Quantification of anaerobic ammonium-oxidizing bacteria in enrichment cultures by quantitative competitive PCR

The anaerobic ammonium-oxidizing （ANAMMOX） bacteria were enriched from a sequencing batch biofilm reactor （SBBR）. A quantitative competitive polymerase chain reaction （QC-PCR） system was successfully developed to detect and quantify ANAMMOX bacteria in environmental samples. For QC-PCR system, PCR primer sets targeting 16S ribosomal RNA genes of ANAMMOX bacteria were designed and used. The quantification range of this system was 4 orders of magnitude, from 10^3 to 10^6 copies per PCR, corresponding to the detection limit of 300 target copies per mL. A 312-bp internal standard was constructed, which showed very similar amplification efficiency with the target amxC fragment （349 bp） over 4 orders of magnitude （10^3-10^6）. The linear regressions were obtained with R^2 of 0.9824 for 10^3 copies, 0.9882 for 10^4 copies, 0.9857 for 10^5 copies and 0.9899 for 10^6 copies, respectively. Using this method, ANAMMOX bacteria were quantified in a shortcut nitrification/denitrification-anammox system which was set for piggery wastewater treatment.

Synchronous Detection of DNA/RNA of Four Shrimp Viruses by Real-time Fluorescence Quantitative RT-PCR

[ Objective] This study aimed to establish a simultaneous detection method of shrimp viruses by real-time fluorescence quantitative RT-PCR, to improve the efficiency of inspection and quarantine. [ Method] A novel real-time fluorescence quantitative RT-PCR assay was established and optimized for simultaneously detecting DNA/RNA of four shrimp viruses （WSSV, IHHNV, TSV and YHV ）. [ Result] The optimized real-time fluorescence quantitative RT-PCR system gener- ated typical amplification curves with high amplification efficiencies （E = 1.06, 1.07, 0.92 and 0.92, respectively）, good hnear relationship （ r = 1 ）, uniform repeatability （ standard deviation = 0.05 - 0.46 ; variation coefficient = 0.26% - 1.62% ） and high sensitivity, exhibiting no significant differences compared with re- al-time fluorescence quantitative PCR （average error of Ct value = 0.04 -0.40; T = 0.53 -2.50; P 〉 0.05 ）. The total detection time was about 1 h. [ Conclusion] The optimized real-time fluorescence quantitative RT-PCR system can be used for rapid detection of WSSV, IHHNV, TSV and YHV.

Detection and clinical significance of multidrug resistance-1 mRNA in bone marrow cells in children with acute lymphoblastic leukemia by real-time fluorescence quantitative RT-PCR

Objective： Multidrug resistance（MDR） is one of the most important reasons for treatment failure and recurrence of acute leukemia. Its manifestations are different in children with acute lymphoblastic leukemia（ALL） which may be due to different detection methods. This study was to detect the expression of MDR1 mRNA in bone marrow cells of children with ALL by real-time fluorescence- quantitative reverse transcription polymerase-chain reaction（FQ-RT-PCR）, and combine minimal residual desease（MRD） detection by flow cytometry（FCM） and to study their relationship with treatment response and prognosis of ALL. Methods：The MDR1 mRNA levels in bone marrow cells from 67 children with ALL[28 had newly diagnosed disease, 27 had achieved complete remission（CR）, 12 recurrent] and 22 children without leukemia were detected by FQ-RT-PCR. MRD was detected by FCM. The patients were observed for 9-101 months, with a median of 64 months. Results：Standard curves of human MDR1 and GAPDH genes were constructed successfully. MDR1 mRNA was detected in all children with a positive rate of 100%. The mRNA level of MDR1 was similar among the newly diagnosed ALL group, CR group, and control group（P 〉 0.05）, but significantly higher in the recurrence group than that in newly diagnosed disease group and control group（0.50 ± 0.55 vs. 0.09 ± 0.26 and 0.12 ± 0.23, P〈 0.05）. 54 ALL patients were followed up, and it was found that MDR1 mRNA level was significantly higher in ALL patients within 3 years duration than that of ALL patients with 3-6 years and over 6 years duration（0.63 ± 0.56 vs. 0.11 ± 0.12 and 0.04 ± 0.06, P〈 0.01）. For the 28 children with newly diagnosed disease, the MDR1 mRNA level was similar between WBC 〉 50 ~ 109 group and WBC〈50 × 10^9 group（P〉 0.05）. In the 33 CR patients, the MDR1 mRNA level was significantly higher in MRD〉10a group than that in MRD〈10a group（0.39 ± 0.47 vs. 0.03 ± 0.03, P 〈 0.05）. Conclusion：The sensitivity and specificity of FQ-RT-PCR in detecting MDR1 mRNA in bone marrowy cells of children with ALL patients are high. MDR1 mRNA is expressed in children with and without leukemia. MDR1 mRNA is highly expressed in the CR ALL patients with high MRD, recurrence and short duration（within 3 years）. Monitoring MRD and the MDR1 mRNA level might be helpful for individual treatment.

THE DETECTION OF MDR1 GENE EXPRESSION USING FLUOROGENIC PROBE QUANTITATIVE RT-PCR METHOD

Objective: To establish a fluoregenic probe quantitative RT-PCR (FQ-RT-PCR) method for detection of the expression of MDR1 gene in tumor cells and to investigate the expression of MDR1 gene in patients with lung cancer. Methods: The fluorogenic quantitative RT-PCR method for detection of the expression of MDR1 gene was established. K562/ADM and K562 cell lines or 45 tumor tissues from patients with lung cancer were examined on PE Applied Biosystems 7700 Sequence Detection machine. Results: the average levels of MDR1 gene expression in K562/ADM cells and K562 cells were (6.86±0.65)× 107 copies/μg RNA and (8.49±0.67)×105 copies/μg RNA, respectively. The former was 80.8 times greater than the latter. Each sample was measured 10 times and the coefficient variation (CV) was 9.5% and 7.9%, respectively. Various levels of MDR1 gene expression were detected in 12 of 45 patients with lung cancer. Conclusion: Quantitative detection of MDR1 gene expression in tumor cells was achieved by using FQ-RT-PCR. FQ-RT-PCR is an accurate, and sensitive method and easy to perform. Using this method, low levels of MDR1 gene expression could be detected in 24% of the patients with lung cancer.

Constructing Competitive Reverse Transcription Polymerize Chain Reaction Inter-Reference of PC mRNA by Intron Approach

Inter-reference of competitive reverse transcription polymerase chain reaction (RT-PCR)was constructed by intron method to detect the change of PC mRNA level in the pathway ofcarbohydrate metabolism. The experiment based on the principle that 81bp intron sequencewas deleted in PC mRNA compared with PC DNA sequence. The 466bp competitive DNA templaterecombinant plasmid of PC mRNA was successfully built by a pair of primer and was clonedonce, PC DNA and PC mRNA could be inter-referred each other. The intron approach used inthe experiment has broken through the traditional method of constructing competitivetemplate.

Establishment of a Real-time Fluorescent Quantitative RTPCR Method for Detecting NP Gene of Class Ⅰ Newcastle Disease Virus(NDV)

Newcastle disease( ND) is one of the most serious infectious diseases that infect the poultry industry.There is only one serotype of Newcastle disease virus( NDV),but NDVs can be divided into two distinct classes( class Ⅰ,and class Ⅱ) according to their genetic relationship.To develop a method for rapid quantitative detection of class Ⅰ NDV,a pair of primers and a TaqM an probe were designed and synthesized according to the conservative sequence of NP gene of class Ⅰ NDV.The positive recombinant plasmid harboring NP gene of JS-18-05 isolate was used as a positive template to establish the standard curve.A real-time fluorescent quantitative RT-PCR method was established for rapid detection of class Ⅰ NDV with strong specificity,high sensitivity and good repeatability.The established method exhibited a good linear relationship within the concentration of 102 to 108 copies of NDV,by which 1 μl of 10 copy of NDV nucleic acid could be detected in the initial template.Compared with conventional virus isolation methods,the established method had similar sensitivity and led to the same results in detecting33 class Ⅰ,class Ⅱ NDV isolates.The study provided the basis for rapid quantitative detection of class Ⅰ NDVs and further clarification of their pathogenicity and pathogenic mechanism in poultry.

定量RT-PCR及其在植物学研究中的应用

定量RT-PCR(Quantitative reverse transcriptase-PCR)是在反转录和定量PCR的基础上发展起来的一种特异性检测基因表达的技术。主要包括相对定量RT-PCR(Relative quantitative RT-PCR)、竞争性定量RT-PCR(Competitive quan-titative RT-PCR)、比较定量RT-PCR(Comparative quantitative RT-PCR)和实时定量RT-PCR(Real time quantitative RT-PCR)四种。目前定量RT-PCR在植物学研究中的应用越来越广泛,如植物营养学研究、植物发育学研究、植物抗逆机理研究、转基因植物的检测、病原菌的检测、植物与微生物互作机理研究、植物抗病性检测等方面。本文综述了定量RT-PCR的原理及在植物学中的应用。

应用内含子法构建PC基因mRNA竞争RT-PCR内参照

运用PC基因mRNA与PC基因DNA相比缺少1个81bp内含子序列的基本原理,应用PCR技术和生物工程原理,通过1对引物,进行1次克隆,成功构建了PC基因mRNA的466bp竞争DNA模板重组质粒,PC基因mRNA与PC基因DNA可以互为内参照。为应用逆转录-聚合酶链反应(RT-PCR)检测糖代谢过程中PC基因mRNA水平奠定方法学基础。

猪IFN-γ mRNA竞争性RT-PCR定量检测方法的建立

无菌分离的猪外周血单个核细胞(PBMC),经ConA体外刺激培养15 h后提取细胞总RNA。以此总RNA为模板,采用RT-PCR技术扩增到了435 bp的IFN-γ基因。把扩增到的IFN-γ基因与pMD18-T载体连接,构建了pMD-IFN435重组质粒。用另一对引物对重组质粒pMD-IFN435内部进行PCR扩增,得到了257 bp(含PstⅠ酶切位点)的基因片段,将此基因片段连接到pMD18-T载体上构建了pMD-IFN257重组质粒。将pMD-IFN257双酶切(PstⅠ+SalⅠ)后回收的目的片段与pMD-IFN435双酶切(PstⅠ+SalⅠ)后回收的目的片段连接,得到了含有367bp目的片段的重组质粒pMD-IFN367,即内标准DNA模板。以定量后的pMD-IFN367与2倍梯度稀释的pMD-IFN435进行竞争PCR扩增,建立了能够准确、方便定量检测猪IFN-γmRNA的标准竞争曲线的线性回归方程(y=0.414x-1.864)。

竞争性RT-PCR法及对大肠杆菌acrA基因mRNA表达水平的定量研究

建立了用于检测大肠杆菌(Escherichia coli)ATCC25922的acrA基因mRNA表达水平的定量竞争性RT-PCR(QC-RT-PCR)体系。PCR合成目标片段的突变型片段(321bp)作为内标准模板(Internal standard,IS),与目标片段一致的片段(389bp)作为目标模板(Target standard,TS),优化两种模板共扩增体系;梯度稀释IS与等量大肠杆菌cDNA样本共扩增,扫描电泳条带,软件分析数据。结果表明,引物设计合适,以IS和TS为模板实现共扩增,产物(321bp和389bp)通过1.5%琼脂糖凝胶电泳有效分离;梯度稀释IS与cDNA共扩增产物出现亮度梯度电泳条带;获得一元回归曲线y=-0.345+0.097x(相关系数r=0.959,标准差s=0.05997)。该研究成功构建内标准模板,优化的共扩增PCR体系实现了对大肠杆菌ATCC25922中acrA基因mRNA表达水平的检测,具有简便、高效、敏感度高等优点。

猪IL-12p40竞争定量RT-PCR检测方法的建立

根据GenBank中猪IL-12p40的序列设计引物,采用RT-PCR技术扩增377 bp的部分基因片段,并克隆到pGEM-T Easy载体中,构建成含IL-12p40部分基因片段的重组质粒.利用反向PCR技术构建与扩增377 bp片段共用同一对引物但扩增255 bp片段的竞争重组子.通过重组质粒与竞争重组子竞争定量PCR方法(qc-PCR),建立了猪IL-12p40的标准竞争曲线和直线回归方程.

猪TNF-α竞争定量RT-PCR标准曲线的建立

根据GenBank中猪TNF-α的序列设计引物,采用RT-PCR技术扩增402 bp的部分基因片段,并克隆到pGEM-T载体中,构建成含TNF-α部分基因片段的重组质粒.利用反向PCR技术构建与扩增402 bp片断共用同一对引物,但缺失137 bp的竞争重组子.通过重组质粒与竞争重组子竞争定量PCR方法(qc-PCR),建立猪TNF-α的标准竞争曲线和直线回归方程.

定量检测CCL20的竞争性内参照RT-PCR的建立及其初步应用

目的 建立检测趋化因子CC亚家族配体2 0 (CCL2 0 )表达水平的内参照定量逆转录聚合酶链反应(RT PCR)方法。方法 将人CCL2 0编码基因克隆到pBs ΔANK质粒中(PAL 2 ) ,将一4 2bp的外源核苷酸片断插入到上述重组质粒的CCL2 0中间,构建内参照质粒PAL- 2 - IS。在该定量系统中以PAL- 2 -IS和PAL- 2为模板,用CCL2 0的特异性引物扩增,根据扩增出的两个不同大小的条带的光密度扫描值对CCL2 0进行相对定量。结果 将PAL -2与已知不同系列浓度的PAL- 2 - IS以内参照竞争定量RT- PCR共扩增定量PAL- 2浓度,PAL- 2计算浓度与实际浓度无差异(P >0 .0 5 )。在同一细胞数量水平(10 5数量级) ,内参照竞争定量RT- PCR检测表明:CCL2 0在L0 2、HepG2、Hepal、Hepa3中表达水平高于Hepa2 ,而在HepG2 .2 .15中最低。结论 建立了检测CCL2 0表达水平的内参照定量RT -PCR方法,该方法可用于细胞中CCL2 0不同表达水平的检测。

猪IFN-γ竞争定量RT-PCR标准曲线的建立

根据GenBank中猪IFN-γ的序列设计引物,采用RT-PCR技术扩增380bp的部分基因片段,并克隆到pGEM-TEasy载体中,构建成含IFN-γ部分基因片段的重组质粒。利用反向PCR技术构建和扩增380 bp片段共用同一对引物但缺失163 bp的竞争重组子。通过重组质粒与竞争重组子,建立猪IFN-γ的标准竞争曲线和直线回归方程,为进一步检测IFN-γ的mRNA的转录水平变化奠定基础。

定量竞争性RT-PCR检测耐受山梨酸钾的大肠杆菌菌株中acrA-mRNA表达水平

采用含有亚抑菌浓度(1/2×MIC)山梨酸钾的LB琼脂平板连续传代的方法,对大肠杆菌(Escherichia coli)进行诱导,获得具有一定耐受性的大肠杆菌菌株;通过定量竞争性RT-PCR检测诱导后的各个菌株与未经诱导的各个菌株的acrA-mRNA的表达水平。结果表明,各个菌株经过含有亚抑菌浓度山梨酸钾的LB琼脂连续培养10代后获得的诱导菌株,与普通LB琼脂平板连续培养10代后获得的菌株相比可以耐受更高浓度的山梨酸钾,并且acrA-mRNA表达水平在诱导后的各个菌株中比未经诱导的各个菌株均有一定程度的提高。说明大肠杆菌主动外排系统AcrAB-TolC中acrA基因的表达水平提高可能与大肠杆菌对山梨酸钾的耐受程度增加有一定相关性。

猪IL-18 mRNA定量RT-PCR检测方法的建立

根据GenBank中猪白介素(IL)-18基因序列,设计1对引物,用RT-PCR技术从猪肺泡巨噬细胞总RNA中扩增出其411 bp cDNA片段,将其与pGEM-T Easy载体连接,经转化、筛选阳性克隆、酶切与测序鉴定后,构建出含猪IL-18 cDNA部分片段的重组质粒。后用反向PCR技术构建出与扩增411 bp片段共用同1对引物,但缺失174 bp的竞争重组质粒。通过上述2种质粒的竞争PCR方法,建立了猪IL-18 mRNA的标准竞争曲线,得到其直线回归方程^y=0.583 2x-2.903 4(R2=0.9898)。

Establishment and Application of Digital RT-PCR Assay for Detection of Avian Influenza Virus H9 Subtype

A digital RT-PCR method for rapid detection of H9 subtype influenza was established by comparing the two methods of digital RT-PCR and real-time quantitative RT-PCR. The sensitivity, specificity and reproducibility of the two methods for H9 were determined by gradient dilution using the same pair of primers and probes. Both methods were able to detect 104 times diluted H9 pathogens, while digital RT-PCR could detect H9 in single droplets, and its sensitivity was higher than real-time quantitative RT-PCR. At the same time, the specificities of both methods were very strong, with no amplification reactions for H3N2, H4N2, H6N2. The reproducibility of the two methods were also good. Digital RT-PCR has a higher sensitivity than real-time quantitative RT-PCR and could play an important role in the rapid detection of H9 subtype influenza virus.

The application of sequence specific primer and RT-PCR to LRRK2 gene polymorphism typing

Objective:To establish a new detecting method for disease susceptibility loci R1628P and G2385R of Parkinson’s disease(PD)related gene LRRK2.Methods:Sequence specific primers were designed to make a genotyping of DNA markers with known genotypes by use of quantitative fluorescence real-time PCR(RT-PCR).100 cases of PD samples with unknown genotypes were tested,and verified by use of polymerase chain reaction linked restriction fragment length polymorphism(PCR-RLFP).Results:The genotyping results of DNA markers proved to be correct,and 100 cases of samples to be tested had a completely consistent genotyping result with PCR-RLFP genotyping result.Conclusions:Sequence specific primer and quantitative fluorescence RT-PCR can successfully make a genotyping for disease susceptibility loci R1628P and G2385R of LRRK2.

基于出行成本的定制公交竞争力研究

作为城市公共交通的一种补充形式,定制公交可以提供高品质服务,有利于通勤出行,能够缓解城市早晚高峰交通压力,满足多样性出行需求。利用问卷调查,考虑经济性、便捷性、快速性、舒适性、准时性、安全性等服务特性对出行成本的影响,探讨基于出行成本的量化模型。以北京市为例,在路线长度、接驳距离、道路拥堵程度3种情景下,探讨定制公交相对常规公交、城市轨道交通、出租车及私家车的出行成本竞争力。结果表明,定制公交在各情景下的出行成本均为最低,在通勤半径内偏向于中长距离出行,对于常规公交在便捷舒适方面优势较大;与城市轨道交通的出行成本相差最小;在经济性方面相比出租车、私家车竞争力较大。