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At least 955 records · Page 53Linked to original sources
PubMed2005

Evaluation of real-time reverse transcriptase PCR and real-time loop-mediated amplification assays for severe acute respiratory syndrome coronavirus detection.

We compared the performance of a recently established real-time loop-mediated amplification (LAMP) assay with the one from a highly sensitive quantitative PCR assay. None of these assays produced false-positive results in this study. For samples isolated from patients within the first 3 days of disease onset, the detection rate of the quantitative PCR assay was higher (14 of 15 were positive) than the LAMP assay (9 of 15 were positive). By contrast, the detection rates of these assays toward specimens sampled from patients with more than 3 days of illness were similar (32 of 44 for PCR and 33 of 44 for LAMP were positive). The simpler operation of LAMP might be a possible solution for on-site diagnosis.

Humans↗
PubMed1997

Quantification of genetically tagged cyanobacteria in Baltic Sea sediment by competitive PCR.

Competitive PCR (cPCR) is a quantitative PCR approach based on the addition of an internal standard to the PCR mixture. In this study, cPCR was used to quantitate genetically tagged cyanobacteria in Baltic Sea sediment. The cyanobacterium Synechocystis 6803-luc has a chromosomal insertion of the firefly luciferase gene, luc, as a marker detectable by PCR. A competitive standard was constructed that contained a 37-bp insertion within the luc DNA region that could be distinguished from the target luc DNA on the basis of size. Synechocystis 6803-luc cells were added to sediment, total bacterial DNA was extracted from sediment and the number of luc DNA copies was quantified by cPCR and phosphor imaging analysis. The internal standard was added either before (co-extraction) or after (post-extraction) isolation of DNA from sediment. The co-extraction method was found to be both more accurate and more precise for the quantitation of added cell numbers (luc DNA copies) by cPCR. When using the co-extraction approach, it was possible to overcome variations in extraction efficiency between replicate samples. The target:competitor PCR product ratio was the only value required for interpolation from standard curves to the luc DNA concentration present in the original sediment sample. The number of luc-tagged cyanobacteria added to the sediment could be calculated after adjustment for the number of chromosomes per cell. This technique should be applicable for quantitation of genetically tagged cyanobacteria in nature.

Autoradiography↗
PubMed2002

Novel competitive PCR methods for quantitation of T-cell receptor delta (TCRD) gene rearrangements.

Since the invention of the polymerase chain reaction (PCR) several quantitative PCR-based approaches have been described. Recently, the real-time PCR method became a standard in quantitative PCR, although high costs of the necessary equipment and reagents make it unaffordable for many laboratories. In this paper we describe two novel competitive PCR techniques, which were used to determine the frequency of T-cell receptor delta gene (TCRD) rearrangements in peripheral blood leukocytes. In the reference gene competitive PCR (rgc-PCR) the rearranged TCRD gene competes with the reference gene (RAG1) for common reagents (dNTPs and Taq polymerase). The intensity ratio of amplification products, TCRD/RAG1, corresponds to the portion of cells containing a rearrangement. A series of reactions was performed, in which RAG1 primers were added to the PCR after different numbers of cycles. On the basis of the number of cycles needed to obtain equal band intensity, the frequency of cells containing a rearrangement was calculated. In the common primer competitive PCR (cpc-PCR), two gene rearrangements, Vdelta1-Jdelta1 and Vdelta2-Jdelta1, compete for the common Jdelta1 primer. The competing genes are amplified from the same genomic DNA template; therefore unlike in the method using the internal competitor, the results are not affected by the quantity or quality of the analysed sample. We showed that the rgc-PCR and cpc-PCR are reliable and give reproducible results. The methods do not require any expensive equipment or reagents, and can be used to determine the frequency of gene rearrangements.

Gene Rearrangement, delta-Chain T-Cell Antigen Rec↗
PubMed2000

Comparison of quantitative cytomegalovirus (CMV) PCR in plasma and CMV antigenemia assay: clinical utility of the prototype AMPLICOR CMV MONITOR test in transplant recipients.

The correlation between the prototype AMPLICOR CMV MONITOR test (Roche Molecular Systems), a quantitative PCR assay, and the cytomegalovirus (CMV) pp65 antigenemia assay was evaluated in transplant recipients. Sequential blood specimens were collected on 29 patients (491 specimens), the leukocyte fraction was tested by CMV antigenemia, and quantitative PCR was performed on plasma specimens. None of the 15 patients (242 specimens) who were antigenemia negative were positive for CMV DNA by PCR, and none of these patients developed active CMV disease. There were 14 antigenemia-positive patients, 8 of whom developed active CMV disease. In all patients, there was a good association between the antigenemia and PCR assays. Ganciclovir-resistant virus was isolated from three patients with active CMV disease. These three patients had persistently elevated levels of antigenemia and CMV DNA by PCR when resistance to ganciclovir developed. This standardized, quantitative CMV PCR assay on plasma has clinical utility for the diagnosis of active disease and in monitoring the response to antiviral therapy in transplant recipients.

Adolescent↗
PubMed1996

Clinical characterization of a competitive PCR assay for quantitative testing of hepatitis C virus.

Rational clinical application of quantitative assessments of hepatitis C virus (HCV) RNA depends on an understanding of factors affecting the assay and its intrinsic variability. The effects of three types of blood collection tubes, two storage temperatures, five processing times, and two laboratories on a commercially available quantitative reverse transcriptase PCR assay (AMPLICOR HCV MONITOR) were evaluated. HCV RNA concentrations were assessed in 356 specimens representing 178 aliquots from nine patients. In a multivariate generalized linear model, HCV RNA concentrations decreased when centrifugation was delayed more than 6 h (P = 0.005) and were marginally different between laboratories (P = 0.06), but precentrifugation storage temperature (P = 1.00) and anticoagulation (P = 0.22) had no effect. After adjusting for other factors, the HCV concentration of 95% of a subject's samples were within 0.44 log. Specimens procured for reverse transcriptase PCR-based quantitative HCV testing should be centrifuged within 6 h of collection. Serial assessments should ideally be performed in the same laboratory, and changes in HCV RNA concentration of less than 0.44 log may not be biologically important.

Adult↗
PubMedDate not supplied

Detection and quantification of SV40 large T-antigen DNA in mesothelioma tissues and cell lines.

SV40 viral DNA sequences, particularly large T-antigen (T-ag) DNA, have been reported in malignant pleural mesothelioma (MPM) and suggested to play a role in the tumorigenesis of this cancer. These results remain somewhat controversial owing to variability among a number of laboratories in reported SV40 DNA and protein detection in MPM tissues. This could be explained in part if SV40 DNA is present in relatively low abundance in many MPM tissues determined to contain viral sequences and is therefore difficult to detect. To this end, we investigated the efficacy of real time quantitative PCR in detecting low copy number SV40 DNA sequences, then we quantified SV40 copy number in MPM tissues and cell lines at our institution. Quantitative PCR demonstrated consistent precision and accuracy in detecting SV40 DNA sequences over a large logarithmic range of viral copy number. In addition, SV40 sequences were found in 2/35 tissues and 3/7 cell lines in relatively low abundance. We conclude that SV40 is not a contributing factor in the pathobiology of the majority of MPM tumors from patients at our institution.

Animals↗
PubMedDate not supplied

Increased expression of protease M in ovarian tumors.

Proteases are known to play important roles in tumor invasion and metastasis. Protease M, which was originally identified by Anisowicz and colleagues in 1996, is a new member of the serine protease family. We also identified the protease M transcript in a differential PCR screen of ovarian tumors and have investigated its expression in 44 ovarian tumors (12 low malignant potential tumors, 32 carcinomas) and 10 normal ovaries using quantitative PCR. The PCR product was labeled with (32)P and a phosphoimager was used to determine the relative expression of the protease M gene compared to internal control beta-tubulin. mRNA expression levels of protease M were significantly elevated in 9 of 12 low malignant potential tumors and 30 of 32 carcinomas. Northern blot hybridization showed that the 1.7-kb protease M transcript was abundant in carcinoma but not detected in normal ovary. Immunohistochemical staining of normal ovary and ovarian tumor tissue sections with antibodies generated to protease M derived peptides corroborated the semi-quantitative PCR and Northern analysis data. Our results suggest that protease M is frequently overexpressed in ovarian tumors and may therefore contribute to the invasive nature or growth capacity of ovarian carcinomas.

Adenocarcinoma, Clear Cell↗
PubMed2000

Epstein-Barr virus (EBV) load and cytokine gene expression in activated T cells of chronic active EBV infection.

To identify the role of T cells in chronic active Epstein-Barr virus (EBV) infection, EBV and cytokine gene expression was quantified by use of real-time polymerase chain reaction (PCR) among 6 patients who fulfilled the diagnostic criteria for chronic active EBV infection. Four of these patients showed clonal expansion of EBV-infected T cells. Quantitative PCR for EBV DNA in peripheral blood of patients with symptomatic chronic active EBV infection showed higher copy numbers of virus (mean, 1.45 x 10(5) copies/mL) than were seen in blood from patients with infectious mononucleosis (3.08 x 10(3) copies/mL) or with EBV-associated hemophagocytosis (2.95 x 10(4) copies/mL). Fractionated CD3(+) HLA-DR(+) cells from patients with chronic active EBV infection contained higher copy numbers than did CD3(+) HLA-DR(-) cells. Quantitative PCR for cytokines revealed that interferon-gamma, interleukin (IL)-2, IL-10, and transforming growth factor-beta genes were expressed at higher levels in HLA-DR(+) than in HLA-DR(-) T cells. These results suggest that activated T cells in chronic active EBV infection expressed high levels of EBV DNA and both Th1 and Th2 cytokines. EBV-infected T cells may contribute to the unbalanced cytokine profiles of chronic mononucleosis.

Adolescent↗
PubMed2004

[Expressions of early growth response 1 and tissue factor in caerulein-induced acute pancreatitis tissues in rats].

OBJECTIVE: To observe the expressions of early growth response 1 (Egr-1) and tissue factor (TF) in rat tissues of acute pancreatitis induced by caerulein and to explore their significance. METHODS: Pancreatitis was induced in rats by high-dose intraabdominal caerulein injection. The changes of Egr-1 mRNA and protein in pancreas were measured by quantitative PCR and Western blotting, and the localization of Egr-1 protein in acinar cells was visualized by immunohistochemistry. TF mRNA levels were also measured by quantitative PCR. High-dose bombesin-stimulated rats served as the negative control. RESULTS: Egr-1 mRNA was rapidly increased in the pancreas of rats stimulated by high-dose cearulein, and reached the peak level 30 min after the stimulation, whereas band for peak Egr-1 protein level was visualized by Western blotting till 2 h after stimulation. Immunohistochemistry showed that almost every acinar cell in the pancreas was Egr-1-positive, especially in the nucleus. In line with Egr-1 activation, TF mRNA was detected 1 h after the stimulation and increased steadily within the initial 4 h. Only a small quantity of Egr-1 mRNA expression was observed in bombesin-stimulated rats, in which no Egr-1 protein or TF mRNA were detected. CONCLUSION: Egr-1 mRNA and protein were up-regulated in the early stage of pancreatitis. Egr-1, as a pro-inflammatory transcriptional factor, probably plays an important role in the initiation of acute pancreatitis, and its action might be partially mediated through the up-regulation of TF expression.

Animals↗
PubMed2005

Conversion of cDNA differential display results (DDRT-PCR) into quantitative transcription profiles.

BACKGROUND: Gene expression studies on non-model organisms require open-end strategies for transcription profiling. Gel-based analysis of cDNA fragments allows to detect alterations in gene expression for genes which have neither been sequenced yet nor are available in cDNA libraries. Commonly used protocols for gel-based transcript profiling are cDNA differential display (DDRT-PCR) and cDNA-AFLP. Both methods have been used merely as qualitative gene discovery tools so far. RESULTS: We developed procedures for the conversion of cDNA Differential Display data into quantitative transcription profiles. Amplified cDNA fragments are separated on a DNA sequencer and detector signals are converted into virtual gel images suitable for semi-automatic analysis. Data processing consists of four steps: (i) cDNA bands in lanes corresponding to samples treated with the same primer combination are matched in order to identify fragments originating from the same transcript, (ii) intensity of bands is determined by densitometry, (iii) densitometric values are normalized, and (iv) intensity ratio is calculated for each pair of corresponding bands. Transcription profiles are represented by sets of intensity ratios (control vs. treatment) for cDNA fragments defined by primer combination and DNA mobility. We demonstrated the procedure by analyzing DDRT-PCR data on the effect of secondary metabolites of oilseed rape Brassica napus on the transcriptome of the pathogenic fungus Leptosphaeria maculans. CONCLUSION: We developed a data processing procedure for the quantitative analysis of amplified cDNA fragments separated by electrophoresis. The system utilizes common software and provides an open-end alternative to DNA microarray analysis of the transcriptome. It is expected to work equally well with DDRT-PCR and cDNA-AFLP data and be useful particularly in research on organisms for which microarray analysis is not available or economical.

Brassica napus↗
PubMed2000

Molecular basis for therapeutic decisions in chronic myeloid leukemia patients after allogeneic bone marrow transplantation.

BACKGROUND AND OBJECTIVES: Recent progress in the development of diagnostic techniques has greatly facilitated the monitoring of minimal residual disease (MRD) in patients with chronic myeloid leukemia (CML) after allogeneic bone marrow transplantation (BMT), the only curative treatment for this disease. The presence of the P210(bcr-abl) rearrangement in CML cells has allowed highly sensitive detection of MRD by polymerase chain reaction (PCR). However, complete eradication of the leukemic clone may not be a necessary prerequisite for long-term remission or cure. This observation limits the value of qualitative PCR analysis for prediction of progressive disease and highlights the need to monitor the proliferative activity of the malignant clone in order to permit timely detection of impending relapse and, thus, early therapy. This article discusses the applicability of several molecular methods to the monitoring of treatment efficacy and early assessment of clonal expansion in patients with CML after BMT. It also presents guidelines for clinical use of PCR analyses and the most effective approaches to treat relapsed patients. INFORMATION SOURCES: The authors have been working in this field, both experimentally and at a clinical level, contributing original papers to peer-reviewed journals. The material examined in this review includes articles published in journals covered by MedLine and reviews from journals with a high impact factor. STATE OF THE ART AND PERSPECTIVES: In view of the very limited value of qualitative PCR in detecting CML patients destined to relapse after BMT, several investigators have developed molecular assays that enable the kinetics of MRD to be monitored over time (e.g. quantitative PCR for P210(bcr-abl), PCR analysis of whole blood/lineage-specific chimerism and qualitative PCR for P190(bcr-abl)). These molecular strategies closely trace the kinetics of leukemic regrowth. Disease evolution in relapsed patients is consistently characterized by the sequential detection of increasing P210(bcr-abl) transcript levels, increasing myeloid mixed chimerism and finally, P190(bcr-abl) positivity preceding cytogenetic relapse. A 10-fold or greater increase in the expression of P210(bcr-abl) confirmed by a minimum of three independent quantitative PCR analyses and/or a progressive increase in the percentage of host myeloid cells in three consecutive chimerism analyses and/or P190(bcr-abl) mRNA detection must be regarded as an indication of incipient disease progression and should provide a rationale for initiation of treatment. There are various approaches to the management of the patient who relapses. The first step, if possible, is to reduce or terminate immune suppression. If the patient is not receiving this therapy, he or she can be treated with hydroxyurea or interferon or can be offered a second transplant. However, infusion to the patient of lymphoid cells (DLI) collected from the original donor has the capacity to restore complete remission in 70-80% of cases. Currently, several strategies are being used to minimize the severity of graft-versus-host disease after DLI (optimization of transfused lymphocyte doses, modification of the transfused lymphocyte subsets, administration of lymphocytes in escalating doses or lymphocyte transfection with a suicide gene), to reduce the incidence of marrow aplasia (stem cell support) and to increase the rate of complete responses (cytokines associated with DLI, leukemia-reactive cytotoxic lymphocytes, tyrosine kinase inhibitors or pre-emptive DLI).

Antineoplastic Combined Chemotherapy Protocols↗
PubMed2001

New developments in the diagnosis of maternal and congenital CMV infection.

Recent advances in the screening of pregnant women with Cytomegalovirus (CMV) IgM, CMV IgG and CMV IgG avidity serologic tests, has led to a more accurate diagnosis of CMV infection. When serologic screening is performed early in gestation, it is possible to identify those women at risk of intrauterine transmission of the virus, i.e., those women with a primary CMV infection, who should be enrolled in prenatal diagnosis. The use of quantitative PCR on amniotic fluid from pregnant women at 21-22 weeks of gestation in prenatal diagnosis is an effective diagnostic tool to distinguish between CMV infection and CMV disease in the fetus and newborn. Quantitative PCR on peripheral blood leukocytes from CMV infected newborns can be used to monitor viral load, especially during treatment with ganciclovir. These advances in serology and quantitative virology should lead to more accurate diagnosis of maternal and congenital CMV infection.

Antibody Affinity↗
PubMed1998

oriGNAI3: a narrow zone of preferential replication initiation in mammalian cells identified by 2D gel and competitive PCR replicon mapping techniques.

The nature of mammalian origins of DNA replication remains controversial and this is primarily because two-dimensional gel replicon mapping techniques have identified broad zones of replication initiation whereas several other techniques, such as quantitative PCR, have disclosed more discrete sites of initiation at the same chromosomal loci. In this report we analyze the replication of an amplified genomic region encompassing the 3'-end of the GNAI3 gene, the entire GNAT2 gene and the intergenic region between them in exponentially growing Chinese hamster fibroblasts. These cells express GNAI3 but not GNAT2 . The replication pattern was first analyzed by two-dimensional neutral-alkaline gel electrophoresis. Surprisingly, the results revealed a small preferential zone of replication initiation, of at most 1.7 kb, located in a limited part of the GNAI3 - GNAT2 intergenic region. Mapping of this initiation zone was then confirmed by quantitative PCR. The agreement between the two techniques exploited here strengthens the hypothesis that preferred sites of replication initiation do exist in mammalian genomes.

AMP Deaminase↗
PubMed2004

Real time PCR quantification of frataxin mRNA in the peripheral blood leucocytes of Friedreich ataxia patients and carriers.

The most common causative mutation of Friedreich ataxia (FRDA) is the unstable hyperexpansion of an intronic GAA triplet repeat that impairs frataxin transcription. Using real time quantitative PCR, we showed that FRDA patients had residual levels of frataxin mRNA ranging between 13% and 30% and that FRDA carriers had about 40% of that of controls. Asymptomatic carriers also showed reduced frataxin mRNA levels. We found an inverse correlation between the number of GAA repeats and frataxin mRNA levels. Real-time quantitative PCR may represent an alternative assay for FRDA molecular diagnosis.

DNA Primers↗
PubMed2004

Quantification of MDR-1 gene expression in canine tissues by real-time reverse transcription quantitative polymerase chain reaction.

MDR-1 gene product mediated multidrug resistance is thought to play a major role in the outcome of chemotherapy in some canine tumors, especially malignant lymphoma. In the present study, MDR-1 RNA expression in normal lymph node and liver tissue as well as in tumor biopsies from 23 dogs with lymphomas and two dogs with liver tumors was measured by real-time RT-quantitative PCR. MDR-1 gene expression was detected in all samples analyzed. Comparably high MDR-1 RNA levels were measured in all normal liver tissues, one of the lymphomas and a cholangiocarcinoma. MDR-1 expression levels in canine lymphomas were found to vary over a wide range with most tumors expressing relative low levels. Interestingly, gastrointestinal lymphomas expressed higher MDR-1 RNA levels than multicentric lymphomas (p = 0.03). In conclusion, real-time RT-quantitative PCR appears to be a suitable method for sensitive and quantitative determination of MDR-1 gene expression in canine normal and neoplastic tissues.

Animals↗
PubMed1997

Detection of hepatitis C virus genomic sequences in the cerebrospinal fluid of HIV-infected patients.

To assess the presence of hepatitis C virus (HCV) in the central nervous system (CNS), HCV-RNA was sought in paired serum and cerebrospinal fluid (CSF) samples of 21 HIV/HCV-positive patients: HCV-RNA was detected in the serum of 19/21 patients (90.4%), and in the CSF of five of the 19 serum-positive patients. The presence of HCV-RNA was confirmed in follow-up CSF samples available for three of these five patients. An identical HCV genotype was found in the paired serum/CSF samples. No correlation was found between the different genotypes and the presence of HCV in CSF of the individual patients. HCV viremia levels measured by branched-DNA and quantitative PCR were not significantly higher in the CSF-positive cases than in the CSF-negative cases (P = 0.3, using b-DNA; 0.5, using quantitative PCR). This report shows the presence of HCV in CSF and raises the possibility that the CNS may act as a reservoir site for HCV.

AIDS-Related Opportunistic Infections↗
PubMed2006

Detection and enumeration of Salmonella enteritidis in homemade ice cream associated with an outbreak: comparison of conventional and real-time PCR methods.

Salmonellosis caused by Salmonella Enteritidis (SE) is a significant cause of foodborne illnesses in the United States. Consumption of undercooked eggs and egg-containing products has been the primary risk factor for the disease. The importance of the bacterial enumeration technique has been enormously stressed because of the quantitative risk analysis of SE in shell eggs. Traditional enumeration methods mainly depend on slow and tedious most-probable-number (MPN) methods. Therefore, specific, sensitive, and rapid methods for SE quantitation are needed to collect sufficient data for risk assessment and food safety policy development. We previously developed a real-time quantitative PCR assay for the direct detection and enumeration of SE and, in this study, applied it to naturally contaminated ice cream samples with and without enrichment. The detection limit of the real-time PCR assay was determined with artificially inoculated ice cream. When applied to the direct detection and quantification of SE in ice cream, the real-time PCR assay was as sensitive as the conventional plate count method in frequency of detection. However, populations of SE derived from real-time quantitative PCR were approximately 1 log higher than provided by MPN and CFU values obtained by conventional culture methods. The detection and enumeration of SE in naturally contaminated ice cream can be completed in 3 h by this real-time PCR method, whereas the cultural enrichment method requires 5 to 7 days. A commercial immunoassay for the specific detection of SE was also included in the study. The real-time PCR assay proved to be a valuable tool that may be useful to the food industry in monitoring its processes to improve product quality and safety.

Colony Count, Microbial↗
PubMed1993

Polymerase chain reaction detection of human cytomegalovirus in over 2000 blood specimens correlated with virus isolation and related to urinary virus excretion.

The polymerase chain reaction (PCR) as applied to human cytomegalovirus (HCMV) detection should provide a valuable tool for rapid, reliable diagnosis of infection, thereby allowing prompt treatment. However, to date the high sensitivity of this technique and the lack of semi-quantitative interpretation have hindered establishing its validity for diagnosing systemic infection. We describe a rapid, simple, semi-quantitative PCR technique for HCMV detection. The validity of the technique was tested objectively by analyzing over 2000 leukocytes specimens by PCR and comparing the results with virus isolation from urine and blood in concomitant samples in the absence of any clinical data. It could thus be established that this technique had a sensitivity and specificity of 97%. When the PCR signal corresponded to > or = 8000 genome equivalents for 10(4) leukocytes, the predictive value for viremia was 86%. This semi-quantitative PCR technique should allow rapid diagnosis of systemic infection and provide a reliable means of monitoring clearance of CMV from blood during drug therapy.

Acquired Immunodeficiency Syndrome↗