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At least 469 records · Page 26Linked to original sources
PubMed2004

Graft-versus-leukemia activity may overcome therapeutic resistance of chronic lymphocytic leukemia with unmutated immunoglobulin variable heavy-chain gene status: implications of minimal residual disease measurement with quantitative PCR.

The aim of this study was to investigate if graft-versus-leukemia (GVL) activity conferred by allogeneic stem cell transplantation (allo-SCT) is effective in chronic lymphocytic leukemia (CLL) with unmutated V(H) gene status. The kinetics of residual disease (MRD) were measured by quantitative allele-specific immunoglobulin heavy chain (IgH) polymerase chain reaction (PCR) in 9 patients after nonmyeloablative allo-SCT for unmutated CLL. Despite an only modest decrease in the early posttransplantation phase, MRD became undetectable in 7 of 9 patients (78%) from day +100 onwards subsequent to chronic graft-versus-host disease or donor lymphocyte infusions. With a median follow-up of 25 months (range, 14-37 months), these 7 patients remain in continuous clinical and molecular remission. In contrast, PCR negativity was achieved in only 6 of 26 control patients (23%) after autologous SCT for unmutated CLL and it was not durable. Taken together, this study shows for the first time that GVL-mediated immunotherapy might be effective in CLL with unmutated V(H).

Adult↗
PubMed2004

Neutrophil microbicidal activity: screening bacterial mutants for survival after phagocytosis using quantitative PCR.

When a constant gene replacement sequence is introduced into bacteria to produce mutants and the flanking chromosomal sequences are known, it is possible to use a quantitative polymerase chain reaction method (QPCR) to compare the concurrent survival of the different bacterial mutants under identical conditions. We describe Escherichia coli survival following neutrophil phagocytosis among three mutants deleted respectively for araB, dps or oxyR. Comparisons were made both by traditional and QPCR methods with similar results and indicate that the survival defect of an oxyR and oxyS mutant described previously can be attributed to the loss of oxyR alone. Deletion of dps, a prominent member of the regulon controlled by the oxyR gene product does not engender a survival defect. We suggest that QPCR analysis can readily compare the relative survival of 10 or more mutants concurrently. QPCR analysis would seem to be especially valuable when experimental conditions are subject to a high degree of sample to sample variability or when the stress producing system involves use of expensive or scarce resources like rare patient cells, cells from children, or the use of genetically modified animal hosts.

Bacterial Outer Membrane Proteins↗
PubMed2000

Basic principles of quantitative PCR.

The polymerase chain reaction (PCR) is an extremely sensitive method owing to the repetitive multiplication of template molecules. This property is a drawback for quantitative measurements because small differences in the multiplication factor lead to large differences in the amount of product. Two methods can be used to solve the problem of quantification: kinetic methods based on the determination or comparison of the amplification factor; and coamplification methods, which compare the amount of product to that of a simultaneously amplified standard template. An overview of the theoretical background of both methods is presented. For selection of a suitable method, both theoretical and practical considerations are important. Kinetic methods are the most convenient if PCR can be performed without opening the tubes, as in some apparatus using fluorescence detection. Coamplification methods can be done without expensive equipment but requires the parallel running of several PCR tubes. When the number of initial template molecules is close to one, as in the limiting dilution technique, statistical considerations become important.

Gene Amplification↗
PubMed2000

Quantitative PCR analysis of different splice forms of NFAT5 revealed specific gene expression in fetal and adult brain.

To investigate sequences or mutations associated with neurodegenerative disorders, we performed analyses for the NFAT5 gene, which is located in the candidate region for the autosomal dominantly inherited spinocerebellar ataxia type 4 (SCA4). PCR based expression analyses detected NFAT5 transcripts with alternative splicing in 27 fetal and adult human tissues. Interestingly, by using quantitative methods on cDNA from fetal and adult human brain a significant difference at the expression level for one splice form could be shown.

Adult↗
PubMed2003

Assessment of thymic activity in human immunodeficiency virus-negative and -positive adolescents by real-time PCR quantitation of T-cell receptor rearrangement excision circles.

Circular DNA molecules known as T-cell receptor rearrangement excision circles (TREC) arise during T-cell development and are present in cells that have recently emigrated from the thymus. In cross-sectional studies, the number of peripheral blood lymphocytes bearing TREC decreases with age, consistent with an anatomically demonstrated loss of thymic epithelial tissue. TREC numbers increase following hematopoietic stem cell transplantation and during therapy for human immunodeficiency virus (HIV) infection. Quantitation of TREC has therefore been proposed as a parameter of thymic activity. In this study, we used real-time PCR to quantify TREC in peripheral blood samples obtained longitudinally from HIV-seronegative adolescents. TREC values in peripheral blood T cells were very stable throughout adolescence, once thought to be a time of rapid involution of the thymus. In addition, in a cross-sectional analysis, we examined TREC values in a cohort of HIV-positive adolescents and found evidence of ongoing thymopoiesis in perinatally infected individuals, despite lifelong infection. These data demonstrate the utility of TREC assessment in adolescents and that HIV infection does not uniformly result in accelerated thymic involution in childhood.

Adolescent↗
PubMed2007

Interaction of quantitative PCR components with polymeric surfaces.

This study investigated the effect of exposing a polymerase chain reaction (PCR) mixture to capillary tubing of different materials and lengths, at different contact times and flow rates and the adsorption of major reaction components into the tubing wall. Using 0.5 mm ID tubing, lengths of 40 cm and residence times up to 45 min, none of the tested polymeric materials was found to affect subsequent PCR amplification. However, after exposure of the mixture to tubing lengths of 3 m or reduction of sample volume, PCR inhibition occurred, increasing with the volume to length ratio. Different flow velocities did not affect PCR yield. When the adsorption of individual PCR components was studied, significant DNA adsorption and even more significant adsorption of the fluorescent dye Sybr Green I was found. The results indicate that PCR inhibition in polymeric tubing results from adsorption of reaction components to wall surfaces, increasing substantially with tubing length or sample volume reduction, but not with contact time or flow velocities typical in dynamic PCR amplification. The data also highlight that chemical compatibility of polymeric capillaries with DNA dyes should be carefully considered for the design of quantitative microfluidic devices.

Artifacts↗
PubMed2006

Development of a real time quantitative PCR assay for the hard clam pathogen Quahog Parasite Unknown (QPX).

Quahog Parasite Unknown (QPX) is a thraustochytrid pathogen responsible for catastrophic mortalities of the northern quahog (hard clam) Mercenaria mercenaria. A real-time quantitative polymerase chain reaction (qPCR) assay was developed to assist research efforts on QPX ecology and pathology. Sensitivity of the assay was evaluated with serial dilutions of QPX-cultured cells to determine the lowest concentration of DNA that remained detectable in both the presence and absence of extraneous environmental substances. QPX cells were quantified before DNA extraction to calibrate standard curves to cell counts. Based on our results, the qPCR assay is able to quantify QPX within the range of 1 to several thousand organisms per reaction. Specificity of the assay was assessed by testing 29 thraustochytrid-like protists isolated from suspension-feeding bivalves from China, Oregon, Maryland, and Virginia. Application of the assay was demonstrated with positive qPCR results from naturally contaminated environmental samples including marine aggregates (i.e. marine snow), clam pseudofeces, and inflammatory nodules from infected clams. This quantitative assay for QPX will provide a valuable tool for characterizing QPX parasite abundances in coastal environments and for improving clam disease diagnostics.

Animals↗
PubMed2005

[Fluorescence quantitative PCR detection of WT1 gene expression in peripheral blood of patients with acute leukemias and its clinical implications].

To elucidate the expression of WT1 in all types of leukemias and its implications for monitoring minimal residual disease in patients with acute leukemia, the peripheral blood from 55 leukemia patients and 10 normal voluteer was detected by using FQ-RT-PCR. Follow-up monitoring of WT1 expression of peripheral blood was performed for 20 patients with acute leukemia. The results showed that the expression of WT1 gene in all types of leukemias was significantly higher than that in normal control (P < 0.001). For ANLL and ALL patients, the survival time in the group of WT1 6.8 x 10(-3), (P = 0.027). Follow-up detection of the expression of WT1 in peripheral blood samples from 20 acute leukemia patients, 7 cases relapsed after complete remission has been done. In 5 of 7 relapsed patients, the expression of WT1 had obviously increased about 2 - 3 months before clinical relapse became apparent. It is concluded that the established FQ-RT-PCR method is accurate and specific. The expression of WT1 gene is relatively high in all types of leukemias compared with normal peripheral blood cells, the higher WT1 expression may associate with poor prognosis in acute leukemia, and the dynamics of WT1 level correlate with the disease status. The quantitative assessment of WT1 expression in peripheral blood samples by FQ-RT-PCR may be a useful tool for monitoring minimal residual disease.

Acute Disease↗
PubMed1995

Quantitative PCR. A survey of the present technology.

PCR-based amplification of nucleic acids has had a major impact in almost every field of basic research and has already found extensive applications in the area of clinical diagnosis. For many of these applications, quantitative data are sought to relate the quantity of amplified product to the amount of original target nucleic acid present in the sample. Since the PCR methodology with its exponential nature can be adapted for this purpose, a lot of different strategies have emerged in the last few years for sensitive and specific PCR product detection and quantification. Basic strategies, including the use of external and internal standards, are presented with respect to statistical aspects, and the advantages as well as the limitations of individual protocols are discussed. Furthermore the suitability of conventional laboratory techniques, such as gel systems or HPLC, nonradioactive labeling procedures, and the principles of advanced solid-phase-mediated strategies for the precise determination of amplification products, are outlined with the help of selected examples.

Polymerase Chain Reaction↗
PubMed2002

[Identification and viability assessment of dermatophytes infecting nail based on quantitative PCR of dermatophyte actin (ACT) mRNA].

The diagnosis and choice of treatment for dermatophytoses are usually based on the result of microscopic observation of hyphal elements and culture. However, false negative cultures have sometimes been encountered and appropriate timing of discontinuation of treatment has not been formulated. In this study, we attempted the identification and viability assessment of dermatophytes based on the quantitative measurement of dermatophyte actin (ACT) mRNA. An internal fragment of the ACT, 725 to 762 bp, was isolated by PCR from the genomic DNA of dermatophytes and sequenced. ACT intron-based primers were dermatophyte species-specific and primer pairs crossing the intron were dermatophyte genus-specific. The LightCycler (LC) instrument, employing the two-step RT-PCR/fluorescent hybridization system, was used to quantify the actin mRNA (ACT) of dermatophytes. A 669 bp ACT cDNA fragment was used as a quantification standard. Several mg of samples were collected from skin scales or nail plates before and after the treatment using oral terbinafine. The results indicated that quantification of ACT mRNA correlated with the results of culture and KOH examination and that copy numbers of dermatophyte ACT mRNA per mg sample decreased with progression of the therapy. This method comprises a sensitive (1 fg), specific, rapid (< 4 h) and quantitative assessment of the viability and identification of dermatophytes in skin tissue.

Actins↗
PubMed2000

The life cycles of the temperate lactococcal bacteriophage phiLC3 monitored by a quantitative PCR method.

We present here a new and general approach for monitoring the life cycles of temperate bacteriophages which establish lysogeny by inserting their genomes site-specifically into the bacterial host chromosome. The method is based on quantitative amplification of specific DNA sites involved in various cut-and-join events during the life cycles of the phages (i.e. the cos, attP, attB, attL and attR sites) with the use of sequence-specific primers. By comparing the amounts of these specific DNA sites at different intervals, we were able to follow the development of the lytic and lysogenic life cycles of the temperate lactococcal bacteriophage phiLC3 after infection of its bacterial host Lactococcus lactis ssp. cremoris IMN-C18.

Bacteriophages↗
PubMed2001

Residual subset population analysis in WBC-reduced blood components using real-time PCR quantitation of specific mRNA.

BACKGROUND: Implementation of WBC reduction of the blood supply increases the importance of measurement of residual WBC subtypes responsible for immunologic and infectious complications of transfusion. STUDY DESIGN AND METHODS: Real-time RT-PCR assays were developed to detect mRNA encoding lineage-specific WBC markers. Primers and fluorescent probes were designed for CD45 (pan-WBC), CD3 (T-lymphocyte), CD19 (B-lymphocyte), CD14 (monocyte), and CD66 (granulocyte), and the specificity was assessed by comparison with flow cytometric analysis of enriched cell populations. WBC subsets were examined in WBC-reduced whole blood prepared with filters (WBF2, Pall; and RZ2000, Baxter) and in platelet concentrates prepared with other filters (Autostop, Pall; and PLX-5, Baxter) and apheresis (COBE Spectra LRS, Gambro). RESULTS: All real-time RT-PCR assays were linear over >5 log concentration range, allowing pre-WBC-reduction and post-WBC-reduction comparisons. Sensitivity limits ranged from 10 cells per mL (CD45) to 200 cells per mL (CD19). Assay specificity was confirmed by the close correlation of real-time RT-PCR and immunophenotyping results by flow cytometry. For all subsets, >3.8 log and >3.1 log reduction was obtained during WBC reduction of whole blood and platelets, respectively. CONCLUSION: Real-time RT-PCR assays are suitable for analysis of subset removal during WBC reduction. There was no significant difference between the two whole-blood filters or between platelet filtration and apheresis in the removal of any WBC subset.

Antigens, CD↗
PubMed1999

Monitoring of residual disease in non-Hodgkin's lymphomas by quantitative PCR (preliminary report).

Highly sensitive PCR techniques are often used in molecular monitoring of hematological malignancies, and a quantification of residual disease is important for further prognosis. Here, the limiting dilution methodology and the multiplex IgH/ras PCR are proposed as approaches to molecular monitoring of NHLs. Applying the limiting dilution methodology as a simple dose-response assay for the translocation t(14,18) and CDR3 clonal rearrangement of IgH, critical amounts of total cells determined with stored consecutive diagnostic samples in the same PCR run are compared. Assuming that specific targets are diluted proportionally in dilution of total genomic DNA, the samples showing lower critical concentrations of total DNA are considered as containing higher portion of cells possessing the specific disease marker and vice versa. So far, the correlation of results with the disease outcome confirmed that this simple semi-quantitative approach may in some cases substitute laborious precisely quantifying techniques in the monitoring of the disease. In optimized multiplex IgH/ras PCR co-amplifying clonal CDR3 rearrangement of IgH and the codon 61 of Hras 1 gene, the amount of CDR3 product as the disease marker is related to the ras product as a standard marker of all cells, and quantitative results are obtained by software analyses of detecting gels. Presumably, both approaches may provide clinically useful information on the disease activity and treatment outcome.

Blood Cells↗
PubMed1998

A synthetic standard for competitive RT-PCR quantitation of 13 GABA receptor type A subunit mRNAs in rats and mice.

We describe a synthetic 769-bp DNA internal standard, GABARQuant 1, for measuring mRNAs of 13 GABA(A) receptor subunits by reverse transcriptase-polymerase chain reaction (RT-PCR). When it is transcribed into cRNA, added in known amounts to target mRNAs in extracts from rat or mouse tissue. competitively reverse transcribed into cDNA, and amplified by the polymerase chain reaction (PCR), the relative intensities of the amplified, stained target and standard DNA bands enable measurement of small amounts of mRNAs for GABA(A) receptor subunits alpha1-6, beta1-3, gamma1-3 and delta and the three cellular markers beta-actin, light neurofilament protein, and glutamine synthetase. For the subunits, most standard products (263-504 bp) differ in size from target products (398-564 bp) by 10-20%. Primer pairs span at least one intron, to prevent interference by genomic DNA, and at least one rat versus mouse restriction fragment length polymorphism (RFLP), to enable rat products to be distinguished from mouse products.

Animals↗
PubMed2005

A real time quantitative PCR analysis and correlation of COX-1 and COX-2 enzymes in inflamed dental pulps following administration of three different NSAIDs.

Dental pain is encountered daily by clinicians. Nonsteroidal anti-inflammatory drugs (NSAIDs) commonly used for pain management are traditionally cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2) inhibitors, and more recently selective COX-2 inhibitors. This study was designed to identify and quantify COX-1 and COX-2 gene expression level in inflamed rat molar pulps after administration of three NSAIDs: Celebrex, Vioxx, and Advil. Fifty male Wistar rats had their first and second molar pulps exposed and sealed with Cavit for 4 days. Rats were randomly divided into the three drug groups and two control groups. RNA was isolated from the rat pulps. Real Time Quantitative Reverse Transcriptase-Polymerase Chain Reaction assay, a relatively new PCR technique, was used to quantify COX-1 and COX-2 mRNA. Statistical analysis demonstrated no significant differences in COX-1 and COX-2 levels among the drug groups. However, Vioxx and Advil significantly reduced COX-2 expression levels compared to inflamed (positive control) pulps (p < 0.05).

Animals↗
PubMed2002

Comparison of real-time, quantitative PCR with molecular beacons to nested PCR and culture methods for detection of Mycobacterium avium subsp. paratuberculosis in bovine fecal samples.

An automated PCR with fluorescent probes (molecular beacons) detected Mycobacterium avium subsp. paratuberculosis in bovine feces. When the PCR was compared with culture in testing 41 fecal samples, kappa scores of 0.94 to 0.96, a sensitivity of 93 to 96%, and a specificity of 92% were obtained. Results were quantitated by using a standard curve derived from a plasmid containing IS900. A minimum quantity of 1.7 x 10(-4) pg of DNA, correlating to 1 to 8 CFU, was detected.

Animals↗
PubMed1995

Differential expression of somatostatin receptors by quantitative PCR in the rat brain.

Five subtypes of somatostatin receptors (sst) have recently been cloned and reported to be expressed in rat brain. However, conventional mRNA measurement techniques do not allow to accurately compare the levels of expression of the 5 sst. Thus, we established a quantitative reverse transcriptase polymerase chain reaction method for the 5 sst. A cRNA internal standard was constructed by inserting in msst1 plasmid sequences corresponding to specific sense primers for amplification of each sst. Using a common reverse primer, a unique primer pair by receptor amplifies both wild type and standard RNAs with the same efficiency. The technique was validated by evaluating sst mRNAs in 3 brain structures in which different somatostatin receptor binding levels were previously reported. While the absolute level of expression is similar between regions, sst3 is the major subtype in cerebellum, sst1 predominates in spinal cord and sst4 and sst2 are equally expressed in the hypothalamus.

Animals↗
PubMed2005

Determination of an internal control to apply reverse transcription quantitative PCR to study stress response in the lactic acid bacterium Oenococcus oeni.

The expression gene pattern reflects, in part, mechanisms involved in adaptation to environmental conditions. Thus, we established and validated a method that enables relative transcript quantification in different conditions in the lactic acid bacteria Oenococcus oeni, notably in a technological medium. First, we determined an internal control in our conditions by reverse transcription quantitative polymerase chain reaction (RT-qPCR) using the SYBR Green I technology. Among the seven presumed housekeeping tested genes, the ldhD gene was retained for further experiments. Then, the PCR reproducibility was verified in our conditions and the comparative critical threshold (2deltadeltaC(T)) method was applied to quantify the transcript level of genes. The quantification of transcript levels of several stress genes already studied in our laboratory by Northern blot after a heat shock and at the entry of stationary phase allowed us to validate this method. RT-qPCR appeared as a powerful tool to study O. oeni response in stress conditions and wine mimetic conditions.

Base Sequence↗