Helveticoside was a biologically active component of seeds extract of Descurainia Sophia.
Ontology highlight
ABSTRACT: This study was designed to identify active component of ethanol extract of the seeds of D. sophia. The dose-dependent expression of genes by treatment of EEDS was measured on A549 cells. Total RNA was isolated and was subject to single channnel microarray.
Project description:To ameliorate the cumbersome processes of reprogramming and subsequent gene-editing in vulnerable iPSCs, we have developed a greatly simplified one-step procedure, simultaneously introducing reprogramming and gene-editing components into human fibroblast cells. This not only serves to save time, labor, and costs, but opens up a new arena of research that is beyond the current application of gene-editing methodologies due to restrictive reprogramming concerns, inhibitory pluripotency maintenance requirements, and vulnerability of single-cell dissociated iPSCs. We generated iPSCs (mALK2-iPSCs) derived from Fibrodysplasia ossificans progressiva (FOP)-fibroblast cells carrying the ACVR1 p.R206H mutation and gene-corrected ALK2-iPSCs (cALK2-iPSCs). To identify gene-correction effects on global gene expression, gene expression profiling was measured in cALK2-iPSCs and mALK2-iPSCs, calibrated to WT-iPSCs with duplication.
Project description:This study was designed to identify molecular changes induced by radiation in mouse lung. Mouse left lung was irradiated with a single dose of radiation. Total RNA from the irradiated lung tissue was subject to single channnel microarray.
Project description:To gain deeper insight into the mechanism of toxicity, it is important to identify and characterize mRNAs profiles involved in responses to specific classes of toxicants in conjunction with their impact on gene expression levels. However, few reports have described the effects of toxicants on mRNA expression profiles. Taking into account the prominent role of mRNAs in cancer development, progression, cell cycle control, and proliferation-related processes, it is likely that mRNAs are involved in the toxic response induced by carcinogens. Aldehydes are a well-characterized class of human carcinogens. In the present study, we documented the different expression profiles of mRNAs in environmental carcinogen-exposed A549 cells by mRNA microarray analysis. To evaluate the change in mRNA expression levels, human alveolar cells(A549) were exposed to seven lower-molecular-weight saturated aliphatic aldehyde (LSAAs) for 48h. mRNA expression analysis was conducted using a 4x44k human whole genome oligo microarray (Agilent Technologies, USA).
Project description:Transcriptome from high throughput sequencing-by-synthesis is a good resource of molecular markers. In this study, we present utility of massively parallel sequencing by synthesis for profiling the transcriptome of red pepper (Capsicum annuum L. TF68) by 454 GS-FLX pyrosequencing. Through the generation of approximately 30.63 megabases (Mb) of Expressed Sequence Tags (ESTs) data with the average length of 375 base pairs (bp), 9,818 contigs and 23,712 singletons were obtained by assembly. Using BLAST alignment against NCBI non-redundant and a UniProt protein database, 30% of the tentative consensus sequences were assigned to specific function annotation, while 24% returned alignments of unknown function, leaving up to 46% with no alignment. Functional classification using FunCat revealed that sequences with putative known function were distributed cross 18 categories. Furthermore, over 200 high quality single nucleotide discrepancies were discovered using the Bukang cDNA collection as a reference database. Moreover, 758 simple sequence repeat (SSR) motif loci were mined from over 600 contigs, from which 572 primer sets were designed. The SSR motifs corresponded to di- and tri- nucleotide motifs (27.03 and 61.92%, respectively). These molecular markers may be of great value for application in linkage mapping and association mapping research. 1 sample TF68 accession examined
Project description:The goal of this study is to explore genes that are differentially expressed in E. coli C strains (wt and a butanol-tolerant mutant) after 1-butanol treatment. The butanol-tolerant mutant strain PKH5000 (denoted by 'E' for 'evolved') were derived from KCTC 2571 (wt) (denoted by 'A' for 'ancestral') by proton beam irradiation. 0 and 1 in sample title mean before and after butanol treatment, respectively. All microarray experiments were carried out in triplicate (rep1-3). Probes were spotted in duplicate on separate area of each microarray slide, which produces two GPR files (a and b suffixes).
Project description:Many of duplicated genes are enriched in signaling pathways. Recently, gene duplication of kinases has been shown to provide genetic buffering and functional diversification in cellular signaling. Transcription factors (TFs) are also often duplicated. However, how duplication of TFs affects their regulatory structures and functions of target genes has not been explored at the systems level. Here, we examined regulatory and functional roles of duplication of three major ARR TFs (ARR1, 10, and 12) in Arabidopsis cytokinin signaling using wild-type and single, double, and triple deletion mutants of the TFs. Comparative analysis of gene expression profiles obtained from Arabidopsis roots in wild-type and these mutants showed that duplication of ARR TFs systematically extended their transcriptional regulatory structures, leading to enhanced robustness and diversification in functions of target genes, as well as in regulation of cellular networks of target genes. Therefore, our results suggest that duplication of TFs contributes to robustness and diversification in functions of target genes by extending transcriptional regulatory structures. Duplication of TFs can confer an extension of transcriptional regulatory structures for target genes by providing new regulatory relationships between duplicated TFs and new or old target genes. To examine the nature of the extension in the regulatory structure, we performed gene expression profiling of Arabidopsis root tissues obtained from wild-type (WT) and deletion mutants of three type-B ARR1, 10, and 12. To examine how the extended regulatory structures by the duplicated ARR TFs are utilized for the responses to external CK, we generated gene expression profiles of WT Arabidopsis roots treated with mock or exogenous CK for 1 hour. Total RNAs were isolated from two biological replicates at each condition and used to measure gene expression level.
Project description:We employed the mRNA-seq method to acquire transcriptome-wide characterization of the crown tissue and provide new insights into the expression profiles of heat- and gibberellin-related genes. The study accompanied application of ATAC-seq strategy to identify open chromatin regions (OCRs) and to characterize their distributions and organizations in crown tissues of three barley (Horedeum vulgare) genotypes carrying different allelic forms of the sdw1 gene encoding Gibberellin 20-oxidase (GA20ox) subjected to high temperature. ATAC-seq and RNA-seq data integration provided results concerning relationships between chromatin openness and gene expression changes.
Project description:This study’s objective was to elucidate plant modifications and crown-specific transcriptome re-modeling that takes place in gibberellin-deficient barley sdw1 NILs exposed to increased temperatures. Experiments were designed to determine whether the phenotypic expression of sdw1 mutants is influenced by the allele-specific expression of the HvGA20ox2 gene or by wider genetic background variance and environmental cues. To achieve this goal, plants were examined considering phenotypic properties, physiological responses, and genomic constitution using high-throughput genotyping and sdw1 gene sequencing. We also employed the mRNA-seq method to acquire transcriptome-wide characterization of the crown tissue and provide new insights into the expression profiles of heat- and gibberellin-related genes.
Project description:This experiment analyses the expression data of the wild type P. syringae pv. tomato DC3000 grown in the absence and in the presence of phloretin and naringenin.
Project description:Clear cell renal cell carcinoma (ccRCC) initiated from the renal epithelium is the most prevalent histological type of adult kidney cancers. Dissecting intratumoral heterogeneity (ITH) of ccRCC has leveraged to extend our knowledge on how primary tumors harboring driver mutations evolve and spread to other sites. The cellular fractions within and across the primary (pRCC) and metastatic RCC (mRCC) are heterogeneous in both their genetic and biological features determining the variability in clinical aggressiveness and sensitivity to the therapy. To achieve sustainable therapeutic benefit with targeted agents in mRCC, the effective target should focus on signaling pathways that are related to driver mutations occurred early in the clonal evolution of the disease and thus should be common to primary tumor and metastatic sites. Considering that extensive genetic heterogeneity may result in drug response variability among patients and treatment resistance, the tailored strategies for metastatic RCC is urgently needed. Here, we analyze single-cell RNA-seq (scRNA-seq) data from a matched primary RCC (pRCC) and lung metastasis (mRCC) to dissect ITH at the highest resolution to date with the objective of discovering the better therapeutic regimen. In order to identify successful clonal propagation from patient to PDX samples and understand pathogenesis from primary to metastatic RCC, we performed whole-exome sequencing (WES, n=4) and matched aCGH (n=4) on bulk tumor samples. And we utilized single-cell RNA sequencing (scRNA-seq) to model and dissect functional heterogeneity acroass primary and metastatic RCC tumors. We checked whether of capturing live one cell, not more cells, in microfluidics by fluorescent microscopic observation. To construct RNA sequencing libraries, we performed further quality controls including adequate quantities and qualities of amplified transcriptomes respectively from single cells. Tumor cells from the parental mRCC (n=34), PDX-mRCC (n=36) and PDX-pRCC (n=46) were finally analyzed in this study after filtering out poor quality cells.