Transcription profiling by array of Arabidopsis roots split and grown in media with or without inorganic phosphate
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: marie-christine thibaud
PROVIDER: E-MEXP-2601 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Arabidopsis nudix hydrolase 7 knock-out mutant Atnudt7-1 exhibits a reduced size phenotype when compared with age-matched Col-0 wildtype plants growing in potting mix of 12 parts vermiculite: 3 parts redi-earth and 1 part sand. In these array experiments the differences in gene expression caused by this mutation is assessed in comparison to wildtype plants.
2010-08-31 | E-MEXP-2711 | biostudies-arrayexpress
Project description:Sugarcane one-eyed seed sets obtained from a variety sensitive to drought conditions (cv. SP90-1638, CTC, Brazil) were cultivated on moist sand for 15 days. The plants were transferred to pots containing moist sand and were irrigated with Hoagland's solution (Hoagland and Arnon, 1950). Regular watering was maintained for 90 days and suppressed after this period for the experimental group. Leaves were collected 24 h, 72 h and 120 h after exposure to drought conditions for the control and experimental groups. Samples were collected and immediately frozen in liquid nitrogen. Leaves from six plantlets were used for each time point. Extraction of total RNA was performed separately on each sample pool. Keywords: time course of stress response RNA from experimental sample and from its respective control sample (untreated plants) was used for hybridization to dual channel arrays. Two biological replicates were used for each experimental point. The quantification of each hybridization was submitted in two files, one for each slide side (technical replicates).
2012-07-31 | E-GEOD-33574 | biostudies-arrayexpress
Project description:affy_nitrogen_medicago - affy_nitrogen_medicago - Experiment has been designed to characterize the molecular expression patterns associated to a contrasted modification of the nitrogen status of the whole plant. The systemic effects of nitrogen status modifications are investigated and compared on non nodulated plant supplied with NO3, NH4 or nodulated plants (Sinorhizobium meliloti 2011) supplied with air. The root systems were separated in two compartments of unequal sizes (split root system). Two treatments were applied on the larger compartment in order to modulate the nitrogen status of the plant: for the S treatment, roots are supplied with nutrient solution containing 10 mM NH4NO3,, whereas for the C treatment, roots are supplied with nitrogen free medium. In the case of N2 fixing plants, N limitation was obtained by replacing air by a mixture of Ar and O2 80 per cent and 20 per cent. The effects of these treatments were investigated on roots of the minor compartment supplied continuously with either NO3 1 mM, NH4 1 mM or air (N2) and on the shoots. We were also interested in the molecular expression patterns associated to the roots deprived of N.-The root system of non-nodulated (NO3- and NH4+) or nodulated (N2) plants is split into two unequal parts and each one is installed in a separate compartment. For the S treatement, the major root part is supplied with NH4NO3 10 mM whereas the minor part is supplied with either NO3- 1mM, NH4+ 1mM or N2. For the C treatement, the major root part is supplied with nitrogen-free nutrient solution whereas the minor part is supplied with either NO3- 1mM, NH4plus 1mM or N2. Each treatement is four days long. Samples of roots of six biological types (NO3S, NO3C, NH4S, NH4C, N2S and N2C) were collected. Two biological repeats per biological types have been analyzed. The effect of the S and C treatments were investigated for each N sources by comparing Affymetrix transcriptomes (NO3C vs NO3S, NH4C vs NH4S, N2C vs N2S). Experiment Overall Design: 26 arrays - medicago
2008-06-17 | E-GEOD-9818 | biostudies-arrayexpress
Project description:In order to decipher the molecular alterations caused by the growing medium, we harvested the roots of plants grown in hydroponics and on soil for 6 weeks under 10-hour short days. The temperature was 20°C (day and night), the relative humidity was 70 %, and the light was provided by cool-white fluorescent tubes at 100 μE.mâ2.sâ1 during the first 10 days, 60 μE.mâ2.sâ1 later. The soil was composed of a mixture of peat compost and sand (3:1 v/v), which was watered daily with tap water. Plants were transferred to 1-liter containers (six plants/container) 18 days after sowing. Plants grown in hydroponics were sown on agar-containing (6.7 g.lâ1; Kalys, France) seed-holders placed on 2-liter black containers and accessories (http://www.araponics.com). The hydroponic solution, changed every two weeks, was prepared as described in Tocquin et al. (2003). During the first three weeks of growth, the number of plants per 2-liter tank was 35 and 18 afterwards. Harvesting was performed 8 hours after the beginning of the light period (16h30), and the roots from 35 to 45 individuals were pooled. Three independent biological replicates were performed for plants grown on both media.
2016-06-30 | E-MTAB-4129 | biostudies-arrayexpress
Project description:We used Arabidopsis thaliana Col-0 for all experiments. The plants were grown hydroponically on nutrient solution as described previously [Plant J 1999, 18(5):509-519]. Briefly, plants were grown on sand, placed in custom-designed styrofoam rafts, in a growth chamber (EGC, Chagrin Falls, OH, USA) at 22°C with 60 mmol photons m-2s-1 light intensity and 8 h/16 h light/dark cycles. The seeds were initially germinated in tap water. After one week, the water was replaced with a complete nutrient solution [Plant J 1999, 18(5):509-519]. All the experiments were performed with 6 week old plants. Nutrient solutions were renewed weekly and on the day before the experiments. For treatments, individual rafts were transferred to containers with 300mL of nutrient solution supplemented with various concentrations of nitrate (as a mix of 2/1 KNO3/Ca(NO3)2) and/or sucrose. The N-free nutrient solutions contained 0.25 mM K2SO4 and 0.25 mM CaCl2 instead of KNO3 and Ca(NO3)2. Plants were transferred to treatments media at the beginning of the light period and were harvested 8h afterwards. Roots and leaves were harvested separately and quickly frozen in liquid N2.
2006-11-30 | E-MEXP-828 | biostudies-arrayexpress
Project description:The global emergence of soil salinization poses a serious challenge to many countries and regions. γ-Aminobutyric acid (GABA) is involved in systemic regulation of plant adaptation to salt stress, but the underling molecular and metabolic mechanism still remains largely unknown. The elevated endogenous GABA level by exogenous application of GABA could significantly improve salt tolerance in creeping bentgrass with the enhancement of antioxidant capacity, photosynthetic characteristics, osmotic adjustment (OA), and water use efficiency. GABA strongly upregulated transcript levels of AsPPa2, AsATPaB2, AsNHX2/4/6, and AsSOS1/20 in roots involved in enhanced capacity of Na+ compartmentalization and mitigation of Na+ toxicity in cytosol. Significant downregulation of AsHKT1/4 expression could be induced by GABA in leaves in relation to maintenance of significantly lower Na+ accumulation and higher K+/Na+ ratio. GABA-depressed aquaporins (AQPs) expression and accumulation induced declines in stomatal conductance and transpiration, thereby reducing water loss in leaves during salt stress. For metabolic regulation, GABA primarily enhanced sugars and amino acids accumulation and metabolism largely contributing to improved salt tolerance through maintaining OA and metabolic homeostasis. Other major pathways could be responsible for GABA-induced salt tolerance including increases in antioxidant defense, heat shock proteins, dehydrins, and myo-inositol accumulation in leaves. Integrative analyses of molecular, protein, metabolic, and physiological changes reveal systemic function of GABA on regulating ions, water, and metabolic homeostasis in non-halophytic creeping bentgrass under salt stress.
2020-01-13 | PXD015066 | Pride
Project description:The efficacy of inoculation of single pure bacterial cultures into complex microbiomes, for example, in order to achieve increased pollutant degradation rates in contaminated material (i.e., bioaugmentation), has been frustrated by insufficient knowledge on the behaviour of the inoculated bacteria under the specific abiotic and biotic boundary conditions. Here we present a comprehensive analysis of global gene expression of the bacterium Sphingomonas wittichii RW1 in contaminated sand, compared to regular suspended batch growth in liquid culture. RW1 is a well-known bacterium capable of mineralizing polycyclic aromatic hydrocarbons such as dioxins, dibenzofurans and other chlorinated congeners. We tested the reactions of the cells both during the immediate transition phase from liquid culture to sand with or without dibenzofuran, as well during growth and stationary phase in sand. Cells during transition resemble going through stationary phase, showing evidence of stress responses and nutrient scavenging, and even of major adjustments in their primary metabolism if they were not pre-cultured on the same contaminant as found in the soil. Cells growing and surviving in soil show very different signatures as in liquid or in liquid culture exposed to chemicals inducing drought stress, and we obtain evidence for numerous soil-specific expressed genes. We conclude that studies focusing on inoculation efficacy should test behavior under conditions as closely as possible mimicking the intended microbiome conditions. We were interested to study the global reactions of bacteria with biodegradative properties under near-environmental as compared to laboratory culture conditions. We compared here the genome-wide responses of RW1 between regular laboratory batch growth on the aromatic substrates DBF and salicylate with growth in sandy soil with or without the same aromatic compounds. We analysed the cellular reactions immediately after introduction into the sand, during exponential growth and at stationary phase, all in carefully controlled and replicated experimental conditions.
2014-06-23 | E-GEOD-54814 | biostudies-arrayexpress
Project description:Arabipdosis thaliana (ecotype Col-0) was infected with the root pathogen Plasmodiophora brassicae. Gene expression of the host plant has been analyzed at two time points after inoculation (10 and 23 days after inoculation) compared to the correspondend control plants.
2005-02-25 | E-MEXP-254 | biostudies-arrayexpress
Project description:Covalent modifications of core histones govern downstream DNA-templated processes such as transcription by altering chromatin structure and function. Previously, we reported that the plant homeodomain protein ALFIN-LIKE 6 (AL6), a bona fide histone reader that preferentially binds trimethylated lysin 4 on histone 3 (H3K4me3), is critical for recalibration of cellular phosphate (Pi) homeostasis and root hair elongation under Pi-deficient conditions. Here, we demonstrate that AL6 is also involved in the response of Arabidopsis seedlings to jasmonic acid (JA) during skotomorphogenesis, possibly by modulating chromatin dynamics that affect the transcriptional regulation of JA-responsive genes. Dark-grown al6 seedlings showed a compromised reduction in hypocotyl elongation upon exogenously supplied JA, a response that was calibrated by the availability of Pi in the growth medium. A comparison of protein profiles between wild-type and al6 mutant seedlings using a quantitative Chromatin Enrichment for Proteomics (ChEP) approach, that we modified for plant tissue and designated ChEP-P (ChEP in Plants), yielded a comprehensive suite of chromatin-associated proteins and candidates that may be causative for the mutant phenotype. Altered abundance of proteins involved in chromatin organization in al6 seedlings suggests a role of AL6 in coordinating the deposition of histone variants upon perception of internal or environmental stimuli.
2021-06-17 | PXD026541 | Pride
Project description:Spingomonas wittichii strain RW1 can completely oxidize dibenzo-p-dioxins and dibenzofurans, which are persistent contaminants of soils and sediments. For successful application in soil bioremediation systems, strain RW1 must cope with fluctuations in water availability, or water potential. The objectives of this study were to characterize how strain RW1 responses to changes in different components of the total water potential (solute and matric potential) and to then connect these responses to more realistic scenarios of soil desiccation. To accomplish this task, transcriptome profiling was used to investigate the effects of decreasing the solute potential with sodium chloride (solute stress), decreasing the matric potential with high-molecular weight polyethylene glycol (matric stress), or inoculating cells directly into unsaturated sand (sand desiccation stress). Transcriptome profiling revealed a general response to solute, matric, and sand desiccation stress that involved synthesizing trehalose and modifying the composition of exopolysaccarides. Transcriptome profiling also revealed responses that were unique to each stress. Only solute and matric stress triggered the down-regulation of flagella genes. Only solute and sand desiccation stress triggered the up-regulation of two RNA polymerase ECF-type sigma factors along with several membrane proteins, mechanosensitive channels, and solute transporters. Finally, only matric stress triggered the up-regulation of the RNA polymerase sigma-32 factor along with several molecular chaperones. Together, this study revealed a general response to solute, matric and sand desiccation stress but also unique responses to only a subset of these stresses, suggesting that each stress affects strain RW1 in a fundamentally different way. Comparative transcriptome profiling was performed to assess the effects of acute (30 min) solute and matric stress (3 samples for acute solute stress, 3 samples for acute matric stress, 3 controls), the effects of chronic (24 hours) solute and matric stress (3 samples for chronic solute stress, 3 samples for chronic matric stress, 3 controls), and the effects of sand desiccation stress (4 samples for sand desiccation treatment, 3 controls).
2011-01-19 | E-GEOD-26705 | biostudies-arrayexpress