Podcasts about quantitative rt pcr

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.24.311274v1?rss=1 Authors: Gao, S., Wang, F., Niran, J., Li, N., Yin, Y., Yu, C., Jiao, C., Yao, M. Abstract: Bacterial spot (BS) disease of pepper, incited by Xanthomonas campestris pv. Vesicatoria ( Xcv ), is one of the most serious diseases. For a comparative analysis of defense response to Xcv infection, we performed a transcriptome analysis of BS -susceptible cultivar ECW and -resistant cultivar VI037601 using the HiSeq TM 2500 sequencing platform. Approximately 140.15 G clean data were generated from eighteen libraries. From the libraries generated, we identified 52,041 genes including 35,336 reference genes, 16,705 novel transcripts, and 4,794 differentially expressed genes (DEGs). There were 1,291, 2,956, 1,795 and 2,448 DEGs in ECW-24h-vs-ECW-0h, ECW-48h-vs-ECW-0h, VI037601-24h-vs-VI037601-0h and VI037601-48h-vs-VI037601-0h groups, respectively. Interestingly, DEGs involved in disease response in the resistant variety were induced at an earlier stage and at higher levels compared with the susceptible variety. Key enriched categories included amino sugar and nucleotide sugar metabolism, sesquiterpenoid and triterpenoid biosynthesis and MAPK signaling pathway. Moreover, 273 DEGs only differentially expressed in VI037601 and 436 overlapping DEGs in ECW and VI037601 post Xcv inoculation, including NBS-LRR genes, oxidoreductase gene, WRKY and NAC transcription factors were identified, which were mainly involved in metabolic process, response to stimulus and biological regulation pathways. Quantitative RT-PCR of sixteen selected DEGs further validated the RNA-seq differential gene expression analysis. Our results will provide a valuable resource for understanding the molecular mechanisms of pepper resistance to Xcv infection and improving pepper resistance cultivars against Xcv . Copy rights belong to original authors. Visit the link for more info

While next generation sequencing enables researchers to unveil expression levels of the entire genome, qRT-PCR remains the gold standard for measuring transcript levels of individual genes for functional studies and for the purposes of publication. In this webinar, you will learn: • Low (1-5 genes) vs medium (~300 genes) throughput experimental design • Pros and cons of self-designed vs “off the shelf” assays • How to set up your wet lab experiments start to finish • Downloadable example step-by-step experiments with real data analysis and tutorial • Biological considerations (time series data, cell population frequency changes + more) • Examples of these techniques in publications • Common pitfalls and how to avoid them • Limitations of the technique • MIQE and publication standards Whether you are interested in a few genes or a few hundred, join Matthew Mule as he takes you through the necessary steps to validate expression levels of target genes using qRT-PCR with single gene assays and other medium-throughput platforms.

The clinical course of renal cell carcinoma (RCC) shows a high variability. Prognostic markers are essential to enable an individualized therapeutic strategy. The objective of this study was the identification of novel independent prognostic markers and potential therapeutic targets in RCC. The focus was on genes involved in epithelial-mesenchymal transition (EMT) and cancer stem cell biology. EMT enhances tumor cell motility and hence plays a critical role in invasion and metastasis in various carcinomas. A set of transcription factors acts as master regulators of EMT. Whether EMT is important for tumor progression in clear cell renal cell carcinoma (RCC) is unknown. Therefore, EMT-related genes were selected from the literature, and their role and prognostic relevance in RCC were analyzed. The known cancer stem cell marker CXCR4 and the associated TPBG gene were also analyzed in this project. Additionally, a novel filter strategy was used to analyze RCC oligonucleotide microarray data for identification of potential prognostic markers: genes with increasing expression during tumor progression (normal kidney < primary tumor < metastases) were selected for outcome analysis because they could be crucial for RCC biology. Expression of 46 EMT-related genes was analyzed using oligonucleotide microarrays and gene set enrichment analysis (GSEA) in tissue samples from normal kidney and G1 and G3 primary RCC, 14 samples each. Expression of selected EMT genes was validated by real-time polymerase chain reaction (PCR) in normal kidney, primary RCC and metastases in an independent cohort of 112 patients and then combined with follow-up data for survival analysis. Immunohistochemistry, Western blot and flow cytometry were performed to further examine the expression of CXCR4 and co-expression of CXCR4 and TPBG on the surface of RCC cells. GSEA and dChip software were used for microarray data analysis. The EMT gene set was preferentially expressed in primary tumors compared to normal tissue (false discovery rate FDR=0.01), but no difference between G1 and G3 tumors was found. Quantitative RT-PCR showed down-regulation of critical EMT genes like CDH2 and ZEB1 in metastases which suggests reversal of EMT during metastasis. Kaplan-Meier analysis demonstrated a significant better outcome for patients with low CXCR4, vimentin, fibronectin and TWIST1 mRNA levels. Multivariate analysis revealed that CXCR4 and vimentin up-regulation represent independent prognostic markers for poor cancer-specific survival of RCC patients. The microarray approach using filtering and further RT-PCR validation of progression-associated genes revealed that ATAD2, TET3, HELLS and TOP2A are independent and previously unknown predictors of poor outcome in RCC patients. Taken together, this study provides strong evidence that EMT occurs in RCC. Modulation of EMT in RCC, therefore, might represent a future therapeutic option. Expression levels of a number of EMT-related genes (like the genes encoding the cancer stem cell marker CXCR4 and vimentin) could be identified as independent prognostic markers. Using a novel filtering approach on array data, additional novel prognostic markers could be identified. These findings contribute to a better risk stratification of RCC patients that can support an individualized and optimized therapeutic strategy.

Background Idiopathic pulmonary fibrosis (IPF) has a poor prognosis and limited responsiveness to available treatments. It is characterised by epithelial cell injury, fibroblast activation and proliferation and extracellular matrix deposition. Serotonin (5-hydroxytryptamine; 5-HT) induces fibroblast proliferation via the 5-HTR2A and 5-HTR2B receptors, but its pathophysiological role in IPF remains unclear. A study was undertaken to determine the expression of 5-HT receptors in IPF and experimental lung fibrosis and to investigate the effects of therapeutic inhibition of 5-HTR2A/B signalling on lung fibrosis in vivo and in vitro. Methods and results Quantitative RT-PCR showed that the expression of 5-HTR1A/B and 5-HTR2B was significantly increased in the lungs of patients with IPF (n = 12) and in those with non-specific interstitial pneumonia (NSIP, n = 6) compared with transplant donors (n = 12). The expression of 5-HTR2A was increased specifically in IPF lungs but not in NSIP lungs. While 5-HTR2A protein largely localised to fibroblasts, 5-HTR2B localised to the epithelium. To assess the effects of 5HTR(2A/B) inhibition on fibrogenesis in vivo, mice were subjected to bleomycin-induced lung fibrosis and treated with the 5-HTR2A/B antagonist terguride (or vehicle) in a therapeutic approach (days 14-28 after bleomycin). Terguride-treated mice had significantly improved lung function and histology and decreased collagen content compared with vehicle-treated mice. Functional in vitro studies showed that terguride is a potent inhibitor of transforming growth factor beta(1)- or WNT3a-induced collagen production. Conclusion The studies revealed an increased expression of 5-HTR2A specifically in IPF. Blockade of 5-HTR2A/B signalling by terguride reversed lung fibrosis and is thus a promising therapeutic approach for IPF.

The architecture and compartmentalization of the kidney has stimulated the development of an array of microtechniques to study the functional differences between the distinct nephron segments. With the vast amounts of genomic sequence data now available, the groundwork has been laid for a comprehensive characterization of the molecular pathways defining the differences in nephron function. With the development of sensitive gene expression techniques the tools for a comprehensive molecular analysis of specific renal microenvironments have been provided: Quantitative RT-PCR technologies now allow the analysis of specific mRNAs from as little as single microdissected renal cells. A more global view of gene expression regulation is a logical development from the application of large scale profiling techniques. In this review, we will discuss the power and pitfalls of these approaches, including their potential for the functional characterization of nephron heterogeneity and diagnostic application in renal disease. Copyright (C) 2002 S. Karger AG, Basel.

Changes in ATP-induced increase in {[}Ca2+], during collecting duct ontogeny were studied in primary monolayer cultures of mouse ureteric bud (UB) and cortical collecting duct (CCD) cells by Fura-PE3 fluorescence ratio imaging. In UB (embryonic day E14 and postnatal day P1) the ATIP-stimulated increase (EC50 approximate to 1 muM) in fluorescence ratio (DeltaR(ATP)) was independent of extracellular Ca2+ and insensitive to the P2 purinoceptor-antagonist suramin (1 mM). From day P7 onward when CCD morphogenesis had been completed DeltaR(ATP) increased and became dependent on extracellular Ca2+. This ATP-stimulated Ca2+ entry into CCD cells was non-capacitative and suramin (11 mM)insensitive, but sensitive to nifedipine (30 muM) and enhanced by Bay K8644 (15 muM), a blocker and an agonist of L-type Ca2+ channels, respectively. Quantitative RT-PCR demonstrated similar mRNA expression of L-type Ca2+ channel alpha1-subunit, P2Y(1), P2Y(2), and P2X(4b) purinoceptors in UB and CCD monolayers while the abundance of P2X(4) mRNA increased with CCD morphogenesis. In conclusion, both embryonic and postnatal cells express probably P2Y(2)-stimulated Ca2+ release from intracellular stores. With development, the CCD epithelium acquires ATP-stimulated Ca2+ entry via L-type Ca2+ channels. This pathway might by mediated by the increasing expression of P2X(4)-receptors resulting in an increasing ATP-dependent membrane depolarization and activation of L-type Ca2+ channels. Copyright (C) 2002 S. Karger AG, Basel.