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At least 253 records · Page 14Linked to original sources
PubMed2006

Real-time, quantitative PCR assays for the detection of virus-specific DNA in samples with mixed populations of polyomaviruses.

Mixtures of polyomaviruses can be present in the central nervous system, the gastrointestinal tract, the genitourinary tract, blood, and urban sewage. We have developed 12 primer/probe sets (four per virus) for real-time, quantitative PCR assays (TaqMan) that can specifically detect BKV, JCV, and SV40 genomes present in mixtures of these viruses. The specificities of these primer/probe sets were determined by evaluating their level of interaction with the DNA from other polyomaviruses and their ability to estimate the number of copies of homologous viral DNA in blinded samples of defined mixtures of three polyomaviral DNAs. Three early region and three late region primer/probe sets determined, within a two-fold range, the number of copies of their respective DNAs. Four sets of SV40 primer/probes also detected 1.1-2.4 copies of SV40 DNA per COS-1 cell, cells estimated to contain a single copy of SV40 DNA. Three JCV primer/probe sets detected 3.7-4.2 copies per cell of JCV DNA in the JCV-transformed cell line M1-HR, cells estimated to contain between 0.5 and 1 copy of the JCV genome. We suggest that the virus-specific primer/probe sets in this study be considered sufficiently characterized to initiate the quantification of polyomavirus DNA in biological samples.

Animals↗
PubMed2003

Quantitative PCR genotyping assay for the Ts65Dn mouse model of Down syndrome.

The Ts65Dn mouse is a segmentally trisomic model for Down syndrome. Until now, Ts65Dn mice have been identified by the laborious methods of either chromosomal analysis of cultured peripheral lymphocytes or fluorescent in situ hybridization (FISH). We report here a quantitative PCR method for genotyping Ts65Dn mice, as well as a phenotypic description for visually preclassifying mice to be genotyped.

Algorithms↗
PubMed2006

Comparison of chicken gut colonisation by the pathogens Campylobacter jejuni and Clostridium perfringens by real-time quantitative PCR.

We compared the colonisation of the chicken gut by the two important pathogens Campylobacter jejuni (frequent food-borne pathogen) and alpha-toxin gene containing Clostridium perfringens (causative agent of necrotic enteritis in chickens) using a new high-throughput automated DNA purification method for microbial biodiversity analyses. The method gave high reproducibility (standard deviation of 1.1 C(T)-values for a universal 16S rDNA real-time PCR), and inhibition was observed in only 0.9% of the individual DNA purifications (n = 753). We analysed 253 randomly collected chicken caecal samples (sampled in 2001 and 2003) from Norwegian chicken flocks by real-time quantitative PCR. Our results showed positive correlation (P = 0.009) in chicken caecal colonisation between C. jejuni and Cl. perfringens. We also found that there was a significant underrepresentation (P = 0.008) of chickens containing high levels of Cl. perfringens and low levels of C. jejuni. This indicates a possible interaction between these bacteria. Potential interaction between pathogens and other bacteria in the gut will certainly be important research fields in the future. As demonstrated here, the development of new tools for high-throughput analyses will be of key importance for these studies.

Animals↗
PubMed2003

[Real-time quantitative PCR detecting minimal residual disease in multiple myeloma patients after autologous peripheral blood stem cell transplantation].

In order to explore the role of real-time PCR in detecting minimal residual disease in multiple myeloma and Waldenstrom's macroglobulinemia after autologous peripheral blood stem cell transplantation (APBSCT), real-time PCR was used to quantitate the IgH rearrangement in 8 patients with multiple myeloma (MM) and 1 case of Waldenstrom's macroglobulinemia before and after APBSCT. The results showed that the copies of IgH rearrangement pre- or post-APBSCT were 3108 +/- 1043 and 549 +/- 660 (P < 0.05) respectively. The number of IgH copies was positively correlated with the amount of plasmocytes in patient 's bone marrow and the M-protein in peripheral blood (r = 0.86, P < 0.05). Similar result was obtained in a case of relapsed Waldenstrom's macroglobulinemia. In conclusion, the quantitative analysis of IgH rearrangement by real-time PCR is a novel way to evaluate the therapeutic efficaciousness and predict the prognoses in MM patients.

Gene Rearrangement↗
PubMed2004

Validation of a rice specific gene, sucrose phosphate synthase, used as the endogenous reference gene for qualitative and real-time quantitative PCR detection of transgenes.

With the development of transgenic crops, many countries have issued regulations to label the genetically modified organisms (GMOs) and their derived products. Polymerase Chain Reaction (PCR) methods are thought to be reliable and useful techniques for qualitative and quantitative detection of GMOs. These methods generally need to amplify the transgene and compare the amplified result with that of the corresponding reference gene to obtain reliable results. In this article, we reported the development of specific primers and probe for the rice (Oryza sativa) sucrose phosphate synthase (SPS) gene and PCR cycling conditions suitable for the use of this sequence as an endogenous reference gene in both qualitative and quantitative PCR assays. Both methods were assayed with 13 different rice varieties, and identical amplification products were obtained with all of them. No amplification products were observed when DNA samples from other species, such as wheat, maize, barley, tobacco, soybean, rapeseed, tomato, sunflower, carrot, pepper, eggplant, lupine, mung bean, plum, and Arabidopsis thaliana, were used as templates, which demonstrated that this system was specific for rice. In addition, the results of the Southern blot analysis confirmed that the SPS gene was a single copy in the tested rice varieties. In qualitative and quantitative PCR analyses, the detection sensitivities were 0.05 and 0.005 ng of rice genomic DNA, respectively. To test the practical use of this SPS gene as an endogenous reference gene, we have also quantified the beta-glucuronidase (GUS) gene in transgenic rice using this reference gene. These results indicated that the SPS gene was species specific, had one copy number, and had a low heterogeneity among the tested cultivars. Therefore, this gene could be used as an endogenous reference gene of rice and the optimized PCR systems could be used for practical qualitative and quantitative detection of transgenic rice.

Blotting, Southern↗
PubMed2000

Application of germline IGH probes in real-time quantitative PCR for the detection of minimal residual disease in acute lymphoblastic leukemia.

Large-scale clinical studies on detection of minimal residual disease (MRD) in acute lymphoblastic leukemia (ALL) have shown that quantification of MRD levels is needed for reliable MRD-based risk group classification. Recently, we have shown that 'real-time' quantitative PCR (RQ-PCR) can be applied for this purpose using patient-specific immunoglobulin (Ig) and T cell receptor (TCR) gene rearrangements as PCR targets with TaqMan probes at the position of the junctional region and two germline primers. Now, we tested an alternative approach on 35 immunoglobulin heavy chain (IGH) gene rearrangements, by designing three germline JH TaqMan probes to be used in combination with one of six corresponding germline JH primers and one allele specific oligonucleotide (ASO) primer complementary to the junctional region. In nine cases in which both approaches were compared, at least similar (n = 4) or slightly higher (n= 5) maximal sensitivities were obtained using an ASO primer. The ASO primer approach reached maximal sensitivities of at least 10(-4) in 33 out of 35 IGH rearrangements. The reproducible range for accurate quantification spanned four to five orders of magnitude in 31 out of 35 cases. In 13 out of 35 rearrangements the stringency of PCR conditions had to be increased to remove or diminish background signals; this only concerned the frequently occurring JH4, JH5 and JH6 gene rearrangements. After optimization of the conditions (mainly by increasing the annealing temperature), only occasional aspecific amplification signals were observed at high threshold cycle (CT) values above 42 cycles and at least six cycles above the CT value of the detection limit. Hence, these rare aspecific signals could be easily discriminated from specific signals. We conclude that the here presented set of three germline JH Taq-Man probes and six corresponding germline JH primers can be used to develop patient-specific RQ-PCR assays, which allow accurate and sensitive MRD analysis in almost all IGH gene rearrangements. These results will facilitate standardized RQ-PCR analysis for MRD detection in large clinical studies.

DNA Probes↗
PubMed2002

Quantitative PCR assay to evaluate ampicillin, ofloxacin, and doxycycline for treatment of experimental leptospirosis.

The susceptibility of Leptospira interrogans serovar icterohaemorrhagiae strain Verdun to selected antibiotics used in medical practice (ampicillin, doxycycline, and ofloxacin) was evaluated in a Syrian hamster model, to determine the efficacy of these antibiotics during the course of the disease. A quantitative PCR assay was used to monitor the density of leptospires in blood and in target organs (liver, kidney, lung, heart, and spleen). Our results demonstrated the ability of ampicillin at a high dose (100 mg/kg of body weight) to clear leptospires from the host, except from kidneys and heart, where 10(2) leptospires/g remained at day 6. Ofloxacin (30 mg/kg) was unable to clear bacteria from blood or kidneys. With doxycycline (10 mg/kg), the clearance of leptospires occurred in 2 days in all the target organs studied, with the exception of liver, which required 3 days. Our data demonstrate the value of monitoring the kinetics of experimental leptospiral infection in order to accurately evaluate the efficacy of antibiotics. We have demonstrated the potential value of doxycycline for the treatment of leptospirosis cases, except in circumstances where it is contraindicated. This experimental model could be used to define better therapeutic strategies for human leptospirosis, by testing associations or new formulations of antibiotics.

Ampicillin↗
PubMed2002

Disseminated toxoplasmosis, resulting from infection of allograft, after orthotopic liver transplantation: usefulness of quantitative PCR.

Disseminated toxoplasmosis is a life-threatening disease in liver transplant recipients that can result from an organ-transmitted infection. We report here a case of fatal disseminated toxoplasmosis after orthotopic liver transplantation from a seropositive donor (immunoglobulin G [IgG](+) and IgM(-)) in a patient who was nonimmune for toxoplasmosis prior to transplantation. Quantitative PCR analyses of various clinical specimens, including serum samples, appeared retrospectively to be a valuable diagnostic tool that might guide therapeutic attitudes.

Adult↗
PubMed2005

Detection of large deletions in the LDL receptor gene with quantitative PCR methods.

BACKGROUND: Familial Hypercholesterolemia (FH) is a common genetic disease and at the molecular level most often due to mutations in the LDL receptor gene. In genetically heterogeneous populations, major structural rearrangements account for about 5% of patients with LDL receptor gene mutations. METHODS: In this study we tested the ability of two different quantitative PCR methods, i.e. Real-Time PCR and Multiplex Ligation-Dependent Probe Amplification (MLPA), to detect deletions in the LDL receptor gene. We also reassessed the contribution of major structural rearrangements to the mutational spectrum of the LDL receptor gene in Denmark. RESULTS: With both methods it was possible to discriminate between one and two copies of the LDL receptor gene exon 5, but the MLPA method was cheaper, and it was far more accurate and precise than Real-Time PCR. In five of 318 patients with an FH phenotype, MLPA analysis revealed five different deletions in the LDL receptor gene. CONCLUSION: The MLPA method was accurate, precise and at the same time effective in screening a large number of FH patients for large deletions in the LDL receptor gene.

DNA Mutational Analysis↗
PubMed2006

Sonic hedgehog mRNA expression by real-time quantitative PCR in normal and tumor tissues from colorectal cancer patients.

Shh is expressed in the early stages of embryogenesis and in the foregut development. Although Shh has been shown to be overexpressed in brain, pancreas, gastric and lung cancers, its role in the development of colorectal cancer has not been examined. We used real-time quantitative PCR to assess Shh mRNA expression levels in tumor and matched normal tissue from 57 colorectal cancer patients and correlated the results with patient clinicopathological characteristics. Shh expression levels were higher in tumor tissue than in normal tissue from the same patient (P=0.00001). Higher levels of Shh expression were associated with early stage disease (P=0.02). Shh overexpression may influence the development of colorectal cancer.

Adult↗
PubMed2004

Quantitation of HTLV-I and II proviral load using real-time quantitative PCR with SYBR Green chemistry.

BACKGROUND: Human T-lymphotropic virus type I (HTLV-I) is linked etiologically with adult T cell leukemia/lymphoma and HTLV-I-associated myelopathy/tropical spastic paraparsis (HAM/TSP). Human T-lymphotropic virus type II (HTLV-II) is associated with HAM/TSP and, in HIV coinfected patients only, rare cases of cutaneous T cell lymphoma. Proviral load may be important in the pathogenesis of HTLV-associated disease. MATERIALS AND METHODS: A real time quantitative PCR assay using SYBR Green intercalation was established. Primers targeting the tax region were standardized against MT2 and MOT cell line DNA for HTLV-I and HTLV-II, respectively. HTLV-I/II copy number was normalized to the amount of cellular DNA by quantitation of the HLA-DQ alpha gene. We measured proviral load in peripheral blood mononuclear cells (PBMCs) in a large cohort of 120 HTLV-I and 335 HTLV-II seropositive former blood donors. We also assessed the intra- and inter-assay reproducibility of the assay. RESULTS: Proviral load for HTLV-I infected patients ranged from 3.1 x 10(0) to 1.8 x 10(5)copies/10(6) PBMCs with a mean of 1.6 x 10(4) and a median of 3.0 x 10(3). HTLV-I was undetectable in 7 of 120 cases (5.8%). Proviral load for HTLV-II infected patients ranged from 1.1 x 10(0) to 1.0 x 10(6)copies/10(6) PBMCs with a mean of 2.8 x 10(4) and a median of 5.0 x 10(2). HTLV-II was undetectable in 31 out of 335 cases (9.3%). CONCLUSION: The assay has excellent dynamic range from 10(6) to 10(0)copies/reaction, good intra- and inter-assay reproducibility, and a lower limit of detection of a single copy per reaction. The sensitivity and high dynamic range allow determination of a broad range of HTLV-I/II proviral load in clinical subjects. This assay will facilitate the study of the relationship between proviral load and pathogenesis.

Benzothiazoles↗
PubMed2006

Prochlorococcus ecotype abundances in the North Atlantic Ocean as revealed by an improved quantitative PCR method.

The cyanobacterium Prochlorococcus numerically dominates the photosynthetic community in the tropical and subtropical regions of the world's oceans. Six evolutionary lineages of Prochlorococcus have been described, and their distinctive physiologies and genomes indicate that these lineages are "ecotypes" and should have different oceanic distributions. Two methods recently developed to quantify these ecotypes in the field, probe hybridization and quantitative PCR (QPCR), have shown that this is indeed the case. To facilitate a global investigation of these ecotypes, we modified our QPCR protocol to significantly increase its speed, sensitivity, and accessibility and validated the method in the western and eastern North Atlantic Ocean. We showed that all six ecotypes had distinct distributions that varied with depth and location, and, with the exception of the deeper waters at the western North Atlantic site, the total Prochlorococcus counts determined by QPCR matched the total counts measured by flow cytometry. Clone library analyses of the deeper western North Atlantic waters revealed ecotypes that are not represented in the culture collections with which the QPCR primers were designed, explaining this discrepancy. Finally, similar patterns of relative ecotype abundance were obtained in QPCR and probe hybridization analyses of the same field samples, which could allow comparisons between studies.

Atlantic Ocean↗
PubMed2006

Role of metal ions in catalysis by HIV integrase analyzed using a quantitative PCR disintegration assay.

Paired metal ions have been proposed to be central to the catalytic mechanisms of RNase H nucleases, bacterial transposases, Holliday junction resolvases, retroviral integrases and many other enzymes. Here we present a sensitive assay for DNA transesterification in which catalysis by human immunodeficiency virus-type 1 (HIV-1) integrase (IN) connects two DNA strands (disintegration reaction), allowing detection using quantitative PCR (qPCR). We present evidence suggesting that the three acidic residues of the IN active site function through metal binding using metal rescue. In this method, the catalytic acidic residues were each substituted with cysteines. Mn2+ binds tightly to the sulfur atoms of the cysteine residues, but Mg2+ does not. We found that Mn2+, but not Mg2+, could rescue catalysis of each cysteine-substituted enzyme, providing evidence for functionally important metal binding by all three residues. We also used the PCR-boosted assay to show that HIV-1 IN could carry out transesterification reactions involving DNA 5' hydroxyl groups as well as 3' hydroxyls as nucleophiles. Lastly, we show that Mn2+ by itself (i.e. without enzyme) can catalyze formation of a low level of PCR-amplifiable product under extreme conditions, allowing us to estimate the rate enhancement due to the IN-protein scaffold as at least 60 million-fold.

Amino Acid Substitution↗
PubMed2005

Biodistribution and general safety of a naked DNA plasmid, GTU-MultiHIV, in a rat, using a quantitative PCR method.

We studied the general safety, biodistribution and persistence of a naked DNA plasmid in a rat model using intramuscular, intradermal and intravenous routes of administration. Clinical signs were followed up throughout the study and at the necropsy. Tissue samples were collected at the necropsy at 2, 14 and 28 days after injection of 200 microg of plasmid DNA and analysed with validated quantitative polymerase chain reaction (QPCR). The plasmid (GTU-MultiHIV) was shown to be well tolerated and no clinical observations related to the vaccine were found. Within 2 days after the intramuscular and intradermal injections, the plasmid could be detected in the lymph nodes and also at 14 days in a few test animals. The quantitative PCR analysis indicated that in positive lymph nodes one of 15-213 dendritic cells could be carrying the plasmid. No plasmid was detected in gonads or brain samples in any of the study groups. In intramuscular and intradermal administration, low amounts of the plasmid DNA persisted at the injection site 28 days after the injection, whereas a complete clearance with intravenous route was observed already at 14 days. The results show that the GTU-MultiHIV plasmid is safe and suitable for human clinical trials.

AIDS Vaccines↗
PubMed1999

Real time quantitative PCR as a method to evaluate simian virus 40 removal during pharmaceutical protein purification.

Continuous cell lines used for pharmaceutical protein manufacturing have the potential to be contaminated by viruses. To ensure the safety of pharmaceutical proteins derived from continuous cell lines, validation of the ability of the manufacturing process to clear potential contaminating viruses is required for product registration. In this paper, a real time quantitative PCR method has been applied to the evaluation of simian virus 40 (SV40) removal during chromatography and filtration procedures. This method takes advantage of the 5'-3' exonuclease activity of Taq DNA polymerase and utilizes the PRISM 7700 sequence detection system of PE Applied Biosystems for automated SV40 DNA quantification through a dual-labeled fluorogenic probe. This method provides accurate and reproducible quantification of SV40 DNA. The SV40 clearance during chromatography and filtration procedures determined by this method is highly comparable with that determined by the cell-based infectivity assay. This method offers significant advantages over cell-based infectivity assays, such as higher sensitivity, greater reliability, higher sample throughput and lower cost. This method can be potentially used to evaluate the clearance of all model viruses during chromatography and filtration procedures. This method can be used to substitute cell-based infectivity assays for process validation of viral removal procedures and the availability of this method should greatly facilitate and reduce the cost of viral clearance evaluations required for new biologic product development.

Antibodies, Monoclonal↗
PubMed1997

A quantitative PCR assay for the detection of low amounts of malignant cells in multiple myeloma.

BACKGROUND: High-dose chemotherapy (HDT) with autografting of hematopoietic stem cells induces up to 50% of complete remissions in patients with multiple myeloma. Cases of molecular remissions have been reported. However, qualitative assays determine only the absence or presence of a monoclonal population depending on their sensitivity. Therefore reliable and sensitive methods to quantitate tumor loads are necessary. MATERIALS AND METHODS: We have established a quantitative PCR assay (qPCR) with allele-specific primers complementary to hypervariable CDR3 regions. Sample DNA was serially diluted in 0.5 log steps and amplified in 10 replicates. PCR results were analysed by likelihood maximization and chi 2 minimization to calculate the tumor load. RESULTS: Three approaches were taken to validate the qPCR. 1) Single copies of the CDR3 region of U266 cells could be detected. 2) Analysis of a bone marrow sample by FACS for CD 38+2 and kappa/lambda restricted plasma cells and by qPCR yielded results of 1.4 and 2.5% respectively. 3) qPCR results with plasmids carrying CDR3 regions simulating different tumor loads diverged by no more than a factor of 1.6 from the expected values. CONCLUSION: We consider the qPCR to be an accurate method for assessing samples with low amounts of malignant cells.

Base Sequence↗
PubMed2005

Real-time quantitative PCR analysis of viral transcription.

Whole-genome profiling using DNA arrays has led to tremendous advances in our understanding of cell biology. It has had similar success when applied to large viral genomes, such as the herpesviruses. Unfortunately, most DNA arrays still require specialized and expensive resources and, generally, large amounts of input RNA. An alternative approach is to query entire viral genomes using real-time quantitative PCR. We have designed such PCR-based arrays for every open reading frame of human herpesvirus 8 and describe here the general design criteria, validation procedures, and detailed application to quantify viral mRNAs. This should provide a useful resource either for whole-genome arrays or just to measure transcription of any one particular mRNA of interest. Because these arrays are RT-PCR-based, they are inherently more sensitive and robust than current hybridization-based approaches and are ideally suited to query viral gene expression in models of pathogenesis.

Base Sequence↗