Analyte detection with DNA-labeled antibodies and polymerase chain reaction

We demonstrate immuno-polymerase chain reaction (PCR) assays for two clinical analytes--human thyroid-stimulating hormone and chorionic gonadotropin (hTSH, hCG)--using DNA-labeled antibodies and PCR for amplification of assay response. DNA-antibody conjugates were synthesized by using heterobifunctional cross-linker chemistries to covalently attach single- or double-stranded DNA labels through amine or sulfhydryl groups on the analyte antibodies. These approaches yielded molecular chimeras possessing both analyte-specific antibody binding and nucleic acid amplification functionalities. Dose-response relationships were demonstrated for immuno-PCR assays of both analytes in a microtiter plate-based, two-antibody sandwich assay format. Detection limits for hTSH (1 x 10(-19) mol, < 1.4 mIU/L) and hCG (5 x 10(-18) mol, 0.025 IU/L) exceeded those of conventional enzyme immunoassays by 2-3 orders of magnitude. We also evaluated various DNA design factors influencing label amplification and assay performance, such as primer sequence, strand number, and DNA length. Our findings, in concert with previous reports, suggest that this hybrid technology could provide the basis for a new generation of ultra-sensitive immunoassays offering multianalyte capabilities.     

The in situ polymerase chain reaction for detection of chlamydia trachomatis

The in situ polymerase chain reaction (PCR) is a technique that has important applications in the diagnosis of viral and bacterial diseases. This study investigated an in situ PCR assay established to detect the presence of Chlamydia trachomatis in endocervical swabs. In addition, histological sections of endocervical squamous cell carcinoma were analyzed because previous studies had revealed a significant association with C. trachomatis. A total of 20 cervical neoplasms (squamous cell carcinoma in situ; n = 10; invasive squamous cell carcinoma; n = 10) and endocervical smears taken from five patients with and without inflammatory changes were analyzed by conventional PCR. Chlamydial DNA was found in 10 histological samples (six carcinomas in situ, four invasive carcinomas) and in one endocervical swab from a patient with known C. trachomatis infection. Positive specimens were used for establishing an in situ PCR assay (IS-PCR). After IS-PCR, these samples showed dense cytoplasmic staining of endocervical cells (smears) and non-neoplastic epithelial cells (cervical neoplasms). The other tumor samples and smears did not demonstrate positive PCR reaction. The results indicate that in situ PCR is an effective technique for localizing C. trachomatis in target cells because IS-PCR detection of chlamydial DNA correlated with histological and cytological features.     

GBV-RNA detection by polymerase chain reaction with several primer pairs

The identification of specific genomic sequences of GB viruses (GBV) has made it possible to utilize the polymerase chain reaction (PCR) for evaluation of the viraemia. Several studies have demonstrated the RNA-GBV presence in sera from different patients amplifying several portions of the virus. In this investigation the PCR results when different regions of GBV (NS3, UTR and putative CORE and E1) were amplified in the same sample. In 245 samples studied there were two (0.8%) discordant results and the NS3 primer showed the greatest sensitivity. The lowest percentage of positivity was obtained with CORE-E1 primers. These results could be because the nucleocapside/E1 region was extremely variable in length and sequences, although degenerated primers and probes were used. Discordances were attributable to laboratory errors, variability in the viral genome, the presence of primer inhibitors in samples or a low viral load.     

Nested polymerase chain reaction for detection of Mycobacterium tuberculosis in clinical samples

The nested polymerase chain reaction technique was compared with the conventional smear and culture methods for detection of Mycobacterium tuberculosis. The nested polymerase chain reaction used in this study showed excellent specificity, sensitivity, and agreement with the conventional methods for 417 clinical samples, indicating a contribution to the rapid diagnosis of mycobacterial infectious diseases.     

Single-fiber polymerase chain reaction for detection of mutant mitochondrial DNA]

Single-fiber PCR amplifies mitochondrial DNA (mtDNA) in single muscle fiber isolated from cross frozen section. The PCR products are digested with a restriction enzyme to distinguish mutant mtDNA from wild-type mtDNA. The proportion of mutant mtDNA is higher in ragged-red fiber (RRF) than in non-RRF in mitochondrial encephalomyopathies with mutations of mtDNA. This method may be applied to evaluate amount of mtDNA and mRNA in single muscle fiber, and become a powerful tool to elucidate the pathogenetic mechanism in mitochondrial encephalomyopathies.     

The polymerase chain reaction in pathology

Membrane-fixed CD14 acts as a receptor for the protein-bound endotoxin (LPS) complex and mediates the cellular effects of endotoxin. Soluble CD14 (sCD14) is suggested to neutralize circulating LPS, i.e., acting as an endotoxin antagonist. The aim of this study was to elucidate the release of both sCD14 and endotoxin in traumatized patients, starting from the earliest phase after trauma. A total of 15 patients (O ISS = 19, 9-75) suffering major trauma were enrolled in this prospective study. Blood samples were collected as early as immediately at the site of accident, on hospital admission, and thereafter hourly, then daily. For patients (O ISS = 47) died within 24 h because of their severe injuries. Immediately after the accident as well as during the first 2 h after hospital admission, the mean sCD14 levels of surviving patients did not differ from those of healthy volunteers (n = 53). Thereafter, however, sCD14 increased continuously in the trauma group. The concentrations remained elevated throughout the entire observation period. There was, however, no relation between the sCD14 release and the pattern or the severity of injury. In contrast, endotoxin levels revealed a pattern-specific release. The highest plasma concentrations of LPS were observed in patients suffering from (additional) thoracic injury. On the basis of these results we conclude that the release of sCD14 after trauma does not reflect a strict principle such as action/reaction caused by the appearance of endotoxin immediately after the injury. Soluble CD14 is more likely release by an endotoxin-independent mechanism.     

Mycoplasma pneumoniae detection from throat swab by two-step polymerase chain reaction

Two-step polymerase chain reaction (PCR) with primers designated against 16S rRNA gene of Mycoplasma pneumoniae for diagnosis of infection was evaluated in comparison with the conventional single-step PCR and culture methods. The two-step PCR method showed specific amplification of M. pneumoniae DNA and higher sensitivity (1.5 fg/assay) than the single-step PCR method. With the two-step PCR method, 76 of 322 throat swabs (23.6%) from patients with acute respiratory complaints gave positive results whereas 20.2% were positive in the culture method. Seven of 13 samples which were negative in the single-step PCR method but positive in either serological or the culture method showed positive results by the two-step PCR method. In addition, 5 samples which were weakly positive in the single-step PCR method showed distinctly positive results in the two-step PCR. These results indicate that the two-step PCR method is a useful tool for detection of M. pneumoniae in clinical specimens, although it requires a relatively sophisticated in technique.     

Quantitative hepatitis C RNA-polymerase chain reaction and detection with DNA-ELISA

BACKGROUND/AIMS: Viral serum concentrations are considered to have a clinical, prognostic and epidemiological impact on patients with hepatitis C infection. The purpose of this study was to test whether quantitation of HCV-RNA is possible by PCR in combination with DNA-ELISA. METHODOLOGY: PCR with 25 to 35 cycles was performed with variable concentrations of cloned HCV-cDNA or the serum of patients with chronic hepatitis C. The amplified PCR-products were detected by agarose gel or by DNA-ELISA. RESULTS: The detection limit of PCR with DNA-ELISA or gel detection decreased with increasing numbers of PCR cycles. However, the correlation of the optical density of the DNA-ELISA with the HCV-cDNA concentration decreased with increasing numbers of PCR as well (r=0.8 vs. r=0.29; 25 vs. 35 PCR-cycles). HCV-RNA was found in the sera of 19 of 30 patients (63%) with chronic hepatitis C by gel detection and in 14 of 30 patients (47%) by DNA-ELISA subsequent to PCR with 35 cycles. CONCLUSIONS: The PCR/DNA-ELISA technique allows a semiquantitative determination of HCV-cDNA concentrations down to 103 genomes/ul. However, to obtain a reasonable sensitivity for HCV concentrations in the serum of patients with hepatitis C, the number of PCR cycles has to be increased to numbers too high to provide reliable quantification. Further studies should be done to evaluate whether the detection systems can be improved to obtain a sufficient sensitivity for quantitative HCV-PCR. A prerequisite for the use of PCR in combination with quantifiable detection systems is that a PCR-cycle number is chosen that keeps amplification within the logarithmic phase.     

Evaluation of polymerase chain reaction for detection of Mycoplasma meleagridis infection in turkeys

Different methods were compared for the detection of the turkey pathogen Mycoplasma meleagridis in a turkey field flock before and after antibiotic (oxytetracycline) treatment. They included culture, serology (detection of antibodies by ELISA) and a polymerase chain reaction (PCR) based assay developed by Boyle et al. [Boyle, J.S., Good, R., Morrow, C.J., 1995. Detection of the turkey pathogens Mycoplasma meleagridis and M. iowae by amplification of genes coding for rRNA. J. Clin. Microbiol. 33, 1335-1338]. Culture and PCR assay with tracheal swab samples were much more sensitive than ELISA with serum samples. Percentages of infected birds detected by culture or PCR for samples collected prior to antibiotic treatment were almost identical but the percentage of positive samples detected after antibiotic treatment was much higher with the PCR test.     

Rapid detection of Shiga-like toxin gene in feces with rapid-cycle polymerase chain reaction

A rapid detection for Shiga-like toxin in feces was developed with the nucleic acid extraction method by silicondioxide-guanidine thiothianate and rapid-cycle polymerase chain reaction by RapidCycler (model 1002; Idaho Technology, RC-PCR here after). Twenty-two fecal samples that were collected from patients with diarrhoea caused by E. coli O157:H7 and frozen for 6 months were examined directly by RC-PCR, conventional PCR assay using by ThermalCycler 9600-R (Roche, TC-PCR here after) and by the culture method using tellurite-cefixime sorbitol MacConkey (direct method). These examinations were done also after being injected into TCV-TSB and incutated at 35 degrees C overnight (indirect method). The sensitivity of RC-PCR and TC-PCR using a diluted suspension of broth enriched at 35 degrees C overnight were 4.1 pg and 410 fg, respectively. Positive results in the direct method were obtained in 7 for RC-PCR, 10 for TC-PCR and 5 for culture. Positive results on indirect assay were obtained in 9 for RC-PCR, 9 for TC-PCR and 7 for culture. It was demonstrated that the RC-PCR assay was able to detect Shiga-like toxin gene in feces in less than 90 minutes after being received at the laboratory.     

Gene sequences of the pcpB gene of pentachlorophenol-degrading Sphingomonas chlorophenolica found in nondegrading bacteria

An optically active, rigid rodlike helical polysilane with 6, 9, 12-trioxatetradecyl and (S)-2-methylbutyl substituents (1) was newly obtained as a very high molecular weight polymer of several million. Due to the presence of trietheral substituent, 1 was readily soluble in a polar solvent such as ethanol and a mixture of ethanol and water, but was insoluble in pure water. Polysilane 1 in pure ethanol at room temperature exhibited an intense and narrow ultraviolet (UV) and circular dichroism (CD) absorptions at 323 nm, associated with an almost mirror imaged fluorescence (FL) at 328 nm, that are characteristics of rigid rodlike, single-screw-sense helical polysilanes reported previously. When solution temperature was changed from 60 degrees C to -104 degrees C, a global shape of 1 expanded associated with an increase of segment length, whereas a screw pitch tended to be wound tightly. On the other hand, as a solvent polarity became poor, a global shape of 1 shrunk associated with an decrease of segment length and formed a chiral motif with an M-helicity between two helical segments with a kink. At a ratio of 50% of ethanol/water of 50:50 (v/v), 1 became insoluble and formed aggregates.     

Direct detection of Streptococcus mutans in human dental plaque by polymerase chain reaction

Streptococcus mutans is an etiological agent in human dental caries. A method for the detection of S. mutans directly from human dental plaque by polymerase chain reaction has been developed. Oligonucleotide primers specific for a portion of the dextranase gene (dexA) of S. mutans Ingbritt (serotype c) were designed to amplify a 1272-bp DNA fragment by polymerase chain reaction. The present method specifically detected S. mutans (serotypes c, e and f), but none of the other mutans streptococci: S. cricetus (serotype a), S. rattus (serotype b), S. sobrinus (serotypes d and g), and S. downei (serotype h), other gram-positive bacteria (16 strains of 12 species of cocci and 18 strains of 12 species of bacilli) nor gram-negative bacteria (1 strain of 1 species of cocci and 20 strains of 18 species of bacilli). The method was capable of detecting 1 pg of the chromosomal DNA purified from S. mutans Ingbritt and as few as 12 colony-forming units of S. mutans cells. The S. mutans cells in human dental plaque were also directly detected. Seventy clinical isolates of S. mutans isolated from the dental plaque of 8 patients were all positive by the polymerase chain reaction. These results suggest that the dexA polymerase chain reaction is suitable for the specific detection and identification of S. mutans.     

Gastric syphilis: polymerase chain reaction detection of treponemal DNA in pseudolymphomatous lesions

Syphilis is an unexpected diagnosis in the stomach. To establish the diagnosis, evidence of Treponema pallidum in the gastric lesion is necessary. However, it is sometimes difficult to prove the presence of the organisms by conventional methods. The authors describe two cases of early gastric syphilis with pseudolymphomatous histology in which T pallidum gene was detected by the polymerase chain reaction (PCR) using paraffin biopsy sections. The gastric lesion of each case endoscopically and histologically simulated that of malignant lymphoma. However, no clonality was proved by immunohistochemistry or PCR gene rearrangement analysis. No spirochetal organisms were detected with certainty by Warthin-Starry silver stain, whereas the organisms were shown by immunofluorescent stain in one patient. A PCR study showed the treponemal DNA in both patients, and its validity was supported by a direct sequencing and a restriction enzyme digestion. Positive results of serological tests for syphilis and regression of the lesions after antisyphilitic treatment were confirmatory of the diagnosis. Gastric syphilis should be considered as a differential diagnosis when an atypical lymphoid infiltrate fails to show monoclonality. The present PCR method would be helpful in showing T pallidum using routinely processed small biopsy specimens as the tissue source.     

Direct in situ reverse transcriptase polymerase chain reaction for detection of measles virus

Behavioral contexts can evoke a variety of autonomic modes of response, characterized by reciprocal, coactive, or independent changes in the autonomic divisions. The present study investigated the modes of autonomic response to visual illusion and mental arithmetic tasks, by the use of noninvasive measures of sympathetic (pre-ejection period; PEP) and parasympathetic (respiratory sinus arrhythmia; RSA) cardiac control. As previously demonstrated, mental arithmetic was associated with a reciprocal pattern of sympathetic activation and vagal withdrawal. The illusion task, however, yielded a distinct mode of vagal activation in the absence of sympathetic change. Responses within tasks were reliable. In contrast to the general intertask consistency reported for stress tasks that yield similar autonomic modes of response, however, neither PEP nor RSA responses were correlated across the illusion and arithmetic tasks. This may be attributable to the dissimilar modes of autonomic control evoked by these tasks. The distinct modes of autonomic response to arithmetic and illusions emphasize the importance of a bivariate model of autonomic control, and may offer important experimental tools for psychophysiological studies of autonomic control.     

Rapid detection of thymidylate synthase gene expression levels by semi-quantitative competitive reverse transcriptase polymerase chain reaction followed by quantitative digital image analysis

We describe a simplified and reliable polymerase chain reaction (PCR) method to quantify thymidylate synthase (TS) gene expression levels from clinical human tumor biopsy samples as small as 100 mg using the beta-actin housekeeping gene as a reference standard. The semiquantitative RT-PCR is carried out by the coamplification of the target template and an external competitor using primer pairs common to both templates in the same reaction vessel. Quantitative digital image analysis is performed directly after electrophoresis, thus mRNA quantification is done quickly and without the use of radioactive substances. The observed relative TS gene expression levels varied between 3- and 40-fold, but most of the values were grouped within a 10-fold range. There is an observed 89% correlation between TS mRNA expression and protein levels. These findings suggest that preliminary experiments used to determine the linear range of RT-PCR amplification in non-competitive semiquantitative PCR experiments, and the use of radioactive substances to quantify PCR products may be unnecessary.