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PubMed2004

Methods of detection of Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis and Tannerella forsythensis in periodontal microbiology, with special emphasis on advanced molecular techniques: a review.

BACKGROUND: Certain specific bacterial species from the subgingival biofilm have demonstrated aetiological relevance in the initiation and progression of periodontitis. Among all the bacteria studied, three have shown the highest association with destructive periodontal diseases: Actinobacillus actinomycetemcomitans (Aa), Porphyromonas gingivalis (Pg) and Tannerella forsythensis (Tf). Therefore, the relevance of having accurate microbiological diagnostic techniques for their identification and quantification is clearly justified. AIM: To evaluate critically all scientific information on the currently available microbial diagnostic techniques aimed for the identification and quantification of Aa, Pg and Tf. SUMMARY: Bacterial culturing has been the reference diagnostic technique for many years and, in fact, most of our current knowledge on periodontal microbiology derives from cultural data. However, the advent of new microbial diagnostics, mostly based on immune and molecular technologies, has not only highlighted some of the shortcomings of cultural techniques but has also allowed their introduction as easy and available adjunct diagnostic tools to be used in clinical research and practice. These technologies, mostly polymerase chain reaction (PCR), represent a field of continuous development; however, we still lack the ideal diagnostic to study the subgingival microflora. Qualitative PCR is still hampered by the limited information provided. Quantitative PCR is still in development; however, the promising early results reported are still hampered by the high cost and the equipment necessary for the processing. CONCLUSION: Quantitative PCR technology may have a major role in the near future as an adjunctive diagnostic tool in both epidemiological and clinical studies in periodontology. However, culture techniques still hold some inherent capabilities, which makes this diagnostic tool the current reference standard in periodontal microbiology.

Aggregatibacter actinomycetemcomitans↗
PubMed2000

Ligation-mediated PCR for quantitative in vivo footprinting.

Ligation-mediated polymerase chain reaction (LM-PCR) is a genomic analysis technique for determination of (1) primary DNA nucleotide sequences (2) cytosine methylation patterns (3) DNA lesion formation and repair, and (4) in vivo protein-DNA footprints. However, LM-PCR can be limited by the multiple steps required and the relatively short stretch of sequence (usually <200 bp) that can be analyzed per reaction. We report here a simplified, one-day LM-PCR protocol in which all pipetting steps can be performed by a robotic workstation and which, moreover, provides longer reads (>350 bp) and enhanced signal quality by use of nonradioactive detection and a LI-COR DNA sequencing instrument. Sensitivity comparable to radiolabeling is achieved using oligonucleotide primers that are 5'-end labeled with infrared fluorochromes. We showed that the technique could be used for sensitive and reproducible in vivo photofootprinting of the human phosphoglycerate kinase 1 (PGK1) promoter, as well as providing good Maxam-Gilbert sequence information. The methods described here should allow high-throughput, high-resolution analysis of transcription factor binding and chromatin structure, and also may be useful for sequencing gaps that are refractory to cloning.

Animals↗
PubMed1999

Rapid detection of chromosome aneuploidies by quantitative fluorescence PCR: first application on 247 chorionic villus samples.

We report the results of the first major study of applying quantitative fluorescence polymerase chain reaction (QF-PCR) assays for the detection of major chromosome numerical disorders. The QF-PCR tests were performed on a total of 247 chorionic villus samples, which were analysed blind, without any knowledge of the results obtained using conventional cytogenetic analysis. The aims of this investigation were to evaluate the detection power and accuracy of this approach by testing a large number of fetal samples and to assess the diagnostic value of each of the chromosome specific small tandem repeat (STR) markers used. In addition, we introduced three more markers specific for chromosomes 13, 18, and X to allow an accurate analysis of samples homozygous for a particular STR. Fluorescent labelled primers were used to amplify 12 STRs specific for chromosomes 21, 18, 13, X, and the amylogenin-like DNA sequence AMXY, expressed on the X and Y chromosomes. In this blind study of 247 fetal samples, 222 were correctly diagnosed by QF-PCR as normal for each of the five chromosomes investigated; 20 were diagnosed by QF-PCR as trisomic for chromosomes 21, 18, or 13, in agreement with the cytogenetic tests. Only one false negative result was observed, probably owing to the mishandling of the sample, which had been transferred through three laboratories before being analysed by QF-PCR. The 247 samples also included four cases of mosaicism or translocation; one case of mosaic trisomy 21 was detected by QF-PCR and the other cases were not identified by QF-PCR. The results of this investigation provide clear evidence that the QF-PCR assays are powerful adjuncts to conventional cytogenetic techniques and can be applied for the rapid and accurate prenatal diagnosis of the most frequent aneuploidies.

Aneuploidy↗
PubMed2000

Quantification of VEGF mRNA expression in non-small cell lung cancer using a real-time quantitative reverse transcription-PCR assay and a comparison with quantitative competitive reverse transcription-PCR.

A reliable quantitative method for measuring gene product expression is important in investigating the relationship between growth factors and tumor biological behavior. In this study, we quantified the expression of vascular endothelial growth factor (VEGF) mRNA in 104 paired samples of lung cancer tissue and the surrounding nontumorous lung tissue using a new kinetic quantitative polymerase chain reaction (PCR) method, ie, real-time quantitative reverse transcription-PCR (RTQ RT-PCR). The samples consisted of 46 squamous cell carcinomas, 50 adenocarcinomas, and 8 undifferentiated cell carcinomas. In 17 cases, the results obtained were compared with those obtained using quantitative competitive RT-PCR (QC RT-PCR). Using RTQ RT-PCR, VEGF mRNA expression was detected and quantified in all 104 (100%) lung cancer samples and their normal counterparts. VEGF mRNA expression in the lung cancer tissue was significantly higher than in the normal counterparts (95% CI: 0.575 approximately 1.727, p < 0.001; paired t test). In 68 (65.4%) cases, VEGF mRNA expression was higher in the cancer tissue than normal tissue. VEGF mRNA expression was higher in nonsquamous cell carcinoma (p = 0.02), and higher in tumor with hilar or mediastinal lymph node metastasis (p = 0.024). QC RT-PCR was able to detect and quantify VEGF mRNA expression in 15/17 (88%) lung cancer samples and 12/17 (70.6%) normal tissue samples. The values for VEGF mRNA expression were higher in the tumor in 13 (76%) cases. Comparison of the values of the VEGF mRNA expression quantified using RTQ RT-PCR or QC RT-PCR showed a good correlation between results obtained using these two methods, both in cancer tissue (r = 0.68, p = 0.0025) and normal counterpart (r = 0.53, p = 0.027). Agreement between the results for the relative expression of VEGF mRNA expression in cancer and normal tissue obtained using these two methods was seen in 14/16 cases (88%). We conclude that RTQ RT-PCR is as accurate as QC RT-PCR and is more sensitive than QC RT-PCR in detecting and quantifying VEGF mRNA expression in lung cancer and normal tissues, and both methods reveal that the VEGF mRNA expression is higher in lung cancer tissue than in healthy lung tissue.

Base Sequence↗
PubMed2006

Evaluation of SAT-1, SAT-2 and GalNAcT-1 mRNA in colon cancer by real-time PCR.

By qualitative and quantitative PCR, we evaluated the expression of three messengers coding for SAT-1, SAT-2 and GalNAcT-1 in human samples of intestinal cancer and some cell lines (breast cancer and melanomas). Qualitative PCR demonstrated, in human tissues but not in the cell lines examined, the presence of an mRNA that lacks hexon 3; experiments performed on transfected SKMEL-28 excluded a regulative role of this noncanonical mRNA. Data from real-time PCR, statistically analysed by ANOVA indicated that the mRNA expression of all the considered glycosyltransferases (SAT-1, SAT-2 and GalNAcT-1) was significantly different in tumours versus their own control. The ganglioside patterns in the examined samples did not correlate with mRNA expression; this finding demonstrates that ganglioside expression is the result of a very complex balance between anabolic and catabolic enzyme activities. Although this study is still preliminary, it opens a new possibility for neoplastic prognosis finding potential molecular markers among the mRNAs that codify for glycosyltransferases.

Acetyltransferases↗
PubMed2001

Fluorogenic PCR-based quantitative detection of a murine pathogen, Helicobacter hepaticus.

Helicobacter hepaticus infection in mice is being used as an animal model for elucidating the pathogenesis of gastrointestinal and biliary diseases in humans. H. hepaticus, which forms a spreading film on selective agar, is not amenable to routine quantitative counts of organisms in tissues using a CFU method. In this study, a fluorogenic PCR-based assay was developed to quantitatively detect H. hepaticus in mouse ceca and feces using the ABI Prism 7700 sequence detection system. A pair of primers and a probe for this assay were generated from the H. hepaticus cdtB gene (encoding subunit B of the H. hepaticus cytolethal distending toxin). Using this assay, the sensitivity for detection of H. hepaticus chromosomal DNA prepared from pure culture was 20 fg, which is equivalent to approximately 14 copies of the H. hepaticus genome based on an estimated genome size of approximately 1.3 Mb determined by pulsed-field gel electrophoresis. H. hepaticus present in feces and cecal samples from H. hepaticus-infected mice was readily quantified. The selected PCR primers and probe did not generate fluorescent signals from eight other helicobacters (H. canis, H. cineadi, H. felis, H. mustelae, H. nemestrinae, H. pullorum, H. pylori, and H. rodentium). A fluorescent signal was detected from 20 ng of H. bilis DNA but with much lower sensitivity (10(6)-fold) than from H. hepaticus DNA. Therefore, this assay can be used with high sensitivity and specificity to quantify H. hepaticus in experimentally infected mouse models as well as in naturally infected mice.

Animals↗
PubMed1991

Rapid analysis and quantitation of PCR products by high-performance liquid chromatography.

HPLC utilizing a high efficiency anion-exchange column provides a rapid and easily automated technique for the qualitative and quantitative analysis of subnanogram to microgram amounts of DNA fragments generated by the PCR. The accuracy, precision and linearity of this method exceed those attainable with electrophoretic techniques. In addition, because of the nondestructive nature of HPLC, the desired PCR amplification product can be purified for subsequent utilization. Thus, liquid chromatography extends the utility of the PCR technique to those applications requiring precise quantitation.

Base Sequence↗
PubMed1999

Cytomegalovirus viraemia has poor predictive value for the development of cytomegalovirus disease in patients with advanced HIV-infection.

OBJECTIVE: Cytomegalovirus (CMV) continues to be one of the most important opportunistic infections associated with human immunodeficiency virus (HIV) infection. This study investigated the value of CMV-viraemia in predicting the development of clinical CMV disease in patients with advanced HIV infection. METHODS: This was a prospective observational study performed over a 2-year period between 1994-96 in the Department of Infection and Tropical Medicine at Leicester Royal Infirmary. Adult HIV-positive patients attending a hospital clinic were included if they were CMV-seropositive with CD4 counts < or =50 cells/mm3. Subjects were seen at approximately 6-weekly intervals in the clinic and were reviewed by an experienced ophthalmologist. Serum for CMV PCR was taken and stored at regular intervals and qualitative and quantitative PCR was performed at the end of the study period. The value of PCR in predicting the development of CMV disease was then assessed. RESULTS: Twenty-six patients were followed up during the study period and 77 evaluable specimens were analysed for CMV PCR. Twenty-three (30%) samples were positive and 54 negative. Seven (27%) patients developed CMV disease (five retinitis alone, and two with retinitis and oesophagitis) during the study period. Viraemia was often intermittent and there was no significant difference in the proportions of patients with positive or negative tests who subsequently developed CMV disease. The sensitivity, specificity, positive and negative predictive values of the qualitative PCR were 71%, 47%, 33% and 82% respectively and 57%, 74%, 44% and 82% respectively for the quantitative PCR (>10(3) copies/ml). CONCLUSIONS: The results from this study, which was performed before the introduction of protease inhibitors, found that cytomegalovirus PCR was of limited clinical value in predicting the patients at greatest risk of developing CMV-disease and provided little useful prognostic information.

AIDS-Related Opportunistic Infections↗
PubMed2006

Quantification of viral inactivation by photochemical treatment with amotosalen and UV A light, using a novel polymerase chain reaction inhibition method with preamplification.

BACKGROUND: In evaluating a photochemical treatment process for inactivating parvovirus B19, there lacked simple culture methods to measure infectivity. The recently developed enzyme-linked immunospot (ELISpot) infectivity assay uses late-stage erythropoietic progenitor cells and is labor intensive and time consuming. We evaluated a novel, efficient polymerase chain reaction (PCR) inhibition assay and examined correlations with reductions in infectivity. METHODS: Contaminated plasma was treated with 150 micromol/L amotosalen and 3 J/cm(2) ultraviolet A light and then tested for DNA modification using conventional PCR inhibition and a novel preamplification approach. The novel assay subjected the samples to preamplification cycles using long-template PCR, followed by quantitative PCR (QPCR) inhibition detection. Both approaches were tested for correlations with reductions in viral infectivity by comparing ELISpot assay results of identical samples. RESULTS: The B19 preamplification inhibition assay showed detection ranges of 2-2.5 log and demonstrated quantitative correlation with up to a 5.8-log reduction in viral infectivity in ELISpot results. Conventional PCR detected a >5 log reduction in amplification, correlated with a 4.4-log reduction in viral infectivity. A range of 4-log inhibition of hepatitis B virus DNA amplification was also achieved. CONCLUSIONS: The results demonstrated that a novel preamplification QPCR assay is a useful tool for predicting reductions in infectivity after photochemical treatment. This assay was extended to show utility in circumstances where practical in vitro assays are unavailable for the determination of the efficacy of pathogen inactivation.

DNA, Viral↗
PubMed2006

Semi-quantitative fluorescent PCR analysis identifies PRKAA1 on chromosome 5 as a potential candidate cancer gene of cervical cancer.

OBJECTIVE: Comparative genomic hybridization has frequently detected amplification of chromosome 5p in cervical cancer, but candidate cancer genes within the region are rarely known. Therefore, we pursued to identify potential candidate gene related to cervical cancer development. METHODS: A series of 128 cervical tumor samples were examined by semi-quantitative fluorescent differential PCR for copy number changes on three candidate genes (PRKAA1, CTNND2 and POLS) mapped to chromosome 5p and one gene (ERBIN) mapped to chromosome 5q12.3. The impact of gene copy number was later analyzed in relation to HPV infection, tumor stage or tumor radiosensitivity. RESULTS: DNA copy numbers of PRKAA1, CTNND2 and ERBIN were significantly different from normal controls (P < 0.05). DNA copy number changes did not correlate with HPV infection, tumor stages or tumor radiosensitivity. Using RT-PCR, PRKAA1 mRNA expression in seven tumor samples with known 5p amplification was amplified from 3- to 15-fold. Over-expression of PRKAA1 was further confirmed by immunohistochemical staining on 125 paraffin-embedded cervical cancer tissues. The expression level in cervical tumor was significantly higher than that in normal epithelium (P < 0.001). CONCLUSIONS: PRKAA1 gene codes for the catalytic alpha 1 subunit of the AMP-activated protein kinase which is an important cellular metabolic stress regulator. It might assist tumor cells growth under stress. Thus, PRKAA1 may be one of the potential candidate genes for cervical carcinogenesis.

AMP-Activated Protein Kinases↗
PubMed1999

Rapid prenatal diagnosis of aneuploidy by quantitative fluorescent PCR on fetal samples from mothers at high risk for chromosome disorders.

We report the results of a prospective study using quantitative fluorescent polymerase chain reaction (QF-PCR) and small tandem repeat markers (STR) for the rapid prenatal detection of aneuploidies in a group of pregnant women at increased risk of having fetuses with numerical chromosome disorders. Amniotic fluid samples (n = 52) were collected from mothers undergoing prenatal invasive testing for fetal abnormalities on ultrasonographic examination or abnormal maternal serum aneuploidy screening results. All samples were tested by cytogenetic analysis, but rapid diagnoses of aneuploidies were offered and performed using QF-PCR analysis with several STRs specific for chromosomes 21, 18, 13 and X. All cases with numerical chromosome aberrations involving chromosomes 21, 18 and 13 (n = 8) were correctly diagnosed. Three gonosomal aneuplodies (one 47,XXY and two 45,X) were not detected because they were uninformative for the X markers. Another sample with a deletion (46,XX,7q-), that the present assay was not designed to detect, was not identified. One sample was heavily contaminated with maternal blood and the results of the QF-PCR assays were uninformative. The remaining samples from normal fetuses provided QF-PCR patterns disomic for chromosomes 21, 18, 13 and X. Our study demonstrates that QF-PCR is a rapid method for the detection of common numerical chromosome disorders and it may play an important role in prenatal diagnosis for women at high risk for fetal aneuploidy.

Amniocentesis↗
PubMedDate not supplied

[Quantitative PCR-analysis: development of a system for determining the level of an amplified DNA fragment].

A new technique is elaborated for quantitative evaluation of the polymerase chain reaction (PCR) results based on a system for yopA gene identification in Yersinia pseudotuberculosis fragment located on p45 plasmid. The analysis schedule includes amplification of the studied DNA sequence under the conditions when the reverse primer carries chemically bound biotin label on the 5'-end, hybridization of the labelled amplified fragment with the probe immobilized on the microplate surface, the probe being complementary to the inner portion of specific DNA, visualization of the label, and calculation of bound labelled DNA quantity. The lower threshold of analysis sensitivity is some picograms. It makes possible the analysis and detection of PCR product in the period of exponential increase of its content, i.e. in the initial period of reaction when the quantity of amplified DNA in the reaction mixture is not enough for reliable identification by ethidium bromide staining.

Bacterial Outer Membrane Proteins↗
PubMed2006

Real-time PCR: housekeeping genes in the INS-1E beta-cell line.

Investigation of gene expression is a developing area with several methods available. One method is quantitative PCR. A major pitfall in quantitative PCR is the normalisation procedure of the gene expression. Many experiments include a housekeeping gene, some use RNA concentration, and others use a geometric mean of several internal, stably expressed genes. This study demonstrates that real-time-PCR results differ with varying housekeeping genes and analysis protocols when applied to insulin-secreting INS-1E cells derived from the pancreas and stimulated by DEDTC (diethyldithiocarbamate, a zinc chelator) and GLP-1.

Animals↗
PubMed1998

Clinical comparison of an enhanced-sensitivity branched-DNA assay and reverse transcription-PCR for quantitation of human immunodeficiency virus type 1 RNA in plasma.

The performance characteristics of an enhanced-sensitivity branched-DNA assay (bDNA) (Quantiplex HIV-1 version 2.0; Chiron Corp., Emeryville, Calif.) and a reverse transcription (RT)-PCR assay (AMPLICOR HIV-1 Monitor; Roche Diagnostic Systems, Inc., Branchburg, N.J.) were compared in a molecular diagnostic laboratory. Samples used in this evaluation included linearity and reproducibility panels made by dilution of a human immunodeficiency virus type 1 (HIV-1) stock culture of known virus particle count in HIV-1-negative plasma, a subtype panel consisting of HIV-1 subtypes A through F at a standardized level, and 64 baseline plasma specimens from HIV-1-infected individuals. Plots of log10 HIV RNA copies per milliliter versus log10 nominal virus particles per milliliter demonstrated that both assays were linear over the stated dynamic ranges (bDNA, r = 0.98; RT-PCR, r = 0.99), but comparison of the slopes of the regression lines (bDNA, m = 0.96; RT-PCR, m = 0.83) suggested that RT-PCR had greater proportional systematic error. The between-run coefficients of variation for bDNA and RT-PCR were 24.3 and 34.3%, respectively, for a sample containing 1,650 nominal virus particles/ml and 44.0 and 42.7%, respectively, for a sample containing 165 nominal virus particles/ml. Subtypes B, C, and D were quantitated with similar efficiencies by bDNA and RT-PCR; however, RT-PCR was less efficient in quantitating subtypes A, E, and F. One non-B subtype was recognized in our clinical specimens based on the ratio of values obtained with the two methods. HIV-1 RNA was quantitated in 53 (83%) baseline plasma specimens by bDNA and in 55 (86%) specimens by RT-PCR. RT-PCR values were consistently greater than bDNA values, with population means of 142,419 and 67,580 copies/ml, respectively (P < 0.01). The results were highly correlated (r = 0.91), but the agreement was poor (mean difference in log10 copies per milliliter +/- 2 standard deviations, 0.45 +/- 0.61) for the 50 clinical specimens that gave discrete values with both methods.

Evaluation Studies as Topic↗
PubMed2000

Quantitative competitive PCR as a technique for exploring flea-Yersina pestis dynamics.

We used a quantitative competitive polymerase chain reaction assay to quantify Yersinia pestis loads in fleas and bacteremia levels in mice that were used as sources of infectious blood meals for feeding the fleas. Xenopsylla cheopis, the Oriental rat flea, achieved higher infection rates, developed greater bacterial loads, and became infectious more rapidly than Oropsylla montana, a ground squirrel flea. Both flea species required about 10(6) Y. pestis cells per flea to be able to transmit to mice. Most fleas that achieved these levels, however, were incapable of transmitting. Our results suggest that at the time of flea feeding, host blood must contain > or = 10(6) bacteria/ml to result in detectable Y. pestis infections in these fleas, and > or = 10(7) bacteria/mL to cause infection levels sufficient for both species to eventually become capable of transmitting Y. pestis to uninfected mice. Yersinia pestis colonies primarily developed in the midguts of O. montana, whereas infections in X. cheopis often developed simultaneously in the proventriculus and the midgut. These findings were visually confirmed by infecting fleas with a strain of Y. pestis that had been transformed with the green fluorescent protein gene.

Animals↗
PubMed2005

Prenatal diagnosis of spinal muscular atrophy: Indian scenario.

OBJECTIVES: To study the psychosocial issues associated with prenatal diagnosis of SMA in India and the use of SMN1 copy number analysis for carrier detection prior to offering prenatal diagnosis. METHODS: Homozygous deletion of SMN1 gene was done by PCR-RFLP. Copy number analysis of SMN1 gene was performed by quantitative PCR. RESULTS: We report our experience of eight cases of prenatal diagnosis for SMA and the use of carrier detection prior to offering prenatal diagnosis. Quantitative PCR results show that SMN1 copy number analysis is useful to identify couples at risk. CONCLUSION: Case analyses depict unique psychosocial issues associated with prenatal diagnosis of SMA from India.

Chorionic Villi Sampling↗
PubMed2001

Quantitative TaqMan PCR without a real-time thermal cycler: an assay for fish insulin-like growth factor I messenger RNA.

The reverse transcriptase-polymerase chain reaction, more commonly known as RT-PCR, has become a widely used tool in molecular biology and is now frequently used in monitoring gene expression levels. A number of variations in the RT-PCR technique now exist including TaqMan PCR (5' nuclease assay), which is a useful nonisotopic detection method for the quantification of PCR products. To monitor the formation of these fluorescent amplification products a "real-time" thermal cycler is normally required. In this study, repeated scanning of PCR products in a 96-well plate format showed that a conventional fluorescent plate reader can be used to generate similar results. To demonstrate the power of this approach, the nutritional regulation of insulin-like growth factor I (IGF-I) was investigated in a marine finfish, the snapper (Pagrus auratus). Hepatic IGF-I messenger RNA levels were shown to significantly decrease after 2 weeks of fasting and returned to fed control levels on refeeding. These results demonstrated that a real-time PCR machine was not required to generate this type of quantitative data and that this technology can be adapted for use in most molecular biology laboratories.

Journal Article↗
PubMed1994

Analysis of mdr-1 gene expression in human leukemic cells by quantitative competitive PCR.

The ability to recognize the acquisition of multidrug resistance (MDR) in leukemia patients would improve our ability to predict the responsiveness of patients to chemotherapy. To quantitate the degree of MDR acquisition, we determined the amount of mdr-1 mRNA in leukemic cells from patients by competitive polymerase chain reaction (PCR) analysis. Twenty-one patients including 12 patients prior to treatment and nine relapsed patients with acute myelogenous or lymphoblastic leukemia were examined. The amount of mdr-1 gene expression in K562, K562/ADR500 cells and their mixtures showed a proportional correlation between the ratio of resistant to non-resistant cells and the amount of the mdr-1 gene. Mean mdr-1 gene expression in relapsed patients was greater than that in pretreatment patients. Patients refractory to chemotherapy (NR) showed higher levels of mdr-1 gene expression than the patients who achieved complete remission (CR). Because of the wide variations in values, no statistical differences were observed between pretreatment and relapsed patients, or CR and NR patients. These results suggest that the competitive PCR technique is a reliable method to quantitatively determine mdr-1 gene expression, but it may be difficult to predict responsiveness to chemotherapy by using this technique alone.

ATP Binding Cassette Transporter, Subfamily B, Mem↗