell cycle-associated transcription in unicellular systems, global patterns of periodic transcription in multicellular tissues remain largely unexplored. Here we define the cell cycle-associated transcriptome of the developing Drosophila wing epithelium and compare it with that of cultured Drosophila S2 cells, revealing a core set of periodic genes as well as a surprising degree of context-specificity in periodic transcription. We further employ RNAi-mediated phenotypic profiling to define functional requirements for over 300 periodic genes, with a focus on those required for cell proliferation in vivo. Finally, we investigate the role of novel genes required for interkinetic nuclear migration. Combined, these findings provide a global perspective on cell cycle control in vivo, and highlight a critical need to understand the context-specific regulation of cell proliferation. Cells from developing Drosophila wing epithelium, and cultured S2 cells are FACS sorted into G1 and G2 populations based on DNA content and compared in triplicate on Affymetrix microarrays to identify differences in the transcriptional program of the cell cycle by cell type.
2014-03-15 | E-GEOD-54926 | biostudies-arrayexpress
Project description:Dietary restriction has shown benefits in physiological, metabolic, and molecular signatures associated with aging. In mice, periodic dietary restriction, that accompanies cyclical periods of reduced calories, mitigates aging phenotypes, yet the effects of this periodic restriction in higher order, genetically heterogenous mammals, have not been investigated. Reducing caloric intake in middle-aged Rhesus Macaques for four days followed by ad libitum eating for ten days, repeated for six cycles, led to significant changes in body composition, metabolome, and microbiome of the restricted monkeys compared to their ad libitum fed (age and sex matched) controls. These changes were also associated with stabilized blood parameters. The changes in metabolome, microbiome, and body compositions were additive, with consistent but increasingly pronounced changes in later cycles, suggesting sustaining benefits in non-human primates. These results suggest this type of cyclical dietary restriction, that is easy to adhere to, will also have translational benefits in humans while enhancing aging-associated parameters.
2023-12-17 | GSE235769 | GEO
Project description:The Oscillation Zone (OZ) of unsynchronized roots was disected and divided into an upper (OZ2) and lower (OZ1) half . Samples were ordered according to DR5:GUS expression as analyzed by real time PCR to find periodic expression patterns
2010-09-12 | GSE21611 | GEO
Project description:Objective. To evaluate the efficacy and safety of canakinumab treatment in active hyperimmunoglobulinemia D with periodic fever syndrome (HIDS). Methods. This is a 3-part open-label study with a 6-month treatment period (P1; 300 mg or 4 mg/kg q6w) a 6-month withdrawal period (P2) and a 24-month treatment period (P3). The primary endpoint was reduction in frequency of flares during treatment period compared with the historical period (HP; period in which patients did not receive drugs other than NSAIDs and/or steroids).
2018-09-17 | GSE97075 | GEO
Project description:The Oscillation Zone (OZ) of unsynchronized roots was dissected and divided into an upper (OZ2) and lower (OZ1) half . Samples were ordered according to DR5:GUS expression as analyzed by real time PCR to find periodic expression patterns Seedlings were grown for 5 days. 39 individual roots were dissected for RNA extraction. These microarray samples profile a specific region of the root tip designated as the Oscillation zone. Arrangement of the samples in the following order: OZ1-1, OZ1-4, OZ1-23, OZ1-14, OZ1-17, OZ1-2, OZ1-6, OZ1-13, OZ1-15, OZ1-16, OZ1-10, OZ1-32, OZ1-3, OZ1-31, OZ1-22, OZ1-35, OZ1-19, OZ1-9, OZ1-33, OZ1-20, OZ2-4, OZ2-23, OZ2-14, OZ2-6, OZ2-13, OZ2-15, OZ2-10, OZ2-32, OZ2-22, OZ2-35, OZ2-19, OZ2-9, OZ2-20, OZ2-36, OZ2-39, OZ2-21, OZ2-40, OZ2-38, OZ2-1, was used to identify periodic expression patterns.
2010-09-12 | E-GEOD-21611 | biostudies-arrayexpress
Project description:This is data from studies on mechanisms compensating for disturbances in the activity of neuronal or humoral neuroimmune communication pathways in the model of intraperitoneal inflammation.
2022-03-24 | GSE199231 | GEO
Project description:The spatial correlation of disturbance is gaining attention in landscape ecology, but knowledge is still lacking on how species traits determine extinction thresholds under spatially correlated disturbance regimes. Here we develop a pair approximation model to explore species extinction risk in a lattice-structured landscape subject to aggregated periodic disturbance. Increasing disturbance extent and frequency accelerated population extinction irrespective of whether dispersal was local or global. Spatial correlation of disturbance likewise increased species extinction risk, but only for local dispersers. This indicates that models based on randomly simulated disturbances (e.g., mean-field or non-spatial models) may underestimate real extinction rates. Compared to local dispersal, species with global dispersal tolerated more severe disturbance, suggesting that the spatial correlation of disturbance favors long-range dispersal from an evolutionary perspective. Following disturbance, intraspecific competition greatly enhanced the extinction risk of distance-limited dispersers, while it surprisingly did not influence the extinction thresholds of global dispersers, apart from decreasing population density to some degree. As species respond differently to disturbance regimes with different spatiotemporal properties, different regimes may accommodate different species.
| S-EPMC4612536 | biostudies-literature
Project description:The shape and dimensions of a micromixer are key elements in the mixing process. Accurately quantifying the mixing efficiency enables the evaluation of the performance of a micromixer and the selection of the most suitable one for specific applications. In this paper, two methods are investigated to evaluate the mixing efficiency: a numerical model and an experimental model with a software image processing technique. Using two methods to calculate the mixing efficiency, in addition to corroborating the results and increasing their reliability, creates various possible approaches that can be selected depending on the circumstances, resources, amount of data to be processed and processing time. Image processing is an easy-to-implement tool, is applicable to different programming languages, is flexible, and provides a quick response that allows the calculation of the mixing efficiency using a process of filtering of images and quantifying the intensity of the color, which is associated with the percentage of mixing. The results showed high similarity between the two methods, with a difference ranging between 0 and 6% in all the evaluated points.
| S-EPMC8469598 | biostudies-literature