The aim of this study was to analyze potential brown planthopper (BPH) resistant genes in Rathu Heenati (RHT) by Affymetrix whole rice genome array,BPH susceptible and resistant rice varieties of TN1Taichung Native 1as control. All the resistant related genes derived from RHT will be analyzed according to the SSR markers interval flanked on the chromosome 3, 4, 6 and 10. It will be benefit to the gene clone and marker assistant breeding for Bph3 gene in the near future.
Microarray analysis of broad-spectrum resistance derived from an indica cultivar Rathu Heenati.
Specimen part, Time
View SamplesTranscriptomic analysis of ZmUbi:ZmNAC111 transgenic maize under under well-watered and 2h dehydration stress conditions
No associated publication
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Specimen part
View SamplesAnalysis of the gene signature of steatosis associated to obesity in hepatocytes of Zucker fa/fa obese rats and their controls; identifying target genes linked to steatosis progression. or Obesity and insulin resistance-associated steatosis can be a non-inflammatory condition affecting hepatocytes or progress to steatohepatitis: a condition that can result in end-stage liver disease. Although molecular events leading to accumulation of lipid droplets in the liver have been identified individually, the complexity of the condition suggested that emergent target would be uncovered by a more comprehensive examination. Then, this study was aimed at establishing a gene signature of steatosis in hepatocytes and at identifying target genes linked to steatosis progression. Using Affymetrix oligonucleotide arrays, we compared transcriptomes of hepatocytes isolated from Zucker "fa/fa" obese rats with three different age-related grades of steatosis with those of their counterpart non-steatotic cells.
A subset of dysregulated metabolic and survival genes is associated with severity of hepatic steatosis in obese Zucker rats.
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Sex, Age, Specimen part, Disease, Disease stage
View SamplesTwo of the most prevalent ovarian diseases affecting women's fertility and health are Primary Ovarian Insufficiency (POI) and Polycystic Ovarian Syndrome (PCOS). Previous studies have shown that exposure to a number of environmental toxicants can promote the epigenetic transgenerational inheritance of ovarian disease, including decreases in the primordial follicle pool of oocytes that are similar to what is seen in POI, and increases in ovarian cysts that are similar to what is seen in PCOS. In the current study, transgenerational changes to the transcriptome and epigenome of ovarian granulosa cells are characterized in F3 generation rats after ancestral vinclozolin or DDT exposures compared to controls. There was an increase in ovarian disease in transgenerational F3 generation vinclozolin and DDT lineage rats at one year of age compared to F3 generation controls. In purified granulosa cells from 20 day old F3 generation females 164 differentially methylated regions (DMRs) (p<1e-06) were found in the F3 generation vinclozolin lineage, and 293 DMRs (p<1e-06) in the DDT lineage, compared to controls. The long non-coding RNAs (lncRNAs) and small non-coding RNAs (sncRNAs) were found to be differentially expressed in both the vinclozolin and DDT lineages with the sncRNAs having 492 sncRNAs (p<1 x 10-4) in the vinclozolin lineage and 1,085 sncRNAs (p<1 x 10-4) in the DDT lineage. The lncRNAs were differentially expressed with 123 and 51 in the vinclozolin and DDT lineages, respectively (p<1 x 10-4). Differentially expressed mRNAs were found in the vinclozolin lineage at 174 mRNAs (p<1 x 10-4) and the DDT lineage at 212 mRNAs (p<1 x 10-4). These transgenerational epigenetic changes contribute to the dysregulation of the ovary and disease susceptibility that can occur in later life. This suggests that ancestral exposure to toxicants is potentially a major risk factor that must be considered in the molecular etiology of ovarian disease.
No associated publication
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No sample metadata fields
View SamplesNine accessions of Arabidopsis were sampled before and after 14d of cold acclimation at 4°C. Transcript data were combined with metabolite data and related to quantitative measurement of plant freezing tolerance as determined by leaf electrolyte leakage assays.
Natural genetic variation of freezing tolerance in Arabidopsis.
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Specimen part
View SamplesFloral organs are extremely sensitive to stress during anthesis and lead to severe yield loss. Rice anthers and pollinated pistils of two cultivars with contrasting tolerance to heat and drought stress under variable conditions, including control, heat, combined heat and drought stress, were used to explore gene expression pattern in male and female reproductive organs during anthesis under control and stress conditions. More gene regulation was induced by combined drought and heat stress than heat in anthers of both cultivars. N22 showed less regulation under combined stress than Moroberekan. The overlap of regulated genes between two cultivars was rather low, indicated the distinct molecular stress responses.
No associated publication
Specimen part
View SamplesDuring cold acclimation plants increase their freezing tolerance in response to low non-freezing temperatures. This is accompanied by many physiological, biochemical and molecular changes that have been extensively investigated. In addition, many cold acclimated plants become more freezing tolerant during exposure to mild, non-damaging sub-zero temperatures. There is hardly any information available about the molecular basis of this adaptation. However, Arabidopsis thaliana is among the species that acclimate to sub-zero temperatures. This makes it possible to use the molecular and genetic tools available in this species to identify components of sub-zero signal transduction and acclimation. Here, we have used microarrays and a qRT-PCR primer platform covering 1880 genes encoding transcription factors to monitor changes in gene expression in the accessions Columbia-0, Rschew and Tenela during the first three days of sub-zero acclimation at -3C. The results indicate that gene expression during sub-zero acclimation follows a tighly controlled time-course. Especially AP2/EREBP and WRKY transcription factors may be important regulators of sub-zero acclimation, although the CBF signal transduction pathway seems to be less important during sub-zero than during cold acclimation. Globally, we estimate that approximately 5% of all Arabidopsis genes are regulated during sub-zero acclimation. Particularly photosynthesis-related genes were down-regulated and genes belonging to the functional classes of cell wall biosynthesis, hormone metabolism and RNA regulation of transcription were up-regulated. Collectively, these data provide the first global analysis of gene expression during sub-zero acclimation and allow the identification of candidate genes for forward and reverse genetic studies into the molecular mechanisms of sub-zero acclimation.
Global changes in gene expression, assayed by microarray hybridization and quantitative RT-PCR, during acclimation of three Arabidopsis thaliana accessions to sub-zero temperatures after cold acclimation.
Specimen part, Time
View SamplesPlant seeds prepare for germination already during seed maturation. We performed a detailed transcriptome analysis of barley grain maturation, desiccation and germination in two tissue fractions (endosperm/aleurone = e/a and embryo = em) using the Affymetrix barley1 chip.
Barley grain maturation and germination: metabolic pathway and regulatory network commonalities and differences highlighted by new MapMan/PageMan profiling tools.
No sample metadata fields
View SamplesWe identified a small zinc finger protein, MBS, as a new mediator of singlet oxygen responses in Chlamydomonas and Arabidopsis. MBS is required for induction of singlet oxygen-dependent gene expression and, upon oxidative stress, accumulates in distinct granules in the cytosol of Arabidopsis cells. First, we recorded changes in light stress-regulated gene expression profiles after genetically perturbing MBS function by isolating mutants for the two MBS genes (MBS1 and MBS2) and by overexpression of MBS1 in Arabidopsis thaliana. Then, these light stress-related gene expression profiles were analyzed with respect to genes specifically responding to singlet oxygen and hydrogen peroxide/superoxide. The results indicated that MBS inactivation leads to an impaired response to singlet oxygen signaling under light stress.
A mediator of singlet oxygen responses in Chlamydomonas reinhardtii and Arabidopsis identified by a luciferase-based genetic screen in algal cells.
Specimen part, Treatment
View Samples- Background and Aims: Oxygen can fall to low concentrations within plant tissues, either because of environmental factors that decrease the external oxygen concentration or because the movement of oxygen through the plant tissues cannot keep pace with the rate of oxygen consumption. Recent studies document that plants can decrease their oxygen consumption in response to relative small changes in oxygen concentrations to avoid internal anoxia. The molecular mechanisms underlying this response have not been identified yet. The aim of this study was to use transcript and metabolite profiling to investigate the genomic response of Arabidopsis roots to a mild decrease in oxygen concentrations.
Transcript and metabolite profiling of the adaptive response to mild decreases in oxygen concentration in the roots of arabidopsis plants.
No sample metadata fields
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