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PCR System (pcr + system)
Selected AbstractsDirect analysis of sulfate reducing bacterial communities in gas hydrate-impacted marine sediments by PCR,DGGEJOURNAL OF BASIC MICROBIOLOGY, Issue S1 2009Christopher E. Bagwell Abstract Molecular investigations of the sulfate reducing bacteria that target the dissimilatory sulfite-reductase subunit A gene (dsr A) are plagued by the nonspecific performance of conventional PCR primers. Here we describe the incorporation of the FailSafeÔ PCR System to optimize environmental analysis of dsr A by PCR amplification and denaturing gradient gel electrophoresis. PCR,DGGE analysis of dsr A composition revealed that SRB diversity was greater and more variable throughout the vertical profile of a marine sediment core obtained from a gas hydrate site (GC234) in the Gulf of Mexico than in a sediment core collected from a nearby site devoid of gas hydrates (NBP). Depth profiled dsr B abundance corresponded with sulfate reduction rates at both sites, though measurements were higher at GC234. This study exemplifies the numerical and functional importance of sulfate reducing bacteria in deep-sea sedimentary environments, and incremental methodological advancements, as described herein, will continue to streamline the analysis of sulfate reducer communities in situ. (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Identification of Helicobacter pylori and the cagA genotype in gastric biopsies using highly sensitive real-time PCR as a new diagnostic toolFEMS IMMUNOLOGY & MEDICAL MICROBIOLOGY, Issue 3 2005Shiho Yamazaki Abstract The CagA protein is one of the virulence factors of Helicobacter pylori, and two major subtypes of CagA have been observed, the Western and East Asian type. CagA is injected from the bacteria into gastric epithelial cells, undergoes tyrosine phosphorylation, and binds to Src homology 2 domain-containing protein-tyrosine phosphatase SHP-2. The East Asian type CagA binds to SHP-2 more strongly than the Western type CagA. Here, we tried to distinguish the CagA type by highly sensitive real-time PCR with the objective of establishing a system to detect H. pylori and CagA subtypes from gastric biopsies. We designed primers and probe sets for Western or East Asian- cagA at Western-specific or East Asian-specific sequence regions, respectively, and H. pylori 16S rRNA. We could detect the H. pylori 16S rRNA gene, Western and East Asian- cagA gene from DNA of gastric biopsies. The sensitivity and specificity for H. pylori infection was 100% in this system. In Thai patients, 87.8% (36/41) were cagA -positive; 26.8% (11/41) were Western- cagA positive and 53.7% (22/41) were East Asian- cagA positive, while 7.3% (3/41) reacted with both types of cagA. These results suggest that this real-time PCR system provides a highly sensitive assessment of CagA type as a new diagnostic tool for the pathogenicity of H. pylori infection. [source] Application of real-time PCR for quantitative detection of Campylobacter jejuni in poultry, milk and environmental waterFEMS IMMUNOLOGY & MEDICAL MICROBIOLOGY, Issue 3 2003Chengbo Yang Abstract Campylobacter jejuni is a leading human food-borne pathogen. The rapid and sensitive detection of C. jejuni is necessary for the maintenance of a safe food/water supply. In this article, we present a real-time polymerase chain reaction (PCR) assay for quantitative detection of C. jejuni in naturally contaminated poultry, milk and environmental samples without an enrichment step. The whole assay can be completed in 60 min with a detection limit of approximately 1 CFU. The standard curve correlation coefficient for the threshold cycle versus the copy number of initial C. jejuni cells was 0.988. To test the PCR system, a set of 300 frozen chicken meat samples, 300 milk samples and 300 water samples were screened for the presence of C. jejuni. 30.6% (92/300) of chicken meat samples, 27.3% (82/300) of milk samples, and 13.6% (41/300) of water samples tested positive for C. jejuni. This result indicated that the real-time PCR assay provides a specific, sensitive and rapid method for quantitative detection of C. jejuni. Moreover, it is concluded that retail chicken meat, raw milk and environmental water are commonly contaminated with C. jejuni and could serve as a potential risk for consumers in eastern China, especially if proper hygienic and cooking conditions are not maintained. [source] Quantitative Analysis of Cytokine mRNA Expression in Hearts from Patients with Nonischemic Dilated Cardiomyopathy (DCM)JOURNAL OF CARDIAC SURGERY, Issue 2003Akira Ukimura To evaluate the role of cytokines in nonischemic DCM, we analyzed the relative quantity of cytokine mRNA expression in the hearts from DCM patients with refractory heart failure, using the ABI PRISM7700 real-time PCR system. We used heart tissues resected from 32 DCM patients at the time of elective partial ventriculectomy (PLV), and five biopsy specimens with normal histological findings as control. Results and Discussion: Interleukin (IL)-1,, IL-10, and Tumor Necrosis Factor (TNF)-, mRNA were expressed at low levels in all normal hearts. The number of IL-10-positive DCM cases was significantly smaller than normal controls (P = 0.0036). One (10%) of 10 DCM patients with IL-10 mRNA expression died after PLV, and 10 (45%) of 22 DCM patients without IL-10 mRNA expression died. IL-1, mRNA was overexpressed (over twice the mean of control subjects) in 15 of 32, and TNF-, mRNA in 10 of 32 patients. We propose the classification of DCM patients into subgroups on the basis of cytokine mRNA expression. Anticytokine therapy or cytokine therapy may have potential in improving the condition of heart failure in certain subgroups of DCM patients. Conclusions: We suggest that DCM patients with heart failure deteriorate without IL-10 mRNA expression in the myocardium. The classification of DCM patients into subgroups on the basis of cytokine mRNA expression may have great value in considering the treatment of this heterogeneous disease state. (J CARD SURG 2003;18 (Suppl 2):S101-S108) [source] Comparative analysis of putative periodontopathic bacteria by multiplex polymerase chain reactionJOURNAL OF PERIODONTAL RESEARCH, Issue 3 2008M. Morikawa Background and Objective:, The polymerase chain reaction (PCR) has been applied for the rapid and specific detection of periodontopathic bacteria in subgingival plaque and is potentially of clinical benefit in the diagnosis and treatment of periodontitis subjects. However, several technical points need to be modified before the conventional PCR detection system can be used by clinicians. Material and Methods:, To develop a PCR-based technique more applicable for clinical use than conventional PCR, we established a multiplex PCR for five putative periodontopathic (Treponema denticola, Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, Prevotella intermedia and Tannerella forsythia) and two nonperiodontopathic (Streptococcus sanguinis and Streptococcus salivarius) species of bacteria using whole-plaque suspension as templates, and detected bacteria in subgingival plaque taken from 85 subjects at the supportive periodontal therapy stage after active periodontal treatments. Results:, Among putative periodontopathic bacteria, the detection frequency of T. denticola and P. gingivalis was elevated in parallel with higher probing pocket depth and clinical attachment loss, and had 4.2,14.1 times increasing odds of the clinical parameters tested. Detection of any of the five species of putative periodontopathic bacteria markedly increased the odds ratio of a higher probing pocket depth, clinical attachment loss and bleeding on probing. Conclusion:, The multiplex PCR system developed in this study enabled the detection of all the bacteria under investigation in one reaction tube in a less time- and labor-intensive manner than conventional PCR. These results support the potential clinical use of multiplex PCR for detecting periodontopathic bacteria and for evaluating therapeutic strategies and predicting the prognosis for each subject. [source] Identification of the M-CSF Receptor in Endometriosis by Immunohistochemistry and RT-PCRAMERICAN JOURNAL OF REPRODUCTIVE IMMUNOLOGY, Issue 5 2004Liselotte Mettler Problem:, The aim of this paper is to provide further evidence that the dystopic proliferation of endometriotic epithelia is caused by the stimulation of peritoneal macrophages. It is essential to show that endometriotic epithelial cells express the macrophage colony-stimulating factor receptor (M-CSFR) which binds the M-CSF produced by the peritoneal macrophages. Method of study:, For the detection of M-CSFR, samples of ectopic endometrium (n = 79) and eutopic endometrium (n = 18) were compared. The specimens were gained at operative laparoscopy in the proliferative phase of the cycle. Cryostat sections were used for immunohistochemical detection. For in vitro reverse transcriptase polymerase chain reaction (RT-PCR) tests, the tissue was immediately shock frozen on paraffin sections. For the in situ RT-PCR technique the specimens were placed in a para-formaldehyde solution, embedded in paraffin and later processed. The Gene Amp 1000 in situ PCR system (Perkin Elmer) was used as the thermal cycler. Results:, M-CSF and the M-CSF receptor are present in eutopic and ectopic endometrium. Qualitatively, with both PCR techniques we found the M-CSF receptor to be present in all samples examined. Using the histochemical detection technique, the M-CSF receptor was found in nearly 70% of endometriosis patients compared with a statistically significant lower percentage in normal endometrium. Conclusions:, The in situ RT-PCR technique and immunohistochemistry elaborated the need to trace the cellular sources of the M-CSF receptor. The identification of the M-CSF receptor in endometriotic tissue and in endometrium is apt to open a new experimental field in endometriosis research. [source] Congenital Cytomegalovirus Infection Diagnosed by Polymerase Chain Reaction With the Use of Preserved Umbilical Cord in Sensorineural Hearing Loss Children,THE LARYNGOSCOPE, Issue 11 2006Hiroshi Ogawa MD Abstract Objectives/Hypothesis: Congenital cytomegalovirus (CMV) infection is estimated to account for 30% of sensorineural hearing loss (SNHL) cases. Differences in clinical characteristics between CMV-related and unrelated SNHL cases were scrutinized. Methods: Using dried umbilical cord, we have recently developed a polymerase chain reaction (PCR)-based assay for the retrospective detection of congenital CMV infection. Medical records of 7 CMV-related patients identified from 31 SNHL patients by the assay were evaluated for the following: type and degree of hearing impairment, computed tomographic scan results, mental retardation, cerebral palsy, autism, and other multiple disorders. Results: Clinical characteristics of the seven CMV-related SNHL cases were as follows: 1) six of the seven exhibited severe bilateral SNHL, whereas one had severe unilateral SNHL in the right ear. Although the hearing levels of CMV-related patients were more greatly impaired than those of CMV-negative patients, there was no hearing impairment pattern specific to the CMV-related patients; 2) five patients had mental retardation, which was more frequent than in CMV-negative patients; 3) birth weights of the CMV-positive cases were relatively lower. Discussion: Although CMV-positive cases are clinically indistinguishable from CMV-negative cases, our PCR system allowed the retrospective diagnosis of CMV-related SNHL. Conclusion: CMV-related SNHL tends to accompany mental retardation and low birth weight more frequently than does CMV-negative SNHL. [source] Prognostic Significance of Occult Bone Marrow Micrometastases of Breast Cancer Detected by Quantitative Polymerase Chain Reaction for Cytokeratin 19 mRNACANCER SCIENCE, Issue 9 2000Noriko Ikeda Amplification of cytokeratin 19 (CK19) transcripts by reverse transcriptase-polymerase chain reaction (RT-PCR) has been shown to be a highly sensitive assay for the detection of bone marrow micrometastases (BMM) of breast cancer, but recent studies have demonstrated the occurrence of false-positive results due to low-level, illegitimately transcribed CK19 in normal bone marrow tissue. One approach to solve this problem is to develop a quantitative CK19 RT-PCR assay and to introduce a cut-off value which can distinguish between illegitimate expression and cancer-specific expression levels. In the present paper, we describe a quantitative CK19 RT-PCR assay using a real-time automated PCR system. The number of CK19 transcripts was normalized to that of GAPDH transcripts as an internal control for quality and quantity of cDNA. The cut-off value for the ratio of CK19 to GAPDH transcripts was set at 10,4 since the ratio never exceeded this value in the control bone marrow samples (n=12). In total, 117 bone marrow aspirates from stage I-III patients with invasive breast cancers were subjected to CK19 RT-PCR assay and immunocytological examination. Forty (34.2%) were found to be BMM-positive by CK19 RT-PCR assay whereas only three (2.6%) were found to be BMM-positive by immunocytology. Multivariate analysis has shown that occult BMM detected by CK19 RT-PCR is a significant risk factor for relapse, being independent of axillary lymph node metastases. [source] Comparison of MY09/11 consensus PCR and type-specific PCRs in the detection of oncogenic HPV typesJOURNAL OF CELLULAR AND MOLECULAR MEDICINE, Issue 4 2007C. E. Depuydt Abstract The causal relationship between persistent infection with high-risk HPV and cervical cancer has resulted in the development of HPV DNA detection systems. The widely used MY09/11 consensus PCR targets a 450bp conserved sequence in the HPV L1 gene, and can therefore amplify a broad spectrum of HPV types. However, limitations of these consensus primers are evident, particularly in regard to the variability in detection sensitivity among different HPV types. This study compared MY09/11 PCR with type-specific PCRs in the detection of oncogenic HPV types. The study population comprised 15, 774 patients. Consensus PCR failed to detect 522 (10.9%) HPV infections indicated by type-specific PCRs. A significant correlation between failure of consensus PCR and HPV type was found. HPV types 51, 68 and 45 were missed most frequently. The clinical relevance of the HPV infections missed by MY09/11 PCR was reflected in the fraction of cases with cytological abnormalities and in follow-up, showing 104 (25.4%) CIN2+ cases. The MY09/11 false negativity could be the result of poor sensitivity, mismatch of MY09/11 primers or disruption of L1 target by HPV integration or DNA degradation. Furthermore, MY09/11 PCR lacked specificity for oncogenic HPVs. Diagnostic accuracy of the PCR systems, in terms of sensitivity (MY09/11 PCR: 87.9%; type-specific PCRs: 98.3%) and specificity (MY09/11 PCR: 38.7%; type-specific PCRs: 76.14%), and predictive values for histologically confirmed CIN2+, suggest that type-specific PCRs could be used in a clinical setting as a reliable screening tool. [source] Parvovirus B19 infection in pregnancy: Quantitative viral DNA analysis using a kinetic fluorescence detection system (TaqMan PCR)JOURNAL OF MEDICAL VIROLOGY, Issue 2 2002Antje Knöll M.D. Abstract Human parvovirus B19 infections are common in the general population, and infection during pregnancy may cause hydrops fetalis and fetal death. To initiate adequate treatment, accurate laboratory diagnosis is essential. The most sensitive tests are nested PCR systems, but these assays provide semiquantitative results at best. A parvovirus B19 DNA assay was developed based on the real time TaqMan PCR. This method was calibrated on the basis of serial plasmid dilutions and tested with an international parvovirus B19 standard. The assay was capable of quantifying parvovirus B19 DNA from one to about 5,×,107 genome equivalents per reaction (corresponding to 100 to 5,×,109 genome equivalents per ml serum). Samples from 51 pregnant women with suspected acute parvovirus B19 infection were tested, and positive PCR results were obtained in at least one of the materials investigated in 41 cases. The median viral DNA load in maternal blood samples was 1.3,×,104 copies/ml (range 7.2,×,102,2.6,×,107). Maternal virus DNA concentration was not associated with the presence of maternal symptoms and/or fetal complications. As the stage of infection was not known in the majority of cases, our data do not exclude an association between peak levels of parvovirus B19 DNA and the development of complications. Maternal sera and corresponding fetal material were available for concurrent testing from 15 DNA-positive cases: in most fetal samples, viral DNA concentrations were several orders of magnitude higher (up to 2.1,×,1012 copies/ml) compared to the corresponding maternal blood samples. J. Med. Virol. 67:259,266, 2002. © 2002 Wiley-Liss, Inc. [source] | |||||||||||||