A.thaliana seedling expression data from ASP treatment
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ABSTRACT:
PROVIDER: PRJNA556253 | ENA |
REPOSITORIES: ENA
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Project description:ASP induces the expression of early auxin response genes by activates auxin response, and affects responses to other signals associated with the auxin signaling pathway. We used microarrays to detail the effect of ASP on Arabidopsis global gene expression, and identified distinct classes of up-regulated or down genes during this process
2019-07-24 | GSE134746 | GEO
Project description:Antibacterial mechanism of the Asp - Asp - Asp - Tyr peptide
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Project description:Previously, we found that ASP-ASP-ASP-TYR (DDDY) from Dendrobium aphyllum has a minimum inhibitory concentration of 36.15 mg/mL against Pseudomonas aeruginosa. Here, we explored the antibacterial mechanism of DDDY and its potential preservation applications. Metabolomic and transcriptomic analyses revealed that DDDY mainly affects genes involved in P. aeruginosa membrane transport and amino acid metabolism pathways. Molecular dynamics simulation revealed that DDDY had a stronger effect on 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine phospholipid membranes than on 1-palmitoyl-2-oleoyl-lecithin or 1-palmitoyl-2-oleoyl phosphatidylglycerol membranes, with high DDDY concentrations displaying stronger efficacy on 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine. Mechanistically, the N-terminal of DDDY first bound to the phospholipid head group, while its C-terminal amino acid residue bound the hydrophobic tail, thereby creating a gap in the membrane when the phospholipids were clustered by hydrogen bonding. Finally, DDDY inhibited the growth of food microorganisms inoculated onto chestnut kernels, suggesting that DDDY is a promising antibacterial agent against multidrug-resistant gram-negative bacteria. Inhibitory effect of ASP-ASP-ASP-TYR (DDDY) from Dendrobium on Pseudomonas aeruginosa
2021-12-24 | GSE192340 | GEO
Project description:Antibacterial mechanism of the Asp - Asp - Asp - Tyr peptide [P. aeruginosa]
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Project description:Indica rice seedlings of IR64 variety were grown hydroponically for 7-days in a culture room with a daily photoperiodic cycle of 14h light and 10h dark. Seedlings were incubated in 0.1% dimethyl sulfoxide (control) or 50 micromolar solutions of indole-3-acetic acid (IAA treatment) and benzyl aminopurine (BAP treatment) for 1h and 3h. Equal amounts of 1h and 3h samoles were pooled for each treatment before RNA isolation. The 5 micrograms of each total RNA sample was processed for microarray analysis according to Affymetrix protocol. Keywords: Rice, seedling, IAA, BAP, hormone response
2009-06-08 | GSE5167 | GEO
Project description:We determined the gene expression profiles of murine melan-a melanocytes treated with ASP or alpha-MSH over a 4 days time course using genome-wide oligonucleotide microarrays. As expected, the gene expression patterns emphasized the opposing effects of the 2 ligands, and there were significant reductions in expression of numerous melanogenic proteins elicited by ASP, which correlates with its inhibition of pigmentation. However, ASP also unexpectidly modulated the expression of genes involved in various other cellular pathways, including glutathione synthesis and redox metabolism. Many genes up-regulated by ASP are involved in morphogenesis, cell adhesion and ECM-receptor interactions. Treatment with ASP or alpha-MSH was performed for 3 hr, 1 day, 2 days, 3 days and 4 days, in triplicate. Each biological replicate was submitted to a direct hybridization (treated/untreated samples) after coupling with Cy5 or Cy3 and to a reverse dye-swap, leading to 2 replicated hybridization for each biological sample. A total of 6 hybridized arrays was used for each of the 5 time points, for each drug.
2009-02-02 | E-GEOD-14089 | biostudies-arrayexpress
Project description:The japonica rice variety Nipponbare was grown under hydroponic condition for 10-days (untreated seedling sample). Seedlings were exposed to once stress conditions for 24 hours (stress treated sample). Seedlings were exposed to one of the following for 24 h: cold stress, incubation at 10 °C; salt stress by adding 150 mM sodium chloride to the planter box; osmotic stress by adding 260 mM mannitol to the planter box; and drought stress by adding 25% polyethylene glycol 6000 to the planter box. Total RNAs were prepared from each sample using an RNeasy Midi Kit (Qiagen, Tokyo, Japan) and the mRNAs were purified with an Oligotex-dT30 Kit (Takara, Shiga, Japan). Purified mRNA was amplified and labeled and we hybridized the 1-mg fluorescent liner amplified Cy3- and Cy5-labeled cRNAs (each cRNA was 500 ng) to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer. Keywords = Rice Keywords = Seedling Keywords = stress treatment Keywords = flood Keywords: other
2006-03-22 | GSE2415 | GEO
Project description:Antibacterial mechanism of peptide Asp-Tyr-Asp-Asp based on multiomics and molecular dynamics [E. coli]
| PRJNA791221 | ENA
Project description:The japonica rice variety Nipponbare was grown under hydroponic condition for 10-days (untreated seedling sample). Seedlings were exposed to once stress conditions for 24 hours (stress treated sample). Seedlings were exposed to one of the following for 24 h: cold stress, incubation at 10 °C; salt stress by adding 150 mM sodium chloride to the planter box; osmotic stress by adding 260 mM mannitol to the planter box; and drought stress by adding 25% polyethylene glycol 6000 to the planter box. Total RNAs were prepared from each sample using an RNeasy Midi Kit (Qiagen, Tokyo, Japan) and the mRNAs were purified with an Oligotex-dT30 Kit (Takara, Shiga, Japan). Purified mRNA was amplified and labeled and we hybridized the 1-mg fluorescent liner amplified Cy3- and Cy5-labeled cRNAs (each cRNA was 500 ng) to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer. Keywords = Rice Keywords = Seedling Keywords = stress treatment Keywords = flood
2010-06-11 | E-GEOD-2415 | biostudies-arrayexpress
Project description:The human pathogenic fungus Aspergillus fumigatus is readily eradicated by the innate immunity of immunocompetent human hosts, but can cause severe infections, such as invasive aspergillosis (IA), in immunocompromised individuals. During infection, the fungal redox homeostasis can be challenged by reactive oxygen (ROS) species, either derived from the oxidative burst of innate immune cells or the action of antifungal drugs. The peroxiredoxin Asp f3 was found to be essential to cause IA in mice, but how Asp f3 integrates to fungal redox homeostasis remains unknown. Here, we show that in vivo, Asp f3 acts as a sensor for ROS. While global transcription in fungal hyphae under minimal growth conditions was fully independent of Asp f3, a robust induction of the oxidative stress response required the presence of the peroxiredoxin. Hyphae devoid of Aspf 3 failed to activate several redox active genes, like members of the gliotoxin biosynthesis gene cluster and integral members of the Afyap1 regulon, the central activator of the ROS defence machinery in fungi. Upon deletion of the asp f3 gene Afyap1 displayed significantly reduced nuclear localization during ROS exposure, indicating that Asp f3 can act as an intracellular redox sensor for several target proteins
2021-06-03 | GSE173349 | GEO