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PubMed2007

Hepatocyte growth factor up-regulates the expression of the bone morphogenetic protein (BMP) receptors, BMPR-IB and BMPR-II, in human prostate cancer cells.

Hepatocyte growth factor (HGF) plays multiple roles in cancer, by acting as a motility, invasion and angiogenesis stimulating factor, which promotes metastasis and tumour growth. Bone morphogenetic proteins (BMPs) are members of the TGF-beta superfamily. The effects of BMPs are mediated by two subgroups of receptors, type I and type II. Recent studies have shown that some BMPs, via their signaling pathways, affect the growth of prostate cancer cells. BMPR-IB and BMPR-II have been reported to be expressed at low levels in prostate cancer. However, little is known about the crosstalk between HGF and BMP pathways. In this study, prostate cancer cells (PC-3 and DU-145) were exposed to HGF at different concentrations (1-75 ng/ml) for 18 h, or were treated with HGF at 40 ng/ml over various time periods (up to 24 h). The effect of HGF on BMP receptor expression was further investigated in a nude mouse PC-3 xenograft model. Mice were treated with either HGF, the HGF antagonist NK4, or a combination of both. The expression of BMPR-IB and BMPR-II mRNA was up-regulated by HGF, as shown by both conventional PCR and quantitative PCR. An elevation of BMPR-IB and BMPR-II at the protein level was confirmed by both Western blot analysis and immunocytochemical staining. In a murine prostate tumour model, infusion of recombinant HGF resulted in an increase in the levels of both BMPR-IB and BMPR-II transcript in prostate tumours. Concomitant delivery of NK4, an HGF antagonist, prevented this effect. In conclusion, HGF up-regulates the expression of the bone morphogenetic protein receptors, BMPR-IB and BMPR-II, in prostate cancer cells, both in vitro and in vivo. This may have important implications in the development of bone metastasis in prostate cancer.

Animals↗
PubMed1995

[Methods of study of the hepatitis C virus genome. Diagnostic tools in human pathology].

The study of the molecular biology of infectious agents involves the examination of their genomes and the products of those genomes. Molecular biology methods may therefore allow us to study either DNAs or RNAs. The study of genomic RNAs (viruses) or messenger RNAs (all infectious agents) is used increasingly in infectious disease pathology. The hepatitis C virus was identified in 1989 and was shown to be responsible for a large number of chronic hepatitis cases in France and worldwide. This virus is a good model for the development of technologies to study RNAs, which will later be applied to the study of other viruses. The molecular biology methods used to study hepatitis C virus RNA may be classified into 3 categories. a) Detection methods evidence nucleic acids in fluid or tissue samples, mainly using the polymerase chain reaction (PCR), but also newly developed techniques, such as the NASBA (nucleic-acid-sequence-based amplification), the Q-beta reaction, and the LCR (ligase chain reaction), and techniques that localize viral RNAs in tissue (in situ hybridization, in situ PCR). b) Quantitative methods determine the amount of RNA present in a sample. These include quantitative PCR and new technologies based on signal amplification, such as the 'branched DNA' assays which have recently been developed. c) Qualitative analysis of the genome uses genotyping methods to classify viral strains into different genotypes and subtypes.

Genome, Viral↗
PubMed2001

Assessment of new markers for the rapid detection of aneuploidies by quantitative fluorescent PCR (QF-PCR).

Rapid prenatal diagnoses of major chromosome aneuploidies have been achieved successfully using quantitative fluoresent PCR (QF-PCR) assays and small tandem repeat (STR) markers. Here we report the results of evaluating the use of previously untested X-linked STRs, (DXS6803) and (DXS6809), together with modified amelogenin (AMXY) sequences and the X22 marker that maps in the pseudoautosomal region PAR2 on the long arm of the X and Y chromosomes. These markers will allow prenatal diagnoses of sex chromosome aneuploidies such as 45,X (pure Turner Syndrome), 47,XXY and 47,XYY, while assessing the sex of the fetuses. Data are also presented concerning the difficulties associated with the evaluation of the frequencies of the various types of sub-populations of cells in amniotic fluid samples collected from fetuses with sex chromosome mosaicism. The results of evaluating the use of new markers for the rapid diagnosis of aneuploidies affecting chromosomes 21,18 and 13 are also presented. Three chromosome 21 specific STRs have been found to produce trisomic triallelic or diallelic patterns from all amniotic samples retrieved from fetuses with Down Syndrome. Since all samples tested were amplified and no false positive or negative results were observed, the present results confirm the diagnostic value of QF-PCR for the prenatal detection of major numerical chromosome disorders.

Aneuploidy↗
PubMed1993

A high-sensitivity electrochemiluminescence-based detection system for automated PCR product quantitation.

A high-sensitivity nonisotopic system has been developed for post-PCR product detection. The probe-based detection system exploits a chemiluminescent reaction that takes place on the electrode surface in an electrochemical cell. The detection system incorporates a biotin-streptavidin capture reaction onto a solid support that permits fast post-PCR product detection at the attomole level. The system precision is within 5% relative standard deviation over a linear dynamic range of greater than three orders of magnitude. In this paper, the principles and features of the electrochemiluminescent-based detection system, together with its application to PCR product quantitation, are described in detail.

Autoanalysis↗
PubMed2004

Insight into the intrinsic sensitivity of the PCR assay used to detect CMV infection in amniotic fluid specimens.

BACKGROUND: PCR detection of human cytomegalovirus (HCMV) DNA in amniotic fluid (AF) is the most sensitive tool for diagnosis of fetal infection, but has sub-optimal sensitivity. It has been suggested that inhibition by AF reduces the sensitivity of this assay, however this assumption has never been thoroughly studied. Several PCR assays have been shown to improve sensitivity, but comparative studies are insufficient to choose the optimal approach. OBJECTIVES: To assess the effect of AF inhibition on PCR sensitivity and to determine the most sensitive assay for diagnosing fetal infection. STUDY DESIGN: Plasmid containing HCMV DNA was tested by PCR, in water and in non-infected AF, to assess the inhibitory effect of AF. Twenty-three AF-infected samples were tested by various PCR protocols. AF supernatant, with or without DNA extraction, and AF cells, were assayed by single-round and semi-nested PCR. Viral load was measured in the supernatant by a commercial quantitative PCR kit. RESULTS: The plasmid model demonstrated that single-round PCR was 2000-fold less sensitive in AF compared with water. Semi-nested PCR was only 10-fold less sensitive. Single-round PCR was 30% sensitive in HCMV-infected AF supernatants, and detected viral loads higher than 2.3 x 10(6) viral copies/ml. Extraction of DNA from the supernatant increased the sensitivity of this assay to 89% and the detection limit to 5.2 x 10(4) copies/ml. Semi-nested PCR performed on supernatant, with and without DNA extraction, was 96% and 100% sensitive, respectively, with a detection threshold of 3.8 x 10(3) copies/ml. Single-round and semi-nested PCR were 89% and 100% sensitive, respectively, in cells. The commercial quantitative PCR assay was 100% sensitive. CONCLUSIONS: AF supernatant is inhibitory to PCR. The two most sensitive assays were semi-nested PCR performed on DNA extracted from the supernatant and the commercial quantitative PCR kit. Of these two, the latter is standardized, non-labor-intensive, and allows minimal opportunity for contamination, thereby making it the preferred method for diagnosis.

Adult↗
PubMed2003

HCMV DNA detection and quantitation in the plasma and PBL of lung transplant recipients: COBAS Amplicor HCMV monitor test versus in-house quantitative HCMV PCR.

BACKGROUND: Human cytomegalovirus (HCMV) reactivation may cause severe disease in immunosuppressed patients. Quantitation of HCMV viral load in the blood has been shown to be important in predicting for HCMV disease, however the particular blood compartment that should be tested, plasma versus peripheral blood leukocytes (PBL), has been subject to debate. OBJECTIVES: To simultaneously compare HCMV viral loads in the PBL using an in-house quantitative HCMV polymerase chain reaction (PCR) assay and in the plasma using the commercially available COBAS Amplicor HCMV monitor test, in a cohort of lung transplant recipients (LTR). STUDY DESIGN: Sequential paired plasma and PBL samples were collected (n=98) from a total of 21 LTR during the first 6 months post lung transplantation. HCMV viral loads were assessed in the PBL using an in-house quantitative HCMV PCR assay and the plasma using the COBAS Amplicor HCMV monitor test. HCMV disease in LTR was defined as histopathologically proven HCMV pneumonitis. RESULTS: HCMV deoxyribonucleic acid (DNA) was detected in 39/98 (40%) of total samples with excellent agreement between the two strategies. HCMV was detected in both the plasma and PBL in 38/39 (97%) of HCMV positive samples. HCMV viral loads were higher in patients with HCMV pneumonitis in both the PBL and plasma compared to patients without HCMV pneumonitis. Greater than 10-fold increases in HCMV DNA levels had a sensitivity of 88% and a specificity of 73% in the plasma for HCMV pneumonitis and a positive and negative predictive value of 70 and 89%, respectively. Greater that 10-fold increases in HCMV DNA levels in the PBL had a sensitivity of 88% and a specificity of 64%, for HCMV pneumonitis and a positive and negative predictive value of 64 and 88%, respectively. CONCLUSIONS: Acknowledging the difference in assay methods used for HCMV DNA quantitation, the in-house PCR PBL assay and the COBAS Amplicor HCMV monitor plasma assay predicted equally well for HCMV pneumonitis in LTR.

Cytomegalovirus↗
PubMedDate not supplied

Validation of PCR methods for quantitation of genetically modified plants in food.

For enforcement of the recently introduced labeling threshold for genetically modified organisms (GMOs) in food ingredients, quantitative detection methods such as quantitative competitive (QC-PCR) and real-time PCR are applied by official food control laboratories. The experiences of 3 European food control laboratories in validating such methods were compared to describe realistic performance characteristics of quantitative PCR detection methods. The limit of quantitation (LOQ) of GMO-specific, real-time PCR was experimentally determined to reach 30-50 target molecules, which is close to theoretical prediction. Starting PCR with 200 ng genomic plant DNA, the LOQ depends primarily on the genome size of the target plant and ranges from 0.02% for rice to 0.7% for wheat. The precision of quantitative PCR detection methods, expressed as relative standard deviation (RSD), varied from 10 to 30%. Using Bt176 corn containing test samples and applying Bt176 specific QC-PCR, mean values deviated from true values by -7to 18%, with an average of 2+/-10%. Ruggedness of real-time PCR detection methods was assessed in an interlaboratory study analyzing commercial, homogeneous food samples. Roundup Ready soybean DNA contents were determined in the range of 0.3 to 36%, relative to soybean DNA, with RSDs of about 25%. Taking the precision of quantitative PCR detection methods into account, suitable sample plans and sample sizes for GMO analysis are suggested. Because quantitative GMO detection methods measure GMO contents of samples in relation to reference material (calibrants), high priority must be given to international agreements and standardization on certified reference materials.

European Union↗
PubMed2005

Intestinal alkaline phosphatase gene expression is activated by ZBP-89.

Intestinal alkaline phosphatase (IAP) is an enterocyte differentiation marker that functions to limit fat absorption. Zinc finger binding protein-89 (ZBP-89) is a Kruppel-type transcription factor that appears to promote a differentiated phenotype in the intestinal epithelium. The purpose of this study was to investigate the regulation of IAP gene expression by ZBP-89. RT-PCR, quantitative real-time RT-PCR, Western blot analyses, and reporter assays were used to determine the regulation of IAP by ZBP-89 in HT-29 and Caco-2 colon cancer cells. ZBP-89 knockdown was achieved by specific short interfering (si)RNA. EMSA and chromatin immunoprecipitation (ChIP) were performed to examine the binding of ZBP-89 to the IAP promoter. The results of RT-PCR, quantitative real-time PCR, and Western blot analyses showed that ZBP-89 was expressed at low levels in Caco-2 and HT-29 cells, whereas IAP was minimally expressed and absent in these cells, respectively. Transfection with ZBP-89 expression plamid increased IAP mRNA and protein levels in both cell lines, whereas knockdown of endogenous ZBP-89 by siRNA reduced basal levels of IAP gene expression in Caco-2 cells. IAP-luciferase reporter assays, EMSA, and ChIP established that ZBP-89 activated the IAP gene through a response element (ZBP-89 response element: 5'-CCTCCTCCC-3') located between -1018 and -1010 bp upstream of the AUG start codon. We conclude that ZBP-89 is a direct transcriptional activator of the enterocyte differentiation marker IAP. These findings are consistent with the role that this transcription factor is thought to play as a tumor suppressor and suggests its possible function in the physiology of fat absorption.

Alkaline Phosphatase↗
PubMed1996

Validation of a quantitative RNA PCR assay for HIV-1 in human plasma.

A quantitative human immunodeficiency virus type 1 (HIV-1) RNA polymerase chain reaction assay has been validated analytically and clinically in > 13,000 samples. The assay is highly reproducible with intra- and inter-assay precision of 16% and 19%, respectively. In 1,542 of 1,548 subjects with CD4+ counts of 0-500 cells per mm3, viral RNA levels were quantifiable and ranged from approximately 3,000-52,200,000 copies per milliliter. Median plasma HIV-1 RNA values were inversely proportional to CD4+ counts from 0-400 cells per mm3. When patients were off antiretroviral therapies for approximately 14 days prior to the initial baseline RNA PCR evaluation, the mean variance between the two baseline values was 23% (0.1 log). Of these patients, 95% had a sufficient plasma viral load to quantitate a 10-fold (1 log) diminution in viral load caused by antiviral therapy. In contrast, only 20% and 45% of these subjects had sufficient p24 and ICD p24 levels to detect a 50% diminution in circulating virus. The high precision and reproducibility of this quantitative RNA PCR assay provide an enhanced means of evaluating therapeutic drug regimens for HIV-1.

Base Sequence↗
PubMed2001

Quantitative nested PCR for human cytomegalovirus DNA: analysis using NucleoScan 2001.

A quantitative nested DNA PCR for human cytomegalovirus (CMV) was developed using PCR mimic DNA as an internal standard. A combination of ultra-thin gel and enhanced detection of ethidium bromide-stained PCR bands allowed us to achieve a 25-fold increase in sensitivity over the conventional gel electrophoreses, down to 0.1 ng of DNA per band. When the technique was applied to measuring CMV load in CMV positive leucocyte DNA preparations its sensitivity spanned the range from single to hundreds of CMV DNA copies in 0.1 microg of total white blood cell DNA.

Cytomegalovirus↗
PubMed2005

Quantitative TaqMan PCR for detection of Pneumocystis jiroveci.

We developed a quantitative real-time PCR assay for detection and quantification of Pneumocystis jiroveci in bronchoalveolar lavage (BAL) specimens based on primers and probe targeting the gene encoding beta-tubulin. The assay was able to detect 50 DNA copies per ml of a standard plasmid containing the target sequence. The intra- and interassay coefficients of variation were 0.46%-4.27% and 0.05-2.00% over 5 log(10) values. Fifty-seven controls of human, viruses, bacteria and fungi DNA samples were amplified and found negative. Fifty-three BAL samples sent to the laboratory for diagnosis of pneumocystosis were prospectively investigated by real-time PCR and direct microscopic examinations (DME) using Giemsa stain and direct immunofluorescence. All PCR negative samples were negative by microscopy. Among the 24 (45%) BAL found PCR positive, 8 were positive by microscopy (35%). The copy numbers of the target gene were between 4.4 x 10(3) and 2.8 x 10(6) per ml for the microscopically positive samples and between 8 and 9.2 x 10(3) per ml for the microscopically negative samples. In conclusion, we developed a rapid, sensitive and specific real time PCR for the diagnosis and quantification of Pneumocystis jiroveci in BAL samples.

Base Sequence↗
PubMed1999

A real time quantitative PCR-based method for the detection and quantification of simian virus 40.

A real time quantitative PCR-based simian virus 40 (SV40) detection and quantification method has been developed. This method takes advantage of the 5' to 3'-exonuclease activity of Taq DNA polymerase and utilizes the PRISM 7700 sequence detection system of PE Applied Biosystems for direct monitoring of PCR product accumulation through a dual-labelled fluorogenic probe. This method provides accurate, precise and reproducible quantification of SV40 DNA over a linear dynamic range of at least 100,000-fold with a minimum detection level of 6.4 copy equivalents/microL of SV40 viral particle in test samples. The sample preparation procedure employed allows for efficient and consistent recovery of SV40 DNA from test samples. High concentrations of protein and cellular DNA presenting in test samples have been demonstrated to have no impact on SV40 quantification. This method offers significant advantages over other PCR methods and cell-based infectivity assays currently available for SV40 detection and quantification. The availability of this method should greatly facilitate the pathogenic investigation of SV40, as well as viral clearance evaluations required for the development of new biological products.

DNA, Viral↗
PubMed2002

Determination of donor-type chimerism using a semi-quantitative PCR-based method in a canine model for bone marrow transplantation.

Dogs are used in preclinical transplantation models to study methods of allogeneic bone marrow transplantation (BMT). The evaluation of chimerism is of major significance for the investigation of graft-vs.-host (GvH) and host-vs.-graft (HvG) reactions. To detect and quantitate male donor cells after a sex-mismatched (male to female) allogeneic BMT, we established a semi-quantitative polymerase chain reaction (PCR) assay. Based on the canine Y-chromosome sex-determining region (Sry) sequence, we designed primer specific for the detection of male DNA and optimised PCR conditions and cycle numbers. Artificial mixtures of male and female leukocytes were used to analyse the sensitivity of the assay. To validate our established method, we determined the percentage of chimerism in three transplanted female dogs. Under optimised conditions, the established PCR assay specifically detected male cells down to 0.01%, which corresponds to 0.1ng of transplanted male DNA. The percentage of chimerism could be quantitated either by agarose gel analysis or Southern blot analysis. Using our assay, we could confirm the percentage of chimerism in blood samples of three transplanted female canines, previously determined by karyotype analysis as 0, 100 and 100%, respectively. The established semi-quantitative PCR assay offers a quick, simple, accurate and sensitive way of evaluating and quantitating the percentage of chimerism in a sex-mismatched canine BMT model.

Animals↗
PubMed2003

Multiplexed, real-time PCR for quantitative detection of human adenovirus.

Adenovirus infection is becoming increasingly recognized as a cause of morbidity and mortality in the immunosuppressed patient population. While early detection and quantitation of adenovirus in peripheral blood has been suggested as a means of directing and monitoring antiviral therapy in these patients, few methods have been published, particularly with respect to viral quantitation. A multiplexed real-time PCR assay was developed that can quantitatively detect a wide range of known serotypes of human adenovirus, including all of subgroups A to C. This assay was compared to a qualitative, Southern blot-based PCR assay by using 45 peripheral blood specimens from 16 patients. There was 100% concordance between the two tests in terms of qualitative results. The real-time assay detected adenovirus in patient samples at levels from <200 to 266,681 copies/ml of blood. By using control viral samples, sensitivity was demonstrated to less than 10 copies of viral genome per reaction and quantitative linearity was demonstrated from 10 to 10(6) copies of input viral DNA. Equivalent sensitivity and linearity were demonstrated for 15 different reference serotypes of adenovirus. Eleven other viral serotypes have complete target region sequence homology to one or more of the strains tested. No cross-reactivity was noted with other commonly isolated viral species. Sequence analysis showed no significant homology with any other human pathogens (bacterial or viral). This assay allows rapid, sensitive, and specific quantitation of adenovirus and may have a significant impact on the care of immunocompromised patients at risk for disseminated viral infection.

Adenovirus Infections, Human↗
PubMed2003

A quantitative LightCycler PCR to detect Streptococcus pneumoniae in blood and CSF.

A quantitative real-time PCR targeting the Pneumolysin (ply) gene of Streptococcus pneumoniae was developed for the LightCycler instrument using Fluorescence Resonance Energy Transfer (FRET) probes. All common S. pneumoniae serotypes were detected while other bacteria and viruses were not. The sensitivity was determined to be between one and ten target copies per reaction. The PCR was applied to six CSF and 16 whole blood specimens from 17 patients with laboratory proven invasive pneumococcal disease. One hundred percent of CSF specimens and 69% of whole blood specimens were PCR positive. The bacterial loads were determined to be 7.6 to 6.01 x 10(5) copies/microL for the six CSF specimens, and 0.08 to 5.4 x 10(2) copies/microL for the 16 whole blood specimens. Ninety-seven percent of 30 culture and Gram's stain negative CSF specimens and 100% of 50 normal whole blood specimens were PCR negative. This highly sensitive and specific PCR assay has the potential to provide sufficiently rapid results to improve antibiotic treatment of S.pneumoniae infections, while bacterial load quantitation has opened up exciting possibilities for patient management.

Bacteremia↗
PubMed2006

[Expression change of TIF3 p36 at different stages of human bronchial epithelial cells transformed and induced by cadmium chloride].

OBJECTIVE: To explore the molecular mechanisms potentially responsible for carcinogenesis due to cadmium by detecting expression change of the translation initiation factor 3 (TIF3 p36) in those malignant transformation of human bronchial epithelial cell lines (16HBE) induced by cadmium chloride (CdCl(2)). METHODS: The expression changes of TIF3 p36 were detected and analyzed at different stages of malignant cells (semi transformed cells, transformed cells and tumorigenic cells) induced by CdCl(2) solution with both reverse transcription PCR technique and sensitive fluorescent quantitative PCR assay. RESULTS: Compared with non-transformed human bronchial epithelial cells, the results of fluorescent quantitative PCR assay showed that the semi-transformed cells, transformed cells and tumorigenic cells all expressed higher levels of TIF3 p36 mRNA (P < 0.01 or P < 0.05). As compared with the control cells, the TIF3 expressions at different stages of malignant transformation were 3.1 times, 5.9 times and 9.9 times higher respectively in the low dosage group of CdCl(2) (5 micromol/L); 7.1 times, 6.8 times and 14.8 times respectively in the middle dosage group of CdCl(2) (10 micromol/L); 3.6 times, 3.0 times and 9.1 times respectively in high of dose of CdCl(2) (15 micromol/L). These results showed that there was the positive correlation between overexpression levels of TIF3 p36 mRNA and the malignant degree of the cells, but they were not related to the dosages of cadmium. CONCLUSION: There is significantly abnormal overexpression of TIF3 gene during malignant transformation of human bronchial epithelial cell line induced by cadmium chloride, and the TIF3 expression is associated with the malignant degree of the cells, which may be one of molecular mechanisms potentially responsible for the carcinogenesis due to cadmium.

Bronchi↗
PubMed1997

A quantitative PCR-ELISA for the rapid enumeration of bacteria in refrigerated raw milk.

We have developed a quantitative PCR-ELISA for the rapid enumeration of bacteria in refrigerated raw milk using primers designed from conserved regions in the 16S ribosomal RNA gene (rRNA). The designed primers permitted the amplification of a 147 bp DNA fragment from a wide selection of bacteria which may grow in milk at refrigeration temperatures. Amplified PCR products generated using a digoxigenin-labelled primer were heat-denatured before being quantified by an enzyme-linked immunosorbent assay (ELISA). A biotinylated probe immobilized onto streptavidin-coated microplates was used to capture the digoxigenin-labelled fragments that were detected with a peroxidase anti-digoxigenin conjugate. Subsequent enzymic conversion of substrate gave distinct absorbency differences when assaying milk samples containing bacteria in the range 10(3)-10(7) cfu ml-1. The detection threshold for the PCR-ELISA assay developed in this work is 103 cfu ml-1.

Animals↗
PubMed1998

Quantitative, competitive PCR assay for HIV-1 using a microplate-based detection system.

We have developed a quantitative competitive PCR (QC-PCR) assay in a microplate format for quantifying human immunodeficiency virus Type 1 (HIV-1) DNA or RNA in a broad range of source materials. Our QC-PCR assay is a modification of technique originally described by Piatak et al. (1993), which is based on the presence of a competitive internal standard containing an internal 80-bp deletion of HIV-1 gag target sequence. For improved detection and quantification of the wild-type and internal-standard PCR products in a microplate format, we introduced a non-HIV, 31-bp insert into the internal standard as a probe hybridization site that does not cross-hybridize with wild-type HIV-1 products. By using a primer pair in which one primer is biotinylated, QC-PCRs can be bound to a streptavidin-coated microplate, denatured and probed with a digoxigenin (Dig)-labeled, wild-type or internal-standard probe. The hybridized Dig-labeled probes are detected with an anti-Dig antibody conjugated to detector molecules for luminometry (aequorin) or optical densitometry (peroxidase), yielding results that are quantifiable over the range of 100-10,000 copies of HIV gag. Tested source materials for HIV-1 DNA or RNA quantification include plasma, vaginal lavage and cultured cells. The application of the QC-PCR assay using the microplate format affords a convenient and cost-effective method for quantifying HIV-1 proviral and viral loads from a variety of body fluids, cells and tissues.

Aequorin↗