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PubMed1996

Comparison of different quantitative PCR procedures in the analysis of the 4977-bp deletion in human mitochondrial DNA.

Four quantitative PCR procedures were compared to analysing the level of the 4977 bp deletion in human mitochondrial DNA. A single preparation of total cellular DNA from the heart of a 69-year-old female subject was used for all four methods. We estimated the deletion to represent 0.005% of total mtDNA molecules using the serial dilution procedure and two internal standard methods with two separate sets of reference recombinant plasmids. However, the value obtained with the kinetic PCR analysis was 0.5%, two orders of magnitude higher. The internal standard procedures are likely to be the most accurate among the four methods used, but the more technically convenient serial dilution method would also be an appropriate choice.

Aged↗
PubMed1991

Generation of competitor DNA fragments for quantitative PCR.

A convenient and generally applicable method for the generation of competitor DNA fragments for quantitative PCR is described. Using mouse-specific primers, fragments are amplified from DNA of an evolutionarily distantly related species under low-stringency annealing conditions. Because these artificially created fragments contain the mouse primer specific ends, they can be used for the quantification of the mouse DNA amplified by these primers. Competitor DNA fragments that differ in size from the corresponding mouse DNA are selected to distinguish both fragments visually by gel electrophoresis. Competitor DNA fragments were generated for mouse beta-actin, interleukin-1, and tumor necrosis factor (TNF). Co-amplification of beta-actin cDNA for adjustment of equal amounts of input cDNA and subsequently TNF cDNA from lipopolysaccharide (LPS)-activated and nonactivated spleen cells with serial dilutions of the respective competitor DNA fragments allowed a semiquantitative comparison of the ratio of TNF mRNA present in both cDNA samples. Under certain conditions, the competitor DNA fragments can be used to determine the approximate molar concentration of a mRNA.

Animals↗
PubMed2001

Comparison of different approaches to quantify Staphylococcus aureus cells by real-time quantitative PCR and application of this technique for examination of cheese.

Two different real-time quantitative PCR (RTQ-PCR) approaches were applied for PCR-based quantification of Staphylococcus aureus cells by targeting the thermonuclease (nuc) gene. Purified DNA extracts from pure cultures of S. aureus were quantified in a LightCycler system using SYBR Green I. Quantification proved to be less sensitive (60 nuc gene copies/microl) than using a fluorigenic TaqMan probe (6 nuc gene copies/microl). Comparison of the LightCycler system and the well-established ABI Prism 7700 SDS with TaqMan probes revealed no statistically significant differences with respect to sensitivity and reproducibility. Application of the RTQ-PCR assay to quantify S. aureus cells in artificially contaminated cheeses of different types achieved sensitivities from 1.5 x 10(2) to 6.4 x 10(2) copies of the nuc gene/2 g, depending on the cheese matrix. The coefficients of correlation between log CFU and nuc gene copy numbers ranged from 0.979 to 0.998, thus enabling calculation of the number of CFU of S. aureus in cheese by performing RTQ-PCR.

Benzothiazoles↗
PubMed2004

Real-time quantitative PCR for assessment of abundance of Pseudoalteromonas species in marine samples.

A real-time quantitative PCR (RTQ-PCR) method for measuring the abundance of Pseudoalteromonas species in marine samples is presented. PCR primers targeting a Pseudoalteromonas-specific region of the 16S rRNA gene were tested at three different levels using database searches (in silico), a selection of pure cultures (in vitro), and a combined denaturing gradient gel electrophoresis and cloning approach on environmental DNA (in situ). The RTQ-PCR method allowed for the detection of SYBR Green fluorescence from double-stranded DNA over a linear range spanning six orders of magnitude. The detection limit was determined as 1.4 fg of target DNA (1,000 gene copies) measured in the presence of 20 ng of nontarget DNA from salmon testes. In this study, we discuss the importance of robust post-PCR analyses to overcome pitfalls in RTQ-PCR when samples from different complex marine habitats are analyzed and compared on a nonroutine basis. Representatives of the genus Pseudoalteromonas were detected in samples from all investigated habitats, suggesting a widespread distribution of this genus across many marine habitats (e.g., seawater, rocks, macroalgae, and marine animals). Three sample types were analyzed by RTQ-PCR to determine the relative abundance of Pseudoalteromonas ribosomal DNA (rDNA) compared to the total abundance of eubacterial rDNA. The rDNA fractions of Pseudoalteromonas compared to all Eubacteria were 1.55% on the green alga Ulva lactuca, 0.10% on the tunicate Ciona intestinalis, and 0.06% on the green alga Ulvaria fusca.

Animals↗
PubMed2000

Evaluation of the kinetics of the bone marrow tumor load in the course of sequential high-dose therapy assessed by quantitative PCR as a predictive parameter in patients with multiple myeloma.

The aim of this investigation was to examine the possible clinical significance of the kinetics of bone marrow (BM) tumor load during the course of sequential high-dose therapy (HDT) as assessed by quantitative PCR in patients with multiple myeloma. In 20 patients with multiple myeloma (MM) treated with two consecutive cycles of HDT followed by autologous peripheral blood stem cell transplantation (PBSCT), clonotypic cells in the peripheral blood (PB) and BM were quantitated by PCR using allele-specific oligonucleotides (ASO) prior to the first, immediately prior to the second, and after the second HDT. The median proportion of clonotypic cells in the BM was 1.27% before the first HDT (range, 0.03-70%), 0.17% after the first (range, 0.001-22%), and 0.05% after the second HDT (range, 0.00009-1.44%). The median number of circulating clonotypic cells was 65/ml (range, 0.9-10842) prior to HDT, 2.7/ml (range, 0-315) after the first, and 3.5/ml PB (range, 0.7-97) after the second HDT. While the median BM tumor load decreased during the first (P = 0.03) and second (P = 0.044) HDT cycles, only the first cycle resulted in a reduction of clonotypic cells in the PB (P = 0.00078 and P= 1.0, respectively). In seven patients, the BM tumor load did not decrease below the initial level after one or two cycles of HDT. All of these patients developed progressive disease (median, 19 months post first cycle; range, 10-21). Of the remaining 13 patients, only four relapsed (18, 19, 21 and 22 months after the first cycle of HDT), while nine remain in response (median followup, 29 months; range, 18-41) (log-rank test P = 0.0009). Our results indicate that the kinetics of the BM tumor load is a predictive parameter in patients with MM and identifies those patients who could benefit from further therapy including new treatment modalities.

Adult↗
PubMed2005

Quantification of vertical transmission of Murine polyoma virus by real-time quantitative PCR.

Pathogenesis studies of viral infections in vivo require sensitive assay methods. A sensitive and specific real-time quantitative PCR (RQ-PCR) assay was developed to detect Murine polyoma virus (MuPyV) DNA sequences. A quantitative assay to measure the single-copy murine wild-type p53 gene was developed to normalize viral gene copies to cell numbers. Both assays were sensitive over a seven-log dynamic range, with a reproducible detection limit of 10 copies per reaction. To determine viral loads and tissue distribution following vertical transmission of MuPyV, pregnant BALB/c mice were inoculated intraperitoneally with virus in late pregnancy. Progeny animals born to infected mothers were followed for 21 days. Viral loads in four tissues (salivary gland, kidney, liver and spleen) were highest at 7 days after birth and dropped to low levels by 14 and 21 days of age, with loads ranging from 5 to 2 million MuPyV copies per 10(3) cells. Significant animal-to-animal variation occurred. Fourteen of 21 (67%) progeny were virus-positive in one or more tissue samples. Transplacental transmission was observed in 6/7 (86%) litters. Infected fetuses per positive litter ranged from 1/7 (14%) to 5/6 (83%) with viral loads ranging from 5 to 25 417 MuPyV copies per 1000 fetal cells. Maternal tissues and blood were frequently highly positive 2 days after inoculation, but viral loads were low by day 14. This study demonstrated the vertical transmission, including transplacental transmission, of MuPyV following acute infection of pregnant mice. It should be considered that there is a possibility that other polyomaviruses, including those in humans, may be vertically transmitted.

Animals↗
PubMed1999

A fluorescent quantitative PCR approach to map gene deletions in the Drosophila genome.

We report the application of TaqMan quantitative PCR (QPCR) to map Drosophila chromosome deficiencies by discrimination of twofold copy number differences. For a model system, we used this technology to confirm the X chromosomal mapping of Dspt6 given the autosomal mapping of Dspt4. We then used this technique on both preexisting deletion mutant flies and flies that we generated with deletions to demonstrate the presence or absence of Dspt6, Dspt4, and swa in various deletion mutant flies. In contrast with in situ hybridization studies, QPCR both vitiates the need to do these more intricate studies, and it is more accurate as the site of deletion can be known down to the 10(2)-bp level. We then successfully applied the technique to the analysis of transcription, demonstrating that the amount of Dspt6 or Dspt4 transcriptional product depended directly on the dosage of the Dspt6 or Dspt4 gene, respectively. The rapidity and precision of this method demonstrates its applicability in Drosophila genetics, the rapid and accurate mapping of Drosophila deletion mutants.

Animals↗
PubMed2004

Application of real-time quantitative PCR to molecular analysis of Candida albicans strains exhibiting reduced susceptibility to azoles.

Real-time quantitative PCR was used to measure expression levels of genes encoding efflux pumps, ERG11 and two control genes, ACT1 and PMA1, in a collection of 14 fluconazole-susceptible Candida albicans isolates. For each gene, average expression levels and variations within the population were determined. These values were then used as reference points to make predictions about the molecular basis of resistance in 38 clinical isolates (the majority of which were resistant to fluconazole) obtained from 18 patients treated with posaconazole for refractory oropharyngeal candidiasis. For each of the 38 isolates, the expression levels of genes encoding efflux pumps, ERG11 and the control genes, were measured as above. Comparison of the two data sets revealed that expression of ACT1 and PMA1 did not vary significantly between the two sets of isolates. In contrast, MDR1, ERG11, CDR1, and CDR2 were overexpressed in 3, 4, 14, and 35, respectively, of the isolates from patients treated with azoles. In addition to these changes, the patient isolates all had at least one and often multiple missense mutations in ERG11. Select ERG11 alleles were expressed in Saccharomyces cerevisiae; all of the alleles tested conferred reduced susceptibility to fluconazole. Despite both the increases in pump expression and the ERG11 mutations, only one of the patient isolates exhibited a large decrease in posaconazole susceptibility.

Actins↗
PubMed2005

Real-time quantitative PCR for determining the burden of Plasmodium falciparum parasites during pregnancy and infancy.

Real-time quantitative PCR (RTQ-PCR) provides a quick, accurate, and reproducible quantification of parasites. However, the value of RTQ-PCR for predicting clinical outcomes of malaria is unknown. Here, we compared RTQ-PCR to microscopy of blood smears, nested PCR (nPCR), and parasite circulating-antigen (CAg) assays for detection of Plasmodium falciparum in pregnant Kenyan women and their infants and related these findings to parity and birth weights in their newborns (n = 554). nPCR was the most sensitive assay for detection of malaria in pregnancy, followed in decreasing order of sensitivity by RTQ-PCR, CAg assays, and blood smears. RTQ-PCR detected a higher frequency of malaria infection (46%) in maternal peripheral blood in primiparous than in multiparous women (35%; P < 0.001), with a >12-fold difference in parasite burden (geometric mean = 25,870 versus 2,143 amplicons/microl blood; P < 0.0001). Similarly, the presence of placental malaria determined by RTQ-PCR was approximately twofold higher in primiparous versus multiparous women (21% versus 13%; P < 0.01). The presence and intensity of malaria infection in pregnant women estimated by RTQ-PCR strongly correlated with low-birth-weight babies, especially in those with high amplicon numbers. RTQ-PCR identified malaria-infected women, missed by blood smear, who were at risk for having underweight offspring. By contrast, malaria detected by nPCR and CAg assay showed a much weaker association with parity or low birth weight. Thus, RTQ-PCR provides an estimate of parasite burden that is more sensitive than blood smear and is predictive of clinical outcomes of malaria infection in pregnant women and newborns.

Animals↗
PubMed2003

Real-time quantitative PCR assay on bacterial DNA: In a model soil system and environmental samples.

Real-time quantitative PCR (RTQ-PCR) was used to quantify the bacterial target DNA extracted by three commonly used DNA extraction protocols (bead mill homogenization, grinding in presence of liquid nitrogen and hot detergent SDS based enzymatic lysis). For the purpose of our study, pure culture of Bacillus cereus (model organism), sterilized soil seeded with a known amount of B. cereus (model soil system) and samples from woodland and grassland (environmental samples) were chosen to extract DNA by three different protocols. The extracted DNA was then quantified by RTQ-PCR using 16S rDNA specific universal bacterial primers. The standard curve used for the quantification by RTQ-PCR was linear and revealed a strong linear relationship (r(2)=0.9968) with a higher amplification efficiency, e5=1.02. High resolution gel electrophoresis was also carried out to observe the effect of these extraction methods on diversity analysis. For the model soil system, the liquid nitrogen method showed the highest target DNA copy number (1.3 x 10(9) copies/microl). However, for both the environmental samples, the bead beating method was found to be suitable on the basis of the high target DNA copy numbers (5.38 x 10(9) and 4.01 x 10(8) copies/ml for woodland and grassland respectively), high yield (6.4 microg/g and 1.76 microg/g of soil for woodland and grassland respectively) and different band patterns on high resolution gel electrophoresis suggesting an overall high extraction efficiency. This difference in the extraction efficiency between the model soil system and environmental samples may be attributed to different affinity of seeded and native DNA to soil particles.

Bacillus cereus↗
PubMed2001

Lymphangiogenesis quantification using quantitative PCR and breast cancer as a model.

The detection of lymphangiogenesis (formation of new lymphatics) has previously been difficult to measure, primarily due to the lack of specific markers for lymphatic endothelium. Using conventional PCR (polymerase chain reaction), DNA sequencing, plasmid synthesis, and real-time quantitative PCR (RTQPCR), we report a new approach to enable the measurement of lymphangiogenesis using LYVE-1, a novel, specific lymphatic marker in breast cancer tissue. By using a Scorpion-based probe system with the RTQPCR analyser, a highly sensitive and specific detection and quantitation of LYVE-1 was possible. It was found that lymphangiogenesis occurred in all breast specimens and that higher levels were found in tumours which had spread to the lymph nodes.

Biomarkers↗
PubMed1999

Quantitative PCR for Listeria monocytogenes with colorimetric detection.

An enzyme-linked immunosorbent assay (ELISA)-mediated polymerase chain reaction (PCR) technique was developed to detect and quantify Listeria monocytogenes in food products. The bacterial DNA was extracted from artificially contaminated food and co-amplified with a synthetic internal standard (IS) using primers specific for the target gene coding for the invasive-associated protein (i.a.p.), a virulence factor of L. monocytogenes (i.a.p.) or IS in the presence of fluorescein-dUTP PCR products were hybridized with biotinylated probes designed for the i.a.p. or IS, and then the hybrids were bound to a streptavidin-coated ELISA plate. An alkaline phosphatase-conjugated antibody to fluorescein was added to the plate and in the presence of substrate, PCR products were quantitated based on an optical density reading. The detection limit for L. monocytogenes experimentally inoculated into milk samples and channel catfish fillets was 20 CFU/ml and 1-2 CFU/g, respectively. Little or no cross reaction was detected in the presence of other spoilage and pathogenic organisms such as Pseudomonas aeruginosa, Aeromonas hydrophila, Escherichia coli, and Staphylococcus aureus. The ELISA-mediated PCR technique, when compared to traditional methods, is more rapid (2 working days) for detecting and quantifying L. monocytogenes.

Animals↗
PubMed2001

Real time quantitative PCR and RT--PCR for analysis of Pneumocystis carinii hominis.

Pneumocystis carinii hominis is a common cause of pneumonia in immunocompromised patients and particularly in those infected by HIV. Giemsa- and Gomori--Grocott-stained smears are widely used for detection and quantification of this opportunistic fungus obtained from biological samples or from in vitro culture. But these methods are fastidious and time-consuming. Thus, instead of performing a count of organisms, we focused our attention on the level of specific DNA by a quantitative PCR technique. This procedure has the advantage of greater precision and more objectivity. To verify the presence of organisms, quantitative RT--PCR based on DHFR and a cell cycle mRNA have been developed. In this current study, we present a detailed description of these methods and their applications for analysis of P. carinii hominis.

Animals↗
PubMed2003

A specific real-time quantitative PCR detection system for event MON810 in maize YieldGard based on the 3'-transgene integration sequence.

The increasing presence of transgenic plant derivatives in a wide range of animal and human consumables has provoked in western Europe a strong demand for appropriate detection methods to evaluate the existence of transgenic elements. Among the different techniques currently used, the real-time quantitative PCR is a powerful technology well adapted to the mandatory labeling requirements in the European Union (EU). The use of transgene flanking genomic sequences has recently been suggested as a means to avoid ambiguous results both in qualitative and quantitative PCR-based technologies. In this study we report the identification of genomic sequences adjacent to the 3'-integration site of event MON810 in transgenic maize. This genetically modified crop contains transgene sequences leading to ectopic expression of a synthetic CryIA(b) endotoxin which confers resistance to lepidopteran insects especially against the European corn borer. The characterization of the genome-transgene junction sequences by means of TAIL-PCR has facilitated the design of a specific, sensitive and accurate quantification method based on TaqMan chemistry. Cloning of event MON810 3'-junction region has also allowed to compare the suitability of plasmid target sequences versus genomic DNA obtained from certified reference materials (CRMs), to prepare standard calibration curves for quantification.

Animals↗
PubMed2004

New real-time quantitative PCR procedure for quantification of bifidobacteria in human fecal samples.

The application of a real-time quantitative PCR method (5' nuclease assay), based on the use of a probe labeled at its 5' end with a stable, fluorescent lanthanide chelate, for the quantification of human fecal bifidobacteria was evaluated. The specificities of the primers and the primer-probe combination were evaluated by conventional PCR and real-time PCR, respectively. The results obtained by real-time PCR were compared with those obtained by fluorescent in situ hybridization, the current gold standard for intestinal microbiota quantification. In general, a good correlation between the two methods was observed. In order to determine the detection limit and the accuracy of the real-time PCR procedure, germfree rat feces were spiked with known amounts of bifidobacteria and analyzed by both methods. The detection limit of the method used in this study was found to be about 5 x 10(4) cells per g of feces. Both methods, real-time PCR and fluorescent in situ hybridization, led to an accurate quantification of the spiked samples with high levels of bifidobacteria, but real-time PCR was more accurate for samples with low levels. We conclude that the real-time PCR procedure described here is a specific, accurate, rapid, and easy method for the quantification of bifidobacteria in feces.

Adult↗
PubMed2000

[Development of a quantitative PCR variant, and use of it for assessing gene expression].

The data on the development of a quantitative PCR technique are presented, including the synthesis of modified primers, the choice of conditions for the removal of reaction-mixture components from the amplified DNA, and the colorimetric detection of the PCR product. The application of this technique to the assessment of the level of gene expression in nonculturable bacterial forms characterized by a drastically reduced metabolism is described.

Colorimetry↗
PubMed2003

[Feasibility of real-time quantitative PCR in assessing the efficiency of gene transfection in vivo].

To explore feasibility of real-time quantitative PCR in assessing efficiency of gene transfection, clonal PCR was employed to analyze efficiency of retroviral-mediated neo gene transfection in primary myoblast, simultaneous real-time PCR were performed for estimation of transfection efficiency; for measuring integrated gene copy number per cell, linear amplification mediated-PCR (LAM-PCR) and retroviral 5'LTR integration analysis also were used. The results showed that: (1) the data from clonal PCR are similar as that from real-time PCR in low efficiency of transfection (< 36%); but in high efficiency of transfection, it is significantly differentiation between clonal PCR and real-time PCR. (2) One copy of transduced gene per cell was observed in retroviral-mediated gene transfection in primary myoblast. It is concluded that real-time PCR can be used to estimate gene transfer vector in vivo, but it is not available for assessing gene transfection in vitro, because high efficiency of transfection could be obtained in most of gene transfection in vitro.

Animals↗
PubMed2003

Developmental validation of a real-time quantitative PCR assay for automated quantification of human DNA.

Our laboratory has developed an automated real-time quantitative PCR assay for detecting human DNA. The assay utilizes an in-house, custom-designed TaqMan-MGB sequence-specific probe (CFS-HumRT) and the ABD 7900HT SDS platform. Developmental validation has followed TWGDAM (1) guidelines and demonstrates that the assay is primate specific, is highly sensitive, yields consistent results, and works with human DNA extracted from a variety of body fluid stains. When operating within the dynamic range of the system using high-quality DNA samples. the technique yields similar quantification results to our current QuantiBlot assay with the added benefit of time saving through automation. Furthermore, the QPCR assay identifies how much amplifiable DNA is in a sample and thus has the potential to predict PCR success in downstream applications such as STR analysis.

Animals↗