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At least 1,297 records · Page 72Linked to original sources
PubMed2005

The use of comparative duplex PCR in monitoring of patients with non-Hodgkin's lymphoma and chronic lymphocytic leukaemia.

Various quantitative PCR approaches have been utilized during the last years to provide information about the treatment efficacy and the risk of recurrent disease in haematological malignancies. Apart from the frequently used real-time PCR, cost-saving modified standard PCR methods may be applied as well. This report evaluates the utility of the end-point comparative duplex PCR. We have used this method for monitoring of 35 patients with either NHL or CLL and observed a good correlation between quantitative molecular results and clinical outcome. There was also an agreement between comparative duplex PCR and real-time PCR in patients who were monitored by both methods. We therefore believe that use of this technique should be strongly considered instead of simple qualitative detection in monitoring of therapeutic outcome in NHL or CLL patients.

Genetic Markers↗
PubMedDate not supplied

[Congenital human cytomegalovirus infection: value of human cytomegalovirus DNA quantification in amniotic fluid].

A quantitative PCR assay (RS Elosa CMV, Lambdatech) was used to quantitate HCMV DNA in maternal amniotic fluid of 12 fetuses with congenital infection (group 1) and of 10 fetuses without congenital infection (group 2). HCMV detection was performed for both groups using culture and qualitative PCR. Histologic examinations of fetal tissues and placenta were carried out for 9 patients from group 1. The amniotic fluid viral loads were negative in all patients of group 2. In group 1, all viral loads were high (from 1.105 to > 107 cop/mL) and no difference was observed between symptomatic and asymptomatic foetuses. Further evaluation on larger samples is needed to define more precisely the pronostic value of HCMV DNA quantification in amniotic fluid.

Amniotic Fluid↗
PubMed2004

Evaluation of antiviral activity against human herpesvirus 8 (HHV-8) and Epstein-Barr virus (EBV) by a quantitative real-time PCR assay.

A real-time quantitative PCR was developed to assess antiviral activity of molecules against human herpesvirus 8 (HHV-8) and the Epstein-Barr virus (EBV). The antiviral activity of the reference molecules acyclovir, ganciclovir, cidofovir, adefovir and brivudin, as assessed by this methodology, proved very similar to the activity as determined by a DNA-DNA hybridisation method.

Acyclovir↗
PubMed2004

Large deletions of the MECP2 gene detected by gene dosage analysis in patients with Rett syndrome.

MECP2 mutations are responsible for Rett syndrome (RTT). Approximately a quarter of classic RTT cases, however, do not have an identifiable mutation of the MECP2 gene. We hypothesized that larger deletions arising from a deletion prone region (DPR) occur commonly and are not being routinely detected by the current PCR-mediated screening strategies. We developed and applied a quantitative PCR strategy (qPCR) to samples referred for diagnostic assessment from 140 patients among whom RTT was strongly suspected and from a second selected group of 31 girls with classical RTT. Earlier MECP2 mutation screening in both groups of patients had yielded a wild-type result. We identified 10 large deletions (7.1%) within the first group and five deletions in the second group (16.1%). Sequencing of the breakpoints in 11 cases revealed that eight cases had one breakpoint within the DPR. Among seven cases, the breakpoint distant to the DPR involved one of several Alu repeats. Sequence analysis of the junction sequences revealed that eight cases had complex rearrangements. Examination of the MECP2 genomic sequence reveals that it is highly enriched for repeat elements, with the content of Alu repeats rising to 27.8% in intron 2, in which there was an abundance of breakpoints among our patients. Furthermore, a perfect chi sequence, known to be recombinogenic in E. coli, is located in the DPR. We propose that the chi sequence and Alu repeats are potent factors contributing to genomic rearrangement. We suggest that routine mutation screening in MECP2 should include quantitative analysis of the genomic sequences flanking the DPR.

Base Sequence↗
PubMed2005

[ISGF3, a critical factor of the IFN-alpha pathway in the antiviral action of HBV].

OBJECTIVE: To study the mechanism of signal transduction in anti-HBV action of IFN-alpha. METHODS: The HBV DNA in HepG 2.2.15 cell line supernatant with/without IFNalpha-2b were monitored by fluorescence real-time quantitive PCR. STAT1, STAT2, ISGF3-gamma, PKR, 2'5'-OAS mRNA levels from HepG 2 and HepG 2.2.15 cell lines that were treated with/without IFNalpha-2b at different times were detected by semi-quantitive RT-PCR. And the ISGF3-gamma protein was detected by Western blot. Then, these items were detected again after inhibiting the JAK-STAT pathway with genistein. RESULTS: The HBV DNA in 2215 supernatant that were treated with IFNalpha-2b for 8 hours decreased 0.72 log 10 copies/ml. But the basal levels of DNA in cells pretreated with genistein? followed by IFNalpha-2b did not decrease. The STAT1, STAT2, ISGF3-gamma, 2'5'-OAS, PKR mRNA levels were upregulated by IFNalpha-2b. The same phenomena were observed with STAT1, STAT2, ISGF3-gamma mRNA when pretreated with genistein then treated with IFNalpha-2b, but the levels of 2'5'-OAS, PKR mRNA were decreased in this situation. The expression of the protein of ISGF3-gamma was also augmented by IFNalpha-2b, and was blocked by genistein. CONCLUSION: The JAK-STAT pathway seems to be a critical pathway in IFNalpha-2b action against HBV? and ISGF3 is most probably a key factor of the route.

Antiviral Agents↗
PubMed2006

Chip-on-beads: flow-cytometric evaluation of chromatin immunoprecipitation.

BACKGROUND: Chromatin immunoprecipitation (ChIP) is a widely used technique for the detection of in vivo DNA-protein interactions underlying epigenetic regulation. The standard readout of ChIP is based on semi-quantitative or quantitative PCR measurements; however, the development of alternative platforms with high throughput potentialities is expected to facilitate the introduction of this method into routine diagnostics. METHODS: We have established a flow-cytometry-based alternative for the evaluation of ChIP data. The method is based on the capture of the products of a conventional PCR run to low cycle numbers, on microbeads. RESULTS: In vivo histone H4 acetylation and H3 lysine 4 methylation was detected at the promoter of the tissue transglutaminase type 2 gene. These results were confirmed by QPCR measurements. The levels of modifications decreased significantly upon apoptosis and were accompanied by the down-regulation of TGM2 mRNA expression. CONCLUSIONS: This method that we named ChIP-on-beads, a combination of flow cytometry and conventional PCR, is a reliable and efficient alternative in the quantitative analysis of ChIP results, especially promising when high throughput monitoring of epigenetic markers of diagnostic importance is required. The method is simple enough to be easily implemented in a routine flow-cytometric laboratory.

Acetylation↗
PubMed1999

Expression of inositol 1,4,5-trisphosphate receptor isoforms in rat cirrhosis.

Ca(2+) signals mediate the hepatic effects of numerous hormones and growth factors. Hepatic Ca(2+) signals are elicited by the inositol trisphosphate receptor, an intracellular Ca(2+) channel. Three isoforms of this receptor have been identified; they are expressed and regulated differently. We investigated the effect of liver fibrosis and cirrhosis on the hepatic expression of the inositol trisphosphate receptor isoforms. Two different rat models were used: bile duct ligation (fibrosis) and chronic exposure to CCl(4)/phenobarbital (cirrhosis). Messenger RNA levels were determined by ribonuclease protection assay (RPA), competitive polymerase chain reaction (PCR) followed by Southern blotting, and real-time quantitative PCR. Protein expression was assessed by Western blotting; tissue distribution was assessed by immunohistology. In control animals, isoform 2 was the predominant isoform, isoform 1 represented less than one third, and isoform 3 less than 1%. After bile duct ligation, expression of types 1 and 3 increased 1.9- and 5.7-fold, and expression of type 2 decreased 2. 5-fold at the protein level. After exposure to CCl(4)/phenobarbital, expression of types 1, 2, and 3 were 2.4-, 0.9-, and 4.2-fold their expression in control animals. Type 2 was localized to the apical domain of hepatocytes, consistent with a role for Ca(2+) signals in canalicular function. Type 3 was detectable in intrahepatic bile duct epithelial cells and not in hepatocytes, suggesting that Ca(2+) signals may be regulated differently in these cells. Signaling through inositol trisphosphate receptor participates in the pathogenesis of cirrhosis, because this process affects the expression of its isoforms.

Animals↗
PubMed1996

Cloning and quantification of galanin-1 receptor expression by mucosal cells lining the human gastrointestinal tract.

Recent studies suggest that galanin receptors may be expressed by mucosal epithelial cells lining the GI tract and play a role in regulating ion transport. However, no information exists as to which receptor subtype is expressed by these mucosal cells, or the relative distribution of such receptors within the GI tract. In this study we cloned the human galanin-1 receptor (huGal 1-R) from small intestinal RNA, and demonstrate its expression in endoscopically obtained mucosal pinch biopsies by RT-PCR from the esophagus to the rectum. Semi-quantitative PCR (SQ-PCR) was performed and revealed the largest amount of huGal 1-R message in the duodenum and the least amount in the gastric fundus. This study for the first time directly demonstrates the presence and quantity of huGal 1-R message in human G1 tract mucosal epithelial cells, and suggests that this subtype is of primary importance in regulating galanin-induced changes in intestinal absorption.

Base Sequence↗
PubMed2002

Biodistribution and toxicity studies of VSVG-pseudotyped lentiviral vector after intravenous administration in mice with the observation of in vivo transduction of bone marrow.

Lentiviral vectors can confer high levels of gene transfer and transgene expression in a variety of cell types. However, the biodistribution and toxicity after intravenous administration have not been reported. To address these issues of biodistribution and toxicity, an HIV-1-based vector, HR'cmvGFP, was administered to normal BALB/c mice by tail-vein injection. Nine different organs and bone marrow were evaluated by real-time quantitative PCR (QPCR) assay capable of a broad range of quantitation (5-log fold) to detect as few as one copy of the green fluorescent protein gene (GFP) per 10(5) cells. Four days after vector administration, high levels of transgene and gene expression were observed in liver, spleen, and bone marrow in all animals. By 40 days after injection, GFP levels had decreased in liver and spleen, but bone marrow exhibited a consistently high level of transgene. This finding was consistent with the increase in both GFP frequency and expression levels observed in peripheral blood by fluorescence-activated cell-sorting (FACS) analysis. Between 0 and 1% transgene was detected in all other organs. No significant pathologic lesions were found attributable to vector in any of the tissues examined. The observation of bone marrow transduction after intravenous vector administration suggests the possibility of an in vivo approach to stem cell gene therapy.

Animals↗
PubMed2003

Innovative tools for detection of plant pathogenic viruses and bacteria.

Detection of harmful viruses and bacteria in plant material, vectors or natural reservoirs is essential to ensure safe and sustainable agriculture. The techniques available have evolved significantly in the last few years to achieve rapid and reliable detection of pathogens, extraction of the target from the sample being important for optimising detection. For viruses, sample preparation has been simplified by imprinting or squashing plant material or insect vectors onto membranes. To improve the sensitivity of techniques for bacterial detection, a prior enrichment step in liquid or solid medium is advised. Serological and molecular techniques are currently the most appropriate when high numbers of samples need to be analysed. Specific monoclonal and/or recombinant antibodies are available for many plant pathogens and have contributed to the specificity of serological detection. Molecular detection can be optimised through the automatic purification of nucleic acids from pathogens by columns or robotics. New variants of PCR, such as simple or multiplex nested PCR in a single closed tube, co-operative-PCR and real-time monitoring of amplicons or quantitative PCR, allow high sensitivity in the detection of one or several pathogens in a single assay. The latest development in the analysis of nucleic acids is micro-array technology, but it requires generic DNA/RNA extraction and pre-amplification methods to increase detection sensitivity. The advances in research that will result from the sequencing of many plant pathogen genomes, especially now in the era of proteomics, represent a new source of information for the future development of sensitive and specific detection techniques for these microorganisms.

Bacteria↗
PubMed2005

Using QPCR to assign infectious potencies to adenovirus based vaccines and vectors for gene therapy: toward a universal method for the facile quantitation of virus and vector potency.

The assignment of infectious potency to test articles of adenovirus has been conducted mainly using classical end-point dilution methods, which rely on virus induced cytopathology to reveal the presence of infectious virus. These assays suffer the disadvantages of labor intensity, duration, throughput restriction and variability. In the course of our development of an Ad5 based HIV vaccine for clinical evaluation, we sought a facile method for the assignment of potency to the numerous test articles generated during the development of bioprocesses for bulk manufacture, downstream purification and formulation. In this paper we describe a quantitative PCR based potency assay (QPA) which uses QPCR to quantitate adenovirus genomes replicated 24h after the inoculation of a test article on 293 cell monolayers, and then relates that mass to potency by interpolation to a standard curve of replicated adenovirus genomes constructed with a reference adenovirus standard to which infectious potency has been previously assigned in the classical end-point dilution assay. The QPA assay for adenovirus is simple and rapid, with a throughput capacity adequate to the potency assay demands of bioprocess development, and with a precision expressed as a root variability of 16.8% R.S.D., allowing for close discriminations of the products of alternative process configurations. The adenovirus QPA principle can be applied to the quantitation of infectious potency of both RNA and DNA viruses and we report briefly on the development of QPA assays for measles and mumps. QPA assays owing to their simplicity and easy automation, rapidity, capacity and precision hold promise to become widely practiced methods for the quantitation of the potency of live virus vaccines and other recombinant virus vectors.

Adenoviridae↗
PubMed2000

Comparison of assays to detect cytomegalovirus shedding in the semen of HIV-infected men.

We sought to determine the optimal assays for cytomegalovirus (CMV) shedding in semen. Over a 2-month period, 149 HIV-1-infected men who have sex with men each provided up to three semen specimens. Specimens were tested for CMV by culture, rapid assay (shell vial) and polymerase chain reaction (PCR). By culture, 30% of seminal plasma and 28% of seminal cell specimens grew CMV. By rapid assay, results were 38 and 33%, respectively. By PCR, 56% of seminal cell specimens demonstrated CMV: 20% in a single semen specimen; 33% in two specimens; and 34% in all three specimens. Overall, 69% of men had CMV detected by PCR in at least one seminal cell specimen. By quantitative PCR, 14% had ten, 14% had 100, 16% had 1000, and 12% had 10000 copies in 6.25 microl of semen analyzed. Adjusting for initial CD4+ cell count, men with CMV shedding demonstrated by PCR at the first visit were approximately four times as likely to shed CMV at a subsequent visit (RR 4.28, CI: 2.30-7.95). CMV shedding was associated with decreased CD4+ cell counts in peripheral blood (P=0.05). It is concluded that the PCR assay provided the greatest sensitivity among the three detection methods.

Adult↗
PubMed2003

Restriction accessibility in isolated nuclei reveals light-induced chromatin reorganization at the PEPC promoter in maize.

Expression of genes necessary to perform C4 photosynthesis in maize is activated by light. It is not known how this activation is regulated on the chromatin level in vivo. We analysed alterations in the chromatin structure of the promoter of the C4-specific isoform of phosphoenolpyruvate carboxylase (PEPC) after illumination of seedlings. A protocol was established that facilitates the preparation of nuclei from maize leaves with intact chromatin structure and resistance to DNA degradation during prolonged incubation at high temperatures. The presence of non-spliced transcripts from the C4-PEPC gene in the nuclei was demonstrated by RT-PCR. The chromatin was partially digested with restriction endonucleases. Quantitative PCR analyses revealed a clear increase in the accessibility of the promoter chromatin to restriction dependent on illumination of the seedlings. The data indicate chromatin reorganization at the C4-PEPC promoter during activation.

Cell Nucleus↗
PubMed2005

Delta24-hyCD adenovirus suppresses glioma growth in vivo by combining oncolysis and chemosensitization.

Replication-competent adenoviruses could provide an efficient method for delivering therapeutic genes to tumors. The most promising strategies among adenovirus-based oncolytic systems are designed to exploit free E2F-1 activity in cancer cells, which in the absence of pRb activates transcription and regulates the expression of genes involved in differentiation, proliferation, and apoptosis. We previously developed Delta24, an E1A-mutant, conditionally replicative oncolytic adenovirus. Here, we examine the ability of a second-generation Delta24 (Delta24-hyCD) engineered to express a humanized form of the Saccharomyces cerevisiae cytosine deaminase gene (hyCD). Real-time quantitative PCR, Western blotting, thin-layer chromatography, and radioisotope quantitative enzymatic assays confirmed the production of a catalytically active hyCD enzyme in the setting of an oncolytic infection in vitro; other experiments assessing local production of 5-fluorouracil and a concomitant bystander effect showed improved cytotoxicity. The IC50 dose of 5-fluorocytosine (5-FC) required for a complete cytopathic effect by the Delta24-hyCD virus was fivefold lower than with Delta24 alone in U251MG and U87MG malignant glioma (MG) cell lines. Intratumoral treatment of mice bearing intracranial U87MG xenografts with Delta24-hyCD+5-FC significantly improved survival, confirming that Delta24-hyCD with 5-FC is a more efficient anticancer tool than Delta24 alone. Histopathologically, Delta24-hyCD replication was accompanied by progressively augmented oncolysis and drug-induced necrosis. These findings demonstrate that Delta24-hyCD with concomitant systemic 5-FC is a significant improvement over the earlier Delta24 oncolytic tumor-selective strategy for therapy of experimental gliomas.

Adenoviridae↗
PubMed2005

Use of broth enrichment and real-time PCR to exclude the presence of methicillin-resistant Staphylococcus aureus in clinical samples: a sensitive screening approach.

A rapid and sensitive method for excluding the presence of methicillin-resistant Staphylococcus aureus (MRSA) in clinical samples was developed and evaluated. The method utilised an MRSA-selective enrichment broth for 16 h, followed by PCR quantification of the nuc gene. Samples below a quantitative PCR threshold were reported as MRSA-negative. Broths from PCR-positive samples were subcultured for MRSA isolation. Clinical samples (n = 334) in a constructed high prevalence population were analysed in parallel with a selective plating method. The new broth-PCR assay increased the number of positive samples by 35% (49 vs. 66), and 94% of negative samples were reported within 24 h. To reduce costs and workload, 665 clinical samples were grown separately in enrichment broth and then pooled in the PCR step. The broth-PCR assay increased the number of MRSA positive samples from 11 to 15 compared with selective plating. Most (89%) of the culture-negative samples were also PCR-negative and could be reported within 24 h. The growth of 25 European EMRSA strains was tested in the selective enrichment broth. On average, the MRSA strains showed a 300 000-fold increase in CFU, compared with 30-fold for the eight methicillin-sensitive Staphylococcus aureus strains tested.

Bacterial Proteins↗
PubMed2005

High level of hepatitis B virus DNA after HBeAg-to-anti-HBe seroconversion is related to coexistence of mutations in its precore and basal core promoter.

AIM: G1896A mutation in precore or A1762T/G1764A mutations in basal core promoter are suspected to be responsible for patients with detectable level of HBV DNA in serum after seroconversion from HBeAg to anti-HBe. However, G1896A variant has impaired, while A1762T/G1764A variant may have intact replication ability. They themselves or their coexistence status may play different roles in such meaningless seroconversion. For these reasons, the significances of these two types of mutations were comparatively investigated in this study. METHODS: One hundred and sixty-five sera with positive anti-HBe and HBV DNA were collected from different patients. Mutations of G1896A and A1762T/G1764A among these serum samples were detected using competitively differentiated PCR. HBV DNA was demonstrated using real-time quantitative PCR. RESULTS: G1896A and/or A1762T/G1764A mutations were detected in 89.1% (147/165) out of patients with detectable HBV DNA in serum after HBeAg-to-anti-HBe seroconversion. The positive rate of G1896A variants was significantly higher than that of A1762T/G1764A mutations (77.6% vs 50.3%, chi2 = 26.61, P<0.01). The coexistence positive rate of these two types of mutations was 38.8% (64/165). Coexistence mutations were found in 77.1% (64/83) out of sera with A1762T/G1764A mutations, and in 50.0% (64/128) out of sera with G1896A mutation. Compared with variants with G1896A mutation only, the coexistence mutations were predominant in patients with high level of serum HBV DNA, and related to higher total bilirubin, lower serum albumin and progressive liver diseases. CONCLUSION: The coexistence of G1896A mutation and A1762T/G1764A mutations is very common, and responsible for the major cases with high level of HBV DNA in serum and progressive liver diseases after HBeAg-to-anti-HBe seroconversion. This coexistence mutation variant may have higher pathogenicity and replication ability.

Adult↗
PubMed2000

[The percentage of hepatitis B virus precore A83 mutant and its dynamicchange in fulminant hepatitis B].

OBJECTIVE: In order to clarify whether hepatitis B virus precore A83 mutant is related to the pathogenesis of fulminant hepatitis B or not. METHODS: The percentage of hepatitis B virus precore A83 mutant and the quantity of HBV DNA in sera from 9 patients with fulminant hepatitis B were assayed by the method of densitometry after mispairing PCR-restriction fragment length polymorphism (mpPCR-RFLP) and quantitative PCR, respectively. RESULTS: The HBV precore A83 mutant was found in sera of 6 out of 9 (66.7%) fulminant hepatitis patients while none of them were infected with the mutant strain alone, and all were mixed with wild strain. The percentage of the mutant over fifty percent is only in 2 cases in whom one was 59.3% (survival) and another 64.8% (died). The percentage below 31.0% was in 4 cases and all of them died. It was observed that appearance or disappearance of the A83 mutant and its dynamic change of percentage were consistent with the fluctuation of HBV DNA level but there was no correlation statistically (r=0.602, 0.583; P>0.05). CONCLUSION: The mutant strain alone has little correlation to the occurrence of fulminant hepatitis. It might be merely a accompaniment to follow the replication of HBV under the highly immune pressure.

Adolescent↗
PubMed2002

[Relationship between amount of HBV DNA in serum/liver tissue and hepatitis G virus (HGV) infection in patients with chronic hepatitis B].

OBJECTIVE: To observe the relationship between the amount of HBV DNA in serum/liver tissue and HGV infection in patients with chronic hepatitis B (CH-B) for exploring the effect of HGV infection on hepatitis B virus (HBV) replication of CH-B. METHODS: HGV RNA in serum, HGV nonstructural region 5 (NS5) antigen (HGV Ag) in liver tissue and the amount of HBV DNA in serum, liver tissue were detected for 56 patients with CH-B by reverse transcription-polymerase chain reaction (RT-PCR) assay, peroxidase antiperoxidase (PAP) immunohistochemical method and fluorescence quantitative PCR assay, respectively. Then the relationship between HGV Ag expression in liver tissue and HGV RNA expression in serum was analysed and the amount of HBV DNA in serum and liver tissues from the serum HGV RNA or liver tissue HGV Ag positive patients were compared with those of the serum HGV-RNA or liver tissue HGV Ag negative patients, respectively. RESULTS: Ten (17.9%) and eight (14.3%) patients were positive for serum and liver tissues,respectively.HGV RNA expression in serum was closely related to HGV Ag expression in liver tissues, but there was HGV RNA in serum from some of the liver tissues HGV Ag negative patients ?cases of HGV RNA and HGV Ag positive or negative,HGV RNA positive but HGV Ag negative, HGV RNA negative but HGV Ag positive, respectively: 5,43,5,3,(P<0.01). There was no significant difference in the amount of HBV DNA in serum and liver tissues between HGV RNA or HGV Ag positive and negative patients (P>0.05). CONCLUSIONS: HGV infection may not affect HBV replication. Liver is the site of HGV replication, but HGV probably also replicates in extrahepatic tissues. HGV hepatic pathogenicity is probably mild and further studies are still needed.

Adult↗