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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Sucrose modulation of the Arabidopsis thaliana guard-cell transcriptome

ABSTRACT: Microarrays were used to evaluate the effect of sucrose on gene expression in guard cells. Strips of Arabidopsis leaves were incubated with sucrose or mannitol or no sugars, then the leaves were freeze dried and guard cells were dissected from the leaf strips and analyzed. RNA was extracted from guard cells dissected from leaf strips that had been treated with sucrose or with mannitol or no sugars as controls. Triplicate biological replicates were prepared for the treatments and controls. The RNA was amplified twice with T7 RNA polymerase and hybridized to Affymetrix ATH1 arrays.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: George Bates

PROVIDER: E-GEOD-37408 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A comparative study of the Arabidopsis thaliana guard-cell transcriptome and its modulation by sucrose.

Bates George W GW Rosenthal David M DM Sun Jindong J Chattopadhyay Maitreyi M Peffer Emily E Yang Jing J Ort Donald R DR Jones Alan M AM

PloS one 20121121 11

Microarray analysis was performed on RNA isolated from guard cells that were manually dissected from leaves of Arabidopsis. By pooling our data with those of two earlier studies on Arabidopsis guard cell protoplasts, we provide a robust view of the guard-cell transcriptome, which is rich in transcripts for transcription factors, signaling proteins, transporters, and carbohydrate-modifying enzymes. To test the hypothesis that photosynthesis-derived sugar signals guard cells to adjust stomatal ope ...[more]

PMID: 23185391

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Sucrose modulation of the Arabidopsis thaliana guard-cell transcriptome

Project description:Microarrays were used to evaluate the effect of sucrose on gene expression in guard cells. Strips of Arabidopsis leaves were incubated with sucrose or mannitol or no sugars, then the leaves were freeze dried and guard cells were dissected from the leaf strips and analyzed.

2012-11-26 | GSE37408 | GEO

Time-resolved metabolomics and proteomics of Brassica napus guard cells under low CO2 concentration

Project description:In order to discover new nodes and edges for low CO2-induced stomata closure, we applied hyphenated mass spectrometry (MS)-based metabolomics and proteomics approaches to analyze short-term low CO2 responses in B. napus (canola) guard cells. A total of 411 metabolites were quantified. We observed decreased trends of primary metabolites biosynthesis (e.g., most common amino acids, nucleotides, and sugars), and changes in the levels of osmoregulators such as sucrose, malate, and mannitol showed increased trends at both early and late time points. Unlike under elevated CO2 levels, JA biosynthesis was not altered. Instead, phytohormones that induces stomatal opening, including cytokinins, auxins, GA4, as well as melatonin increased at early time points. This study also highlights the utility of single cell-type metabolomics in discovering and testing new nodes and edges in cellular signaling and metabolic networks.

2018-10-26 | PXD005787 | Pride

Transcriptome analysis of Arabidopsis thaliana G protein subunit mutants in response to abscisic acid (ABA)

Project description:Heterotrimeric G proteins mediate crucial and diverse signaling pathways in eukaryotes. To gain insights into the regulatory modes of the G protein and the co-regulatory modes of the G protein and the stress hormone abscisic acid (ABA), we generated and analyzed gene expression in G protein subunit single and double mutants of the model plant Arabidopsis thaliana. Through a Boolean modeling approach, our analysis reveals novel modes of heterotrimeric G protein action. Keywords: transcriptome analysis; G protein subunit mutants; abscisic acid (ABA) Microarray data were generated from four genotypes (wild type, gpa1-4 mutant, agb1-2 mutant, agb1-2 gpa1-4 double mutant) with or without ABA treatment. Arabidopsis plants were grown in growth chambers with an 8 hr light/16hr dark. Three hundred Arabidopsis leaves excised from 60-70 five-week-old plants were used as the starting material for each guard cell microarray. Ten mature leaves taken from 3-4 plants grown side-by side with the plants for guard cell isolation were used for each leaf sample. Excised leaf and isolated guard cell samples were treated with ABA (50 μM) or EtOH (solvent control) for 3 hrs. For each type of sample (guard cells or leaves), three independent biological replicates were performed, resulting in a total of 48 microarray hybridizations (2 sample types ´ 4 genotypes ´ two treatments ´3 replicates).

2010-12-06 | E-GEOD-19520 | biostudies-arrayexpress

Transcription profiling of Arabidopsis response to sucrose feeding to detached leaves

Project description:The effect of sucrose feeding on gene expression in Arabidopsis thaliana leaves was investigated using affymetrix ATH1 microarrays. For this, petioles of detached leaves were put in a solution containing either sucrose or sorbitol (control). Sugars were taken up into the leaf via the respiration stream for 13 hours. After that, leaves were frozen in liquid nitrogen and RNA was extracted for analysis. Experiment Overall Design: The effect of sucrose feeding on gene expression was investigated using affymetrix ATH1 microarrays. For this, petioles of detached leaves were put in a solution containing either sucrose or sorbitol (control). Sugars were taken up into the leaf via the respiration stream for 13 hours. After that, leaves were frozen in liquid nitrogen and RNA was extracted for analysis.

2008-06-12 | E-GEOD-4022 | biostudies-arrayexpress

Transcription profiling by array of Arabidopsis guard cells and mesophyll cells in response to ABA treatment

Project description:Transcriptional profiling of guard cells and mesophyll cells in response to ABA treatment

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Improved post thaw function and genetic changes for mesenchymal stromal cells cryopreserved using multicomponent osmolyte solutions

Project description:We report genome-wide expression changes that occur in H9-iMSCs frozen with different freezing methods that include DMSO and non-DMSO experimental solutions such as SGC (sucrose-glycerol-creatinine, SMC (sucrose-mannitol-creatinine), and SGI (sucrose-mannitol-isoleucine). mRNA-Seq analysis shows that DMSO samples cluster with fresh samples in the same clade, while all samples using the experimental solutions cluster together. In addition, we also see that cells frozen using experimental solutions have upregulation of a number of key molecular function pathways including extracellular matrix structural genes, receptor binding, and growth factor expression.

2016-12-30 | GSE88946 | GEO

Comparison of pan-inhibitor of HDACS (TSA) to specific HDAC8 inhibitor (HDAC Inhibitor XIX, Compound 2) in human myometrium

Project description:To compare gene expression in human myometrium after TSA treatment to gene expression after treatment with a specific HDAC8 inhibitor Four Control, four TSA and four Compound 2 samples (2 patients, replicated) derived from non-pregnant myometrial strips

2012-02-07 | E-GEOD-27124 | biostudies-arrayexpress

Arabidopsis Me-0 vs tetraploid Col

Project description:To investigate gene expression differences related to the regulation of stomatal aperture between two Arabidopsis accessions, Me-0 and tetraploid Col, we performed microarray analysis on guard cell protoplasts from these two accessions. We identified 1,777 probes as up-regulated and 1,706 probes as down-regulated differentially expressed genes (DEGs) in Me-0 compared with tetraploid Col (adjusted P-value < 0.001 and log 2 fold change of greater than 1 or less than -1). Using gene set analysis to functionally characterize DEGs, there were eight significant gene sets (at the level of P-value < 0.01) among the up-regulated genes and seven significant gene set among the down-regulated genes. Genes with the lowest P-value among the up-regulated genes were related to âplant-type cell wall looseningâ, an essential step in guard cell swelling. Most of the down-regulated genes were related to the defense responses for immunity, hypoxia, and ozone, which also influence stomatal responses or gas exchange. We propose that these gene expression differences may cause the difference in stomatal aperture between Me-0 and tetraploid Col. Four samples from Me-0 and three samples from tetraploid Col are used for a microarray analysis.

2016-01-14 | E-GEOD-71914 | biostudies-arrayexpress

Gene expression analysis of IL-17 induced mice small intestinal smooth muscle strips with or without 6-shogaol.

Project description:The etiology of post-inflammatory gastrointestinal (GI) motility dysfunction, after resolution of acute symptoms of inflammatory bowel diseases (IBD) and intestinal infection, is largely unknown. Here, using an established mouse model of experimental enteritis, we show that enhancement of smooth muscle cell (SMC) contraction by interleukin (IL)-17A may be involved in postinflammatory GI hypermotility. To examine the effect of IL-17 in the small intestinal smooth muscle, we used whole genome microarray expression profiling to find out the genes which respond to IL-17 stimulus. The smooth muscle strips were peeled off from mouse small intestine and incubated 24h with or without IL-17. And we also examined the effect of 6-shogaol, which is one of the ingredients of Japanese traditional medicine for intestinal mortor disorder, Daikenchuto, in IL-17 stimulated small intestinal smooth muscle strip. The smooth muscle strips were peeled off from mice small intestine and incubated in the culture media for 24h with or without IL-17. A part of IL-17 stimulated strips were co-incubated with 6-shogaol. Six independent experiments were performed.

2012-09-15 | E-GEOD-39573 | biostudies-arrayexpress

Identification of DIR1-dependant cellular responses required for systemic acquired resistance in guard cells

Project description:After localized invasion by bacterial pathogens, systemic acquired resistance (SAR) is induced in uninfected plant tissues, resulting in enhanced defense against a broad range of pathogens. Although SAR requires mobilization of signaling molecules via the plant vasculature, the specific mechanisms remain elusive. The lipid transfer protein-defective in induced resistance 1-1 (DIR1-1) was identified in Arabidopsis thaliana by screening for mutants that were defective in SAR. Since then, the structure and lipid-binding properties of DIR1 have been determined, showing that its barrel structure can bind two, long-chain fatty-acid molecules. Several SAR mobile signals, including dehydroabietinal (DA), azelaic acid (AzA), and glycerol-3-phosphate (G3P) are dependent on DIR1 for transport to systemic leaves. Closure of stomata, controlled by guard cells, is a local response to bacteria. Here we demonstrate that stomatal response to pathogens is altered in systemic leaves by SAR, and this guard cell SAR defense requires DIR1. Using a multi-omics approach, we have determined potential SAR signaling mechanisms specific for guard cells in systemic leaves by profiling metabolite, lipid, and protein differences between guard cells in wild type and dir1-1 mutant during SAR. We identified two 18C fatty actyls and two 16C wax esters as putative SAR-related molecules dependent on DIR1. Proteins and metabolites related to amino acid biosynthesis and response to stimulus were altered in guard cells of dir1-1 compared to wild type. Identification of guard cell-specific SAR-related molecules will lead to new avenues of genetic modifications/molecular breeding for disease resistant plants.

2022-02-17 | PXD024991 | Pride

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