Dual Polymerase Chain Reaction Research Articles

Analyzing the Impact of Diesel Exhaust Particles on Lung Fibrosis Using Dual PCR Array and Proteomics: YWHAZ Signaling.

Air pollutants are associated with exacerbations of asthma, chronic bronchitis, and airway inflammation. Diesel exhaust particles (DEPs) can induce and worsen lung diseases. However, there are insufficient data to guide polymerase chain reaction (PCR) array proteomics studies regarding the impacts of DEPs on respiratory diseases. This study was performed to identify genes and proteins expressed in normal human bronchial epithelial (NHBE) cells. MicroRNAs (miRNAs) and proteins expressed in NHBE cells exposed to DEPs at 1 μg/cm2 for 8 h and 24 h were identified using PCR array analysis and 2D PAGE/LC-MS/MS, respectively. YWHAZ gene expression was estimated using PCR, immunoblotting, and immunohistochemical analyses. Genes discovered through an overlap analysis were validated in DEP-exposed mice. Proteomics approaches showed that exposing NHBE cells to DEPs led to changes in 32 protein spots. A transcriptomics PCR array analysis showed that 6 of 84 miRNAs were downregulated in the DEP exposure groups compared to controls. The mRNA and protein expression levels of YWHAZ, β-catenin, vimentin, and TGF-β were increased in DEP-treated NHBE cells and DEP-exposed mice. Lung fibrosis was increased in mice exposed to DEPs. Our combined PCR array-omics analysis demonstrated that DEPs can induce airway inflammation and lead to lung fibrosis through changes in the expression levels of YWHAZ, β-catenin, vimentin, and TGF-β. These findings suggest that dual approaches can help to identify biomarkers and therapeutic targets involved in pollutant-related respiratory diseases.

Establishment and Clinical Application of a RPA-LFS Assay for Detection of Capsulated and Non-Capsulated Haemophilus influenzae.

A recombinase polymerase amplification-lateral flow strip assay was established for detection of the outer membrane protein P6 (omp6) and the capsule encoding gene bexA of Haemophilus influenzae and the detection limit, sensitivity, and specificity were determined. Specific primers and probes were designed based on the published nucleotide sequences of omp6 and bexA. The minimum detection limit was determined with standard strains and the practical applicability of the RPA-LFS assay was assessed by detection of 209 clinical samples. The results confirmed that the RPA-LFS assay was both specific and sensitive for the detection of capsulated and non-capsulated H. influenzae with a detection limit of 1 CFU/µL. The detection rate of the 209 clinical samples was 97.1%, while the detection rate of capsulated H. influenzae was 63.2%. The detection results were consistent with the traditional culture method and dual polymerase chain reaction (PCR), confirming the applicability of the RPA-LFS assay.

Clinical Impact of Clostridium difficile PCR Cycle Threshold-Predicted Toxin Reporting in Pediatric Patients.

Reliance on tests that detect only the presence of toxigenic Clostridium difficile can result in overdiagnosis and overtreatment of C difficile infection (CDI). The C difficile polymerase chain reaction (PCR) cycle threshold (CT) can sensitively predict the presence of free C difficile toxins; however, the clinical application for this testing strategy remains unexplored. We evaluated the impact of dual PCR and toxin result reporting, as predicted by the CT, on CDI management and outcomes in children. Before the intervention, results for C difficile testing at Lucile Packard Children's Hospital Stanford were reported as PCR positive (PCR+) or negative (PCR-) according to the GeneXpert C diff Epi tcdB PCR assay (Cepheid, Sunnyvale, California). Beginning October 5, 2016, the presence of free toxins, as predicted by the CT, was reported also. The CDI treatment rates 1 year before and 18 months after implementation of toxin reporting were compared. Demographic and treatment-related data were collected, and patient outcomes were followed up 8 weeks later. CDI treatment decreased 22% after the intervention (96% [preintervention] vs 74% [postintervention]; P < .001). During the postintervention period, there were 152 PCR+C difficile results, and 94 (62%) of them were toxin positive (toxin+) according to the CT. Of the 58 PCR+/toxin-negative (toxin-) results, 38 (66%) did not result in CDI treatment. Seven (18%) of the untreated PCR+/toxin- patients underwent repeat testing within 8 weeks, and 5 (13%) of them were subsequently PCR+/toxin+ and treated. No CDI-related complications were identified. Addition of the CT-predicted C difficile toxin result to PCR reporting reduces the proportion of PCR+ children treated for CDI.

Chlamydia trachomatis Antibody in Fitz-Hugh-Curtis Syndrome

Fitz-Hugh-Curtis (FHC) syndrome is inflammation of the liver capsule associated with pelvic inflammatory disease. We measured Chlamydia trachomatis antibodies in 30 female patients with acute abdominal pain for diagnosis of FHC-syndrome, and the results were compared with other tests. A dual-polymerase chain reaction was used for the detection of C. trachomatis in the cervix, and a micro-immunofluorescence test was performed to measure the antibody to C. trachomatis in serum. Cervical specimens were stained with Gram stain and cultured on chocolate agar for detection of Neisseria gonorrhoeae, and abdominal computed tomography (CT) and pelvic examinations were performed. Of the 30 patients examined, 19 were diagnosed as having FHC-syndromes and 11 abdominal pains without FHC-syndrome. C. trachomatis was detected from one of the five patients studied, and no N. gonorrhoeae was isolated from the patients with FHC-syndrome. High titers of IgG antibody (1:512-1:1,024) to C. trachomatis were demonstrated in all patients with FHC-syndrome. The CT scan revealed perihepatitis in 14 patients with FHC-syndrome. All patients with FHC-syndrome are associated with C. trachomatis infections, and a high titer of C. trachomatis antibody (IgG) is a very useful marker for FHC-syndrome.

Molecular Identification of Bacteria from Aseptically Loose Implants

Polymerase chain reaction (PCR) assays have been used to detect bacteria adherent to failed orthopaedic implants, but some PCR assays have had problems with probable false-positive results. We used a combination of a Staphylococcus species-specific PCR and a universal PCR followed by DNA sequencing to identify bacteria on implants retrieved from 52 patients (92 implants) at revision arthroplasty. We addressed two questions in this study: (1) Is this method able to show the existence of bacterial DNA on presumed aseptic loosed implants?; and (2) What proportion of presumed aseptic or culture-negative implants was positive for bacterial DNA by PCR? Fourteen implants (15%) were believed infected, whereas 74 implants (85%) were believed aseptic. Each implant was sonicated and the resulting solution was submitted for dual real-time PCR assay and culture. All implants believed aseptically loose were culture-negative, but nine of the 74 (12%) had bacterial DNA by PCR; two (2.7%) were PCR-positive and also showed histologic findings suggestive of infection. Uniquely developed PCR and bacterial sequencing assays showed bacterial DNA on 12% of implants removed for presumed aseptic loosening. Additional studies are needed to determine the clinical importance of bacterial DNA detected by PCR but not by conventional culture. Level III, diagnostic study.

Isolation of microsatellite markers from Pinus densiflora Sieb. et Zucc. using a dual PCR technique

AbstractWe developed seven microsatellite loci from Pinus densiflora using a dual polymerase chain reaction (PCR) technique. Of 186 clones from a library based on suppression PCR, 127 contained microsatellite sequences. Of these, 43 candidates were determined sequences of both flanking regions, and 16 regions from this group were chosen as development markers. Seven of these primer pairs successfully amplified polymorphic single loci among 83 resistant trees against pine wood nematode. The observed heterozygosity of the seven microsatellite markers ranged from 0.247 to 0.843. Mendelian inheritance was confirmed using megagametophytes.

Purification of Forensic Specimens for the Polymerase Chain Reaction (PCR) Analysis

Purification methods of deoxyribonucleic acid (DNA) from degraded and contaminated forensic samples were investigated for polymerase chain reaction (PCR) analysis. DNA extracted from putrefied tissue or bloodstains sometimes contained the copurified contaminant, that was identified as the porphyrin compound (hematin). When contaminated but less degraded DNA was analyzed by PCR, it was necessary to eliminate the impurity by anion exchange column chromatography or chelating resin preparation, and ultrafiltration using Centricon microconcentrators. When highly degraded DNA was analyzed, trace amounts of high molecular weight DNA was recovered by electroelution method, and then further purified by both column chromatography and ultrafiltration. From thus purified samples, the amelogenin gene for sex determination could be amplified by dual PCR technique.

Sex determination of forensic samples by dual PCR amplification of an X-Y homologous gene

Sex determination by polymerase chain reaction (PCR) analysis of the X-Y homologous amelogenin gene is highly reliable since the detection of an X-specific amplified fragment validates the procedure. Previously, we reported that 250 ng of template DNA are required for sex determination by this method. We report here a refinement of the technique to include dual PCR. Dual PCR using two sets of primers results in the detection of X- and Y-specific amplified fragments from as little as 0.005 ng of template DNA. This is a powerful technique for the analysis of trace forensic samples and its application is discussed.

Absence of fetal cells in maternal circulation at a level of 1 in 25,000

A dual polymerase chain reaction (PCR) technique is developed which enables the detection of one part male DNA in 25,000 parts female DNA. The technique amplifies a part of the X-Y homologous amelogenin gene in which the Y counterpart has a 189 bp deletion within one of the introns. This deletion has made it possible to identify individual X and Y counterparts based on the difference in size between them. None of the 18 pregnant women studied showed a positive Y-signal although eight of them bear male fetuses excluding the presence of fetal cells at one in 25,000 maternal cells. The results presented here show that a sensitivity of greater than one in 25,000 is required for detection of fetal genetic disease using maternal peripheral blood.