Detection of ornamental transgenic fish by real-time PCR and fluorescence microscopy

Transgenic Research - Numbers of ornamental transgenic fish are increasing, and some of them are illegally imported into Europe. The fish are modified to display different fluorescent colors under...     

牙菌斑形成早期微生物定植规律的定量PCR研究

目的观察牙面彻底清洁后24 h内牙面上定植的变异链球菌、伴放线放线杆菌和总微生物的数量变化。方法 8名健康成人接受全口洁治后,分别于6、12和24 h收集龈上菌斑,提取菌斑内细菌的基因组DNA。设计变异链球菌、伴放线放线杆菌和总菌特异性引物,获得目的基因,克隆于大肠埃希菌DH5α感受态细胞,测序后获得质粒标准品。将样本和梯度稀释的质粒标准品进行SYBR Green I实时荧光定量PCR检测,绘制标准曲线,确定样本中变异链球菌、伴放线放线杆菌和总菌DNA拷贝数。结果牙面彻底清洁6 h后即有大量变异链球菌定植,变异链球菌拷贝数占总菌的0.32%,24 h后增加到0.67%。12 h时定植的变异链球菌拷贝数高于6 h,差异有统计学意义（P=0.031）,24 h后继续增加（P=0.024）。12 h时定植的总菌拷贝数高于6 h,差异有统计学意义（P=0.004）,24 h后继续增加（P=0.042）。牙菌斑中伴放线放线杆菌的拷贝数低于103。结论早期牙菌斑中12 h定植的变异链球菌和总菌数量高于6 h,且24 h内不断增加,仅有少量伴放线放线杆菌定植。     

Enumeration and detection of acetic acid bacteria by real-time PCR and nested PCR

Acetic acid bacteria play a negative role in wine making because they increase the volatile acidity of wines. They can survive in the various phases of alcoholic fermentation and it is very important to control their presence and ulterior development. The main objective of the present work is to test fast, sensitive and reliable techniques such as real-time PCR (rt-PCR) and nested PCR for enumerating and detecting the presence of this bacterial group without plating. Primers were designed on the basis of the available 16S rRNA gene sequences and tested successfully with reference acetic acid bacteria strains. The usefulness of rt-PCR was demonstrated by comparing the results with traditional techniques (colony and microscope counting). The results were similar with all the techniques. Optimized rt-PCR enabled numbers between 10(7) and 10(1) cells mL(-1) to be enumerated, while nested PCR detected less than 10 cells mL(-1). Although this latter technique cannot be used for enumeration, it has several advantages in routine laboratory analysis.     

美国白蛾核型多角体病毒实时荧光定量PCR检测方法的建立及应用

为了建立对昆虫核型多角体病毒（nucleopolyhedrovirus）进行定量检测方法,本研究选用美国白蛾Hyphantria cunea核型多角体病毒的polyhedrin基因为目的基因,经引物设计、PCR 扩增、目的片段与载体连接转化以及重组质粒的鉴定,并对重组质粒标准品和样品DNA进行检测,构建出美国白蛾核型多角体病毒SYBR GreenⅠ荧光定量标准曲线。统计学分析显示标准品浓度的对数值与Ct 值之间存在良好的线性关系（R=0.998）。该方法的检测灵敏度为10¹～10²拷贝/μL,线性范围达5个数量级,扩增产物形成单一的特异性熔解峰,组内组间的变异系数均小于3%。根据已建立的方法对不同感染时间段的感病幼虫进行检测,每毫克幼虫样本内病毒polyhedrin基因拷贝数增殖倍数对数值与感染时间（d）呈正相关（R=0.987）。这些结果表明,建立的美国白蛾核型多角体病毒荧光定量 PCR检测方法是可靠的,具有灵敏度高、重复性好等特点,可为昆虫核型多角体病毒体内增殖动态研究及昆虫病毒的标准化生产提供参考。     

Evaluation of progesterone receptor expression in eosinophils using real-time quantitative PCR

Progesterone has been shown in many instances to have immune-suppressant activities. Most of these activities have been investigated in the light of general immune suppression or with a focus on lymphocytes. However, many clinical and in vitro studies have shown that progesterone also has a suppressive effect on eosinophilia. This effect so far has not been thoroughly investigated. The purpose of this study was to evaluate whether the effect is mediated via the classical progesterone receptor (PR). We developed a new real-time quantitative PCR (RQ-PCR) for the analysis and quantification of expression of the classical PR. The test was first validated both on breast cancer cell lines and on breast cancer biopsies. Subsequently, when using eosinophils isolated from peripheral blood of healthy volunteers, we could not find evidence for the expression of PR. These data suggest that the effects of progesterone on eosinophils are not mediated by the classical PR.     

Aggregate Size Distribution of Ammonia-Oxidizing Bacteria and Archaea at Different Landscape Positions

To quantify the spatial distribution of ammonia-oxidizing bacteria (AOB) and archaea (AOA) and to determine nitrification activity in soil aggregates along a landscape, soil samples were collected from three landscape positions (shoulder, backslope, and toeslope) at two pasture sites with contrasting climatic conditions. The abundance of AOB and AOA was estimated by quantifying their respective bacterial and archaeal amoA gene copies using real-time polymerase chain reaction. Soil organic C (SOC), total N (TN), and the potential nitrification rate (PNR) were measured in aggregate size ranges (4–1, 1–0.25, and 0.25–0.05 mm). At site 1, a decreasing trend in PNR was observed as the size of aggregates decreased. Both bacterial and archaeal amoA genes were higher in the macroaggregates (4–1 and 1–0.25 mm) than in the microaggregates (0.25–0.05 mm) along the landscape. At site 2, PNR was higher in the smallest size of aggregates. In the 0.25–0.05-mm fraction, the abundance of bacterial and archaeal amoA genes was equal to, or greater than, those found in larger aggregate sizes. The relative abundance of archaeal amoA gene and the PNR correlated with relative SOC and TN contents along the landscapes. The positive relationship between relative archaeal amoA gene abundance and PNR suggests that nitrification in the studied pastures is probably driven by ammonia-oxidizing Thaumarchaeota.     

Detection and Enumeration of Sulphate-Reducing Bacteria in Estuarine Sediments by Competitive PCR

The distribution of sulphate-reducing bacteria (SRB) in the sediments of the Colne River estuary, Essex, UK covering different saline concentrations of sediment porewater was investigated by the use of quantitative competitive PCR. Here, we show that a new PCR primer set and a new quantitative method using PCR are useful tools for the detection and the enumeration of SRB in natural environments. A PCR primer set selective for the dissimilatory sulphite reductase gene (dsr) of SRB was designed. PCR amplification using the single set of dsr-specific primers resulted in PCR products of the expected size from all 27 SRB strains tested, including Gram-negative and positive species. Sixty clones derived from sediment DNA using the primers were sequenced and all were closely related with the predicted dsr of SRB. These results indicate that PCR using the newly designed primer set are useful for the selective detection of SRB from a natural sample. This primer set was used to estimate cell numbers by dsr selective competitive PCR using a competitor, which was about 20% shorter than the targeted region of dsr. This procedure was applied to sediment samples from the River Colne estuary, Essex, UK together with simultaneous measurement of in situ rates of sulphate reduction. High densities of SRB ranging from 0.2 ? 5.7 × 10⁸ cells ml^{? 1} wet sediment were estimated by the competitive PCR assuming that all SRB have a single copy of dsr. Using these estimates cell specific sulphate reduction rates of 10^{? 17} to 10^{? 15} mol of SO₄ ^{2 ?} cell^{? 1} day^{? 1} were calculated, which is within the range of, or lower than, those previously reported for pure cultures of SRB. Our results show that the newly developed competitive PCR technique targeted to dsr is a powerful tool for rapid and reproducible estimation of SRB numbers in situ and is superior to the use of culture-dependent techniques.     

实时荧光定量PCR检测金山醋酸乳杆菌的方法与应用

[目的] 建立基于实时荧光定量PCR （RT-qPCR）的金山醋酸乳杆菌特异性检测方法,并将其应用于食醋和白酒发酵过程样品的快速检测。[方法] 筛选金山醋酸乳杆菌基因组中特异性强的基因序列作为模板设计特异性引物,通过标准菌株、醋醅样品进行PCR验证引物的特异性和准确性,建立RT-qPCR方法分析金山醋酸乳杆菌在不同地区酒醅、醋醅和食醋样品中的含量。[结果] 以金山醋酸乳杆菌的苯丙氨酰-tRNA合成酶α亚基（编码pheS基因）为参考序列,设计了一对GC含量55%、T_m值59℃、可扩增199 bp片段的引物。建立的RT-qPCR方法特异性强、灵敏度高且重复性好,检测浓度范围为2.24-10.24 lg （copies/μL）,成功应用于4个地区的酒醅、醋醅和食醋样品检测。对镇江香醋醋酸发酵过程的研究表明,醋醅中的金山醋酸乳杆菌数量先迅速增加,随后稳定在10⁸ copies/g干醅。[结论] 本研究建立的RT-qPCR方法可对食醋和白酒发酵过程中金山醋酸乳杆菌进行特异性鉴定和快速定量。     

High-throughput assessment of transgene copy number in sugarcane using real-time quantitative PCR

Accurate and timely detection of transgene copy number in sugarcane is currently hampered by the requirement to use Southern blotting, needing relatively large amounts of genomic DNA and, therefore, the continued growth and maintenance of bulky plants in containment glasshouses. In addition, the sugarcane genome is both polyploid and aneuploid, complicating the identification of appropriate genes for use as references in the development of a high-throughput method. Using bioinformatic techniques followed by in vitro testing, two genes that appear to occur once per base genome of sugarcane were identified. Using these genes as reference genes, a high-throughput assay employing RT-qPCR was developed and tested using a group of sugarcane plants that contained unknown numbers of copies of the nptII gene encoding kanamycin resistance. Using this assay, transgene copy numbers from 3 to more than 50 were identified. In comparison, Southern blotting accurately identified the number of transgene copies for one line and by inference for another, but was not able to provide an accurate estimation for transgenic lines containing numerous copies of the nptII gene. Using the reference genes identified in this study, a high-throughput assay for the determination of transgene copy number was developed and tested for sugarcane. This method requires much less input DNA, can be performed much earlier in the production of transgenic sugarcane plants and allows much more efficient assessment of numerous potentially transgenic lines than Southern blotting.     

Rapid detection and quantification of Prorocentrum minimum by loop-mediated isothermal amplification and real-time fluorescence quantitative PCR

The dinoflagellate Prorocentrum minimum was successfully detected using loop-mediated isothermal amplification (LAMP) and real-time fluorescence quantitative PCR (RTFQ-PCR). Both specificity and sensitivity testing in the two methods have been validated. In the LAMP assay, the specific ladder-like pattern of bands only appeared in those templates containing P. minimum. The sensitivity of LAMP was tenfold higher than conventional PCR. In RTFQ-PCR assay, only positive amplifications were detected from those samples containing P. minimum. RTFQ-PCR can detect 0.1 cells and 10 pg of DNA within 40 cycles, showing its high sensitivity. Cells could be quantified according to standard curves in agreement with the quantification by standard microscopy counting methods. The LAMP method therefore is appropriate for on-the-spot testing because of its rapidity and simplification, and the RTFQ-PCR is fit for laboratory testing owing to its accurate quantification. The two methods are of significance in forecasting red tides.     

早晚牙菌斑变异链球菌定植差异的定量PCR检测

目的 采用实时荧光定量PCR检测白天和晚上所形成牙菌斑生物膜中变异链球菌的数量,比较早晚牙菌斑中变异链球菌定植的差异.方法 收集30名健康成人全口口腔洁治后白天和晚上形成的龈上菌斑,提取细菌基因组DNA.合成变异链球菌特异性引物,纯化PCR产物获得目的基因连接于pTA-TA载体,克隆于大肠埃希菌DH5 α感受态细胞.选取阳性克隆测序后纯化质粒DNA,获得质粒标准品.将样本和梯度稀释的质粒标准品进行SYBR Green Ⅰ实时荧光定量PCR检测,确定标准曲线,定量样本中变异链球菌DNA的拷贝数.结果 早晚牙菌斑细菌基因组DNA样本的扩增曲线均在标准品的扩增曲线范围内.晚上所形成牙菌斑中定植的变异链球菌数量(对数值7.67 ±0.77)高于白天定植的变异链球菌数量(对数值7.25±0.62)(P =0.007).结论 牙菌斑的微生物定植存在日夜节奏变化,晚上所形成牙菌斑中变异链球菌数量多于白天.     

东海原甲藻细胞色素b基因实时荧光定量PCR检测体系优化

为定量检测现场样品中东海原甲藻的细胞色素b(cytochrome b,Cytb)基因,本研究设计了该基因的特异性引物,并对现场样品反转录反应体系中加入的模板数量和定量PCR反应条件进行了优化.结果表明:设计的引物具有较好的特异性,可有效区分不同的藻类;针对现场样品,在20μL的反转录体系中,适宜加入的RNA模板的量为50 ～ 200 ng;PCR模板稀释10倍或向定量PCR反应体系中加入终浓度为0.2μg·μL-1的牛血清蛋白(BSA)均能有效降低现场样品中抑制物的抑制作用,减小干扰.该方法的建立对从分子水平探讨东海原甲藻暴发和消亡的内在机制具有重要意义.     

临床皮炎外瓶霉荧光定量PCR检测方法的建立

目的 建立基于TaqMan探针技术的皮炎外瓶霉荧光定量PCR检测方法.方法 通过对皮炎外瓶霉ITS区域基因组序列（GenBank：JN675373.1）进行分析,设计合成特异性引物和荧光标记探针,优化荧光定量PCR反应条件.以临床标本中分离的皮炎外瓶霉为阳性菌株,及其他种类真菌和细菌作为阴性对照菌株,从特异性、敏感性及重复性方面对该方法检测效果进行评价.结果 该研究设计的引物和探针能扩增皮炎外瓶霉特异性序列.临床分离得到的皮炎外瓶霉在反应中有明显扩增曲线,而甄氏外瓶霉、棘状外瓶霉、烟曲霉、白色念珠菌、新生隐球菌、马内菲青霉等20株菌在CT值≤38范围内均未有扩增;利用基因重组构建的标准品完成了标准曲线的绘制,在1.0×103～1.0×107拷贝数（Cp）内具有良好的线性关系（R2=1.000）,最低可检出量为10 Cp/μL.结论 成功建立了荧光定量PCR检测皮炎外瓶霉方法,该法特异度强、敏感度高、重复性好,将有助于临床皮炎外瓶霉感染的早期诊断和针对性治疗.     

Quantification of class 1 integron abundance in natural environments using real-time quantitative PCR

Integrons are bacterial genetic elements capable of capturing and expressing potentially adaptive genetic material. Class 1 integrons constitute the most intensely studied group of these elements to date, mainly due to their well-established role in the acquisition and dissemination of antibiotic resistance genes in clinical environments. However, virtually nothing is known about the distribution or abundance of class 1 integrons outside of the clinical context. Here we develop a SYBR Green-based real-time quantitative PCR assay capable of quantifying the abundance of class 1 integrons in environmental samples. It was shown that the abundance of the intI1 gene in creek sediment correlates with ecological condition, implying that class 1 integrons provide selective advantages relevant to environmental pressures other than the use of antibiotics. By comparing the quantities of intI1 and 16S rRNA gene in each sample, it was demonstrated that approximately 2.7% of cells potentially harbour a class 1 integron. These findings suggest that class 1 integrons are widespread in natural environments removed from clinical settings and occur in a broader range of host organisms than had previously been assumed on the basis of culture-dependent estimates.     

Comparative assessment of human and farm animal faecal microbiota using real-time quantitative PCR

Pollution of the environment by human and animal faecal pollution affects the safety of shellfish, drinking water and recreational beaches. To pinpoint the origin of contaminations, it is essential to define the differences between human microbiota and that of farm animals. A strategy based on real-time quantitative PCR (qPCR) assays was therefore developed and applied to compare the composition of intestinal microbiota of these two groups. Primers were designed to quantify the 16S rRNA gene from dominant and subdominant bacterial groups. TaqMan^® probes were defined for the qPCR technique used for dominant microbiota. Human faecal microbiota was compared with that of farm animals using faecal samples collected from rabbits, goats, horses, pigs, sheep and cows. Three dominant bacterial groups ( Bacteroides/Prevotella, Clostridium coccoides and Bifidobacterium ) of the human microbiota showed differential population levels in animal species. The Clostridium leptum group showed the lowest differences among human and farm animal species. Human subdominant bacterial groups were highly variable in animal species. Partial least squares regression indicated that the human microbiota could be distinguished from all farm animals studied. This culture-independent comparative assessment of the faecal microbiota between humans and farm animals will prove useful in identifying biomarkers of human and animal faecal contaminations that can be applied to microbial source tracking methods.     

Quantification of ratios of Bacteria and Archaea in methanogenic microbial community by fluorescence in situ hybridization and fluorescence spectrometry

16S rRNA-targeted oligonucleotide probes for Bacteria (Eub338) and Archaea (Arc915) were used for whole-cell, fluorescence in situ hybridization (FISH) to quantify the ratio of these microbial groups in an anaerobic digester. The quantity of specifically bound (hybridized) probe was measured by fluorescence spectrometry and evaluated by analysing the dissociation curve of the hybrids, by the measurement of the binding with a nonsense probe, and by the competitive inhibition of the binding of the labelled probe by the corresponding unlabelled probe. Specific binding of oligonucleotide probes with the biomass of anaerobes was 40–50% of their total binding. The ratio of Arc915 and Eub338 probes hybridized with rRNAs of the cells in anaerobic sludge was 0.50. Measurement of FISH by fluorescence spectrometry appears to be a suitable method for quantification of the microbial community of anaerobes.     

实时荧光定量PCR快速鉴别新型冠状病毒主要变异株北大核心CSCD

为建立一种快速鉴别严重急性呼吸综合征冠状病毒2 (severe acute respiratory syndrome coronavirus 2,SARS-CoV-2)的5种主要变异株的Taq Man探针实时荧光定量PCR(real-time quantitative PCR, RT-qPCR)体系,基于SARS-CoV-2野生型及变异株alpha (N501Y、HV69-70del)、beta (E484K、K417N)、gamma (K417T、V1176F)、delta (L452R、T478K)和omicron (H655Y、N679K、P681H)序列设计特异性引物、探针,建立和优化一种鉴别新型冠状病毒(SARS-CoV-2) 5种主要变异株的Taq Man探针RT-qPCR方法,并进行该方法的特异性、敏感性、鉴别能力评价。该方法可准确区分出SARS-CoV-2野生型和突变型,与其他呼吸道病原体(n=21)无交叉,显示高特异性。该方法最低检测限为2×10;拷贝/mL,操作简单、快速、成本廉价,可用于监测SARS-CoV-2毒株的变异,精准指导疫情识别与防控。