Gene expression profiling of rice seedling with 2-azahypoxanthine
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa Oryza sativa Japonica Group
PROVIDER: GSE14778 | GEO | 2011/04/14
SECONDARY ACCESSION(S): PRJNA112207
REPOSITORIES: GEO
Similar Datasets
Project description:Rings or arcs of fungus-stimulated plant growth occur often on the floor of woodlands which are commonly called “fairy rings”. We purified a plant growth-stimulating compound, 2-azahypoxanthine (AHX), from the fairy ring-forming fungus Lepista sordida, and the detection of AHX in the fungus-infected soil near the growth-stimulated turfgrass roots. The growth-promoting activity of AHX towards rice was further analyzed by oligo DNA microarrays. Immediately after germination, rice seedlings were treated with AHX and incubated for 2 weeks. Total RNA was isolated from the seedlings using an RNeasy plant mini kit (Qiagen). cDNA was synthesized to provide 400 ng of total RNA (Agilent Technologies). This cDNA was used as a template to synthesize cRNA. The cRNA was labeled with Cyanine-3 (Cy3) CTP or Cyanine-5 (Cy5) CTP. Cy3-labeled cRNA was mixed with the same amount of Cy5-labeled cRNA and the mixture was used for hybridization. After hybridization for 17 h at 65°C, the slides were washed and scanned with an Agilent Microarray Scanner. Genes showing a signal value below 300 in the Cy3 channel of the control were excluded from the analysis. Feature extraction and image analysis software (version A.6.1.1; Agilent Technologies) were used to locate and delineate each spot in the array and to integrate each spot’s intensity, filtering, and normalization. We attempted dye swap experiments to estimate the error of technical and dye labelling. Three-condition experiment, control vs. compound-treated rice (0.05 and 0.2 mM). Biological replicates: control, 0.05 mM AHX-treated, 0.2 mM AHX-treated rice independently grown and harvested. One replicate per array.
2011-04-14 | E-GEOD-14778 | biostudies-arrayexpress
Project description:Fairy rings are zones of stimulated grass growth by the interaction between the fungi and the plant. In the previous research, we reported the identification of the “fairy”, ICAproduced by the fairy ring-forming fungus and the mechanism of its growth-inhibiting activity using DNA microarray. We invetigate expression profiling of rice seedlings treated with ICA for the mechanism of its growth-inhibiting activity.
2019-07-26 | GSE100899 | GEO
Project description:Fairy rings are zones of stimulated grass growth by the interaction between the fungi and the plant. In the previous research, we reported the identification of the “fairy”, 2-azahypoxanthine (AHX), produced by the fairy ring-forming fungus and the mechanism of its growth-promoting activity using DNA microarray. We discovered AOH, a common metabolite of AHX in plants. We investigate expression profiling of rice seedlings treated with AHX or AOH for the mechanism of their growth-promoting activity.
2014-01-01 | GSE38844 | GEO
Project description:Fairy rings are zones of stimulated grass growth by the interaction between the fungi and the plant. In the previous research, we reported the identification of the M-bM-^@M-^\fairyM-bM-^@M-^], 2-azahypoxanthine (AHX), produced by the fairy ring-forming fungus and the mechanism of its growth-promoting activity using DNA microarray. We discovered AOH, a common metabolite of AHX in plants. We investigate expression profiling of rice seedlings treated with AHX or AOH for the mechanism of their growth-promoting activity. Three-condition experiment, control vs. AHX-treated rice (50 and 200 mM) and AOH-treated rice (50 and 200 mM).
2014-01-01 | E-GEOD-38844 | biostudies-arrayexpress
Project description:The presence of genetic groups of the entomopathogenic fungus Metarhizium anisopliae in soil is shaped by its adaptability to specific soil and habitat types, and by soil insect populations. Although the entomopathogenic life style of this fungus is well studied, its saprophytic life style has received little consideration. While a set of functionally related genes can be commonly expressed for the adaptability of this fungus to different environments (insect cuticle, insect blood and root exudates), a different subset of genes is also expected for each environment. In order to increase the knowledge of the potential use of M. anisopliae as a rhizosphere competent organism, in this study we evaluated the genetic expression of this fungus while growing on plant root exudates in laboratory conditions during a time course.
2010-12-29 | GSE16848 | GEO
Project description:Specific Aims ; To identify novel transcriptional events associated with angiogenesis in VEGF and Ang-1 stimulated rat aortic rings. Our studies take advantage of the capacity of rat aortic rings to generate new vessels in collagen gels. Rat aortic rings embedded in collagen gel immediately after excision from the animal produce a self-limited angiogenic response under serum-free conditions and in the absence of exogenous stimuli. This angiogenic response can be dose-dependently promoted by vascular endothelial growth factor (VEGF) and angiopoietin-1 (Ang-1), which are critical regulators of the angiogenic process during embryonal development and postnatal angiogenesis. Aortic rings lose their capacity to spontaneously generate new vessels if embedded in collagen gels 10-14 days after excision. VEGF has the capacity to turn back âonâ these quiescent rings producing florid angiogenesis. Conversely, Ang-1 potentiates an existing angiogenic response, but is unable to turn the quiescent system âonâ. Since VEGF-mediated induction of angiogenic sprouting occurs 1-2 days of treatment, we hypothesize that this process is regulated by a unique set of âangiogenesis inducer genesâ that are activated by VEGF and not by Ang-1. Identification of the proteins encoded by these genes may advance our understanding of the molecular mechanisms that regulate the earliest stages of the angiogenic cascade. Experiment Overall Design: Rat thoracic aortic rings will be excised from 1 month old Fisher 344 rats and placed into suspension culture. 15-20 individual rings will be isolated from each animal and cultured in suspension in serum free medium. The rings will be divided into three groups as described below. (Assay is described in; Nicosia et al., 1997 Am.J.Pathol, 151). Experiment Overall Design: All individual aortic rings isolated from a single animal will be split into three groups, VEGF treated, Ang-1 treated, and untreated controls. Rings dissected from proximal and distal portions of the aorta will be mixed so that positional bias will not be carried through to the RNA preparation. Experiment Overall Design: 13 days post isolation, one set of aortic rings will be treated with 10ng/ml of recombinant human VEGF in serum free EBM media, a second set of rings will be treated with 100ng/ml of human recombinant Ang-1 (R&D Systems 923-AN) in conjunction with 5ug/ml poly-His antibody (R&D Systems MAB050), and a third set of rings will be incubated in serum free medium alone. Experiment Overall Design: All samples were incubated for 18 hours post VEGF and Ang-1 treatment and then RNA was harvested. Experiment Overall Design: With the number of aortic rings typically obtained, we anticipate having 4-6 individual rings from each animal for each experimental condition. Furthermore, 10-100ng of total RNA will be collected per aortic ring, corresponding to 400-600ng of total RNA for each experimental condition per animal. Experiment Overall Design: In order to have a minimum of three independent samples from each experimental condition, three animals were sacrificed, each of which gave rise to three individual RNA samples. The resulting 9 individual RNA samples to be compared with respect to transcriptional profiles. Experiment Overall Design: Total RNA will be extracted from each aortic ring using the Trizol reagent (Invitrogen) protocol. RNA will be stored at â80C until all 9 individual samples have been prepared. Trizol extracted total RNA will be further purified/concentrated using the MicroRNAEasy Kit (Qiagen) with DNAseI digestion.
2007-11-06 | E-GEOD-3355 | biostudies-arrayexpress
Project description:During plant life, roots support beneficial associations with soil inhabiting microbes, mainly fungi and bacteria. Increasing evidence suggests that plant-associated microorganisms can promote plant growth and expand immune functions of the plant host. The beneficial entomopathogenic fungus Beauveria bassiana colonizes plant tissues in an asymptomatic way, triggering poorly characterized plant metabolic changes, which negatively affect both pest insects and plant pathogens. B. bassiana has an extremely broad host spectrum, including tomato (Solanum lycopersicum L.). In order to obtain a great overall snapshot of molecular events regulating tomato-B. bassiana interaction, plant proteome and hormonome changes induced over the time by the fungus have been in-depth analyzed by using a combination of high throughput profiling techniques and bioinformatics tools. The proteomics data highlighted interesting molecular pathways affected by B. bassiana related to primary and secondary metabolism and plant growth. Additionally, downregulation of a member of the endochitinase family and upregulation of calcium channel and transporter proteins suggested well-established plant-fungus symbiosis. The molecular pathways linked to protein/amino acids turn-over and to the biosynthesis of energy compounds shed some light on the strategies exploited by the plant to get the most out of the beneficial interaction in improving growth and development.
2023-05-09 | PXD029422 | Pride
Project description:Fire is a crucial event regulating the structure and functioning of many ecosystems. Yet few studies focused on how fire affects both the taxonomic and functional diversity of soil microbial communities, along with plant diversity and soil carbon (C) and nitrogen (N) dynamics. Here, we analyze these effects for a grassland ecosystem 9-months after an experimental fire at the Jasper Ridge Global Change Experiment (JRGCE) site in California, USA. Fire altered soil microbial communities considerably, with community assembly process analysis indicating that environmental selection pressure was higher in burned sites. However, a small subset of highly connected taxa were able to withstand the disturbance. In addition, fire decreased the relative abundances of most genes associated with C degradation and N cycling, implicating a slow-down of microbial processes linked to soil C and N dynamics. In contrast, fire stimulated plant growth, likely enhancing plant-microbe competition for soil inorganic N. To synthesize our findings, we performed structural equation modeling, which showed that plants but not microbial communities were responsible for the significantly higher soil respiration rates in burned sites. In conclusion, fire is well-documented to considerable alter the taxonomic and functional composition of soil microorganisms, along with the ecosystem functioning, thus arousing feedback of ecosystem responses to affect global climate.
2022-02-19 | GSE126737 | GEO
Project description:The presence of genetic groups of the entomopathogenic fungus Metarhizium anisopliae in soil is shaped by its adaptability to specific soil and habitat types, and by soil insect populations. Although the entomopathogenic life style of this fungus is well studied, its saprophytic life style has received little consideration. While a set of functionally related genes can be commonly expressed for the adaptability of this fungus to different environments (insect cuticle, insect blood and root exudates), a different subset of genes is also expected for each environment. In order to increase the knowledge of the potential use of M. anisopliae as a rhizosphere competent organism, in this study we evaluated the genetic expression of this fungus while growing on plant root exudates in laboratory conditions during a time course. One fungal strain: Metarhizium anisopliae ARSEF 2575; Five time conditions: 0h, 1h, 4h, 8h, 12h; Five-condition experiment: Time0h vs. Time1h, Time1h vs. Time4h, Time4h vs. Time8h, Time8h vs. Time12h and Time12h vs. Time0h. Two Biological replicates: independently grown and harvested. Three replicates per array. Dye-swap was performed on replicate 2.
2010-12-29 | E-GEOD-16848 | biostudies-arrayexpress
Project description:Verticillium dahliae is a soil-borne fungus with a broad host range, including the model plants Nicotiana benthamiana and Arabidopsis thaliana. The plant immunity can be activated by Vd-derived patterns while V. dahliae secreted effectors. We report here the RNAseq analyses of samples from N. benthamiana infected by V. dahliae strains 592 and 171 at different time points. The data showed dynamic expression patterns of genes not only from plant defense signaling but also plant developmental signaling.
2023-07-13 | GSE236729 | GEO