Relative impacts of biotic and abiotic factors on the oak microbiota
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PROVIDER: PRJEB86320 | ENA |
REPOSITORIES: ENA
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Project description:Biotic and abiotic stresses limit agricultural yields, and plants are often simultaneously exposed to multiple stresses. Combinations of stresses such as heat and drought or cold and high light intensity, have profound effects on crop performance and yeilds To analyze such responses, we initially compared transcriptome changes in ten Arabidopsis thaliana ecotypes using cold, heat, high light, salt and flagellin treatments as single stress factors or their double combinations.
2013-01-31 | GSE41935 | GEO
Project description:Biotic and abiotic stresses limit agricultural yields, and plants are often simultaneously exposed to multiple stresses. Combinations of stresses such as heat and drought or cold and high light intensity, have profound effects on crop performance and yeilds To analyze such responses, we initially compared transcriptome changes in ten Arabidopsis thaliana ecotypes using cold, heat, high light, salt and flagellin treatments as single stress factors or their double combinations. Arabidopsis thaliana plants of ecotypes (Col, Ler, C24, Cvi, Kas1, An1, Sha, Kyo2, Eri and Kond) were subjected to the following stress treatments: Salt, Cold, Heat, High Light (HL), Salt+Heat, Salt+HL, Cold+HL, Heat+HL, as well as FLG (Flagellin, flg22 peptide), Cold+FLG, Heat+FLG
2013-01-31 | E-GEOD-41935 | biostudies-arrayexpress
Project description:The periderm is basic for land plants due to its protective role during radial growth, which is achieved by the polymers deposited in the cell walls. Despite the research on the topic has unravelled the role of several enzymes and transcription factors, many questions remain open, especially those regarding cell development. Here we use the outer bark of cork oak (cork), holm oak (rhytidome), and their natural hybrids’ to further understand the mechanisms underlying periderm development. Cork is an outstanding model as it consists of a thick and very homogeneous periderm produced by a permanent mother-cell layer (phellogen). Conversely, holm oak contains a more heterogeneous bark including several thin periderms mixed with phloem, also known as a rhytidome. The inclusion of hybrid samples showing rhytidome-type and cork-type barks is valuable to approach cork development, allowing an accurate identification of candidate genes and processes. The present study underscores that biotic stress and cell death signalling are enhanced in rhytidome-type barks while lipid metabolism and cell cycle are enriched in cork-type barks. Based on the DEGs most expressed related to development, we highlight that cell division, cell expansion, and cell differentiation could account for the differences found between cork and rhytidome-type barks.
2024-06-12 | GSE227020 | GEO
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: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:Transcript profiles of H. annosum from different tissues and mycelium grown on different substrates and under different stresses were analyzed. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, Department of Energy) H. irregulare genome sequence version 1. One aim of this study was to compare gene expression profiles of H. annosum grown on different substrates and under different biotic and abiotic stresses.
2013-11-01 | GSE39805 | GEO
Project description:Here we provide a set of 16 comparable transcriptome measures to monitor early changes in gene expression upon NP exposure. We evaluated A. thaliana response to 8 different types of NPs (metallic, carbonaceous and ranging from 10 to 80 nm) in comparison to biotic and abiotic stress inducers that represent most common environmental challenges for plants. Biotic stress was induced by infection with a necrotizing fungus (Alternaria brassicicola) or a hemibiotrophic bacterium (Pseudomonas syringae). Abiotic stresses induced by hypersaline conditions, drought and mechanical wounding were assayed in our plant growth model. The effect of abscisic acid (ABA), the most studied stress-responsive phytohormone which mediates stomatal closure and other reponses to drought and osmotic stress (ref), was also tested in the gene expression and phenotypes of NP-exposed plants. PART 1: Alternaria brassicicola (Abr), Pseudomonas syringae (Pst), saline stress (NaC), drought (drou), wounding (wou), 10nm TiO2 NPs (TiO2 10), 10nm AgNPs (Ag 10), bulk TiO2 (TiO), bulk AgNO3 (NO), Carbon Nanotubes NPs plus ABA (CNTs+). susana.garcias@ehu.es<a href=susana.garcias@ehu.es>additional contact details for submitter</a>
2015-04-29 | E-MTAB-3331 | biostudies-arrayexpress
Project description:This research was undertaken to investigate the global role of inositol phosphorylceramide synthase (IPCS) activity in plants and reveal its potential as a herbicide target. The non-mammalian enzyme is a key component in the plant sphingolipid biosynthetic pathway and is shown here to be a possible herbicide target. RNA-Seq analyses demonstrated that over-expression of inositol phosphorylceramide synthase isoforms AtIPCS1, 2 or 3 in Arabidopsis thaliana resulted in the down-regulation of genes involved in plant response to pathogens. In addition, genes associated with the abiotic stress response to salinity, cold and drought were found to be similarly down-regulated. Detailed analyses of transgenic lines over-expressing AtIPCS1-3 at various levels revealed that the degree of down-regulation is specifically correlated with the level of IPCS expression. Singular enrichment analysis of these down-regulated genes showed that AtIPCS1-3 expression affects biological signaling pathways involved in plant response to biotic and abiotic stress. The up-regulation of genes involved in photosynthesis and lipid localization was also observed in the over-expressing lines.
2019-05-07 | GSE129016 | GEO
Project description:In this study a complete characterization of the STS multigenic family in grapevine has been performed, commencing with the identification, annotation and phylogenetic analysis of all members and integration of this information with a comprehensive set of gene expression analyses including healthy tissues at differential developmental stages and in leaves exposed to both biotic (downy mildew infection) and abiotic (wounding and UV-C exposure) stresses. At least thirty-three full length sequences encoding VvSTS genes were identified, which, based on predicted amino acid sequences, cluster in 3 principal subgroups designated A, B and C. The majority of VvSTS genes cluster in subgroups B and C and are located on chr16 whereas the few gene family members in subgroup A are found on chr10. Microarray and mRNA-seq expression analyses revealed different patterns of transcript accumulation between the different groups of VvSTS family members and between VvSTSs and VvCHSs. Indeed, under certain conditions the transcriptional response of VvSTS and VvCHS genes appears to be diametrically opposed suggesting that flow of carbon between these two competing metabolic pathways is tightly regulated at the transcriptional level. Examination of transcriptome profile in Vitis vinifera cv Pinot noir leaf discs pools trated upon biotic and abiotic stresses. 7 samples examined: Control (=wounded 0h), wounded 24h, wounded 48h, UV-C treated 24h, UV-C treated 48h, Plasmopara viticola infected 24h, Plasmopara viticola infected 48h.
2012-05-21 | E-GEOD-37743 | biostudies-arrayexpress
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2018-02-07 | PXD004991 | Pride