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At least 559 records · Page 31Linked to original sources
PubMed2006

Detection of hepatitis C virus (HCV) RNA in the liver of healthy, anti-HCV antibody-positive, serum HCV RNA-negative patients with normal alanine aminotransferase levels.

BACKGROUND: It is unknown whether hepatitis C virus (HCV) is present in the liver of anti-HCV antibody-positive patients with persistently normal alanine aminotransferase (ALT) levels and undetectable serum HCV RNA levels. METHODS: We determined the presence of genomic and antigenomic HCV RNA strands in liver biopsy specimens and peripheral blood mononuclear cell (PBMC) samples obtained from 12 anti-HCV antibody-positive patients who had normal ALT levels and who had been serum HCV RNA negative for at least 12 months, according to the results of quantitative, strand-specific, real-time reverse-transcription-polymerase chain reaction and, also, in situ hybridization of liver cells. Intrahepatic HCV RNA was cloned and sequenced. RESULTS: All patients remained anti-HCV antibody positive and serum HCV RNA negative, and all had normal ALT values during follow-up (mean duration +/- SD, 29.2 +/- 19.8 months). Genomic HCV RNA was detected in liver biopsy specimens obtained from 10 (83%) of 12 patients, and the antigenomic strand was detected in 10 (100%) of 10 liver biopsy specimens in which genomic HCV RNA was detected. Results were confirmed by in situ hybridization. Intrahepatic HCV was of genotype 1b, and HCV sequencing demonstrated no cross-contamination among samples. Genomic HCV RNA was found in 6 (50%) of 12 PBMC samples, and antigenomic HCV RNA was also detected in 5 (83%) of these 6 PBMC samples. CONCLUSION: HCV may persist and replicate in the liver and PBMCs of healthy, anti-HCV antibody-positive, serum HCV RNA-negative patients who have persistently normal ALT levels. These patients should be followed up, because they have an ongoing viral infection.

Adult↗
PubMed1991

Detection and quantification of human immunodeficiency virus RNA in patient serum by use of the polymerase chain reaction.

Human immunodeficiency virus (HIV) RNA was detected and quantified in the serum of HIV-seropositive individuals using the polymerase chain reaction (PCR) and a nonisotopic enzyme-linked affinity assay. Of 55 HIV-infected patients who were not receiving therapy, serum HIV RNA was detected in 9 of 19 who were asymptomatic, 11 of 16 with AIDS-related complex (ARC), and 18 of 20 with AIDS, with copy numbers ranging from 10(2) to greater than or equal to 5 x 10(4) 200 microliters of serum based on a relationship between absorbance and known copy number of gag gene RNA. Linear regression analysis demonstrated a correlation between infectious titer in 42 patient sera cocultured with donor peripheral blood mononuclear cells (PBMC) and PCR product absorbance (r = .70, P less than .01). Serum HIV RNA detected by PCR also correlated with serum p24 antigen positivity, CD4 counts less than 400/mm3, and the presence of HIV-related symptoms or disease. Quantification of infectious HIV RNA in cell-free serum by PCR may be useful as a marker for for disease progression or in monitoring antiviral therapy.

AIDS-Related Complex↗
PubMed1997

Detection of rhinovirus RNA in lower airway cells during experimentally induced infection.

Rhinovirus (RV) infections are presumed to be localized to the upper airway, yet can cause severe lower airway symptoms in children and adults with asthma. To test the hypothesis that rhinovirus infection of the upper airway may be associated with the presence of virus in lower airway cells, we used the techniques of reverse transcription-polymerase chain reaction (RT-PCR) and Southern blotting to detect RV RNA in lower airway cells from eight allergic volunteers experimentally infected with RV16. Bronchoscopy with bronchoalveolar lavage (BAL) was done 1 mo before, and 2 and 4 d after an experimental infection with RV16. All subjects developed cold symptoms, and infection was confirmed by culturing RV16 from nasal secretions. Rhinovirus RNA was detected in both nasal lavage and lower airway cells from all eight subjects 2 to 4 d after an experimental inoculation, but not in any of the precold specimens from either the nose or the lower airway. These findings suggest that RV can infect cells of the lower airway, and raise the possibility that such an effect can promote asthma exacerbations in the susceptible host through direct enhancement of local inflammation.

Adolescent↗
PubMed1991

Strand-specific detection of enteroviral RNA in myocardial tissue by in situ hybridization.

In this report we describe the development and application of single-stranded RNA probes for strand-specific detection of enterovirus RNA in infected heart tissue by in situ hybridization. For synthesis of RNA probes a full-length reverse-transcribed, recombinant CVB3 cDNA was inserted into the transcription vector pSPT18. Run-off transcripts of plus-strand and minus-strand orientation were produced using either T7 or SP6 RNA polymerase. Binding specificity and sensitivity of the radioactively labelled RNA probes were determined by slot-blot hybridization. Due to the high degree of genetic identity among enteroviruses, the in vitro transcribed CVB3 RNA probes hybridized with various enterovirus serotypes, including group A and B coxsackieviruses and echoviruses, which are commonly implicated in human viral heart disease. Strand-specific in situ hybridization led to detection of viral plus-strand or minus-strand RNA in infected cell cultures and in myocardial tissue sections of infected mice. In consecutive sections either viral genomic plus-strand RNA or complementary minus-strand RNA were localized in the same infected myocardial cells. In situ hybridization with enterovirus-specific and highly sensitive single-stranded RNA probes is of particular interest for the diagnosis of myocardial infections and for studies concerning viral RNA replication.

Animals↗
PubMed2006

[Development of methods for detection of H5N1 from human clinical specimens].

BACKGROUND: To establish a method for H5N1 RNA detection and laboratory diagnosis of suspected human avian influenza (H5N1) virus infected cases. METHODS: The typing and sub-typing primers were designed according to M and H5 and N1 gene respectively, and the RT-PCR and real-time PCR were developed using these primers. RESULTS: The RT-PCR and real-time PCR could be used for H5N1 detection specifically, and there was no cross reaction with other influenza subtypes such as H1 and H3. The sensitivity for RT-PCR and real-time PCR was 1 TCID50 and 0.01 TCID50 respectively. Thirteen laboratory confirmed human H5N1 cases were detected from 42 suspected cases by using these methods. CONCLUSION: The established RT-PCR and real-time PCR methods can be used for laboratory detection of suspected human H5N1 cases.

Animals↗
PubMed1993

Expression of mRNA encoding the macrophage colony-stimulating factor receptor (c-fms) is controlled by a constitutive promoter and tissue-specific transcription elongation.

The gene encoding the receptor for macrophage colony-stimulating factor 1 (CSF-1), the c-fms protooncogene, is selectively expressed in immature and mature mononuclear phagocytes and trophoblasts. Exon 1 is expressed only in trophoblasts. Isolation and sequencing of genomic DNA flanking exon 2 of the murine c-fms gene revealed a TATA-less promoter with significant homology to human c-fms. Reverse transcriptase primer extension analysis using exon 2 primers identified multiple clustered transcription initiation sites. Their position was confirmed by RNase protection. The same primer extension products were detected in equal abundance from macrophage or nonmacrophage sources of RNA. c-fms mRNA is acutely down-regulated in primary macrophages by CSF-1, bacterial lipopolysaccharide (LPS), and phorbol myristate acetate (PMA). Each of these agents reduced the abundance of c-fms RNA detectable by primer extension using an exon 3 primer without altering the abundance of presumptive short c-fms transcripts detected with exon 2 primers. Primer extension analysis with an intron 2 primer detected products at greater abundance in nonmacrophages. Templates detected with the intronic primer were induced in macrophages by LPS, PMA, and CSF-1, suggesting that each of the agents caused a shift from full-length c-fms mRNA production to production of unspliced, truncated transcripts. The c-fms promoter functioned constitutively in the RAW264 macrophage cell line, the B-cell line MOPC.31C, and several nonhematopoietic cell lines. Macrophage-specific expression and responsiveness to selective repression by LPS and PMA was achieved by the incorporation of intron 2 into the c-fms promoter-reporter construct. The results suggest that expression of the c-fms gene in macrophages is controlled by sequences in intron 2 that act by regulating transcription elongation.

Animals↗
PubMed2005

Can highly active antiretroviral therapy be interrupted in patients with sustained moderate HIV RNA and > 400 CD4+ cells/microl? Impact on immunovirological parameters.

Because the effects of treatment interruption on patients with >400 CD4(+) cells/microl and prolonged moderate HIV loads is unknown, their HIV1 RNA and DNA loads, plasma, and PBMC resistance mutations and CD4+ kinetics were studied during 12 months of treatment interruption. Fifty-seven patients were included: 28 with undetectable (median 40 months) and 29 with moderate (>1 year) HIV1 RNA levels (3.3 log10 copies/ml) at the baseline M0. HIV1 RNA and CD4+ counts were determined monthly. PBMC HIV1 DNA was quantified (real-time PCR) and its reverse transcriptase (RT) and protease (PR) genotypes analyzed (M0, M6, M12). Regardless of HIV1 RNA detectability at the baseline M0, all patients had comparable HIV1 RNA (median 4.6), DNA (median 2.9), CD4+ (median 455) at month 12 (M12). The decisive moment was month 1 (M1), when the HIV1 RNA increase and CD4 decline stabilized, rendering M0 differences non-significant and predicting outcome. The lower the CD4+ nadir was before HAART, the steeper the CD4+ decline at M1. HIV1 DNA shifted to wild-type genotype in 47% (M6) and 79% (M12) of RT; 64% of PR major resistance mutations disappeared (M12). Treatment interruption is possible, regardless of the baseline M0 HIV RNA status, but it must take into consideration the CD4+ nadir, an outcome predictor, to initiate HAART before too severe depletion to preserve the possibility of treatment interruption. HIV1 DNA genotyping helps monitor patients with undetectable HIV RNA at M0.

Anti-HIV Agents↗
PubMed2005

Suppression of RNA recognition by Toll-like receptors: the impact of nucleoside modification and the evolutionary origin of RNA.

DNA and RNA stimulate the mammalian innate immune system through activation of Toll-like receptors (TLRs). DNA containing methylated CpG motifs, however, is not stimulatory. Selected nucleosides in naturally occurring RNA are also methylated or otherwise modified, but the immunomodulatory effects of these alterations remain untested. We show that RNA signals through human TLR3, TLR7, and TLR8, but incorporation of modified nucleosides m5C, m6A, m5U, s2U, or pseudouridine ablates activity. Dendritic cells (DCs) exposed to such modified RNA express significantly less cytokines and activation markers than those treated with unmodified RNA. DCs and TLR-expressing cells are potently activated by bacterial and mitochondrial RNA, but not by mammalian total RNA, which is abundant in modified nucleosides. We conclude that nucleoside modifications suppress the potential of RNA to activate DCs. The innate immune system may therefore detect RNA lacking nucleoside modification as a means of selectively responding to bacteria or necrotic tissue.

Antigens, CD↗
PubMed2004

[Comparison of hepatitis C viral RNA and core antigen kinetics in the therapeutic follow up of hepatitis C virus and human immunodeficiency virus co-infected patients, treated by bitherapy interferon-ribavirin, within the framework of RIBAVIC protocol].

AIM OF STUDY: The RIBAVIC protocol, established by ANRS in 2001 and closed in 2003, compared the efficacy and the tolerance of two bitherapy anti-Hepatitis C Virus for HIV-HCV co-infected patients: IFN-ribavirin and PEG-IFN-ribavirin for 48 weeks. Two hundred patients from protocol were tested for hepatitis C virus core antigen, to study this viral marker kinetics, before and under treatment, in comparison with hepatitis C virus RNA evolution. MATERIAL AND METHODS: The available samples for the 204 patients of our study were tested for RNA detection (COBAS AMPLICOR v2.0, Roche Diagnostics) and quantification (VERSANT HCV RNA v3.0, Bayer Diagnostics) and for quantification of core antigen (Ortho trak-C Assay, Ortho Clinical Diagnostics). The viral kinetics were established from samples quantified at D0, W2, W4, W12, W24, W48, W52, W72 (W =week), according to virological response assessed by PCR, six month after the end of treatment (non responders, sustained responders, relapsers et breakthroughs). RESULTS: We obtained, for each type of response, similar evolution of both viral markers. Trak-C assay show to be enough sensitive, with similar results whatever genotype of hepatitis C virus. The Pearson's correlation is excellent (R =0.94; P <0.001). The intergenotype correlation is correct too, whatever HCV genotype (1, 2, 3, 4). CONCLUSIONS: The HCV core antigen quantification by trak-C assay is a new tool for the follow-up of the treatment of patients with chronic hepatitis C and HIV co-infected.

Antigens, Viral↗
PubMed2003

Pair hidden Markov models on tree structures.

MOTIVATION: Computationally identifying non-coding RNA regions on the genome has much scope for investigation and is essentially harder than gene-finding problems for protein-coding regions. Since comparative sequence analysis is effective for non-coding RNA detection, efficient computational methods are expected for structural alignments of RNA sequences. On the other hand, Hidden Markov Models (HMMs) have played important roles for modeling and analysing biological sequences. Especially, the concept of Pair HMMs (PHMMs) have been examined extensively as mathematical models for alignments and gene finding. RESULTS: We propose the pair HMMs on tree structures (PHMMTSs), which is an extension of PHMMs defined on alignments of trees and provides a unifying framework and an automata-theoretic model for alignments of trees, structural alignments and pair stochastic context-free grammars. By structural alignment, we mean a pairwise alignment to align an unfolded RNA sequence into an RNA sequence of known secondary structure. First, we extend the notion of PHMMs defined on alignments of 'linear' sequences to pair stochastic tree automata, called PHMMTSs, defined on alignments of 'trees'. The PHMMTSs provide various types of alignments of trees such as affine-gap alignments of trees and an automata-theoretic model for alignment of trees. Second, based on the observation that a secondary structure of RNA can be represented by a tree, we apply PHMMTSs to the problem of structural alignments of RNAs. We modify PHMMTSs so that it takes as input a pair of a 'linear' sequence and a 'tree' representing a secondary structure of RNA to produce a structural alignment. Further, the PHMMTSs with input of a pair of two linear sequences is mathematically equal to the pair stochastic context-free grammars. We demonstrate some computational experiments to show the effectiveness of our method for structural alignments, and discuss a complexity issue of PHMMTSs.

Algorithms↗
PubMed2005

RNA secondary structural alignment with conditional random fields.

MOTIVATION: The computational identification of non-coding RNA regions on the genome is currently receiving much attention. However, it is essentially harder than gene-finding problems for protein-coding regions because non-coding RNA sequences do not have strong statistical signals. Since comparative sequence analysis is effective for non-coding RNA detection, efficient computational methods are expected for structural alignment of RNA sequences. Several methods have been proposed to accomplish the structural alignment tasks for RNA sequences, and we found that one of the most important points is to estimate an accurate score matrix for calculating structural alignments. RESULTS: We propose a novel approach for RNA structural alignment based on conditional random fields (CRFs). Our approach has some specific features compared with previous methods in the sense that the parameters for structural alignment are estimated such that the model can most probably discriminate between correct alignments and incorrect alignments, and has the generalization ability so that a satisfiable score matrix can be obtained even with a small number of sample data without overfitting. Experimental results clearly show that the parameter estimation with CRFs can outperform all the other existing methods for structural alignments of RNA sequences. Furthermore, structural alignment search based on CRFs is more accurate for predicting non-coding RNA regions than the other scoring methods. These experimental results strongly support our discriminative method employing CRFs to estimate the score matrix parameters. AVAILABILITY: The program which is implemented in C++ is available at http://phmmts.dna.bio.keio.ac.jp/ under the GNU public license.

Base Sequence↗
PubMed1998

Hepatitis C virus-associated hepatitis following treatment of HIV-infected patients with HIV protease inhibitors: an immune restoration disease?

OBJECTIVE: To report observations from case studies on the pathogenic mechanisms underlying the acute hepatitis that sometimes occurs in hepatitis C virus (HCV) and HIV coinfected patients following treatment with potent antiretroviral therapy that includes a HIV protease inhibitor. METHODS: Cases of acute hepatitis were identified from a group of 133 patients enrolled in a retrospective study of pathogen-associated inflammatory disease following the use of potent antiretroviral therapy. Data on serum alanine aminotransferase concentrations, clinical events, HCV antibodies, and liver biopsies were collected from medical records. HCV RNA assays and additional HCV antibody assays were undertaken on stored plasma or sera. RESULTS: Three of the 133 patients (2%) developed symptomatic hepatitis. One was HCV antibody-positive prior to commencing antiretroviral therapy and developed hepatitis subsequent to an episode of Mycobacterium avium complex disease associated with immune restoration. However, the other two patients had previously undiagnosed HCV infection for up to 2 years prior to antiretroviral therapy, with HCV RNA detected but anti-HCV antibody repeatedly undetectable in stored plasma or sera. HCV antibody was only detectable after antiretroviral therapy-induced decrease in plasma HIV RNA and immunological reconstitution. Plasma HCV RNA increased after therapy in one of these patients, but in the other the level was not increased at a time of active hepatitis demonstrated by liver biopsy. CONCLUSIONS: Hepatitis in HCV-HIV-coinfected patients following treatment with potent antiretroviral therapy may reflect restoration of anti-HCV immune responses rather than increased HCV replication or a hepatotoxic effect of antiretroviral therapy.

AIDS-Related Opportunistic Infections↗
PubMed1990

Identification and characterization of the virus causing rabbit hemorrhagic disease.

Liver tissue from animals that died of rabbit hemorrhagic disease (RHD) was used to identify the causative agent. After extraction of liver homogenates and sucrose density gradient ultracentrifugation, distinct bands were obtained. The respective gradient fractions reacted positively in an enzyme-linked immunosorbent assay as well as in hemagglutination assays and were infective for rabbits. These fractions contained virions which had a diameter of 40 nm and resembled morphologically those of the family Caliciviridae. By immunoblotting, a major structural protein with a molecular weight of 60,000 was identified. Highly pure RNA of about 8 kilobases was isolated from virions. Labeled cDNA synthesized from virion RNA detected two RNAs of 8 and 2 kilobases in Northern (RNA) blots of liver RNA from animals infected with RHD virus. Finally, isolated virion RNA injected into the liver of rabbits produced a disease with clinical symptoms and pathological findings typical of RHD. We conclude that a calicivirus represents the causative agent of RHD.

Animal Diseases↗
PubMed1991

Deletion analysis of brome mosaic virus 2a protein: effects on RNA replication and systemic spread.

Brome mosaic virus (BMV) genomic RNA2 encodes the 94-kDa 2a protein, which is one of two BMV nonstructural proteins required for RNA replication and subgenomic mRNA transcription. 2a contains a central polymeraselike region, which has extensive sequence similarity with the Sindbis virus nsP4 and tobacco mosaic virus (TMV) 183-kDa replication proteins, and also contains N- and C-terminal flanking segments without counterparts in the Sindbis virus and TMV nonstructural proteins. To further investigate the roles of the central and flanking segments in 2a, we have constructed a series of deletion and frameshift mutants in a biologically active BMV RNA2 cDNA clone and tested their ability to support viral RNA replication in barley protoplasts and systemic infection in whole barley plants. The entire 125-amino-acid C-terminal segment following the polymeraselike region was dispensable for RNA replication and transcription. Within the 200-amino-acid N-terminal flanking segment, deletion of the first 50 residues dramatically reduced genomic and subgenomic RNA accumulation, and deletion of 100 or more residues abolished detectable RNA synthesis. All mutations removing residues from the central polymeraselike domain also blocked RNA replication in trans. Sequences required in cis for RNA2 replication or stability were found to occur within the first 300 nucleotides of the 2a coding region. In whole barley plants, systemic infection was inhibited even by 2a deletions that supported strong RNA replication in protoplasts. Some replication-competent 2a variants failed to spread to uninoculated leaves, while other showed 10- to 500-fold-reduced virus yield in both inoculated and uninoculated leaves. These reductions were not due to any defects in RNA2 encapsidation.

Capsid↗
PubMed1993

Primary structure, neural-specific expression, and dendritic location of human BC200 RNA.

Primate BC200 RNA is a 200-nucleotide-long, nontranslatable RNA that is prevalently expressed in the nervous system. We have determined the primary structure of human BC200 RNA, using cDNA cloning and PCR techniques. BC200 RNA can be subdivided into three structural domains. The 5' region is homologous to Alu repetitive elements that are found in high copy numbers in primate genomes. The central part of BC200 RNA is characterized by a high percentage of A-residues, with a few interspersed other nucleotides. The 3' sequence is unique to BC200 RNA and shows no apparent similarity with known human DNA sequences. Sequence similarity with rodent BC1 RNA is limited to several short elements, and BC1/BC200 sequence comparisons indicate that the two genes have evolved via separate phylogenetic routes. Probes directed against the 3' unique part of BC200 RNA detected a single band corresponding to approximately 200 nucleotides on RNA blots. This band was identified only with RNA isolated from human brain, not with RNA from non-neural organs such as lung or kidney. In situ hybridization to selected areas of the human nervous system showed that BC200 RNA is expressed by a subpopulation of neurons that is analogous to the BC1 RNA-expressing subset of neurons in the corresponding areas of the rat nervous system. Moreover, like rat BC1 RNA, human BC200 RNA was localized to dendrite-rich neuropil areas, for example, in the inner plexiform layer of the retina. These results indicate that BC1 RNA and BC200 RNA, although of different evolutionary pedigree, may play analogous functional roles, in rodents and primates, respectively, in somatodendritic domains of nerve cells.

Base Sequence↗
PubMed1993

Frequency and significance of antibodies to hepatitis C virus in polyarteritis nodosa.

We tested sera from 56 patients to determine the seroprevalence of antibodies to hepatitis C virus (HCV) in polyarteritis nodosa (PAN), to assess the specificity of these antibodies for hepatitis C virus encoded antigens, and to evaluate the clinical features in patients with HCV infection and PAN. Eleven (20%) were positive for anti-HCV by an enzyme immunoassay. Three (5%) had specific antibodies to HCV encoded antigens detected by recombinant immunoblot assay (RIBA II) and had HCV RNA detected by polymerase chain reaction. Patients with HCV infection were more likely to have liver and skin involvement and a diminished serum complement.

Adult↗
PubMed1998

High performance Nanogold-silver in situ hybridisation.

Conventional in situ hybridisation (ISH) usually requires the presence of at least 10-50 copies of the nucleic acid sequence in question per cell. In situ PCR has been proposed as an alternative method, which may yield single-copy sensitivity, but shows a relatively high rate of false-negative or even false-positive reactions. Very recently, possible alternatives have been described, which can be performed in routine laboratories without the need for expensive equipment. Streptavidin-Nanogold-Silver ISH is an easy-to-perform assay, which can be applied to detect low copy numbers of nucleic acid sequences in paraffin sections and cytological preparations. Its combination with labelled tyramides (TSATM = tyramide signal amplification, also known as CARD = catalysed reporter deposition) can achieve single gene copy sensitivity in detecting DNA viruses and also shows very high sensitivity for RNA detection. Possible applications include the early recognition of viral infection, cancer-associated genes, genetic diseases, and also the specific detection of mRNA.

Acetates↗
PubMed1994

Detection of hepatitis C virus RNA in the ultrasonic dissector irrigating solution used in liver surgery.

Hepatitis C virus (HCV) RNA was detected in the irrigating solution aspirated by the ultrasonic dissector system used in liver surgery with a reverse transcription polymerase chain reaction technique and was then compared with HCV RNA in the serum to clarify the risk of viral transmission to hospital personnel. The positivity of HCV RNA in the aspirated irrigating solution was approximately equal in all patients whose serum was positive for HCV RNA. However, viral RNA was not detected in the aspirated irrigating solution of any patient who was seronegative for HCV RNA. These results indicate that it is necessary to be cautious regarding the transmission of HCV during liver surgery when using the ultrasonic dissector in HCV RNA seropositive patients, because the irrigating solution aspirated by this device appears to be highly infectious.

Aged↗