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PubMed1998

Time course analysis of semi-quantitative PCR and antigenaemia assay for prevention of cytomegalovirus disease after bone marrow transplantation.

Cytomegalovirus (CMV) disease is a serious complication after bone marrow transplantation (BMT). Recently, semi-quantitative polymerase chain reaction (SQ-PCR) analysis for CMV-DNA has been developed. We compared the time course of SQ-PCR and that of antigenaemia assay after BMT. Our findings suggested that SQ-PCR is more sensitive than antigenaemia assay in the detection of CMV infection and that quantitation of CMV-DNA could discriminate patients with positive PCR but without the risk for CMV disease. We considered that SQ-PCR could be a useful guide for starting pre-emptive therapy against CMV disease.

Adolescent↗

PubMed2001

Quantitative PCR determination of human cytomegalovirus in blood cells.

We evaluated a rapid and sensitive method to determine human cytomegalovirus (CMV) DNA levels in blood cells using a quantitative polymerase chain reaction (PCR) technique. This method is based on real-time detection of PCR using a dual fluorescence-labeled probe and a sequence detector. Ten copies of CMV DNA were detected, when 1 microg of DNA from blood samples was used with this method, and a good correlation was obtained between increased concentrations of copy numbers calculated and measured copy numbers of CMV DNA (r = 0.999). Forty normal subjects exhibited no copies of CMV DNA. On the other hand, a 6-month-old girl tested positive for increased levels 4 weeks after liver transplant. This method is simple, accurate, and sensitive for the quantitative detection of CMV DNA in vivo, indicating possible applications for the diagnosis and monitoring of CMV infection.

Cytomegalovirus↗

PubMed2006

Quantitative PCR method for sensitive detection of ruminant fecal pollution in freshwater and evaluation of this method in alpine karstic regions.

A quantitative TaqMan minor-groove binder real-time PCR assay was developed for the sensitive detection of a ruminant-specific genetic marker in fecal members of the phylum Bacteroidetes. The qualitative and quantitative detection limits determined were 6 and 20 marker copies per PCR, respectively. Tested ruminant feces contained an average of 4.1 x 10(9) marker equivalents per g, allowing the detection of 1.7 ng of feces per filter in fecal suspensions. The marker was detected in water samples from a karstic catchment area at levels matching a gradient from negligible to considerable ruminant fecal influence (from not detectable to 10(5) marker equivalents per liter).

Animals↗

PubMed2005

Assessment of NMYC amplification: a comparison of FISH, quantitative PCR monoplexing and traditional blotting methods used with formalin-fixed, paraffin-embedded neuroblastomas.

OBJECTIVE: To determine the degree of agreement between fluorescence in situ hybridization (FISH), Southern blot analysis and LightCycler monoplex polymerase chain reaction (PCR) analysis in the assessment of NMYC gene amplification status in neuroblastoma. STUDY DESIGN: We performed a retrospective analysis of NMYC amplification, using FISH, LightCycler monoplex PCR and Southern blot techniques to assess NMYC amplification in a series of 18 neuroblastomas and 20 histologically normal tissues (15 lymph nodes, 2 pancreas specimens, 1 section each of thyroid, prostate and uterus). RESULTS: Nine neuroblastomas were NMYC amplified, and the remaining cases were nonamplified. All cases yielded interpretable results by Southern blotting and PCR monoplexing techniques. A single case of neuroblastoma was difficult to interpret by FISH due to high background debris. A single case demonstrated low-level NMYC amplification by LightCycler PCR monoplexing but was nonamplified by the other 2 techniques. FISH analysis in 1 case showed amplification, while the other 2 techniques demonstrated nonamplified status. The case in which FISH analysis incorrectly demonstrated amplification was the same one in which there was high background debris. The Southern blot results were reported as amplified or nonamplified, while numeric amplification ratios were obtained by both FISH and PCR LightCycler monoplex analysis. Comparison of these techniques demonstrated FISH to underestimate the degree of amplification in cases in which the amplification level was high by PCR. In fact, FISH appeared to saturate at amplification ratios > 10. CONCLUSION: The study revealed a high level of concordance between the 3 techniques for assessment of NMYC amplification status. However, FISH analysis has the advantage of allowing concurrent assessment of NMYC amplification status and architecture. LightCycler PCR monoplexing appears to have the advantage of more accurately quantitating high levels of NMYC amplification, including those amplified 20-fold or higher. Both FISH and PCR LightCycler monoplexing have the advantage of being performable on formalin-fixed, paraffin-embedded tissue.

Blotting, Southern↗

PubMed2002

Human kallikrein gene 5 (KLK5) expression by quantitative PCR: an independent indicator of poor prognosis in breast cancer.

BACKGROUND: KLK5 is a newly discovered human kallikrein gene. Many kallikrein genes have been found to be differentially expressed in various malignancies, and prostate-specific antigen (PSA; encoded by the KLK3 gene) is the best tumor marker for prostate cancer. Like the genes that encode PSA and other kallikreins, the KLK5 gene was found to be regulated by steroid hormones in the BT-474 breast cancer cell line. METHODS: We studied KLK5 expression in 179 patients with different stages and grades of epithelial breast carcinoma by quantitative reverse transcription-PCR (RT-PCR), using LightCycler((R)) technology. An optimal cutoff point equal to the detection limit (65th percentile) was used. KLK5 values were then compared with other established prognostic factors in terms of disease-free (DFS) and overall survival (OS). RESULTS: High KLK5 expression was found more frequently in pre-/perimenopausal (P = 0.026), node-positive (P = 0.029), and estrogen receptor-negative (P = 0.038) patients. In univariate analysis, KLK5 overexpression was a significant predictor of reduced DFS (P <0.001) and OS (P <0.001). Cox multivariate analysis indicated that KLK5 was an independent prognostic factor for DFS and OS. KLK5 remained an independent prognostic variable in the subgroups of patients with large tumors (>2 cm) and positive nodes. Hazard ratios derived from Cox analysis and related to DFS and OS were 2.48 (P = 0.005) and 2.37 (P = 0.009), respectively, for the node-positive group and 3.03 (P = 0.002) and 2.94 (P = 0.002), respectively, for patients with tumor sizes >2 cm. KLK5 expression was also associated with statistically significantly shorter DFS (P = 0.006) and OS (P = 0.004) in the subgroup of patients with grade I and II tumors. CONCLUSIONS: KLK5 expression as assessed by quantitative RT-PCR is an independent and unfavorable prognostic marker for breast carcinoma.

Adult↗

PubMed1997

Quantitative PCR analysis reveals novel expression of prothrombin mRNA and regulation of its levels in developing mouse muscle.

Precise determination of mRNA levels is an essential element in any investigation of complex regulatory systems. Classical methodologies such as Northern hybridization suffer from requirements for significant samples of material and also a degree of nonspecificity. Recently, quantitative techniques involving PCR amplification have been devised. We have developed and applied such procedures to the determination of prothrombin messages in skeletal muscle cells during development. In addition to its role in the blood coagulation cascade, the serine protease thrombin has been shown to participate in several signaling events in the neuromuscular system. The inactive precursor, prothrombin, primarily produced in the liver, has also been shown to be synthesized and developmentally-regulated in the brain. In skeletal muscle, thrombin is a mediator of activity-dependent polyneuronal synapse elimination (ADPSE) which occurs in early postnatal development. Recent experiments showing that thrombin is released from myotubes in culture under the influence of acetylcholine suggest that locally-synthesized prothrombin may be the source of this Hebbian synaptic interaction. We have determined that prothrombin is expressed in skeletal muscle, as the likely source of thrombin involved in ADPSE, and the current results show the quantitative expression of muscle prothrombin during this time of intense synapse remodeling.

Animals↗

PubMed2003

Real-time PCR quantitation of FE65 a beta-amyloid precursor protein-binding protein after traumatic brain injury in rats.

In cases of traumatic brain injury (TBI) in which the patient survived for only a short period of time and was without macroscopic changes at autopsy, it is difficult to diagnose TBI. To detect early diagnostic markers of diffuse axonal injury (DAI), real-time quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) in an experimental head trauma model of rat was chosen. The beta-amyloid precursor protein (beta-APP) is a well-known diagnostic marker of DAI which can be detected by immunolabeling as early as 1.5 h after injury. beta-APP has a binding protein, FE65, which is expressed in the brain of Alzheimer's disease patients along with beta-APP, but no involvement with brain injury has been reported. Neuron-specific enolase (NSE) is also a useful marker of DAI. We found that FE65 expression increased dramatically as early as 30 min after injury and decreased after peaking 1 h post-injury, although NSE showed no significant changes. These results suggest that real-time PCR of FE65 mRNA is useful for the diagnosis of DAI in forensic cases.

Amyloid beta-Protein Precursor↗

PubMed2005

Real-time quantitative PCR for enteric adenovirus serotype 40 in environmental waters.

Adenoviruses 40 and 41 have been recognized as important etiological agents of gastroenteritis in children. A real-time PCR method (TaqMan assay) was developed for rapid quantification of adenovirus 40 (Ad40) by amplifying an 88 bp sequence from the hexon gene. To establish a quantification standard curve, a 1090 bp hexon region of Ad40 was amplified and cloned into the pGEM-T Vector. A direct correlation was observed between the fluorescence threshold cycle number (Ct) and the starting quantity of Ad40 hexon gene. The quantification was linear over 6-log units and the amplification efficiency averaged greater than 95%. Seeding studies using various environmental matrices (including sterile water, creek water, brackish estuarine water, ocean water, and secondary sewage effluent) suggest that this method is applicable to environmental samples. However, real-time PCR was sensitive to inhibitors present in the environmental samples. Lower efficiency of PCR amplification was found in secondary sewage effluent and creek waters. Application of the method to fecal contaminated waters successfully quantified the presence of Ad40. The sensitivity of the real-time PCR is comparable to the traditional nested PCR assay for environmental samples. In addition, the real-time PCR assay offers the advantage of speed and insensitivity to contamination during PCR set up. The real-time PCR assay developed in this study is suitable for quantitative determination of Ad40 in environmental samples and represents a considerable advancement in pathogen quantification in aquatic environments.

Adenoviruses, Human↗

PubMed2001

Quantitative PCR in EBV-infected renal transplant patients.

In this study we investigated the levels of Epstein Barr virus (EBV) DNA by quantitative polymerase chain reaction (Q-PCR) in serum, whole blood and peripheral blood mononuclear cells (PBMC) from anti-EA IgG seropositive or anti-EA IgG seronegative EBV infected renal transplant recipients. We compared serological data with the viral load to monitor the risk of developing post-transplant lymphoproliferative disorders (PTLD). All patients were asymptomatic and none of them developed PTLD at the time of the study. EBV DNA quantitation for each patient varied in whole blood and PBMC samples probably due to different numbers of mononuclear cells present in samples from which DNA was extracted (whole blood vs. purified PBMC). In 92% of the serum samples EBV DNA was undetectable probably due to absence of free genomes since the number of DNA copies detected in samples from whole blood and PBMC does not reach very high levels. The correlation between the presence of EA-antibody, considered serological evidence of EBV reactivation, and the viral load showed that 60% of EA-positive patients had quantifiable EBV DNA, whereas in 40% of EA-positive patients EBV DNA was undetectable, showing serological reactivity but no viral replication. Of the remaining EA-negative patients, EBV DNA could be detected in 71% of them, whereas 29% did not show EBV DNA, indicating no EBV replication. In conclusion, our results confirm that the presence of serum IgG anti-EA antibody is not a reliable marker of active EBV infection whereas the evaluation of the viral load in blood samples is a useful diagnostic tool to monitor and to better understand the course of EBV infection in immunocompromised renal transplant patients at risk of developing PTLD.

Adult↗

PubMed1999

[Isolating candidate inserted fragment from positive fused phage clones using quantitative PCR].

OBJECTIVE: To isolate quickly and exactly the specific inserted fragment from fused phage clones which were obtained from cDNA library by hybridization. METHODS: According to the amplification principle of quantitative polymerase chain reaction (PCR) and based on the difference of original template quantity,target cDNA fragment was isolated and identified by two PCRs. RESULTS: A positive clone with specific cDNA fragment of HumGT-H1 gene was obtained from a two-phage fused clone by using this method,and the inserted fragment was verified to be the 5' cDNA sequence of HumGT-H1,1.9kb in length. So another hybridization screening is not necessary. CONCLUSION: The method presented is effective and rapid in gene cloning and can greatly save time and materials.

Bacteriophages↗

PubMed2003

Quantitative PCR analysis of FosB mRNA expression after short duration oxygen and light stress.

Quantitative polymerase chain reaction (QPCR) was used to examine changes in FosB mRNA expression in models of oxygen and light stress to the retina. C57BL/6 mice or Sprague-Dawley (SD) albino rats were subjected to several experimental paradigms: short-term light or oxygen stress, extended hyperoxia (75% oxygen), or a model of oxygen-induced retinopathy (OIR). Control animals were subjected to room air and 5 lux cyclic light. FosB expression dramatically increases in response to light stress as well as in a model of OIR, but not in response to sustained 75% oxygen. These data suggest that both hypoxia and light stress induce expression of FosB in the retina.

Animals↗

PubMed1997

Minimal effect of delayed sample processing on results of quantitative PCR for cytomegalovirus DNA in leukocytes compared to results of an antigenemia assay.

Quantitative cytomegalovirus antigenemia and DNAemia were determined in peripheral leukocytes of 25 patients stored for up to 72 h at room temperature (RT) and 4 degrees C before processing. Numbers of antigen-positive cells significantly decreased with time. The decline was greater at RT than at 4 degrees C. In contrast, no significant alterations in DNAemia occurred.

Antigens, Viral↗

PubMed2002

Real-time quantitative PCR for detection of Helicobacter pylori.

Helicobacter pylori is one of the most common chronic infections in humans, in whom it is a key etiological factor in peptic ulcer disease, gastric mucosa-associated lymphoid tissue lymphoma, and gastric adenocarcinoma. Humans are the bacterium's only host. Here we report the development of a real-time quantitative (Q) PCR-based assay to measure ureC gene copy number to detect H. pylori, based on the fact that there is only one copy of the ureC gene per bacterium. Upon optimization of LightCycler Q-PCR conditions, we obtained a standard curve with a linear range (correlation coefficient = 1) across six logs of DNA concentration. We were able to accurately quantify as few as 1,000 bacteria in our assay. Analysis of variance on 15 randomly selected clinical samples showed good reproducibility of this assay. Comparison of Q-PCR results with bacterial culture and histopathological results from an additional 85 clinical biopsy samples showed a significant difference for the presence of H. pylori. Many samples that were negative for H. pylori by culture and histopathology were positive by Q-PCR. Contamination of PCR by H. pylori or H. pylori genetic material could not be ruled out. In summary, we developed a rapid, sensitive, and real-time Q-PCR method for detecting H. pylori. This technique offers a significant improvement over other available methods for detecting H. pylori in clinical and research samples.

Computer Systems↗

PubMed2004

IFN-gamma induced persistent Chlamydia pneumoniae infection in HL and Mono Mac 6 cells: characterization by real-time quantitative PCR and culture.

Growth of Chlamydia pneumoniae during gamma interferon (IFN-gamma) induced persistent infection in epithelial (HL) and monocyte-macrophage (Mono Mac 6) cell lines was studied by a quantitative real-time PCR and passage. When HL cultures were treated with IFN-gamma (25 U/ml), the replication of C. pneumoniae DNA was unaffected while differentiation into infectious elementary bodies (EB) was strongly inhibited, and in contrast to the untreated cultures, no second cycle of infection was observed. The estimated doubling time of C. pneumoniae genomes was 6-7 h in both IFN-gamma treated and untreated HL cultures. At 72 h post inoculation, most infectious EBs were released from untreated cultures, whereas in IFN-gamma treated HL cells >90% of C. pneumoniae genomes were in non-infectious form. A higher dose (1000 U/ml) of IFN-gamma was needed to restrict growth of C. pneumoniae in Mono Mac 6 cells. In untreated Mono Mac 6 cultures, the growth curve of C. pneumoniae resembled that observed in HL cells, except that no second cycle of infection could be detected. In IFN-gamma treated Mono Mac 6 cultures, the number of infectious C. pneumoniae EBs recovered decreased gradually after 3 days post inoculation, while C. pneumoniae genome load remained unaltered suggesting persistence of C. pneumoniae also in these cells.

Algorithms↗

PubMed2002

Tracking T cell clonotypes in complex T lymphocyte populations by real-time quantitative PCR using fluorogenic complementarity-determining region-3-specific probes.

The T cell receptor (TCR) alpha and beta chains are encoded by a series of stochastic rearrangements between variable (V), diversity (D) for TCR beta chain only, and joining (J) gene segments, creating hypervariable complementarity-determining region 3 (CDR3) regions that contact the peptide/MHC complex and confer specificity. In the present paper, we applied the recently developed real-time quantitative RT-PCR technique to the detection of rearranged TCR beta chain mRNA transcripts. We designed BV- and BJ-specific primers together with TaqMan probes specific for the CDR3 regions of the clones of interest. As an external reference, we used plasmids containing the entire TCR beta chains, making it possible to normalize the number of specific rearranged BV-J mRNA copies among the total number of TCR beta chains. Here, we present data validating this fluorogenic PCR-based method for the quantification of several TCR clonotypes characteristic of the CD4 T cell response to hen egg white lysozyme (HEL) in mice of the H-2d haplotype. This accurate and sensitive procedure permits the precise determination of T cell clone frequencies ranging from 10(-2) to less than 10(-5) in normal biological samples; it may provide an alternative approach when frequencies are too low to be assessed by flow cytometry.

Animals↗

PubMed2004

[Significance of detecting HBV-DNA by the fluorescence quantitative PCR].

BACKGROUND: To study the correlativity between HBV-DNA and the markers of hepatitis B virus infection and different clinical types of hepatitis B. METHODS: The fluorescence quantitation (FQ) of HBV-DNA of 105 patients with hepatitis B was performed by PCR, and the correlativity between the fluorescence quantitation of HBV-DNA and the markers of hepatitis B virus and different clinical types of hepatitis B was analyzed. RESULTS: Ninety-seven percent of the patients were found HBsAg(+), HBeAg(+), HBcAb(+); 75% were HBsAg(+), HBeAb(+), HBcAb(+); 60% were HBsAg(+), HBcAb(+); 40% were HBsAg(+); in HBsAb(+), HBeAb(+), HBcAb(+) (or both HBsAb and HBcAb were positive) group the HBV DNA was undetectable. The analysis indicated that there was a significant difference among different groups (P less than 0.05).HBV-DNA was detected in 72.2% in acute hepatitis B group, in 75% of chronic hepatitis B group, and in 70% of cases of liver cirrhosis with hepatitis B group. The analysis indicated that there was no significant difference among the different clinical types of hepatitis (P greater than 0.05). CONCLUSION: The levels of viral replication were not correlated with different clinical types of hepatitis B; the concentration of HBV-DNA in serum was related to hepatitis B antigen.

Adolescent↗

PubMed2003

Cloned plasmid DNA fragments as calibrators for controlling GMOs: different real-time duplex quantitative PCR methods.

Analytical real-time PCR technology is a powerful tool for implementation of the GMO labeling regulations enforced in the EU. The quality of analytical measurement data obtained by quantitative real-time PCR depends on the correct use of calibrator and reference materials (RMs). For GMO methods of analysis, the choice of appropriate RMs is currently under debate. So far, genomic DNA solutions from certified reference materials (CRMs) are most often used as calibrators for GMO quantification by means of real-time PCR. However, due to some intrinsic features of these CRMs, errors may be expected in the estimations of DNA sequence quantities. In this paper, two new real-time PCR methods are presented for Roundup Ready soybean, in which two types of plasmid DNA fragments are used as calibrators. Single-target plasmids (STPs) diluted in a background of genomic DNA were used in the first method. Multiple-target plasmids (MTPs) containing both sequences in one molecule were used as calibrators for the second method. Both methods simultaneously detect a promoter 35S sequence as GMO-specific target and a lectin gene sequence as endogenous reference target in a duplex PCR. For the estimation of relative GMO percentages both "delta C(T)" and "standard curve" approaches are tested. Delta C(T) methods are based on direct comparison of measured C(T) values of both the GMO-specific target and the endogenous target. Standard curve methods measure absolute amounts of target copies or haploid genome equivalents. A duplex delta C(T) method with STP calibrators performed at least as well as a similar method with genomic DNA calibrators from commercial CRMs. Besides this, high quality results were obtained with a standard curve method using MTP calibrators. This paper demonstrates that plasmid DNA molecules containing either one or multiple target sequences form perfect alternative calibrators for GMO quantification and are especially suitable for duplex PCR reactions.

Calibration↗

PubMed1998

RT-PCR quantitation of cytokine responses in vivo from specimens containing small numbers of cells during bioimmunotherapy.

A Standard Template method has been developed to carry out semiquantitative RT-PCR analysis on mRNA extracted from small specimens that contain low yields of RNA. Using easily prepared templates (made from previously tested reference specimens), standard calibration curves were generated for each of two cytokine products of interest, specifically IL-10 and IFN-gamma. Also, internal standardization was accomplished by quantitating a well-characterized housekeeping gene (GAPDH). Simple densitometry of the RT-PCR product did not demonstrate sufficient reliability for quantitation since a logarithmic relationship was shown between product and template input. Peritoneal exudate cell specimens that were obtained from ovarian cancer patients during intraperitoneal immunotherapy were utilized for the demonstration of IL-10 and IFN-gamma transcript in vivo. Briefly, this method consists of: (1) template preparation: a PCR product for the cytokine of interest is generated from a previously identified positive specimen, purified and stored at -20 degrees C. (2) RT-PCR: cDNAs are produced from RNA extracted from patient specimens. Replicates of each cDNA and serial dilutions of the corresponding template are amplified with primers specific for each cytokine of interest. (3) Quantitation: photographs are made of the PCR products displayed on an agarose gel and are analyzed by densitometry. Determinations of fold-differences in cytokine transcript expression are normalized to the mRNA content of each specimen (based on the expression of GAPDH).

Ascitic Fluid↗