scholarly journals Efficient Extraction of RNA and Analysis of Gene Expression in a Long-Term Taxus Cell Culture Using Real-Time RT-PCR

2009 ◽  
Vol 64 (1-2) ◽  
pp. 125-130 ◽  
Author(s):  
Li-Qin Li ◽  
Chun-Hua Fu ◽  
Chun-Fang Zhao ◽  
Juan Xia ◽  
Wen-Juan Wu ◽  
...  
Keyword(s):  
Cell Culture ◽  
Real Time ◽  
Rna Extraction ◽  
Rt Pcr ◽  
Metabolite Level ◽  
Transcript Levels ◽  
Total Rna ◽  
Taxus Media ◽  
Key Enzyme

A simple, quick and efficient method for isolating total RNA from heavy browning cells was developed by adding polyvinylpyrrolidone, mercaptoethanol and 3 M NaAc during the process of the Trizol (a kind of a widely used RNA extraction buffer) method. High-quality total RNA was isolated and synthesized to cDNA. Transcript levels of four paclitaxel biosynthetic pathway genes: dxr, hmgr, ggpps and dbat were assayed by real-time RT-PCR. The results demonstrated that the transcript levels of these genes experienced a coincident descent in the past three years as well as a decreasing paclitaxel productivity. According to these results, the possible reason for the descending paclitaxel productivity during long-term Taxus media cv. Hicksii cell culture maybe due to a decreasing transcripts level of mass genes in close with a gross secondary metabolite level. Gene manipulation emphasized only on key enzyme genes in the paclitaxel biosynthesis pathway may not hamper the somaclonal variation trend of Taxus media cv. Hicksii cell culture.

scholarly journals Comparison of Six RNA Extraction Methods for the Detection of Classical Swine Fever Virus by Real-Time and Conventional Reverse Transcription–PCR

2005 ◽  
Vol 17 (6) ◽  
pp. 574-578 ◽  
Author(s):  
Ming Y. Deng ◽  
He Wang ◽  
Gordon B. Ward ◽  
Tammy R. Beckham ◽  
Thomas S. McKenna
Keyword(s):  
Real Time ◽  
Classical Swine Fever Virus ◽  
Rna Extraction ◽  
Classical Swine Fever ◽  
Extraction Methods ◽  
Rt Pcr ◽  
Total Rna ◽  
Reverse Transcription Pcr ◽  
Rna Extraction Methods ◽  
Positive Results

Six RNA extraction methods, i.e., RNAqueous kit, Micro-to-midi total RNA purification system, NucleoSpin RNA II, GenElute mammalian total RNA kit, RNeasy mini kit, and TRIzol LS reagent, were evaluated on blood and 7 tissues from pig infected with classical swine fever virus (CSFV). Each of the 6 extraction methods yielded sufficient RNA for positive results in a real-time reverse transcription–PCR (RT-PCR) for CSFV, and all RNA, except the one extracted from blood by TRIzol LS reagent, yielded positive results in both a conventional RT-PCR for CSFV and a conventional RT-PCR for an endogenous gene encoding β-actin. The RNA extracted from blood by TRIzol LS reagent became positive in both conventional RT-PCR assays when it was diluted to 1:2, 1:4, or up to 1:64 in nuclease-free water. It is concluded that all 6 methods are more or less useful for the detection of CSFV by real-time and conventional RT-PCR in swine blood and tissues. However, some of the 6 reagents offer certain advantages not common to all 6 extraction procedures. For example, RNA extracted by the TRIzol LS reagent constantly had the highest yield; that by the RNAqueous kit had the highest A260/A280 ratio for almost all samples; and that by the NucleoSpin RNA II and the GenElute mammalian total RNA kit was most likely to be free of contaminations with genomic DNA.

scholarly journals Real-time reverse transcription polymerase chain reaction development for rapid detection of Tomato brown rugose fruit virus and comparison with other techniques

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7928 ◽  
Author(s):  
Stefano Panno ◽  
Susana Ruiz-Ruiz ◽  
Andrea Giovanni Caruso ◽  
Ana Alfaro-Fernandez ◽  
Maria Isabel Font San Ambrosio ◽  
...  
Keyword(s):  
Real Time ◽  
Crude Extract ◽  
Rna Extraction ◽  
Leaf Disk ◽  
Quantitative Detection ◽  
Rt Pcr ◽  
Total Rna ◽  
End Point ◽  
Crude Extracts ◽  
Total Rna Extraction

Background Tomato brown rugose fruit virus (ToBRFV) is a highly infectious tobamovirus that causes severe disease in tomato (Solanum lycopersicum L.) crops. In Italy, the first ToBRFV outbreak occurred in 2018 in several provinces of the Sicily region. ToBRFV outbreak represents a serious threat for tomato crops in Italy and the Mediterranean Basin. Methods Molecular and biological characterisation of the Sicilian ToBRFV ToB-SIC01/19 isolate was performed, and a sensitive and specific Real-time RT-PCR TaqMan minor groove binder probe method was developed to detect ToBRFV in infected plants and seeds. Moreover, four different sample preparation procedures (immunocapture, total RNA extraction, direct crude extract and leaf-disk crude extract) were evaluated. Results The Sicilian isolate ToB-SIC01/19 (6,391 nt) showed a strong sequence identity with the isolates TBRFV-P12-3H and TBRFV-P12-3G from Germany, Tom1-Jo from Jordan and TBRFV-IL from Israel. The ToB-SIC01/19 isolate was successfully transmitted by mechanical inoculations in S. lycopersicum L. and Capsicum annuum L., but no transmission occurred in S. melongena L. The developed real-time RT-PCR, based on the use of a primer set designed on conserved sequences in the open reading frames3, enabled a reliable quantitative detection. This method allowed clear discrimination of ToBRFV from other viruses belonging to the genus Tobamovirus, minimising false-negative results. Using immunocapture and total RNA extraction procedures, the real-time RT-PCR and end-point RT-PCR gave the same comparable results. Using direct crude extracts and leaf-disk crude extracts, the end-point RT-PCR was unable to provide a reliable result. This developed highly specific and sensitive real-time RT-PCR assay will be a particularly valuable tool for early ToBRFV diagnosis, optimising procedures in terms of costs and time.

141 EXPRESSION STATUS OF AQUAPORINS 3, 7, AND 9 IN BOVINE PRE-IMPLANTATION EMBRYOS

2016 ◽  
Vol 28 (2) ◽  
pp. 200
Author(s):  
T. Fujii ◽  
H. Hirayama ◽  
S. Kageyama ◽  
A. Naito ◽  
S. Fukuda ◽  
...  
Keyword(s):  
Real Time ◽  
Cellular Response ◽  
Transcript Level ◽  
Bovine Embryos ◽  
Rt Pcr ◽  
Transcript Levels ◽  
Total Rna ◽  
Expression Status

The aquaporins (AQP) are a family of small integral membrane proteins that work as channels for rapid water transport. In mouse embryos, AQP3, AQP7, and AQP9 were found to play important roles in the pre-implantation development or adaptive cellular response to osmotic stress. In addition, because AQP3, AQP7, and AQP9 permeate not only water but also cryoprotectant, such as glycerol, these AQP thought to be involved in the process of cryopreservation. However, little information is available for AQP in bovine embryos. The understanding of the mechanisms mediated by AQP that embryos utilise to survive during culture and the process of cryopreservation will contribute to development of in vitro culture systems and cryopreservation procedures for bovine embryos. The aims of present study were to clarify the expression status of AQP3, AQP7, and AQP9 in bovine pre-implantation embryos, and to evaluate the expression level of AQP3 in in vivo-derived (IVD) and IVF bovine embryos. For production of IVF embryos, cumulus-oocyte complexes (COC) were aspirated from ovaries collected at a local slaughterhouse. The COC were in vitro matured, fertilized, and then cultured for 7 days. The IVD embryos at early blastocyst (EB) and blastocyst (BC) stage were obtained from donor cows treated with superovulation and AI. In experiment 1, in order to clarify the expression of AQP3, AQP7, and AQP9 mRNA in bovine pre-implantation embryos, total RNA was extracted from pools of 30 IVM oocytes, pools of 15 IVF embryos at 2- to 4-cell, 8- to 16-cell, compaction morula (CM), EB, BC, and expanded blastocyst (ExBC) stage, and RT-PCR was performed followed by agarose gel electrophoresis. In experiment 2, in order to clarify the expression status of AQP3, AQP7, and AQP9 during bovine pre-implantation development after zygotic gene activation, total RNA was extracted from pools of 15 IVF embryos at 8- to 16-cell, CM, EB, BC and ExBC stage (n = 5), and relative quantifications of AQP mRNA were performed using real-time RT-PCR. Data were analysed by Scheffé’s method. In experiment 3, AQP3 transcript levels in single IVD and IVF embryos at EB and BC stages (n = 10) was evaluated by real-time RT-PCR. Data were analysed by Mann-Whitney’s U test. In experiment 1, AQP3 and AQP7 transcripts were detected in IVM oocytes and all stages of embryos. AQP9 mRNA was detected in IVM oocytes and in 2- to 4-cell, 8- to 16 cell, CM, and EB stage embryos, but was not detected in BC and ExBC stage embryos. In experiment 2, AQP3 and AQP7 transcript levels were significantly increased from 8- to 16-cell to CM and EB stage, and significantly decreased from EB to BC and ExBC stages (P < 0.05). AQP9 transcript level was significantly decreased from 8- to 16-cell to CM and EB stage (P < 0.05). In experiment 3, AQP3 transcript level in IVF embryos was significantly lower than that in in vivo embryos at the BC stage (P < 0.05). Our results indicate that AQP3 and AQP7 may have specific roles at morula and EB stage in bovine embryos. In addition, AQP3 expression is influenced by developmental condition of bovine embryos.

Per-unit-living tissue normalization of real-time RT-PCR data in ischemic rat hearts

2012 ◽  
Vol 44 (12) ◽  
pp. 651-656 ◽  
Author(s):  
S. Ellefsen ◽  
M. Bliksøen ◽  
A. Rutkovskiy ◽  
I. B. Johansen ◽  
M.-L. Kaljusto ◽  
...  
Keyword(s):  
Infarct Size ◽  
Real Time ◽  
Reference Genes ◽  
Stable Expression ◽  
Unit Weight ◽  
Living Tissue ◽  
Rt Pcr ◽  
Internal Reference ◽  
Total Rna ◽  
Rat Hearts

In studies of gene expression in acute ischemic heart tissue, internal reference genes need to show stable expression per-unit-living tissue to hinder dead cells from biasing real-time RT-PCR data. Until now, this important issue has not been appropriately investigated. We hypothesized that the expression of seven internal reference genes would show stable per-unit-living tissue expression in Langendorff-perfused rat hearts subjected to ischemia-reperfusion. This was found for cyclophilin A, GAPDH, RPL-32, and PolR2A mRNA, with GAPDH showing the highest degree of stability ( R = 0.11), suggesting unchanged rates of mRNA transcription in live cells and complete degradation of mRNA from dead cells. The infarct size-dependent degradation of GAPDH was further supported by a close correlation between changes in GAPDH mRNA and changes in RNA quality measured as RNA integrity number (R = 0.90, P < 0.05). In contrast, β-actin and 18S rRNA showed stable expression per-unit-weight tissue and a positive correlation with infarct size (R = 0.61 and R = 0.77, P < 0.05 for both analyses). The amount of total RNA extracted per-unit-weight tissue did not differ between groups despite wide variation in infarct size (7.1–50.1%). When β-actin expression was assessed using four different normalization strategies, GAPDH and geNorm provided appropriate per-unit-living expression, while 18S and total RNA resulted in marked underestimations. In studies of ischemic tissues, we recommend using geometric averaging of carefully selected reference genes for normalization of real-time RT-PCR data. A marked shift in the mRNA/rRNA ratio renders rRNA as useless for normalization purposes.

scholarly journals A Simplified Quantitative Real-Time PCR Assay for Monitoring SARS-CoV-2 Growth in Cell Culture

mSphere ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Christian Shema Mugisha ◽  
Hung R. Vuong ◽  
Maritza Puray-Chavez ◽  
Adam L. Bailey ◽  
Julie M. Fox ◽  
...  
Keyword(s):  
Cell Culture ◽  
Real Time ◽  
Real Time Pcr ◽  
Rna Extraction ◽  
Quantitative Real Time Pcr ◽  
Pcr Assay ◽  
Dna Viruses ◽  
Culture Supernatants ◽  
Hiv 1 ◽  
Rna And Dna

ABSTRACT Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected millions within just a few months, causing severe respiratory disease and mortality. Assays to monitor SARS-CoV-2 growth in vitro depend on time-consuming and costly RNA extraction steps, hampering progress in basic research and drug development efforts. Here, we developed a simplified quantitative real-time PCR assay that bypasses viral RNA extraction steps and can monitor SARS-CoV-2 growth from a small amount of cell culture supernatants. In addition, we show that this approach is easily adaptable to numerous other RNA and DNA viruses. Using this assay, we screened the activities of a number of compounds that were predicted to alter SARS-CoV-2 entry and replication as well as HIV-1-specific drugs in a proof-of-concept study. We found that E64D (inhibitor of endosomal proteases cathepsin B and L) and apilimod (endosomal trafficking inhibitor) potently decreased the amount of SARS-CoV-2 RNA in cell culture supernatants with minimal cytotoxicity. Surprisingly, we found that the macropinocytosis inhibitor ethylisopropylamiloride (EIPA) similarly decreased SARS-CoV-2 RNA levels in supernatants, suggesting that entry may additionally be mediated by an alternative pathway. HIV-1-specific inhibitors nevirapine (a nonnucleoside reverse transcriptase inhibitor [NNRTI]), amprenavir (a protease inhibitor), and allosteric integrase inhibitor 2 (ALLINI-2) modestly inhibited SARS-CoV-2 replication, albeit the 50% inhibitory concentration (IC50) values were much higher than that required for HIV-1. Taking the data together, this simplified assay will expedite basic SARS-CoV-2 research, be amenable to mid-throughput screening assays (i.e., drug, CRISPR, small interfering RNA [siRNA], etc.), and be applicable to a broad number of RNA and DNA viruses. IMPORTANCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of the coronavirus disease 2019 (COVID-19) pandemic, is continuing to cause immense respiratory disease and social and economic disruptions. Conventional assays that monitor SARS-CoV-2 growth in cell culture rely on costly and time-consuming RNA extraction procedures, hampering progress in basic SARS-CoV-2 research and development of effective therapeutics. Here, we developed a simple quantitative real-time PCR assay to monitor SARS-CoV-2 growth in cell culture supernatants that does not necessitate RNA extraction and that is as accurate and sensitive as existing methods. In a proof-of-concept screen, we found that E64D, apilimod, EIPA, and remdesivir can substantially impede SARS-Cov-2 replication, providing novel insight into viral entry and replication mechanisms. In addition, we show that this approach is easily adaptable to numerous other RNA and DNA viruses. This simplified assay will undoubtedly expedite basic SARS-CoV-2 and virology research and be amenable to use in drug screening platforms to identify therapeutics against SARS-CoV-2.

scholarly journals Lyophilized Matrix Containing Ready-to-Use Primers and Probe Solutions for Standardization of Real-Time PCR and RT-qPCR Diagnostics

Proceedings ◽  
2020 ◽  
Vol 50 (1) ◽  
pp. 7
Author(s):  
Remi N Charrel ◽  
Laurence Thirion
Keyword(s):  
Real Time ◽  
Molecular Techniques ◽  
Cold Chain ◽  
Rt Pcr ◽  
Emerging Viruses ◽  
Valley Fever ◽  
Term Stability ◽  
E Gene ◽  
Long Term Stability

Real-time molecular techniques have become the reference methods for the direct diagnosis of pathogens. The reduction of steps is a key factor in order to decrease the risk of human errors resulting in invalid series and delayed results. We describe here a process involving the preparation of oligonucleotide primers and a hydrolysis probe in a single tube at predefined optimized concentrations that are stabilized via lyophilization (Lyoph-P&P). Lyoph-P&P was compared to the classic protocol using extemporaneously prepared liquid reagents, assaying (i) sensitivity, (ii) long-term stability at 4 °C, and (iii) long-term stability at 37 °C, mimicking transportation without a cold chain. Two previously published molecular assays were selected for this study. They target two emerging viruses that are listed on the blueprint of the WHO to be considered for preparedness and response actions: chikungunya virus (CHIKV) and Rift Valley fever phlebovirus (RVFV). The results of our study demonstrate that (i) Lyoph-P&P is stable for at least four days at 37 °C, supporting shipping without the need of a cold chain, (ii) Lyoph-P&P rehydrated solution is stable at 4 °C for at least two weeks, (iii) the sensitivity observed with Lyoph-P&P is at least equal to, and often better than, that observed with liquid formulation, and (iv) the validation of results observed with low-copy specimens is rendered easier by higher fluorescence levels. In conclusion, Lyoph-P&P holds several advantages over extemporaneously prepared liquid formulations and merits consideration as a novel real-time molecular assay for implementation into a laboratory with routine diagnostic activity. Since the meeting, this concept has been applied to the COVID-19 situation: two diagnostic assays (E gene and RdRp) have been developed and can be ordered on the European Virus Archive catalog (https://www.european-virus-archive.com/detection-kit/lyophilized-primers-and-probe-rt-pcr-2019-ncov-e-gene; https://www.european-virus-archive.com/detection-kit/lyophilized-primers-and-probe-rt-pcr-sars-cov-2-rdrp-gene).

Cell culture demonstrates superior sensitivity over one step real time RT PCR and nested VP1 amplification for Enteroviruses

2021 ◽  
Vol 287 ◽  
pp. 113994
Author(s):  
Auwal Idris Kabuga ◽  
Ahmad Nejati ◽  
Parastoo Soheili ◽  
Soodeh Yousefipoor ◽  
Maryam Yousefi ◽  
...  
Keyword(s):  
Cell Culture ◽  
Real Time ◽  
Rt Pcr ◽  
One Step

scholarly journals Quantitative Analysis of the Relative Transcript Levels of ABC Transporter Atr Genes in Aspergillus nidulans by Real-Time Reverse Transcription-PCR Assay

2002 ◽  
Vol 68 (3) ◽  
pp. 1351-1357 ◽  
Author(s):  
Camile Pizeta Semighini ◽  
Mozart Marins ◽  
Maria Helena S. Goldman ◽  
Gustavo Henrique Goldman
Keyword(s):  
Quantitative Analysis ◽  
Real Time ◽  
Aspergillus Nidulans ◽  
Abc Transporter ◽  
Reverse Transcription ◽  
Wild Type ◽  
Rt Pcr ◽  
Transcript Levels ◽  
Reverse Transcription Pcr ◽  
Nitroquinoline Oxide

ABSTRACT The development of assays for quantitative analysis of the relative transcript levels of ABC transporter genes by real-time reverse transcription-PCR (RT-PCR) might provide important information about multidrug resistance in filamentous fungi. Here, we evaluate the potential of real-time RT-PCR to quantify the relative transcript levels of ABC transporter Atr genes from Aspergillus nidulans. The AtrA to AtrD genes showed different and higher levels in the presence of structurally unrelated drugs, such as camptothecin, imazalil, itraconazole, hygromycin, and 4-nitroquinoline oxide. We also verified the relative transcript levels of the Atr genes in the A. nidulans imazalil-resistant mutants. These genes displayed a very complex pattern in different ima genetic backgrounds. The imaB mutant has higher basal transcript levels of AtrB and -D than those of the wild-type strain. The levels of these two genes are comparable when the imaB mutant is grown in the presence and absence of imazalil. The imaC, -D, and -H mutants have higher basal levels of AtrA than that of the wild type. The same behavior is observed for the relative transcript levels of AtrB in the imaG mutant background.

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