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At least 1,423 records · Page 79Linked to original sources
PubMed2005

Rapid quantification of semen hepatitis B virus DNA by real-time polymerase chain reaction.

AIM: To examine the sensitivity and accuracy of real-time polymerase chain reaction (PCR) for the quantification of hepatitis B virus (HBV) DNA in semen. METHODS: Hepatitis B viral DNA was isolated from HBV carriers' semen and sera using phenol extraction method and QIAamp DNA blood mini kit (Qiagen, Germany). HBV DNA was detected by conventional PCR and quantified by TaqMan technology-based real-time PCR (quantitative polymerase chain reaction (qPCR)). The detection threshold was 200 copies of HBV DNA for conventional PCR and 10 copies of HBV DNA for real time PCR per reaction. RESULTS: Both methods of phenol extraction and QIAamp DNA blood mini kit were suitable for isolating HBV DNA from semen. The value of the detection thresholds was 500 copies of HBV DNA per mL in the semen. The viral loads were 7.5X10(7) and 1.67X10(7) copies of HBV DNA per mL in two HBV infected patients' sera, while 2.14X10(5) and 3.02X10(5) copies of HBV DNA per mL in the semen. CONCLUSION: Real-time PCR is a more sensitive and accurate method to detect and quantify HBV DNA in the semen.

DNA, Viral↗
PubMedDate not supplied

CDRAP is expressed in adult articular cartilage, but its expression is not significantly regulated in osteoarthritic chondrocytes.

OBJECTIVE: In this study we assessed the differential in vivo mRNA expression levels of CDRAP, a potential marker of cartilage degeneration. METHODS: Conventional and real time PCR in a large series of normal (n = 18) and late stage osteoarthritic (n = 24) cartilage specimens were performed. RESULTS: Conventional PCR analysis could demonstrate the presence of CDRAP mRNA in normal and osteoarthritic chondrocytes. Real time quantitative PCR confirmed the presence of CDRAP mRNA expression in normal articular chondrocytes in vivo (and in vitro). No significant up-regulation of CDRAP was observed in osteoarthritic chondrocytes in vivo. CONCLUSION: The presented results confirm expression of CDRAP by normal and osteoarthritic articular chondrocytes, but indicate that increased expression levels by chondrocytes are not the cause of the increased levels of CDRAP in the synovial fluid of patients with osteoarthritis.

Adult↗
PubMed1997

Two variants of quantitative reverse transcriptase PCR used to show differential expression of alpha-, beta- and gamma-fibrinogen genes in rat liver lobes.

Quantitative reverse transcriptase PCR (RT-PCR) is a sensitive method for the measurement of mRNA copy number. However, the methodology has gained a reputation for poor reproducibility, leading to concern over the validity of much of the data generated using this technique. We have developed two variants of quantitative competitive RT-PCR using a synthesized RNA as an internal standard to measure precisely the relative levels of alpha-, beta- and gamma-fibrinogen mRNAs in the four lobes of the rat liver. In the first of these variants we altered only the amount of total RNA in the RT-PCR reaction, keeping the amount of internal standard RNA and the number of PCR cycles constant. In the second variant only the number of PCR cycles was altered, and the amounts of total RNA and standard RNA were kept constant. Both variants of RT-PCR allowed calculation of the number of mRNA copies, which did not differ significantly between the two techniques. Of the two variants, the second gave better reproducibility, and the intra-assay coefficient of variation for this technique was 14% (n = 20). Using these two variants we have shown that there are different numbers of fibrinogen mRNAs in the four liver lobes for each of the three genes (alpha-fibrinogen F = 14.64, P = 0.0003; beta-fibrinogen F = 3.74, P = 0.04; gamma-fibrinogen F = 3.75, P = 0.04). In conclusion, by using two variants of quantitative competitive RT-PCR we have shown that this technique can be used to give reproducible results, and the low intra-assay coefficient of variation suggests that quantitative RT-PCR should be the technique of choice for accurate measurement of mRNA copy number.

Animals↗
PubMed2000

Glutamate transporter EAAT2 splice variants occur not only in ALS, but also in AD and controls.

OBJECTIVE: To ascertain the specificity of alternatively spliced mRNA variants of the astroglial glutamate transporter EAAT2 for ALS. BACKGROUND: An important hypothesis for ALS pathogenesis is that motor neuron injury may result from chronically elevated glutamate levels in the CNS. Supporting this idea are reports of decreased glutamate transport in ALS. This in turn has recently been suggested to be due to the presence of aberrant mRNA splice variants for EAAT2 in ALS. METHODS: Postmortem human brain tissue was obtained from different brain regions of patients with ALS, normal controls (NC), and patients with AD and Lewy body dementia (LB)-neurodegenerative diseases in which motor neurons are unaffected. Brain RNA was analyzed for EAAT2 isoforms using reverse transcription PCR and cDNA cloning/sequencing methods. RESULTS: Splice variants lacking exons 7 or 9 were present in ALS brain, as previously reported, but were also present in brains from NC, AD, and LB patients. PCR product sequence analyses from non-ALS brain show variant splicing identical to that reported for ALS. Quantitative PCR analysis shows that these isoforms may be somewhat more abundant in ALS than AD, LB, and NC brains. CONCLUSIONS: EAAT2 mRNA splice variants are found in the brains of NC and AD patients, as in ALS. The authors cannot exclude the possibility that quantitative changes in variant EAAT2 isoforms might relate directly, or indirectly, to ALS pathology. However, the qualitative presence of these "abnormal" EAAT2 splice variants does not appear to be sufficient to explain motor neuron degeneration in ALS.

Alternative Splicing↗
PubMed2004

Development of a 16S rDNA-targeted PCR assay for monitoring of Lactobacillus plantarum and Lact. rhamnosus during co-cultivation for production of inoculants for silages.

AIMS: This paper reports a simple, rapid approach for the parallel detection of Lactobacillus plantarum and Lact. rhamnosus in co-culture in order to produce an inoculant mixture for silage purposes. METHODS AND RESULTS: The 16S rDNA-targeted PCR primers were established for parallel detection of Lact. plantarum and Lact. rhamnosus in a single multiplex PCR. A protocol for application of these primers in direct PCR as well as colony-direct (CD) PCR was developed. These primers were also applicable for the estimation of the relative amount of each DNA type in mixed probes (semi-quantitative PCR). CONCLUSIONS: The PCR assay presented in this study is a robust, fast and semi-quantitative approach for detection of Lact. plantarum and Lact. rhamnosus in liquid cultures as well as on agar plates. SIGNIFICANCE AND IMPACT OF THE STUDY: This method provides an effective tool for the establishment of a regime for co-cultivation of Lact. plantarum and Lact. rhamnosus. This would enable faster and thus cost-reduced production of ensiling inoculants.

Coculture Techniques↗
PubMed2003

Human immunodeficiency virus type 1 nucleocapsid zn(2+) fingers are required for efficient reverse transcription, initial integration processes, and protection of newly synthesized viral DNA.

Human immunodeficiency virus type 1 (HIV-1) containing mutations in the nucleocapsid (NC) Zn(2+) finger domains have greatly reduced infectivity, even though genome packaging is largely unaffected in certain cases. To examine replication defects, viral DNA (vDNA) was isolated from cells infected with viruses containing His-to-Cys changes in their Zn(2+) fingers (NC(H23C) and NC(H44C)), an integrase mutant (IN(D116N)), a double mutant (NC(H23C)/IN(D116N)), or wild-type HIV-1. In vitro assays have established potential roles for NC in reverse transcription and integration. In vivo results for these processes were obtained by quantitative PCR, cloning of PCR products, and comparison of the quantity and composition of vDNA generated at discrete points during reverse transcription. Quantitative analysis of the reverse transcription intermediates for these species strongly suggests decreased stability of the DNA produced. Both Zn(2+) finger mutants appear to be defective in DNA synthesis, with the minus- and plus-strand transfer processes being affected while interior portions of the vDNA remain more intact. Sequences obtained from PCR amplification and cloning of 2-LTR circle junction fragments revealed that the NC mutants had a phenotype similar to the IN mutant; removal of the terminal CA dinucleotides necessary for integration of the vDNA is disabled by the NC mutations. Thus, the loss of infectivity in these NC mutants in vivo appears to result from defective reverse transcription and integration processes stemming from decreased protection of the full-length vDNA. Finally, these results indicate that the chaperone activity of NC extends from the management of viral RNA through to the full-length vDNA.

Base Sequence↗
PubMed2003

Real-time quantitative RT-PCR assay of gene expression in plant roots during fungal pathogenesis.

Real-time quantitative RT-PCR is becoming the preferred method for high-sensitivity, rapid-throughput RNA transcript quantification. However, due to the significant developmental costs of dedicated fluorogenic probes, a real-time assay that is simple to establish, comparatively inexpensive, and readily adaptable would be advantageous for the detailed analysis of large sets of expressed sequences. We have devised a flexible real-time quantitative RT-PCR assay that employs a nonspecific DNA binding dye for product detection and uses a relative quantification formula to account for differences in PCR amplification efficiency between the target and reference products. The latter permits the use of an exogenous reference transcript and therefore avoids the normal requirement for the construction of a recombinant RNA reference transcript or extensive characterization of housekeeping gene expression. In an investigation of class II chitinase expression in two varieties of Bermuda grass (Cynodon spp.), following infection with the fungal root pathogen Ophiosphaerella narmari, this assay identified 16- and 28-fold peaks in gene expression at 24 and 96 h after inoculation, respectively.

Chitinases↗
PubMed2004

A one step quantitative RT-PCR for detection of SARS coronavirus with an internal control for PCR inhibitors.

In this study, we report a one step quantitative RT-PCR assay for severe acute respiratory syndrome (SARS) diagnosis. The overall detection rate for clinical samples collected from Days 1 to 9 of disease onset is 86.2% and the specificity of the assay is 100%. To detect false negative results due to PCR inhibitors or faulty RNA extraction, we have further modified this one step RT-PCR assay for simultaneous detection of severe acute respiratory syndrome (SARS) coronavirus (CoV) and 18S ribosomal RNA (rRNA) as an internal positive control.

DNA, Ribosomal↗
PubMed2006

Advantages of real-time PCR assay for diagnosis and monitoring of canine leishmaniosis.

The aim of the present study is to highlight the advantages of real-time quantitative PCR intended to aid in the diagnosis and monitoring of canine leishmaniosis. Diagnosis of canine leishmaniosis is extremely challenging, especially in endemic areas, due to the diverse and non-specific clinical manifestations, and due to the high seroprevalence rate in sub-clinical dogs. Veterinarian clinicians are usually confronted with cases that are compatible with the disease, and with several diagnostic tests, sometimes with contradictory results. We have developed a new TaqMan assay, targeting the kinetoplast, applied to 44 samples of bone marrow aspirate or peripheral blood. The dynamic range of detection of Leishmania DNA was established in 7 logs and the limit of detection is 0.001 parasites in the PCR reaction. At the time of diagnosis parasitemia ranges from less than 1 to 10(7)parasites/ml. The ability to quantify the parasite burden allowed: (i) to elucidate the status of positive dogs by conventional PCR, although larger studies are necessary to clarify the dividing line between infection and disease, (ii) to estimate the kinetics of the parasite load and the different response to the treatment in a follow-up and (iii) to validate blood as less invasive sample for qPCR. The continuous data provided by real-time qPCR could solve the dilemma for the clinician managing cases of canine leishmaniosis by differentiating between Leishmania-infected dogs or dogs with active disease of leishmaniosis.

Animals↗
PubMed1997

Alteration in mRNA levels of Fas splice variants in hepatitis C-infected liver.

The Fas receptor (APO-1/CD95) is expressed on hepatocytes and is thought to be important in triggering apoptosis after ligation by the Fas ligand carried on cytotoxic T cells. Recent evidence has shown that several splice variants of Fas exist, the major one of which (FasTMDel) may produce a soluble protein which can modulate apoptosis by interacting with ligand. There are no data on the expression of splice variants of Fas in liver disease. RNA was extracted from needle biopsies from 13 patients with hepatitis C virus (HCV) infection and six normal liver samples. By reverse transcriptase polymerase chain reaction (RT-PCR) FasTMDel expression was demonstrated at the mRNA level, in both normal and HCV-infected liver. Quantitative PCR demonstrated an increase in Fas transcript relative to FasTMDel in HCV infection. This difference is due to an induction of Fas, with FasTMDel remaining at constant levels in the two groups. If translated into protein, liver cells may express more Fas and thus be susceptible to apoptosis inducible by ligand-bearing cytotoxic T cells. These findings suggest that mechanisms exist to regulate the differential splicing of Fas and FasTMDel dependent on the cell's environment. The degree of alteration in the levels of Fas relative to FasTMDel occurred independently of the ALT levels and histological grading of the HCV-infected cases. However, an association was noted between increasing Fas:FasTMDel ratio and log viral load in the liver, measured by competitive PCR.

Alanine Transaminase↗
PubMed2001

Minimal residual disease in thyroid carcinoma.

The detection of disseminated tumor cells in differentiated (DTC) and medullary thyroid carcinomas (MTC) is one of the main topics in current thyroid cancer research. Immunocytochemistry and polymerase chain reaction (PCR) provide the tools for the identification of a small number of thyroid cancer cells in peripheral blood and cervical lymph nodes. Thyroid-specific markers, such as thyroglobulin (Tg) mRNA and thyroid peroxidase (TPO) mRNA, have been detected with RT-PCR in blood samples of tumor patients and healthy control subjects. To prevent false-positive results, quantitative PCR systems were established. Tumor-specific markers, such as telomerase activity and cytokeratin 20 (CK20), have been detected in various epithelial tumors. Amplification products of these markers were found in blood samples and in fine-needle aspiration (FNA) biopsies of patients with thyroid carcinomas. Using molecular detection of disseminated tumor cells in cervical lymph nodes with CK20 RT-PCR, a higher percentage of involved lymph nodes was detected compared to immunohistochemistry. The results of the presented studies may help researchers to develop more sensitive methods for early tumor cell dissemination, and refine risk groups that might benefit from more extensive surgical procedures or adjuvant therapy. However, the prognostic value of minimal residual disease (MRD) in thyroid carcinoma has to be confirmed in large or multicenter prospective studies.

Humans↗
PubMed2004

Detection and quantitation of human immunodeficiency virus type-1 particles by confocal microscopy.

A method is described to visualise directly human immunodeficiency virus type-1 (HIV-1) particles. HIV-1 containing samples were adsorbed onto a plastic surface and doubly labeled with antibodies specific for viral proteins and sensitive nucleic acids dyes. Laser scanning confocal microscopy detected co-localization of viral proteins and nucleic acids, thus allowing specific identification of HIV. Using this technique, we have quantified eight different HIV-1 sub-types and three HIV-1 groups in tissue culture supernatants from infected peripheral blood mononuclear cells (PBMCs). Confocal counts correlated well with electron microscopy (EM) counts and HIV-1 RNA loads as determined by quantitative PCR. Confocal microscopy may prove to be a simple alternative to electron microscopy for virus identification and quantitation.

Cell Line↗
PubMed2003

Incomplete DJH rearrangements of the IgH gene are frequent in multiple myeloma patients: immunobiological characteristics and clinical implications.

DH-JH rearrangements of the Ig heavy-chain gene (IGH) occur early during B-cell development. Consequently, they are detected in precursor-B-cell acute lymphoblastic leukemias both at diagnosis and relapse. Incomplete DJH rearrangements have also been occasionally reported in mature B-cell lymphoproliferative disorders, but their frequency and immunobiological characteristics have not been studied in detail. We have investigated the frequency and characteristics of incomplete DJH as well as complete VDJH rearrangements in a series of 84 untreated multiple myeloma (MM) patients. The overall detection rate of clonality by amplifying VDJH and DJH rearrangements using family-specific primers was 94%. Interestingly, we found a high frequency (60%) of DJH rearrangements in this group. As expected from an immunological point of view, the vast majority of DJH rearrangements (88%) were unmutated. To the best of our knowledge, this is the first systematic study describing the incidence of incomplete DJH rearrangements in a series of unselected MM patients. These results strongly support the use of DJH rearrangements as PCR targets for clonality studies and, particularly, for quantification of minimal residual disease by real-time quantitative PCR using consensus JH probes in MM patients. The finding of hypermutation in a small proportion of incomplete DJH rearrangements (six out of 50) suggests important biological implications concerning the process of somatic hypermutation. Moreover, our data offer a new insight in the regulatory development model of IGH rearrangements.

Clone Cells↗
PubMed1992

Simultaneous use of two retroviral vectors in human gene marking trials: feasibility and potential applications.

Two Moloney murine leukemia virus (Mo-MLV)-based neoR retroviral vectors--LNL6 and G1Na--were used to transduce various human tumor-infiltrating lymphocytes (TIL) populations. These groups included bulk CD(8+)- and CD(4+)-enriched TIL from human renal cell carcinomas and melanomas. Transduction efficiencies averaged 5% for single 4-hr supernatant infections. Integrated provirus could be detected for up to 4 weeks of in vitro culture. LNL6 provirus could be distinguished from G1Na provirus using specific polymerase chain reaction (PCR) primers. A single neomycin phosphotransferase (neoR) gene copy could be detected in 10(5) TIL. Using quantitative PCR, the relative ratio of LNL6 to G1Na copies in the same sample could be determined even at low copy numbers. These preclinical studies demonstrate the feasibility of using two retroviral marking vectors in human gene therapy efforts.

Base Sequence↗
PubMed2004

Application of RT-PCR to clinical diagnosis of micrometastasis of colorectal cancer: A translational research study.

We previously reported in a retrospective study that CEA-based RT-PCR was useful for predicting the prognosis of patients with node-negative colorectal cancer. RT-PCR is well established for laboratory use, but many issues remain to be resolved prior to its clinical application. In addition to the false positive rate of RT-PCR, we addressed several issues, including the timing of lymph node sampling, stability of RNA after surgery, and reproducibility of results. After appropriate modification, including development of a tissue sampling kit, a multi-institutional clinical study was commenced prospectively from November 2001, and 100 patients were enrolled for examination of micrometastasis. RNA was stable in lymph nodes for up to 3 h after surgical resection. This range of sampling time was acceptable to the surgeons. RNA was well preserved in RNA later at -20 degrees C for 3 weeks. Dilutions of MKN45 and LoVo cells served as positive controls for conventional PCR since these controls were found to be highly stable and ensured reproducibility. Moreover, simultaneous use of quantitative PCR (Light Cycler) ensured double confirmation of the results. Our clinical study showed that the quality of RNA was excellent or good in most samples (98 of 100; 98%). Twenty-four of 98 (24.5%) cases were judged to be micrometastasis-positive. In conclusion, the current translational research study established a clinically feasible RT-PCR system for micrometastasis. Our system could potentially be useful as a clinical tool.

Colorectal Neoplasms↗
PubMed1995

[Methods for DNA diagnosis in military medicine].

The article makes a review of achievements in the sphere of biotechnology and genetic engineering as far as military medicine is concerned. A special attention is drawn on diagnostic capacities of molecular genetic methods which analyse DNA and RNA objects. Principles of modern diagnostical methods are described which are based on molecular hybridization of nucleic acids with a use of specific DNA probes or polymerize chain reaction (PCR). The advantages of the latter are shown in the comparison with immunochemical methods. Peculiarities of new quantitative PCR modifications are studied. The article contains data concerning the use of DNA probes and PCR for estimation of radiation injuries and during formation of maximal tolerance level of physical and chemical influence.

Base Sequence↗
PubMed2004

Real-time PCR designs to estimate nuclear and mitochondrial DNA copy number in forensic and ancient DNA studies.

We explore different designs to estimate both nuclear and mitochondrial human DNA (mtDNA) content based on the detection of the 5' nuclease activity of the Taq DNA polymerase using fluorogenic probes and a real-time quantitative PCR detection system. Human mtDNA quantification was accomplished by monitoring the real-time progress of the PCR-amplification of two different fragment sizes (113 and 287 bp) within the hypervariable region I (HV1) of the mtDNA control region, using two fluorogenic probes to specifically determine the mtDNA copy of each fragment size category. This mtDNA real-time PCR design has been used to assess the mtDNA preservation (copy number and degradation state) of DNA samples retrieved from 500 to 1500 years old human remains that showed low copy number and highly degraded mtDNA. The quantification of nuclear DNA was achieved by real-time PCR of a segment of the X-Y homologous amelogenin (AMG) gene that allowed the simultaneous estimation of a Y-specific fragment (AMGY: 112 bp) and a X-specific fragment (AMGX: 106 bp) making possible not only haploid or diploid DNA quantitation but also sex determination. The AMG real-time PCR design has been used to quantify a set of 57 DNA samples from 4-5 years old forensic bone remains with improved sensitivity compared with the slot-blot hybridization method. The potential utility of this technology to improve the quality of some PCR-based forensic and ancient DNA studies (microsatellite typing and mtDNA sequencing) is discussed.

Amelogenin↗
PubMed2003

[Clinical significance of CEA mRNA detection in pleural and peritoneal effusions by real-time fluorescent quantitative RT-PCR].

OBJECTIVES: To detect CEA mRNA levels in benign and malignant pleural and peritoneal effusions and evaluate their clinical significance. METHODS: Samples of pleural and peritoneal effusions from 58 patients with malignant diseases and 76 patients with benign diseases were collected and total RNAs were prepared and subjected to real-time fluorescent quantitative RT-PCR to determine the CEA mRNA levels in these samples. The positive rate of this examination was compared with that of shed cell pathological examination. RESULTS: Nineteen samples (32.8%) of pleural and peritoneal effusions from the 58 patients with malignant diseases showed positive results in shed cell examination, while the number of CEA mRNA >1 CN was 46 (79.3%) (chi(2) = 21.81, P = 0.000). Nineteen samples of pleural and peritoneal effusions from the 76 patients with benign diseases showed CEA mRNA > 1 CN (25.0%), which was significantly different from that of the patients with malignant diseases (chi(2) = 38.85, P = 0.000). CONCLUSION: CEA mRNA levels in pleural and peritoneal effusions can be quantified by real-time fluorescent quantitative PCR, which is more sensitive than shed cell pathological examination. This technique is helpful in discrimination of benign and malignant pleural and peritoneal effusions.

Ascitic Fluid↗