Speciation of human microsporidia by polymerase chain reaction single-strand conformation polymorphism.

We describe the application of single-strand conformation polymorphism (SSCP) analysis to the speciation of human microsporidia after polymerase chain reaction (PCR) amplification with the panmicrosporidian primers PMP1 and PMP2. We compared the DNA extracted and amplified from different genotypes or isolates of Enterocytozoon bieneusi, Encephalitozoon cuniculi, E. hellem, and E. intestinalis plus an isolate of Vittaforma corneae. The PCR-SSCP, when performed at 20 degrees C, generated 2 bands in distinctive, reproducible patterns in polyacrylamide gels for each species of microsporidia tested, regardless of genotype or isolate. We found PCR-SSCP to be an easy and reproducible method for speciation of human microsporidia when the primer pair PMP1 and PMP2 is used.     

Novel DNA amplification on chromosomes 2p25.3 and 7q11.23 in cholangiocarcinoma identified by arbitrarily primed polymerase chain reaction

Purpose: To detect and characterize amplified DNA sequences in cholangiocarcinoma (CCA). Patients and methods: We extracted DNA from tumor and corresponding normal tissues of 30 patients with CCA and amplified with 30 random ten-mer arbitrary primers by the arbitrarily primed polymerase chain reaction (AP-PCR) technique. Results: Our results showed gains of genomic sequences at high frequency. Using the AX-11 arbitrary primer, we determined an amplified DNA fragment occurred frequently in the tumors analyzed. The DNA fragment was isolated and identified as two sequences mapped to chromosomes 2p25.3 and 7q11.23. Specific primers were designed employing these sequences and used for detecting amplification by real-time quantitative PCR. The amplification of the DNA sequences on chromosomes 2p25.3 and 7q11.23 was detected in 10 (33%) and 6 (20%) cases, respectively. Thirteen (43%) cases showed amplification on both or one of the chromosomes. In addition, amplification of the DNA on chromosome 2p25.3 was predominantly observed in poorly differentiated tumors. Conclusions: Our findings suggest that the novel amplified DNA on chromosomal regions at 2p25.3 and 7q11.23 might be involved in the development and progression of CCA.     

Detection of specific DNA sequences by fluorescence amplification: a color complementation assay.

We have developed a color complementation assay that allows rapid screening of specific genomic DNA sequences. It is based on the simultaneous amplification of two or more DNA segments with fluorescent oligonucleotide primers such that the generation of a color, or combination of colors, can be visualized and used for diagnosis. Color complementation assay obviates the need for gel electrophoresis and has been applied to the detection of a large and small gene deletion, a chromosomal translocation, an infectious agent, and a single-base substitution. DNA amplification with fluorescent oligonucleotide primers has also been used to multiplex and discriminate five different amplified DNA loci simultaneously. Each primer set is conjugated to a different dye, and the fluorescence of each dye respective to its amplified DNA locus is scored on a fluorometer. This method is valuable for DNA diagnostics of genetic, acquired, and infectious diseases, as well as in DNA forensics. It also lends itself to complete automation.     

Genotyping of Chlamydia trachomatis from a trachoma-endemic village in the Gambia by a nested polymerase chain reaction: identification of strain variants.

Direct amplification of the major outer membrane protein (MOMP) gene by polymerase chain reaction (PCR) was used to identify Chlamydia trachomatis in eye swabs from clinically active cases of endemic trachoma in a Gambian village. Chlamydial DNA was detected in 51% of 96 subjects with clinically active disease and in 5% of 37 clinically negative individuals. The PCR detection was combined with typing, using nested primers to variable sequences (VS) 1, 2, and 4 of the MOMP genes to distinguish between trachoma genotypes A, B, and C, respectively. Genotypes A and B were detected in the village, with some individuals harboring both genotypes within the same eye. DNA sequencing revealed strain variants of both genotypes. Typing of genotype and strain variants is now in progress to study trachoma transmission within the village.     

乙型肝炎病毒基因型(A-F)多引物PCR分型法的初步建立

目的：建立一种简便易行的乙型肝炎病毒基因分型方法（只需PCR）。方法:对GenBank中查获的114例HBV全序列进行比较分析，找出每种基因型相对于其他5种基因型的独特序列，并根据这些独特序列设计出6对分别针对A－F基因型的特异引物。用这6对引物分别对标本进行PCR，根据阳性结果判断出标本的基因型。进一步简化该方法，用多引物对PCR法（PCR with several primer sets in a single tube,Multiplex PCR)将B，C，D3种基因型的特异引物混合进行PCR，根据扩增片断的大小判断基因型。用此方法对已鉴定的B，C，D型标本进行比较和验证。结果：单引物对PCR与多引物对PCR的分型结果一致，且与以前用PCR－RFLP法的分型结果一致。结论：用多引物对PCR分型法准确易行，灵敏性高，便于推广应用。     

乙型肝炎病毒逆向点杂交基因分型法建立及应用

目的 利用逆向点杂交技术建立乙型肝炎病毒(HBV)基因分型新方法，通过对HBV DNA阳性血清抽样标本进行基因分型，了解佛山地区HBV基因型分布状态。方法 以HBV基因组的X区序列为主设计分型引物与探针，将活性氨基标记的探针依次固定在尼龙膜上，制成检测膜条。用标记生物素的引物进行HBV DNA扩增，将扩增产物与检测膜条杂交，以POD与TMB显色，判断基因分型结果，通过与基因测序结果比较确定新方法的有效性。从佛山地区HBVDNA阳性患者血清中随机抽取300份，用新建方法进行HBV基因分型检测。结果 新建HBV逆向点杂交基因分型方法可对拷贝数在10^3～10^9／ml之间的300份HBV DNA阳性抽检血清进行基因分型，发现B型147例，占49.0％；C型136例，占45．3％；D型1例，占0．3％；B、C混合型12例，占4．0％；C、D混合型4例，占1．3％；未发现A、E和F型。新方法基因分型结果与测序结果一致。结论 利用逆向点杂交技术可以准确有效和简便经济的进行HBV基因分型，适用于临床检测与流行病学研究；在佛山地区，人群中感染的HBV以B、C型为主。     

PCR-ELISA检测疟原虫DNA的研究

目的：介绍一种诊断疟疾的新方法ＰＣＲ－ＥＬＩＳＡ。方法：根据业已报道的疟原虫ＳＳＵｒ－ＲＮＡ基因保守序列，设计并合成一对通用于恶性疟原虫和间日疟原虫的引物，其中一引物的５’端加以生物素标记。经ＰＣＲ扩增后，携带有生物素的扩增产物与先期包被于ＥＬＩＳＡ板上的亲和素结合，再经与恶性疟原虫、间日疟原虫特异、荧光素标记的寡核苷酸探针分别杂交，底物显色等步骤，使ＰＣＲ产物得以半定量地检出。结果：对于恶性疟原虫和间日疟原虫，本法检出最低原虫密度阈值分别为４和１０个原虫／μｌ血（取血２０μｌ），本法检测两种疟原虫未发现交叉反应。结论：本试验具有较高的敏感度和特异性，可望用于疟疾流行病学调查     

随机引物PCR法分型大肠艾希菌及其在判断医院感染中的应用

目的对大肠艾希菌(艾希菌)进行随机引物PCR(AP—PCR)法基因分型并应用于医院感染的判断。方法以优化的随机引物、反应体系和扩增条件对临床分离的161株艾希菌进行AP—PCR法基因分型并按指纹图上DNA条带数及片段大小绘制基因分型图谱，同时对艾希菌的医院内感染进行了观察与分析。结果161株艾希菌共得AP—PCR型120种；艾希菌的医院内感染确实存在。结论AP—PCR法可对艾希菌有效分型并可用于艾希菌医院内感染的判断。     

广州东部HPV基因型分布及其优势基因型E6／E7核酸序列分析

目的研究广州东部人乳头瘤病毒基因型分布特征,并获取优势基因型早基因E6／E7的核酸序列,进行变异分析,为本课题组下一步新型分子诊断方法的研发提供目标序列。方法通过导流杂交基因芯片技术进行宫颈脱落细胞标本的人乳头瘤病毒基因分型检测,分析本地区基因型分布特征,确定优势基因型;根据GenBank序列设计特异性引物,用于扩增优势基因型的早基因E6／E7的编码区序列,克隆后测序并对序列进行变异分析。结果通过导流杂交基因芯片技术进行宫颈脱落细胞标本的分型检测,检测了536份宫颈脱落细胞标本,HPV阳性占27.2％（146／536）,其中多基因型感染占29.5％（43／146）,高危型感染中52型为优势基因型,频数达23.3％（37／159）。HPV感染与52型HPV感染的年龄分布显示低年龄组（即A组,≤25岁）妇女最高。3份52型HPV感染阳性标本的核酸模板,通过特异性引物均成功扩增出大小接近750bp的目的序列;分别克隆到T载体上并测序,得到3条人乳头瘤病毒52型早表达基因E6／E7的编码区序列,克隆后测序并对序列进行变异分析;3条序列经BLAST分析,与GenBank数据库HPV52型序列（Accession：X74481）的E6／E7编码区序列一致性均为99％,三条序列（EU924143、EU924144、EU924145）存在6种碱基置换,其中2种可引起所编码的相应氨基酸残基改变。结论本研究可确认广州东部地区妇女宫颈感染HPV中A组（17-25岁）具有最高的感染率;宫颈感染HPV的优势基因型为52型;我们通过克隆策略得到了与HPV高危型52型X74481高度相似的E6／E7编码序列,为课题组后续进行的HPV致病机制和新型分子检测方法研究提供了重要基础。     

Genetic typing of human platelet antigen 1 (HPA-1) by oligonucleotide ligation assay in a specific and reliable semi-automated system

Genotyping of platelet alloantigens with the possibility of using any type of cellular material as a source of DNA has become a preferred procedure, particularly in thrombocytopenic patients when platelet counts are too low for phenotyping. Recently human platelet antigen 1 (HPA-1) has been identified as an inherited risk factor for coronary thrombosis. The different detection methods currently used have disadvantages for large-scale DNA diagnosis, including the need for electrophoresis (allele-specific restriction enzyme analysis, amplification with sequence-specific primers) or the potential risk of reduced specificity (allele-specific oligonucleotide hybridization). In this report we describe the adaptation of an automated oligonucleotide ligation assay to genotype HPA-1 in polymerase chain reaction (PCR)-amplified DNA samples. HPA-1a and HPA-1b phenotypes corresponded to the results of the different genotyping assays. The genotypes determined with the ELISA-based PCR-oligonucleotide ligation assay were in 100% concordance with the results obtained by conventional allele-specific restriction enzyme site analysis and PCR amplification with sequence-specific primers. The automated oligonucleotide ligation assay provides a rapid, reliable, nonisotopic method to genotype human platelet antigens that can rapidly be applied to large population screening.     

山西省HBV基因型及亚型分布调查

目的了解山西省乙型肝炎病毒(HBV)的基因型及亚型分布情况。方法对136例乙型肝炎表面抗原(HBsAg)阳性者血清采用PCR-PFLP结合基因型特异性引物-PCR法进行HBV基因型及亚型检测。结果 136例HBV感染者的血清标本经PCR-PFLP分析,B基因型18例,均为Ba亚型,占13.2%;C基因型113例,占83.1%,除4例未分型外均为Ce亚型;D基因型5例,占3.7%。经型特异性引物-PCR分析,18例HBV B基因型中有4例为B/C基因型混合感染;5例经PCR-PFLP确定的D基因型病毒经型特异性引物法分析有2例扩增出E基因型条带。C、B基因型病毒感染者的平均年龄分别为(39.5±13.1)岁和(30.5±14.1)岁,差异有统计学意义(P<0.05);与B基因型相比,C基因型病毒感染者的HBeAg阴转率减慢。结论山西省HBV基因型主要为C(Ce),有少量的B(Ba)和D基因型,且存在B/C混合基因型,且可能存在D和E基因型病毒的重组体;与B基因型比较,感染C基因型病毒更难被机体清除,疾病更易慢性化。     

HBV基因型与HBeAg的表达关系及其临床意义

目的观察慢性乙型肝炎病毒（HBV）感染者HBV基因型与HBeAg表达和病情轻重的关系。方法利用型特异性引物多重PCR方法检测HBV基因型,时间分辨荧光法检测HBV DNA。结果在120例慢性乙型肝炎病毒感染者中HBV基因型C型84例（70%）、B型31例（25.8%）,BC混合型5例（4.2%）,未发现A、D、E、F基因型;C型在慢性重型肝炎组最高（P〈0.05）;在C基因型中HBeAg（＋）患者较HBeAg（-）患者多见（P〈0.05）,在B基因型中,HBeAg（＋）和HBeAg（-）患者分布无明显差别。结论徐州地区HBV基因型以C型和B型多见,e抗原的表达率在C型中较高;基因型B型与C型相比,C型引起肝脏损伤重。     

Molecular epidemiology survey of toxinogenic Clostridium perfringens strain types by multiplex PCR

Toxin genotypes of 95 C. perfringens strains collected within a 45-year period were analysed by a multiplex PCR. A set of primers designed for 4 different genes encoding the alpha, beta, epsilon, and iota toxins was used in a single reaction with a sensitivity of gene detection of 200 fg for DNA extracted from pure culture. Most of the strains (97%) conformed to the A biotype, and the remaining to the C or E biotypes. For biotype determination, seroneutralization of lethality in mice was performed by intravenous injection. Toxin phenotype and genotype profile were concordant in 94% of strains. Our results documented the presence of rare toxin genotypes of C. perfringens in a Polish geographical region and indicated the suitability of multiplex PCR as a method supplementing classical techniques and providing better insight into the prevalence of toxinogenic C. perfringens strains.     

Newer developments in the identification of beta-thalassemia

One of the easiest and most sensitive methods of detecting mutations in the beta-globin gene leading to beta-thalassemia is by the use of oligonucleotide probes. The current method involves digestion of 5-10 micrograms of genomic DNA followed by gel electrophoresis, and blotting onto nitrocellulose. The membrane is then hybridized with a 32P-radiolabeled oligonucleotide probe containing the specific point mutation of interest. Finally, the membrane is subjected to X-ray film for 3-10 days. We wish to report a method for detecting these mutations which involves 1 microgram of genome DNA or less. The method involves the use of a gene amplification technique. A series of primers are synthesized which span the beta-globin gene. In each primer set, one primer is complementary to the beta-gene and the other primer is complementary to the non-coding strand. The suspected mutation point is located between these two primers. With the use of this primer set, the beta-globin gene region is amplified by denaturing, annealing, and DNA synthesis. The amplification cycle is repeated 25 to 30 times. The amplification is conducted using the Klenow fragment of DNA polymerase I or Taq polymerase in the presence of all four deoxynucleotide triphosphates. The resulting amplified DNA is applied to a nylon membrane with the aid of a dot-blot apparatus and directly hybridized with normal and mutant deoxynucleotide probes. The entire process requires one to two days. More than 300 beta-thalassemia homozygotes have been identified in our laboratories; over 20 different mutations have been observed.     

Genotyping 238 HBV strains using type-specific primer PCR combined with type-specific nucleotide analysis]

OBJECTIVE: To establish a set of suitable and reliable methods for HBV genotyping and to study the distribution of HBV genotypes. METHODS: Type-specific nucleotides were searched through alignment of S genes (more than 1000 sequences) listed in GenBank. Then, type-specific primers were designed and type-specific primer PCR was used to genotype the 238 HBV strains. S genes of the untyped strains were further amplified and sequenced to find out their genotypes with type-specific nucleotide analysis. RESULTS: All the 238 HBV strains were genotyped. 159 (66.8%) cases were genotype B, 69 (28.9%) were genotype C, 6 (2.5%) were mixtures of genotypes B and C and 4 (1.6%) were mixtures of genotypes B and D. No genotypes of A, E, F, G, and H were found. CONCLUSION: Genotypes B and C are the most common types for HBV strains. Mixtures of genotypes B and C or genotypes B and D coinfection rarely existed. There is no relationship between the gender of the patients and HBV genotypes (X2 = 0.794, P more than 0.05).     

优化的多重扩增阻滞突变系统-PCR 对载脂蛋白E 基因的简易分型

目的通过改进和优化多重扩增阻滞突变系统-PCR（multi-ARMS-PCR）条件,建立载脂蛋白E（ApoE）基因的简易分型方法。方法基于multi-ARMS-PCR的原理和特点,针对文献报道方法中存在的缺陷和错误,重新设计或改进引物。以外周血白细胞基因组DNA为模板,应用4个等位基因特异性寡核酸上游引物、1个通用下游引物和一对内参引物,分A,B两个管同步进行多重PCR反应。PCR扩增产物经过琼脂糖凝胶电泳分离-EB染色,根据电泳带型的差异,实现对ApoE 6种基因型的判定。结果新引物显著提高了扩增效率和反应特异性,排除了非特异条带的干扰,减少了ApoE基因分型的错判。结论采用优化后的multi-ARMS-PCR方法对ApoE基因型进行鉴定,具有操作简便、时间短、效率高、成本低的优点,值得推广。     

Comparative study of PCR-based Cryptosporidium discriminating techniques with a review of the literature

We identified the species or genotypes of the six Cryptosporidium isolates from patients and C. parvum strain HNJ-1 using the seven previously described species-differentiation and genotyping PCR protocols for detection of Cryptosporidium parasites. In addition, we also discussed about the usefulness of these PCR-based protocols on the basis of the reports previously published. Cryptosporidium diagnostic fragment was amplified by PCR with each primer pair, targeting the 18S ribosomal RNA (18SrRNA), Cryptosporidium oocyst wall protein (COWP). Heat shock protein 70 (HSP70), Polythreonine (Poly-T), Thrombospondin related adhesive protein of Cryptosporidium-1 (TRAP-C1), and unknown gene locus, in all isolates from patients and the strain HNJ-1. The RFLP profiles of 18SrRNA, COWP, HSP70, Poly-T, and TRAP-C1 PCR products in all isolates from patients were found to be the same among isolates, and were correspondent to those of C. parvum human genotype. While the RFLP profiles of HNJ-1 were strictly different from those of isolates from patients, and were correspondent to C. parvum cattle genotype. In addition, nucleotide sequences in 18 SrRNA gene of all isolates from patients and HNJ-1 were found to be identical to that of C. parvum, human or cattle genotype, respectively. Therefore, the isolates from patients and HNJ-1 were identified as C. parvum human and cattle genotype, respectively. According to the reports related to the PCR-based protocols applied in the present study, RFLP profiles targeting the HSP70, Poly-T, TRAP-C1 genes had been revealed in only a few species or genotypes, but those of 18SrRNA and COWP genes were in all species and genotypes. However, we supposed that it was difficult to distinguish between human or cattle genotype and other species or genotypes by RFLP profiles of 18SrRNA or COWP because the RFLP profiles of human or cattle genotype were identical or similar to those of other species or genotypes. On the other hand, it has been known that the nucleotide sequences in 18SrRNA or COWP gene are different among Cryptosporidium species and/or genotypes. Therefore, the direct sequencing method targeting the variable regions which can be used to distinguish among Cryptosporidium species, as well as the genotypes within C. parvum in either 18SrRNA or COWP gene is the most useful tool for accurate identification of Cryptosporidium isolates.     

血清皮质醇水平与重型肝炎预后的相关性

目的探讨重型肝炎患者血清皮质醇水平与预后的关系,为临床判断预后及探讨治疗提供理论依据。方法对临床诊断的重型肝炎患者进行血清皮质醇、TNFα含量检测;比较重型肝炎、急性肝炎和慢性肝炎患者血清皮质醇水平的差异以及重型肝炎患者中死亡组和存活组的差异;检测血清皮质醇含量与TNFα含量的相关性。结果重型肝炎患者血清皮质醇水平明显低于急、慢性肝炎患者,尤以死亡组患者更为明显;血清皮质醇水平与TNFα含量呈显著负相关。结论重型肝炎患者存在肾上腺皮质功能不全,且与患者预后密切相关。