Fluorescence-based Multiplex PCR-Single Strand Conformation Polymorphism (SSCP) Analysis of 16S Ribosomal DNA Using Capillary Electrophoresis

The rRNA genetic locus is found in all prokaryotic organisms, and is highly conservative, although its relatively stable variations are found frequently in different bacteria. The utility of this locus as a taxonomic and phylogenetic tool has been reported widely. This study, aimed at 16S rRNA gene (16S rDNA) and with the help of biomolecular methods, attempted to achieve the goal of rapid identification of common pathogens. In this study, 333 clinical isolated pathogenic bacteria were collected. Two pairs of primers were chosen and labeled with different fluorescent dyes and then used to amplify the genomic DNA extracted from bacteria. The PCR products were then detected by capillary electrophoresis-single strand conformation polymorphism (CE-SSCP). In order to pursue higher resolution and peak-separation effect, a high efficient separating medium, liner polyacrylamidedel (LPA), was put to use in this study. Finally, every bacteria colony generated distinct patterns from each other, which were easily to be used for identification. These results indicated that PCR-CE-SSCP was a rapid identification method for bacterial identification, with the aspects of high efficiency and high precision. Compared with traditional method, this technology is of great utility for clinical use especially for its high sensitivity.

Poly(ADP-ribose) polymerase-1 gene polymorphism in various Chinese nationalities

Poly （ADP-ribose） polymerase-1 （PARP-1） can exacerbate ischemic brain injury and lessen ischemic neuronal death, which may be associated with PARP-1 polymorphisms. The present study investigated human PARP-1 gene polymorphisms in various Chinese nationalities, the results of which could potentially help in the treatment and prevention of neurologic diseases. Genetic polymorphisms of seven exons in the PARP-1 gene, in 898 Chinese Han, Buyi, Shui, Miao, and Zhuang subjects, were investigated by PCR-single-strand conformation polymorphism. A single-strand conformation polymorphism variant in exons 12, 13, 16, and 17 of the PARP-1 gene was identified in 148 people, with two stationary bands showing three degenerative single strands. Results showed that the PARP-1 gene polymorphisms exist in various nationalities, and may act as a biomarker for susceptibility to disease.

Interleukin-10 promoter polymorphisms in patients with hepatitis B virus infection or hepatocellular carcinoma in Chinese Han ethnic population

BACKGROUND: Since single nucleotide polymorphisms (SNPs) can serve as gene markers, polymorphism profiles may help scientists to identify the full collection of genes that contribute to the development of complex diseases such as cancer. The distribution of interleukin-10 (IL-10) promoter polymorphisms in Chinese Han ethnic patients with hepatitis B virus (HBV) infection and hepatocellular carcinoma (HCC) was investigated in this study. METHODS: The polymorphisms of IL-10 promoter region were detected by pulymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and sequencing. Sixty-six health controls, 42 patients with HBV infection, 30 HCC patients, and cell line SMMC-7721 were examined this way. RESULTS: Polyrnorphisms of T/C or T/N on-872 site occurred frequently in Han ethnic population. Pulyrnorphisms were detected in HBV and HCC patients and cell line SMMC-7721. The hotspot among the pulymorphisms was inserting base A between-1058 and-1057. CONCLUSION: Polymorphisms of IL-10 promoter in HBV and HCC patients may be associated with HBV infection and HCC development.

Single nucleotide polymorphisms in the CDH17 gene of colorectal carcinoma

AIM:To investigate the relationship between c.343A>G and c.2216A>C polymorphism sites in the CDH17 gene and colorectal carcinoma.METHODS:Ninety-three non-consanguineous colorectal carcinoma patients admitted to the Department of Oncology at the First Affiliated Hospital of Zhengzhou University were included in this study.Ninety-three peripheral venous blood samples,of approximately one milliliter from each patient,were collected betweenDecember 2009 and August 2010.The genomic DNA of these peripheral venous blood samples were extracted and purified using a Fermentas Genomic DNA Purification Kit(Fermentas,CA) according to the manufacturer' s protocol.The single nucleotide polymorphisms(SNPs) of the liver-intestine cadherin(CDH17) gene c.343A>G and c.2216A>C were determined by the polymerase chain reaction-single strand conformation polymorphism method(PCR-SSCP) in 93 peripheral venous blood samples from patients suffering with colorectal carcinoma.Typical samples that showed different migration bands in SSCP were confirmed by sequencing.Directed DNA sequencing was used to check the correctness of the genotype results from the PCR-SSCP method.RESULTS:There was a significant association between the c.2216 A>C SNPs of the CDH17 gene and the tumor-node-metastasis(TNM) grade,as well as with lymph node status,in 93 peripheral venous blood samples from colorectal carcinoma patients.The genotype frequencies of A/C,A/A,and C/C were 12.90%,33.33% and 53.76%,respectively.There was a significant correlation between lymph node metastasis,TNM grade,and the genotype distribution(P < 0.05).The C/C genotype raised the risk of lymph node metastasis and the TNM grade.There was a significant difference in the TNM grade and lymph node metastasis between the A/A and C/C genotypes(P = 0.003 and P = 0.013,respectively).Patients with colorectal carcinoma carrying the C allele tended to have a higher risk of lymph node metastasis and have a higher TNM grade.The difference between the TNM grades,as well as the lymph node metastasis of the two alleles,was statistically significant(P < 0.01).CONCLUSION:The SNPs of the CDH17 gene c.2216 A>C might be clinically important in the prognosis of colorectal carcinoma.

Application of PCR-SSCP in detecting rpoB drug resistant gene polymorphism of M. tuberculosis L-form from pneumoconiosis patients with tuberculosis

Objective: To study the relationship between the polymorphism of drug resistant gene rpoB and drug resistance against rifampicin(RFP) of M. tuberculosis L-forms, and to evaluate its clinical application. Methods: A total of 52 clinical isolated strains of M. tuberculosis L-forms were collected. rpoB gene polymorphism was analyzed by polymerase chain reaction and single-strand conformation polymorphism (PCR-SSCP) and conventional antimicrobial susceptibility test (AST). Their results were compared. Results: AST results showed that 38 of 52 clinical isolated strains were drug resistance (73.08％),while PCR-SSCP indicated 65.38％ (32/52) rpoB gene polymorphism. There was no statistic significance(χ2= 2.4914) between the 2 methods. Conclusion:Combined the application of PCR-SSCP with AST in detecting rpoB drug resistant gene polymorphism of M. tuberculosis L-form from pneumoconiosis patients with tuberculosis may have advantages at earlier diagnosis and guidance of clinical medications.

中国家驴TYRP1基因第二内含子多态性分析

为了探究TYRP1基因对中国家驴毛色的影响,试验采集410只不同毛色中国家驴的血液样本,采用聚合酶链式反应及单链构象多态性(polymerase chain reaction and single-strand conformation polymorphism, PCR-SSCP)方法检测中国家驴TYRP1基因第二内含子中的单核苷酸多态性(single nucleotide polymorphism, SNP)位点,对不同毛色中国家驴个体进行基因分型,并计算基因型频率和等位基因频率,分析TYRP1基因第二内含子多态性与中国家驴不同毛色之间的关系。结果表明:在中国家驴TYRP1基因第二内含子中检测到1个SNP位点(g.1 702A→G),该位点存在AA、AG、GG三种基因型;乌头、黑三粉、青三粉、灰三粉、白色和白化家驴的优势等位基因均为A。乌头、黑三粉和青三粉均为AA基因型频率最高,GG基因型频率最低;灰三粉为AA基因型频率最高,AG基因型频率最低(0)。在乌头、黑三粉、青三粉、灰三粉家驴中,AA基因型频率为灰三粉最高,然后依次为青三粉、黑三粉和乌头;以黑毛色为主色调的家驴(乌头、黑三粉、青三粉)GG基因型频率低于以灰毛色为主色调的家驴(灰三粉),有白毛混杂的黑三粉和青三粉的GG基因型频率低于纯黑的乌头。样本中的白色家驴和白化家驴各有2头,其基因型均为AA纯合子。说明随着中国家驴黑色被毛比例的增加,TYRP1基因g.1 702A→G位点的AA基因型频率逐渐降低,推测该位点可能与中国家驴毛色性状有关。

结核分枝杆菌耐乙胺丁醇分子机制的研究

目的 了解结核分枝杆菌耐乙胺丁醇分子机制 ,建立快速分子药敏试验方法。方法 通过聚合酶链反应 (PCR) -单链构象多态性 (SSCP)、PCR-限制性片段长度多态性 (RFL P)和 PCR-直接测序 (DS)技术分析 10 7株结核分枝杆菌临床分离株 emb B基因。结果 以 H3 7Rv标准株为对照 ,10 7株结核分枝杆菌临床分离株的 16 S r DNA SSCP电泳图谱均与结核分枝杆菌标准相同。 38株药物敏感株的 emb B基因、SSCP均泳动正常 ,RFL P和 DS分析与对照株相同。 6 9株耐乙胺丁醇 (EMB)分离株中 ,2 5株 (36 .2 % ) emb B基因 SSCP泳动异常 ;8株 RFL P分析异常 ;DS分析 2 5株均为 30 6位密码子突变 ,其中 1株合并有 2 74位 CGC→ CCC突变 ,其 EMB MICs均≥ 2 0 μg/ml;8株为 30 6位 ATG→ATA或 ATT突变 ,17株为 ATG→GTG或 CTG突变 ,后者 EMB MICs均≥ 30μg/ml。结论 部分结核分枝杆菌耐乙胺丁醇是由于其 emb B基因 (尤其是 30 6位密码子 )突变所致 ,PCR- SSCP技术可能成为测定部分结核分枝杆菌乙胺丁醇耐药基因型的简便。

藏绵羊DQA1基因多态性分析

【目的】研究藏绵羊DQA1基因多态性,确定其等位基因数、核苷酸多态位点、氨基酸多态位点及各等位基因间的遗传关系,同时分析其进化意义。【方法】采用PCR-SSCP方法检测了900只藏绵羊DQA1基因第2外显子多态性;克隆、测序群体内变异产生的各等位基因序列,并分析序列数据。【结果】发现了17个DQA1的等位基因,包括缺失的1种基因,其中5个为发现的新等位基因。16个单倍型序列中发现56个核苷酸多态位点,27个氨基酸多态位点。【结论】藏绵羊DQA1基因第2外显子具有丰富的多态性,群体中可能蕴藏着更多的遗传资源;藏绵羊DQA1基因最初可能是由2个等位基因突变分化成两大类等位基因的;藏绵羊DQA1基因第2外显子序列与牛的DQA1基因第2外显子序列具有较高的同源性,预示绵羊和牛的DQA1基因最早可能来源于它们分歧以前的共同祖先原始序列;DQA1基因在与其相关的特定抗原刺激下发生的免疫应答反应在绵羊和牛上具有相似性;新等位基因C的139位发现了1个新的核苷酸突变位点(A/G),属同义突变;5个新发现的DQA1等位基因遗传关系较近,可能由同一等位基因突变产生。

DNA芯片鉴定分枝杆菌的研究

目的评价DNA芯片技术鉴定分枝杆菌菌种的应用价值,为临床实际应用提供科学依据。方法收集以BACTECMGIT960从结核病患者分离到的分枝杆菌阳性培养物,以传统分枝杆菌菌种鉴定方法为对照,应用DNA芯片技术进行菌种鉴定。结果两种方法鉴定结果一致和基本一致共112株,吻合率为83.6%(112/134),包括胞内分枝杆菌50株,龟分枝杆菌14株,结核分枝杆菌14株,戈登分枝杆菌9株,鸟分枝杆菌7株,偶然分枝杆菌7株,堪、瘰、胃和猿分枝杆菌6株,土分枝杆菌和海分枝杆菌各1株;未分类NTM3株。应用DNA芯片未能分类的17株分枝杆菌中,传统方法分别鉴定为戈登分枝杆菌5株、胞内分枝杆菌3株、龟分枝杆菌2株、蟾分枝杆菌、耻垢分枝杆菌和浅黄分枝杆菌各1株,未分类NTM4株。结论用DNA芯片检测技术,可以简便、快速、灵敏、特异地将大多数分枝杆菌鉴定到种,但有待进一步完善。

毛细管电泳-单链构象多态性分析检测K-ras基因突变

K ras癌基因的点突变在结直肠癌的发生起重要作用。以异丙醇为聚合反应链转移剂,水相法合成 特性粘度为0.70×10-3m3/kg,分子量为6.5×104的低粘度短链线性聚丙烯酰胺。以6%线性聚丙烯酰胺为 筛分介质,分离温度27℃,分离电压9kV为电泳条件,建立了检测K ras基因突变的毛细管电泳 单链构象多 态性方法。利用该方法检测36例结直肠癌患者肿瘤组织,发现12例K ras基因突变。结果表明:该方法具有 快速、高灵敏的优点,为大规模进行结直肠肿瘤的早期诊断提供了可靠方法。

基因hMSH2、hMLH1与p53突变型在散发性大肠癌患者的表达

目的:探讨错配修复基因hMSH2、hMLH1与p53突变型在散发性大肠癌发生中的作用。方法:用聚合酶链反应和单链DNA多态性分析(PCR-SSCP)对45例散发性大肠癌患者肿瘤组织及正常组织基因hMSH2、hMLH1、p53进行检测。结果:45例散发性大肠癌患者中,发生hMSH2、hMLH1、p53基因突变分别为2、6、22例,分别占4.44%、13.33%和48.89%。hMLH1、hMSH2基因在突变型p53患者中的突变率为27.27%明显高于在p53未发生突变的患者中的突变率8.69%(P<0.05)。结论:一定比例的散发性大肠癌患者中存在MMR基因缺陷,其中hMLH1所起的作用大于hMSH2,散发性大肠癌中MMR基因突变与p53突变密切相关。

PCR－SSCP分析实践

介绍了一种在一般实验室都能使用的适用于ＳＳＣＰ分析电泳的改良方法．并对如何设计引物、选择ＰＣＲ条件和分析结果进行了讨论．

PCR-SSCP及克隆测序法研究燃煤型砷中毒患者p53基因突变与皮肤癌的关系

[目的 ]分析燃煤型砷中毒患者外周血中p5 3基因突变情况。 [方法 ]采用聚合酶链反应 单链构象多态性(PCR -SSCP)技术对 60例燃煤型砷中毒患者外周血中p5 3基因 5～ 8外显子的突变情况进行初筛 ,并进一步克隆测序 ,以确定突变位点及类型。 [结果 ]癌变组p5 3基因突变率为 3 0 % ( 3 /10 ) ;癌前组为 16.67% ( 2 /12 ) ;一般病变组未发现突变 ( 0 /3 8)。对筛查出来的 5例突变阳性者进行克隆测序 ,突变均为G :C→A :T的转换 ,分别位于密码子 14 3、14 6及 15 1。[结论 ]燃煤型砷中毒患者外周血中p5 3基因突变的检出 。

喹乙醇致线粒体DNA基因损伤的SSCP分析

为研究喹乙醇对mtDNA基因的致突变效应,以1日龄的健康艾维因商品代肉鸡为试材,运用改进的碱变性法提取肝脏的mtDNA,设计4对引物扩增mtDNA的tRNALeu(UUR)t、RNAIlet、RNALys、ATPase8 4个基因,同时运用SSCP技术对扩增产物进行突变分析。结果表明:喹乙醇处理Ⅵ组tRNALeu(UUR)有突变发生,序列测定结果表明该突变为4 007位的C→A点突变,其他各组的tRNALeu(UUR)基因无任何突变发生。该结果提示喹乙醇中毒可以导致mtDNA tRNALeu(UUR)基因突变。

鲁道夫对盲囊线虫rDNAITS遗传标记的研究

本实验通过对鲁道夫对盲囊线虫(Contracaecumrudolphii)rDNA的第一及第二内转录间隔区(ITS- 1及ITS -2 )进行PCR扩增、PCR SSCP分析及序列分析,以明确ITS 1及ITS 2是否可作为C. rudolphii分子分类的遗传标记。结果发现:C .rudolphiirDNAITS序列存在种间差异,并且差异显著,但是种内序列一致,没有差异。本实验证明C rudolphii确为由两个种(C .rudolphiiA和C rudolphiiB)组成的复合种,ITS -1及ITS- 2可作为两个姊妹种的遗传标志。

聚合酶链反应-单链构象多态性技术快速检测脑脊液中病原菌的初步研究

目的探讨聚合酶链反应单链构象多态性(PCR-SSCP)快速检测病原菌的可行性,初步评价该法检测脑脊液中病原菌的意义。方法设计通用引物对不同细菌进行PCR-SSCP,同时利用该法直接检测脑脊液中的病原菌,并与细菌培养比较。结果不同细菌的SSCP图谱呈多态性可相互区别;标准菌株和临床菌株的SSCP图谱完全一致;6份化脑的脑脊液,PCR-SSCP检出5份有细菌,而细菌培养只检出1份有细菌;7份病脑两种方法均未检出细菌。结论PCR-SSCP技术可快速、敏感地检测脑脊液中的病原菌。

四川地区结核分枝杆菌喹诺酮耐药基因突变研究

目的 研究结核分枝杆菌耐喹诺酮类药物的分子机制 ,探索四川地区耐喹诺酮结核分枝杆菌临床分离株的耐药基因突变特征。方法 采用绝对浓度法检测结核分枝杆菌临床分离株的最小抑菌浓度 (MIC) ,再通过聚合酶链反应 -单链构象多态性 (PCR- SSCP)和直接测序检测结核分枝杆菌耐喹诺酮类药物临床分离株 gyr A耐药决定区 (QRDR)突变 ,并和标准株 H 37Rv比较。结果 6 8株临床分离株中 ,14株喹诺酮药物敏感株和 8株低耐药株未发现 gyr A耐药决定区基因突变 ,2 5株高耐药株、11株低耐药株和 10株药物敏感株检测到 gyr A基因突变 ,高耐药株突变率为 10 0 % ,低耐药株突变率为 5 8% ,敏感株突变率为 4 2 % ,总的突变率为 6 8%。根据 SSCP条带 ,gyr A突变可分成 4种类型 ,测序发现分别为 Ser95 Thr、Asp94 Gly、Ala90 Val、Ala83Val突变。结论 结核分枝杆菌耐喹诺酮与 gyr A基因突变密切相关 ,gyr A基因突变是耐喹诺酮结核分枝杆菌耐药性的主要分子机制。

厌氧活性污泥微生物群落的SSCP分析条件优化

针对厌氧活性污泥微生物群落结构复杂,群落中相似基因序列较多等特点,对影响单链构像多态性(SSCP)图谱分辨率的电泳温度、甘油、交联度和影响聚合酶链式反应(PCR扩增)的BSA等因素进行了实验研究。结果表明,选择细菌16SrDNAV3区(约200bp)PCR扩增片段,在凝胶浓度为12%、丙烯酰胺与双丙烯酰胺质量比为49:1、无甘油等条件下,恒压260V,4℃电泳17h,可获得较为理想的SSCP图谱;BSA的使用,有助于降低样品中残留腐殖酸和棕黄酸等杂质对PCR扩增的抑制作用,提高SSCP图谱的分辨率和可读性,为厌氧活性污泥细菌群落结构解析提供了有效手段。

结核分支杆菌异烟肼耐药的分子机制及其快速鉴定

目的探讨快速检测结核分支杆菌异烟肼耐药的分子药敏方法。方法用聚合酶链反应-单链构象多态性(PCR-SSCP)检测了20株异烟肼(INH)敏感的结核杆菌临床分离株,20株INH耐药株的katG基因,随后用SSCP方法鉴定扩增产物有无突变,以结核分支杆菌H37RV作对照。结果所有INH敏感株均观察到katG基因扩增产物,20株INH耐药株中19株观察到katG基因扩增产物。以H37RV标准株为对照,20株敏感株SSCP带谱与对照相同;19株INH耐药株中8株与对照相同,11株有不同程度的差异,INH耐药katG基因突变或缺失的阳性率为60%。结论多数结核分支杆菌耐INH是由于其katG基因突变所致,用PCR-SSCP筛选突变株可达到快速检测结核分支杆菌INH耐药的目的。

胃癌组织中PTEN基因突变的研究

目的:研究抑癌基因PTEN突变高发区外显子5穴exon5雪和外显子8穴exon8雪在胃癌组织中的突变频率,探讨其突变与胃癌病理组织学分级和临床病理分期的关系。方法:应用聚合酶链反应鄄单链构像多态性分析(PCR鄄SSCP)方法检测胃癌组织和相应癌旁正常组织中PTEN基因的突变,并对突变样本的PCR产物进行测序分析。结果:42例胃癌组织中检测到PTEN基因突变3例,其中exon5突变1例,exon8突变2例,突变率为7.14%(3/42);42例相应癌旁正常组织未检测到突变,二者差异无统计学意义(P>0.05)。对42例胃癌进行组织学分级,低分化腺癌突变率为12.00%(3/25),中、高分化腺癌突变率为0(0/17),二者差异无统计学意义(P>0.05)。对42例胃癌临床病理分期,Ⅰ、Ⅱ期突变率为5.88%(1/17)熏Ⅲ、Ⅳ期突变率为8.00%(2/25),二者差异无统计学意义(P>0.05)。结论:胃癌组织中存在PTEN基因突变;主要发生在低分化腺癌中;而PTEN基因突变与胃癌病理组织学分级和临床病理分期之间无明显相关性。