Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA353754 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5028670_1.fastq.gz | Fastqsanger.gz | |||
| SRR5028670_2.fastq.gz | Fastqsanger.gz | |||
| SRR5028667_1.fastq.gz | Fastqsanger.gz | |||
| SRR5028667_2.fastq.gz | Fastqsanger.gz | |||
| SRR5028668_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 8 |
Similar Datasets
Project description:Pathak2013 - MAPK activation in response to various abiotic stresses
MAPK activation mechanism in response to various abiotic stress conditions, such as cold, salt, drought, H2O2, heavy metal and ethylene, in plants
This model is described in the article:
Modeling of the MAPK machinery activation in response to various abiotic and biotic stresses in plants by a system biology approach.
Pathak RK, Taj G, Pandey D, Arora S, Kumar A.
Bioinformation 2013; 9(9): 443-449
Abstract:
Mitogen-Activated Protein Kinases (MAPKs) cascade plays an important role in regulating plant growth and development, generating cellular responses to the extracellular stimuli. MAPKs cascade mainly consist of three sub-families i.e. mitogen-activated protein kinase kinase kinase (MAPKKK), mitogen-activated protein kinase kinase (MAPKK) and mitogen activated protein kinase (MAPK), several cascades of which are activated by various abiotic and biotic stresses. In this work we have modeled the holistic molecular mechanisms essential to MAPKs activation in response to several abiotic and biotic stresses through a system biology approach and performed its simulation studies. As extent of abiotic and biotic stresses goes on increasing, the process of cell division, cell growth and cell differentiation slow down in time dependent manner. The models developed depict the combinatorial and multicomponent signaling triggered in response to several abiotic and biotic factors. These models can be used to predict behavior of cells in event of various stresses depending on their time and exposure through activation of complex signaling cascades.
This model is hosted on BioModels Database
and identified
by: BIOMD0000000491
.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource
for published quantitative kinetic models
.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to the public
domain worldwide. Please refer to CC0 Public Domain
Dedication
for more information.
2024-09-02 | BIOMD0000000491 | BioModels
Project description:Pathak2013 - MAPK activation in response to various biotic stresses
MAPK activation mechanism in response to various biotic (fungal and bacterial pathogens) stress conditions in plants
This model is described in the article:
Modeling of the MAPK machinery activation in response to various abiotic and biotic stresses in plants by a system biology approach.
Pathak RK, Taj G, Pandey D, Arora S, Kumar A.
Bioinformation 2013; 9(9): 443-449
Abstract:
Mitogen-Activated Protein Kinases (MAPKs) cascade plays an important role in regulating plant growth and development, generating cellular responses to the extracellular stimuli. MAPKs cascade mainly consist of three sub-families i.e. mitogen-activated protein kinase kinase kinase (MAPKKK), mitogen-activated protein kinase kinase (MAPKK) and mitogen activated protein kinase (MAPK), several cascades of which are activated by various abiotic and biotic stresses. In this work we have modeled the holistic molecular mechanisms essential to MAPKs activation in response to several abiotic and biotic stresses through a system biology approach and performed its simulation studies. As extent of abiotic and biotic stresses goes on increasing, the process of cell division, cell growth and cell differentiation slow down in time dependent manner. The models developed depict the combinatorial and multicomponent signaling triggered in response to several abiotic and biotic factors. These models can be used to predict behavior of cells in event of various stresses depending on their time and exposure through activation of complex signaling cascades.
This model is hosted on BioModels Database
and identified
by: BIOMD0000000492
.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource
for published quantitative kinetic models
.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to the public
domain worldwide. Please refer to CC0 Public Domain
Dedication
for more information.
2024-09-02 | BIOMD0000000492 | BioModels
Project description:Environmental stresses influence the growth of plants and the productivity of crops. Salinity is one of the most important abiotic stresses for agricultural crops. PCD is induced by various biotic and abiotic stresses in algae and higher plants, including high salinity treatment. OsPDCD5, an ortholog to mammalian-programmed cell death 5, is up-regulated under low temperature and NaCl treatments. We found that the transgenic rice which constitutively expressed anti-OsPDCD5 increased salt stress tolerance in unique ways. By using the Rice Genome Microarray, we identified target genes that were regulated in transgenic rice plants by anti-OsPDCD5.
2011-11-01 | GSE28209 | GEO
Project description:Environmental stresses influence the growth of plants and the productivity of crops. Salinity is one of the most important abiotic stresses for agricultural crops. PCD is induced by various biotic and abiotic stresses in algae and higher plants, including high salinity treatment. OsPDCD5, an ortholog to mammalian-programmed cell death 5, is up-regulated under low temperature and NaCl treatments. We found that the transgenic rice which constitutively expressed anti-OsPDCD5 increased salt stress tolerance in unique ways. By using the Rice Genome Microarray, we identi?ed target genes that were regulated in transgenic rice plants by anti-OsPDCD5. Leaf tissues of 2-week-old transgenic and nontransgenic seedlings (10 plants each) before 200mM NaCl treatment, 20mins and 3 hours after 200mM NaCl treatment, respectively, were selected.
2011-11-01 | E-GEOD-28209 | biostudies-arrayexpress
Project description:Protein kinases are major regulatory components in almost all cellular processes in eukaryotic cells. By adding phosphate groups, protein kinases regulate the activity, localization, protein-protein interactions and other profiles of their target proteins. It is known that protein kinases such as SNF1 related protein kinase 2 and 3 (SnRK2 and SnRK3), calcium dependent protein kinases (CDPKs), and mitogen activated protein kinases (MAPKs) are central components in plant response to environmental stresses such as drought, high salinity, cold and pathogen attack. Although the phosphorylation-dependent signaling plays critical roles in plant stress biology, only a few targets of these protein kinases have been identified. How these protein kinases regulate the downstream biological processes and mediate the stress responses are still largely unknown. In this study, we developed an isotope labeled protein kinase assay-based approach with enriched phosphoproteome as kinase-substrates pool to identify the putative substrates of 8 protein kinases that function in plant abiotic and biotic stress responses. As a result, we identified more than 5,081 putative targets of osmotic stress-activated SnRK2.4 and SnRK2.6, ABA activated protein kinases SnRK2.6 and Casein-Kinase Like 2 (CKL2), elicitor-activated protein kinase CDPK11 and MPK6, cold-activated protein kinase MPK6, H2O2-activated protein kinase OXI1 and MPK6, salt-induced protein kinase SOS1 and MPK6, as well as the low-potassium-activated protein kinase CIPK23. We also analyzed the conserved motif and functional ontology of these putative kinase targets. These results provide comprehensive information on the role of these protein kinases in the control of cellular activities and could be valuable resource for further study on the mechanism underlying plant response to environmental stresses.
2020-01-16 | PXD010053 | Pride
Project description:Background: Mechanical ventilation causes ventilator-induced lung injury in animals and humans. Mitogen-activated protein kinases have been implicated in ventilator-induced lung injury though their functional significance remains incomplete. We characterize the role of p38 mitogen-activated protein kinase/ mitogen activated protein kinase kinase-3 and c-Jun-NH2-terminal kinase-1 in ventilator-induced lung injury and investigate novel independent mechanisms contributing to lung injury during mechanical ventilation. Methodology and Principle Findings: C57/BL6 wild-type mice and mice genetically deleted for mitogen-activated protein kinase kinase-3 (mkk-3-/-) or c-Jun-NH2-terminal kinase-1 (jnk1-/-) were ventilated, and lung injury parameters were assessed. We demonstrate that mkk3-/- or jnk1-/- mice displayed significantly reduced inflammatory lung injury and apoptosis relative to wild-type mice. Since jnk1-/- mice were highly resistant to ventilator-induced lung injury, we performed comprehensive gene expression profiling of ventilated wild-type or jnk1-/- mice to identify novel candidate genes which may play critical roles in the pathogenesis of ventilator-induced lung injury. Microarray analysis revealed many novel genes differentially expressed by ventilation including matrix metalloproteinase-8 (MMP8) and GADD45a. Functional characterization of MMP8 revealed that mmp8-/- mice were sensitized to ventilator-induced lung injury with increased lung vascular permeability. Conclusions: We demonstrate that mitogen-activated protein kinase pathways mediate inflammatory lung injury during ventilator-induced lung injury. C-Jun-NH2-terminal kinase was also involved in alveolo-capillary leakage and edema formation, whereas MMP8 inhibited alveolo-capillary protein leakage. Keywords: response to injury, genetically modified mouse
2007-05-08 | GSE7742 | GEO
Project description:Being a sessile organism, plants are constantly confronted by various biotic (pest and pathogen) and abiotic (drought, salinity, flood, extreme temperatures, etc.) stresses. In response to these environmental stresses, plants have developed numerous defense mechanisms. One of the basal defense responses in plants are mediated by trypsin inhibitors (TIs). Putranjiva roxburghii trypsin inhibitor (PRTI), a potent trypsin inhibitor from P. roxburghii showing sequence similarity with a group of genes known to have defense and storage function such as wound inducible (WIN) proteins, vegetative storage proteins (VSPs), and Bark storage protein (BSPs) was overexpressed in Citrus aurantifolia. PRTI overexpressing lines were tolerant to various abiotic stresses (salinity, drought, and alkalinity) and two pests namely, Scirtothrips citri and Papilio demoleus. The molecular insights underlying the heterologous overexpression of PRTI at the transcriptomic level reveals the upregulation of stress responsive genes and involvement of hormonal signal transduction and transporters. Further, genes related to DNA repair, amino acid synthesis, and development were also found to be upregulated. Our study also reveals the nuclear-cytoplasmic localization and alteration phytohormone profile by PRTI overexpression in transgenic lines as compared to wild-type which clearly indicates the role of abscisic acid ABA in stress tolerance.
2022-12-31 | GSE208104 | GEO
Project description:Plants will meet various abiotic stresses during their growth and development. One of the important strategies for plants to deal with the stress is involved in metabolic regulation, causing the dramatic changes of metabolite profiles. Metabolomic studies have been intensively conducted to reveal the responses of plants to abiotic stress, but most of them were limited to one or at most two abiotic stresses in a single experiment. In this study, we compared the metabolite profiles of barley seedlings exposed to seven abiotic stresses simultaneously, including drought, salt stress, aluminum (Al), cadmium (Cd), deficiency of nitrogen (N), phosphorus (P) and potassium (K). The results showed that metabolite profiles of barley under these stresses could be classified into three types: osmotic stresses (drought and salt); metal stresses (Al and Cd) and nutrient deficiencies (N, P and K deficiencies). Compared with the control, some metabolites (including polyamines, raffinose and piperonic acid) in plants exposed to all abiotic stresses changed significantly, while some other metabolites showed the specific change only under a certain abiotic stress, such as proline being largely increased by osmotic stress (drought and salinity), the P-containing metabolites being largely decreased under P deficiency, some amino acids (lysine, tyrosine, threonine, ornithine， glutamine and so on) showing the dramatic reduction in the plants exposed to N deficiencies, respectively. The current meta-analysis obtained a comprehensive view on the metabolic responses to various abiotic stress, and improved the understanding of the mechanisms for tolerance of barley to abiotic stress.
2021-01-07 | ST001648 | MetabolomicsWorkbench
Project description:This research trial is testing a combination of two experimental drugs, MSC1936369B (Mitogen-activated protein extracellular signal-regulated kinase (MEK) Inhibitor) and SAR245409 (Phosphatidylinositol 3-kinase (Pi3K)/Mammalian Target of Rapamycin (mTOR) inhibitor), in the treatment of locally advanced or metastatic solid tumors. The primary purpose of the study is to determine the maximum tolerated dose of the drug combination.
| 2109499 | ecrin-mdr-crc
Project description:A novel cold-inducible GSK3/Shaggy-like kinase cDNA (TaSK5) was isolated from winter wheat by a macroarray-based differential screening approach. Sequence analysis of TaSK5 revealed high similarity to Arabidopsis subgroup I GSK3/Shaggy-like kinases ASK-alpha, ASK-gamma and ASK-epsilon. Transgenic Arabidopsis plants overexpressing TaSK5 cDNA under the control of CaMV 35S promoter showed enhanced tolerance to salt and drought stresses. In contrast, the tolerance of the transgenic plants to freezing stress was not altered. To identify genes which are differentially regulated in the 35S:TaSK5 over-expressing Arabidopsis plants under non-stress conditions, we compared the genome-wide expression profiles of Col-0 and plants over-expressing TaSK5 using DNA microarrays. Sixty seven genes were found to be expressed at least 2-fold more strongly in 35S:TaSK5 plants than in Col-0, and 17 genes were found to be expressed at least 2-fold more strongly in Col-0 than in 35S:TaSK5 plants. Most of the TaSK5 up-regulated genes were also induced by abiotic stresses, including cold, salt and drought. These results support the involvement of TaSK5 in abiotic stress signal transduction. Keywords: transgenic vs wt Col.-0 comparison
2014-11-02 | GSE59556 | GEO