Thalassiosira pseudonana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA13883 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Diatoms are photosynthetic unicellular algae and this species has served as a model for diatom physiology studies
| PRJNA9562 | ENA
Project description:Thalassiosira pseudonana TAG accumulation Project
| PRJNA79899 | ENA
Project description:T. pseudonana gene-specific arrays were used for differential gene expression. Seven hundred nine genes were differentially expressed by more than 2-fold (Bayesian t-test, p< 0.001) under at least one growth-limiting condition relative to nutrient-replete conditions. A striking result of the hierarchical cluster analysis was the identification of a common set of genes that were upregulated by both iron and silicon limitation, but no other treatment. Together, these two treatments accounted for about one fourth of all differentially expressed genes but almost two thirds of the differentially expressed novel genes, further emphasizing the distinctive aspects of silicon manipulation in diatoms. Keywords: silicon, stress response, cell wall, iron, temperature, carbon dioxide
2008-01-09 | GSE9660 | GEO
Project description:Experimental evidence suggests that the novel conserved DNA-binding protein (BIG1) identified in Thalassiosira pseudonana and other centric diatoms increases resilience under harsh environmental settings, leading to a faster growth response upon return to more favorable growth conditions. To assess the effects of a BIG1 overexpression cell line compared to wild -type, we undertook transcriptome analysis via microarrays.
2024-08-31 | E-MTAB-14049 | biostudies-arrayexpress
Project description:Biomineral forming organisms produce inorganic materials with complex, genetically encoded morphologies that are inaccessible by current synthetic chemistry. It is poorly understood which genes are involved in biomineral morphogenesis and how the encoded proteins guide this process. We addressed these questions using diatoms, which are paradigms for the self-assembly of hierarchically meso- and macroporous silica under mild reaction conditions. By isolating the intracellular organelle for silica biosynthesis, we identified a suite of new biomineralization proteins. Three of these, dAnk1-3, are specific to diatoms and contain a common protein-protein interaction domain indicating a role in coordinating assembly of the silica biomineralization machinery. Knocking out individual dank genes led to characteristic structural aberrations in silica biogenesis that point to a liquid-liquid phase separation process as underlying mechanism for pore pattern morphogenesis. Our work provides an unprecedented path for the synthesis of tailored meso- and macroporous silicas using Synthetic Biology.
2022-11-21 | PXD033943 | Pride
Project description:Nutrient-starvation induced lipid accumulation has been reported in diverse algae, including diatoms. Molecular mechanisms underlying lipid accumulation in nutrient-starved algae are of interest to inform genetic engineering strategies aimed at improving lipid productivity. Diatom cell walls are made of nanostructured silica which is a unique feature of the group and silicon deprivation induces both growth arrest and lipid accumulation. In this work, we report the whole cell transcript level response during silicon starvation induced lipid accumulation.
2015-12-31 | GSE75651 | GEO
Project description:T. pseudonana gene-specific arrays were used for differential gene expression. Seven hundred nine genes were differentially expressed by more than 2-fold (Bayesian t-test, p< 0.001) under at least one growth-limiting condition relative to nutrient-replete conditions. A striking result of the hierarchical cluster analysis was the identification of a common set of genes that were upregulated by both iron and silicon limitation, but no other treatment. Together, these two treatments accounted for about one fourth of all differentially expressed genes but almost two thirds of the differentially expressed novel genes, further emphasizing the distinctive aspects of silicon manipulation in diatoms. We analyzed 6 different sets of arrays from 6 growth conditions. Four biological replicates (=4 arrays) were used for each growth condition.
2010-05-26 | E-GEOD-9660 | biostudies-arrayexpress
Project description:Phytoplankton and bacteria form the base of marine ecosystems and their interactions drive global biogeochemical cycles. The effect of bacteria and bacteria-produced compounds on diatoms range from synergistic to pathogenic and can affect the physiology and transcriptional patterns of the interacting diatom. Here, we investigate physiological and transcriptional changes in the marine diatom Thalassiosira pseudonana induced by extracellular metabolites of a known antagonistic bacterium Croceibacter atlanticus. Mono-cultures of C. atlanticus released compounds that inhibited diatom cell division and elicited a distinctive phenotype of enlarged cells with multiple plastids and nuclei, similar to what was observed when the diatom was co-cultured with the live bacteria. The extracellular C. atlanticus metabolites induced transcriptional changes in diatom pathways that include recognition and signaling pathways, cell cycle regulation, carbohydrate and amino acid production, as well as cell wall stability. Phenotypic analysis showed a disruption in the diatom cell cycle progression and an increase in both intra- and extracellular carbohydrates in diatom cultures after bacterial exudate treatment. The transcriptional changes and corresponding phenotypes suggest that extracellular bacterial metabolites, produced independently of direct bacterial-diatom interaction, may modulate diatom metabolism in ways that support bacterial growth.
2022-06-24 | GSE197934 | GEO
Project description:To test whether elevated CO2 , which drives seawater below pH 7.9, would shift the dynamical expression patterns diatoms in a more natural environment, we designed a controlled mesocosm study at Friday Harbor Laboratories (FHL) Ocean Acidification Environmental Laboratory (OAEL). Briefly, four independent mesocosm tanks were set up with continuous flow (10-12 mL/min) of filtered seawater from the Puget Sound to simulate mid-century (pH 7.9) and acidified oceanic conditions (pH 7.6) in duplicate. Mesocosm reservoirs were supplemented with nutrients and inoculated with T. pseudonana acclimated in FHL seawater. Mesocosms were outfitted with custom enclosures to simulate a 12:12 light:dark diel cycle. Cells for RNA extraction were sampled in the middle of the light and dark cycle and sequenced on Illumina NextSeq 500 platform.
2021-03-13 | GSE168812 | GEO
Project description: Not available
| EMPIAR-12142 | biostudies-other