Transcriptome profiling of sugarcane root in response to low-K stress
ABSTRACT: To explore the molecular mechanism of low-K tolerance in sugarcane, we have employed whole genome microarray expression profiling to identify sugarcane genes in response to low-K stress. seeldings were transplanted to low-K hydroponic (containing 0.1 mmol.L-1 K+) and the roots were collected at 0 (CK), 8, 24 and 72 h after exposure to low-K condition. The expressions of genes in sugarcane roots were detected by microarray analysis. Totally 1545 genes at 8 h, 1053 genes at 24 h and 3155 at 72 h differentially expressed under low-K stress, when the 2-fold change was adopted as the threshold for determining differentially expressed genes. Among these genes, a certain amount of transcription factors, transporters, kinases, oxidative stress-related genes and genes in Ca+ and ethylene signaling pathway were detected to differentially express. Seeldings were treated with low-K hydroponic (containing 0.1 mmol.L-1 K+) and after 0 (CK), 8, 24 and 72 h exposure to low -K stress, the roots of sugarcane were collected. Four independent experiments were performed using roots collected at different time points
Project description:we characterized the rice alkaline tolerant mutant, alt1. Map-based cloning revealed that alt1 harbors a mutation in a putative chromatin remodeling ATPase gene. ALT1-RNAi transgenic plants mimicked the alt1 phenotype, exhibiting tolerance to alkali stress in a transcript dosage-dependent manner. We found that the predicted ALT1 protein belonged to the Ris1 subgroup of the Snf2 family and was localized in the nucleus. qRT-PCR analysis showed that ALT1 was predominantly expressed in leaf blades and sheaths, and that ALT1 transcription was rapidly suppressed after alkaline treatment. These results support the notion that ALT1 is a negative regulator of alkaline tolerance. Roots of two-leaf stage alt1 and WT seedlings grown under normal conditions were sampled for microarray analysis. The transcriptomic profiles were investigated using an Agilent-015241 Rice Gene Expression 4×44 K Microarray (Agilent Technology) containing 32,325 probes corresponding to cDNA, 6,934 probes corresponding to expressed sequence tags (ESTs), and 2,612 probes corresponding to gene predicted loci, respectively, with three independent biological replicates. Roots of two-leaf stage alt1 and WT seedlings grown under normal conditions were sampled for microarray analysis
Project description:Previous studies showed that S100A8 and S100A9 are involved in neovascularization as well as in tumor development. At high concentrations, S100A8 and S100A9 cause inflammatory response or apoptosis mediated damage in vascular endothelial cells. But the effect of low concentrations of such proteins on endothelial cells remains unknown. This assay was performed to screen for genes that are involved in the response of Human Unbilican Vascular Endothelial Cells to low concentrations of S100A8. Human Umblical Vascular Endothelial Cells (HUVEC) were cultuered and treated with 10ug/mL S100A8 proteins for 4 or 24 hours. Gene profiling was carried out using two-color microarray. Two-condition experiment, S100A8 treatment vs. non-treatment. Two time points: 4 hours and 24 hours. Biological replicates at each time point: 3 control replicates, 3 treatment replicates.
Project description:We profiled plasma miRNA expression in workers exposed to Cr(VI), and assessed genetic damage on chromosome and DNA to compare the sensitivity between epigenetic changes and genetic damage for biomarkers We screened differently expressed plasma miRNAs between high and low Cr(VI) exposed workers using Agilent miRNA microarray. low exposure : <5.49 ng/ml; high exposure >5.49 ng/ml
Project description:Compared to wild type plants, overexpression of NROB results leaf early senescence, biomass and seeds yield decreased more than 70%. Microarray analysis the differential expression genes induced by NROB Young leaves of DAG 30 were harvested from WT and 35S: NROB #2 plants and frozen immediately in liquid nitrogen. Total RNA was extracted using the RNeasy plant mini kit (Qiagen) and was checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100. Qualified and purified total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, Two-Color (Agilent technologies, US). Regulated genes were identified with a stringent significance threshold, namely a mean >2.0-fold change (transformants relative to WT control samples) and based on at least two replicates. Microarray analysis result was verified by real-time PCR
Project description:Potential components of the barrier to radial oxygen loss (ROL) are suberin and/or lignin, which accumulate at the cell wall in the cells of peripheral cell layers of the root. Chemical composition of the apoplastic barrier in rice roots was characterized and it was suggested that ROL can be restricted by the formation of a suberized exodermis and/or lignified sclerenchyma in the outer part of the root. To characterize reorganization of primary carbon metabolism in rice roots during the ROL barrier formation, we obtained the profiles of polar metabolites and the profiles of fatty acids of different zones of rice roots from plants growing in stagnant (anaerobic) and in well aerated medium. Biochemical data are combined with the results of microarray analysis. Nine days after germination, the seedlings were transferred to well aerated nutrient solution or stagnant deoxygenated nutrient solution. Stagnant solution contained 0.1% (w/v) dissolved agar and was deoxygenated (dissolved oxygen, <0.5 mg l–1) prior to use by flushing with N2 gas. After 14 d (23 d old), adventitious roots, 100-150 mm long, were harvested from rice plants grown either in aerated or stagnant conditions and RNA was extracted from 10 mm segments from the regions 0-10 mm, 10-20 mm and 20-30 mm from the root apex have been cut with sterile razor blade and collected and processed separately. Total RNAs were labeled with a Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions. Aliquots of Cy5-labeled and Cy3-labeled cRNA (825 ng each) were used for hybridization in a rice 44K oligo-DNA microarray.
Project description:Analysis of 96-hours-old-rice seedlings with promoted-growth induced by implantation with low-energy nitrogen ion beam. Ion-beam implantation can induce changes in 351 up-regulated transcripts and 470 down-regulated transcripts, including signaling proteins, kinases, plant hormones, transposable elements, transcription factors, non-coding protein RNAs, secondary metabolites, resistance proteins, peroxidase, chromatin modification and even miRNAs. Results provide insight into the molecular basis of biological effects of plants that implanted by ion beam. Three sample groups—the controls, the ion-beam implanted samples and vacuum-treated samples. Three replicates were included in each sample group. Radiation induced gene expression rice seedlings was measured at 96 hours after germination of the seeds.
Project description:To explore the molecular mechanism of low-K tolerance in sugarcane, we have employed whole genome microarray expression profiling to identify sugarcane genes in response to low-K stress. seeldings were transplanted to low-K hydroponic (containing 0.1 mmol.L-1 K+) and the roots were collected at 0 (CK), 8, 24 and 72 h after exposure to low-K condition. The expressions of genes in sugarcane roots were detected by microarray analysis. Totally 1545 genes at 8 h, 1053 genes at 24 h and 3155 at 72 h differentially expressed under low-K stress, when the 2-fold change was adopted as the threshold for determining differentially expressed genes. Among these genes, a certain amount of transcription factors, transporters, kinases, oxidative stress-related genes and genes in Ca+ and ethylene signaling pathway were detected to differentially express. Overall design: Seeldings were treated with low-K hydroponic (containing 0.1 mmol.L-1 K+) and after 0 (CK), 8, 24 and 72 h exposure to low -K stress, the roots of sugarcane were collected. Four independent experiments were performed using roots collected at different time points
Project description:Endometrial stromal sarcomas (ESSs) are a genetically heterogeneous group of rare uterine neoplasms that are frequently driven by recurrent gene rearrangements. In conventional low-grade ESSs, JAZF1-SUZ12, PHF1-JAZF1, EPC1-PHF1 and MEAF6-PHF1 chimeric fusions have been reported in > 50% of cases. The recently described t(10;17)(q22;p13) translocation yields YWHAE-FAM22A/B chimeric proteins that are associated with histologically high-grade and clinically more aggressive ESS. Integrating whole-transcriptome paired-end RNA sequencing with fluorescence in situ hybridization (FISH) and conventional cytogenetics, we identified MBTD1 (Malignant Brain Tumor Domain-containing 1) and CXorf67 (Chromosome X open reading frame 67) as the genes involved in the novel reciprocal t(X;17)(p11.2;q21.33) translocation in two independent low-grade ESS of classical histology. The presence of the MBTD1-CXorf67 fusion transcript was validated in both cases using RT-PCR followed by Sanger sequencing. A specific FISH assay to be used on paraffin tissues was developed to detect the novel t(X;17) translocation, and resulted in identification of an additional low-grade ESS case positive for the MBTD1-CXorf67 fusion among 14 uterine stromal tumours [9 ESSs and 5 undifferentiated endometrial sarcomas (UESs)] that were negative for JAZF1 and YWHAE rearrangements. Gene expression profiles of 3 ESSs with YWHAE- and 4 classical ESSs with JAZF1-rearrangements, and 4 UESs without known gene rearrangements, indicated clustering of tumours with MBTD1-CXorf67 fusion together with low-grade JAZF1-associated ESSs. The chimeric MBTD1-CXorf67 fusion identifies yet another cytogenetically distinct subgroup of low-grade ESS and offers the opportunity to shed light on the functions of two poorly characterized genes. Genomic DNA extracted from 2 low-grade ESS frozen tumor samples; Agilent CGH+SNP 4x180K array. Reference female DNA supplied with the SureTag Complete DNA Labeling Kit was used for the aCGH experiments.
Project description:To further development of our gene expression approach to biodosimetry, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish radiation dose across an exposure range relevant for medical decision-making in a radiological emergency. Human peripheral blood from healthy donors was irradiated ex vivo, and a 74-gene consensus signature was identified that distinguished between four radiation doses (0.5, 2, 5 and 8 Gy) and control samples. The same set of genes separated samples by exposure level at both six and 24 hours after treatment, with overlap evident only at the highest two doses (5 and 8 Gy). Expression of five genes (CDKN1A, FDXR, SESN1, BBC3 and PHPT1) from this signature was quantified in the same RNA samples by real-time PCR, confirming low variability between donors as well as the predicted radiation response pattern. Heat and shake stress induced gene expression in rat jejunum was measured with or without 3 days stressed (Control and S3d groups) The conditions of the treatment for rats were as follows: 35°C with a vibration of 0.1 × g for 3 days， 2 h/day in a temperature shake. each group had 3 sample replications, and each sample were mixed by 3 rats total RNA