Qualitative PCR Detection Research Articles

Establishment of <I>Phytase</I>-Specific Qualitative PCR Detection Method and Construction of a Positive Plasmid Molecule

Establishment of <I>Phytase</I>-Specific Qualitative PCR Detection Method and Construction of a Positive Plasmid Molecule

Validation of Artemisia Genus-Specific Gene, GEL4, for Use as an Endogenous Reference Gene in Qualitative PCR Detection of Putative Transgenic Artemisia annua

Abstract Artemisia annua L. is a popular medical plant used against malaria. Transgenic A. annua plants have been developed to increase the artemisinin content using genetic engineering. To develop a reliable PCR method of detecting transgenic A. annua, one Artemisia specific gene, GEL4, was selected and validated as suitable. Qualitative PCR methods were assayed with 16 different A. annua ecotypes and four Artemisia plants, and identical amplified products were obtained. No amplified products were observed when genomic DNA samples were extracted from 15 different plant species. An LOD of 0.05 ng of A. annua DNA was also determined. Furthermore, the results of a Southern blot method showed that the GEL4 gene was in three copies of the six A. annua ecotypes tested. To determine whether there was intraspecific variability in the GEL4 region between different A. annua ecotypes, the GEL4 region corresponding to the 10 A. annua ecotypes was cloned and sequenced. Alignment of the obtained sequences presented a highly conserved amplification product region in 10 A. annua ecotypes. Therefore, it is concluded that the GEL4 gene can be used as an endogenous reference gene of A. annua, and that the qualitative PCR system was reliable for the detection of transgenic A. annua.

Assessment of DNA extraction methods for PCR testing of discontinued or unapproved biotech events in single seeds of canola, flax and soybean

The purpose of the study was to assess the suitability of three DNA extraction methods (Fast ID, SDS-based and relatively high-throughput methods) for single seeds (kernels) of canola, flax and broken pieces of soybean seeds. The extracted DNA was used for conventional and real-time qualitative PCR detection of the biotech events OXY235 canola, FP967 flax and DP305423 soybean. The mean weight of single canola and flaxseeds ranged from 2.3 to 3.2 mg and 5.5 to 5.8 mg, respectively. For canola, mean total DNA yields of 216, 796 and 377 ng per seed were obtained for Fast ID, SDS and relatively high-throughput DNA extraction methods, respectively. For flax, mean total DNA yields of 329, 826 and 957 ng per seed were obtained for Fast ID, SDS and relatively high-throughput DNA extraction methods, respectively. For soybean, mean DNA yields of 58, 102 and 175 ng per mg of broken seed were obtained for Fast ID, SDS and relatively high-throughput DNA extraction methods, respectively. Comparison of mean DNA yields indicated statistically significant differences among the three DNA extraction methods for all the three grain types. There was either weak or no correlation between seed weight and DNA yield for all the three DNA extraction methods. Abs260/280 ratio of ≥1.8 was obtained for DNA extracted with Fast ID and SDS-based methods. DNA isolated with all three extraction methods had low Abs260/230 ratios indicating the presence of contaminants that absorb at 230 nm. Consistent and repeatable PCR amplification was obtained for DNA extracted with the Fast ID and SDS-based extraction methods. Inhibition of PCR was observed for flax DNA extracted using relatively high-throughput method; however, reducing the amount of DNA to 10 ng in the PCR resulted in consistent amplification. Overall, all three DNA extraction methods can be used for fast DNA-based detection of unapproved or discontinued biotech events in single seeds of canola and flax as well as broken pieces of soybean seeds.

Interlaboratory Study of DNA Extraction from Multiple Ground Samples, Multiplex Real-Time PCR, and Multiplex Qualitative PCR for Individual Kernel Detection System of Genetically Modified Maize

In many countries, the labeling of grains, feed, and foodstuff is mandatory if the genetically modified (GM) organism content exceeds a certain level of approved GM varieties. We previously developed an individual kernel detection system consisting of grinding individual kernels, DNA extraction from the individually ground kernels, GM detection using multiplex real-time PCR, and GM event detection using multiplex qualitative PCR to analyze the precise commingling level and varieties of GM maize in real sample grains. We performed the interlaboratory study of the DNA extraction with multiple ground samples, multiplex real-time PCR detection, and multiplex qualitative PCR detection to evaluate its applicability, practicality, and ruggedness for the individual kernel detection system of GM maize. DNA extraction with multiple ground samples, multiplex real-time PCR, and multiplex qualitative PCR were evaluated by five laboratories in Japan, and all results from these laboratories were consistent with the expected results in terms of the commingling level and event analysis. Thus, the DNA extraction with multiple ground samples, multiplex real-time PCR, and multiplex qualitative PCR for the individual kernel detection system is applicable and practicable in a laboratory to regulate the commingling level of GM maize grain for GM samples, including stacked GM maize.

Interlaboratory Study of DNA Extraction from Multiple Ground Samples, Multiplex Real-Time PCR, and Multiplex Qualitative PCR for Individual Kernel Detection System of Genetically Modified Maize

Abstract In many countries, the labeling of grains, feed, and foodstuff is mandatory if the genetically modified (GM) organism content exceeds a certain level of approved GM varieties. We previously developed an individual kernel detection system consisting of grinding individual kernels, DNA extraction from the individually ground kernels, GM detection using multiplex real-time PCR, and GM event detection using multiplex qualitative PCR to analyze the precise commingling level and varieties of GM maize in real sample grains. We performed the interlaboratory study of the DNA extraction with multiple ground samples, multiplex real-time PCR detection, and multiplex qualitative PCR detection to evaluate its applicability, practicality, and ruggedness for the individual kernel detection system of GM maize. DNA extraction with multiple ground samples, multiplex real-time PCR, and multiplex qualitative PCR were evaluated by five laboratories in Japan, and all results from these laboratories were consistent with the expected results in terms of the commingling level and event analysis. Thus, the DNA extraction with multiple ground samples, multiplex real-time PCR, and multiplex qualitative PCR for the individual kernel detection system is applicable and practicable in a laboratory to regulate the commingling level of GM maize grain for GM samples, including stacked GM maize.

Analysis of Junction Sequence in the Transgenic Maize MON88017 and the Methods of Qualitative PCR Detection

The experiment was conducted to investigate the integration site of transgene in maize MON88017 and to establish event specific methods for qualitative detection of MON88017 based on the left border junction fragment, which was isolated with the amended GenomeWalker and Nested-PCR methods. Sequence alignment between the T-DNA sequence and isolated junction fragments showed a 504 bp junction fragment of MON88017 including 336 bp of T-DNA sequence and 168 bp of MON88017 genome DNA. MON88017 event-specific qualitative PCR method was established with the primers (MON88017-1F/R) targeting the junction regions to produce a 446 bp product. The limit of detection for qualitative PCR assay was 0.1%. The method developed in this work is highly specific, sensitive and suitable for MON88017 sample detection.

혹명나방저항성 GM 벼의 분자생물학적 특성 및 특이 마커를 이용한 검정

Abstract In recent years, several genetically modified (GM) crops have been developed worldwide through the recombinant DNA technology and commercialized by various agricultural biotechnological companies. Commercialization of GM crops will be required the assesment of risks associated with the release of GM crops. In advance of the commercial release of GM crops, developer should submit the several information on GM crops for approval. In this study, we carried out to provide the molecular data for the risk assessment of GM rice containing insect-resistant gene, modified Cry1Ac (CryIAc1). Through the molecular analysis with CryIAc1 induced GM rice, we confirmed the steady integration and expression of transgene, the transgene copy number, the adjacent region sequences of inserted gene into rice genome, and the transgene stability in progenies. For the qualitative PCR detection methods, specific primer pairs were designed on the basis of integration sequences, and construct- and event-specific detection markers were developed for leaf folder-resistant rice, Cr7-1 line. From these results, we demonstrated that the molecular data and the PCR detection methods of leaf folder- resistant GM rice could be acceptable to conduct the biosafety and environment risk assessment.

국내개발 stack gene GM 벼(LS28 X Cry1Ac)에 대한 정성 PCR 분석

For the development of qualitative PCR detection method of genetically modified (CM) rice, rice species-specific gene, OsCc-1 (rice cytochrome c gene), was selected as suitable far use as an endogenous gene in rice. The primer pair OsCytC-5`/3`with 111 bp amplicon was used for PCR amplification of the rice endogenous gene, OsCc-1 and no amplified product was observed from 8 different crops as templates. Qualitative PCR method was carried out with stack traits of L528CryIAc1 GM rice developed in Korea. For the qualitative PCRs, some primer pairs were designed with a construct-specific and event-specific type based on T-DNA and junction sequences of T-DNA in GM rice. Actck-5`/3` amplifying between actin promoter and OsCK1 gene introduced in LS28 gave rise to an amplicon 306 bp; also, CrLB-5`/3` from CryIAcl and CKRB-5`/3`amplifying the junction region of T-DNA and genome sequence from LS28 as event-specific primers gave rise to an amplicon 142 bp and 91 bp, respectively. These primer pairs for the detection of event-specific targets not produced PCR amplicons on non-CM rice and various crops in contrast to event lines. Therefore, in this study we verified that event-specific primers were effective to specifically detect stack trait lines and demonstrated that this method presented could be provided with the detection-method data for risk assessment analysis of GM rice to be commercialized.

Qualitative and Quantitative PCR Methods for Event-specific Detection of Genetically Modified Cotton Mon1445 and Mon531

Based on the DNA sequences of the junctions between recombinant and cotton genomic DNA of the two genetically modified (GM) cotton varieties, herbicide-tolerance Mon1445 and insect-resistant Mon531, event-specific primers and probes for qualitative and quantitative PCR detection for both GM cotton varieties were designed, and corresponding detection methods were developed. In qualitative PCR detection, the simplex and multiplex PCR detection systems were established and employed to identify Mon1445 and Mon531 from other GM cottons and crops. The limits of detection (LODs) of the simplex PCR were 0.05% for both Mon1445 and Mon531 using 100 ng DNA templates in one reaction, and the LOD of multiplex PCR analysis was 0.1%. For further quantitative detection using TaqMan real-time PCR systems for Mon1445 and Mon531, one plasmid pMD-ECS, used as reference molecule was constructed, which contained the quantitative amplified fragments of Mon1445, Mon531, and cotton endogenous reference gene. The limits of quantification (LOQs) of Mon1445 and Mon531 event-specific PCR systems using plasmid pMD-ECS as reference molecule were 10 copies, and the quantification range was from 0.03 to 100% in 100 ng of the DNA template for one reaction. Thereafter, five mixed cotton samples containing 0, 0.5, 0.9, 3 and 5% Mon1445 or Mon531 were quantified using established real-time PCR systems to evaluate the accuracy and precision of the developed real-time PCR detection systems. The accuracy expressed as bias varied from 1.33 to 8.89% for tested Mon1445 cotton samples, and from 2.67 to 6.80% for Mon531. The precision expressed as relative standard deviations (RSD) were different from 1.13 to 30.00% for Mon1445 cotton, and from 1.27 to 24.68% for Mon531. The range of RSD was similar to other laboratory results (25%). Concluded from above results, we believed that the established event-specific qualitative and quantitative PCR systems for Mon1445 and Mon531 in this study are acceptable and suitable for GM cotton identification and quantification.

Quantitative Detection System for Maize Sample Containing Combined-Trait Genetically Modified Maize

Various countries have established regulations that stipulate the labeling of agricultural commodities, feed, and food products that contain or are made from genetically modified (GM) material or that contain adventitious GM material in amounts that exceed certain threshold levels. While regulations in some countries refer to GM material on a weight per weight (w/w) percentage, the currently applied detection methods do not directly measure the w/w percentage of the GM material. Depending on the particular method and the sample matrix it is applied to, the conversion of analytical results to a w/w percentage is challenging or not possible. The first rapid PCR system for GM maize detection on a single kernel basis has been developed. The equipment for the grinding of individual kernels and a silica membrane-based 96-well DNA extraction kit were both significantly revised and optimized for this particular purpose, respectively. We developed a multiplex real-time PCR method for the rapid quantification of GM DNA sequences in the obtained DNA solutions. In addition, a multiplex qualitative PCR detection method allows for the simultaneous detection of different GM maize traits in each kernel and thereby for identification of individual kernels that contain a combination of two or more GM traits. Especially for grain samples that potentially contain combined-trait GM maize kernels, the proposed methods can deliver informative results in a rapid, precise, and reliable manner.

Significance of qualitative PCR detection method for pre-emptive therapy of cytomegalovirus infection in patiens after allogeneic hematopoietic stem cell transplantation—single-centre experience

Background: Cost-effectiveness analyses of clinical preventive services are a potential means to aid public health resource allocation. Cost-utility analysis (CUA) is a specific form of cost-effectiveness analysis where results are expressed in terms of cost per quality-adjusted life year (QALY) gained. To increase the transparency and comparability of CUAs, standardization of methods has been recommended.Objectives: The purposes of this study were as follows: (1) identify published articles with original CUAs of primary and secondary clinical preventive services, (2) summarize the ratios found in these analyses, (3) identify articles employing comparable methods, and (4) explore analytic methods employed over time.Methods: As part of a larger study we conducted a comprehensive search of published CUAs in the area of clinical preventive services and systematically collected data on the results of the analyses and analytic methods employed. Cost-effectiveness ratios were standardized and organized into a table.Results: We found 50 CUAs pertaining to clinical preventive services (primary, n=22, 44%; and secondary, n=28, 56%) and 174 cost-effectiveness ratios. These ratios ranged from cost-savings up to $27,000,000/QALY, with a median of $14,000/QALY. Only three (6%) of the CUAs met minimum reference case requirements. There was no apparent improvement of methods over time.Conclusions: Immunizations and chemoprophylaxis have the most favorable cost-effectiveness ratios, and preventive services are more cost-effective when targeted at high-risk populations. However, there is wide variation in the methods used in these analyses. This study allows us to define where improvements in methodologic rigor need to occur, provides a base-line for future audits, and highlights disease areas in clinical preventive services that have been omitted or underevaluated.