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At least 289 records · Page 16Linked to original sources
PubMed1997

Hepatitis C virus infection in pregnancy and the risk of mother-to-child transmission.

The risk of vertical transmission of the hepatitis C virus (HCV) from infected mothers to their children during pregnancy and delivery was determined in 120 children born to HCV-positive mothers. Methods included enzyme immunoassay and immunoblot for detection of HCV antibodies and reverse transcription polymerase chain reaction (RT-PCR) for detection of viral RNA. Six (5%) children were perinatally infected with HCV as shown by RT-PCR. None of the infected children had clinical signs of hepatitis. None of the pregnancies was complicated by abortion, stillbirth, premature birth, or malformation of the child. Special concern was given to the possibility of HCV transmission via breast milk. In no breast milk sample obtained from 34 HCV-infected mothers was HCV RNA detected. These observations indicate that HCV infection is not necessarily a contraindication for breast-feeding.

Breast Feeding↗
PubMed2005

Estimating the probability of freedom of classical swine fever virus of the East-Belgium wild-boar population.

A report of the Scientific Committee on Animal Health and Animal Welfare of the European Commission (CEC, 1999.) includes recommendations for setting up monitoring programmes for classical swine fever (CSF) infection in a wild-boar population, based on the assumption that one would detect at least 5% prevalence in a CSF-infected wild-boar population. This assumption, however, is not science based. We propose an alternative method to provide evidence for a wild-boar population being free of CSF and evaluate the efficiency of a surveillance programme that was implemented in Belgium in 1998. In our study, the probability of freedom of CSF-virus was estimated based on 789 samples; these were collected from wild-boars within the surveillance programme (within the three provinces which include 95% of the Belgian wild-boar population) and examined by three diagnostics methods (antibody detection, virus detection and virus RNA detection). A Bayesian framework was used for the estimation, accounting for the diagnostic test characteristics without the assumption of the presence of a gold standard. The median probability of freedom of CSF-virus was estimated at 0.970, with a 95% credibility interval of 0.149-1.000. Independent on the choice of the prior information, the posterior distributions for the probability of freedom of CSF-virus were always skewed close to the upper boundary of 1. This represents a big gain of knowledge since we did not use any prior information for the probability of freedom of CSF-virus and took the uncertainty about the accuracy of the diagnostic methods into account.

Animals↗
PubMed1995

Hepatitis C infection and viremia in Dutch hemophilia patients.

Serum samples from 316 patients visiting the Dutch National Hemophilia Center were collected from 1979 to 1993 and stored at -30 degrees C. Patients were placed into three different groups: 1) patients ever treated with large pool non-hepatitis C virus (HCV)-safe concentrate (n = 179); 2) patients treated with cryoprecipitate (n = 125); and 3) patients treated exclusively with HCV-save concentrate (n = 12). In order to examine the prevalence of HCV infection in the different treatment groups serum samples were tested retrospectively for anti-HCV antibody using second generation enzyme-linked immunosorbent assay (ELISA) and recombinant immunoblot assay (RIBA-2). Significant differences in the prevalence of HCV infection were found between these 3 groups (group 1: 99%, group 2: 66%, group 3: 0%). The safety of currently administered clotting products is demonstrated in 57 patients who remained without HCV markers between 1989 and 1993. To examine the natural course of HCV infection fresh-frozen plasma samples were obtained recently from a subgroup of 277 hemophilia patients for HCV-RNA detection by a well-validated cDNA-PCR assay. In contrast to other reports, no evidence was found for seronegative HCV carriers. None of 52 patients without anti-HCV had detectable HCV-RNA. Of 225 patients with anti-HCV, 182 (81%) were HCV-RNA positive. None of 39 anti-HCV positive patients with a negative HCV-RNA reaction had serum alanine aminotransferase (ALT) levels above 50 U/l, whereas 44% of HCV-RNA positive patients had persistently elevated ATL levels above 50 U/l.(ABSTRACT TRUNCATED AT 250 WORDS)

Alanine Transaminase↗
PubMed1984

Excision of an intact intron as a novel lariat structure during pre-mRNA splicing in vitro.

To study the mechanisms of RNA splicing we have analyzed the products generated by in vitro processing of a truncated 32P-labeled human beta-globin RNA precursor that contains the first two exons and the first intervening sequence (IVS1). Six major RNA products were detected and characterized. The first detectable RNA processing event is cleavage at the 5' GT of IVS1. Subsequently, accurately spliced RNA and the excised, intact IVS1 are simultaneously observed. The IVS1-containing RNA processing products have several unusual properties, which include: anomalous electrophoretic mobilities on polyacrylamide gels; a block to reverse transcription near the 3' end of IVS1; the presence of a nuclease-resistant component within IVS1. The block to reverse transcription and the nuclease-resistant component map to the same site near the 3' end of IVS1. The nuclease-resistant component appears to be a modified adenosine residue that contains an RNA branch. Based upon these and other structural studies we propose that the 5' end of IVS1 is joined by a 2'-5' phosphodiester linkage to the A residue in the RNAase T1 oligonucleotide ACTCTCTCTG located 28-37 nucleotides upstream from the IVS1 3' end. The IVS1 is therefore in the form of a lariat. These results imply that sequences within IVS1 actively participate in splicing.

Base Sequence↗
PubMed2006

Human endogenous retroviral pol RNA and protein detected and identified in the blood of individuals with schizophrenia.

Retrovirus has been speculated as one of the potential infectious agents involved in the development of schizophrenia. Here we used nested RT-PCR to detect the RNA of HERV pol gene in blood from schizophrenic patients and normal human. We found retroviral pol genes expressed in blood from 20 of 58 (34.5%) individuals with recent-onset schizophrenia, but not from 38 normal persons (p<0.01). Sequence analysis revealed that the expressed gene was homologous to those of the human endogenous retroviral (HERV) family. The ERV9 family was the closest, with 90% homology in the gene sequence. In addition, Western blots showed that antibody against ERV9 pol protein in serum from the HERV+ schizophrenia patients, but not from control (p<0.01). Our data suggested that the transcriptional activation of certain retroviral elements might be associated with the development of schizophrenia in some patients. Further characterization of retroviral elements in subjects with schizophrenia may aid in better diagnosis and treatment of this disorder.

Adolescent↗
PubMed2003

A new quantitative HIV load assay based on plasma virion reverse transcriptase activity for the different types, groups and subtypes.

BACKGROUND: Plasma viral load monitoring is an integral part of the standard of care for HIV-infected patients in industrialized countries. In developing countries, viral load assay is either unaffordable or hindered by on-site maintenance and/or technical problems. OBJECTIVES: To evaluate a new and simple quantitative assay for plasma HIV reverse transcriptase (RT) activity; and to compare RT activity-based and RNA-based quantification in plasma samples from patients infected by different subtypes of HIV-1 group-M, HIV-1 group-O and HIV-2. METHODS: The RT-based viral load assay involves separation of the virion-protected RT and quantification of its activity with an enzyme immunoassay. Plasma viraemia was quantified both by RT activity and by RNA copies in 322 samples from 236 HIV-1 group M-infected patients, including serial samples from 54 patients. Samples from 49 patients infected by HIV-1 group O or HIV-2 were also tested. RESULTS: RT activity and RNA copies were detected in 70% of plasma samples; respectively 25% and 1% of samples contained detectable RNA copies or RT activity alone. Measured RT activity corresponded to 48%, 96% and 100% of samples with 1.7-4.0 log(10), 4.1-4.8 log(10) and 4.9-6.7 log(10) RNA copies/ml, respectively. The values of the two assays correlated independently of the HIV subtype (P < 0.0001) and group/type (P < 0.03). Patient follow-up showed a similar pattern of viraemia with the two assays. CONCLUSION: Plasma RT activity assay is a simple, cheap and reliable alternative for HIV viral load determination. As such, it could be particularly valuable for diagnosis and treatment monitoring in developing countries.

HIV Infections↗
PubMed2005

Mature human spermatozoa do not transcribe novel RNA.

Mature spermatozoa contain subsets of mRNA that have been found in human testes before. Based on this finding it was hypothesized that the mRNAs of spermatozoa are transcribed during spermatogenesis. However, up to now there is no proof of the transcriptional inactivity of human sperm. To address this issue we performed in vitro labelling experiments with radio-labelled uridine triphosphate followed by analysis of cellular RNA. There was virtually no radioactive RNA detectable in the RNA purified from human spermatozoa proving the transcriptional inactivity of mature spermatozoa. The spermatozoal RNA obviously results from transcription during spermatogenesis and can be used for diagnostic purposes. These findings might have diagnostic and - possibly - therapeutic value in infertility patients as spermatozoal RNAs might complement the RNA pool of the oocyte after fertilization.

Base Sequence↗
PubMed2001

[Detection of astrovirus RNA from sewage works, seawater and native oysters samples in Chiba City, Japan using reverse transcription-polymerase chain reaction].

Through a year from April, 1999 to March, 2000, 20 samples, which consisted of raw sewage (2), chlorine-treated sewage (2), seawater (10) and naturally grown oysters (6), were collected monthly both from the sewage works at Mihama-ku, Chiba City and at a yacht harbor in Chiba City Bay, Japan. Astrovirus RNA were detected by reverse transcription-polymerase chain reaction (RT-PCR) and was typed by direct sequencing. Astrovirus positive products were detected from 9 samples (raw sewage; 1/2, chlorine-treated sewage; 2/2, seawater; 5/10 and oysters; 1/6) collected in April, 1999. In May, positive products were detected from 4 samples (raw sewage; 2/2 and seawater; 2/10). In June, only 1 positive product was detected from raw sewage. The number of positive samples showed a tendency to decrease and no positive products were detected from samples collected in July, 1999 to January, 2000. After that period, positive products were again detected from 3 samples (raw sewage; 1/2, chlorine-treated sewage; 2/2) collected in February, 2000. In March, the number of positive samples showed the peak and positive products were detected from 12 samples (raw sewage; 2/2, chlorine-treated sewage; 2/2, seawater; 7/10 and oysters: 1/6). Astrovirus positive products detected in April, May, June, July, 1999 and February, 2000 were classified into type 1 or 2 by sequencing, whereas in March, 2000 were type 1, 2, 3, 6 and 7.

Animals↗
PubMed1983

Defective Interference in the Killer System of Saccharomyces cerevisiae.

The K(1) killer virus (or plasmid) of Saccharomyces cerevisiae is a noninfectious double-stranded RNA genome found intracellularly packaged in an icosahedral capsid. This genome codes for a protein toxin and for resistance to that toxin. Defective interfering virus mutants are deletion derivatives of the killer virus double-stranded RNA genome; such mutants are called suppressive. Unlike strains carrying the wild-type genome, strains with these deletion derivatives are neither toxin producers nor toxin resistant. If both the suppressive and the wildtype virus are introduced into the same cell, most progeny become toxin-sensitive nonkillers (J. M. Somers, Genetics 74:571-579, 1973). Diploids formed by the mating of a killer with a suppressive strain were grown in liquid culture, and RNA was extracted from samples taken up to 41 generations after the mating. The ratio of killer RNA to suppressive RNA decreased with increasing generations; by 41 generations the killer RNA was barely detectable. The copy numbers of the suppressive genome and its parental killer were virtually the same in isogenic strains, as were the growth rates of diploid strains containing either virus alone. Therefore, suppressiveness, not being due to segregation or overgrowth by faster growing segregants, is likely due to preferential replication or maintenance of the suppressive genome. Three suppressive viruses, all derivatives of the same killer virus (T. K. Sweeney et al., Genetics 84:27-42, 1976), did not coexist stably. The evidence strongly indicates that the largest genome of the three slowly suppressed both of the smaller genomes, showing that larger genomes can suppress smaller ones and that suppression can occur between two suppressives. Of 48 isolates of strains carrying the suppressive viruses, 5 had newly detectable RNA species, all larger than the original suppressive genomes. At least seven genes necessary for maintenance of the wild-type killer virus (MAK genes) were needed by a suppressive mutant. No effect of ski mutations (affecting regulation of killer virus double-stranded RNA replication) on suppressiveness was observed.

Journal Article↗
PubMed2005

A yeast RNA-hybrid system for the detection of RNA-RNA interactions in vivo.

RNA-RNA interactions play a crucial role at many different levels of the cellular metabolism such as plasmid replication control, viral encapsidation, or transcriptional and translational regulation. Therefore, methods are necessary to investigate the molecular determinants of given interactions, including their stabilities, or to screen for new interacting partners. We designed an RNA-hybrid system in S. cerevisiae, based on the yeast three-hybrid system. In this setup, the activation of a reporter gene is dependent on the interaction of two RNAs. A loop-loop interaction similar to the dimerization initiation site of the HIV genome was used as a model system, demonstrating that in this novel RNA-hybrid system only cognate RNAs promote the activation of the reporter gene. Levels of reporter activation correlate well with interaction stabilities determined in vitro by UV melting analyses, suggesting that conditions used for the analysis of in vitro structural stabilities translate well into the intracellular environment. Furthermore, the system was applicable for a screen against a test library. Nine out of ten selected clones were identified as predicted interaction partners for the bait RNA. In summary, we present a yeast reporter system depending on RNA-RNA interactions, which can be used alternatively for analysis of known interactions or for screening libraries in search for new interaction partners.

Base Pairing↗
PubMed1999

[Study of the 3'noncoding region of Chinese hepatitis C virus genome].

OBJECTIVE: To analyze the 3' noncoding region (3' NCR) of HCV genome from Chinese hepatitis C patients so as to facilitate further study of mechanism of HCV gene replication. METHODS: Two different strategies were employed to amplify the full-length of the 3' noncoding region of HCV genome from sera of HCV infected patients in Shanghai area: one was to amplify the full-length fragment directly by nested PCR and the other amplify two overlapping fragments. The PCR products were further analyzed by sequencing and nucleotide alignments. A HCV genome 3'NCR based RT-PCR was developed and its specificity and sensitivity for HCV RNA detection in sera was compared with the established 5'NCR based RT-PCR. RESULTS: Sequence analysis showed that Chinese HCV genomic 3' NCR consists of three parts: the 5' region, poly (U-UC) tract and the 98-base region. Sequence alignments revealed that, while the 98-base regions were completely conserved in different isolates and were identical to the reported sequences, the poly (U-UC) region shared highly diversities. A high degree of concordance(95%) between the 3'NCR and 5'NCR RT-PCR for detection of HCV RNA in sera was found. CONCLUSION: The high conservation at the 3' NCR(98 bases) of HCV genome among different isolates indicated that this region may be critical for HCV gene replication The 3'NCR based RT-PCR may be a useful addition to available systems to diagnosis HCV infection.

3' Untranslated Regions↗
PubMed1996

Single molecule detection of RNA reporter probes by amplification with Q beta replicase.

The addition of target-specific probe sequences within MDV RNA, an otherwise efficient template for Q beta replicase, generally resulted in RNA molecules with inferior replication properties, including reduced replication rates and poor sensitivities. We have discovered that the replication characteristics of MDV RNA molecules with internally placed probe sequences are dramatically affected by short RNA sequences (spacer elements) at the 5' and 3' ends of the probe sequence. For a given probe sequence, the sequences of the flanking spacer elements effected replication sensitivity by six orders of magnitude and replication rate by three fold. By taking advantage of spacer elements, internal MDV probes were developed that permitted the reproducible, real time, fluorescence detection of a single RNA molecule in less than 25 min through amplification with Q beta replicase. RNA structural analysis of such probes suggested that the spacer elements functioned by allowing the RNA to fold in a way which substantially maintained the tertiary structure of the MDV domain. MDV reporter probes with suitable replication properties were obtained from libraries of RNA molecules in which the probe sequence was flanked by many different spacer elements (generated by random nucleotide synthesis). We demonstrated that this is a general method for developing RNA reporter molecules which are rapidly and reproducibly amplified by Q beta replicase, even from a single molecule.

Base Sequence↗
PubMed2006

Male-specific RNA coliphages detected by plaque assay and RT-PCR in tropical river waters and animal fecal matter.

Male-specific RNA coliphages (FRNA) have been recommended as indicators of fecal contamination and of the virological quality of water. In this study, 16 river water and 183 animal fecal samples were examined for the presence of FRNA coliphages by a plaque assay using Salmonella typhimurium WG49 and WG25 to differentiate between male-specific and somatic phages, a RNase spot test to differentiate between DNA and RNA phages and a reverse transcriptase-polymerase chain reaction (RT-PCR) for the specific identification of FRNA phages. The overall recovery rate for F-specific coliphages was 8.0%. (4.4% from animal fecal matter and 50% from river water samples). Plaque counts were generally low (< 6 x 10(2) pfu per g feces or ml water), with FRNA (6.5%) and Male-specific DNA coliphages (FDNA) (7.0%) phages occurring at almost equal frequencies. The RT-PCR was positive in all FRNA plaques and was able to identify FRNA phages in mixed populations of FRNA, FDNA and somatic phages.

Animals↗
PubMedDate not supplied

Prevalence and outcome of hepatitis C infection among heart transplant recipients.

BACKGROUND: Hepatitis C virus infection is common in organ transplant recipients, and can be associated with significant morbidity and mortality. A unique feature of this infection among immunosuppressed patients is that it can progress without the development of hepatitis C virus antibodies. METHODS: To define the prevalence of hepatitis C virus infection in patients undergoing heart transplantation and identify clinical syndromes associated with hepatitis C virus infection in heart transplant recipients, we collected sera from 59 consecutive heart transplant recipients and their donors. Samples were tested before and after transplantation for hepatitis C virus antibodies with the use of a second-generation recombinant immunoblot assay and for hepatitis C virus RNA by means of reverse transcriptase polymerase chain reaction. RESULTS: Four of 59 patients (7%) had hepatitis C virus-RNA detected in posttransplantation serum samples; but only one of these was anti-hepatitis C virus antibody positive. Two of the four patients with hepatitis C virus RNA detected after transplantation received organs from donors who were positive for hepatitis C virus RNA/anti-hepatitis C virus. One of these two recipients tested positive for hepatitis C virus antibody and hepatitis C virus RNA before transplantation. The other two patients received organs from hepatitis C virus negative donors and possibly acquired infection after transplantation from blood or immunoglobulin preparations. One patient was anti-hepatitis C virus positive before transplantation but had no detectable hepatitis C virus RNA, and hepatitis C virus infection did not develop after transplantation. Progressive hepatitis C virus-induced cholestatic liver disease that led to hepatic failure and death after heart transplantation occurred in one of the four patients. CONCLUSION: Hepatitis C virus infection may occur after heart transplantation in the absence of anti-hepatitis C virus antibodies, and a syndrome of severe cholestatic liver disease may complicate heart transplantation in the presence of hepatitis C virus infection.

Adult↗
PubMed1993

Chemical cleavage method for the detection of RNA base changes: experience in the application to collagen mutations in osteogenesis imperfecta.

We discuss the definition of mutations in osteogenesis imperfecta (OI) using a chemical cleavage method for detecting mismatched bases in patient mRNA: control cDNA heteroduplexes. The method is based on the increased chemical modification of cytosines (Cs) by hydroxylamine and thymines (Ts) by osmium tetroxide when they are not paired with their complementary base. The DNA is then cleaved at the modified base with piperidine and the use of radioactively labeled DNA probes allows the position of the mismatched base to be determined by electrophoresis of the cleavage-product. The precise mutations are then determined by specific amplification and sequencing of the region containing the mismatched base. In perinatally lethal OI (OI type II) mismatches have been detected in all 17 cases studied; 12 of these have been fully characterized. In 7 of these 12 cases the mismatches were point mutations in the genes for pro alpha 1(I) or pro alpha 2(I) which resulted in glycine substitutions in the triple helical region of the protein. Sequence variation was detected in addition to the glycine substitutions in 2 cases. In 2 cases the RNA mismatch resulted from changes in the amino acid sequence of the C-propeptide domain. In the 3 remaining cases the mismatch resulted from silent nucleotide sequence variants. In the less severe forms of OI we have studied, mismatches have been detected and characterized in 8 of 12 cases. In 4 of these 8 cases the mismatch resulted from presumably neutral sequence variation and in the other 4 cases mutations have been defined.(ABSTRACT TRUNCATED AT 250 WORDS)

Cells, Cultured↗
PubMed1995

Single-tube reverse transcription and heminested polymerase chain reaction of hepatitis C virus RNA to detect viremia in serologically negative hemodialysis patients.

Detection of hepatitis C virus genome is the only method currently available for detecting viremia in infected individuals. We describe a substantial simplification of current methods for viral RNA reverse transcription and polymerase chain reaction amplification, which allows cDNA synthesis and nested amplification in a single tube; this is achieved through compartmentalization of the reagents for the two reactions with a wax barrier. This procedure retains a high sensitivity: analysis of serum samples from hemodialysis patients, a high-risk group for hepatitis C virus infection, confirmed the presence of the virus in 88% of antibody-positive patients and detected viremia in patients without serological or biochemical evidence of hepatitis C virus infection.

Adult↗
PubMed2001

Linear 2' O-Methyl RNA probes for the visualization of RNA in living cells.

U1snRNA, U3snRNA, 28 S ribosomal RNA, poly(A) RNA and a specific messenger RNA were visualized in living cells with microinjected fluorochrome-labeled 2' O-Methyl oligoribonucleotides (2' OMe RNA). Antisense 2' OMe RNA probes showed fast hybridization kinetics, whereas conventional oligodeoxyribonucleotide (DNA) probes did not. The nuclear distributions of the signals in living cells were similar to those found in fixed cells, indicating specific hybridization. Cytoplasmic ribosomal RNA, poly(A) RNA and mRNA could hardly be visualized, mainly due to a rapid entrapment of the injected probes in the nucleus. The performance of linear probes was compared with that of molecular beacons, which due to their structure should theoretically fluoresce only upon hybridization. No improvements were achieved however with the molecular beacons used in this study, suggesting opening of the beacons by mechanisms other than hybridization. The results show that linear 2' OMe RNA probes are well suited for RNA detection in living cells, and that these probes can be applied for dynamic studies of highly abundant nuclear RNA. Furthermore, it proved feasible to combine RNA detection with that of green fluorescent protein-labeled proteins in living cells. This was applied to show co-localization of RNA with proteins and should enable RNA-protein interaction studies.

Animals↗