Ontology highlight
ABSTRACT:
PROVIDER: PRJNA688555 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13325886_1.fastq.gz | Fastqsanger.gz | |||
| SRR13325886_2.fastq.gz | Fastqsanger.gz | |||
| SRR13325887_1.fastq.gz | Fastqsanger.gz | |||
| SRR13325887_2.fastq.gz | Fastqsanger.gz | |||
| SRR13325888_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 6 |
Similar Datasets
Project description:Amino acid utilizing bacterium
| PRJNA33685 | ENA
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:Amino acid availability is a crucial factor for survivability of cancer cells. Leukemia cells have been shown to resist asparagine depletion by utilizing GSK3-dependent proteasomal degradation, termed Wnt-dependent stabilization of proteins (Wnt/STOP), to replenish their amino acid pool. Inhibition of GSK3a halts the sourcing of amino acids, which subsequently leads to cancer cell vulnerability towards asparaginase therapy. Leveraging RNA sequencing we show that GSK3a inhibition leads to temporally dynamic downregulation of distinct ribosomal proteins upon amino acid starvation.
2023-09-13 | GSE234800 | GEO
Project description:The nucleotide (p)ppGpp is crucial for viability during amino acid limitation in bacteria, yet how it accomplishes this remains unknown. We found that the absence of (p)ppGpp in Bacillus subtilis cells leads to multiple amino acid auxotrophy, and that (p)ppGpp allows for prototrophy by reducing GTP levels. We provide evidence that reduction of GTP levels relieves the requirements for branched-chain amino acids primarily by preventing hyperactivity of the GTP-dependent transcriptional regulator CodY, but that GTP levels can also play an important role in regulating transcription of many amino acid biosynthesis genes independently of CodY. Thus, CodY-dependent and independent regulation of transcription by GTP levels plays overlapping yet distinct physiological roles in allowing amino acid prototrophy. Finally, supplementing these required amino acids does not protect against cell death upon nutrient downshift, but allows for sustained growth following this transition. We conclude that regulation of GTP levels by (p)ppGpp allows cells to adapt to conditions of amino acid limitation by first allowing survival during shifting nutrient conditions, and then allowing amino acid prototrophy by transcriptionally regulating amino acid biosynthesis. This strategy may be used to ensure viability during amino acid limitation in evolutionarily divergent bacteria.
2013-11-01 | GSE41501 | GEO
Project description:The neurotoxic amino acid, domoic acid, is naturally produced by marine phytoplankton and presents a significant health threat to marine mammal and human populations. Currently, diagnostic tools to assess exposure are not available, yet concerns regarding health impacts associated with low-level repetitive exposure are growing. Here we applied a laboratory zebrafish model to assess exposure to asymptomatic doses of domoic acid in a nine-month low-level repetitive exposure study. Blood analyses, whole brain gene expression, and functional lymphocyte proliferation assays analyzed at 11 time points revealed a quantifiable antibody response that was temporally correlated with upregulated immune response genes and significantly increased spontaneous lymphocyte proliferation. The antibody response was further validated in field exposed California sea lions and provides the first biomarker for chronic exposure assessment. Time series domoic acid exposure of zebrafish.
2013-01-03 | E-GEOD-34716 | biostudies-arrayexpress
Project description:The nucleotide (p)ppGpp is crucial for viability during amino acid limitation in bacteria, yet how it accomplishes this remains unknown. We found that the absence of (p)ppGpp in Bacillus subtilis cells leads to multiple amino acid auxotrophy, and that (p)ppGpp allows for prototrophy by reducing GTP levels. We provide evidence that reduction of GTP levels relieves the requirements for branched-chain amino acids primarily by preventing hyperactivity of the GTP-dependent transcriptional regulator CodY, but that GTP levels can also play an important role in regulating transcription of many amino acid biosynthesis genes independently of CodY. Thus, CodY-dependent and independent regulation of transcription by GTP levels plays overlapping yet distinct physiological roles in allowing amino acid prototrophy. Finally, supplementing these required amino acids does not protect against cell death upon nutrient downshift, but allows for sustained growth following this transition. We conclude that regulation of GTP levels by (p)ppGpp allows cells to adapt to conditions of amino acid limitation by first allowing survival during shifting nutrient conditions, and then allowing amino acid prototrophy by transcriptionally regulating amino acid biosynthesis. This strategy may be used to ensure viability during amino acid limitation in evolutionarily divergent bacteria. Twelve-condition experiment: wt, wt+RHX, wt+Guo, (p)ppGpp0, (p)ppGpp0+RHX, (p)ppGpp0+Guo, M-NM-^TcodY (p)ppGpp0, M-NM-^TcodY (p)ppGpp0+RHX, M-NM-^TcodY (p)ppGpp0+Guo, guaB- (p)ppGpp0, guaB- (p)ppGpp0+RHX, guaB- (p)ppGpp0+Guo. Biological replicates: 3 for each sample. Reference: a mixture of wt RNA from different growth phases and wt backgrounds.
2013-11-01 | E-GEOD-41501 | biostudies-arrayexpress