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At least 325 records · Page 18Linked to original sources
PubMed1994

Detection of hepatitis C viral sequences in formalin-fixed, paraffin-embedded liver tissue: effect of interferon alpha therapy.

To determine the effect of interferon-alpha (IFN) therapy on hepatitis C virus (HCV) in liver, reverse transcription "nested" polymerase chain reaction (RT-PCR) was applied to detect HCV RNA in formalin-fixed, paraffin-embedded liver biopsy specimens obtained before and at the end of IFN therapy in 42 patients with chronic HCV infection. Results were correlated with the clinical and biochemical outcome in 36 cases. Fifteen patients were nonresponders to IFN; 13 patients had a complete response to IFN but relapsed shortly after IFN was stopped (responders who relapsed); and 8 patients showed a complete and sustained response to IFN therapy (sustained responders). Total RNA was extracted using proteinase K digestion and phenol/chloroform/isoamyl alcohol extraction, and HCV RNA was detected by standard RT-PCR using primers from the highly conserved 5' untranslated region. HCV RNA was detected in 41 of the 42 pretreatment specimens. Of the 36 patients with paired posttreatment samples, HCV RNA was detected in all 15 patients who did not respond to IFN and 9 of 13 who responded to IFN but relapsed shortly after IFN was stopped. In contrast, only one of the eight patients who had a sustained response to IFN therapy had HCV RNA detected by RT-PCR (P < 0.04). These data confirm 1) the feasibility of detecting HCV RNA in formalin-fixed, paraffin-embedded tissue from patients with chronic HCV infection, 2) show that sustained response to IFN is associated with loss of liver HCV RNA at the end of IFN therapy, and 3) offer an explanation for recurrence in patients who relapse.

Base Sequence↗
PubMed1984

High resolution autoradiographical detection of RNA in the interchromatin granules of DRB-treated cells.

Isolated rat liver cells were pulse-labelled with tritiated uridine and post-incubated in the presence of an excess of unlabelled uridine and of adenosine analog DRB (5-6-dichloro-1-beta-D-ribofuranosyl benzimidazole). Nuclear radioactivity was detected with high resolution autoradiography. A significant labelling of the interchromatin granules was revealed in these conditions. Pretreatments of cells with low doses of actinomycin D in order to preferentially inhibit ribosomal RNA (rRNA) synthesis prevented the labelling of the interchromatin granules during subsequent DRB treatments. These observations indicate that in DRB-treated cells, the interchromatin granules are sites of transfer or of accumulation of nucleolar RNA. Our results are discussed in connection with our knowledge of the action of DRB on RNA metabolism in mammalian cells and with recent data concerning the still enigmatic interchromatin granules which are present in the nuclei of most cells.

Animals↗
PubMed1997

Quantitative comparison of pretreatment regimens used to sensitize in situ hybridization using oligonucleotide probes on paraffin-embedded brain tissue.

Paraffin embedding of tissue is generally perceived to dramatically reduce RNA detectability. As a consequence, in situ hybridization on paraffin-embedded tissue is largely confined to detection of high-copy RNA species (e.g., viral RNA) and/or to detection using typically more sensitive cDNA probes or riboprobes. In this study, several procedures for in situ hybridization on paraffin-embedded rat tissue using oligonucleotide probes complementary to cellular transcripts were developed and quantitatively compared. Certain pretreatments showed marked increases in sensitivity compared to untreated sections. Furthermore, through quantitative assessment using image analysis, sensitivity of optimal pretreatments was equal to that of routinely used fresh-frozen, postfixed tissue sections. The development of such techniques permitting in situ hybridization to be carried out on paraffin-embedded tissue allows a comparison of protein and mRNA distribution to be made in adjacent sections and provides the potential for double labeling by in situ hybridization and immunohistochemistry which may not be possible on post-fixed frozen sections.

Animals↗
PubMed2004

Evaluation of three molecular biology-based assays for the detection of GB virus C/hepatitis G virus in clinical specimens.

OBJECTIVE: The present study was performed to evaluate the reliability of three reverse transcription-polymerase chain reaction (RT-PCR) assays, one commercial and two 'homebrew', for GB virus C (GBV-C)/hepatitis G virus (HGV) RNA detection in clinical specimens. We, therefore, investigated the virus prevalence with the method that gave us the best performances. METHODS: The commercial assay amplified sequences from the viral 5'-untranslated region (5'UTR) and non-structural 3 (NS3) region. The non-commercial assays 1 and 2 were based on different primers for the 5'UTR consensus sequence. RESULTS: The percentage of overall concordance by the three methods was 91.7%, raising to 93.0% when only the two non-commercial methods were compared. Assay 1 showed low sensitivity (57.1% vs. the commercial assay, 58.8% vs. assay 2), with 100% specificity. The commercial assay gave 18 of 54 (33.3%) 'false-negative' results, concordantly negative by the other assays. The prevalence of GBV-C/HGV RNA among the HIV+ patients was 27.0 and 32.6% in HIV/HCV co-infected patients. CONCLUSION: These data suggest that assay 2 has higher reliability as compared to the other two methods and may be used for an accurate GBV-C/HGV RNA detection in clinical and epidemiological studies.

5' Untranslated Regions↗
PubMed2004

Use of the minimum spanning tree model for molecular epidemiological investigation of a nosocomial outbreak of hepatitis C virus infection.

The minimum spanning tree (MST) model was applied to identify the history of transmission of hepatitis C virus (HCV) infection in an outbreak involving five children attending a pediatric oncology-hematology outpatient ward between 1992 and 2000. We collected blood samples from all children attending since 1992, all household contacts, and one health care worker positive for antibody to HCV (anti-HCV). HCV RNA detection was performed with these samples and with smears of routinely collected bone marrow samples. For all isolates, we performed sequence analysis and phylogenetic tree analysis of hypervariable region 1 of the E2 gene. The MST model was applied to clinical-epidemiological and molecular data. No additional cases were detected. All children, but not the health care worker, showed genotype 3a. On six occasions, all but one child had shared the medication room with another patient who later seroconverted. HCV RNA detection in bone marrow smears revealed, in some cases, a delay of several months in anti-HCV responses. Sequence analysis and phylogenetic tree analysis revealed a high identity among the isolates. The MST model applied to molecular data, together with the clinical-epidemiological data, allowed us to identify the source of the outbreak and the most probable patient-to-patient chain of transmission. The management of central venous catheters was suspected to be the probable route of transmission. In conclusion, the MST model, supported by an exhaustive clinical-epidemiological investigation, appears to be a useful tool in tracing the history of transmission in outbreaks of HCV infection.

Child↗
PubMed1991

Molecular hybridization with cloned fragments of tick-borne encephalitis (TBE) virus cDNA in acute and chronic TBE infection.

Recombinant plasmid DNA was used as a probe to detect tick-borne encephalitis (TBE) virus RNA during incubation period, acute disease and persistent infection of syrian hamsters. Within the first three weeks post-infection the results of direct virus isolation and RNA detection in the brain agreed by a rate of 100%, the virus titre ranging between 10(1.9) to 10(10.5) LD50/ml and viral RNA concentration at 1-1000 pg. At the same time TBE virus RNA was detected in the spleen when the virus titre was greater than or equal to 10(6.5) LD50/ml. By 8 months post infection (p.i.) viral RNA was found in the brain, liver, and spleen in the absence of infectious TBE virus. No viral RNA was present in the thymus. In addition, electron microscopic findings in hamster brain confirmed the hypothesis that TBE virus persistence was accompanied by formation of virus-specific structures but impaired virion maturation.

Acute Disease↗
PubMed1994

Absence of FMR-1 gene expression can be detected with RNA extracted from dried blood specimens.

Fragile X syndrome is a genetic disorder caused by abnormal function of the FMR-1 gene. The majority of fragile X syndrome patients carry an expansion of the CGG tri-nucleotide repeat in the FMR-1 gene, whereas others have a deletion or a point mutation in the FMR-1 structural gene. In this report, we analyzed a typical family with three male patients. RNA from Epstein-Barr virus transformed lymphoblastoid cells was used for RNase protection assay and reverse transcription-polymerase chain reaction (RT-PCR) analysis. Five normal individuals and one asymptomatic heterozygote from this family expressed detectable FMR-1 transcripts, whereas three fragile X patients showed no sign of expression with either assay. To extend the application of this PCR-based assay to laboratory diagnosis of fragile X syndrome, we confirmed that dried blood samples collected on screening filter papers for newborns are an adequate source of RNA for RT-PCR. Moreover, fragile X patients from the study family and another family were reliably identified by the absence of the FMR-1-specific PCR product from the dried blood specimens. Our studies indicate that this simple assay can be used to diagnose the fragile X syndrome for the majority of male patients.

Base Sequence↗
PubMed1990

Serum hepatitis delta virus RNA in patients with delta hepatitis and in liver graft recipients.

We have investigated the usefulness of serum hepatitis delta virus (HDV) RNA detection using a slot hybridization analysis of serum samples from ten patients with acute hepatitis and delta markers (group I), from 28 patients with chronic delta hepatitis (group II) and from seven liver graft recipients with hepatitis B virus (HBV) and HDV related cirrhosis or fulminant hepatitis (group III). The slot-blots were hybridized with both HDV-complementary DNA and single-stranded RNA probes. With the single-stranded RNA probe, HDV RNA was detected in the first serum sample available in 9/10 of the patients with acute hepatitis (group I). In addition, HDV RNA was detected in 8/9 and 7/8 of the samples obtained within and after 1 month of the onset of hepatitis. Five of the ten patients scored positive for HDV RNA and negative for hepatitis delta antigen (HDAg) while one was negative for HDV RNA and positive for HDAg. The same RNA probe enabled the detection of serum HDV RNA in 21/28 chronic hepatitis patients (liver HDAg and/or IgM anti-HD positive) (group II). Among the liver graft recipients (group III), 7/7 had a recurrent delta infection. Serum HDAg, liver HDAg and anti-HD IgM were identified in 3/7, 6/7 and 5/7 of the patients, respectively. HDV RNA was detected in the seven patients with either persistent (4/7) or transient (3/7) positivity. In addition, HBsAg and HBV RNA were persistently shown in 4/7 patients with continuous HDV replication. In the remaining three patients, HDV RNA was detectable despite the absence of HBsAg.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed1982

A critical evaluation of Bernhard's EDTA regressive staining technique for RNA.

The EDTA regressive staining procedure to detect RNA (Bernhard's technique) is based on the proposition that after staining ultrathin sections with uranyl the stain is preferentially removed from DNA rather than RNA by the action of the chelating agent EDTA. Whilst attempting to use the EDTA regressive staining procedure to detect the presence of RNA in the large granule complexes of chicken erythrocyte nuclei, certain anomalous staining patterns were observed in the chromatin of these nuclei. Essentially, these were that the edges of condensed chromatin bodies stained positively for RNA even though this molecule is known not to be present there in significant quantities. The staining patterns suggested that chromatin was retaining its stain in a manner expected of RNA but not DNA as a consequence of EDTA-containing species failing to pass freely through the section. This hypothesis was tested by carrying out the EDTA procedure on embedded specimens of a DNA-containing virus, simian virus 40 (SV40), small enough not to be exposed at the surface of the section. In this way it has been shown that virus particles completely surrounded by resin destain so much more slowly than chromatin, which is accessible at the surface of the section, that without any other information it would be concluded that the viruses contained RNA, not DNA. This apparently anomalous result arises because the difficulties encountered by stain or EDTA molecules in passing through a plastic section were not appreciated at the time of the initial publication of the technique. The observations are discussed in the light of recent knowledge that has been gained on the kinetics of staining by measuring the electron-scattering densities of stained sections, similar measurements having been made on sections stained by Bernhard's technique. A model for the mechanism of the EDTA regressive staining technique consistent with the experimental observations is proposed and the conditions under which Bernhard's staining procedure retains its specificity are defined. Briefly, these conditions are that: (a) the sections be stained for only a short period with uranyl before treating them with EDTA even though such brief staining is undesirable for quantitative measurements of stain uptake into biological material; and (b) that sections stained in lead only be compared as controls with sections stained by Bernhard's technique so that any specificity of lead for sub-cellular components is not confused with a positive indication of the presence of RNA. Unless these conditions are fulfilled, results obtained by the use of the regressive staining technique may be highly misleading.

Animals↗
PubMed1993

Detection of hepatitis C virus RNA in peripheral blood mononuclear cells and in saliva.

The nested polymerase chain reaction (PCR) technique was applied to investigate hepatitis C virus (HCV) RNA in the peripheral blood mononuclear cells (PBMCs), saliva, and serum of patients with chronic type C hepatitis. The specificity of the amplified products was analyzed and confirmed by agarose gel electrophoresis, Southern blot hybridization, and restriction endonuclease pattern analysis. HCV RNA was detectable in the PBMCs of 24% (12/50) of the patients. The HCV RNA detected in PBMCs was not due to the contamination from plasma, since no viral sequences could be detected in the third washing of PBMCs. Of the 12 patients with HCV RNA in PBMCs, five were negative for HCV RNA sequences in the serum. Thus the presence of HCV RNA in PBMCs was not strictly correlated to the results for sera. Among 25 patients with HCV RNA in their saliva, 18 were negative for PBMCs. Among 25 patients without HCV RNA in their saliva, five had HCV RNA in PBMCs. In conclusion, PBMCs are an extrahepatic target for chronic HCV infection. However, we do not suggest that PBMCs act as a vehicle for carrying HCV to saliva, since the presence of HCV RNA in PBMCs and in saliva was not closely correlated.

Base Sequence↗
PubMed1988

Detection of enterovirus RNA in experimentally infected mice by molecular hybridisation: specificity of subgenomic probes in quantitative slot blot and in situ hybridisation.

Subgenomic cDNA clones representing defined regions of the genome of Coxsackie B3 virus were used as hybridisation probes to detect RNA of various enteroviruses in cell culture and mouse model systems. Radiolabelled probes were used in slot blots to quantitate the RNA in samples; biotinylated probes were used to localise virus RNA at the cellular level by in situ hybridisation with monolayers of infected cells or thin sections of tissue samples. Probes derived from the 5' or 3' terminal regions of Coxsackie virus RNA, which are highly conserved in the genus Enterovirus, detected RNA of various serotypes in infected cell cultures, but failed to hybridise with hepatitis A virus (HAV) RNA. Although HAV is clearly a Picornavirus, our data support the view that its taxonomic position within the enteroviruses should be reconsidered. The biotinylated probes were also used to detect in situ virus RNA in paraffin-embedded tissue samples from experimental mouse models of Coxsackie B3 virus-induced myocarditis or Coxsackie B1 virus-induced myositis. Since the integrity of the tissues was preserved during the process, and viral RNA was localised in the affected muscle fibres, this has enabled us unequivocally to relate the infecting virus to the underlying tissue injury.

Animals↗
PubMed1993

Hepatitis C virus infection and disease. Diagnostic problems.

Hepatitis C virus (HCV) is a lipid-enveloped single-stranded RNA virus with an unknown physical structure as only putative HCV particles have been identified by electron microscopy. Although HCV lacks the retroviral properties of being able to integrate into host DNA, it causes chronic infection in a considerable number of infected individuals (40-60%). Chronic infection is associated with a wide spectrum of liver diseases ranging from normal presentation to the different forms of chronic hepatitis, cirrhosis (about 20% of cases) and hepatocellular carcinoma. HCV therefore is not invariably and equally pathogenic, and genetic heterogeneity could be a major cause of such variability. Diagnosis of HCV infection relies on anti-HCV and HCV-RNA detection. Using second-generation assays, diagnostic sensitivity has increased to about 95%, but detection of anti-HCV does distinguish past from present infections. Only rising anti-HCV titres or anti-HCV seroconversion confirm a recent HCV infection. In anti-HCV-negative infections and cases of early acute hepatitis, HCV-RNA detection by RT-PCR represents a valid diagnostic alternative. In patients undergoing interferon therapy, testing for anti-HCV by immunoblotting represents a valid routine tool to monitor response. Anti-C-22 has the highest titre and persists longer while anti-C-100 is the earliest antibody to disappear in responders. The significant association between serum anti-C-100, HCV-RNA and liver disease suggests that anti-C-100 is an indirect marker of hepatitis C, but true markers of HCV-induced liver disease are still lacking.

Diagnosis, Differential↗
PubMed1999

Rapid and specific detection of RNA base sequence using fluorescence polarization.

Rapid and specific determination of the RNA gene of hepatitis C virus (HCV), which had been multiplied by NASBA, was performed using a fluorescence polarization assay. The polarization of the probe DNA in the presence of HCV positive sample, amplified by NASBA, was obviously different from those in the presence of negative control samples. The total time for the gene amplification and detection was about 90 min, while the polarization detection was completed within 10 min. The slight increase of polarization was also confirmed with the hybridization between probe oligo-DNA 25-mers and the synthesized complementary oligo-RNA 25-mers. The polarization of positive and negative samples showed excellent agreement with the results obtained from electrophoresis and dot-blot hybridization.

Base Sequence↗