Comparison of direct fecal smear microscopy,culture,and polymerase chain reaction for the detection of Blastocystis sp.in human stool samples

Objective:To compare the sensitivity and specificity of direct fecal smear microscopy,culture,and polymerase chain reaction in the detection of Blastocystis sp.in human stool.Methods:Human stool samples were collected from a community in San Isidro,Rodriguez,Rizal,Philippines.These samples were subjected to direct fecal smear microscopy,culture and polymerase chain reaction to detect the presence of Blastocystis sp.Results:Of the 110 stool samples collected,28(25%)were detected positive for the presence of Blastocystis sp.by two or more tests.Culture method detected the highest number of Blastocystis-positive stool samples(n=36),followed by PCR of DNA extracted from culture(n=26),PCR of DNA extracted from stool(n=10),and direct fecal smear(n=9).Compared to culture,the sensitivity of the other detection methods were 66.7%for PCR from culture and 19.4%for both PCR from stool and direct fecal smear.Specificity of the methods was high,with PCR from culture and direct fecal smear having97.3%,while PCR from stool at 95.9%.Conclusions:In this study,in vitro culture is the best method for detecting Blastocystis sp.in human stool samples.

Detection of the Pandemic H1N1/2009 Influenza A Virus by a Highly Sensitive Quantitative Real-time Reverse-transcription Polymerase Chain Reaction Assay

A quantitative real time reverse-transcription polymerase chain reaction （qRT-PCR） assay with specific primers recommended by the World Health Organization （WHO） has been widely used successfully for detection and monitoring of the pandemic H1N1/2009 influenza A virus. In this study, we report the design and characterization of a novel set of primers to be used in a qRT-PCR assay for detecting the pandemic H1N1/2009 virus. The newly designed primers target three regions that are highly conserved among the hemagglutinin （HA） genes of the pandemic HlN1/2009 viruses and are different from those targeted by the WHO-recommended primers. The qRT-PCR assays with the newly designed primers are highly specific, and as specific as the WHO-recommended primers for detecting pandemic H1N1/2009 viruses and other influenza viruses including influenza B viruses and influenza A viruses of human, swine, and raccoon dog origin. Furthermore, the qRT-PCR assays with the newly designed primers appeared to be at least 10-fold more sensitive than those with the WHO-recommended primers as the detection limits of the assays with our primers and the WHO-recommended primers were 2.5 and 25 copies of target RNA per reaction, respectively. When tested with 83 clinical samples, 32 were detected to be positive using the qRT-PCR assays with our designed primers, while only 25 were positive by the assays with the WHO-recommended primers. These results suggest that the qRT-PCR system with the newly designed primers represent a highly sensitive assay for diagnosis of the pandemic HIN1/2009 virus infection.

Primary application of a real-time quantitative polymerase chain reaction for the detection of human breast cancer related novel gene-Metadherin expression

Objective:The aim of this study was to detect the expression level of Metadherin (MTDH) in peripheral blood of the breast cancer patients by real-time fluorescence quantitative polymerase chain reaction (PCR),and to explore the relationship between expression of Metadherin gene in the patients peripheral blood and the clinic-pathological features in breast cancer. Methods:Real-time fluorescence quantitative polymerase chain reaction was employed to determine the expression level of Metadherin gene in 80 peripheral blood samples of breast cancer patients and healthy donors. Results:The expression of Metadherin gene in breast cancer patients peripheral blood were positive,in which 34 breast cancer patients were highly expressed,accounting for 55.7%,while the expression of Metadherin gene in normal females peripheral blood were negative,there was statistical significance (Ratio = 2.02±0.81,P < 0.05); Ratio of the Metadherin expression in breast cancer patients peripheral blood and the glyceraldehyde-3-phosphate dehydrogenase expression was 1.15 ± 0.36. REST software analysis showed that the expression of Metadherin gene was significantly up-regulated in breast cancer. Conclusion:The SYBR Green I quantitative real-time polymerase chain reaction method can successfully detect the expression level of Metadherin gene. Expression level of Metadherin gene in breast cancer patients peripheral blood is closely related to survival,and it maybe involved in the development of breast cancer and used as an indicator of prognosis.

USE OF THE POLYMERASE CHAIN REACTION (PCR) TO DETECT MONOCLONALITY OF B CELL LYMPHO-PROLIFERATIVE DISORDERS

A technique has been developed using PCR to detect monoclonality of B-lymphoproliferative disorders. DNA was extracted from the blood, tissue and paraffin embedded sections by biochemical means or boiling. Forty cases of B-non Hodgkin's lymphoma (NHL), 15 cases of T-NHL, 8 cases of chronic lymphocytic leukemia, 17 cases of reactive lymphadenopathy and 12 cases of various non-lym-phocytic tumor were examined. Monoclonality of B-lymphocytes was detected in 86-92% of cases with B-lymphoproliferative diseases, but none in T-NHL, reactive disorders and non-lymphatic tumors. This technique provides a new molecular biologic method to diagnose malignant B-lymphoproliferative dicor-ders. It may be useful in Ig gene rearrangement study, differential diagnosis and retrospective investigation of lymphoproliferative disorders.

Sensitivity assay of polymerase chain reaction for detection of Canine Parvo Virus infection in dogs

A polymerase chain reaction was performed using re-ported primers for detection of Canine Parvo virus (CPV) in the stool sample obtained from repository. The PCR primers were specific to VP1/VP2 gene of CPV. Sensi-tivity assay of PCR detection was performed by making dilutions of CPV positive DNA extracted from fecal sample, carrying out PCR for each dilution and visualiz-ing amplicons in ethidium bromide stained agarose gel under UV radiation. Study was valuable in determining the efficiency of PCR. The sensitivity of PCR in present study was determined to be equivalent to detection of .00 2pg/μl of CPV DNA. The study was conducted to analyze the variation, sensitivity and repeatability.

Detection of Human Papillomavirus DNA in Oral Cancer Tissue Using Polymerase Chain Reaction

Using polymerase chain reaction (PCR), 25 specimens from 22 patients with oral carcinomas were examined by 6 selected primers of human papillomavirus (HPV). Eighteen of the 22 patients (18/22) gave positive reaction with a positive rate of 81.8%. The positive rates of HPV 6, 11, 16 and 18 were 27.3%, 18.2%, 63.6% and 40.9% respectively. 13.6% positive for mixed infection of HPV 16 and 18 (3/22) and 18.2% positive for mixed infection of HPV, 6, 11, 16 and 18 (4/22). Examining enlarged cervical lymph nodes in three cases with suspecting metastases to cervical lymph nodes from oral carcinomas. It revealed HPV DNA 16 and 18 in two cases and HPV DNA 18 in one case. These results suggested that there was a tendency for HPV 16 and 18 to metastasinze via lymphatics. Only one case of the three had a pathologic diagnosis of lymph node metastasis. Of the 30 non tumor controls, HPV DNA positivity was 10%, all being HPV 18. χ 2 test gave a P<0.005. It strongly indicated that HPV 16 and 18 were related to oral carcinomas.

Investigation on detection of Haemophilus ducreyi by Polymerase Chain Reaction

Objective:To investigate the application of polymerase chain reaction (PCR) detection of Haemophilus ducreyi in clinical diagnosis of chancroid. Methods: Nucleotide sequences of 16srRNA gene specific for H. dureyi were used to develop primer sets for amplification of two strains. The amplified products were tested via PCR and sequenced by electrophoresis in a 1.5% gel.These products were compared with those of heterogeneous species or related bacteria to test the specificity of the PCR assay. PCR amplification with different concentrations of H.ducreyi was performed to test its sensitivity. Results: PCR amplification of two strains of H. ducreyi produced a single band of expected 438bp length. The sequence was identified with genomic DNA. None of the other 19 reference species amplified under the same conditions gave this result. The highest sensitivity of PCR assay in the present test was 10ng/L. Conclusions: PCR assay for detection of H. ducreyi is a rapid, specific, and sensitive detection method. If laboratory conditions are strictly controlled, PCR assay is a potentially useful laboratory test for H. ducreyi infection diagnosis.

Sperm Mediated Transfer of Genes into Goldfish and Detection by Polymerase Chain Reaction

Goldfish sperms were mixed with eggs for fertilization after incubation with antifreeze protein gene(AFP)from ocean pout for 30 min.A number of embryos and 145 adult goldfish were obtained.DNA from adult goldfish and embryos was extracted separately.Results of the amplification by PCRand Southern blot molecular hybridization indicate the integration of exogenous antifreeze gene intothe genome of a part of the recipient goldfish.Of the 45 samples detected by PCR,twelve showedpositive reaction with distinct hybridization band.The positive rate was 26%.

基于主成分分析的多重定量PCR荧光串扰校正

聚合酶链式反应(PCR)是分子生物学常用的检测手段,主要用于对生物的DNA或RNA进行检测。由于荧光光谱重叠和滤光片过滤带宽限制,检测时所获得的荧光数据通常会包含荧光通道之间的串扰,串扰的存在使PCR结果分析变得复杂,并可能影响最终的检测结果。选择合适的光学元件,并确定通道间的补偿矩阵,可以降低甚至消除荧光串扰。目前荧光补偿矩阵大多通过迭代计算获得,还没有一种简单的方法可以从混合的多通道荧光数据中找到荧光补偿矩阵。为了快速获得荧光补偿矩阵,减小计算量,采用主成分分析法(PCA)中确定主成分的方式,基于搭建的测试平台进行单一染料实验,获得染料的荧光信号在各个检测通道的分布情况,计算得到荧光补偿矩阵。通过分析补偿矩阵,发现对于搭建的硬件系统,Cy5染料对Cy5.5通道串扰较大,串扰比例为8.76%,同时Cy5.5染料对Cy5通道串扰影响也相对较大,比例约为6.2%;其次是ROX染料对HEX通道串扰,比例约为2.68%;HEX染料对FAM通道串扰,比例约为1.58%;FAM染料对HEX通道串扰相对较小,比例约为0.25%,其余通道无明显串扰,与荧光光谱反映的结果一致。采用得到的荧光补偿矩阵对单一染料实验得到的原始荧光数据进行处理,有效去除了非目标通道的荧光串扰,实现了荧光通道数据的解耦,验证了方法的可行性。最后设计了染料颜色分辨实验,将不同浓度的多种染料进行组合测试,并采用所提出的方法将得到的数据进行荧光补偿。实验结果表明,荧光通道各自的线性相关性较高,五个荧光通道的线性相关系数r均大于0.99,该结果进一步验证了该补偿方法的有效性。

位点特异性PCR鉴别水牛角及其伪品

目的:开发一种针对水牛角的特异性聚合酶链式反应(PCR)鉴别方法,快速、准确地鉴别水牛角与其他混伪品。方法:通过比对水牛、黄牛、牦牛、山羊等动物的细胞色素C氧化酶亚基Ⅰ(COⅠ)基因序列差异,筛选水牛的特异性单核苷酸多态性(SNP)位点,设计出相应的鉴别引物,并对影响PCR体系的相关条件进行优化,考察验证方法的耐受性和适用性。结果:PCR条件为扩增体系20μL、退火温度60℃、循环次数32次、DNA模板量为100 ng、10μmol·L^(-1)正反引物对各0.8μL时,使用设计的鉴别引物SN1对水牛角进行PCR扩增,产物经琼脂糖凝胶电泳后出现约358 bp的特异性条带,其他物种的样品均无条带出现。结论:该PCR鉴别方法特异性好,能迅速、准确地鉴别水牛角和其他常见动物角类样品,为水牛角的真伪鉴别提供参考。

帕利亚姆病毒实时荧光定量RT-PCR检测方法的建立与应用

本研究拟建立帕利亚姆病毒(Palyam virus,PALV)血清型特异性实时荧光定量RT-PCR(qRT-PCR)方法用于临床样本或媒介中PALV血清型鉴定。根据我国流行PALV毒株的基因节段2序列,设计扩增引物和TaqMan探针,建立PALV血清型特异型qRT-PCR方法,对方法的特异性、灵敏性与重复性进行评估;以我国分离的28株PALV和90份核酸阳性血液样本评估检测方法的可靠性;利用建立的方法对采集库蠓样本中携带的PALV进行血清型鉴定。结果显示,建立的PALV血清型qRT-PCR检测方法具有良好的特异性与灵敏性,可检出核酸拷贝数下限在22至28 copies·μL^(-1)。对28株PALV的qRT-PCR检测结果与病毒测序鉴定结果一致;对PALV不同感染阶段哨兵动物血液(90份)中的qRT-PCR鉴定结果与分离病毒的血清型鉴定结果一致;建立的方法可准确鉴定库蠓中携带PALV的血清型。本研究建立的PALV血清型qRT-PCR定型方法具有良好的特异强、敏感性与重复性,可用于PALV感染动物与媒介中PALV血清型的鉴定,具有良好的应用价值。

基于PCR-LFIA的非洲猪瘟病毒核酸检测方法研究

该文利用聚合酶链式反应(PCR)技术进行扩增后,以侧流免疫层析方法(LFIA)对核酸进行检测,建立了一种非洲猪瘟病毒核酸的快速检测方法。通过设计引物,构建了pUC57-ASFV-(1-1941)质粒作为阳性质控品,采用柠檬酸三钠还原法制备胶体金颗粒用于标记抗体建立免疫分析方法。通过优化实验条件,在质粒浓度1.6×10^(-2)~1.6×10^(8)copies/μL范围内,得到pUC57-ASFV-(1-1941)阳性质粒的检出限为1.6 copies/μL。该方法与其他猪病毒无交叉,特异性良好,可作为非洲猪瘟现场筛查的辅助方法。

仰口线虫PCR检测方法的建立及应用

为特异性检测羊感染仰口线虫的情况,基于仰口线虫ITS基因序列设计特异性引物,进行退火温度及反应条件的优化,建立其属特异性PCR检测方法。应用该方法对仰口线虫、食道口线虫、毛尾线虫、捻转血矛线虫、细颈线虫、奥斯特线虫、夏伯特线虫、筒线虫、毛圆线虫的DNA样本进行扩增,仅能特异性扩增出仰口线虫的目的条带;该方法成功从仰口线虫中扩增出约500 bp的特异性片段,最低检测浓度为3.6×10^(3)copies/μL;该PCR检测方法对临床奶山羊粪便样品的检测结果显示,羊粪便样品中仰口线虫卵的阳性率为10%,且与显微镜镜检所得的结果一致。结果表明,建立的仰口线虫PCR检测方法敏感性较高且特异性良好,可以应用于临床羊粪便样品中仰口线虫的虫卵检测,为羊仰口线虫病的诊断与防治提供了一种技术支持。

基于嵌入式ARM的微流控PCR检测系统设计

为了实现微流控设备功能的集成化、提高交互系统的可操作性,提出一种基于嵌入式ARM的微流控聚合酶链式反应(PCR)控制系统及上位机软件的设计方案。系统硬件采用多个嵌入式ARM控制器与功能模块相互协调,制定可扩展的通信机制和协议,实现微流控PCR检测过程中的流路运动、温度控制、荧光信号采集等功能的集成控制。采用Qt结合SQLite数据库设计了上位机软件,利用多线程和节点映射,实现对硬件模块的协调控制以及检测信息存储。实验表明:该系统运行稳定,人机交互效果好,可操作性高,满足微流控PCR的集成功能需求。

A quantitative polymerase chain reaction assay for the enumeration of brown tide algae Aureococcus anophagefferens in coastal waters of Qinhuangdao

Aureococcus anophagefferens, a small pelagophyte algae, has caused brown tide blooms in coastal waters of Qinhuangdao in recent years, presenting significant negative impacts on the shellfish mariculture industry. Under standard light microscopy, it is visually indistinguishable from other small algae in field samples due to its extremely small size. In this study, quantitative polymerase chain reaction（q PCR） based on 18 S r DNA sequences was developed and used to detect and enumerate A. anophagefferens. A linear regression（R2 = 0.91） was generated based on cycle thresholds value（Ct） versus known concentrations of A. anophagefferens. Twenty-two field samples collected in coastal waters of Qinhuangdao were subjected to DNA extraction and then analyzed using q PCR. Results showed that A. anophagefferens had a wide distribution in coastal waters along Qinhuangdao. Elevated A. anophagefferens abundance, category 3 brown tide blooms（〉200 000 cells/m L） occurred at Dongshan Beach and Tiger-stone Beach in August in 2013. In shellfish mariculture areas along coastal waters of Qinhuangdao, 4 stations had category 3 blooms, and 6 stations had category 2 blooms（35 000–200 000 cells/m L） in August and all stations had category 1 blooms（〉0 to ≤35 000 cells/m L） in October. Quantitative PCR allows for detection of A. anophagefferens cells at low levels in filed samples, which is essential to effective management and prediction of brown tide blooms.

旋转式三温区微流控PCR扩增平台的研制

微流控芯片用于聚合酶链式反应(PCR)可提高检测效率和自动化程度,但目前把核酸提取、扩增、检测功能集成到一块芯片上仍比较困难,此外,微流控芯片专用PCR仪也存在温度控制不够快速、精准的问题。作者采用空间上温度循环代替时间上温度循环的设计思路,搭建了一套旋转式三温区微流控PCR扩增平台,对大肠杆菌进行核酸提取和扩增。结果表明,旋转式三温区微流控PCR扩增平台拥有较好的热均匀性和热稳定性,平台的升降温速率分别为3.5℃/s和2.67℃/s,单次循环时间为110 s。与9700型PCR仪相比,所建平台的温度控制方案更为简单、升降温速率更高、循环时间更短。本研究结果可为实现核酸提取、扩增一体化的微流控PCR设备的研发提供参考。

利用mPCR方法检测巴氏奶中致病菌的鲁棒性研究

为解决巴氏奶货架期短与致病菌传统检测方法耗时长相矛盾问题,建立一种检测巴氏奶中的阪崎克罗诺杆菌、大肠杆菌和沙门氏菌的鲁棒性多重聚合酶链式反应(multiple polymerase chain reaction,mPCR)方法。旨在常规mPCR的基础上深入研究,提高方法的准确性和稳定性。首先,针对每个目标菌株选择两种基因,并设计两组特异性引物,建立两套mPCR扩增体系,进行双重检测;然后,在不改变方法灵敏度的前提下,对优化了的退火温度进行范围稳定性选择;最后,将提出方法与国标方法 GB 4789.40-2016、GB 4789.38-2012、GB 4789.4-2016进行比较,同时检测人工污染样品并评价应用效果。结果表明,第一套mPCR检测巴氏奶中三种致病菌可在退火温度59~59.5℃(温差0.5℃)的范围内,具有较好的检测准确性和稳定性,灵敏度为10 CFU/mL。第二套mPCR检测巴氏奶中三种致病菌可在退火温度57.5~58.5℃(温差1℃)的范围内,不影响方法的准确性和稳定性,灵敏度为10 CFU/mL。采用建立的鲁棒性mPCR方法对人工污染的50份巴氏奶样品进行检测,检测结果与国标方法一致。在检测时效上需要4 h,较国标方法(检测时间为62~148 h)显著(P<0.05)缩短检测时间。该方法对微生物流行病学调查和研究,尤其是对巴氏奶中致病菌的快速检测和安全控制具有一定的实际应用价值。

BORRELIA BURGDORFERI DNA IN BIOLOGICAL SAMPLES FROM PATIENTS WITH SARCOIDOSIS USING THE POLYMERASE CHAIN REACTION TECHNIQUE

Polymerase chain reaction (PCR) was used to detect the presence of Barrelia burgdoferi DNA in biological samples from patients with sarcoidosis. The target DNA sequence was of chromosomal origin. The amplified DNA sequence was analyzed by agarose gel electrophoresis, PAGE with silver staining, and the identity of amplified DNA was confirmed by restriction enzyme cleavage and DNA-DNA hybridization with a 32P-labelled probe. The assay was sensitive to fewer than two copies of B. burgdorferi genome, even in the presence of a 104-fold excess of human eukaryotic DNA , and was also specific to different B. burgdorferi strains tested. Sera serologically positive to B. burgdcrferi (n=26), bronchoalveolar lavage fluid and supernatant of BALF (n=26) and peripheral blood (n=9) from sarcoidosis patients were tested. The positive rate was low (4/26, 2/26. and 0/9, respectively). It was considered that DNA from B. burgdor ferimay be identified in a minority of patients with sarcoidosis, and it may play a pathogenetic role in such cases. More studies need to be done before advancing the hypothesis of an etiologic role of B. burgdorferi in sarcoidosis.

Quantum dots induce hot-start effects for Taq-based polymerase chain reaction

Decent hot-start effects were here reported in Taq DNA polymerase-based polymerase chain reaction (PCR) when water-soluble CdTe quantum dots (QDs) were employed. The hot-start effects were revealed by the higher amplicon yields and distinguished suppression of nonspecific amplification after pre-incubation of PCR mix with quantum dots between 30°C and 56°C. DNA targets were well amplified even after PCR mixture was pre-incubated 3 hr at 30°C or 1 hr at 50°C. Importantly, the effects of QDs nanoparticles could be reversed by increasing the polymerase concentration, suggesting that there was an interaction between QDs and Taq DNA polymerase. Moreover, control experiment indicated that hot-start effect is not primarily due to the reduced polymerase concentration resulted from the above interaction. This study provided another good start to investigate potential implications of quantum dots in key molecular biology techniques.

鹦鹉喙羽症病毒PCR检测方法的建立与应用

为建立一种灵敏特异的检测鹦鹉喙羽症病毒PCR方法,给临床快速诊断鹦鹉喙羽症提供技术支持,根据Genbank上公开的鹦鹉喙羽症病毒基因序列,比对分析找出高保守区域,设计了1对检测引物,提取鹦鹉喙羽症病毒阳性样品DNA模板,对扩增体系和反应条件进行一系列调整,确定理想的PCR反应方案;通过10倍梯度稀释DNA模板法,确定该检测方法的灵敏度极限;应用该方法检测传染性法氏囊炎病毒、鸡传染性支气管炎病毒、新城疫病毒、传染性喉气管炎病毒、鸡痘病毒和Ⅰ群禽腺病毒4型这6种禽病病原,确定方法的特异性;运用该PCR方法检测90份临床样品,测试其实用性。结果表明,设计的检测引物能特异性扩增鹦鹉喙羽症病毒,其它6种家禽病毒均为阴性,其检测DNA浓度的下限是3.725×10^(-6)ng/μL。临床应用表明,90份疑似病料有28份为阳性,阳性率为31.1%。成功建立了一种灵敏度高、特异性好的鹦鹉喙羽症病毒PCR方法。