A real‐time PCR for the detection of hepatopancreatic parvovirus (HPV) of penaeid shrimp

Hepatopancreatic parvovirus (HPV) causes a common shrimp disease that occurs in many shrimp farming regions, especially in the Indo Pacific, and infects most of the cultured penaeid species. There are seven geographic HPV isolates known, so a method to detect different HPV types is needed. We developed a sensitive and generic real‐time PCR assay for the detection of HPV. A pair of primers and TaqMan probe based on an HPV sequence obtained from samples of Fenneropenaeus chinensis from Korea were selected, and they were used to amplify a 92 bp DNA fragment. This real‐time PCR was found to be specific to HPV and did not react with other shrimp viruses. A plasmid (pHPV‐2) containing the target HPV sequence was constructed and used for determination of the sensitivity of this assay. The assay could detect a single copy of plasmid DNA, and it was used successfully in finding HPV in shrimp samples from the China‐Yellow Sea region, Taiwan, Korea, Thailand, Madagascar, New Caledonia and Tanzania.     

A quantitative method for detecting ammonia‐oxidizing bacteria in coastal aquaculture systems

There is a need to quantify autotrophic nitrifiers in coastal aquaculture systems for evolving a bioremediation strategy. Autotrophic nitrifiers are extremely slow‐growing organisms, which cannot be detected by traditional methods as they are notoriously difficult to culture. Molecular techniques based on functional genes could be deployed for the detection of nitrifiers. Ammonia monooxygenase (amoA), that catalyses the oxidation of ammonia to hydroxylamine in the rate‐determining step of nitrification is largely unique to ammonia‐oxidizing bacteria (AOB). In the present study, a quantitative real‐time polymerase chain reaction assay targeting amoA was developed to estimate AOB population size in coastal soil, ammonia‐removing bioaugmentors and the solid matrix. To achieve this objective, different set of primers and a dual labelled probe have been designed for SYBR Green and TaqMan real‐time assays. The abundance of AOB ranged from 10⁴ to 10⁶ order of magnitude in the samples. In the present study, biofilm formation of the consortium of nitrifying bacteria onto bagasse has also been quantified. The results demonstrate that the developed method is a rapid and sensitive tool for the quantitative detection of nitrifying bacteria in aquatic and related environment. This helps in making the bioremediation approach for ammonia removal by immobilization of nitrifying bacteria onto the natural substrate.     

Latent entry and spread of Colletotrichum acutatum (species complex) in strawberry fields

Anthracnose, caused by Colletotrichum acutatum (species complex), has become a troublesome problem in strawberry production worldwide. This paper reports (i) an optimized sampling method combined with a real‐time PCR technique to detect the latent presence of C. acutatum in cold‐stored strawberry plants used as planting material in several European countries, and (ii) a study of the spread of C. acutatum following a point inoculation under field conditions. Screening of different parts of planting material suggested that C. acutatum is most likely to be present on runners and old petioles. In addition, in seven out of nine batches of planting material from different nurseries, latent infection by C. acutatum was detected in at least one of five replicate samples. Field experiments in 2009 and 2010 showed extensive latent within‐field spread of the pathogen on strawberry leaves, with a within‐row dispersal distance up to at least 1·75 m in 1 week. A straw ground cover between the rows did not decrease C. acutatum spread, probably because introduced (and/or subsequent) inoculum was confined to the plant bed (within the row) and was not present between the beds. Moreover, the number of C. acutatum spores on the symptomless leaves, as estimated using a real‐time PCR method, was significantly (P < 0·05) correlated with the incidence of fruit rot at harvest and post‐harvest (r = 0·56–0·66). These results illustrate the importance of detecting latent infections in planting material and strawberry leaves in the field.     

甲基茉莉酸和草酸诱导油菜BN10基因的表达

利用实时荧光定量PCR方法,观察油菜BN10基因在根、茎、叶中的表达差异,并分析甲基茉莉酸(MeJA)和草酸(OA)对该基因的诱导表达的动态变化。结果表明:BN10基因在油菜根、茎、叶中均能表达,其中在根中的表达量最高,茎中的表达量次之,在叶中的表达量最低,且在抗病毒品种苏油1号中的表达量高于感病品种中双9号;BN10的表达受MeJA和OA的诱导影响。MeJA诱导处理感病品种中双9号叶片后,BN10基因表达先升后降,在24h时表达量最高,为诱导前的2.58倍,之后有所下降,但诱导后的表达量始终高于诱导前,72h时的表达量仍为诱导前的1.13倍;OA诱导处理中双9号后,BN10表达量也是先增加后降低,在12h时达到最大值,为诱导前的2.5倍,72h时下降至最低,仅为诱导前的25%。MeJA诱导处理抗病品种苏油1号后,BN10的表达趋势与中双9号相似,但各时间点的表达量均高于中双9号;OA诱导处理苏油1号后,对BN10的诱导更强烈,表达量在6h时即达到峰值,为诱导处理前的3.05倍,之后逐渐下降。     

山羊C D 4基因的克隆及组织表达分析

CD4基因是质膜上的转运系统之一,为动物辅助性T细胞(TH)和部分胸腺细胞的共受体与信号传导分子,参与TCR介导的TH细胞活化和胸腺细胞分化过程.该研究首次克隆了山羊CD4基因(GenBank登录号:EU913093),并分析了该基因的组织表达情况.结果表明:所克隆的山羊CD4全长cDNA序列为1 555bp,开放阅读框(ORF)为1 368bp,编码455个氨基酸的蛋白,相对分子质量为5.05×104,等电点为9.52.山羊CD4蛋白前体由信号肽、胞外区、跨膜区和胞浆区4个部分构成.胞外区含有4个Ig样结构域,2个二硫键(C41—C109和C143—C180)及3个N糖基化位点(N231,N263和N343).氨基酸序列比对表明山羊CD4与绵羊CD4的氨基酸相似性为98%,与猪、人、兔、狗、猫、蝙蝠以及小鼠的氨基酸相似性分别为81%,74%,73%,72%,70%,70%和66%.系统发育树表明山羊CD4与绵羊和猪的CD4蛋白聚成一支,表明它们有较近的亲缘关系,其中山羊与绵羊的亲缘关系最近,而与狗、蝙蝠、兔、人和小鼠的亲缘关系相对较远.实时荧光定量PCR分析发现,CD4在山羊淋巴中的表达量最高,在睾丸中表达量较低,表明山羊CD4是一种免疫分子.     

11种杀虫剂对松墨天牛肌肉LIM蛋白基因表达的影响

松墨天牛（MonochamusalternatusHope）是松树的重要蛀干害虫,也是松材线虫（Bursaphelenchusxylophilus）的主要传播媒介。试验从松墨天牛文库中分离得到肌肉LIM蛋白基因的部分cDNA序列,长度为871 bp,命名为MaLIM（GenBank：KJ872589）;与赤拟谷盗（Tribolium castaneum）和家蚕（Bombyxmori）氨基酸相似性分别为77%和75%。用RT-qPCR测定了11种杀虫剂对MaLIM相对表达量的影响,结果表明,杀虫剂处理后MaLIM基因的表达量均有所下降,仅为对照的0.03~0.53。     

转录因子Relish在斑节对虾不同发育阶段的表达分析

对克隆获得的转录因子NF-κB/Rel家族成员Relish基因在斑节对虾发育阶段的表达特征进行分析。所获的PmRelish是Relish基因的亚型之一,与凡纳滨对虾LvRelish高度相似,结构域组成相同,其中RHD、IPT和DD结构域均具有100%的同源性,ANK结构域的相似性也高达97.7%。NF-κB/Rel家族进化树分析显示,PmRelish与对虾、昆虫等节肢动物的Relish聚为一支,并与P105(NF-κB1)和P100(NF-κB2)最为相近。PmRelish的表达在4个幼体发育时期都存在显著性差异,其中糠虾阶段表达量最高。PmRelish在不同发育阶段的精巢和卵巢中的表达特征相似,即未成熟期的表达相对较低,其中PmRelish在10～12 cm体长雄虾精巢中表达量最高,卵巢中的表达则在成熟期(V期)最高,为卵原细胞期的14.3倍。     

鸡减蛋综合征病毒Hexon基因SYBR GreenⅠ实时荧光定量PCR检测方法的建立

用PCR方法扩增出鸡减蛋综合征病毒（EDSV）Hexon基因保守片段,经琼脂糖凝胶电泳及序列测定分析扩增产物的特异性。以构建的阳性重组质粒作为标准品,建立SYBR GreenⅠ实时荧光定量PCR反应的扩增曲线和溶解曲线,并绘制标准曲线。结果表明,建立的EDSV荧光定量PCR标准曲线Ct值与1×10^1～1×10^6拷贝/μL的基因拷贝数呈现良好线性关系,灵敏度可达10拷贝,且特异性及重复性良好;说明本试验建立的SYBR GreenⅠ实时荧光定量PCR检测方法可用于EDSV的诊断及病原的定量分析。     

Relative importance of seed‐tuber and soilborne inoculum in causing black dot disease of potato

Controlled‐environment and field experiments were done to quantify the individual contribution of seed‐tuber and soilborne inoculum of Colletotrichum coccodes in causing black dot disease of potato tubers. Seed‐tuber and soilborne inocula of C. coccodes were quantified using an existing real‐time PCR assay and related to subsequent incidence and severity of disease. In four field trials, a controlled‐environment experiment and through the monitoring of 122 commercial crops, seed‐tuber inoculum was found to be relatively less important than soilborne inoculum in causing black dot, and the level of seed‐tuber inoculum did not significantly affect either the incidence or severity of disease or the percentage of progeny tubers deemed unmarketable. By contrast, soilborne inoculum had the potential to result in high levels of disease and the level of C. coccodes soil infestation (pg DNA g^?1 soil) was found to have a significant effect. At soil infestation levels below 100 pg DNA C. coccodes g^?1 soil, 7% of commercial crops had an incidence of black dot greater than 20%, increasing to 40% and 57% of crops at levels of 100–1000 pg g^?1 and >1000 pg g^?1 soil, respectively. These arbitrary threshold levels for soilborne inoculum related to disease risk are discussed. Interpretation of disease risk based on inoculum levels must, in the future, be informed by agronomic variables and potential control strategies.