Conticribra weissflogii
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA298677 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2645750.fastq.gz | Fastqsanger.gz | |||
| SRR2645751.fastq.gz | Fastqsanger.gz | |||
| SRR2645752.fastq.gz | Fastqsanger.gz | |||
| SRR2645747.fastq.gz | Fastqsanger.gz | |||
| SRR2645748.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 6 |
Similar Datasets
Project description:The salinity gradient separating marine and freshwater environments is a major ecological divide, and the mechanisms by which most organisms adapt to new salinity environments are poorly understood. Diatoms are a lineage of ancestrally marine microalgae that have repeatedly colonized and diversified in freshwaters. Cyclotella cryptica is a euryhaline diatom that naturally tolerates a broad range of salinities, thus providing a powerful system for understanding the genomic mechanisms for mitigating and acclimating to low salinity. To understand how diatoms mitigate acute hypoosmotic stress, we abruptly shifted C. cryptica from seawater to freshwater and performed transcriptional profiling at 8 time points across 10 hours. We found substantial remodeling of the transcriptome, with over half of the genome differentially expressed in at least one time point. The peak response occurred within 1 hour, with strong repression of genes involved in functions related to cell growth and osmolyte production, and strong induction of genes implicated in stress defense such as scavenging reactive oxygen species and maintaining osmotic balance. Notably, transcripts largely returned to baseline levels within 4–10 hours, with growth resuming shortly thereafter, suggesting that gene expression dynamics may be useful for predicting acclimation. Moreover, comparison to a study of expression profiling following months-long acclimation of C. cryptica to freshwater revealed little overlap between the genes and processes differentially expressed in cells exposed to acute stress versus fully acclimated conditions. Altogether, this study highlights the power of time-resolved transcriptomics to reveal fundamental insights into how cells dynamically respond to an acute environmental shift and provides new insights into how diatoms mitigate natural salinity fluctuations and have successfully diversified across freshwater habitats worldwide.
2022-06-23 | GSE206725 | GEO
Project description:Conticribra weissflogii Transcriptome or Gene expression
| PRJNA922708 | ENA
Project description:Photosynthetic diatoms are exposed to rapid and unpredictable changes in irradiance and spectral quality, and must be able to adapt their light harvesting systems to varying light conditions. Molecular mechanisms behind light acclimation in diatoms are largely unknown. We set out to investigate the mechanisms of high light acclimation in Phaeodactylum tricornutum using an integrated approach involving global transcriptional profiling, metabolite profiling and variable fluorescence technique. Algae cultures were acclimated to low light (LL), after which the cultures were transferred to high light (HL). Molecular, metabolic and physiological responses were studied at time points 0.5 h, 3 h, 6 h, 12 h, 24 h and 48 h after transfer to HL conditions. The integrated results indicate that the acclimation mechanisms in diatoms can be divided into an initial response phase (0.5 h), an intermediate acclimation phase (3-12 h) and a late acclimation phase (12-48 h). The initial phase is recognized by strong and rapid regulation of genes encoding proteins involved in photosynthesis, pigment metabolism and reactive oxygen species (ROS) scavenging systems. A significant increase in light protecting metabolites occur together with the induction of transcriptional processes involved in protection of cellular structures at this early phase. During the following phases, the metabolite profiling display a pronounced decrease in light harvesting pigments, whereas the variable fluorescence measurements show that the photosynthetic capacity increases strongly during the late acclimation phase. We show that P. tricornutum is capable of swift and efficient execution of photoprotective mechanisms, followed by changes in the composition of the photosynthetic machinery that enable the diatoms to utilize the excess energy available in HL. Central molecular players in light protection and acclimation to high irradiances have been identified.
2009-11-06 | GSE17237 | GEO
Project description:Photosynthetic diatoms are exposed to rapid and unpredictable changes in irradiance and spectral quality, and must be able to adapt their light harvesting systems to varying light conditions. Molecular mechanisms behind light acclimation in diatoms are largely unknown. We set out to investigate the mechanisms of high light acclimation in Phaeodactylum tricornutum using an integrated approach involving global transcriptional profiling, metabolite profiling and variable fluorescence technique. Algae cultures were acclimated to low light (LL), after which the cultures were transferred to high light (HL). Molecular, metabolic and physiological responses were studied at time points 0.5 h, 3 h, 6 h, 12 h, 24 h and 48 h after transfer to HL conditions. The integrated results indicate that the acclimation mechanisms in diatoms can be divided into an initial response phase (0.5 h), an intermediate acclimation phase (3-12 h) and a late acclimation phase (12-48 h). The initial phase is recognized by strong and rapid regulation of genes encoding proteins involved in photosynthesis, pigment metabolism and reactive oxygen species (ROS) scavenging systems. A significant increase in light protecting metabolites occur together with the induction of transcriptional processes involved in protection of cellular structures at this early phase. During the following phases, the metabolite profiling display a pronounced decrease in light harvesting pigments, whereas the variable fluorescence measurements show that the photosynthetic capacity increases strongly during the late acclimation phase. We show that P. tricornutum is capable of swift and efficient execution of photoprotective mechanisms, followed by changes in the composition of the photosynthetic machinery that enable the diatoms to utilize the excess energy available in HL. Central molecular players in light protection and acclimation to high irradiances have been identified. The experiment was designed as a time series, with diatom cultures were harvested at time points 0.5 h, 3 h, 6 h, 12 h, 24 h and 48 h after transfer to high light conditions. The reference samples were kept at low light and harvested in parallel with the treated samples. Three biological replicates were harvested for all samples.
2009-11-05 | E-GEOD-17237 | biostudies-arrayexpress
Project description:Conticribra weissflogii strain:CCMP1051 Transcriptome or Gene expression
| PRJNA288683 | ENA
Project description:Conticribra weissflogii strain:CCMP 1336 Genome sequencing and assembly
| PRJNA665191 | ENA
Project description:In estuaries and coastal areas, salinity regimes vary with river discharge, seawater evaporation, morphology of the coastal waterways, and dynamics of marine water mixing. Therefore, microalgae have to respond to salinity variations at various time scales, from daily to annual cycling. They might also adapt to physical alteration that might induce loss of connectivity and enclosure of water bodies. Here we integrate physiological-based assays, morphological plasticity with functional genomics approach to examine the regulatory change that occur during the acclimation to salinity in an estuary diatom, Thalassiosira weissflogii. We found that this diatom respond to salinity (i.e. 21, 28 and 35 psu) with minute adjustments of its physiology (i.e., carbon and silicon metabolisms, pigments concentration and photosynthetic parameters). In contrast after short- (~ 5 generations) or long-term (~ 700 generations) culture at the different salinity we found a large transcriptome reprogramming. With most of the genes being down-regulated in long-term, and only a few genes in common between short and long term experiments.
2018-10-02 | GSE73987 | GEO
Project description:Background: Fucoxanthin (FX), a xanthophyll pigment which occurs in marine brown algae with remarkable biological properties, has been proven to be safe for consumption by animals. Although FX has various pharmacological effects including anti-inflammatory, anti-tumor, anti-obesity, antioxidant, anti-diabetic, anti-malarial, and anti-lipid, in vivo protective effect against sepsis has not been reported. In this study, we aimed at evaluation the efficacy of the FX in a model of sepsis mouse. Methods: FX was successfully isolated from Conticribra weissflogii ND-8 for the first time. The FX was identified by thin-layer chromatography (TLC), high-performance liquid chromatography-mass spectrometry (HPLC-MS), and nuclear magnetic resonance (NMR). Animals were randomly divided into 9 groups, including Sham group (mouse received an intraperitoneal injection of normal saline 1.0 ml/kg), FX-treated (0.1-1.0 ml/kg), Lipopolysaccharide (LPS)-treated (20 mg/kg), FX+LPS-treated (0.1-10.0 mg/kg and 20 mg/kg, respectively), and urinastatin groups (104 U/kg). Nuclear factor (NF)-κB activation could be potential treatment for sepsis. NF-κB signaling components were determined by western-blotting. IL-6, IL-1β, TNF-α production, and NF-κB activation were evaluated by ELISA and immunofluorescent staining in vitro. Results: FX was found to decrease the expression of inflammatory cytokines including IL-6, IL-1β, and TNF-α, in a prophylactic manner in the LPS-induced sepsis mouse model. Meanwhile, FX significantly inhibits phosphorylation of the NF-κB signaling pathway induced by LPS at the cellular level and reduces the nuclear translocation of NF-κB. The IC50 for suppressing the expression of NF-κB was 11.08 ± 0.78 μM in the THP1-Lucia™ NF-κB cells. Furthermore, FX also inhibits the expression of inflammatory factors in a dose-dependent manner with the IC50 inhibition of IL-6 production was 2.19 ± 0.70 μM in Raw267.4 macrophage cells. It is likely that the molecules with the ability of targeting NF-κB activation and inflammasome assembly, such as fucoxanthin, are interesting subjects to be used for treating sepsis.
| S-EPMC6722224 | biostudies-literature
Project description:In low rainfall regions soils are naturally conditioned with frequent co-occurrence of salinity and alkalinity. Plant salinity responses both at physiological and molecular level have been extensively researched. However, effects of the combined treatment of alkaline salinity that could greatly reduce plant growth and the mechanisms responsible for tolerance remain indeterminate. In Brassica juncea, large reductions in biomass and increased leaf Na+ concentration under alkaline salinity indicates that the combined treatment had greater negative effect than salinity on both growth and the physiological responses of the plant. To determine molecular mechanisms potentially controlling adaptive tolerance responses to salinity and alkaline salinity, the moderately tolerant genotype NDR 8501 was further investigated using microarray analysis. The transcripts of treated leaf tissues verses those of the untreated control sample were analysed after prolonged stress of four weeks. In total, 528 salinity responsive and 1245 alkaline salinity responsive genes were indentified and only 101 genes were expressed jointly in either of the two treatments. Transcription of 37% more genes involved in response to alkaline salinity than salinity alone, which suggests the increased impact and severity of the combined stress on the plant, indicating the transcription of a far greater number of genes likely involved in mitigation and damage control. Transcription of KUP2 and KUP7 genes involved in potassium homeostasis under salinity alone and NHX1 and ENH1 genes for ion (K+ and Na+) homeostasis under alkaline salinity, clearly demonstrated that different genes and genetic pathways are involved in response to each stress. They further provide supporting evidence for the physiological responses that occur in the plant, with massive reprogramming of the transcriptome leading to partial ion exclusion, shuttling and compartmentation. Salinity and alkaline salinity induced gene expression in Brassica juncea leaf was measured at 4 weeks of prolonged treatment of 50 mM NaCl alone and combined with 2.5 mM HCO3- versus non-stressed control. A single experiment was conducted using Brassica juncea genotype NDR 8501 at a single time point (fours weeks after treatment) with three replications per treatment.
2012-06-25 | E-GEOD-38905 | biostudies-arrayexpress