两种不同方法提取人粪便进行DNA检测的有效性研究

目的分析两种不同方法提取人粪便进行DNA检测的效果。方法收集108例研究者的粪便,采用粪便DNA提取试剂盒及酚一氯仿法提取DNA,比较两种方法提取DNA的效果。结果采用酚．氯仿的方法及试剂盒提取的DNA浓度分别为（232．51±41．24）ng／μl、（67．35±13．17）ng／μ1（P〈0．01）;试剂盒提取粪便DNA在纯度（0D260／280）、溶液澄清度及电泳结果等方面,均高（优）于酚．氯仿提取的DNA（P〈0．01）。酚-氯仿及试剂盒首次提取的DNA能进行PCR扩增的阳性率分别为5％（1／20）和91．67％（99／108）（P〈0．01）。另有9例采用试剂盒未能提取足够的DNA量,加大粪便量后,再次提取的DNA能够满足实验要求。结论试剂盒提取的DNA质量较高,能满足DNA甲基化检测的条件。酚一氯仿的提取方法有待进一步研究才可能获得质量较高的DNA。     

Rapid quantification of semen hepatitis B virus DNA by real-time polymerase chain reaction

AIM: To examine the sensitivity and accuracy of real-time polymerase chain reaction (PCR) for the quantification of hepatitis B virus (HBV) DNA in semen. METHODS: Hepatitis B viral DNA was isolated from HBV carriers' semen and sera using phenol extraction method and QIAamp DNA blood mini kit (Qiagen, Germany). HBV DNA was detected by conventional PCR and quantified by TaqMan technology-based real-time PCR (quantitative polymerase chain reaction (qPCR)). The detection threshold was 200 copies of HBV DNA for conventional PCR and 10 copies of HBV DNA for real time PCR per reaction. RESULTS: Both methods of phenol extraction and QIAamp DNA blood mini kit were suitable for isolating HBV DNA from semen. The value of the detection thresholds was 500 copies of HBV DNA per mL in the semen. The viral loads were 7.5x10~7 and 1.67x10~7 copies of HBV DNA per mL in two HBV infected patients' sera, while 2.14x10~5 and 3.02x10~5 copies of HBV DNA per mL in the semen. CONCLUSION: Real-time PCR is a more sensitive and accurate method to detect and quantify HBV DNA in the semen.     

Evaluation of a quantitative real-time PCR assay for the detection of JC polyomavirus DNA in cerebrospinal fluid without nucleic acid extraction

The JC polyomavirus (JCV) is the causative agent of progressive multifocal leukoencephalopathy (PML), a fatal demyelinating disease. The current diagnostic standard for PML is real-time PCR testing of extracted DNA for assessing the presence of JCV DNA in cerebrospinal fluid (CSF). This study was aimed at evaluating the feasibility of a real-time PCR assay without nucleic acid extraction for the rapid quantification of JCV DNA in CSF. CSF samples were heat-treated or treated with DNAzol Direct, a commercially available reagent for direct PCR, and the performances of the real-time PCR assays using templates obtained by either treatment were compared with that using DNA extracts. JCV DNA was detected in the heat- or DNAzol Direct-treated samples containing only a few copies of the viral genome per reaction, and a linear relationship was noted between the copy number detected and the amount of input virus ascertained by the DNA extraction method. The sensitivities of the assays using the heat and DNAzol Direct treatments were 85.7 and 90.5%, respectively, with the results of the DNA extraction method being used as reference. These data demonstrate that the real-time PCR assay introduced in this study can serve as a rapid and cost-effective method of testing for JCV without DNA extraction and thereby facilitate the assessment of PML.     

不同方法抽提血清HBV DNA得率的比较

目的：比较不同的HBV DNA抽提方法对PCR产物量的影响,方法：将HBV DNA阳性血清及投入了HBV DNA质粒的HBV DNA阴性血清,分别采用7种不同方法抽提核酸,抽提物作PCR后,产物行琼脂糖凝胶电泳,并对阳性扩增条带进行密度定量,结果：血清直接煮沸法,经典的蛋白酶裂解加酚／氯仿抽提法,蛋白酶裂解加酚／氯仿抽提法省缺乙醇沉淀和柱抽提法的HBV DNA抽提得率分别为75．2％,13．8％,21．9％,用碱变性裂解和蛋白酶裂解后煮沸所得上清液,以及血清直接作为模板,行PCR后不能得到阳性扩增条带。结论：核酸抽提方法选择不当能直接影响基因检测的灵敏度,导致基因定量准确性下降,血清直接煮沸法抽提HBV DNA得率高,操作简便,省时和经济,值得推荐。     

Optimised sample DNA preparation for detection of Chlamydia trachomatis in synovial tissue by polymerase chain reaction and ligase chain reaction

OBJECTIVE: Molecular biology techniques such as polymerase chain reaction (PCR) and ligase chain reaction (LCR) are routinely used in research for detection of C trachomatis DNA in synovial samples, and these methods are now in use in some clinical laboratories. This study aimed at determining the method best suited to molecular diagnosis of C trachomatis by examining four standard DNA preparation methods using chlamydia spiked synovial tissue and chlamydia infected monocytes. METHODS: Synovial tissue from a chlamydia negative patient with rheumatoid arthritis was spiked with defined numbers of C trachomatis elementary bodies (EB). Purified human peripheral monocytes from normal donors were infected with the organism at a multiplicity of infection 1:1 in vitro and harvested after four days. DNA was prepared from all samples by four methods: (1) QIAmp tissue kit; (2) homogenisation in 65 degrees C phenol; (3) incubation at 97 degrees C; (4) proteinase K digestion at 97 degrees C. DNA from methods 1 and 2 was subjected to PCR using two different primer sets, each targeting the C trachomatis omp1 gene. LCR was done on DNA prepared by each method. RESULTS: In synovial tissue samples spiked with EB, and in monocytes persistently infected with the organism, preparation of template using the QIAmp tissue kit (method 1) and the hot phenol extraction technique (method 2) allowed sensitive detection of C trachomatis DNA. These methods also produced template from both sample types for LCR. DNA prepared by heat denaturation (method 3) allowed only low sensitivity chlamydia detection in LCR and did not work at all for PCR. Proteinase K digestion plus heat denaturation (method 4) gave template that did not allow amplification in either PCR or LCR assays. CONCLUSIONS: The sensitivity of detection for C trachomatis DNA in synovial tissue by PCR and LCR depends strongly on the method used for preparation of the amplification template. LCR targeting the multicopy chlamydial plasmid and two nested PCR assay systems targeting the single copy omp1 gene showed roughly equivalent sensitivity. Importantly, template preparation method and the specific PCR primer system used for screening must be optimised in relation to one another for highest sensitivity.     

微小隐孢子虫卵囊DNA提取及用于PCR检测

目的采用3种方法提取微小隐孢子虫卵囊DNA,并用于PCR检测以进行比较。方法 微小隐孢子虫卵囊经多次冻融加热破壁后,采用螯合树脂(Chelex-100)、酚/氯仿和基因组DNA纯化系统试剂盒3种方法提取微小隐孢子虫卵囊DNA,并根据微小隐孢子虫基因序列(L16996)设计一对寡核苷酸引物,分别对3种方法制备模板进行PCR扩增分析。Chelex-100提取的DNA也用于观察PCR检测的敏感性。结果3种方法制备的微小隐孢子虫卵囊模板用于PCR检测均获得1条446 bp条带,Chelex-100提取的DNA用于PCR检测的敏感性至少达0.5个卵囊。结论3种方法提取的微小隐孢子虫卵囊DNA均可用于PCR检测,Chelex-100法是一种高效而快速的微量提取DNA方法,适用于对隐孢子虫DNA的检测。     

Comparison of five DNA extraction methods and optimization of a b1 gene nested PCR (nPCR) for detection of Toxoplasma gondii tissue cyst in mouse brain

Toxoplasmosis, caused by Toxoplasma gondii, is an important parasitic disease worldwide. Different techniques have been developed for T. gondii detection. At present, polymerase chain reaction (PCR) has been widely used. However, PCR for identifying T. gondii remains unsatisfactory in many laboratories because of lack of standardization and variations in efficiency. In the present study, we optimized a nested PCR protocol (n-PCR) in order to compare the amplification of T. gondii DNA, after being extracted from mouse brain by five different DNA extraction methods including phenol chloroform, QIAamp DNA minikit, Genomic DNA purification kit and Chelex with or without proteinase K. All DNA extraction methods were able to extract DNA from a single tissue cyst from mouse brain. However, among the five DNA extraction methods, the Chelex without proteinase K appeared to be the most rapid and easiest.     

Rapid DNA extraction for molecular epidemiological studies of malaria

DNA isolation from blood samples collected in molecular epidemiological studies is crucial for the quality and reproducibility of data. Blood samples from two malaria endemic sites have been prepared by four different DNA isolation methods with subsequent PCR amplification of the msp2 locus of Plasmodium falciparum. We tested a rapid boiling method; the guanadine isothiocyanate DNA extraction; QIAmp blood kit; and the ISOCODE STIX PCR template preparation dipstick, and analysed the numbers of concurrent infections/sample. The rapid boiling method and the ISOCODE STIX provided overall the best sensitivity combined with ease of handling. The possibility to store and ship the ISOCODE STIX at ambient temperature adds further advantage to this method.     

生菜污染隐孢子虫卵囊洗脱与巢式PCR检测方法的研究

目的 比较生菜表面污染隐孢子虫卵囊的洗脱与检测方法。方法 对生菜表面人工“种植”的隐孢子虫卵囊的洗脱次数、振荡方式、振荡频率、振荡时间、洗脱液种类等进行比较,以及3种商业化DNA提取试剂盒提取水溶液中隐孢子虫卵囊DNA的效果进行比较。结果 采取往返振荡,振荡频率为100次/min,振荡时间为1 h,洗脱液采用1% Alconox^○R时,其总体回收率最高,达71.40%。不同DNA试剂盒比较显示,土壤DNA提取试剂盒与粪便DNA提取试剂盒较组织DNA提取试剂盒提取水溶液中隐孢子虫卵囊DNA的质与量均高。结论 本研究建立了巢式PCR检测生菜表面微小隐孢子虫卵囊的检测方法,为蔬菜的食品安全提供新的技术方法。     

DNA extraction from archival Giemsa-stained bone-marrow slides: comparison of six rapid methods

The ability of six rapid DNA extraction procedures to provide DNA for the polymerase chain reaction from archival Giemsa-stained bone marrow slides was tested on 120 samples. Boiling in distilled water, freeze–thaw method, boiling in 10% Chelex-100 resin solution, proteinase K/Tween 20/NP-40 method coupled with simplified phenol/chloroform/isoamyl alcohol protocol or salting-out procedure using saturated NaCl and modification of commercial QIAamp procedure (Qiagen, Chatsworth, Calif.) gave DNA extraction efficiencies of 50%, 70%, 85%, 95%, 100% and 100%, respectively. Our results demonstrate that rough DNA extraction methods have decreased efficiencies compared to complete DNA extraction protocols and that the latter are required to ensure highly reproducible results from archival Giemsa-stained bone marrow slides.     

Simple method for DNA extraction from pancreatic juice for PCR amplification assays.

CONCLUSION: Preparation of DNA from pancreatic juice for subsequent polymerase chain reaction (PCR) is difficult, but manageable. The protocol presented offers a simple and fast solution. This method might be applicable to other complicated samples, such as saliva, would secretions, or stool washings. BACKGROUND: Of all the biological samples used for PCR amplification, pancreatic juice is the most problematic because of the presence of potential inhibitory substances and the amount of nucleases. This demands a DNA preparation procedure that is suitable for routine diagnostic PCR, and is therefore efficient and safe. This is particularly true for pancreatic juice obtained during routine endoscopy. METHODS: We describe here a simple method utilizing modified phenol/chloroform extraction and precipitation directly from native pancreatic juice suitable for diagnostic PCR applications, such as oncogenes. RESULTS: DNA could be prepared in quantitative amounts from routine endoscopic specimens. DNA could also be prepared from samples kept several days at room temperature.     

A simple and rapid method for extracting bacterial DNA from intestinal microflora for ERIC-PCR detection

AIM： To develop a simple and convenient method for extracting genomic DNA from intestinal microflora for enterobacterial repetitive intergenic consensus （ERIC）-PCR detection.
METHODS： Five methods of extracting bacterial DNA, including Tris-EDTA buffer, chelex-100, ultrapure water, 2% sodium dodecyl sulfate and 10% Triton-100 with and without sonication, were compared with the commercial fecal DNA extraction kit method, which is considered as the gold standard for DNA extraction. The comparison was based on the yield and purity of DNA and the indexes of the structure and property of micro-organisms that were reflected by ERIC-PCR.
RESULTS： The yield and purity of DNA obtained by the chelex method was similar to that obtained with the fecal DNA kit. The ERIC-PCR results obtained for the DNA extracted by the chelex method and those obtained for DNA extracted with the fecal DNA kit were basically the same.
CONCLUSION： The chelex method is recommended for ERIC-PCR experiments in view of its simplicity and costeffectiveness; and it is suitable for extracting total DNA from intestinal micro-organisms, particularly for handling a large number of samples.     

粪便DNA中MGMT、XAF1基因启动子甲基化联合检测在结直肠癌筛查中的应用研究

目的使用甲基化特异性PCR(MSP)方法检测粪便DNA中O6-甲基鸟嘌呤-DNA甲基转移酶(MGMT)、X染色体连锁凋亡抑制蛋白相关因子1(XAF1)基因启动子甲基化情况,并探讨其在结直肠肿瘤诊断中的意义。方法收集40例结直肠腺癌、40例腺瘤性息肉、52例正常对照住院患者粪便标本,使用试剂盒提取其粪便中肠道脱离细胞DNA,通过MSP方法检测其MGMT、XAF1基因启动子甲基化情况。结果 MGMT、XAF1基因启动子甲基化在结直肠腺癌中的阳性率分别为50.0%、55.9%;在腺瘤性息肉中的阳性率分别为42.1%、52.6%;二者联合检测在结直肠腺癌及腺瘤性息肉中的阳性率分别为73.5%、68.4%;特异性为52.0%。结直肠腺癌患者粪便中粪便潜血阳性率为35.3%,CEA阳性率为35.3%。结论通过试剂盒提取粪便DNA具有较高成功率;粪便DNA中MGMT、XAF1基因启动子甲基化状态用于检测结直肠腺癌及腺瘤性息肉具有较高的敏感性。检测粪便基因甲基化有望成为CRC高风险人群筛查的一个重要途径。     

两种国产乙型肝炎病毒核酸定量检测试剂的检测效能评价

比较两种国产不同核酸提取方法定量检测乙型肝炎病毒（HBV）核酸试剂的检测效能。方法选择经抗病毒治疗且HBV DNA 载量在﹤1×10^4 IU/ml的乙型肝炎患者血清标本36份,采用两种国产HBV核酸定量检测试剂盒平行检测HBV DNA,对阳性血清进行梯度稀释后再检测,从定量线性范围、准确性、灵敏度、特异性等方面比较两种试剂的差异。结果在36例临床血清中,14份经科华试剂检测的结果为﹤500 IU/ml,而圣湘试剂检测的结果仍﹥1.00×10^3 IU/ml;对其中获得检测数据的31份标本进行两种试剂检测结果的相关性分析,发现一致性较好（r=0.817,P﹤0.05）;两种方法检测乙型肝炎患者血清HBV DNA的阳性率分别为55.6％和94.4％,差异具有统计学意义（x2=12.07,P=0.000）;对强阳性血清进行梯度稀释后定量检测显示,两种试剂检测水平的平均值与理论水平的线性相关性较好（湖南圣湘r=0.999,上海科华r=0.992）,但圣湘所有检测的相对偏差均在±0.3logIU/ml之内,而科华有两次检测的相对偏差超出了±0.3logIU/ml范围,提示圣湘试剂检测结果更稳定,使用纳米磁珠核酸提取法的检测结果较煮沸法更加准确。结论以纳米磁珠为提取核酸方法不仅具有更广的线性范围,同时可显著提高国产HBV DNA检测试剂的灵敏度和准确性。     

Simple method for DNA extraction from pancreatic juice for PCR amplification assays

Summary Conclusion: Preparation of DNA from pancreatic juice for subsequent polymerase chain reaction (PCR) is difficult, but manageable. The protocol presented offers a simple and fast solution. This method might be applicable to other complicated samples, such as saliva, wound secretions, or stool washings. Background: Of all the biological samples used for PCR amplification, pancreatic juice is the most problematic because of the presence of potential inhibitory substances and the amount of nucleases. This demands a DNA preparation procedure that is suitable for routine diagnostic PCR, and is therefore efficient and safe. This is particularly true for pancreatic juice obtained during routine endoscopy. Methods: We describe here a simple method utilizing modified phenol/chloroform extraction and precipitation directly from native pancreatic juice suitable for diagnostic PCR applications, such as oncogenes. Results: DNA could be prepared in quantitative amounts from routine endoscopic specimens. DNA could also be prepared from samples kept several days at room temperature.     

High prevalence of pfcrt K76t mutants among Plasmodium falciparum isolates from Sabah, Malaysia

Chloroquine (CQ) remains the first line drug for the prevention and treatment of malaria in Malaysia in spite of the fact that resistance to CQ has been observed in Malaysia since the 1960s. CQ-resistance is associated with various mutations in pfcrt, which encodes a putative transporter located in the digestive vacuolar membrane of P. falciparum. Substitution of lysine (K) to threonine (T) at amino acid 76 (K76T) in pfcrt is the primary genetic marker conferring resistance to CQ. To determine the presence of T76 mutation in pfcrt from selected areas of Kalabakan, Malaysia 619 blood samples were screened for P. falciparum, out of which 31 were positive. Blood samples were collected on 3 MM Whatman filter papers and DNA was extracted using QIAmp DNA mini kit. RFLP-PCR for the detection of the CQ-resistant T76 and sensitive K76 genotype was carried out. Twenty-five samples were shown to have the point mutation in pfcrt whereas the remaining samples were classified as CQ-sensitive (wild-type). In view of the fact that CQ is the first line anti-malarial drug in Malaysia, this finding could be an important indication that treatment with CQ may no longer be effective in the future.     

Colonic short chain fatty acids mediate jejunal growth by increasing gastrin.

Colonic exfoliated epithelial cells in faecal material provide a source of human DNA which has been analysed for the presence of the tumour marker ras, in order to detect early tumour cells. The stool samples were subjected to a preliminary sample preparation step followed by centrifugation. DNA was extracted from both the centrifugation pellet and supernatant fractions, as well as from endoscopy washings, using a conventional phenol chloroform extraction method and was then purified on glass milk or spin columns. The purified DNA was amplified using mitochondrial primers and analysed for ras mutations using a non-radioactive, allele specific mismatch method. Corresponding tumour DNA was analysed for mutations using the same method. The results show that approximately 50% of the faecal samples analysed exhibited the presence of ras mutations which were also observed in the corresponding tumours. A double mutation was detected in one supernatant. Our findings represent an important stage in the development of a diagnostic test for the early detection of colorectal cancer.     

An improved DNA isolation technique for PCR detection of Strongyloides stercoralis in stool samples

Strongyloides stercoralis is a nematode that causes severe infections in immunocompromised patients. The low parasitic burden of chronically infected patients makes diagnosis difficult to achieve by conventional methods. Here, an in-house (IH) method for the isolation of parasite DNA from stools and a PCR assay for the molecular diagnosis of S. stercoralis were optimized. DNA yield and purity improved with the IH method which included a step of incubation of stool samples with a glycine–SDS buffer and mechanical disruption prior to DNA extraction. For the PCR assay, the addition of bovine serum albumin was required to neutralize inhibitors present in stool. The analytical sensitivity of the PCR using DNA as template, isolated with the IH method, was superior to the commercial one. This study demonstrates that a combined method that adds the step of glycine–SDS buffer incubation plus mechanical disruption prior to DNA isolation with the commercial kit increased PCR sensitivity to levels of the IH method. Finally, our assay was tested on 17 clinical samples. With the IH method for DNA isolation, a S. stercoralis specific band was detected by PCR in the first stool sample in all patients (17/17), while with the commercial kit, our S. stercoralis-specific band was only observed in 7 samples. The superior efficiency of the IH and combined methods over the commercial kit was demonstrated when applied to clinical samples with low parasitic burden. These results show that the DNA extraction procedure is a key to increase sensitivity of the S. stercoralis PCR assay in stool samples. The method developed here could help to improve the molecular diagnosis of S. stercoralis.     

Real-Time Polymerase Chain Reaction for Detection of Strongyloides stercoralis in Stool

The use of real-time polymerase chain reaction (PCR) for detection of Strongyloides stercoralis in stool has recently been described. We compared five DNA extraction methods by using normal human stool spiked with Strongyloides ratti and tested by using a real-time PCR. The PowerSoil kit was found to be the best technique in terms of sensitivity and ease of use. The PCR detected DNA extracted from one spiked S. ratti larva diluted 10⁻². The PowerSoil kit was then used to extract DNA from 160 human survey samples. All culture positive specimens with a high and moderate larval load were identified by real-time PCR, but only 15% of specimens with low larval load were positive. Specificity was greater than 99%. The combination of the PowerSoil kit and real-time PCR reliably detected high to moderate larval numbers of S. stercoralis in stools but was less sensitive when the larval load was low.     

循环肿瘤DNA定量方法的建立及其临床应用的初步研究

目的 建立荧光核酸染料PicoGreen用于循环肿瘤DNA定量的方法并以乳腺癌为例初步探讨其在肿瘤辅助诊断中的作用. 方法 采用QIAamp DNA blood kit提取血清中的循环肿瘤DNA并分析其提取效率,分析PicoGreen荧光分光光度法对微量DNA进行精确定量的范围和可靠性.以受试者工作特征曲线(ROC)判断循环肿瘤DNA应用于乳腺癌辅助诊断的可行性. 结果 QIAamp DNA blood kit提取血清中DNA的效率在37.8%～46.2%,平均43.4%.用PicoGreen荧光法,可检出低至1 ng的循环肿瘤DNA,并且在1～500 ng范围内呈现良好的直线关系.用此法检测乳腺癌组血清DNA浓度为(169.70±124.10)μg/L,对照组乳腺良性病变为(51.70±29.04)μg/L,健康人为(54.30±36.84)μg/L.经Mann-Whitney检验二者差异有统计学意义.ROC下面积为0.899(95%CI为0.848～0.951),当DNA诊断界值为96.0/μg/L时,灵敏度为78.2%,特异度为90.0%,提示血清DNA浓度有较好的诊断应用价值. 结论 应用PicoGreen荧光分光光度法可有效检测微量的血清循环肿瘤DNA,且乳腺癌组循环肿瘤DNA浓度明显高于对照组,提示循环肿瘤DNA为有价值的乳腺癌辅助诊断指标之一.