Selective control of primer usage in multiplex one-step reverse transcription PCR

Abstract Background Multiplex RT-PCR is a valuable technique used for pathogen identification, disease detection and relative quantification of gene expression. The simplification of this protocol into a one-step procedure saves time and reagents. However, intensive PCR optimization is often required to overcome competing undesired PCR primer extension during the RT step. Results Herein, we report multiplex one-step RT-PCR experiments in which the PCR primers contain thermolabile phosphotriester modification groups. The presence of these groups minimizes PCR primer extension during the RT step and allows for control of PCR primer extension until the more stringent, elevated temperatures of PCR are reached. Results reveal that the use of primers whose extension can be controlled in a temperature-mediated way provides improved one-step RT-PCR specificity in both singleplex and multiplex reaction formats. Conclusions The need for an accurate and sensitive technique to quantify mRNA expression levels makes the described modified primer technology a promising tool for use in multiplex one-step RT-PCR. A more accurate representation of the abundances in initial template sample is feasible with modified primers, as artifacts of biased PCR are reduced because of greater improvements in reaction specificity

Detection of Porcine DNA in Processed Beef Products Using Real Time – Polymerase Chain Reaction

Meat is one of food materials which has protein source and mostlyconsumed by non-vegetarian. Consuming halal food is an obligation for every Muslim. Meat processed products usually contaminated by pork. One of technique that is often chosen as an authentication process for proofing halalness of the product is PCR technique, one of PCR technique which most commonly used is RT-PCR. RT-PCR technique was chosen as identification method because it has high accuration for detection of porcine DNA in fresh meat and processed products. RT-PCR is the amplification technique in the specific regions that are restricted by two oligonucleotide with the help of polymerase enzymes. Annealing is the first process of RT-PCR analysis who was primary attachment to the DNA template that determines the specificity and amount of DNA produced. In this study, extraction kit and detection kit were used for analysis Porcine DNA in meatballs. The results obtained from this study were from whole DNA samples, which had DNA purity ranging from 1.82 to 1.93. From the all samples three of them containing porcine DNA. The positive samples shown from amplification curves who was specifically formed when probes reacts with porcine gene

Multiplex Detection of Aspergillus fumigatus Mycoviruses.

© 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).Mycoviruses are viruses that naturally infect and replicate in fungi. They are widespread in all major fungal groups including plant and animal pathogenic fungi. Several dsRNA mycoviruses have been reported in Aspergillus fumigatus. Multiplex polymerase chain reaction (PCR) amplification is a version of PCR that enables amplification of different targets simultaneously. This technique has been widely used for detection and differentiation of viruses especially plant viruses such as those which infect tobacco, potato and garlic. For rapid detection, multiplex RT-PCR was developed to screen new isolates for the presence of A. fumigatus mycoviruses. Aspergillus fumigatus chrysovirus (AfuCV), Aspergillus fumigatus partitivirus (AfuPV-1), and Aspergillus fumigatus tetramycovirus-1 (AfuTmV-1) dsRNAs were amplified in separate reactions using a mixture of multiplex primer pairs. It was demonstrated that in the presence of a single infection, primer pair mixtures only amplify the corresponding single virus infection. Mixed infections using dual or triple combinations of dsRNA viruses were also amplified simultaneously using multiplex RT-PCR. Up until now, methods for the rapid detection of Aspergillus mycoviruses have been restricted to small scale dsRNA extraction approaches which are laborious and for large numbers of samples not as sensitive as RT-PCR. The multiplex RT-PCR assay developed here will be useful for studies on determining the incidence of A. fumigatus mycoviruses. This is the first report on multiplex detection of A. fumigatus mycovirusesPeer reviewe

Comparisons of competitive enzyme-linked immunosorbent assay and one step RT-PCR tests for the detection of Bluetongue virus in south west of Iran

Bluetongue is a noncontagious, arthropod-borne viral disease of both domestic and wild ruminants. Bluetongue virus (BTV) is the type of species of the genus Orbivirus within the family Reoviridae. BTV is endemic in some areas with cattle and wild ruminants serving as reservoirs for the virus. Clinical symptoms are often seen in sheep. There are several methods for the detection of Bluetongue virus, among them the molecular technique like RT-PCR is considered as the most sensitive and reliable one. The aim of this study was to comprise competitive enzyme-linked immunosorbent assay (C-ELISA) with one step RT-PCR test for the detection of BTV in sheep. A total of 770 blood samples were obtained from sheep (265 serum positive samples and 505 serum negative samples in C-ELISA). According to our data, out of the 265 serum positive samples in ELISA test, 234 were positive in RT-PCR assay whereas all serum negative samples were negative in RT-PCR experiment. According to the results, the PCR assay was more sensitive and reliable than ELISA technique for the diagnosis of Bluetongue virus.Key words: Bluetongue virus, C-ELISA, RT- PCR, Sheep, Iran

Evaluation of five diagnostic methods for Strongyloides stercoralis infection in Amhara National Regional State, northwest Ethiopia

Background: Strongyloides stercoralis is an intestinal parasite that can cause chronic infection, hyperinfection and/or a dissemination syndrome in humans. The use of techniques targeting ova fails to detect S. stercoralis, as only larvae of the parasite are excreted in faeces. Due to the absence of "Gold" standard diagnostic method for S. stercoralis, there is a paucity of reported data worldwide. Objective: This study aimed to evaluate the performance of diagnostic methods of S. stercoralis infection by taking the composite reference as a "Gold" standard. Methods: A cross-sectional study was conducted among 844 schoolchildren in Amhara Region, Ethiopia, from April to December 2019. Stool samples were collected and processed with formol-ether concentration technique (FECT), spontaneous tube sedimentation technique (STST), Baermann concentration technique (BCT), agar plate culture (APC) and real-time polymerase chain reaction (RT-PCR). Sensitivity, specificity, positive predictive value, and negative predictive value of each diagnostic method were computed against the composite reference. The agreements of diagnostic methods were evaluated by Kappa value at 95% CI. Results: The composite detection rate of S. stercoralis by the five diagnostic methods was 39.0% (329/844). The detection rate of the parasite from stool samples by FECT, STST, BCT, APC and RT-PCR was 2.0% (17/844), 4.0% (34/844), 10.2% (86/844), 10.9% (92/844) and 28.8% (243/844), respectively. The highest detection rate (37.8%; 319/844) of S. stercoralis was recorded by a combination of BCT, APC, and RT-PCR followed by a combination of STST, BCT, APC and RT-PCR (37.3%; 315/844). The sensitivity of FECT, STST, BCT, APC and RT-PCR against the composite reference was 5.2%, 10.3%, 26.4%, 28.0% and 73.9%, respectively. The diagnostic agreements of RT-PCR, APC, BCT, STST and FECT with the composite reference in detection of S. stercoralis were substantial (0.775), fair (0.321), fair (0.305), slight (0.123), and slight (0.062), respectively. Conclusion: RT-PCR detected the highest number of S. stercoralis infections. A combination of RT-PCR with APC and/or BCT better detected S. stercoralis from stool samples compared to other combinations or single diagnostic methods. Therefore, RT-PCR and combination of RT-PCR with APC and/or BCT diagnostic methods should be advocated for detection of S. stercoralis infection.The fund obtained from Bahir Dar University and Mundo Sano Foundation was used for data collection and laboratory detection purpose.N

Simultaneous detection of enteropathogenic viruses in buffalos faeces using multiplex reverse transcription-polymerase chain reaction (mRT-PCR)

A multiplex reverse transcription- polymerase chain reaction (mRT-PCR) assay that detects Bovine Viral Diarrhoea Virus, Bovine Coronavirus, and Group A Rotaviruses in infected cell-culture fluids and clinical faecal samples is described. One hundred twenty faecal samples from buffalo calves with acute gastroenteritis were tested. The mRT-PCR was validated against simplex RT-PCR with published primers for Pestivirus, Coronavirus and Rotavirus. The multiplex RT-PCR was equally sensitive and specific in detecting viral infections compared with simplex RT-PCR. The mRT-PCR readily identified viruses by discriminating the size of their amplified gene products. This mRT-PCR may be a sensitive and rapid assay for surveillance of buffalo enteric viruses in field specimens. This novel multiplex RT-PCR is an attractive technique for the rapid, specific, and cost-effective laboratory diagnosis of acute gastroenteritis

On joint maximum-likelihood estimation of PCR efficiency and initial amount of target

We consider the problem of estimating unknown parameters of the real-time polymerase chain reaction (RTPCR) from noisy observations. The joint ML estimator of the RT-PCR efficiency and the initial number of DNA target molecules is derived. The mean-square error performance of the estimator is studied via simulations. The simulation results indicate that the proposed estimator significantly outperforms a competing technique

Optimization of the reverse transcriptase polymerase chain reaction for the detection of circulating prostate cells

The reverse transcriptase polymerase chain reaction (RT-PCR) is a sensitive technique that can detect prostate-specific messenger RNA in circulating blood. Many authors have studied the potential of RT-PCR as a staging technique in prostate cancer (PC). Clinical sensitivity and in some cases specificity has been disappointing. Few authors have been able to correlate RT-PCR result with patient stage. We have compared the results of using two different RT-PCR protocols with different sensitivities on blood samples from prostate cancer patients. An 80-amplification-cycle nested primer RT-PCR assay had a detection limit of 10 prostate cells and a 50-cycle RT-PCR could detect 20 cells in 5 ml blood. The 80-cycle assay detected prostate mRNA in four of 10 female samples, whereas the 50-cycle assay detected it in none. There was little difference in the assays’ ability to detect prostate mRNA in advanced PC patients. The 50-cycle assay could differentiate between hormone-escaped, stable hormone-treated and untreated localized PC patients, whereas the 80-cycle assay could not. Each blood sample must be assayed several times with RT-PCR to avoid false-negative results and, if this is done, assay specificity can be increased with little effect on clinical sensitivity. © 2000 Cancer Research Campaig

Evaluation of RT-PCR and hemi-nested RT-PCR in brain samples from dogs with neurologic signs compatible with distemper

Foi comparado o valor diagnóstico das técnicas de RT-PCR e heminested RT-PCR (hnRT-PCR) em amostras de cérebro de cães com sintomatologia nervosa compatível com cinomose. Fragmentos do sistema nervoso central (SNC) colhidos de 68 animais foram testados pela Imunofluorescência direta (IFD) e, independentemente do resultado, foram armazenados a -20°C por pelo menos três anos. Após esse período, foram submetidos a RT-PCR e a hnRT-PCR com oligonucleotídeos iniciadores direcionados ao gene codificador da nucleoproteína N. As proporções de resultados positivos/examinados foram: 59/68 para a IFD, 40/68 para a RT-PCR (Kappa = 0,358) e 54/68 quando associada à heminested PCR (Kappa = 0,740). Houve nove resultados negativos nas três técnicas empregadas. Os resultados do coeficiente Kappa entre a IFD e hnRT-PCR demonstram que apesar das condições de armazenamento, a hnRT-PCR pode ser utilizada em estudos retrospectivos.The diagnostic value of RT-PCR and hemi-nested RT-PCR (hnRT-PCR) was compared in brain samples of dogs presenting neurological signs compatible with canine distemper. Samples of central nervous system (CNS) were collected from 68 dogs and tested by direct immunofluorescence test (RFID) and, independent of the results, they were stored at -20°C for at least three years. They were submitted to the RT-PCR and hnRT-PCR techniques aiming to determine the gene responsible for the viral nucleoprotein decoding. Fifty-nine samples were positive for RIFD, 40 for RT-PCR (Kappa = 0.358) and 54 for hnRT-PCR (Kappa = 0.740). All nine RIFD negative samples were also negative for RT-PCR and hnRT-PCR. In spite of the storage duration and proper sample conditions, the estimated accordance between hnRT-PCR and RIFD demonstrated that hnRT-PCR technique can be applied in retrospective studies