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An improved, low-cost, hydroponic system for growing Arabidopsis and other model plant species under sterility conditions (Arabidopsis transcriptional profile in early response to Pi starvation)

ABSTRACT: Transcriptional profiling of roots from 12 days-old Arabidopsis thaliana seedlings transfered to Pi-deficient medium in hydroponic solution in a 10 min, 30 min, and 2 hrs time course period.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE53114 | GEO | 2013/12/12

SECONDARY ACCESSION(S): PRJNA231123

REPOSITORIES: GEO

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An improved, low-cost, hydroponic system for growing Arabidopsis and other model plant species under sterility conditions (Arabidopsis transcriptional profile in early response to Pi starvation)

Project description:Transcriptional profiling of roots from 12 days-old Arabidopsis thaliana seedlings transfered to Pi-deficient medium in hydroponic solution in a 10 min, 30 min, and 2 hrs time course period. A dye balanced modified loop design was implemented. This experiment involved a total of twelve sets of microarray hybridizations, including direct and dye swap comparisons between treatments as well as across time points for the same treatment. This design allowed us to determine differences in gene expression between Pi-deprived and control seedlings, and whether the differences were time dependent. Four biological replicates representing each sampling point were obtained.

2013-12-12 | E-GEOD-53114 | biostudies-arrayexpress

An improved, low-cost, hydroponic system for growing Arabidopsis and other plant species under aseptic conditions.

Project description:BackgroundHydroponics is a plant growth system that provides a more precise control of growth media composition. Several hydroponic systems have been reported for Arabidopsis and other model plants. The ease of system set up, cost of the growth system and flexibility to characterize and harvest plant material are features continually improved in new hydroponic system reported.ResultsWe developed a hydroponic culture system for Arabidopsis and other model plants. This low cost, proficient, and novel system is based on recyclable and sterilizable plastic containers, which are readily available from local suppliers. Our system allows a large-scale manipulation of seedlings. It adapts to different growing treatments and has an extended growth window until adult plants are established. The novel seed-holder also facilitates the transfer and harvest of seedlings. Here we report the use of our hydroponic system to analyze transcriptomic responses of Arabidopsis to nutriment availability and plant/pathogen interactions.ConclusionsThe efficiency and functionality of our proposed hydroponic system is demonstrated in nutrient deficiency and pathogenesis experiments. Hydroponically grown Arabidopsis seedlings under long-time inorganic phosphate (Pi) deficiency showed typical changes in root architecture and high expression of marker genes involved in signaling and Pi recycling. Genome-wide transcriptional analysis of gene expression of Arabidopsis roots depleted of Pi by short time periods indicates that genes related to general stress are up-regulated before those specific to Pi signaling and metabolism. Our hydroponic system also proved useful for conducting pathogenesis essays, revealing early transcriptional activation of pathogenesis-related genes.

| S-EPMC3999955 | biostudies-literature

Increased sensitivity to salt stress in tocopherol-deficient Arabidopsis mutants growing in a hydroponic system.

Project description:Recent studies suggest that tocopherols could play physiological roles in salt tolerance but the mechanisms are still unknown. In this study, we analyzed changes in growth, mineral and oxidative status in vte1 and vte4 Arabidopsis thaliana mutants exposed to salt stress. vte1 and vte4 mutants lack α-tocopherol, but only the vte1 mutant is additionally deficient in γ-tocopherol. Results showed that a deficiency in vitamin E leads to reduced growth and increased oxidative stress in hydroponically-grown plants. This effect was observed at early stages, not only in rosettes but also in roots. The vte1 mutant was more sensitive to salt-induced oxidative stress than the wild type and the vte4 mutant. Salt sensitivity was associated with (i) high contents of Na(+), (ii) reduced efficiency of PSII photochemistry (Fv/Fm ratio) and (iii) more pronounced oxidative stress as indicated by increased hydrogen peroxide and malondialdeyde levels. The vte 4 mutant, which accumulates γ- instead of α-tocopherol showed an intermediate sensitivity to salt stress between the wild type and the vte1 mutant. Contents of abscisic acid, jasmonic acid and the ethylene precursor, 1-aminocyclopropane-1-carboxylic acid were higher in the vte1 mutant than the vte4 mutant and wild type. It is concluded that vitamin E-deficient plants show an increased sensitivity to salt stress both in rosettes and roots, therefore indicating the positive role of tocopherols in stress tolerance, not only by minimizing oxidative stress, but also controlling Na(+)/K(+) homeostasis and hormonal balance.

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Arabidopsis seedling hydroponic treatment with Streptomyces AGN23 culture supernatants

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RNA-seq analysis of bread wheat grown under hydroponic Fe deficient conditions

Project description:Bread wheat (Triticum aestivum L., cv. Fielder) plants were grown under iron (Fe) deficient hydroponic conditions to analyise transcriptomic changes in leaf and root tissue.

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Gene expression profiling of ramie roots during hydroponic induction and adaption to aquatic environment

Project description:Transcriptome analysis of root development related genes in terrestrial and hydroponic ramie. Ramie seedlings were cultivated in soil, and in hydroponic with the shoot-cutting propagation method. The root samples from hydrophonic ramie were collected from the early stage (5-day-old seedling) and the late stage (30-day-old seedling) of acquatic roots induction. The roots of ramie seedling cultivated in soil were also collected for comparative analysis. Our study represents the detailed analysis of ramie root transcriptomes with biologic replicates.

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Expression data from +Pi and -Pi treeatment between WT and spx1spx2 double mutant

Project description:Fourteen days plants growth under hydroponic +P condition (200 µM) were treated with +P(200µM) or –P (no phosphate) for another 7 days, shoot of plants from 3 biological repeats were sampled for Affymetrix microarray analysis. We used microarrays to detail the global programme of gene expression underlying +Pi and -Pi condition between WT and spx1spx2 double mutant. Fourteen days plants growth under hydroponic +P condition (200 µM) were treated with +P(200µM) or –P (no phosphate) for another 7 days, shoot of plants from 3 biological repeats were sampled for Affymetrix microarray analysis.

2014-10-03 | E-GEOD-60823 | biostudies-arrayexpress

Expression data from +Pi and -Pi treeatment between WT and spx1spx2 double mutant

2014-10-03 | GSE60823 | GEO

cDNA Microarray Analysis of Soybean NILs under Fe Sufficient Hydroponic Conditions

Project description:The purpose of this experiment was to identify any genes differentially expressed between the Soybean Near Isogenic Lines iron efficient Clark and iron inefficient IsoClark under iron sufficient hydroponic conditions. These genes would represent constituative genetic differences between the NILs. Keywords: Near Isogenic Line Comparison of Unstressed Soybean Plants

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Protein-protein interaction network dynamics induced by nitrogen starvation in Arabidopsis root membranes

Project description:With the information gathered through mass-shift- and correlation-analysis, we predict PPi on a proteomic scale and describe the results in form of a network. This experiment was done with 3 week old Arabidopsis thaliana wt seedlings grown in hydroponic culture (1/2 MS-Medium) under different nutritional conditions (N-Starvation, Full supply and Resupply after 15 min)

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