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Transcriptomic response of Anoxybacillus sp. SK 3-4 to aluminum exposure

ABSTRACT: By comparing the gene expression profiling in Anoxybacillus sp. SK 3-4 with and without aluminum exposure, the sets of gene up-regulated and down-regulated by aluminum were identified. The function of genes or proteins induced under these conditions can a reflection of the mechanism of resistance. Transcriptome profiling of Anoxybacillus sp. SK 3-4 treated by aluminum would allow a better understanding of the gene involving in tolerance and removal of aluminum.

ORGANISM(S): Anoxybacillus ayderensis

PROVIDER: GSE78908 | GEO | 2016/08/05

REPOSITORIES: GEO

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Transcriptomic response of Anoxybacillus sp. SK 3-4 to aluminum exposure

Project description:By comparing the gene expression profiling in Anoxybacillus sp. SK 3-4 with and without aluminum exposure, the sets of gene up-regulated and down-regulated by aluminum were identified. The function of genes or proteins induced under these conditions can a reflection of the mechanism of resistance. Transcriptome profiling of Anoxybacillus sp. SK 3-4 treated by aluminum would allow a better understanding of the gene involving in tolerance and removal of aluminum. Global transcriptomic response of Anoxybacillus sp. SK 3-4 to aluminum exposure

2016-08-05 | E-GEOD-78908 | biostudies-arrayexpress

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Project description:Gene expression profiling in soybean under aluminum stress: mechanisms of magnesium amelioration of aluminum toxicity at gene expression level. Micro-molar concentrations of magnesium in culture solution has been shown to ameliorate Al toxicity in soybean and other leguminous species. Different theories have been proposed to explain the chemical mechanisms of how the two ions interact to neutralize the toxic effect of aluminum in the plant root system. To understand the molecular mechanisms of the phenomenon at the gene expression level in soybean, we undertook a comparative transcriptome analysis in Al-tolerant and Al-sensitive genotypes treated with aluminum alone or aluminum plus magnesium using DNA microarrays. The results revealed magnesium enhances Al-tolerance level in the Al-tolerant genotype by down-regulating genes commonly induced in response to Al toxicity. We hypothesized that the magnesium-mediated alleviation of Al toxicity in the Al-tolerant genotype emanates from reduction in energy expenditure of gene expression induced in response to Al stress. Conversely, magnesium appears to ameliorate Al toxicity in the sensitive genotype by dual mechanisms of increasing the expression level of several genes involved in Al-tolerance and decreasing the expression level of most genes. Keywords: Soybean, aluminum toxicity, magnesium, transcriptome

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2010-10-04 | E-GEOD-18518 | biostudies-arrayexpress

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Genome-wide maps of H3K27me3 modification sites in sk-hep-1,sk-hep-1-shEZH2 and LO2 cells.

Project description:We report the application of chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) for high-throughput profiling of H3K27me3 modifications in sk-hep-1(sk), sk-hep-1-shEZH2 (sks) and LO2 cells. Following standard ChIP procedure, 10 ng of each DNA sample was used for Illumina sequencing. Statistically significant ChIP-enriched regions (peaks) were identified by sk vs sks (p-value threshold of 10-2) or sk vs LO2 (p-value threshold of 10-3). Enriched peaks were annotated by the nearest gene using the newest UCSC RefSeq database. We identify genes modified by EZH2-mediated H3K27me3. This study provides insights into these down stream genes modified by EZH2 regulated H3K27me3 in HCC cell lines.

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Transcriptomic analysis of Col responding to aluminum

Project description:Our objective is to study root development under aluminum stress. We isolated total RNA from the roots of 7-day-old Col-0 seedlings. New genes after responding to aluminum treatment, during the root development, are discovered.

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Gene expression profiling in Al-tolerant and Al-sensitive soybean under aluminum stress

Project description:Gene expression profiling in soybean under aluminum stress: genes differentially expressed between Al-tolerant and Al-sensitive genotypes. Aluminum toxicity is the most important constraint of crop production on acid soils. Understanding the molecular and genetic mechanisms of tolerance is crucial for developing efficient breeding programs to improve Al tolerance. This research was undertaken to identify candidate Al-tolerance genes in soybean. Two soybean genotypes PI 416937 (Al-tolerant) and Young (Al-sensitive) seedlings were exposed to zero or 10 µM Al in a growth chamber under hydroponic conditions for four time spans of 2, 12, 48 or 72 hrs. Microarray analysis was made on mRNA isolated from 1 cm long tap root tips using an Affymetrix soybean genome array. Both novel and previously reported aluminum-responsive genes were identified. The differentially expressed genes were enriched for metabolism, stress response and transporters. Multiple putative Al-tolerance genes uniquely induced in the tolerant genotype includes the up-regulation of previously identified transcription factors auxin down regulated-like protein (ADR6-like) and basic leucine zipper (bZIP 94), sulfur transmembrane transport protein and lipid transfer protein (Sec 14 ) and novel genes that include rare cold inducible protein (RCI2B ), GPI-transamidase, malonyl-COA: Isoflavone 7-O-glucoside-6˝-O-malontransferase, a cell proliferation protein (WPP2), Oleosin protein, pectinestrease inhibitor, and impaired sucrose induction1. The genes identified in this study will be utilized as important genetic resources for future improvement of Al tolerance in soybean. Key words: Soybean, Al tolerance, gene expression, microarray Two genotypes: PI 416937 (p) and Young (y); two treatments: aluminum or untreated; four time points: 2, 12, 48, and 72 hrs; 2 or 3 replicates.

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