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At least 595 records · Page 33Linked to original sources
PubMed2006

Differential roles of MDA5 and RIG-I helicases in the recognition of RNA viruses.

The innate immune system senses viral infection by recognizing a variety of viral components (including double-stranded (ds)RNA) and triggers antiviral responses. The cytoplasmic helicase proteins RIG-I (retinoic-acid-inducible protein I, also known as Ddx58) and MDA5 (melanoma-differentiation-associated gene 5, also known as Ifih1 or Helicard) have been implicated in viral dsRNA recognition. In vitro studies suggest that both RIG-I and MDA5 detect RNA viruses and polyinosine-polycytidylic acid (poly(I:C)), a synthetic dsRNA analogue. Although a critical role for RIG-I in the recognition of several RNA viruses has been clarified, the functional role of MDA5 and the relationship between these dsRNA detectors in vivo are yet to be determined. Here we use mice deficient in MDA5 (MDA5-/-) to show that MDA5 and RIG-I recognize different types of dsRNAs: MDA5 recognizes poly(I:C), and RIG-I detects in vitro transcribed dsRNAs. RNA viruses are also differentially recognized by RIG-I and MDA5. We find that RIG-I is essential for the production of interferons in response to RNA viruses including paramyxoviruses, influenza virus and Japanese encephalitis virus, whereas MDA5 is critical for picornavirus detection. Furthermore, RIG-I-/- and MDA5-/- mice are highly susceptible to infection with these respective RNA viruses compared to control mice. Together, our data show that RIG-I and MDA5 distinguish different RNA viruses and are critical for host antiviral responses.

Animals↗
PubMed2000

Assessment of decalcifying protocols for detection of specific RNA by non-radioactive in situ hybridization in calcified tissues.

For the best performance of in situ analysis of specific RNA expression in calcified tissues, it is necessary to choose an appropriate protocol to decalcify the tissues. We evaluated the usefulness of various acid-based decalcifying reagents with reference to 28 S rRNA staining by in situ hybridization using a thymine-thymine dimerized oligonucleotide probe. The reagents evaluated were 10% nitric acid, 10% HCl, 5% formic acid, 5% trichloroacetic acid, Morse's solution, Plank-Rychlo's solution, and K-CX solution, all of which are commonly used to decalcify tissues, and their effects on retention of morphology and RNA were compared with EDTA-based solutions. When normal mouse mandible was used as a model tissue, well-preserved morphology of ameloblasts was obtained from sections decalcified with Morse's solution, 10% HCl, Plank-Rychlo's solution, and K-CX solution, and best retention of 28 S rRNA was obtained with 5% formic acid and Morse's solution. We recommend Morse's solution to decalcify tissues to be processed for the rapid analysis of specific RNA expression. Indeed, we detected specific mRNAs strongly in sections treated with Morse's solution, and quantitative analysis showed that the ratio of signal intensities of 28 S rRNA and the specific mRNAs correlated with each other depending on decalcifying solutions.

Animals↗
PubMed1979

Ribonucleic acid in plasma from normal adults and multiple myeloma patients.

Reports of the presence of RNA in human plasma have been numerous, often suggesting that RNA in plasma is correlated with human disease. We critically examined the methods for determination of RNA in plasma. Lack of method specificity has caused previous workers to overestimate plasma RNA concentrations by more than 50-fold. To isolate RNA from plasma, we used both a phenol-chloroform extraction and a modified Schmidt-Thannhauser procedure. We show that RNA in plasma can be identified and quantified by alkaline hydrolysis of the plasma extract and subsequent separation of the resulting 2'- and 3'-mononucleotides by "high-performance" liquid chromatography. We could not detect RNA in plasma from either apparently healthy, normal adults or multiple myeloma patients, but found 1.1 mg/L in the plasma of a patient with Waldenström's macroglobulinemia. Our method is useful for the specific determination of RNA in plasma and will detect as little as 600 micrograms/L.

Chromatography, High Pressure Liquid↗
PubMed2005

Occurrence of hepatitis A virus genotype III in Germany requires the adaptation of commercially available diagnostic test systems.

BACKGROUND: A blood donation, obtained in 2003 in Germany during the preseroconversion diagnostic window period of a hepatitis A virus (HAV) infection, tested HAV-negative by commercially available HAV reverse transcription-polymerase chain reaction (RT-PCR) detection assays. STUDY DESIGN AND METHODS: The virus responsible for this infection was identified as HAV genotype IIIA by characterization of the nearly complete genome sequence. RESULTS: Thereby, this HAV variant, which was named strain HMH, was detected in Germany for the first time. Because the commercially available HAV RNA detection systems failed to detect this genotype, a real-time RT-PCR kit was developed that allows quantification and detection of all HAV genotypes. The first nearly full-length nucleotide sequence so far available for HAV genotype IIIA is also provided. CONCLUSION: This case demonstrates that owing to the genetic variability of HAV, constant monitoring and adaptation of the diagnostic nucleic acid assays are required to guarantee the safety of blood and blood products.

Alanine Transaminase↗
PubMed2001

Study of the infection of human blood derived monocyte/macrophages with hepatitis C virus in vitro.

Hepatitis C virus (HCV) is essentially hepatotropic, but clinical observations based on quasispecies composition in different compartments or on viral RNA detection in cells suggest that the virus is able to infect and persist in cells other than liver cells. It was shown previously that peripheral blood mononuclear cells (PBMCs) are permissive to HCV replication in vitro but at a very low rate. Since different viruses associated with chronic infections are known to persist in monocyte/macrophages, it is important to determine whether these mononuclear blood cells are susceptible preferentially to HCV. In order to study HCV interaction with monocytes/macrophages, these cells were isolated from the blood of healthy donors and incubated with HCV genotype 1b positive sera. The detection by RT-PCR of the positive- and negative-strand RNA in the cells at different times and the increase in the amount of intracellular viral RNA measured by the branched DNA assay suggest that monocyte/macrophages can support HCV RNA replication. The rate, however, is very low. The analysis of hypervariable region 1 (HVR-1) nucleotide sequences indicated that some minor variant present in the inoculum might display a specific tropism for the monocytes/macrophages. These results provide evidence that human monocytes/macrophages might represent a reservoir for HCV. This cell tropism may be a crucial factor in the pathogenesis of hepatitis C.

Base Sequence↗
PubMed1990

Organ-specific modulation of gene expression in transgenic plants using antisense RNA.

We have shown leaf-specific inhibition GUS gene expression in transgenic Nicotiana plants using an antisense RNA with a 41-base homology spanning the translation start codon of the gene. GUS was expressed from the nominally constitutive 35S promoter and the antisense RNA was expressed from the light-regulated ca/b promoter of Arabidopsis thaliana. A range of GUS inhibition from 0 to 100% was obtained by screening a small population of transgenic plants and the specific levels of inhibition observed were stably inherited in two generations. An antiGUS 'gene' dosage effect was observed in plants which were homozygous for antiGUS. RNA detection results suggest that duplex formation with the 41 base pair antiGUS RNA destabilized the GUS mRNA and that an excess of antisense RNA was not required. Our results demonstrate the potential of antisense RNA as a strategy for obtaining plant mutants, especially 'down mutations' in essential genes where only a short 5' sequence of the mRNA is required. They also suggest that the 'position effect' on gene expression could be used in conjunction with an antisense RNA strategy to provide a versatile approach for crop improvement.

Base Sequence↗
PubMed1993

Cloning and sequence analysis of the alpha subunit of the cat flea sodium pump.

We have cloned a cDNA that encodes the sodium pump alpha-subunit of the cat flea Ctenocephalides felis. The deduced amino acid sequence of 1037 residues is 90% homologous with the Drosophila alpha-subunit sequence and shows 75% similarity to the sheep kidney alpha-subunit. One characteristic unique to the insect polypeptides is an extended sequence at the N-terminus. Northern blot analysis of C. felis RNA detects two alpha-subunit transcripts with lengths of 3.8 and 4.4 kb. Sodium pump alpha-subunit sequences were readily detected in homogenates of flea midguts and in cDNA synthesized from midgut RNA.

Amino Acid Sequence↗
PubMed1972

Hybridization of Rous sarcoma virus deoxyribonucleic acid polymerase product and ribonucleic acids from chicken and rat cells infected with Rous sarcoma virus.

Rous sarcoma virus (RSV)-specific ribonucleic acid (RNA) in virus-producing chicken cells and non-virus-producing rat cells infected with RSV was studied by hybridization with the endogenous deoxyribonucleic acid (DNA) product of the RSV virion DNA polymerase system. By hybridizing the total DNA product with excess virion RNA, the product DNA was separated into hybridized ("minus") and nonhybridized ("plus") DNA. The "minus" DNA was complementary to at least 20% of the RNA from RSV which remained of high molecular weight after denaturation. A maximum of approximately 65% hybridization was observed between "minus" DNA and RSV RNA or RSV-infected chicken cell RNA. A maximum of about 60% hybridization was observed between "minus" DNA and RSV-infected rat cell RNA. RSV-infected chicken cells contained RSV-specific RNA equivalent to about 6,000 virions per cell. RSV-infected rat cells contained RSV-specific RNA equivalent to approximately 400 virions per cell. Neither cell type contained detectable RNA complementary to virion RNA. The RSV-specific RNA in RSV-infected rat cells did not appear to be qualitatively different from that in RSV-infected chicken cells.

Animals↗
PubMed1995

Chronic hepatitis C in alcoholic patients: prevalence, genotypes, and correlation to liver disease.

BACKGROUND: Only one-fifth of chronic alcoholic patients develop chronic liver disease in spite of continuous alcohol abuse. Hepatitis C has been proposed to be one of several suggested factors contributing to the development of liver disease. METHODS: In 201 consecutive chronic alcoholic patients admitted to the hospital for detoxification, antibodies to hepatitis C virus (HCV) were determined, using second-generation enzyme-linked immunosorbent assay (ELISA) and recombinant immunoblot assay (RIBA) tests. Sera from patients with antibodies were tested with polymerase chain reaction (PCR) to detect HCV RNA and subsequently genotyped. RESULTS: Twenty-nine patients (14%) were positive in the ELISA and RIBA tests. HCV RNA was detected in 23 of the 29 (79%); 21 could be genotyped. Previous intravenous drug abuse was present in 18 of 29 (58%) in the positive group versus 3 of 172 (2%) in the negative group (p < 0.001), whereas the prevalence of previous blood transfusions did not differ between the groups. In one-third of the positive cases no obvious route of transmission was found. On the basis of clinical and biochemical variables and, if available, histology, altogether 6 of 29 (21%) HCV-positive patients were classified as having severe liver disease as compared with 12 of 172 (7%) HCV-negative patients (p < 0.05). HCV-positive patients with liver disease were younger than HCV-negative patients with liver disease (p < 0.05). CONCLUSIONS: Hepatitis C virus infection is common among chronic alcoholic patients in Stockholm, especially among patients with a history of intravenous drug abuse. To confirm ongoing infection, detection of HCV RNA is necessary. This infection seems to be a factor contributing to the development of liver disease in alcoholic patients.

Adult↗
PubMed1983

[Neural apparatus of the heart in a cardiopulmonary conduit in an experiment].

In 20 dogs with a corrugated stenosis of the pulmonary trunk, the state of the intramural neural system has been studied by means of some histological techniques. For correction a by-pass cardio-pulmonary shunt has been used. Fifteen dogs have been used as controls, in 5 of them stenosis of the pulmonary trunk without correction has been induced, in 5--the right ventricular wall has been dissected and the heart wound has been saturated ; in 5--thoracotomy has been performed. Various parts of the cardiac wall have been investigated during the interval 2 hours--360 days. Changes in the cardiac intramural apparatuses at the time up to the 7th day can be considered as nonspecific in response to the surgical trauma. They are similarly manifested in all parts of the cardiac wall in the animals of all the groups studied. Subsequently, destructive changes of neurocytes are the most pronounced. The cells decrease in their size, the nuclei are not detected, RNA content is sharply decreased. When stained after Nissl, "ghost-cells" are seen. Thick neural fibers undergo fragmentation and granular decay. The receptors are subjected to the most sharp changes. These processes are most pronounced up to the 30th day. Further (when stenosis of the pulmonary trunk is corrected with the conduit), restorative processes prevail. In the bodies of neurocytes pironinophilia increases, RNA content rises, young receptors with soft weakly argerophile fibrillae are often detected. Thus, up to 4-6 months the state of the intramural neural apparatuses approaches the normal state. The results of the investigation performed make it possible to conclude that the correction method for the pulmonary trunk stenosis is effective. Owing to this method it is possible to avoid destructive changes that progressively develop in animals with a noncorregated stenosis of the pulmonary trunk.

Animals↗
PubMed1993

Molecular cloning and sequence of a novel ommochrome-binding protein cDNA from an insect, Manduca sexta.

An ommochrome-binding protein (OBP) from the hemolymph of Manduca sexta has recently been purified and characterized. A cDNA clone was isolated from a fifth instar larval cDNA expression library utilizing antiserum against OBP. Northern blot analysis of total fat body RNA detected a transcript of approximately 1.2 kilobases in fifth instar wandering larvae RNA. The complete nucleotide sequence of the 905-base pair cDNA insert was determined by the dideoxy chain termination method. The OBP cDNA encodes a polypeptide of 274 residues with a predicted molecular weight of 30,580 and with one consensus N-linked glycosylation site. Comparison of the NH2-terminal sequence of the mature protein and the cDNA sequence revealed a typical signal peptide of 18 amino acids. In wandering stage larvae, the OBP transcript appeared to be at least 250-fold less abundant than ribosomal RNA.

Amino Acid Sequence↗
PubMed1998

Measles virus RNA is not detected in inflammatory bowel disease using hybrid capture and reverse transcription followed by the polymerase chain reaction.

Recent epidemiological and immunohistochemical studies have indicated a possible link between measles virus and inflammatory bowel disease (IBD). The aim of this study was to use a sensitive and robust method for the detection of measles virus RNA in IBD and control clinical samples. Peripheral blood mononuclear cells and intestinal resection tissue from IBD and control patients were studied. Two methods were used to determine the presence of measles virus RNA: hybrid capture, using measles virus-specific oligonucleotides linked to paramagnetic solid-phase supports, was carried out on total cellular RNA to enrich for measles virus RNA sequences. Reverse transcription followed by the polymerase chain reaction (RT-PCR) using rTth DNA polymerase was employed for amplification of measles virus N-gene sequences amongst the enriched species. Total RNA was also used for RT-PCR of a housekeeping mRNA species to assess RNA quality. RT-PCR for another region of the measles genome (the haemagglutinin (H) gene) was also undertaken in order to confirm the results obtained using N-gene primers for analysis of these samples. None of the samples were positive for measles N- or H-gene RNA using RT-PCR. Positive control samples confirmed the sensitivity of the methods employed. These results show that either measles virus RNA was not present in the samples, or was present below the sensitivity limits known to have been achieved.

Adolescent↗
PubMed2002

Development and evaluation of a nucleic acid sequence based amplification (NASBA) protocol for the detection of enterovirus RNA in cerebrospinal fluid samples.

A nucleic acid sequence based (NASBA) assay for the generic detection of enterovirus RNA in cerebrospinal fluid (CSF) samples was developed and compared with an established reverse transcription/nested polymerase chain reaction (PCR) protocol. The sensitivity of NASBA followed by detection of amplicons with a biotinylated oligonucleotide probe was < or = ten copies of enterovirus RNA, indicating that enterovirus NASBA achieves a similar sensitivity as nested PCR. Moreover, NASBA detected a panel of 22 different serotypes of the species poliovirus, human enterovirus A, human enterovirus B and human enterovirus C completely. For evaluating NASBA as a diagnostic tool, 61 CSF samples of patients suffering from aseptic meningitis were tested in parallel with NASBA and nested PCR. NASBA detected enterovirus RNA in four CSF samples, two of these were also positive by nested PCR and two other CSF samples were positive only by nested PCR (in total six positive samples). All other 55 of 61 CSF samples were concordantly enterovirus negative by both methods. In conclusion, the more simple to handle 'one step' NASBA is as sensitive as nested PCR and may be used as an alternative method for the detection of enterovirus RNA in CSF samples. Enterovirus NASBA is a 'one step' RNA amplification procedure that is less prone to cross-contamination compared to a three step nested PCR.

Base Sequence↗
PubMed2002

Development of a chemiluminescence-based ribonuclease protection assay.

The ribonuclease protection assay (RPA) is a widely used method for the detection and quantification of specific mRNA transcripts in a complex mixture of total RNA or mRNA molecules. While exhibiting many advantages over other RNA detection methods, RPAs are traditionally performed using radiolabeled probes that often require gel purification steps and lengthy exposure times to visualize results. Moreover, these probes can only be used for 1-2 weeks because of their short isotopic half-life and radiolysis. We report a method that improves the traditional RPA by replacing radiolabeled probes with biotinylated probes and lengthy exposure times with quick, streptavidin/HRP-based chemiluminescent detection technology. Biotinylated probes can be used without get purification and are stable for years, as opposed to weeks. Most importantly, our streptavidin/HRP-based chemiluminescent technology enables us to achieve sensitivity results similar to radioactive RPAs and to detect multiple transcripts in a single sample more efficiently. Furthermore, this new protocol addresses and eliminates the one major drawback unique to using biotinylated probes in chemiluminescent RPAs: a confounding artifact, not seen when running radioactive RPAs but commonly detected when using certain biotinylated rare message probes.

Actins↗
PubMed1992

Detection of hepatitis C virus RNA by in situ hybridization.

Persistent infection with hepatitis C virus (HCV) is associated with chronic hepatitis and cirrhosis which may eventually develop into primary hepatocellular carcinoma. The mechanism of pathogenesis is ill-defined and nothing is known of the distribution, frequency or type of infected cell in the liver of HCV-infected individuals. In this study we have examined liver tissue taken at autopsy from 2 anti-HCV-positive patients by in situ hybridization for the presence of HCV RNA. Viral RNA was detected by autoradiography after hybridization with 125I-labelled riboprobes, representing approximately 35% of the HCV genome. Only a few positive cells were identified in the HCV-infected liver samples, but not in a normal liver sample. Hybridization with an unrelated probe was negative in all samples. The HCV RNA-positive cells were detected with anti-sense but not sense RNA probes, suggesting that they contained a high ratio of genomic:antigenomic RNA. The appearance and distribution of the HCV RNA-positive cells suggested that they were not hepatocytes and were more likely to be lymphocytes or macrophages.

Autoradiography↗
PubMed1991

Ultrasensitive chemiluminescent and colorigenic detection of DNA, RNA, and proteins in plant molecular biology.

Nonradioactive detection methods for DNA, RNA, and protein analysis have been the subject of research for several years. In this paper the application of the digoxigenin nucleic acid labeling system, in combination with the new alkaline phosphatase substrate 3-(2'-spiroadamantane)-4-methoxy-4-(3"-phosphoryloxy)-phenyl -1,2-dioxetane, to the special requirements of the analysis of transgenic plants is described. Earlier detection systems lacked the required ultrasensitive limits of detection necessary because of the large genomes found in plant cells. Routine detection of single-copy genes from transgenic plant species requires the detection of bands of picograms of specific DNA, which is easily achieved by employing the AMPPD substrate. Optimal conditions of genomic Southern analysis have been successfully adapted for Northern blotting techniques. Detection of foreign proteins in transgenic plants has proven difficult because of the very small amounts of detectable specific protein. Until now, utilization of biotinylated antibodies in combination with a streptavidin-alkaline phosphatase conjugate has been the most sensitive procedure. By introducing the AMPPD substrate, a further significant enhancement of sensitivity leading to detectable signals in the picogram range can be obtained.

Adamantane↗
PubMed1998

Rapid detection of enteroviral RNA in cerebrospinal fluid (CSF) from patients with aseptic meningitis by reverse transcription-nested polymerase chain reaction.

The aim of this study was to compare conventional enterovirus isolation with rapid detection of enteroviral RNA by a reverse transcription-nested polymerase chain reaction (RT-nPCR) method amplifying the 5' nontranslated region of the enteroviral genome in specimens from patients with aseptic meningitis. Reference enterovirus strains and clinical enterovirus isolates were analyzed to evaluate assay sensitivity and specificity. All known enteroviral serotypes tested, but one (echovirus type 22), were detected by RT-nPCR. A series of unrelated viral isolates as well as CSF samples from patients with meningitis/encephalitis or neurological syndromes unrelated to enterovirus infection were included as controls. A total of 47 specimens (31 CSF, 12 rectal swabs, 4 throat swabs) from 30 patients with aseptic meningitis were available for the study. Of the 31 CSF samples tested from 30 patients, 17 from 17 patients (54.8%) were positive by RT-nPCR, while only 10 from 10 patients (32.2%) were positive by culture. Thus, RT-nPCR allowed diagnosis of enterovirus meningitis in 7 additional patients compared to cell culture. The cytopathic effect was observed 5-15 days after inoculation of CSF specimens onto cell cultures, while direct detection of viral RNA in CSF samples by RT-nPCR permitted diagnosis of enteroviral meningitis within 1-2 days. On the whole, viral isolation was positive in 12/47 (25.5%) specimens, whereas viral RNA was detected by RT-nPCR in 11 additional samples (23/47, 48.9%). Specimens of the control group were consistently negative by both viral isolation and RT-nPCR. Restriction endonuclease analysis of PCR products (RFLP) was applied to differentiate poliovirus (PV) from non-polio enteroviruses (NPEV). All enterovirus strains detected in clinical samples (n = 23) were identified as NPEV by RFLP. Clinical isolates were typed by neutralization as echovirus type 30 (n = 6), while 6 were not typed. In conclusion, detection of enteroviral RNA in CSF by RT-nPCR allows: i) rapid diagnosis of enteroviral meningitis; ii) increased sensitivity with respect to virus isolation; iii) differentiation between PV and NPEV infections of the central nervous system.

Adolescent↗
PubMed2003

[An inter-laboratory study of anti-HCV antibody detection in saliva samples].

AIM: The purpose of this study was to evaluate the efficacy of anti-hepatitis C virus (HCV) antibody detection in the saliva samples of 108 drug users in an inter-laboratory study. METHODS: Between January and June 2001, 108 subjects in Lille, Metz and Lens received a test to detect anti-HCV antibodies in their saliva. Two consecutive saliva samples were taken in each subject (Salivette system, Sarstedt). An HCV serology (Axsym HCV 3.0, Abbott) was also performed and serum HCV RNA detection by Amplicor HCV 2.0 (Roche) was performed when HCV serology was positive. Sixty three patients had a negative HCV serology, 45 had a positive HCV serology, and 31 of these had positive HCV RNA as well. Tests for the detection of the anti HCV antibody in saliva samples were performed as a blind study in both the Lille and the Thionville laboratories. RESULTS: The sensitivity of saliva anti-HCV antibody tests was respectively 71% (32/45) and 78% (35/45) in Lille and Thionville. In the event of positive HCV viremia, the sensitivity was respectively 90% (28/31) and 93% (29/31). The specificity was respectively 97% (61/63) and 98.5% (62/63). Results from the two laboratories agreed for 101 saliva tests while discrepancies were found in 7 (Kappa Concordance Coefficient: 0.85). CONCLUSIONS: This study confirms, in a large, unselected population sample, that anti-HCV antibody detection tests in saliva allow the detection of 90% of viremic HCV-antibody-positive patients with excellent specificity. The simplicity and reproductibility of this technique makes it a precious tool for epidemiological studies.

Hepatitis C Antibodies↗