Multivariate Optimization of Polymerase Chain Reaction for Microbial Community Analysis

A multivariate regression, partial least square (PLS) approach was used to optimize a polymerase chain reaction (PCR) method for mixed communities. This approach, in contrast to univariate ones, provided information on the relative influence of the different factors to be optimized, as well as the interactions between factors. Models that predicted the outcome of further optimization were constructed from the initial experiments and verified experimentally. The models constructed were able to predict the outcome of a second set of experiments with high accuracy. PCR-amplification of DNA from environmental samples is often the first step in microbial community fingerprinting. Inhibitors and low cell numbers in the samples can cause problems with yield, for which compensation is normally made by increasing the number of cycles in the PCR-amplification reaction. Increasing the number of cycles, however, can cause other problems such as heteroduplex formation and increased bias. To avoid these problems the effects of different times of denaturing, annealing, and extension on yield were investigated for 2 different samples, one that consisted of a mixture of 9 laboratory strains, and one that represented the microbial community from the surface of the red alga Delisea pulchra. The multivariate approach showed, in addition to the successful optimization of yield, that the different factors affected the PCR depending on sample type. Annealing time had the largest effect on yield for the mixture of laboratory strains, whereas extension time was most important for the D. pulchra community. We suggest that multivariate optimization is a useful tool for PCR optimization and can be used irrespectively of the particular factors that are being investigated.     

Improvements of Polymerase Chain Reaction and Capillary Electrophoresis Single-Strand Conformation Polymorphism Methods in Microbial Ecology: Toward a High-throughput Method for Microbial Diversity Studies in Soil

The molecular signature of bacteria from soil ecosystems is an important tool for studying microbial ecology and biogeography. However, a high-throughput technology is needed for such studies. In this article, we tested the suitability of available methods ranging from soil DNA extraction to capillary electrophoresis single-strand conformation polymorphism (CE–SSCP) for high-throughput studies. Our results showed that the extraction method does not dramatically influence CE–SSCP profiles, and that DNA extraction of a 0.25 g soil sample is sufficient to observe overall bacterial diversity in soil matrices. The V3 region of the 16S rRNA gene was amplified by PCR, and the extension time was found to be critical. We have also found that proofreading DNA polymerases generate a better signal in CE–SSCP profiles. Experiments performed with different soil matrices revealed the repeatability, efficiency, and consistency of CE–SSCP. Studies on PCR and CE–SSCP using single-species genomic DNA as a matrix showed that several ribotypes may migrate at the same position, and also that single species can produce double peaks. Thus, the extrapolation between number of peaks and number of species remains difficult. Additionally, peak detection is limited by the analysis software. We conclude that the presented method, including CE–SSCP and the analyzing step, is a simple and effective technique to obtain the molecular signature of a given soil sample.     

An Easier Method for Locating Replication Origins Based on Real-Time Polymerase Chain Reaction

Locating replication origins (ROs) is an old problem to which diverse answers have been previously given. However, a better and more convenient method still remains desirable because previously reported methods are time-consuming. In this study, we report an easier method for locating ROs based on real-time polymerase chain reaction. The feasibility of this method was demonstrated using Escherichia coli K-12 and Halobacterium salinarium NRC-1 as models. Our results show that this method is easy, fast, and accurate in locating ROs.     

RT—PCR技术检测呼吸道合胞病毒RNA方法的建立

为了建立一种快速诊断呼吸道合胞病毒（RSV）感染的方法,根据RSVN基因的核苷酸序列,设计合成了一对引物,经RT-PCR扩增,可检出RSVRNA该引物不能检测流感病毒、副流感病毒RNA。应用该法可检出疑为RSV感染的婴幼儿鼻咽分泌物中的病毒RNA且比病毒分离法敏感,特异性与免疫荧光法一致。结果表明RT－PCR法具有快速、敏感、特异的优点,可用于RSV感染患儿的临床诊断。     

Homologous-Restraint Polymerase Chain Reaction: An Efficient and Rapid Protocol to Clone Multiple Homologous Genes

In this article, we present a novel protocol, called homologous-restraint polymerase chain reaction (HRPCR), for cloning multiple homologous genes. One of the homologous genes was cloned by consensus-degenerate hybrid oligonucleotide (CODEHOP) polymerase chain reaction (PCR) and sequenced. Primers of HRPCR were designed with 20 to 30 nt inverted to the known gene before the 5' end of the CODEHOP primers. The amplification of the known gene was restricted owing to the loop of the PCR product or the incorrect binding of the primers and the template. As a result, only unknown genes could be cloned. This protocol proved to be simple, rapid, and efficient. We applied this protocol to clone the multiple homologous genes of beta-1,4-N,6-O-diacetylmuramidase from the genomic DNA of Streptomyces griseus.     

用PCR法直接快速筛查重组阳性克隆

本研究目的是应用PCR法快速筛查插入有苯丙氨酸脱氨酶（PAL）cDNA重组阳性克隆,用于PCR扩增的引物是位于载体pET23b启动子处的T7启动子引物和位于目的基因PALc DNA3’端终止密码TAA处的引物,以灭菌吸头挑一单菌落加PCR体系扩增。结果：在筛查的3个克隆中,有2个阳性克隆,并且插入方向正确,经DNA序列测定得到进一步证实,结果表明,以PCR方法筛查重组阳性克隆,可以简便快速鉴定插入片段的大小和方向,不需提取质粒。     

A Simple RNA Probe System for Analysis of Listeria monocytogenes Polymerase Chain Reaction Products

[This corrects the article on p. 2796 in vol. 59.].     

Gut Microbial Diversity in Rat Model Induced by Rhubarb

Rhubarb is often used to establish chronic diarrhea and spleen (Pi)-deficiency syndrome animal models in China. In this study, we utilized the enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) method to detect changes in bacterial diversity in feces and the bowel mucosa associated with this model. Total microbial genomic DNA from the small bowel (duodenum, jejunum, and ileum), large bowel (proximal colon, distal colon, and rectum), cecum, and feces of normal and rhubarb-exposed rats were used as templates for the ERIC-PCR analysis. We found that the fecal microbial composition did not correspond to the bowel bacteria mix. More bacterial diversity was observed in the ileum of rhubarb-exposed rats (P<0.05). Furthermore, a 380 bp product was found to be increased in rhubarb-exposed rats both in faces and the bowel mucosa. The product was cloned and sequenced and showed high similarity with regions of the Bacteroides genome. AS a result of discriminant analysis with the SPSS software, the Canonical Discriminant Function Formulae for model rats was established.     

单纯疱疹病毒的PCR直接基因分型

本文利用ＰＣＲ技术建立一种对ＨＳＶ直接基因分型的方法。在ＨＳＶ－Ⅰ、Ⅱ两型的ＤＮＡ多聚酶基因上设计了一条两型共同的上游引物（ＨＤＰ－Ｂ）和两条型特异的下游引物（ＨＤＰ－１、ＨＤＰ－２）。三条引物共同组成一个扩增反应体系,在ＨＳＶ－Ⅰ产生５４３ｂｐ条带,ＨＳＶ－Ⅱ产生３７２ｂｐ条带,据此在基因水平上对ＨＳＶ进行分型。５株不同来源的ＨＳＶ（２株Ⅰ型,３株Ⅱ型）分型结果与病毒分离及血清学方法完全一致。该反应体系与其它来源的ＤＮＡ不产生特异反应,敏感性可达１ｆｇ。应用该法对１５１份临床可疑ＨＳＶ感染的标本进行检测并分型,结果与免疫学方法完全一致。     

PCR在猴B病毒鉴定中的应用研究

目的为鉴定新分离毒株是否为B病毒.方法根据ScinicarielloF报道的引物,用PCR方法扩增BV147、HSV-1、HSV-2,对扩增产物进行SacⅡ内切酶消化.结果这一对引物可同时对这3种病毒进行扩增,但只有BV147的扩增产物可被SacⅡ内切酶切开.对BV147扩增片段克隆测序的结果证实,其与美国B病毒E2490株部分基因(UL27)相对应位置的核苷酸同源性为100%.结论初步建立了检测B病毒DNA的PCR方法并测定了新分离病毒毒株的部分基因序列,证明新分离的病毒为B病毒.     

Diagnosis of Genital Herpes by Polymerase Chain Reaction Amplification

A new polymerase chain reaction (PCR) method employing type-specific primers and probes was applied to 114 clinical specimens obtained from 58 female patients with genital lesions or who had a history of genital herpes. Ten and 15 specimens, respectively, were positive for herpes simplex virus (HSV)-1 and HSV-2 by cell culture. All of 10 culture-confirmed HSV-1 cases and 11 of 15 (73%) culture-confirmed HSV-2 cases were identified by PCR. Although there were several cases with discrepancy between cell culture and PCR for HSV-2, the results suggest that this PCR procedure could be applied to clinical specimens from the female genital tract.     

聚合酶链反应技术检测禽网状内皮组织增殖病病毒

目的建立聚合酶链反应(PCR)技术检测禽网状内皮组织增殖病病毒(REV)的方法。方法提取感染REV-T和脾坏死病毒(SNV)的SPF鸡胚成纤维细胞DNA为模板,利用前病毒长末端重复序列(LTR)区引物进行扩增。采集肿瘤病鸡,以及人工感染REV 28 d后鸡肝脏、脾脏、肾脏、心脏、胸腺、法氏囊等器官,进行扩增。同时将采集的脏器组织,进行HE染色和免疫组化试验(IHC)。结果REV-T感染的组织未检测出电泳条带,而SNV感染的细胞中检测到了一条300bp特异而清晰的电泳条带,而且SNV感染的鸡组织中,PCR方法检测到了特异的条带。通过HE染色和免疫组化技术观察到了肿瘤组织,肿瘤细胞的形态、分布。结论PCR检测REV更快捷,特异更好。     

A Fast-and-Robust Profiler for Improving Polymerase Chain Reaction Diagnostics

Polymerase chain reaction (PCR) is an in vitro technology in molecular genetics that progressively amplifies minimal copies of short DNA sequences in a fast and inexpensive manner. However, PCR performance is sensitive to suboptimal processing conditions. Compromised PCR conditions lead to artifacts and bias that downgrade the discriminatory power and reproducibility of the results. Promising attempts to resolve the PCR performance optimization issue have been guided by quality improvement tactics adopted in the past for industrial trials. Thus, orthogonal arrays (OAs) have been employed to program quick-and-easy structured experiments. Profiling of influences facilitates the quantification of effects that may counteract the detectability of amplified DNA fragments. Nevertheless, the attractive feature of reducing greatly the amount of work and expenditures by planning trials with saturated-unreplicated OA schemes is known to be relinquished in the subsequent analysis phase. This is because of an inherent incompatibility of ordinary multi-factorial comparison techniques to convert small yet dense datasets. Treating unreplicated-saturated data with either the analysis of variance (ANOVA) or regression models destroys the information extraction process. Both of those mentioned approaches are rendered blind to error since the examined effects absorb all available degrees of freedom. Therefore, in lack of approximating an experimental uncertainty, any outcome interpretation is rendered subjective. We propose a profiling method that permits the non-linear maximization of amplicon resolution by eliminating the necessity for direct error estimation. Our approach is distribution-free, calibration-free, simulation-free and sparsity-free with well-known power properties. It is also user-friendly by promoting rudimentary analytics. Testing our method on published amplicon count data, we found that the preponderant effect is the concentration of MgCl₂ (p<0.05) followed by the primer content (p<0.1) whilst the effects due to either the content of the deoxynucleotide (dNTP) or DNA remained dormant (p>0.1). Comparison of the proposed method with other stochastic approaches is also discussed. Our technique is expected to have extensive applications in genetics and biotechnology where there is a demand for cheap, expedient, and robust information.     

一种高效提取杨树发病树皮总RNA的方法及应用

对杨树发病树皮总RNA的高效提取是开展杨树抗溃疡病基因表达调控的基础,为了探讨杨树发病树皮RNA的高效提取方法,本研究以欧美杨细菌性溃疡病菌侵染后的‘中林46’杨为材料,比较了包括本研究提出的RNA提取新方法（RNA试剂盒改良法）在内的6种方法提取的总RNA的质量和浓度。结果显示,通过RNA试剂盒改良法提取的总RNA 28S rRNA条带亮度约为18S rRNA条带亮度的2倍且浓度高,表明该方法更适合感染欧美杨细菌性溃疡病的‘中林46’杨发病树皮总RNA的提取。为了验证RNA试剂盒改良法对健康杨树树皮及不同胁迫处理、组织RNA提取的适用性,进一步用该方法提取了‘中林46’杨、‘107’杨、‘北京’杨健康树皮,低氮、低磷处理的毛白杨组培苗以及白玉兰花的总RNA。结果表明,用RNA试剂盒改良法均能获取高质量的总RNA。所提取的总RNA已成功用于感染欧美杨细菌性溃疡病的杨树树皮转录组测序,以及低氮处理的毛白杨组培苗RT-PCR和荧光定量PCR实验,表明用RNA试剂盒改良法提取的总RNA可以用于后续分子实验。     

A Polymerase Chain Reaction Method for Identification of Five Major Meloidogyne Species

A polymerase chain reaction (PCR) method for discriminating Meloidogyne incognita, M. arenaria, M. javanica, M. hapla, and M. chitwoodi was developed. Single juveniles were ruptured in a drop of water and added directly to a PCR reaction mixture in a microcentrifuge tube. Primer annealing sites were located in the 3'' portion of the mitochondrial gene coding for cytochrome oxidase subunit II and in the 16S rRNA gene. Following PCR amplification, fragments of three sizes were detected. The M. incognita and M. javanica reactions produced a 1.7-kb fragment; the M. arenaria reaction, a 1.1-kb fragment; and the M. hapla and M. chitwoodi reactions resulted in a 0.52-kb fragment. Digestion of the amplified product with restriction endonucleases allowed discrimination among species with identically sized amplification products. Dra I digestions of the 0.52-kb amplification product produced a characteristic three-banded pattern in M. chitwoodi, versus a two-banded pattern in M. hapla. Hinf I digestion of the 1.7-kb fragment produced a two-banded pattern in M. javanica, versus a three-banded pattern in M. incognita. Amplification and digestion of DNA from juveniles from single isolates of M. marylandi, M. naasi, and M. nataliei indicated that the diagnostic application of this primer set may extend to less frequently encountered Meloidogyne species.     

聚合酶链扩增技术用于药品中沙门菌的快速检查

目的:由于中国药典中规定的沙门菌检查采用微生物培养法,其操作繁琐、培养周期长,本研究拟建立一种快速定性检测沙门菌的方法以替代药典中繁琐耗时的微生物培养法。方法:取10 m L含动物类药材的口服制剂,分别加入0.096~96 cfu的沙门菌,同时以大肠埃希菌作为干扰对照菌,设置沙门菌污染组、大肠埃希菌污染组、沙门菌及大肠埃希菌混合污染组及阴性对照组共4个实验组,采用多重聚合酶链扩增技术(PCR)对供试品溶液进行扩增检测,分别考察该方法对沙门菌检出的专属性、准确性、灵敏度以及适用性。结果:所建立的方法检验周期短,仅需30小时;专属性好,能准确区分沙门菌与干扰对照菌;结果准确,检测结果与药典方法检验结果一致;灵敏度高,最低检测限为1 cfu。结论:本方法便捷高效、结果准确,可为药品检验中的沙门菌检查提供一种新手段。