肠球菌TaqMan实时荧光定量PCR检测方法的建立及初步应用

目的利用TaqMan荧光定量PCR方法,建立肠球菌实时荧光PCR检测方法,并初步应用于粪便中肠球菌的检测。方法根据GenBank发表的肠球菌23S rRNA基因序列的保守区域参考国外文献设计合成特异性的引物和探针[1];利用构建的质粒标准品优化Mg2 的浓度和引物探针浓度,并考核检测体系的保守性、灵敏性和重复性;初步应用于粪便标本的检测分析。结果Mg2 终浓度为4.5 mmol/L,上下游引物终浓度为0.4μmol/L,灵敏度为6拷贝数/反应;绘制两种标准曲线,构建了基因拷贝数、细菌数为分析指标的定量分析模型,检测粪便标本结果显示TaqMan荧光定量PCR方法较平板计数法敏感、快捷、简便。结论本研究建立了一种灵敏、特异、简便易行的肠球菌定量检测方法。     

猪轮状病毒RT-LAMP检测方法的建立及应用

为了建立一种适用于猪轮状病毒(PoRV)的逆转录-环介导等温核酸扩增(RT-LAMP)的快速、灵敏检测方法。依据GenBank上登录的PoRV VP7基因保守序列,设计了6条特异性引物,通过对外引物与内引物浓度比、Bst DNA聚合酶浓度、Mg2+浓度、dNTP浓度和反应条件等进行优化。结果显示,当外引物与内引物浓度比为200nmol/L∶2 400nmol/L(1∶12)、Bst DNA聚合酶浓度为0.64 U/μL、Mg2+浓度为2.5 mmol/L、dNTP浓度为1.0mmol/L,在恒温(60℃)条件下作用60min,扩增效果出现明显"梯状"条带,同时对建立的RT-LAMP检测方法进行特异性和敏感性验证,其只有PoRV获得特异性扩增条带,与其他猪流行性腹泻病毒、猪传染性胃肠炎病毒、猪瘟病毒等无交叉反应,具有良好的特异性,最低检测分子拷贝数为1.0×102拷贝/μL,具有极高的敏感性。反应结束后肉眼可见阳性扩增产物出现白色沉淀,加入SYBR GreenⅠ观察颜色变化可以判定结果。该方法适用于野外、基层部门和海关快速检测PoRV的新方法,在临床上有良好的推广意义。     

大鼠结肠平滑肌细胞的钙库操纵性通道

目的:探讨大鼠结肠平滑肌细胞是否存在钙库操纵性通道(SOC)。方法:荧光探针Fura-2/AM标记细胞内游离Ca2+后,用荧光分光光度计检测毒胡萝卜素(thapsigargin)和咖啡因(caffeine)耗竭胞内钙库后激活的SOC通道对酶解分离的大鼠结肠平滑肌细胞[Ca2+]i的影响。结果:在无Ca2+缓冲液中,thapsigargin(1μmol/L)以及caf-feine(10 mmol/L)分别使[Ca2+]i由静息时(68.32±3.43)nmol/L升高至(240.85±12.65)nmol/L(、481.25±34.77)nmol/L,继之,向细胞外液中引入两种浓度的Ca2+(1.5 mmol/L和3.0 mmol/L),导致[Ca2+]i进一步升高,分别为(457.55±19.80)nmol/L、(1005.93±54.62)nmol/L;(643.88±34.65)nmol/L、(920.16±43.25)nmol/L。且上述升高效应对维拉帕米(verapamil,5μmol/L)以及KCl引起的细胞膜去极化不敏感,但可被La3+(1 mmol/L)抑制。结论:在酶解分离的大鼠结肠平滑肌细胞上,存在胞内钙库耗竭激活的SOC通道,为支持在电兴奋性细胞上存在库容性Ca2+内流提供了实验和理论依据。     

沙门氏菌荧光实时定量PCR检测试剂的研制及应用

荧光实时定量PCR技术是近年来广泛应用于沙门氏菌快速检测的现代方法之一,本研究建立了检测沙门氏菌快速、敏感、特异以及准确定量的FQ-PCR方法。采用沙门氏菌fimY基因序列,设计特异引物和探针,通过对Taq酶、Mg2 和引物探针浓度等反应体系和条件的优化,然后进行特异性和适用性实验。最优化结果为:Taq酶用量2.5U;Mg2 浓度为3.75×10-3mol/L;引物浓度为0.65×10-6mol/L,探针浓度为0.30×10-6mol/L;循环条件为step1:95℃2min,step2:95℃5s,60℃40s,40cycles。结果表明该FQ-PCR检测试剂具有快速、简单、灵敏度高、特异性强和适用范围广等优点,可应用于食品卫生监管、商品检验检疫以及临床诊断等领域。     

云南野生油菜RAPD反应体系的优化

针对RAPD反应体系中Mg2+、dNTPs、引物等3个主要影响因素,设计了一组3因素3水平试验。筛选出了云南野生油菜RAPD反应优化体系。即Mg2+浓度为1.25mmol/L、dNTPs浓度为0.15mmol/L、引物浓度为0.5umol/L。     

丹参ISSR-PCR反应体系的建立与正交优化

利用正交试验设计的方法,从引物浓度、Taq DNA聚合酶浓度、Mg2+浓度、dNTP浓度4种因素3个水平,对丹参ISSR-PCR反应体系进行优化分析,并在此基础上对模板DNA浓度、PCR反应过程中的退火温度进行梯度检测。结果表明:20μL ISSR-PCR反应体系中各因素的最佳浓度为1×PCR buffer、200μmol/L dNTP、1.0μmol/L引物、1.5mmol/L Mg2+和1 U Taq DNA聚合酶,最佳模板DNA浓度为20～60ng,引物UBC 835的最佳退火温度为51.7℃。     

3种菊花病毒/类病毒实时荧光定量RT-PCR检测体系的构建与准确性评价

菊花容易受到病毒感染而造成品质下降,目前国内对菊花病毒的检测主要根据外观表现或者定性PCR检测,无法准确判定病毒载量。为构建一种可同时用于检测菊花B病毒(Chrysanthemum virus B,CVB)、番茄不孕病毒(Tomato aspermy virus,TAV)和菊花褪绿斑驳类病毒(Chrysanthemum chloritic mottle viroid,CChMVd)的实时荧光定量RT-PCR检测方法,本研究分别以保守区域作为靶标设计相应的引物探针,通过优化扩增体系中CVB、TAV、CChMVd 3种病毒/类病毒探针浓度、引物浓度、Mg²⁺浓度、dNTPs浓度,摸索扩增程序中反转录时间、退火温度和扩增循环数,构建了一种可同时用于CVB、TAV、CChMVd的3重实时荧光定量RT-PCR检测体系,优化后的扩扩增体系中CVB、TAV和CChMVd的探针浓度分别为100 nmol/L、120 nmol/L和80 nmol/L,引物浓度分别为200 nmol/L、240 nmol/L和160 nmol/L,Mg²⁺浓度为3.0 mmol/L;dNTPs浓度200μmol/L;最适反转录时间为25 min,退火温度为60℃,循环数为40。敏感性实验结果表明,该反应体系对3种病毒/类病毒的敏感性为1.0×¹⁰3拷贝/mL,敏感性好;定量线性范围为1.0×¹⁰3拷贝/mL~1.0×¹⁰10拷贝/mL,线性范围宽;特异性好,对菊花矮化类病毒、烟草花叶病毒和黄瓜花叶病毒核酸检测结果为阴性;对1.0×¹⁰4拷贝/mL的低浓度参考品平行检测10次,定量结果lg值偏差(CV%)为4.81%,重复性好。在南京农业大学"中国菊花种质资源保存中心"基地随机选择菊花20株进行本研究试剂检测,检出6例CVB病毒株和4例TAV病毒株,其病毒载量为2.5×¹⁰4拷贝/mL~5.5×¹⁰7拷贝/mL,随机选择1株CVB病毒株定量PCR,产物进行TA克隆后经测序与NCBI Blast比对,其与MH678704.1的同源性为100%。因此,本研究建立了一种能同时检测CVB、TAV、CChMVd 3种菊花常见病毒/类病毒的灵敏、快速、可定量的检测方法。     

TaqMan—MGB荧光定量RT-PCR技术快速检测H5亚型禽流感病毒

建立以TaqMan-MGB荧光探针为特点的荧光定量RT-PCR方法,用于检测H5亚型禽流感病毒。针对H5亚型禽流感病毒血凝素(HA)基因保守区域设计特异性引物与TaqMan-MGB荧光探针,筛选并优化荧光定量RT-PCR反应体系与反应条件,用以提高方法的特异性、敏感性与准确性;并通过体外克隆技术建立病毒基因拷贝数进行定量分析。结果表明:引物与探针的优化浓度分别640nmol/L和480nmol/L,体系具有良好的保守性和特异性,与其他呼吸道病毒均无交叉反应。方法检测灵敏度为100拷贝/反应,标准曲线线性范围为107～102拷贝/反应,从病毒核酸提取至检测完成仅需3h左右,操作简便,重现性好。本研究建立的TaqMan-MGB荧光定量PCR方法特异、敏感、快速,适合于临床实验室进行H5亚型禽流感病毒的快速定量检测。     

TaqMan-MGB荧光定量RT-PCR技术快速检测H5亚型禽流感病毒

建立以TaqMan-MGB荧光探针为特点的荧光定量RT-PCR方法,用于检测H5亚型禽流感病毒.针对H5亚型禽流感病毒血凝素(HA)基因保守区域设计特异性引物与TaqMan-MGB荧光探针,筛选并优化荧光定量RT-PCR反应体系与反应条件,用以提高方法的特异性、敏感性与准确性;并通过体外克隆技术建立病毒基因拷贝数进行定量分析.结果表明引物与探针的优化浓度分别640nmol/L和480nmol/L,体系具有良好的保守性和特异性,与其他呼吸道病毒均无交叉反应.方法检测灵敏度为100拷贝/反应,标准曲线线性范围为107～102拷贝/反应,从病毒核酸提取至检测完成仅需3h左右,操作简便,重现性好.本研究建立的TaqMan-MGB荧光定量PCR方法特异、敏感、快速,适合于临床实验室进行H5亚型禽流感病毒的快速定量检测.     

沙门菌、大肠杆菌和金黄色葡萄球菌的多重PCR检测*

根据沙门菌invA基因、大肠杆菌phoA基因和金黄色葡萄球菌nuc基因序列,设计3对特异性引物进行多重PCR并对反应条件进行优化。结果表明3对引物能特异地扩增出284bp、622bp、484bp的目的条带;最佳反应条件为沙门菌、大肠杆菌、金黄色葡萄球菌的引物浓度分别为40nmol/L、40nmol/L、80nmol/L,Mg²⁺浓度2.4mmol/L,dNTP浓度200μmol/L,TaqDNA聚合酶1.5U,退火温度55.0℃~57.4℃之间;在此条件下多重PCR同时检测DNA的敏     

Incidence of Prunus necrotic ring spot virus on Malus domestica in India

In surveys of apple (Malus domestica) orchards in various parts of Himachal Pradesh, samples from trees showing necrotic symptoms on the leaves were collected and tested for detection of Prunus necrotic ringspot virus (PNRSV) initially by ELISA followed by RT‐PCR using coat protein gene primers. Positive results were obtained in samples from Kullu and Kalpa regions. The virus gene sequences showed 88–97% similarity to corresponding sequences of other PNRSV isolates deposited in the GenBank database using ncbi.nih.nlm.gov. Although the similarity was high, there were some distinct differences with the Spanish isolate. This is the first report of PNRSV in apple from India.     

Engineering cherry rootstocks with resistance to Prunus necrotic ring spot virus through RNAi‐mediated silencing

Prunus necrotic ringspot virus (PNRSV) is a major pollen‐disseminated ilarvirus that adversely affects many Prunus species. In this study, an RNA interference (RNAi) vector pART27–PNRSV containing an inverted repeat (IR) region of PNRSV was transformed into two hybrid (triploid) cherry rootstocks, ‘Gisela 6’ (GI 148‐1) and ‘Gisela 7’(GI 148‐8)’, which are tolerant and sensitive, respectively, to PNRSV infection. One year after inoculation with PNRSV plus Prune Dwarf Virus, nontransgenic ‘Gisela 6’ exhibited no symptoms but a significant PNRSV titre, while the transgenic ‘Gisela 6’ had no symptoms and minimal PNRSV titre. The nontransgenic ‘Gisela 7’ trees died, while the transgenic ‘Gisela 7’ trees survived. These results demonstrate the RNAi strategy is useful for developing viral resistance in fruit rootstocks, and such transgenic rootstocks may have potential to enhance production of standard, nongenetically modified fruit varieties while avoiding concerns about transgene flow and exogenous protein production that are inherent for transformed fruiting genotypes.     

Tests for Transmission of Prunus Necrotic Ringspot and Two Nepoviruses by Criconemella xenoplax

In two of three trials, detectable color reactions in ELISA for Prunus necrotic ringspot virus (PNRSV) were observed for Criconemella xenoplax handpicked from the root zone of infected peach trees. Criconemella xenoplax (500/pot) handpicked from root zones of peach trees infected with PNRSV failed to transmit the virus to cucumber or peach seedlings. The nematode also failed to transmit tomato ringspot (TomRSV) or tobacco ringspot viruses between cucumbers, although Xiphinema americanum transmitted TomRSV under the same conditions. Plants of peach, cucumber, Chenopodium quinoa, and Catharanthus roseus were not infected by PNRSV when grown in soil containing C. xenoplax collected from root zones of PNRSV-infected trees. Shirofugen cherry scions budded on Mazzard cherry seedling rootstocks remained symptomless when transplanted into root zones of PNRSV-infected trees. Virus transmission was not detected by ELISA when C. xenoplax individuals were observed to feed on cucumber root explants that were infected with PNRSV and subsequently fed on roots of Prunus besseyi in agar cultures. Even if virus transmission by C. xenoplax occurs via contamination rather than by a specific mechanism, it must be rare.     

Prunus necrotic ringspot virus isolates in stone fruit germplasm accessions and cultivars in Israel

Prunus necrotic ringspot virus (PNRSV) was detected in almonds, plum and apricot germplasm accessions and local almond cultivars in Israel. PNRSV was widespread both in wild and cultivated almond trees and uncommon in wild apricots and plums. The possible variation among the PNRSV isolates was initially evaluated by restriction analysis of PCR products representing the CP gene with the endonuclease RsaI and followed by nucleotide sequence analysis of selected isolates. It was concluded that all 13 isolates belong to group PV96, the largest cluster of PNRSV isolates, described previously. Two PNRSV isolates, one from a plum accession and one from an almond cultivar, were found to be distinct members of group PV96 with unique nucleotide modifications not found in other documented isolates of this virus. However, no PNRSV isolate typical to a specific host and/or to the Middle East region could be identified. This study expands the body of data on variability of PNRSV isolates and highlights the importance of assessing the virus status of germplasm collections by applying reliable diagnostic and differentiating methods.     

Rootstock‐to‐scion transfer of transgene‐derived small interfering RNAs and their effect on virus resistance in nontransgenic sweet cherry

Small interfering RNAs (siRNAs) are silencing signals in plants. Virus‐resistant transgenic rootstocks developed through siRNA‐mediated gene silencing may enhance virus resistance of nontransgenic scions via siRNAs transported from the transgenic rootstocks. However, convincing evidence of rootstock‐to‐scion movement of siRNAs of exogenous genes in woody plants is still lacking. To determine whether exogenous siRNAs can be transferred, nontransgenic sweet cherry (scions) was grafted on transgenic cherry rootstocks (TRs), which was transformed with an RNA interference (RNAi) vector expressing short hairpin RNAs of the genomic RNA3 of Prunus necrotic ringspot virus (PNRSV‐hpRNA). Small RNA sequencing was conducted using bud tissues of TRs and those of grafted (rootstock/scion) trees, locating at about 1.2 m above the graft unions. Comparison of the siRNA profiles revealed that the PNRSV‐hpRNA was efficient in producing siRNAs and eliminating PNRSV in the TRs. Furthermore, our study confirmed, for the first time, the long‐distance (1.2 m) transfer of PNRSV‐hpRNA‐derived siRNAs from the transgenic rootstock to the nontransgenic scion in woody plants. Inoculation of nontransgenic scions with PNRSV revealed that the transferred siRNAs enhanced PNRSV resistance of the scions grafted on the TRs. Collectively, these findings provide the foundation for ‘using transgenic rootstocks to produce products of nontransgenic scions in fruit trees'.     

Decline and other effects of five virus infections on three varieties of plum (Prunus domestica L.)

The effects of five different virus inocula on three varieties of plum (Prunus domestica L.) were studied in a field trial of 10 years duration. The viruses causing line pattern, ringspot, prune dwarf and bark split had no effect on the growth of Marjorie's Seedling and Cambridge Gage, and only that causing prune dwarf stunted Oullins Gage trees. However, these viruses diminished the fruit yield of one or more varieties, and prune dwarf virus seriously decreased the yield of all three. Decline disease, probably caused by a strain of Prunus necrotic ringspot virus, developed in Marjorie's Seedling but not in the other varieties. The symptoms first appeared after 5 years and then the trees declined progressively with necrotic ‘incompatibility’ between rootstock and scion.     

Preparation and Characterization of a Monoclonal Antibody to Prunus necrotic ringspot virus

A cell line named PVRSV1D11 secreting monoclonal antibody (McAb) against the prokaryotically expressed coat protein (CP) of Prunus necrotic ringspot virus (PNRSV) was developed using hybridoma technology including animal immunization, cell fusion, cell line culture and enzyme‐linked immunosorbent assay (ELISA)‐based for screening. The specificity, titre and detection sensitivity of the McAb were determined by indirect ELISA to establish optimal conditions. The antibody reacted strongly with PNRSV and showed no cross‐reactions with the proteins of Plum pox virus, Prunus dwarf virus, Apple stem pitting virus, Apple stem grooving virus, Apple mosaic virus or Apple chlorotic leafspot virus. The ascites developed with PNRSV1D11 cell line showed high absorbance until it was diluted to over 6.6 × 10⁷ fold. The McAb belonged to IgG_2a isotype and was diluted by 1.28 × 10⁵ folds as an optimal detection concentration. The detection sensitivity of the monoclonal antibody was 11.7 ng/ml protein of PNRSV. The results indicated that the McAb against the CP of PNRSV is suitable for PNRSV detection in the plants and for monitoring the dynamics of the virus by using indirect ELISA.     

An efficient viral vector for functional genomic studies of Prunus fruit trees and its induced resistance to Plum pox virus via silencing of a host factor gene

RNA silencing is a powerful technology for molecular characterization of gene functions in plants. A commonly used approach to the induction of RNA silencing is through genetic transformation. A potent alternative is to use a modified viral vector for virus‐induced gene silencing (VIGS) to degrade RNA molecules sharing similar nucleotide sequence. Unfortunately, genomic studies in many allogamous woody perennials such as peach are severely hindered because they have a long juvenile period and are recalcitrant to genetic transformation. Here, we report the development of a viral vector derived from Prunus necrotic ringspot virus (PNRSV), a widespread fruit tree virus that is endemic in all Prunus fruit production countries and regions in the world. We show that the modified PNRSV vector, harbouring the sense‐orientated target gene sequence of 100‐200 bp in length in genomic RNA3, could efficiently trigger the silencing of a transgene or an endogenous gene in the model plant Nicotiana benthamiana. We further demonstrate that the PNRSV‐based vector could be manipulated to silence endogenous genes in peach such as eukaryotic translation initiation factor 4E isoform (eIF(iso)4E), a host factor of many potyviruses including Plum pox virus (PPV). Moreover, the eIF(iso)4E‐knocked down peach plants were resistant to PPV. This work opens a potential avenue for the control of virus diseases in perennial trees via viral vector‐mediated silencing of host factors, and the PNRSV vector may serve as a powerful molecular tool for functional genomic studies of Prunus fruit trees.     

The detection by serological methods of viruses infecting the rose

Homogenates of herbaceous test plants infected with arabis mosaic virus (AMV), prunus necrotic ringspot virus (PNRSV), or strawberry latent ringspot virus (SLRV), and purified virus preparations were used to assess the sensitivities of four serological methods (the enzyme-linked immunosorbent assay - ELISA, immunodiffusion in gels, the latex flocculation assay, and serologically specific electron microscopy -SSEM) for the detection of these viruses. The latex test was up to 250 times more sensitive than gel immunodiffusion, but SSEM and ELISA were respectively up to 1000 and 200 times more sensitive than the latex test. Gel immunodiffusion and latex tests failed to detect any of the viruses in infected roses. Although ELISA reliably detected PNRSV and SLRV when leaves from infected roses were homogenised in a leaf: buffer ratio of 1 g:10 ml, AMV was occasionally undetected. However, when a modified ELISA technique, which reduced non-specific reactions, was used some PNRSV-infected roses were also not detected. Detection by SSEM was c. twice as sensitive as ELISA for all three viruses in rose extracts. The relative advantages of ELISA and SSEM for the detection of plant viruses are discussed.