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At least 235 records · Page 13Linked to original sources
PubMed1999

Reverse transcription-nested polymerase chain reaction for detecting p40 RNA of Borna disease virus, without risk of plasmid contamination.

Several methods for the detection of Borna disease virus (BDV) RNA have been reported, one being the reverse transcription-nested polymerase chain reaction (RT-nested PCR) method. However, due to the possibility of contamination of the cloned DNA in a reaction tube, false-positive results might be obtained by RT-nested PCR. To detect only BDV RNA without anxiety of contamination, we developed an RT-nested PCR system using "mRNA selective PCR kit". Using this system, cDNA of BDV p40 in the plasmid (up to 5 x 10(7) molecules) was not amplified. BDV specific sequence was amplified from total RNA (more than 50 pg) of MDCK/BDV cells, which were persistently infected with BDV. These results indicate that this mRNA selective RT-nested PCR system can specifically amplify target RNA as distinguished from plasmid contaminated.

Animals↗
PubMed1995

Two different PCR assays to detect enteroviral RNA in CSF samples from patients with acute aseptic meningitis.

Two polymerase chain reaction (RT-PCR) assays were developed to allow rapid detection of enteroviral RNA in cerebrospinal fluid samples (CSF). Primers homologous to the conserved 5' noncoding region of the enterovirus genome were designed. The RT-PCR product size was approximately 500 bp (479 bp for Poliovirus, 500 bp for Coxsackievirus) and was visualized using ethidium bromide-stained gels. Assay 1 utilized Moloney Murine Leukaemia Virus Reverse Transcriptase (MMLV-RTase) for reverse transcription and Taq polymerase for subsequent PCR. Assay 2 utilized a thermoactive DNA polymerase of Thermus thermophilus (rTth enzyme) for both reverse transcription and DNA amplification. In addition, in Assay 2 reverse transcription and PCR were accomplished within the same reaction tube. Both assays detected between 1 and 0.02 TCID50 of prototype strains of Polio and Coxsackie type B viruses propagated in VERO cell and spiked in a pooled preparation of CSF samples from patients with noninfective neurological disorders. However, Assay 1 was 10-fold more sensitive than Assay 2 when applied to the detection of enteroviral RNA in CSF samples from patients with etiologically well characterized acute aseptic meningitis.

Acute Disease↗
PubMed2005

Quenched probes for highly specific detection of cellular RNAs.

Nucleic acid-based RNA detection is a promising field in molecular biotechnology that is leading to the rapid and accurate identification of microorganisms, diagnosis of infections and imaging of gene expression. The specificity of short synthetic DNA probes raises the hope of distinguishing small differences in sequence, ultimately achieving single nucleotide resolution. Recent work using quenched fluorescently labeled oligonucleotide probes as sensors for RNA in bacterial and human cells has overcome several difficult hurdles on the way to these goals, including delivery of probes to live cells, accessing RNA sites containing a high degree of secondary structure, and eliminating many sources of background. Two new classes of quenched oligonucleotide probes, molecular beacons and quenched auto-ligation probes, have shown the most promise for in situ RNA detection. High-specificity detection, at the single-nucleotide resolution level, is now possible in solution with these classes of probes. However, for applications in intact cells, signal and background issues still need to be addressed before the full potential of these methods is achieved.

Animals↗
PubMed2025

MapID-based quantitative mapping of chemical modifications and expression of human transfer RNA.

Detection and quantification of tRNA chemical modifications are critical for understanding their regulatory functions in biology and diseases. However, tRNA-seq-based methods for modification mapping encountered challenges both experimentally (poor processivity of heavily modified tRNAs during reverse transcription or RT) and bioinformatically (frequent reads misalignment to highly similar tRNA genes). Here, we report "MapID-tRNA-seq" where we deployed an evolved reverse transcriptase (RT-1306) into tRNA-seq and developed "MapIDs" that reduce redundancy of the human tRNA genome and explicitly annotate genetic variances. RT-1306 generated robust mutations against m1A and m3C, and RT stops against multiple bulky roadblock modifications. MapID-assisted data processing enabled systematic exclusion of false-positive discoveries of modifications which arise from reads misalignment onto similar genes. We applied MapID-tRNA-seq into mapping m1A, m3C and expression levels of tRNAs in three mammary cell lines, which revealed cell-type dependent modification sites and potential translational regulation of the reduced mitochondrial activities in breast cancer.

Humans↗
PubMed1990

[Features of mutated changes of genomic RNA of cold-adapted and hr-variants of influenza group A virus, detected by RNA:RNA hybridization].

The presence of mutations in the majority of the genes of cold-adapted strains A/Leningrad/134/17/57 (H2N2), A/Leningrad/134/47/57 (H2N2) and A/PR/8/59/1 (H1N1) of influenza A virus has been demonstrated by the RNA-RNA hybridization with the subsequent electrophoresis of double-stranded RNA in 7.5% polyacrylamide gel. The strains were cultivated 17, 47 and 59 passages in the chicken embryos at 25 degrees C. In the genomes of variants passaged in chicken embryos at optimal temperature of incubation 36 degrees C (hr-variants) the used technique permits identification of a single mutant gene. The obtained data suppose the attenuation of cold-adapted vaccine strains of influenza A virus and their high genetic stability to be a result of selection of the variants obtaining multiple mutations in the genome during passaging of the virions at cold temperature. The attenuation of hr-variants is defined by 1-2 mutations (first of all in HA-gene) that makes understandable their inability to serve as donors for recombinant live influenza vaccines construction.

Antigens, Viral↗
PubMed1998

Coxsackie B virus infection and beta cell autoantibodies in newly diagnosed IDDM adult patients.

BACKGROUND: Environmental agents such as viruses have been identified as potentially important determinants of insulin-dependent diabetes mellitus (IDDM). Enterovirus infections, Coxsackievirus B especially, could be linked to the beta cell damaging process and to the onset of clinical IDDM. OBJECTIVES: Enteroviral (EV) infection and beta cell autoimmunity were studied in adult patients at the onset of IDDM. STUDY DESIGN: A total of 14 newly diagnosed-IDDM patients with ketosis or ketoacidosis were compared to, anteriorly diagnosed IDDM patients with metabolic decompensation, non-IDDM patients with metabolic decompensation and healthy adults. EV infection was studied by genomic RNA detection in whole blood using a RT-PCR assay. In order to assess the level of beta cell autoantibodies at the time of the initial metabolic decompensation, serum specimens from IDDM patients were tested for GAD65 antibodies and islet cell antibodies (ICAs). RESULTS: Coxsackie B3 or B4 virus genome was detected and genotyped in five of 14 (35.7) newly diagnosed IDDM patients and in one of 12 (8%) patients in the course of IDDM. By contrast, none of the 12 non-IDDM patients and none of the 15 healthy adults was positive for enterovirus RNA detection in whole blood. Positive GAD65 antibodies and ICAs assays were not significantly correlated to a positive EV-RNA detection. CONCLUSION: The present study demonstrates that Coxsackie B virus RNA sequences can be detected in the peripheral blood from adult patients at the onset or in the course of IDDM and suggests that a Coxsackie B virus infection could initiate or accelerate beta cell autoimmune damaging process.

Adult↗
PubMed1997

Effective detection of active HCV infection: HCV RNA carrier state in a context free of hepatitis symptoms.

HCV immunological assays have limited specificity due to considerable variability of genomic coding sequences. Accordingly, PCR RNA detection also shows variable incidence of HCV in a non-A, non-B (NANB) hepatitis context. We used in-house designed nested PCR applying primers from the 5' untranslated region in 150 thalassemic patients classified in four groups according to anti-HCV screening and glutamic-pyruvate transaminase (GPT) levels. Group A: anti-HCV+/high GPT levels; group B: anti-HCV+/normal GPT levels; group C: anti-HCV(-)+high GPT levels; group D: anti-HCV(-)+normal GPT levels. Viral incidence and concentration, both high in group A, decreased towards group D. Group C RNA incidence was unexpectedly high and, moreover, one control case proved HCV-RNA+. Compared with the Amplicor kit or primers were considerably more sensitive.

Adolescent↗
PubMed2004

Transmission of enterotropic mouse hepatitis virus from immunocompetent and immunodeficient mice.

Mouse hepatitis virus (MHV) is the most prevalent virus that infects mice, and most MHV strains are enterotropic. Experiments were performed to elucidate the duration of enterotropic MHV-Y shedding by immunocompetent BALB/ c and C57BL/6 mice and immunocompromised B and T cell-deficient mice. Although the use of molecular diagnostics to detect MHV infection is increasing, it is unclear whether the viral RNA detected is always infectious. The ability to detect MHV-Y transmission to sentinel mice exposed directly to infected mice or to soil bedding from infected mice was compared with reverse transcriptase-polymerase chain reaction-based detection of viral RNA in the feces. The BALB/c mice developed subclinical intestinal infection, and transmitted MHV-Y for four weeks. The C57BL/6 mice also developed subclinical intestinal infection, but only transmitted virus for two weeks. The T cell-deficient mice developed severe disseminated disease by two weeks and transmitted virus for four weeks. The B cell-deficient mice developed subclinical intestinal infection and transmitted virus for longer than three months, although virus RNA was not detected in feces late in the infection. Viral RNA detected in the feces of infected mice was almost always infectious. Non-infectious RNA was detected in a few mice for several days after transmission had ceased. In addition, constant exposure of naive mice to infected mice, via the use of serial sentinels, prolonged viral transmission.

Animals↗
PubMed2005

Simultaneous in situ detection of RNA, DNA, and protein using tyramide-coupled immunofluorescence.

The use of tyramide-coupled immunofluorescence at the single cell level provides expedient, clean, and sensitive signals for detection of DNA, RNA, or proteins. The principle is based on the ability of horseradish peroxidase (HRP) to cleave tyramides into a free radical species with a very short diffusion radius. The free radicals are then covalently bound to electron-rich moieties such as tyrosine in proteins proximal to the targets. Here we present protocols for tyramide fluorescent in situ hybridization (T-FISH), which detects unique DNA species using DNA probes as short as approx 300-500 bp, or unique RNA species with probes as small as an oligonucleotide. We also present a protocol for tyramide immunofluorescence (T-IF) to detect protein antigens. By combining these protocols with several tyramide-coupled fluorophores, multiple targets can be detected simultaneously in situ, which is ideal for in-depth analyses at the molecular and cellular levels. Finally, we describe the detection of nascent viral RNA transcripts simultaneously with integrated viral genomes or chromosomal domains in single cells or tissue sections.

Clinical Laboratory Techniques↗
PubMed1994

The duration of fixation influences the yield of HCV cDNA-PCR products from formalin-fixed, paraffin-embedded liver tissue.

The extent of hepatitis C virus (HCV) RNA loss during increasing periods of fixation of liver tissue in formalin was examined. For this purpose human liver tissue, known to be HCV RNA positive and stored at -70 degrees C until use, was cut into small slices (n = 9), which were fixed in phosphate-buffered formalin for increasing periods of time before embedding in paraffin. Nucleic acids were extracted from each slice of formalin-fixed, paraffin-embedded liver tissue and HCV RNA loss during fixation was semi-quantified by testing 10-fold dilutions of each extract in an HCV cDNA-PCR assay. The endpoint dilution for HCV RNA detection by cDNA-PCR in liver slices fixed in buffered formalin for 8-24 h was comparable to the endpoint dilutions found for 'fresh', non-fixed liver slices. After fixation for 2-3 days the endpoint dilution for HCV RNA detection was 10(2) to 10(3)-fold less. After 2-4 weeks of formalin-fixation, HCV RNA was detectable from undiluted nucleic acid extracts only. It is concluded that formalin-fixed, paraffin-embedded liver biopsies can be used for HCV RNA detection by cDNA-PCR, on condition that the liver tissue has been embedded in paraffin within 24 h of formalin-fixation.

Biopsy↗
PubMed1979

Changes in the activity of RNA polymerase detected in situ and the intensity of 3H uridine incorporation into the nucleolus and the nucleus of interphase cells in antheridial filaments of Chara vulgaris L.

Analogously as in the 32-cell stage [20], in the 4-, and 8-cell generations of antheridial filaments of Chara vulgaris, the activity of DNA dependent RNA polymerase detected in situ as well as the 3H uridine incorporation increase in the middle S phase and in the middle G2 phase, while they decrease considerably at the end of S phase and in late G2 phase. The diphasic changes occur both in the nucleolar and extranucleolar (nucleoplasmic) activity of RNA polymerase as well as in the 3H uridine incorporation. However, the maximum nucleolar activity, in both S and G2 phases, precedes the peak of nucleoplasmic activity. During the increased nucleolar activity RNA polymerase (as calculated per nucleus) shows a higher level as compared with nucleoplasmic RNA polymerase, whereas the intensity of 3H uridine incorporation into nucleous and nucleoplasm is similar. It may be supposed that the incubation environment containing Mg2+ used in vitro is more stimulating for the nucleolar RNA polymerase than for the nucleoplasmic RNA polymerase. The mean transcriptional activity of the nucleus and the activity of RNA polymerase in the 8-cell generation is about 20% lower than in the 4-cell generation, in proportion to the decrease in cell sizes.

Cell Cycle↗
PubMed1995

Hepatitis C genotypes in liver transplant recipients: distribution and 1-year follow-up.

Chronic hepatitis C infection (CH-C) accounts for a significant number of patients undergoing orthotopic liver transplantation (OLT). Recently, hepatitis C virus (HCV) genotype-dependent differences in disease outcome and therapeutic responses have been suggested. The objectives of our study were to determine (1) the recurrence of HCV infection after OLT; (2) distribution of HCV genotypes in patients with CH-C who required liver transplantation compared with those who did not; and (3) the 1-year transplantation outcome in patients infected with different hepatitis C genotypes. RNA was extracted from sera of 20 patients who underwent OLT for end-stage liver disease secondary to CH-C (group I) and 52 patients with CH-C who did not require OLT (group II). For viral RNA detection, reverse transcriptase and polymerase chain reaction (RT/PCR) of 5'UT region was performed on all OLT patients both before and after OLT. For genotyping, RT-PCR of the NS 5 region was performed, followed by automated sequencing of the amplification products. Nineteen OLT patients had viral RNA detected by PCR both before and after OLT. One patient had no RNA detected before OLT but became viremic after OLT. The prevalence of HCV genotype 1b was significantly higher in group I patients compared with group II (53% v 23% respectively, P = .01). Examination of outcome at 1 year after OLT showed that 9 of 10 patients with HCV genotype 1b had histological evidence of hepatitis compared with 4 of 9 patients with other genotypes (non-1b) (P = .06). However, the number of patients who had one or more episodes of rejection, underwent retransplantation, or died at 1 year after OLT were similar. Recurrence of HCV infection after OLT was shown in all studied patients. Hepatitis C genotype 1b is more prevalent in our patients who underwent transplantation compared with a group with chronic hepatitis C who did not require transplantation (P = .01). Patients infected with HCV genotype 1b may have a higher risk of histological hepatitis after transplantation.

DNA Primers↗
PubMed1984

A rapid screening assay for detecting individual RNA species in field isolates of rotaviruses.

A method is described that allows the rapid screening of field isolates of rotavirus for the detection of specific viral RNA segments. Cloned cDNA copies of viral genomic RNAs are employed for detection in the assay which makes use of the dot-hybridization technique of Thomas (1980). The assay developed was shown to be sufficiently sensitive and specific to allow the genetic composition of virions to be determined over a wide range of concentrations. The feasibility of using the method developed for both the analysis of genetic reassortants prepared in vitro and for screening field isolates to detect putative genome reassortment events is demonstrated.

DNA, Recombinant↗
PubMed2005

Diagnostic cues for natural killer cell lymphoma: primary nodal presentation and the role of in situ hybridisation for Epstein-Barr virus encoded early small RNA in detecting occult bone marrow involvement.

Natural killer (NK) cell lymphomas are rare, and atypical features might lead to diagnostic pitfalls. This report describes an unusual patient in whom lymphoma occurred initially as isolated lymph node involvement, an exceptional presentation of an almost exclusively extranodal disease. Furthermore, during the terminal haemophagocytosis in the bone marrow, lymphoma cells lost the expression of the NK cell marker, CD56, making the histopathological diagnosis of bone marrow involvement difficult. This was resolved by in situ hybridisation for Epstein-Barr virus encoded small RNA, which detected occult bone marrow infiltration.

Bone Marrow Neoplasms↗
PubMed1982

Detection of RNA complementary to herpes-simplex virus in mononuclear cells from patients with Behçet's syndrome and recurrent oral ulcers.

Viral DNA probes were used in in-situ hybridisation to detect the complementary RNA in mononuclear cells from the blood of normal subjects and patients with Behçet's syndrome and recurrent oral ulcers. Hybridisation of 125I-labelled DNA probes was detected by means of autoradiography and quantitated with a video image-analysis technique. Hybridisation between herpes-simplex virus type 1 (HSV-1) DNA and the complementary RNA in mononuclear cells was significantly greater in 10 of 20 patients with Behçet's syndrome than in controls. Consistently, mononuclear cells from fewer patients showed significant hybridisation with the HSV-2 probe, and the grain counts were also lower. Control DNA probes from adenovirus 2, bacteriophage lambda, and Micrococcus lysodeikticus did not show significant hybridisation. Further separation of the patients into the four types of Behçet's syndrome revealed that mononuclear cells in 8 of 10 patients with the ocular or arthritic types showed significant hybridisation of RNA to the HSV-1 DNA probe, compared with 2 of 10 patients with the mucocutaneous or neurological types. Mononuclear cells from 4 of 8 patients with minor but not major aphthous ulcers also showed significant RNA hybridisation to HSV-1 DNA. The results suggest that at least part of the HSV genome is present and transcribed in peripheral-blood mononuclear cells--probably lymphocytes--of patients with the ocular and arthritic types of Behçet's syndrome and minor aphthous ulcers. The immunopathogenesis of these diseases might therefore be associated with HSV-1.

Behcet Syndrome↗
PubMed2006

Hybridisation of F+ RNA coliphages detected in shellfish samples with oligonucleotide probes to assess the origin of microbiological pollution of shellfish.

Current measures for controlling the public health risks associated with bivalve molluscan shellfish consumption rely on the use of Escherichia coli to indicate the sanitary quality of shellfish harvesting areas. However, it has been demonstrated that E. coli is an inadequate indicator of the viral risk associated with shellfish. An alternative indicator, male-specific B+ coliphages, have been investigated as viral indicators of faecal contamination that may provide source-specific information for impacted environmental waters. This study compared the distribution of E. coli and F+ RNA bacteriophages in shellfish grown in harvesting areas of Greece and also examined the presence and proportions of the different subgroups of F+ RNA coliphages in shellfish. F+ RNA bacteriophages were present in shellfish at higher concentrations than E. coli. Elevated numbers of F+ RNA bacteriophages observed in the winter concur with the known increased viral risk associated with shellfish harvested at that time of year in Greece. The majority of F+ RNA coliphages detected in shellfish samples belonged to group IV which indicated the possible presence of animal faecal material in sample harvesting areas. Phages of groups II and III (human waste and human faecal material, respectively) were present at low levels. Finally, 8% of the phages hybridised were found to belong to group I. The presence of group IV showed seasonal distribution (more in winter, less in summer) whereas the other groups did not show any difference. Monitoring of F+ coliphage subgroups may indicate the presence and major sources of microbial inputs to surface waters; however, environmental effects on the relative occurrence of different groups need to be considered.

Animals↗
PubMed1996

A tri-hybrid system for the analysis and detection of RNA--protein interactions.

A modification of the two-hybrid system is described for the in vivo reconstruction of specific RNA-protein interactions. In this tri-hybrid system, the DNA binding and transcription activation domains of the yeast transcriptional activator GAL4 are brought together via the interaction of recombinant fusion proteins with a recombinant RNA. The method provides a system for studying RNA-protein interactions with the genetic advantages of the two-hybrid system. It may be used to detect specific RNA-binding proteins or target RNAs from a library of cDNAs, or to analyse the structural specificity of identified RNA-protein interactions.

Binding Sites↗