Parameters for specific detection ofClavibacter michiganensis subsp.sepedonicus in potato stems and tubers by multiplexed PCR-ELISA

A multiplex PCR-ELISA protocol for detection ofClavibacter michiganensis subsp.sepedonicus (Cms) was developed that is based on primers for amplification of three single-copy, unique DNA sequences, Cms50, Cms72, and Cms85. The three sequences were simultaneously amplified from the genomes of all 42 strains of Cms that were tested including variant mucoid forms, but not from strains representing five related subspecies, andRathayibacter rathayi andRhodococcus faciens. The lowest limit of detection by gel electrophoresis was estimated to be approximately 300 CFU per mL when cells were spiked into potato core fluid, but sensitivity increases approximately 10-fold using PCR-ELISA. Inclusion of a sea anemone DNA fragment engineered so it could be amplified from the Cms72 primer set provided the simultaneous signal that the system functioned properly when any sample was free of the pathogen. The addition of hydrolyzed casein to the reaction mix was demonstrated to markedly reduce or eliminate inhibition of PCR by plant cell components or contaminants. Multiplex PCR-ELISA detection of Cms was determined to be verifiable for analysis of both stems and tubers based on the amplification of multiple sites in its genome, it provides absolute specificity, and it was more sensitive than detection based on gel electrophoresis of PCR products and serological approaches.     

水稻细菌性谷枯病菌的实时荧光PCR检测技术研究

 水稻细菌性谷枯病菌Burkholderia glumae于2007年被列为我国进境植物检疫性有害生物,国内急需建立针对该菌切实可行的检测技术, 以有效控制它在我国的传播。采用实时荧光PCR（real time fluorescence PCR）和经典PCR技术进行水稻细菌性谷枯病菌检测。研究结果表明,供试所有谷枯病菌都能产生139 bp左右的特异性片段,非谷枯菌株均无特异性片段产生。两种检测方法的灵敏度比较发现,常规PCR技术在病菌浓度为104CFU/mL时即可检测到,实时荧光PCR技术在病菌浓度为102CFU/mL时即可检测到,后者比前者的灵敏度高100倍。将模拟带菌种子与灭菌种子按1∶100混合,实时荧光PCR技术可以检测到该菌的存在。     

Comparison of distribution of virulence determinants in clinical and environmental isolates of Vibrio cholera

Background: The virulence of a pathogenic Vibrio cholerae is dependent on a discrete set of genetic determinants. In this study, we determined the distribution of virulence determinants among the clinical and environmental isolates of V. cholerae. Methods: The antibiotic resistance profiles of the isolates were determined using standard disk diffusion assay. PCR assay was performed to analyze the presence of toxin genes of ctx, zot and ace. The composition of cholera toxin encoding element (CTX) region flanking of the V. cholerae isolates was also analyzed. Results: All of the clinical isolates (100%) showed a complete set of virulence genes and also the attachment site of the filamentous bacteriophage CTXphi. None of the environmental isolates contained the virulence genes and the attachment site of the CTXphi. Analysis of the flanking regions including the toxin-linked cryptic element and repeat in toxin genes revealed their integrity in the clinical isolates while in the environmental isolates they were absent or contained incomplete sequences. Comparison of the antibiotic resistance assay of the environmental and clinical isolates showed a significant difference in the resistance profiles of the isolates obtained from the two sites. High rates of resistance to co-trimoxosol, streptomycin and chloramphenicol were found with clinical isolates. Conclusion: The absence of all virulence determinants in the environmental strains may suggest that certain ecological features must be present for V. cholerae to acquire a complete set of virulence determinants and to turn them into pathogenic strains.     

Evaluation of a PCR kit for the detection ofErwinia carotovora subsp.atroseptica on potato tubers

Summary A PCR-based kit, Probelia^TM, for the detection ofErwinia carotovora subsp.atroseptica (Eca) on potatoes was evaluated at five laboratories in four countries. The kit is based on DNA-specific PCR amplification followed by detection of amplicons by hybridization to a peroxidase-labelled DNA probe in a microplate. Specificity of the PCR primers for Eca, regardless of serogroups, was confirmed by testing against 246 bacterial, fungal and plant species. Detection limits of the assay varied little between six Eca strains in pure cultures (1.3×10² to 1.5×10³ cells ml⁻¹). When Eca-free tuber peel extract from four cultivars was inoculated with known numbers of 15 Eca strains, detection limits were more variable (1.0×10¹ to 6.2×10³ cells ml⁻¹ peel extract), attributed probably to inconsistency in the recovery of DNA during extraction. When the PCR assay was compared with three current commercial Eca detection methods, using naturally contaminated tubers, results matched most closely those from viable counts on a selective medium, the most sensitive method (88%), followed by enrichment ELISA (72%) and last ELISA (30%), the least sensitive method.     

Rapid and Accurate Identification by Real-Time PCR of Biotoxin-Producing Dinoflagellates from the Family Gymnodiniaceae

The identification of toxin-producing dinoflagellates for monitoring programmes and bio-compound discovery requires considerable taxonomic expertise. It can also be difficult to morphologically differentiate toxic and non-toxic species or strains. Various molecular methods have been used for dinoflagellate identification and detection, and this study describes the development of eight real-time polymerase chain reaction (PCR) assays targeting the large subunit ribosomal RNA (LSU rRNA) gene of species from the genera Gymnodinium, Karenia, Karlodinium, and Takayama. Assays proved to be highly specific and sensitive, and the assay for G. catenatum was further developed for quantification in response to a bloom in Manukau Harbour, New Zealand. The assay estimated cell densities from environmental samples as low as 0.07 cells per PCR reaction, which equated to three cells per litre. This assay not only enabled conclusive species identification but also detected the presence of cells below the limit of detection for light microscopy. This study demonstrates the usefulness of real-time PCR as a sensitive and rapid molecular technique for the detection and quantification of micro-algae from environmental samples.     

Real-time Fluorescence PCR Method for Detection of Burkholderia glumae from Rice

Burkholderia glumae causing seedling rot and grain rot of rice was listed as a plant quarantine disease of China in 2007. It's quite necessary to set up effective detection methods for the pathogen to manage further dispersal of this disease. The present study combined the real-time PCR method with classical PCR to increase the detecting efficiency, and to develop an accurate, rapid and sensitive method to detect the pathogen in the seed quarantine for effective management of the disease. The results showed that all the tested strains of B. glumae produced about 139 bp specific fragments by the real-time PCR and the general PCR methods, while others showed negative PCR result. The bacteria could be detected at the concentrations of 1×104 CFU/mL by general PCR method and at the concentrations below 100 CFU/mL by real-time fluorescence PCR method. B. glumae could be detected when the inoculated and healthy seeds were mixed with a proportion of 1:100.     

Detection methods forVerticillium species in naturally infested and inoculated soils

The detection and identification of threeVerticillium species in field soils with a polymerase chain reaction (PCR)-based assay was compared to the traditional plating assay method. The two methods were both able to detect the commonVerticillium species in soils although the PCR method detectedV. tricorpus in three soil samples that the traditional method did not. In addition, the PCR assay was rapid, efficient, and required only 1 to 2 days for positive identification whereas the traditional methods required 4 to 8 weeks. The traditional method provided a quantitative measure of pathogen propagules in the soil with population levels ranging from 0 to 21, 625 colony-forming units per gram of soil. However, it was not able to differentiate between the weakly pathogenicV. albo-atrum strain 2 and the more aggressiveV. albo-atrum strain 1, but these two were distinguished with the PCR assay. Results from this study demonstrate that when symptoms of verticillium wilt are observed in potato plants in the field, the major verticillium wilt pathogens present in field soils can be rapidly and reliably detected by the PCR assay.     

Controlled expression of cholera toxin B subunit from Vibrio cholerae in Escherichia coli

The ctxB gene, the causative agent of cholera epidemic was successfully cloned from V. cholerae in E. coli. The insertion of the gene was confirmed by PCR as well as restriction digestion analyses. The sequencing results for the gene confirmed that the insert was in the correct orientation and in-frame with the P(BAD) promoter and it showed that the gene was 99% homologous to the published ctxB sequence. The CTB protein was successfully expressed in E. coli using the pBAD/His vector system. The expected protein of approximately 14 kDa was detected by SDS-PAGE and Western blot. The use of pBAD/His vector to express the cholera toxin gene in E. coli would facilitate future study of toxin gene products.     

橡胶树红根病病原菌LAMP检测方法的建立及应用

由灵芝菌（Ganoderma pseudoferreum）引起的红根病是橡胶上危害面积最广、影响最大的世界性根部传染性病害。本研究利用环介导等温扩增技术（LAMP）,以G. pseudoferreum线粒体Large rDNA特异片段为靶标序列,设计出G. pseudoferreum 特异性LAMP引物,以SYBR Green I为指示剂,建立基于颜色判断的直观、快速、灵敏的G. pseudoferreum LAMP检测方法,优化了反应体系和条件,进行了特异性、灵敏度及田间疑似病样的检测验证。结果表明：整个试验检测时间仅需80 min,在等温64 ℃条件下反应1 h能特异性检测出G. pseudoferreum;特异性检测中,G. pseudoferreum菌株扩增后呈阳性（绿色）,而其他真菌均为阴性（橙色）。该技术最低检测限为1′10^-5 ng/μL。田间疑似病样LAMP体系检测,病原检出率为85%。本研究建立的LAMP检测技术为橡胶树红根病菌的快速鉴定提供了新技术。     

Detection and quantification ofSpongospora subterranea f. sp.subterranea by PCR in host tissue and naturally infested soils

A polymerase chain reaction (PCR) assay using primers SsF and SsR designed from the internal transcribed spacer (ITS) regions ofSpongospora subterranea f. sp.subterranea was developed for the specific identification and quantification ofS. subterranea. These primers amplified a 434 bp product from DNA ofS. subterranea spore balls, but not from DNA of healthy potato, common scab tuber, and taxonomically related plasmodiophorids. This PCR assay was successfully used for the detection ofS. subterranea in naturally infected symptomatic and asymptomatic potato tubers.Spongospora subterranea in other infected symptomless host plants was detected by PCR. The PCR assay was modified with improved soil DNA extraction methods to detectS. subterranea in soil. The assay was sensitive, and one spore ball per gram of soil could be detected. Following the design of a heterologous competitor DNA template from the sequence of λDNA, a competitive PCR assay for the quantification ofS. subterranea in soil was developed and provided accurate quantification in the range of 1 to 10⁴ spore balls per 0.25 g of soil. In a preliminary survey of naturally infested field soil samples, spore ball concentrations were estimated to vary from ca 0 to 3600 spore balls per 0.25-g soil sample by this competitive PCR assay. The spore ball levels were compared with the powdery scab disease incidence of potatoes in these fields, and a correlationship between spore ball levels and subsequent disease incidence was found. The PCR assays developed in this investigation can be routinely used to detect and quantifyS. subterranea in diseased plant tissue, asymptomatic plant tissue, and infested soil.     

马铃薯S病毒的RT-PCR检测

根据马铃薯S病毒(PVS)的外壳蛋白基因序列,设计合成了一对寡核苷酸引物。以感染PVS的马铃薯组织和健康的组织为材料,对提取植物总RNA的两种方法进行了比较,并对总RNA的提取方法进行改进,获得了纯度较高,完整性较好的总RNA。以此为模板,进行cDNA合成及PCR扩增,从感病组织扩增得到一段长度约642bp的特异PCR扩增产物,与理论设计的外壳蛋白基因大小一致,而健康组织无此扩增产物。从而建立了检测PVS快速灵敏简便的新方法,在基因水平上为PVS的检测提供了新手段。     

Simplified extraction method for ELISA and PCR detection of potato leafroll luteovirus primary infection in dormant potato tubers

This report describes a simple, rapid and inexpensive procedure for sampling large numbers of dormant tubers for analysis of potato leafroll luteovirus (PLRV) infection. The procedure uses a common electric drill to simultaneously remove and macerate tuber-eye samples for detection of PLRV by the enzyme-linked immunosorbant assay (ELISA) and the polymerase chain reaction (PCR). By using these sampling and analysis approaches, 19 of 20 different PLRV isolates were detected in dormant tubers from plants with primary infections. Results from the dormant tuber analysis, were verified by planting the tubers and testing leaf tissue by ELISA and PCR. Similar sampling and testing done on healthy dormant tubers and sprouts from the tubers consistently gave negative results as expected.     

The comparison of the effectiveness of a modified conformation sensitive gel electrophoresis with denaturing high performance liquid chromatography

Background: Several methods have been developed for detection of sequence variation in genes and each has its advantages and disadvantages. A disadvantage of them is that the simpler, cost-effective methods are commonly perceived as being less sensitive in their detection of sequence variation, whereas those with proven sensitivity have a requirement for complex or expensive laboratory equipment. In this context, we undertook improvements to the conformation sensitive gel electrophoresis (CSGE) method which provides a cost-effective approach to mutation detection and compared the results with scanning carried out using denaturing high performance liquid chromatography (DHPLC) which utilises a dedicated analyser. Methods: We designed PCR primers to amplify the seven protein-coding exons of the human SPP2 gene which encodes secreted phosphoprotein 24 (spp24) such that the amplified products included the immediately-adjacent intronic regions. Five improvements were made to the CSGE method that was used to the scan the PCR-amplified DNA. The scanning was then repeated using DHPLC and the results were compared. Results: Using CSGE, a single nucleotide polymorphism was discovered in exon 2 and another in intron 2 of the gene. Re-scanning of the same regions by DHPLC detected no additional sequence polymorphisms. Conclusion: With modification of the original protocol, CSGE is capable of providing a simple and cost-effective approach to the detection of DNA sequence polymorphisms that appears to be comparable in sensitivity to DHPLC.     

小麦和玉米籽粒赤霉菌产毒类型的PCR检测

为了建立一种准确、快速鉴定赤霉菌毒素的方法,根据赤霉菌毒素生物合成调控路径T ri5-T ri6基因保守序列,设计了一对通用引物,用于检测和鉴别产生脱氧雪腐镰刀菌烯醇(DON)和雪腐镰刀菌烯醇(N IV)毒素的赤霉菌特异DNA片断。结果表明,产生毒素DON的赤霉菌具有一个300 bp的特异DNA片断,而产生毒素N IV的则为360 bp。PCR检测与HPLC或GC/M S化学分析结果完全一致。利用这一方法分析检测了小麦、玉米籽粒中赤霉菌产毒类型,发现除健康籽粒外,在所有轻微、中度、严重感染赤霉病的小麦或玉米籽粒中,均同时检测到DON及N IV的两种DNA片断,表明这一对通用引物对两种毒素特异DNA片断的扩增效率相同。这些结果说明,该技术是一种经济、快速、可靠的PCR检测技术,可广泛用于赤霉菌及其毒素检测鉴定中。     

建兰花叶病毒RT-LAMP检测方法的建立

建兰花叶病毒（Cymbidium mosaic virus,CyMV）是侵染兰花的主要病毒,严重影响其观赏价值,建立快速、灵敏的检测方法显得尤为重要。根据CyMV的外壳蛋白基因序列设计4对特异性引物,经过优化反应条件,建立该病毒的RT-LAMP 检测方法,并进行LAMP检测的特异性、敏感性检测。该方法能特异扩增CyMV,与其他4种病毒（齿兰环斑病毒、菜豆黄花叶病毒、黄瓜花叶病毒和小苍兰花叶病毒）不发生反应;灵敏度为RT-PCR的10倍。田间检测20份样品中,RT-LAMP和RT-PCR检测结果一致,检出率为60%。在产物中加入荧光染料SYBR GreenⅠ,直接用肉眼观察就可判断样品是否感染CyMV,可省去电泳分析的时间。针对CyMV建立的RT-LAMP方法具有特异性强、灵敏度高、操作简单、快速等特点,适用于在进境检疫及种苗繁育过程中的检测鉴定。     

新型花生内源特异参照基因的开发与应用研究

一个物种的内源特异参照基因是该物种区别其它物种的特异性标志之一。本研究通过对GeneBank中花生基因信息的检索分析,筛选出花生几丁质酶基因chi2.2作为该物种内源特异参照基因的候选基因。通过对该基因的特定区域设计引物,建立了花生产品特异性定性PCR检测方法。利用该方法分别对16个花生品种的DNA进行PCR扩增,均能扩增出81bp的片段。利用相同引物分别对其他油料作物、粮食作物和蔬菜等（油菜,大豆,芝麻,向日葵,油棕,棉花,水稻,玉米,长豆角,豌豆,土豆,萝卜,辣椒,茄子,拟南芥,烟草）的DNA进行PCR扩增,均未发现特异性扩增产物。 结果表明,本研究建立的花生产品检测方法具有很好的物种特异性,且其灵敏度达到0.05ng基因组DNA。该方法可用于花生源成分鉴定,如确定食品中是否含有花生源成分,本研究为识别掺假使杂和保障食品安全提供有效手段。     

海南桑树青枯病病原菌鉴定及其分子鉴定

桑树青枯病是由青枯雷尔氏菌引起的细菌性病害,热带、亚热带地区发病严重,严重影响蚕桑产业的可持续发展。雷尔氏菌不同种间致病力和宿主各不相同,其防治策略也相应不同,准确地分离鉴定病原菌是青枯病有效防控的先决条件。本研究采集、分离了海南省琼中县桑青枯病发病桑园（‘桂桑优62’）桑树根部、茎部病原菌,并通过致病性、生理小种、生化变种测定,结合16S rDNA、特异性引物、复合PCR检测体系、序列变种等分子鉴定方法初步确定了病原菌的种类和分类地位。结果表明,引发海南省琼中县桑青枯病的病原菌属于青枯雷尔氏菌（Ralstonia solanacearum）、生理小种5（race 5）、生化变种Ⅴ（biovar Ⅴ）,病原菌遗传进化分析结果显示病原菌属演化型Ⅰ（phylotype Ⅰ）即亚洲分支菌株,序列变种12（sequevar 12）。这些结果将为海南桑青枯病的有效防控奠定基础。     

多重PCR技术检测4种大豆镰孢菌根腐病病原

镰孢菌是引起大豆根腐病的常见病原菌,传统检测病原镰孢菌的方法存在操作繁琐、时间长、成本高和 效率低等缺点,建立一种快速检测方法显得尤为重要。本研究基于翻译延伸因子序列（EF-1α）建立了检测镰孢菌 （Fusarium species）的多重PCR反应体系,检测了多重PCR体系灵敏度,模拟侵染样本验证多重PCR技术的可行性。 实验结果表明,该方法能够通过扩增片段的大小区分锐顶镰孢菌（Fusarium acuminatum）、尖孢镰刀菌（Fusarium oxysporum）、茄病镰孢菌（Fusarium solani）和禾谷镰孢菌（Fusarium graminearum）。灵敏度检测显示,最低检测基因 组DNA浓度达1×10-4 ng/μL;模拟侵染样本实验表明,使用镰孢菌和大豆基因组混合样本作为模板,在DNA浓度为 100 ng/μL时仍能准确检测出目的条带。因此。以翻译延伸因子序列为靶标建立的多重PCR技术,能够灵敏、特异 性地检测出该四种镰孢菌,可在复合侵染引起大豆镰孢菌根腐病的病原菌鉴定中准确检测。     

PCR-ELISA法对大豆品种的转基因定性检测研究

以共价交联在PCR管壁上的寡核苷酸作为固相引物进行PCR扩增,对PCR扩增的固相和液相产物分别进行杂交和凝胶电泳检测的PCR-ELISA法,对黑龙江省常规选育品种合丰35和黑农37、外源DNA直接导入大豆的分子育种所获品种黑生101、及大连进口的美国2号等大豆,进行转基因定性检测.结果表明:该方法高效可靠,可作为一种快速定性检测转基因产品的方法;检测结果:美国2号为转基因大豆,黑生101、合丰35和黑农37为非转基因大豆.上述结果对分子育种、生态保护、安全监测及对建立黑龙江省非转基因大豆生产保护区等具有重要意义.     

Modification of serological techniques and their evaluation for detection of potato viruses in seed certification related activities

Development of alternative serological techniques to ELISA for detection of potato viruses offers advantages for monitoring virus incidence and for seed potato certification systems. Several trials showed that multiplex tissue print immunoassay (TPIA) and dot blot immunoassay (DBIA) might represent fast, practical, and sensitive alternatives for the detection of: Potato leaf roll virus (PLRV), Potato virus S (PVS), Potato virus X (PVX) and Potato virus Y (PVY), from green and/or tuber tissues. In TPIA, the specific precipitation patterns in infected tissues of leaf petioles or stem cross sections, observed with each virus, allowed identification of the specific virus or mixed infections in a single multiplex assay. For detection of PVY in green tissues, DBIA was shown to be over 50 times more sensitive than ELISA. TPIA and ELISA from the tuber stem end or from eyes might be used for rapid detection of PVY and PVS in seed potato tubers without prior germination. PVS was evenly distributed in potato tuber tissue, while PVY was localized in the vascular tissue beneath the epidermis, with irregular distribution along the periphery of the potato tuber. For laboratories in developing countries lacking time and facilities for tests based on tuber germination, monitoring for PVS and PVY using TPIA in tuber tissue may be a suitable alternative to ELISA.