Performance evaluation of five commercial real-time PCR reagent systems using TaqMan assays for B. anthracis detection

BackgroundReal-time PCR assay sensitivity is affected by the choice and concentrations of reaction mix constituents among other factors such as primers, probes, and analytical assay platforms. Commercially available reagent mixes facilitate PCR assay set-up with fewer steps and timeliness. However, determination of analytical assay framework is important for ready-to-use real-time PCR reagent systems for rapid, quantitative and accurate detection of bioterror pathogens such as Bacillus anthracis.MethodsIn this study, performance characteristics of five commercially available quantitative PCR reagent mixes were evaluated using TaqMan-based real-time PCR. The reagent systems were tested for compatibility on the ABI 7000 assay platform and compared for their distinctive analytical characteristics using the B. anthracis rpoB and pag gene real-time PCR assays.Results and conclusionsKnowledge of distinctive assay performance characteristics of commercially available qPCR reagent mixes is critical for carefully designing analytical assay systems. The ABI, ABgene and Eppendorf reagent systems performed consistently overall for the two TaqMan assays for B. anthracis detection that were used in the current study. However, the use of Eppendorf reagent system requires shorter thermal cycling time. In addition, while the ABI and Eppendorf systems have similar assay sensitivity for both the rpoB and pag assays, the Eppendorf system achieves the same with lower C_T values.     

一种可用于溶瘤病毒M1体内组织定量的TaqMan RT-qPCR检测法的建立与评价

目的:监测溶瘤病毒M1在组织中的传播情况,以更好地控制给药剂量,确保安全性。方法:建立一种基于TaqMan的实时定量PCR检测法,用于对组织中溶瘤病毒M1的检测和定量,并检测静脉注射病毒后多种实验动物体内的病毒载量和分布。结果:我们以一对特异的引物(Q3)和标准RNA开始SYBR Green RT-qPCR研究。通过优化实验方法发现当退火温度高于62℃时可降低基质效应,但却影响了扩增效率。因此我们建立了一步法TaqMan RT-qPCR实验,重新设计了一对Q3短引物(Q3S)。运用一步TaqMan RT-qPCR检测法和Q3S引物,在混有SD大鼠或食蟹猴基质RNA的背景下,均能特异性检测到低拷贝数的标准RNA。经验证,该方法适用于检测M1病毒在小鼠、SD大鼠和食蟹猴体内的组织分布。结论:利用Q3S引物构建的TaqMan一步法RT-qPCR能够定量检测不同动物不同组织样品中的M1病毒,具有特异性和敏感性,可进一步应用于临床样品的检测。     

Consistency of quantitation of HCV genotype 4 from egypt across three HCV‐RNA amplification assays

Different quantitative assays for HCV‐RNA are available that report test results in International Units (IU)/ml based on the WHO International Standard. Thus, assays have been calibrated with standard material containing HCV genotype 1, so the consistency of quantitation might differ between assays for other HCV genotypes. Three commercial HCV nucleic acid amplification techniques (HCV–NAT) were compared for quantitation consistency of genotype 4 and 1 specimens from an Egyptian blood donor panel (n = 92). Consistency of quantitation between HCV–NATs was higher for genotype 1 than for genotype 4. Most quantitative results reported by the assays were in the same range, but some genotype 4 samples were missed by two of the assays. The Abbott assay showed higher concentrations for genotype 4 than the two Roche assays. Follow‐up investigations of individuals should use the same assay unless another assay has been validated properly. Standardization of HCV–NAT assays remains an issue. J. Med. Virol. 80:2086–2091, 2008. © 2008 Wiley‐Liss, Inc.     

High-resolution typing for HLA-DRB1*15 amd -DRB1*16 by fluorescence-marked sequence-specific priming (TaqMan assay)

Sequence-specific primed polymerase chain reaction (PCR-SSP) is widely used in HLA laboratories. The TaqMan method, which is described here for high-resolution typing of HLA-DRB1*15 and -DRB1*16, does not require elaborate and time-consuming post-PCR detection steps. In this one-tube assay, conventional PCR-SSP and fluorescence detection of the amplicon with a doubly labeled fluorescent probe are combined: a fluorogenic hybridization probe (FHP) labeled with a spectral resolvable fluorescent reporter dye (FAM or TET) at its 5' terminus and a common quencher dye (TAMRA) at its 3' terminus is cleaved by the 5' nuclease activity of Taq DNA polymerase only if the target sequence is amplified. An increase of fluorescence intensity indicates a successful amplification. For high-resolution typing of HLA-DRB1*15 and -DRB1*16 alleles we designed two FHPs and 14 specific primer mixes (7 for DR15 and 7 for DR16). Amplification of the specific sequence was detected by a FAM-labeled FHP, whereas amplification of the internal control was detected by a TET-labeled FHP. We were able to type all heterozygous DRB1*15/DRB1*16 subtype combinations. For evaluation, 60 HLA-DRB1*15-positive and 40 HLA-DRB1*16-positive individuals were typed and the results were compared with conventional PCR-SSP DR15/16 subtyping. There were no discrepancies between the two methods. The TaqMan method is an alternative to conventional PCR-SSP typing which is suitable for routine use in HLA laboratories.     

Epithelialized tunnels are a source of inflammation in hidradenitis suppurativa

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Comparison of <Emphasis Type="Italic">SYBR Green I</Emphasis> and <Emphasis Type="Italic">TaqMan</Emphasis> real-time PCR formats for the analysis of <Emphasis Type="Italic">her2</Emphasis> gene dose in human breast tumors

We compared two technologies of real-time PCR (with the use of fluorescent SYBR Green I dye and specific TaqMan probe) for quantification of the dose of her2 gene in breast tumors. The maximum increase in the gene dose in TaqMan and SYBR Green I analyses was 10-and 5-fold, respectively. In was found that TaqMan and SYBR Green I technologies allow detection of the matrix in amounts corresponding to 1–100 and 2.5–40.0 ng genomic DNA, respectively. Tenfold increase in the gene dose leads to incorrect evaluation of multiplication ratio in the SYBR Green I analysis. These results suggest that TaqMan technology is more preferable for correct evaluation of her2 gene dose. __________ Translated from Byulleten’ Eksperimental’noi Biologii i Meditsiny, Vol. 145, No. 2, pp. 201–205, February, 2008     

葡萄糖浓度对变形链球菌srtA基因表达影响的研究

目的观察不同浓度葡萄糖对变形链球菌初始黏附相关基因srtA表达的影响。方法变形链球菌分别在0.2%、1.0%、5.0%葡萄糖条件下培养,提取总RNA,逆转录成cDNA,利用TaqMan实时荧光定量PCR技术检测不同浓度葡萄糖环境中变形链球菌初始黏附相关基因srtA的表达情况。结果在0.2%-5.0%葡萄糖浓度范围内,黏附较强的变形链球菌菌株srtA基因的表达随糖浓度的增加而明显增强,黏附较弱的菌株也呈现这样的趋势,但差异不具有统计学意义。在0.2%和1.0%葡萄糖的环境中,黏附较强的菌株srtA基因表达显著高于黏附较弱的菌株。结论在一定浓度范围内(0.2%-5.0%),葡萄糖浓度升高所致变形链球菌srtA基因高表达可能是其促进变形链球菌初始黏附的机制之一;变形链球菌对牙面的黏附力可能与其srtA表达量有关。     

Traumatic injury-induced BMP7 expression in the adult rat spinal cord

It has been reported that bone morphogenetic proteins (BMPs) are involved in the generation of the central nervous system during development. However, the roles of BMPs in mature spinal cord have not been clarified. We examined the expression of BMP7 mRNA before and after traumatic injury of the adult rat spinal cord. BMP7 mRNA was already detectable at a relatively low level in uninjured spinal cord, but was dramatically increased after injury. Semiquantitative RT-PCR study further confirmed upregulation of BMP7 mRNA in injured spinal cord. In situ hybridization indicated that expression of BMP7 mRNA was present only in glial cells in uninjured spinal cord. After injury, the number of BMP7-expressing glial cells was increased, BMP7 expression also became apparent in motor neurons. It has been suggested that BMPs promote survival of subventricular zone cells in adult rats. Thus, our results suggest that increase in the expression of BMP7 promotes survival of neurons and glial cells after acute traumatic injury. In contrast, there is increasing evidence that BMPs inhibit neurogenesis and alternatively promote gliogenesis of neural progenitors, which are also present in adult spinal cord, suggesting that injury-upregulated BMP7 may regulate differentiation of glial cells from neural progenitors and may induce gliosis after central nervous system injury.     

High-throughput genotyping of KIR2DL2/L3, KIR3DL1/S1, and their HLA class I ligands using real-time PCR

Killer immunoglobulin-like receptors (KIRs) expressed on natural killer cells are critical components of innate immunity. Interactions between KIRs and their human leukocyte antigen (HLA) ligands have been shown to influence autoimmune and infectious disease course in defined populations. However, the low throughput and high cost of current methods impede confirmation of the universality of these findings. To support large epidemiology surveys, we developed a high-throughput real-time polymerase chain reaction-based assay to identify carriers of KIR3DL1, KIR3DS1, KIR2DL2, and KIR2DL3 and their HLA ligands. The platform performed with 100% sensitivity and specificity in detection of carrier and non-carrier on reference samples. The application of this platform will further clarify the nature and impact of the KIR–HLA epistatic interaction on disease course in large global population-based studies.     

实时荧光定量-聚合酶链反应检测食品中金黄色葡萄球菌方法的研究

目的利用实时荧光定量-聚合酶链反应（real-time PCR）技术,建立食品中金黄色葡萄球菌（金葡萄）污染的快速敏感特异的检测方法。方法以金葡菌的IFemB/I基因作为靶序列,设计一对引物和探针,以金葡菌菌株提取核酸DNA作为模板,优化引物和探针的浓度比和Mgsup2+/sup浓度,以金葡菌和10种相关细菌考核检测体系的灵敏性、稳定性和特异性。并初步应用于样品的检测。结果本研究建立的反应体系在引物和探针的浓度为0.8 mol/L、0.6 mol/L,Mgsup2+/sup浓度为3.5 mmol/L时,具有良好的特异性和敏感性。在10株相关菌株的检测中,除金葡菌出现很好的阳性外,其余菌株均为阴性。在纯菌条件下,最低检测限为44 cfu/ml。稳定性分析表明:同一样品重复检测3次IC/It值的变异系数均5％。检测样品结果显示real-time PCR方法较传统方法敏感、快捷、简便。结论该方法特异性强,稳定性高,操作简便快捷,适应食品微生物检验发展需要,具有较大的推广及应用价值。