利用实时荧光定量PCR法检测转基因水稻外源基因拷贝数的研究

转基因植物中外源基因拷贝数是影响目的基因表达水平和遗传稳定性的重要因素,因此外源基因拷贝数的检测成为转基因研究的关键．利用高通量、快速、灵敏的SYBR Green Ⅰ荧光定量实时PCR法,检测了转大麦烟酰胺合成酶基因（NASl）水稻中外源基因拷贝数．以蔗糖磷酸合成酶基因（SPS）作为水稻的内源参照基因．通过梯度稀释法．分别获得了NAS1和SPS基因的Ct值与起始模板数的相关性标准曲线,相关系数分别为0．99976和0．99571,相关性高．通过目的基因NAS1和水稻内源参照基因SPS起始模板数的比较,获得了目的基因在转基因水稻中的拷贝数。在8株转基因株系中,1株为假阳性,1株拷贝数为1,3株拷贝数为2,其余3株拷贝数分别为3、4和7．而阴性对照拷贝数为0．这种方法快速、简便、准确,可以满足转基因育种工作中对后代优良株系的选择．     

实时荧光定量PCR法检测转基因小鼠拷贝数

目的利用实时荧光定量PCR法鉴定转基因小鼠外源基因插入拷贝数。方法以TG-CARK转基因首见鼠为研究对象,选取小鼠的高度保守基因Fabpi为内参,利用绝对定量的实时荧光PCR法鉴定转基因小鼠拷贝数,并与传统的Southern blot方法的定量结果进行比较。结果实时定量PCR鉴定的转基因拷贝数与Southernblot法完全一致,三只TG-CARK首见小鼠的拷贝数分别为1,7,45。结论实时定量PCR技术具有高准确性、高稳定性、高通量和低成本的优点,是比传统杂交技术更好的鉴定小鼠转基因拷贝数的方法。     

利用实时荧光定量比较Ct法检测转基因小鼠外源基因拷贝数

目的：在建立转基因小鼠模型时,外源基因拷贝数是影响其表达水平和遗传稳定性的重要因素之一。外源基因拷贝数的精确测定,是建立转基因动物模型的重要环节。方法：合成cagA基因和内参基因GAPDH的引物,用标准曲线法测得cagA和GAPDH基因的扩增效率分别为97．6％和98．6％;将128拷贝阴性小鼠基因组和128拷贝c0鲥打靶质粒的混合物作为参照样品,取6只来自同一母本的F2阳性小鼠的128拷贝基因组作为待测样品;选取GAPDH作为内源参照基因,用比较Ct法对待测样品进行定量。结果：经计算,6只待测小鼠的cagA基因拷贝数平均值为8。结论：利用实时荧光定量PCR仪,呆用改良后的比较Ct法对转基因小鼠的外源基因拷贝数进行了精确测定。     

实时荧光定量PCR(TaqMan)法测定外源基因的拷贝数

实时荧光定量PCR是近年新兴的一项技术,因其快速、方便、便宜,需要DNA样品量少,无需放射性检测等优点被广泛应用于基因的定量分析。该文就实时荧光定量PCR(TaqMan)技术的发展、基本原理及测定外源基因拷贝数的技术流程做一介绍。     

转红色荧光蛋白基因唐鱼外源基因拷贝数的测定

目的:测定转红色荧光蛋白基因唐鱼的外源基因拷贝数。方法:以杂合F5代和杂合F6代转红色荧光蛋白基因唐鱼为材料,以其外源插入片段(pDsRed-mylz2)与基因组插入位点5′侧翼区之间的边界序列作为特异性内参片段,同时以外源整合的红色荧光表达载体序列(pDsRed-mylz2)作为目的基因,采用实时荧光定量PCR技术测定外源基因整合的拷贝数。结果:运用外源基因与特异内参在同批次实时荧光定量PCR中的初始拷贝数比值,得到杂合F5代和杂合F6代转红色荧光蛋白基因唐鱼中插入的外源红色荧光表达载体序列pDsRed-mylz2的拷贝数均值均为3。结论:转红色荧光蛋白基因唐鱼的外源基因拷贝数为3。     

利用荧光定量PCR分析c-Ha-ras基因在C57-ras转基因小鼠中的拷贝数

目的:利用real-time PCR建立检测C57-ras转基因小鼠中外源c-Ha-ras基因拷贝数的简便方法,为药物安全性评价C57-ras转基因小鼠模型的繁殖和筛选提供数据支持。方法:以自建的人原癌基因c-Ha-ras转基因小鼠为研究对象,利用SYBR GreenⅠ荧光定量PCR的绝对定量法测定3个C57-ras转基因小鼠系的c-Ha-ras基因Ct值,通过与内参基因GAPDH比较计算获得转基因的拷贝数。结果:内参基因GAPDH的标准曲线为lg NGAPDH=-2.852Ct+26.236,外源基因c-Ha-ras的标准曲线为lg NRAS=-3.068Ct+39.186;经计算,NO.2、NO.3、NO.5系的F6代拷贝数分别为4、4和3,并且系内不同个体间拷贝数一致。结论:利用SYBR GreenⅠreal-time PCR技术建立了检测C57-ras转基因小鼠中外源基因拷贝数的方法,该方法操作简单,节约成本,为C57-ras致癌性模型的选留和应用提供了基础和技术手段,也为其他类似转基因品系中转基因拷贝数的确定提供了一种参考方法。     

SYBR Green Ⅰ实时荧光定量RT-PCR测定猴免疫缺陷病毒RNA拷贝数方法的建立

目的 建立SYBR Green Ⅰ荧光染料实时定量RT-PCR方法,测定猴免疫缺陷病毒(SIV)RNA拷贝数.方法 巢式RT-PCR扩增SIV病毒RNA gag基因上1360-1837之间的长度为477 bp的片段,将该片段克隆到pGEM T载体上,构建pGEM-SIVgag477质粒.该质粒经限制性内切酶Not I酶切后,进行体外转录,转录出的RNA产物(RS)纯化后10倍系列稀释,作出标准曲线,作为SIV病毒RNA荧光定量检测的外标准品.结果 应用Qiagen公司QuantiTect SYBR GREEN RT-PCR Kit,该标准品可精确定量到100 copies/μL.结论 制备的RS外标准品纯度高,SYBR Green Ⅰ荧光染料实时定量RT-PCR法特异性、敏感性高,稳定性好,可用于定量测定猴免疫缺陷病毒(SIV)RNA拷贝数.     

实时荧光定量PCR技术及其应用

实时荧光定量PCR技术是一种多色荧光检测核酸定量技术,该简要介绍实时荧光定量PCR技术的原理及其应用。     

SYBR Green实时荧光PCR高通量检测转基因大豆油

采用SYBR Green实时荧光PCR技术,建立了食用大豆油转基因成分的检测方法.根据转基因大豆中内源参照基因lectin和外源基因35S启动子、NoS终止子和ep4 epsps基因,设计特异性引物,在Roche荧光PCR仪上进行实时荧光PCR扩增.荧光曲线表明,SYBR Green实时荧光PCR可特异性地检测大豆油中的转基因成分,方法准确、快速,并运用熔解曲线进行产物分析,验证了试验结果的特异性和准确性,检测方法灵敏度高.     

应用RNAi干扰eGFP转基因小鼠胎儿成纤维细胞中FGF5基因的表达

在小鼠FGF5基因干扰的研究中,针对小鼠FGF5 mRNA的第316～335 bp区域、第499～518 bp区域和第766～785 bp区域分别设计了发夹式RNA干扰片段,并将干扰片段连接到带有H1启动子的红色荧光表达载体上,将载体以脂质体法转染到eGFP转基因小鼠胎儿成纤维细胞中,搜集转染后的细胞提取总RNA,并反转录成cDNA.用SYBR GREEN Ⅰ荧光定量PCR方法对转染了不同干扰载体的细胞cDNA进行检测,结果干扰载体对eGFP转基因小鼠成纤维细胞中的FGF5表达有较强的抑制作用.     

琼脂糖凝胶直接杂交快速鉴定低拷贝数转基因

采用常规的PCR方法检测低拷贝数转基因有一定困难.提出一种使用琼脂糖凝胶直接杂交的方法,结果明确、简单可行,是转基因动物中低拷贝数转基因鉴定的一种较好方法.     

转基因猪中外源基因拷贝数和整合位点的研究

主要采用了绝对定量PCR和热不均一交错PCR(thermal asymmetric interlaced PCR,TAIL-PCR),检测了体细胞核移植技术生产的绿色荧光蛋白转基因猪中外源基因拷贝数和整合位点,并利用旁侧PCR(Junction PCR)对整合位点进行确定,同时进一步分析了整合位点的纯合性．结果表明,绝对定量PCR可以准确有效地检测外源基因拷贝数,标准曲线为：log₂N (拷贝数) =-0.935 4ΔCt + 3.411 6 (R²=0.997 4,P < 0.001),两只转基因猪中外源基因拷贝数分别为30.85 ± 1.77和18.87 ± 1.34;TAIL-PCR能成功地克隆转基因猪中外源基因整合位点,得到25条特异性条带,经BLAST比对,共获得TgInS1 (1 440 bp)、TgInS2 (1 263 bp)和TgInS3 (1 861 bp) 3个整合位点．以整合位点侧翼序列特异性引物与外源基因特异性引物的组合引发Junction PCR,得到预计大小的特异性片段,确定了整合位点上、下游侧翼序列的准确性．采用整合位点5′上游和3′下游侧翼序列特异性引物与外源基因特异性引物的组合,进行Junction PCR,在两只转基因猪中都得到与野生型猪一致的侧翼序列特异性引物扩增片段,表明我们获得的转基因猪都为整合位点杂合子．初步建立了绝对定量PCR和TAIL-PCR对外源基因拷贝数和整合位点检测的体系,为今后研究外源基因在转基因猪中遗传和表达的稳定性打下了基础．     

GUS基因拷贝数对转基因在受体植物烟草中表达的影响

GUS基因拷贝数对转基因在受体植物烟草中表达的影响     

Determining Fungi rRNA Copy Number by PCR

The goal of this project is to improve the quantification of indoor fungal pollutants via the specific application of quantitative PCR (qPCR). Improvement will be made in the controls used in current qPCR applications. This work focuses on the use of two separate controls within a standard qPCR reaction. The first control developed was the internal standard control gene, benA. This gene encodes for β-tubulin and was selected based on its single-copy nature. The second control developed was the standard control plasmid, which contained a fragment of the ribosomal RNA (rRNA) gene and produced a specific PCR product. The results confirm the multicopy nature of the rRNA region in several filamentous fungi and show that we can quantify fungi of unknown genome size over a range of spore extractions by inclusion of these two standard controls. Advances in qPCR have led to extremely sensitive and quantitative methods for single-copy genes; however, it has not been well established that the rRNA can be used to quantitate fungal contamination. We report on the use of qPCR, combined with two controls, to identify and quantify indoor fungal contaminants with a greater degree of confidence than has been achieved previously. Advances in indoor environmental health have demonstrated that contamination of the built environment by the filamentous fungi has adverse impacts on the health of building occupants. This study meets the need for more accurate and reliable methods for fungal identification and quantitation in the indoor environment.     

Standard Addition Quantitative Real-Time PCR (SAQPCR): A Novel Approach for Determination of Transgene Copy Number Avoiding PCR Efficiency Estimation

Quantitative real-time polymerase chain reaction (qPCR) has been previously applied to estimate transgene copy number in transgenic plants. However, the results can be erroneous owing to inaccurate estimation of PCR efficiency. Here, a novel qPCR approach, named standard addition qPCR (SAQPCR), was devised to accurately determine transgene copy number without the necessity of obtaining PCR efficiency data. The procedures and the mathematical basis for the approach are described. A recombinant plasmid harboring both the internal reference gene and the integrated target gene was constructed to serve as the standard DNA. It was found that addition of suitable amounts of standard DNA to test samples did not affect PCR efficiency, and the guidance for selection of suitable cycle numbers for analysis was established. Samples from six individual T₀ tomato (Solanum lycopersicum) plants were analyzed by SAQPCR, and the results confirmed by Southern blot analysis. The approach produced accurate results and required only small amounts of plant tissue. It can be generally applied to analysis of different plants and transgenes. In addition, it can also be applied to zygosity analysis.     

A New Approach Using the SYBR Green-Based Real-Time PCR Method for Detection of Soft Rot Pectobacterium odoriferum Associated with Kimchi Cabbage

Pectobacterium odoriferum is the primary causative agent in Kimchi cabbage soft-rot diseases. The pathogenic bacteria Pectobacterium genera are responsible for significant yield losses in crops. However, P. odoriferum shares a vast range of hosts with P. carotovorum, P. versatile, and P. brasiliense, and has similar biochemical, phenotypic, and genetic characteristics to these species. Therefore, it is essential to develop a P. odoriferum-specific diagnostic method for soft-rot disease because of the complicated diagnostic process and management as described above. Therefore, in this study, to select P. odoriferum-specific genes, species-specific genes were selected using the data of the P. odoriferum JK2.1 whole genome and similar bacterial species registered with NCBI. Thereafter, the specificity of the selected gene was tested through blast analysis. We identified novel species-specific genes to detect and quantify targeted P. odoriferum and designed specific primer sets targeting HAD family hydrolases. It was confirmed that the selected primer set formed a specific amplicon of 360 bp only in the DNA of P. odoriferum using 29 Pectobacterium species and related species. Furthermore, the population density of P. odoriferum can be estimated without genomic DNA extraction through SYBR Green-based real-time quantitative PCR using a primer set in plants. As a result, the newly developed diagnostic method enables rapid and accurate diagnosis and continuous monitoring of soft-rot disease in Kimchi cabbage without additional procedures from the plant tissue.     

Detection of MET Gene Copy Number in Cancer Samples Using the Droplet Digital PCR Method

Purpose

The analysis of MET gene copy number (CN) has been considered to be a potential biomarker to predict the response to MET-targeted therapies in various cancers. However, the current standard methods to determine MET CN are SNP 6.0 in the genomic DNA of cancer cell lines and fluorescence in situ hybridization (FISH) in tumor models, respectively, which are costly and require advanced technical skills and result in relatively subjective judgments. Therefore, we employed a novel method, droplet digital PCR (ddPCR), to determine the MET gene copy number with high accuracy and precision.

Methods

The genomic DNA of cancer cell lines or tumor models were tested and compared with the MET gene CN and MET/CEN-7 ratio determined by SNP 6.0 and FISH, respectively.

Results

In cell lines, the linear association of the MET CN detected by ddPCR and SNP 6.0 is strong (Pearson correlation = 0.867). In tumor models, the MET CN detected by ddPCR was significantly different between the MET gene amplification and non-amplification groups according to FISH (mean: 15.4 vs 2.1; P = 0.044). Given that MET gene amplification is defined as MET CN >5.5 by ddPCR, the concordance rate between ddPCR and FISH was 98.0%, and Cohen''s kappa coefficient was 0.760 (95% CI, 0.498–1.000; P <0.001).

Conclusions

The results demonstrated that the ddPCR method has the potential to quantify the MET gene copy number with high precision and accuracy as compared with the results from SNP 6.0 and FISH in cancer cell lines and tumor samples, respectively.     

Determination of Transgene Copy Number in Stably Transfected Mammalian Cells by PCR-Capillary Electrophoresis Assay

The quantitative determination of transgene copy number in stably transfected mammalian cells has been traditionally estimated by Southern blot analysis. Recently, other methods have become available for appraisal of gene copy number, such as real-time PCR. Herein we describe a new method based on a fluorescently labeled PCR, followed by capillary electrophoresis. We amplified our target gene (prothrombin) and the internal control originating from genomic DNA (18S rRNA) in the same PCR tube and calculated the mean peak height ratio of the target:control gene for every cell clone sample. With this approach we identified stably transfected cell clones bearing the same transgene copy number. The results of our assay were confirmed by real-time PCR. Our method proves to be fast, low-cost, and reproducible compared with traditionally used methods. This assay can be used as a rapid screening tool for the determination of gene copy number in gene expression experiments.