Gene expression of yeast fermentor culture after circadian temperature entrainment
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ABSTRACT:
PROVIDER: PRJNA503841 | ENA |
REPOSITORIES: ENA
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Project description:This gene expression experiment aimed to discover circiadian clock genes in yeast cells grown in a 1L fermentor culture Yeast were entrained for a period of time after the culture was released to a freerun (see growth protocol below). Samples were taken from fermenter cultures (1 × 109 yeast cells) every 3 hours over the first day of constant conditions (free-run), starting 1h before the temperature transition from 21°C to 28°C
2018-11-06 | GSE122152 | GEO
Project description:Setaria viridis (A10.1) circadian expression after light or temperature entrainment
2017-07-01 | GSE97739 | GEO
Project description:In this study we investigate and compare DEGs of K. aerogenes macrocolonies during temperature entrainment (12:12, 35°C:36°C) and subsequent free running conditions (35°C). The goal of this experiment was to identify rhythmically expressed genes in K. aerogenes, the first human gut commensal bacterium with described circadian clock (Paulose et al. 2016). K. aerogenes circadian clock is sensitive to temperature entrainment (Paulose et al. 2019). To further investigate this temperature entrainment of K. aerogenes we performed RNA sequencing experiment. We identified 48 differentially expressed genes when comparing timepoints ZT6 to ZT18, 427 differentially expressed genes when comparing timepoints ZT6 to CT6, 6 differentially expressed genes between timepoints CT6 and CT18, and 2 differentially expressed genes between timepoints ZT18 and CT18.
2023-10-09 | GSE185502 | GEO
Project description:Differential gene expression of K. aerogenes during temperature entrainment
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Project description:The microbiota drives circadian entrainment of tryptophan metabolism in the stressed gut
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Project description:Gould2011 - Temperature Sensitive Circadian
Clock
This model is a temperature sensitive
version of Pokhilko
et al. 2010 (PMID:
20865009),
which is
BIOMD0000000273
in BioModels.
This model is described in the article:
Network balance via CRY
signalling controls the Arabidopsis circadian clock over
ambient temperatures.
Gould PD, Ugarte N, Domijan M, Costa
M, Foreman J, Macgregor D, Rose K, Griffiths J, Millar AJ,
Finkenstädt B, Penfield S, Rand DA, Halliday KJ, Hall
AJ.
Mol. Syst. Biol. 2013; 9: 650
Abstract:
Circadian clocks exhibit 'temperature compensation', meaning
that they show only small changes in period over a broad
temperature range. Several clock genes have been implicated in
the temperature-dependent control of period in Arabidopsis. We
show that blue light is essential for this, suggesting that the
effects of light and temperature interact or converge upon
common targets in the circadian clock. Our data demonstrate
that two cryptochrome photoreceptors differentially control
circadian period and sustain rhythmicity across the
physiological temperature range. In order to test the
hypothesis that the targets of light regulation are sufficient
to mediate temperature compensation, we constructed a
temperature-compensated clock model by adding passive
temperature effects into only the light-sensitive processes in
the model. Remarkably, this model was not only capable of full
temperature compensation and consistent with mRNA profiles
across a temperature range, but also predicted the
temperature-dependent change in the level of LATE ELONGATED
HYPOCOTYL, a key clock protein. Our analysis provides a
systems-level understanding of period control in the plant
circadian oscillator.
This model is hosted on
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and identified by:
BIOMD0000000564.
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2024-09-02 | BIOMD0000000564 | BioModels
Project description:A defining property of circadian clocks is temperature compensation, characterized by the resilience of circadian free-running periods against changes in environmental temperature.We quantify global changes in 3´UTR length as well as gene and protein expression between wild type and CPSF6 knock-down cells and their dependency on temperature.
2023-05-23 | PXD029343 | Pride
Project description:Most organisms have an endogenous circadian clock that is synchronized to environmental signals such as light and temperature. Although circadian rhythms have been described in the nematode C. elegans at the behavioral level, these rhythms appear to be relatively non-robust. Moreover, in contrast to other animal models, no circadian transcriptional rhythms have been identified. Thus, whether this simple nematode contains a bona fide circadian clock remains an open question. We used microarray experiments to identify light- and temperature-regulated transcriptional rhythms in C. elegans, and show that subsets of these transcripts are regulated in a circadian manner. In addition, we find that light and temperature also globally drive the expression of many genes, indicating that C. elegans exhibits systemic responses to these stimuli. Populations of growth-synchronized wild-type C. elegans L1 larvae were entrained for 5 days until adulthood to 12:12 hr light/dark (LD) cycles (500-1000 lux) at a constant temperature of 18°C, or for 4 days to 12:12 hr temperature cycles (25:15°C - warm/cold or WC) in constant darkness. RNA was collected every 4 hrs during the last entrainment and the subsequent free-running days and analyzed via hybridization of Affymetrix GeneChips. L4 larvae were transferred to FUDR-containing plates to inhibit embryonic development.
2010-08-31 | E-GEOD-23528 | biostudies-arrayexpress
Project description:Circadian rhythms are essential for temporal (~24 h) regulation of molecular processes in diverse species. Dysregulation of circadian gene expression has been implicated in the pathogenesis of various disorders, including hypertension, diabetes, depression, and cancer. Recently, microRNAs (miRNAs) have been identified as critical modulators of gene expression post-transcriptionally, and perhaps involved in circadian clock architecture or their output functions. The aim of the present study is to explore the temporal expression of miRNAs among entrained breast cell lines. For this purpose, we evaluated the temporal (28 h) expression of 2006 miRNAs in MCF-10A, MCF-7, and MDA-MB-231 cells using microarrays after serum shock entrainment. We noted hundreds of miRNAs that exhibit rhythmic fluctuations in each breast cell line, and some of them across two or three cell lines. Afterwards, we validated the rhythmic profiles exhibited by miR-141-5p, miR-1225-5p, miR-17-5p, miR-222-5p, miR-769-3p, and miR-548ay-3p in the above cell lines, as well as in ZR-7530 and HCC-1954 using RT-qPCR. Our results show that serum shock entrainment in breast cells lines induces rhythmic fluctuations of distinct sets of miRNAs, which have the potential to be related to endogenous circadian clock, but extensive investigation is required to elucidate that connection.
2017-07-15 | GSE101461 | GEO
Project description:Circadian clocks are temporally aligned to the environment via signals, or Zeitgebers, such as daily light and temperature cycles, food availability, and social behavior. In this study, we show that genome-wide expression profiles from temperature-entrained flies show a dramatic difference in the presence or absence of a thermocycle. Whereas transcription appears to be modified globally by changes in temperature, there is a specific set of transcripts that continue to oscillate in constant conditions following temperature entrainment. These transcripts show a significant overlap with a previously defined set of transcripts oscillating in response to a photocycle. Further, these overlapping transcripts maintain the same mutual phase relationships after entrainment by temperature or light. Comparison of the collective temperature- and light-entrained circadian phases indicates that natural environmental light and temperature cycles cooperatively entrain the circadian clock. These findings suggest that a single transcriptional clock in the adult fly head is able to integrate information from both light and temperature. Keywords: circadian time course
2007-12-09 | GSE6493 | GEO