Project description:An experiment was performed to determine the similarities on the RNA level between different conditions where cell division stops in the diatom Phaeodactylum tricornutum. Many of these conditions also increase the accumulation of lipids within the cell or impair photosynthesis. The different metabolic responses were evaluated and the dataset was mined for potential transcriptional regulators of these changes. The experimental setup was as follows: Cells from the pennate diatom Phaeodactylum tricornutum were grown in ESAW medium under continous fluorescent light at 21C in baffled shakeflasks. Exponentially growing cells were harvested by centrifugation and washed twice in 21gr/L NaCL to remove nutrients. Cells were subsequently resuspended in the five different media/conditions (control, darkness, no nitrate, no phosphate, nocodazole).

2015-12-07 | E-MTAB-4096 | biostudies-arrayexpress

Whole genome McrBC-chip on DNA methylation of diatom Phaeodactylum tricornutum

Project description:Extensive gene methylation correlated strongly with transcriptional silencing and differential expression under specific conditions. DNA methylation and its role in gene regulation is conserved in stramenopile. Methylome of the whole genome of diatom phaeodactylum tricornutum.

2013-06-15 | E-GEOD-47947 | biostudies-arrayexpress

Regulatory mechanism of diurnal fluctuated laminarin in diatom Phaeodactylum tricornutum

Project description:Diatoms played an essential role in marine primary productivity. Polysaccharide chrysolaminarin and neutral lipid, mainly TAG, were necessary carbon fixation in diatom Phaeodactylum tricornutum. Our study speculated on the metabolism pathway of chrysolaminarin, fatty acid, fatty acid β-oxidation and TAG. Transcriptional levels coordinated with carbon fixation metabolism pathway were conjoint analysis in this study.

2022-08-03 | GSE210141 | GEO

Investigating mixotrophic metabolism in the model diatom Phaeodactylum tricornutum.

Project description:Diatoms are prominent marine microalgae, interesting not only from an ecological point of view, but also for their possible use for biotechnology applications. They can be cultivated in phototrophic conditions, using sunlight as the only energy source. Some diatoms, however, can also grow in mixotrophic mode, where both light and external reduced carbon contribute to biomass accumulation. In this study, we investigated the consequences of mixotrophy on the growth and metabolism of the pennate diatom Phaeodactylum tricornutum, using glycerol as a source of reduced carbon. Transcriptomic, metabolomic and physiological data indicate that glycerol affects the central-carbon, carbon-storage and lipid metabolism of the diatom. In particular, glycerol addition mimics some typical responses of nitrogen limitation on lipid metabolism at the level of TAG accumulation and fatty acid composition. However, this compound does not diminish photosynthetic activity and cell growth, at variance with nutrient limitation, revealing essential aspects of the metabolic flexibility of these microalgae and suggesting possible biotechnological applications of mixotrophy.

2017-03-31 | GSE91004 | GEO

Transcriptional response of the marine pennate diatom Phaeodactylum tricornutum to Fe limitation

Project description:Diatoms, which are responsible for up to 40% of the 45 to 50 billion metric tons of organic carbon production each year in the sea, are particularly sensitive to Fe stress. Here we describe the transcriptional response of the pennate diatom Phaeodactylum tricornutum to Fe limitation using a partial genome microarray based on EST and genome sequence data. Processes carried out by components rich in Fe, such as photosynthesis, mitochondrial electron transport and nitrate assimilation are down-regulated to cope with the reduced cellular iron quota. This retrenchment is compensated by nitrogen (N) and carbon (C) reallocation from protein and storage carbohydrate degradation, adaptations to chlorophyll biosynthesis and pigment metabolism, removal of excess electron s by mitochondrial alternative oxidase (AOX), augmented Fe-independent oxidative stress responses, and sensitized iron capture mechanisms. Keywords: Marine phytoplankton, pinnate diatom Wild-type Phaeodactylum tricornutum was grown under Fe replete (10,000 nM) and Fe limiting (5nM) conditions. Partial genome gene expression analysis of iron-inducible genes was conducted using a two-color competitive hybridization microarray.

2010-05-27 | E-GEOD-8675 | biostudies-arrayexpress

Evolutionary and functional analysis of DNA methyltransferases in micro-eukaryotes: Insights from the model diatom Phaeodactylum tricornutum [Bisulfite-Seq]

Project description:DNA methylation has been associated with transcriptional repression of transposable elements. Here we describe the first DNA methylation deficient cell line of a diatom by generating DNMT5:KOs in Phaeodactylum tricornutum. These data show the extend of the loss of DNA methylation in DNMT5:KOs compared to the reference strain. All DNA methylation is lost in DNMT5:KOs.

2023-03-15 | GSE186855 | GEO

Plastid Proteome of diatom Phaeodactylum tricornutum

Project description:In this study, gradient density centrifugation was used to obtain high quality plastids of diatom Phaeodactylum tricornutum. Then, the purified plastid protein composition was analyzed by label-free quantitative proteomics technology

2023-02-01 | PXD039751 | iProX

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