scholarly journals Identification of novel and conserved microRNAs involved in fruit development and ripening in Fragaria vesca

2019 ◽  
Vol 88 (2) ◽  
Author(s):  
Yuanfang Han ◽  
Guosong Chen ◽  
Heying Zhou ◽  
Qing Zhang ◽  
Ling Qin ◽  
...  
Keyword(s):  
Fruit Development ◽  
Molecular Mechanisms ◽  
Transcriptional Level ◽  
Fragaria Vesca ◽  
Chain Reaction ◽  
Regulate Gene Expression ◽  
Qrt Pcr ◽  
Endonucleolytic Cleavage ◽  
Fruit Development And Ripening ◽  
Polymerase Chain

MicroRNAs (miRNAs) are class of noncoding RNAs that regulate gene expression at the post-transcriptional level, either by endonucleolytic cleavage or by translational inhibition. Strawberry is a popular worldwide fresh fruit and is believed to benefit human health. However, the function of miRNAs during this fruit development and ripening remains unknown and miRNAs for specific for these processes are expected to be discovered. In the study, we identified 218 conserved miRNAs and 87 novel miRNAs in <em>Fragaria vesca</em>. Expression profiling of miRNAs during fruit development and ripening was performed, and the expression of targets of the miRNAs was validated by qRT-PCR (quantitative reverse transcription polymerase chain reaction). This study provided data for further research on molecular mechanisms involved in fruit development and ripening.

scholarly journals MiRNA-107 enhances the malignant progression of pancreatic cancer by targeting TGFBR3

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0249375
Author(s):  
Tingke Tian ◽  
Quanzhong Yang ◽  
Cuijuan Zhang ◽  
Xiaokun Li ◽  
Jiancheng Cheng
Keyword(s):  
Pancreatic Cancer ◽  
Molecular Mechanisms ◽  
Bioinformatics Analysis ◽  
Therapeutic Targets ◽  
Biological Functions ◽  
Chain Reaction ◽  
Invasion And Migration ◽  
Qrt Pcr ◽  
Polymerase Chain ◽  
And Migration

Background The prognosis of pancreatic cancer (PC) is relatively dismal due to the lack of effective therapy. In this study, we explored the specific functions and molecular mechanisms of miR-107 to uncover effective therapeutic targets for PC. Method The miR-107 expression in PC cell lines was assessed via quantitative real-time polymerase chain reaction (qRT-PCR). Besides, online bioinformatics analysis was adopted to predict the underlying targets of miR-107. Meanwhile, TCGA database was employed to explore the prognosis of PC patients. In addition, MTT and transwell assays were conducted to explore the PC cells’ biological functions. Result MiR-107 was remarkably increased in PC cells which could promote the proliferation, invasion and migration of PC cells. In addition, miR-107 could directly down-regulate TGFBR3 expression through binding to TGFBR3 3’UTR. Survival analysis from TCGA suggested that PC patients with higher miR-107 expression was significantly involved in poorer prognosis. Conclusion We concluded that miR-107 promoted proliferation, invasion and migration of PC cells via targeting TGFBR3, which may provide novel underlying therapeutic targets.

scholarly journals Analysis and validation of a highly sensitive one-step nested quantitative real-time polymerase chain reaction assay for specific detection of severe acute respiratory syndrome coronavirus 2

2020 ◽  
Vol 17 (1) ◽  
Author(s):  
Yang Zhang ◽  
Chunyang Dai ◽  
Huiyan Wang ◽  
Yong Gao ◽  
Tuantuan Li ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Real Time ◽  
Quantitative Polymerase Chain Reaction ◽  
Clinical Samples ◽  
Chain Reaction ◽  
Pcr Assay ◽  
Qrt Pcr ◽  
Highly Sensitive ◽  
One Step ◽  
Polymerase Chain

Abstract Background Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, is posing a serious threat to global public health. Reverse transcriptase real-time quantitative polymerase chain reaction (qRT-PCR) is widely used as the gold standard for clinical detection of SARS-CoV-2. Due to technical limitations, the reported positive rates of qRT-PCR assay of throat swab samples vary from 30 to 60%. Therefore, the evaluation of alternative strategies to overcome the limitations of qRT-PCR is required. A previous study reported that one-step nested (OSN)-qRT-PCR revealed better suitability for detecting SARS-CoV-2. However, information on the analytical performance of OSN-qRT-PCR is insufficient. Method In this study, we aimed to analyze OSN-qRT-PCR by comparing it with droplet digital PCR (ddPCR) and qRT-PCR by using a dilution series of SARS-CoV-2 pseudoviral RNA and a quality assessment panel. The clinical performance of OSN-qRT-PCR was also validated and compared with ddPCR and qRT-PCR using specimens from COVID-19 patients. Result The limit of detection (copies/ml) of qRT-PCR, ddPCR, and OSN-qRT-PCR were 520.1 (95% CI: 363.23–1145.69) for ORF1ab and 528.1 (95% CI: 347.7–1248.7) for N, 401.8 (95% CI: 284.8–938.3) for ORF1ab and 336.8 (95% CI: 244.6–792.5) for N, and 194.74 (95% CI: 139.7–430.9) for ORF1ab and 189.1 (95% CI: 130.9–433.9) for N, respectively. Of the 34 clinical samples from COVID-19 patients, the positive rates of OSN-qRT-PCR, ddPCR, and qRT-PCR were 82.35% (28/34), 67.65% (23/34), and 58.82% (20/34), respectively. Conclusion In conclusion, the highly sensitive and specific OSN-qRT-PCR assay is superior to ddPCR and qRT-PCR assays, showing great potential as a technique for detection of SARS-CoV-2 in patients with low viral loads.

Metformin Attenuates the Metabolic Disturbance and Depression-like Behaviors Induced by Corticosterone and Mediates the Glucose Metabolism Pathway

2021 ◽  
Author(s):  
Yong Hao ◽  
Yingpeng Tong ◽  
Yanhong Guo ◽  
Xiaoe Lang ◽  
Xinxin Huang ◽  
...  
Keyword(s):  
Glucose Metabolism ◽  
Tricarboxylic Acid Cycle ◽  
Antidepressant Activity ◽  
Tricarboxylic Acid ◽  
Serum Glucose ◽  
Metabolomic Analysis ◽  
Chain Reaction ◽  
Qrt Pcr ◽  
Metabolism Pathway ◽  
Polymerase Chain

Abstract Background Metabolism disturbances are common in patients with depression. The drug metformin has been reported to exhibit antidepressant activity. The purpose of this study was to investigate metabolism disturbances induced by corticosterone (CORT) and determine if metformin can reverse these effects and their accompanying depression-like behaviors. Methods Rats were exposed to corticosterone with or without metformin administration. Depression-like behaviors were tested. Gene expression was confirmed by quantitative real-time polymerase chain reaction (qRT-PCR) and western blot analysis. In addition, the metabolites were quantified by LC-MS/MS analysis. Results Metformin attenuated the depression-like behaviors induced by CORT. Furthermore, metformin reversed disturbances in body weight, serum glucose, and triglyceride levels, as well as hepatic TG levels induced by CORT. Metformin normalized the alterations in the expression of glucose metabolism-related genes (PGC-1α, G6pc, Pepck, Gck, PYGL, Gys2, PKLR, GLUT4) and insulin resistance-related genes (AdipoR1, AdipoR2) in the muscles and livers of rats induced by CORT. Metabolomic analysis showed that metformin reversed the effects of CORT on 11 metabolites involved in the pathways of the tricarboxylic acid cycle, glycolysis, and gluconeogenesis (3-phospho-D-glycerate, β-D-fructose 6-phosphate, D-glucose 6-phosphate, and pyruvate). Conclusion Our findings suggest that metformin can attenuate metabolism disturbances and depression-like behaviors induced by CORT mediating the glucose metabolism pathway.

scholarly journals Ligation-Mediated Polymerase Chain Reaction Detection of 8-Oxo-7,8-Dihydro-2′-Deoxyguanosine and 5-Hydroxycytosine at the Codon 176 of the p53 Gene of Hepatitis C-Associated Hepatocellular Carcinoma Patients

2020 ◽  
Vol 21 (18) ◽  
pp. 6753
Author(s):  
Andrea Galli ◽  
Armelle Munnia ◽  
Filippo Cellai ◽  
Mirko Tarocchi ◽  
Elisabetta Ceni ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Polymerase Chain Reaction ◽  
Hepatitis C ◽  
Molecular Mechanisms ◽  
Active Oxygen Species ◽  
Dietary Exposure ◽  
P53 Gene ◽  
Chain Reaction ◽  
Specific Sequence ◽  
Polymerase Chain

Molecular mechanisms underlying Hepatitis C virus (HCV)-associated hepatocellular carcinoma (HCC) pathogenesis are still unclear. Therefore, we analyzed the levels of 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodG) and other oxidative lesions at codon 176 of the p53 gene, as well as the generation of 3-(2-deoxy-β-d-erythro-pentafuranosyl)pyrimido[1,2-α]purin-10(3H)-one deoxyguanosine (M1dG), in a cohort of HCV-related HCC patients from Italy. Detection of 8-oxodG and 5-hydroxycytosine (5-OHC) was performed by ligation mediated-polymerase chain reaction assay, whereas the levels of M1dG were measured by chromatography and mass-spectrometry. Results indicated a significant 130% excess of 8-oxodG at –TGC– position of p53 codon 176 in HCV-HCC cases as compared to controls, after correction for age and gender, whereas a not significant increment of 5-OHC at –TGC– position was found. Then, regression models showed an 87% significant excess of M1dG in HCV-HCC cases relative to controls. Our study provides evidence that increased adduct binding does not occur randomly on the sequence of the p53 gene but at specific sequence context in HCV-HCC patients. By-products of lipid peroxidation could also yield a role in HCV-HCC development. Results emphasize the importance of active oxygen species in inducing nucleotide lesions at a p53 mutational hotspot in HCV-HCC patients living in geographical areas without dietary exposure to aflatoxin B1.

scholarly journals Long non-coding RNA H19 deficiency ameliorates bleomycin-induced pulmonary inflammation and fibrosis

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Xiaoyu Wan ◽  
Xinbei Tian ◽  
Jun Du ◽  
Ying Lu ◽  
Yongtao Xiao
Keyword(s):  
Pulmonary Fibrosis ◽  
Pulmonary Inflammation ◽  
Chain Reaction ◽  
Potential Therapeutic Target ◽  
Qrt Pcr ◽  
Stat3 Signaling ◽  
Non Coding Rna ◽  
Poor Understanding ◽  
Polymerase Chain ◽  
Long Non Coding Rna

Abstract Background The poor understanding of pathogenesis in idiopathic pulmonary fibrosis (IPF) impaired development of effective therapeutic strategies. The aim of the current study is to investigate the roles of long non-coding RNA H19 (lncRNA H19) in the pulmonary inflammation and fibrosis of IPF. Methods Bleomycin was used to induce pulmonary inflammation and fibrosis in mice. The mRNAs and proteins expression in lung tissues was determined by quantitative real-time polymerase chain reaction (qRT-PCR) and western blot. H19 knockout (H19−/−) mice were generated by CRISPR/Cas9. Results The expression of H19 mRNA was up-regulated in fibrotic lungs patients with IPF as well as in lungs tissues that obtained from bleomycin-treated mice. H19−/− mice suppressed bleomycin-mediated pulmonary inflammation and inhibited the Il6/Stat3 signaling. H19 deficiency ameliorated bleomycin-induced pulmonary fibrosis and repressed the activation of TGF-β/Smad and S1pr2/Sphk2 in the lungs of bleomycin-treated mice. Conclusions Our data suggests that H19 is a profibrotic lncRNA and a potential therapeutic target for IPF.

scholarly journals Quantitation of 35S Promoter in Maize DNA Extracts from Genetically Modified Organisms Using Real-Time Polymerase Chain Reaction, Part 2: Interlaboratory Study

2005 ◽  
Vol 88 (2) ◽  
pp. 558-573 ◽  
Author(s):  
Max Feinberg ◽  
Sophie Fernandez ◽  
Sylvanie Cassard ◽  
Chrystèle Charles-Delobel ◽  
Yves Bertheau ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Real Time ◽  
Genetically Modified Organisms ◽  
Genetically Modified ◽  
Interlaboratory Study ◽  
Performance Criteria ◽  
Tolerance Interval ◽  
Chain Reaction ◽  
Qrt Pcr ◽  
Polymerase Chain

Abstract The European Committee for Standardization (CEN) and the European Network of GMO Working Laboratories have proposed development of a modular strategy for stepwise validation of complex analytical techniques. When applied to the quantitation of genetically modified organisms (GMOs) in food products, the instrumental quantitation step of the technique is separately validated from the DNA extraction step to better control the sources of uncertainty and facilitate the validation of GMO-specific polymerase chain reaction (PCR) tests. This paper presents the results of an interlaboratory study on the quantitation step of the method standardized by CEN for the detection of a regulatory element commonly inserted in GMO maize-based foods. This is focused on the quantitation of P35S promoter through using the quantitative real-time PCR (QRT-PCR). Fifteen French laboratories participated in the interlaboratory study of the P35S quantitation operating procedure on DNA extract samples using either the thermal cycler ABI Prism® 7700 (Applied Biosystems, Foster City, CA) or Light Cycler® (Roche Diagnostics, Indianapolis, IN). Attention was focused on DNA extract samples used to calibrate the method and unknown extract samples. Data were processed according to the recommendations of ISO 5725 standard. Performance criteria, obtained using the robust algorithm, were compared to the classic data processing after rejection of outliers by the Cochran and Grubbs tests. Two laboratories were detected as outliers by the Grubbs test. The robust precision criteria gave values between the classical values estimated before and after rejection of the outliers. Using the robust method, the relative expanded uncertainty by the quantitation method is about 20% for a 1% Bt176 content, whereas it can reach 40% for a 0.1% Bt176. The performances of the quantitation assay are relevant to the application of the European regulation, which has an accepted tolerance interval of about ±50%. These data were fitted to a power model (r2 = 0.96). Thanks to this model, it is possible to propose an estimation of uncertainty of the QRT-PCR quantitation step and an uncertainty budget depending on the analytical conditions.

scholarly journals Inhibition of miR-155 attenuates abdominal aortic aneurysm in mice by regulating macrophage-mediated inflammation

2018 ◽  
Vol 38 (3) ◽  
Author(s):  
Zhidong Zhang ◽  
Kai Liang ◽  
Gangqiang Zou ◽  
Xiaosan Chen ◽  
Shuaitao Shi ◽  
...  
Keyword(s):  
Opposite Effect ◽  
Abdominal Aortic Aneurysms ◽  
Aortic Aneurysms ◽  
Chain Reaction ◽  
Monocyte Chemoattractant ◽  
Qrt Pcr ◽  
Abdominal Aortic ◽  
Polymerase Chain ◽  
And Migration ◽  
Proliferation And Migration

The aim of the present study was to identify abdominal aortic aneurysms (AAA)-associated miR-155 contributing to AAA pathology by regulating macrophage-mediated inflammation. Angiotensin II (AngII)–infused apolipoprotein E-deficient (ApoE-/-) mice and THP-1 cells model of miR-155 overexpression and deficiency were used in the experiments. The expression of miR-155 was detected by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Cytokines were evaluated using enzyme-linked immunoabsorbent assay (ELISA). Western blotting was used to measure the levels of MMP-2, MMP-9, iNOS, and monocyte chemoattractant protein (MCP)-1 proteins. Immunostaining and transwell were used to determine CD68, elastic collagen, proliferation, and migration of vascular smooth muscle cells (VSMCs). The results showed that miR-155 and cytokines were up-regulated in AAA patients or ApoE-/- mice. Overexpression of miR-155 enhanced MMP-2, MMP-9, iNOS, and MCP-1 levels, and stimulated the proliferation and migration of VSMCs. Meanwhile, inhibition of miR-155 had the opposite effect. In addition, histology demonstrated accumulation of CD68 and elastic collagen-positive areas significantly decreased in miR-155 antagomir injection group. In conclusion, the results of the present study suggest that inhibiting miR-155 is crucial to prevent the development of AAA by regulating macrophage inflammation.

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