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Effects of darkness on the gene expression in Cosmarium crenatum

ABSTRACT: Darkness-induced effects on gene expression in Cosmarium crenatum (Zygnematophyceae) from a polar habitat

PROVIDER: PRJEB30351 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2993164_1.fastq.gz	Fastqsanger.gz
	ERR2993164_2.fastq.gz	Fastqsanger.gz
	ERR3005810.fastq.gz	Fastqsanger.gz
	ERR3005820.fastq.gz	Fastqsanger.gz
	ERR3005811.fastq.gz	Fastqsanger.gz

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Proteomic insight into the response of Arabidopsis chloroplasts to darkness

Project description:Chloroplast function in photosynthesis is essential for plant growth and development. It is well-known that chloroplasts respond to various light conditions, however, it remains poorly understood about how chloroplasts respond to darkness. In this study, we found 90 darkness-responsive proteins in Arabidopsis chloroplasts under 8 h darkness treatment. Most of the proteins are nucleus-encoded, indicating that chloroplast darkness response is closely regulated by the nucleus. Among them, 17 ribosome proteins were obviously reduced after darkness treatment. The protein expressional patterns and physiological characters revealed the mechanisms in chloroplasts in response to darkness, e.g., (1) inhibition of photosystem II resulted in preferential cyclic electron flow around PSI; (2) promotion of starch degradation; (3) inhibition of chloroplastic translation; and (4) regulation by redox and jasmonate signaling. The results have improved our understanding of molecular regulatory mechanisms in chloroplasts under darkness.

2016-04-20 | PXD003516 | Pride

RNA-seq analysis on the liver of darkness rats treated with Limosilactobacillus reuteri

Project description:We have previously demonstrated that the arrhythmic expressions of circadian clock genes due to constant darkness induce glycometabolic and reproductive hallmarks of polycystic ovary syndrome (PCOS) in rats. Limosilactobacillus reuteri (L.reuteri) is a promising dietary intervention for host dysmetabolism, while its potential effect on circadian dysrhythmia-induced PCOS remains elusive. Here, we evaluated the amelioration of L.reuteri regimen on constant darkness-induced PCOS-like rats through detecting hepatic gene expression profiles by RNA-seq.

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Dynamics of mRNA abundance and translation in response to darkness and reillumination

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della-regulation in darkness versus light-DELLAs contribute to skotomorphogenesis

Project description:rs09-09_della-dark - della-regulation in darkness versus light - Identification of DELLA-dependent downstream targets in darkness - Aim was to determine downstream target of DELLA proteins involved in skotomorphogenesis. Wt, ga1-3, ga1-3_rga_gai_rgl1_rgl2_rgl3 global seeds were sterilized, sown on MS agar plates then put for stratification for 3 days at 4°C. Plates were placed in growth cabinet at 22°C for 5 days in darkness or in continous light. Keywords: gene knock out

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ppGpp controls global gene expression in light and in darkness in S. elongatus

Project description:ppGpp controls global gene expression in light and in darkness in S. elongatus

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Project description:We used RNA-Seq to ask whether the transcripts for the proposed BCKDH subunits are upregulated in wild-type plants subjected to prolonged darkness. These experiments were performed using rosette leaves from 5-week-old, short-day-grown (8h light/16h dark) Col-0 wild-type plants moved to constant darkness for 6h, 24h, 48h and 72h, and grown in short day for 72h as control. The transcripts of eight BCAA catabolism genes were increased nine- to 400-fold within the first 6h of prolonged darkness, and remained high until the last time point. These results are consistent with the hypothesis that BCAA catabolic enzymes - including BCKDH subunits E1A1, E1B1, E1B2 and E2 - have one or more physiological roles in the dark.

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Project description:Analysis of urinary bladder in wild-type C57BL/6 females sacrificed every 4 hours at six time points under constant darkness after acclimation for 2 weeks under 12-hour light and 12-hour dark conditions. Results provide insight into circadian gene expression patterns in normal urinary bladder.

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Darkness-induced effects on gene expression in Cosmarium crenatum (Zygnematophyceae) from a polar habitat.

Project description:Light is a key environmental regulator in all photosynthetic organisms. Many studies focused on the physiologic response to changes in light availability of species from the Zygnematophyceae, but the impact of the absence of light and the molecular acclimation process on the other side have been poorly understood. Here we present transcriptomic analyses of Cosmarium crenatum from a polar habitat exposed to darkness. The algae were cultured in dark for one week; cell number and quantum yield of photosystem II (Fv/Fm) were monitored. Cell number was stable, but the Fv/Fm decreased in both groups, darkness-treated and control. Gene expression analysis revealed a strong repression of transcripts associated with photosynthesis, photorespiration and cell wall development. General carbohydrate and lipid metabolism were differentially regulated, but starch is shown to be the primary energy source in these conditions. Additionally, C. crenatum induced mRNA responsible for epigenetic modifications which may be a specific response to an adaption and acclimation to polar conditions. Our study sheds light on the molecular acclimation process to darkness and provides ecological implications for new perspectives in this specialized group of green algae.

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Dynamics of mRNA abundance and translation in response to darkness and reillumination

Project description:Gene expression analysis of 14d-old Arabidopsis seedlings exposed to 1h darkness and 10 min reillumination after 1 h darkness to evaluate the regulation of gene expression at the level of translation. 12 samples, 3 conditions (1h light control, 1 h darkness treatment, 1 h darkness plus 10 min reillumination), 2 RNA pools (Total mRNA and polysomal mRNA), 2 bioreplicates

2012-03-30 | E-GEOD-34231 | biostudies-arrayexpress

Microarray studies of darkness stress and bleaching in the Caribbean coral Montastraea faveolata

Project description:Coral bleaching occurs in response to numerous abiotic stressors, the ecologically most relevant of which is hyperthermic stress due to increasing seawater temperatures. Bleaching events can span large geographic areas and are currently a potent threat to coral reefs worldwide. Much effort has been focused on understanding the molecular and cellular events underlying bleaching, and these studies have mainly utilized heat and light stress regimes. In an effort to determine whether different stressors share common bleaching mechanisms, we used cDNA microarrays for the corals Acropora palmata and Montastraea faveolata (containing > 10,000 features) to measure differential gene expression during darkness stress. This is the first coral microarray experiment aimed at darkness stress, and the first for these species to interrogate gene expression at such a large scale. Our results reveal a striking transcriptomic response to darkness in A. palmata involving chaperone and antioxidant up-regulation, growth arrest, and metabolic modifications. As these responses were also measured during thermal stress, our results suggest that different stressors may share common bleaching mechanisms. Furthermore, our results point to ER stress as a critical cellular event involved in darkness-specific (and possibly more general) molecular bleaching mechanisms. On the other hand, we identified a meager transcriptomic response to darkness in M. faveolata where gene expression differences between host colonies and/or sampling locations were greater than differences between control and stressed fragments. To this end, we discuss the importance of factors related to host genotype, Symbiodinium genotype, and the abiotic environment that influence host gene expression and thereby can hinder an investigator’s ability to measure gene expression during a condition of interest.

2011-03-23 | GSE27024 | GEO

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