Project description:The effects of fasting have been studied extensively, predominantly on isolated processes, within a specific organ. No comprehensive study of the adaptations was available for different organs including heart.The gene expression profiles of heart, liver, and muscle were investigated in this experiments.
Project description:Chromochloris zofingiensis has been proposed as a potential producer of lipids and the high-value carotenoid astaxanthin. Previous studies have demonstrated that TAG (triacylglycerol) and astaxanthin accumulated in a well-coordinated manner in response to different stresses in C. zofingiensis. The integrated production of lipids with co-products emerges as a new research direction and is proposed to be a promising approach toward offsetting the algal biodiesel production cost. Therefore, it is suggested C. zofingiensis can serve as research models for the integrated production. Sulfur starvation stress simultaneously induced TAG and astaxanthin accumulation in C. zofingiensis. To understand the mechanism underlying TAG and astaxanthin accumulation induced by sulfur starvation stress, we applied time-resolved high-throughput mRNA sequencing in C. zofingiensis.
Project description:Altered nutrient conditions can trigger massive transcriptional reprogramming in plants, leading to the activation and silencing of thousands of genes. To gain a deeper understanding of the phosphate starvation response and the relationships between transcriptional and epigenetic changes that occur during this reprogramming, we conducted a time-resolved analysis of transcriptome and chromatin alterations in root hair cells of Arabidopsis thaliana during phosphate (P) starvation and subsequent resupply. We found that 96 hours of P starvation causes induction or repression of thousands of transcripts, and most of these recover to pre-starvation levels within 4 hours of P resupply. Among the phosphate starvation-induced genes are many polycomb targets with high levels of H3K27me3 and histone variant H2A.Z. When induced, these genes show increased H3K4me3 consistent with active transcription, but surprisingly minimal loss of H3K27me3 or H2A.Z. These results indicate that the removal of silencing marks is not a prerequisite for activation of these genes. Our data provide a cell type- and time-resolved resource for studying the dynamics of a systemic nutrient stress and recovery and suggest that our current understanding of the switch between silent and active transcriptional states is incomplete.
Project description:Altered nutrient conditions can trigger massive transcriptional reprogramming in plants, leading to the activation and silencing of thousands of genes. To gain a deeper understanding of the phosphate starvation response and the relationships between transcriptional and epigenetic changes that occur during this reprogramming, we conducted a time-resolved analysis of transcriptome and chromatin alterations in root hair cells of Arabidopsis thaliana during phosphate (P) starvation and subsequent resupply. We found that 96 hours of P starvation causes induction or repression of thousands of transcripts, and most of these recover to pre-starvation levels within 4 hours of P resupply. Among the phosphate starvation-induced genes are many polycomb targets with high levels of H3K27me3 and histone variant H2A.Z. When induced, these genes show increased H3K4me3 consistent with active transcription, but surprisingly minimal loss of H3K27me3 or H2A.Z. These results indicate that the removal of silencing marks is not a prerequisite for activation of these genes. Our data provide a cell type- and time-resolved resource for studying the dynamics of a systemic nutrient stress and recovery and suggest that our current understanding of the switch between silent and active transcriptional states is incomplete.
Project description:Altered nutrient conditions can trigger massive transcriptional reprogramming in plants, leading to the activation and silencing of thousands of genes. To gain a deeper understanding of the phosphate starvation response and the relationships between transcriptional and epigenetic changes that occur during this reprogramming, we conducted a time-resolved analysis of transcriptome and chromatin alterations in root hair cells of Arabidopsis thaliana during phosphate (P) starvation and subsequent resupply. We found that 96 hours of P starvation causes induction or repression of thousands of transcripts, and most of these recover to pre-starvation levels within 4 hours of P resupply. Among the phosphate starvation-induced genes are many polycomb targets with high levels of H3K27me3 and histone variant H2A.Z. When induced, these genes show increased H3K4me3 consistent with active transcription, but surprisingly minimal loss of H3K27me3 or H2A.Z. These results indicate that the removal of silencing marks is not a prerequisite for activation of these genes. Our data provide a cell type- and time-resolved resource for studying the dynamics of a systemic nutrient stress and recovery and suggest that our current understanding of the switch between silent and active transcriptional states is incomplete.
Project description:Altered nutrient conditions can trigger massive transcriptional reprogramming in plants, leading to the activation and silencing of thousands of genes. To gain a deeper understanding of the phosphate starvation response and the relationships between transcriptional and epigenetic changes that occur during this reprogramming, we conducted a time-resolved analysis of transcriptome and chromatin alterations in root hair cells of Arabidopsis thaliana during phosphate (P) starvation and subsequent resupply. We found that 96 hours of P starvation causes induction or repression of thousands of transcripts, and most of these recover to pre-starvation levels within 4 hours of P resupply. Among the phosphate starvation-induced genes are many polycomb targets with high levels of H3K27me3 and histone variant H2A.Z. When induced, these genes show increased H3K4me3 consistent with active transcription, but surprisingly minimal loss of H3K27me3 or H2A.Z. These results indicate that the removal of silencing marks is not a prerequisite for activation of these genes. Our data provide a cell type- and time-resolved resource for studying the dynamics of a systemic nutrient stress and recovery and suggest that our current understanding of the switch between silent and active transcriptional states is incomplete.
Project description:Altered nutrient conditions can trigger massive transcriptional reprogramming in plants, leading to the activation and silencing of thousands of genes. To gain a deeper understanding of the phosphate starvation response and the relationships between transcriptional and epigenetic changes that occur during this reprogramming, we conducted a time-resolved analysis of transcriptome and chromatin alterations in root hair cells of Arabidopsis thaliana during phosphate (P) starvation and subsequent resupply. We found that 96 hours of P starvation causes induction or repression of thousands of transcripts, and most of these recover to pre-starvation levels within 4 hours of P resupply. Among the phosphate starvation-induced genes are many polycomb targets with high levels of H3K27me3 and histone variant H2A.Z. When induced, these genes show increased H3K4me3 consistent with active transcription, but surprisingly minimal loss of H3K27me3 or H2A.Z. These results indicate that the removal of silencing marks is not a prerequisite for activation of these genes. Our data provide a cell type- and time-resolved resource for studying the dynamics of a systemic nutrient stress and recovery and suggest that our current understanding of the switch between silent and active transcriptional states is incomplete.
Project description:This data set consists of a long term glucose starvation time course of E. coli grown in minimal media for up to two weeks. Unlike previous studies of long term starvation,Our study focuses on the physiological response of E. Coli in stationary phase as a result of being starved for glucose, not on the genetic adaptation of E. coli to utilize alternative nutrients.
Project description:MicroRNAs are central regulators of the T cell function. We explored RNA expression profiles over the initial 24 h of human CD4+ T cell activation. We found high similarity in time-resolved miRNA expression courses comparing independent activations and different donors. The detected miRNA expression patterns could be grouped into six classes only, each with a defined time course. MiR-155-5p known for its role in T cell immunity showed the most prevalent expression changes, quantified with an hourly increase of about 60 molecules/cell. As demonstrated for miRNA-155-5p, the analysis of time-resolved miRNA and mRNA expression data allowed to increase the validation rate of predicted miRNA targets to close to 90 %. Combining our time-resolved expression analysis with an absolute quantification of miRNA expression changes, gives new insights into miRNA regulatory networks and indicates the functional dominance of specific miRNAs within the early T cell activation.