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

Regional expression of dopamine D1 and D2 receptor proteins in the cerebral cortex of asphyxic newborn infants

Dopamine D(1) and D(2) receptor protein expression was examined by Western blotting in newborn infants dying from cerebral asphyxia between 31 and 42 weeks' gestation, and matched controls. Frontal, occipital, temporal, and motor cortex tissue samples were obtained at autopsy (median postmortem interval 35 hours) and frozen for storage at -80 degrees C. A total of 2 immunoreactive bands were detected with each primary antibody in infant brain, whereas a single band was present in adult human and rat tissue. Immunoreactivity varied between cortical areas for both receptors, but their regional patterns differed significantly. D(1) protein levels were higher in motor and temporal cortex than in frontal or occipital cortex. D(2) protein showed graded expression frontal > motor > occipital > temporal cortex. Asphyxia cases showed lower expression of the upper D(2) immunoreactive band, but no difference in regional pattern. Lower D(2) receptor expression may attenuate stress responses and underlie increased vulnerability to hypoxia at birth.

Advantages of in situ hybridisation over direct or indirect in situ reverse transcriptase-polymerase chain reaction for localisation of galanin mRNA expression in rat small intestine and pituitary

In situ hybridisation (ISH) and direct or indirect in situ reverse transcriptase-polymerase chain reaction (RT-PCR) were used to detect galanin mRNA in paraffin sections of rat intestine and pituitary. With conventional ISH, a subset of intestinal neuronal ganglion cells and anterior pituitary endocrine cells were labelled. Direct in situ RT-PCR also labelled some cells in pituitary but not in intestine. Negative controls were unlabelled, but sections with 3' primer alone for RT-PCR appeared positive. No signal was apparent using the indirect in situ RT-PCR method. Investigation of the specificity of solution phase RT-PCR using RNA extracts from pituitary or intestine revealed that additional PCR products were detected under some conditions. The sequences of these PCR products suggested that one was the result of mispriming and single primer PCR, which could also have occurred in situ. Alternative galanin primers gave only the predicted RT-PCR product in solution phase yet still gave artefacts in tissue sections using direct in situ RT-PCR. ISH with probes transcribed from the correct PCR product gave identical labelling to the original galanin riboprobe. In conclusion, direct in situ RT-PCR is unreliable and requires validation, while indirect in situ RT-PCR may fail even though sufficient target exists for detection with conventional sensitive riboprobe ISH.

Development of a direct in situ RT-PCR method using labeled primers to detect cytokine mRNA inside cells

We have developed an original protocol of direct in situ RT-PCR with biotinylated labeled primers to detect cytokine mRNA inside cells. This label improved the specificity of the technique compared with the use of digoxigenin or fluorescein-labeled primers. We found a reliable correlation between the known expression of cytokine mRNA in a given cell and a positive signal with in situ RT-PCR. Nuclear counterstaining demonstrated that the positive signal obtained was distributed in the cytoplasm in accordance with mRNA localization. In addition, direct demonstration of the presence of the expected PCR product in cell extracts without non-specific parasitic DNA amplification provided strong support for the specificity of the method. Designing the primers in order to prevent DNA amplification, the use of recombinant Thermus thermophilus (rTth) DNA polymerase and a decreased duration of each cycle of PCR by combining the annealing and hybridization steps improved the reproducibility and reliability of the technique and morphological preservation of the cells. Experiments in which different proportions of cytokine mRNA positive and negative cells were mixed argue against significant diffusion of PCR product into initially cytokine mRNA negative cells, thereby leading to false-positive results. In comparison with the direct incorporation of labeled dNTP during amplification, our procedure appears to ensure greater specificity and does not need DNAse treatment which is often difficult to standardize. Detection of IL-2 and IFNgamma mRNA induction after T cell activation using this direct in situ RT-PCR method showed that the technique may be helpful for monitoring cytokine gene expression at a single cell level.

Comparison of procedures for the detection of enteroviruses in murine heart samples by in situ polymerase chain reaction

A protocol for the in situ polymerase chain reaction (IS-PCR) detection of viral nucleic acid in the heart tissue of four-to-five-week-old CD1 mice infected with coxsackievirus B3 (CBV3) Nancy strain is described. To compare the effects of formalin concentration on the IS-PCR process, two different concentrations (10 and 37%) were employed. Using 37% formalin, 25 PCR cycles were sufficient and a permeabilization step could be omitted. However, postfixation of tissues with 4% paraformaldehyde and 100% ethanol after the deparaffinization, reverse transcriptase and amplification steps was required in order to minimize artefacts. When the tissues were fixed in 10% formalin, postfixation with 4% paraformaldehyde was not required, but a permeabilization step had to be employed and 40 cycles of PCR amplification were needed. To detect the PCR product in the 10% formalin-fixed samples, incubation with 0.3 U/ml of an anti-digoxigenin antibody conjugated to alkaline phosphatase was performed for 90 min. When 37% formalin-fixed samples were used, the concentration of the antibody conjugate had to be increased to 3 U/ml and the exposure time was decreased to 30 min. Enterovirus (EV) nucleic acid was detected in the cytoplasm of myocytes. Thus, IS-PCR was successful in localizing EV nucleic acid in the cytoplasm of myocytes in mice infected with a cardiotropic strain of CBV3. Using this technique, 10% formalin-fixed tissues gave better results than 37% formalin-fixed tissues.

A comparison of RT-PCR, in-situ hybridisation and in-situ RT-PCR for the detection of rhinovirus infection in paraffin sections

We describe an in-situ RT-PCR method for the amplification of rhinovirus (RV) in fixed, paraffin-embedded HeLa cells employed as a model for human respiratory epithelium. HeLa cells were infected in-vitro with inocula of rhinovirus-16 ranging from 10(2) to 10(6) 50% tissue culture infective doses (TCID50), incubated for 18 h then fixed and processed into paraffin blocks. Sections of the cell preparation were subjected to standard RT-PCR, in-situ hybridisation (ISH) or in-situ RT-PCR using specific oligonucleotide primers or probes directed against the 5' non-coding region of RV RNA. RT-PCR was found to be capable of detecting RV16 RNA in one 8 microns-thick section of cells infected with the lowest virus titre. ISH using digoxigenin labelled oligonucleotide probes located RV16 signal in the majority of HeLa cells at the highest virus titre, but in few or no cells with the lowest virus titre. In contrast, in-situ RT-PCR detected RV16 in the majority of cells infected with this amount of RV16. There was a slight loss of morphology and fine localisation associated with the in-situ thermal cycling process. However, the sensitivity of in-situ RT-PCR is comparable to standard RT-PCR and greater than ISH for the detection of RV. In-situ RT-PCR has wide applications for sensitive localization of low copy viral and RNA sequences within cells to investigate the role of viruses in a variety of clinical conditions.

Direct in situ transcriptase polymerase chain reaction for the detection of Enterovirus genome in liver tissues

Adolescent female mice were inoculated intraperitoneally with coxsackievirus B3 Nancy strain, sacrificed 3 and 5 days later and the livers harvested. A protocol for direct reverse transcriptase in situ PCR (RT-ISPCR) detection of enteroviral RNA in paraffin-embedded liver tissues was developed. The optimal conditions for the assay were determined. The best results were obtained when the tissue was fixed in formalin, prior to being embedded in paraffin, then cut in 5 micron thick sections, and mounted onto silanized slides. After deparaffination the slides were incubated in 1 microgram/m1 Proteinase K for 10 min and cDNA synthesis was carried out. For successful RT-ISPCR 40-50 cycles of amplification were necessary. The optimal concentrations of dNTP, primers and Taq Polymerase for RT-ISPCR were determined by serial dilution assays. Primers were selected from highly conserved sequences in the 5' non-coding region (5'NTR). To detect the viral RNA in the liver, digoxigenin-dUTP was incorporated during amplification, subsequently bound with an antidigoxigenin antibody conjugated to alkaline phosphatase (AP), followed by colorimetric detection with nitroblue tetrazolium salt (NBT) and 5-brom-4chloro-3indolyl-phosphate (BCIP). The result was a blue precipitate in the cytoplasm of hepatocytes from infected mice. Fibroblasts, endothelial cells, lymphocytes and the nuclei of hepatocytes were negative. Thus, RT-ISPCR is a specific method for the detection of enterovirus RNA in the hepatocytes of infected mice, and can be of use for the determination of EV liver disease in man.