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At least 199 records · Page 11Linked to original sources
PubMed2000

Effects of delayed freezing of liver biopsies on the detection of hepatitis C virus RNA strands.

BACKGROUND/AIMS: There are no data about the influence of handling conditions of liver biopsies on the integrity of viral RNAs. We studied the influence of the time delay between obtaining and freezing the liver biopsy on the stability of intrahepatic positive and negative hepatitis C virus RNA (HCV-RNA) strands. METHODS: Liver samples from 30 anti-HCV patients were included. For each case, one portion of the liver biopsy (first sample) was immediately frozen (20-28 s), while the other section (second sample) was kept at room temperature (1-30 min) before freezing. Each experimental time point was performed in triplicate using liver samples from three different patients. Semi-quantitative analysis of the positive and negative HCV-RNA strands and of the al-antitrypsin mRNA was performed by a Tth-based reverse-transcription polymerase chain reaction. RESULTS: A significant time-related decrease in both positive (r=-0.8412, p=0.001) and negative (r=-0.8539, p=0.001) HCV-RNA strand titres was found in the second liver fractions. There were no appreciable changes in RNA titres in those samples frozen after less than 3 min. The RNA titres decreased in all but two samples incubated for 4-30 min. Thus, 3/15 (20%) and 7/11 (64%) of these samples lost positive and negative HCV-RNA strands, respectively. Alpha-1-antitrypsin mRNA titres decreased significantly (r=-0.8935, p=0.01) in those samples kept at room temperature for more than 4 min. CONCLUSION: Freezing of liver samples immediately after extraction is crucial to avoid false negative HCV-RNA detection results, especially for the antigenomic RNA strand.

Biopsy↗
PubMed1998

Detection of human immunodeficiency virus type 1 (HIV-1) RNA in pools of sera negative for antibodies to HIV-1 and HIV-2.

A total of 234 pools were prepared from 10,692 consecutive serum samples negative for antibodies to human immunodeficiency virus type 1 (HIV-1) and HIV-2 collected at five virological laboratories (average pool size, 45 serum samples). Pools were screened for the presence of HIV-1 RNA by a modified commercial assay (Amplicor HIV-1 Monitor test) which included an additional polyethylene glycol (PEG) precipitation step prior to purification of viral RNA (PEG Amplicor assay). The sensitivity of this assay for HIV-1 RNA detection in individual serum samples within pools matches that of standard commercial assays for individual serum samples, i.e., 500 HIV-1 RNA copies per ml. Five pools were identified as positive, and each one contained one antibody-negative, HIV-1 RNA-positive serum sample, corresponding to an average of 1 infected sample per 2,138 serum samples. Retrospective analysis revealed that the five HIV-1 RNA-positive specimens originated from individuals who had symptomatic primary HIV-1 infection at the time of sample collection and who were also positive for p24 antigenemia. We next assessed the possibility of performing the prepurification step by high-speed centrifugation (50,000 x g for 80 min) of 1.5-ml pools containing 25 microl of 60 individual serum samples, of which only 1 contained HIV-1 RNA (centrifugation Amplicor assay). The sensitivity of this assay also matches the sensitivities of standard commercial assays for HIV-1 RNA detection in individual serum samples. The results demonstrate that both assays with pooled sera can be applied to the screening of large numbers of serum samples in a time- and cost-efficient manner.

Centrifugation↗
PubMed1995

In situ DNA PCR and RNA hybridization detection of herpes simplex virus sequences in trigeminal ganglia of latently infected mice.

The presence of herpes simplex virus (HSV-1) DNA in the trigeminal ganglia of latently infected mice was detected by an in situ DNA polymerase chain reaction (PCR), which includes a DNA:DNA hybridization step (indirect in situ PCR). These results were compared to the number of neurons possessing the HSV-1 latency associated transcript (LAT), as detected by in situ RNA hybridization with LAT probes. Sensitivity assays were shown to detect a single copy cellular gene in 48% of neuronal cell bodies. The results suggest that in situ PCR is an effective method to locate and detect HSV-1 within latently infected neurons. Moreover, the number of neurons found to be harboring HSV-1, by the method of in situ PCR, which does not depend upon virus gene expression, is within threefold of the number detected by in situ hybridization for LAT. Therefore, this report describes the first detection of HSV-1 DNA in latently infected murine trigeminal ganglia by the method of indirect in situ PCR, and compares the findings to the number of neurons expressing LAT, as assessed by conventional in situ hybridization.

Animals↗
PubMed2001

Performance characteristics of a transcription-mediated nucleic acid amplification assay for qualitative detection of hepatitis C virus RNA.

The detection of hepatitis C virus (HCV) RNA by nucleic acid amplification techniques is the method of choice to differentiate between ongoing and past infection, and can be used to monitor the course of HCV infection. In this study, we evaluated the performance characteristics of a newly developed transcription-mediated amplification (TMA)-based assay, the VERSANT HCV RNA qualitative assay, which was designed to qualitatively detect HCV RNA. Samples tested by the TMA assay included 100 HCV antibody negative sera; serial dilutions of an HCV genotype 1a panel; the WHO HCV RNA standard 76/790; an HCV genotyping panel; and 150 clinical specimens, including sera from patients who had received alpha interferon (IFN) treatment or liver transplants. TMA test results were compared with the Cobas Amplicor HCV polymerase chain reaction (PCR) assay. The analytical specificity of the HCV TMA assay was > 98%. No carry-over contaminations were observed. The assay demonstrated an analytical sensitivity of 100% at 41 HCV RNA copies/mL (genotype 1a panel) and 5 IU/mL (WHO standard), respectively. HCV genotypes and subtypes did not affect the results. Qualitative RNA detection by diagnostic Amplicor PCR and TMA was in agreement in > 97% of all 150 clinical samples tested. In our study, the TMA-based assay proved to be a specific and sensitive method for qualitative HCV RNA detection. The test may turn out to be an attractive alternative to already established techniques for HCV RNA amplification in routine clinical laboratories.

Enzyme-Linked Immunosorbent Assay↗
PubMed2025

Northern Blotting: Protocols for Radioactive and Nonradioactive Detection of RNA.

Northern blotting is a common technique in RNA biology, allowing to detect and quantify RNAs of interest following separation by gel electrophoresis, transfer to a membrane, and hybridization of specific anti-complementary labelled probes. In this chapter, we describe our protocol for efficient RNA extraction from yeast, separation on agarose gel, and capillary transfer to a membrane. We provide two different methods for strand-specific detection of several types of RNAs using oligonucleotide probes, the first using radioactive 32P-labelled probes, the second based on nonradioactive digoxigenin-labelled probes.

Blotting, Northern↗
PubMed2002

Recruitment of intron-encoded and co-opted proteins in splicing of the bI3 group I intron RNA.

Detectable splicing by the Saccharomyces cerevisiae mitochondrial bI3 group I intron RNA in vitro is shown to require both an intron-encoded protein, the bI3 maturase, and the nuclear-encoded protein, Mrs1. Both proteins bind independently to the bI3 RNA. The bI3 maturase binds as a monomer, whereas Mrs1 is a dimer in solution that assembles as two dimers, cooperatively, on the RNA. The active six-subunit complex has a molecular mass of 420 kDa, splices with a k(cat) of 0.3 min(-1), and binds the guanosine nucleophile with an affinity comparable to other group I introns. The functional bI3 maturase domain is translated from within the RNA that encodes the intron, has evolved a high-affinity RNA-binding activity, and is a member of the LAGLIDADG family of DNA endonucleases, but appears to have lost DNA cleavage activity. Mrs1 is a divergent member of the RNase H fold superfamily of dimeric DNA junction-resolving enzymes that also appears to have lost its nuclease activity and now functions as a tetramer in RNA binding. Thus, the bI3 ribonucleoprotein is the product of a process in which a once-catalytically active RNA now obligatorily requires two facilitating protein cofactors, both of which are compromised in their original functions.

Amino Acid Sequence↗
PubMed1996

Detection of RNA polymerase II promoters and polyadenylation sites in human DNA sequence.

Detection of RNA polymerase II promoters and polyadenylation sites helps to locate gene boundaries and can enhance accurate gene recognition and modeling in genomic DNA sequence. We describe a system which can be used to detect polyadenylation sites and thus delineate the 3' boundary of a gene, and discuss improvements to a system first described in Matis et al. (1995) [Matis S., Shah M., Mural R. J. & Uberbacher E.C. (1995) Proc. First Wrld Conf. Computat. Med., Public Hlth, Biotechnol. (Wrld Sci.) (in press).], which predicts a large subset of RNA polymerase II promoters. The promoter system used statistical matrices and distance information as inputs for a neural network which was trained to provide initial promoter recognition. The output of the network was further refined by applying rules which use the gene context information predicted by GRAIL. We have reconstructed the rule-based system which uses gene context information and significantly improved the sensitivity and selectivity of promoter detection.

Algorithms↗
PubMed1982

Sensitive detection of RNA using strand-specific M13 probes.

We have extended the method of Hu and Messing (Gene 17 (1982) 271-277) to prepare highly radioactive M13 probes suitable for use in RNA-DNA hybridization experiments. Single strands of M13 DNA carrying cloned sequences are rendered partially double-stranded by primed synthesis using a synthetic oligonucleotide primer complementary to a region 5' to the cloning site. The newly synthesized radioactive complementary strand is then covalently cross-linked to the M13 phage DNA by UV irradiation in the presence of 4,5,8-trimethylpsoralen (trioxsalen). Since the cross-linked probe is stable to heat denaturation, and the region of cloned sequence is kept single-stranded, these complexes may be used as strand-specific hybridization probes to detect RNA sequences under conditions which would denature DNA-DNA duplexes.

Base Sequence↗
PubMed1993

Rabies RNA synthesis, detected with cDNA probes, as a marker for virus transport in the rat nervous system.

The kinetics of viral RNA synthesis in different parts of the rat brain, infected with fixed or street rabies virus strains, is correlated with their anatomical neuronal connections with the masseter muscles, using hybridization with rabies cDNA probes. Viral RNA synthesis is first detected in the brain-stem and in the pons where the direct anatomical projection of the masseter muscle nervous arborization into the sensory and motor nuclei is located, through the trigeminus nerve. Rabies RNA detection is delayed in the other regions of the rat brain depending on the time course of virus transport from the trigeminal nuclei through multiple nervous connections.

Afferent Pathways↗
PubMed2001

Screening of blood donations by hepatitis C virus polymerase chain reaction (HCV-PCR) improves safety of blood products by window period reduction.

Introduction of the nucleic acid amplification technique (NAT) as a screening test for blood donors to detect HCV RNA became mandatory on 1 April 1999. Few automated commercial systems are available for HCV RNA detection at the moment. The Cobas Amplicor HCV 2.0 System is able to perform fully automated amplification and detection of nucleic acids. A concentration of 98 IU HCV RNA/ml can be detected by the Cobas Amplicor HCV 2.0 System (n = 233, in 100% of the cases). With a pool size of 40 donor samples, the guidelines of the Paul-Ehrlich-Institute concerning sensitivity (5,000 IU HCV RNA per mL in a single donation) were followed. One whole blood donation was identified as HCV-RNA positive (anti-HCV IgG negative, GPT < 30 U/L) during a period of 5 months. No false positive test results could be observed. The internal control and the run control are primarily helpful to monitor methodological problems.

Autoanalysis↗
PubMed1988

Detection of mononuclear cells expressing hepatitis B virus in peripheral blood from HBsAg positive and negative patients by in situ hybridisation.

In situ hybridisation was used to detect RNA of Hepatitis B virus (HBV) in peripheral mononuclear blood cells. Presence of HBV-RNA was detected in 10/17 HBsAg positive HBeAg positive patients, in 8/18 HBsAg positive HBeAg negative patients, in 1/3 anti-HBs positive subjects. Four control subjects were negative. The frequency of labelled cells varied from 1 to 10% of mononuclear cells. These results indicate that the DNA detected so far in mononuclear blood cells may be transcriptionally active.

Adolescent↗
PubMed2000

Hepatitis C virus in the hemodialysis setting: detecting viral RNA from blood port caps by reverse transcription-polymerase chain reaction.

BACKGROUND: A widely observed increased risk of hepatitis C virus (HCV) infection in chronic hemodialysis patients has been previously attributed to violations of "Universal Precautions" for the control of blood-borne pathogens, as well as in part, to other risk factors, such as a history of blood transfusion or injection drug use. However, specific factors responsible for transmission have not been identified and the possibility that flaws in dialysis procedures, including sterilization, could increase the risk of transmission, has not been excluded. METHODS: We investigated reuse procedures for hemodialysis equipment and tested dialyzer blood port caps for detection of hepatitis C virus RNA (HCV RNA) by reverse transcription-polymerase chain reaction (RT-PCR). RESULTS: Following artificial contamination of the blood port caps with blood or fluids from human HCV-positive patients, and overnight soaking in 1% Renalin, HCV RNA was detected on 4 of 20 caps contaminated with blood, 1 of 10 contaminated with serum and 8 of 24 contaminated with dialyzer blood compartment residue. HCV RNA was also detected on 1 of 111 pairs of blood port caps collected post dialysis from HCV positive patients, after soaking the caps overnight in 1% Renalin. CONCLUSION: The results suggest that HCV RNA might be detectable on reused dialysis equipment post sterilization procedures, if residual blood or serum is not entirely or almost entirely removed prior to sterilization. This may warrant evaluation of sterilization procedures to ensure that procedures are adequate and that protocols are rigorously followed. Further studies of sterilization procedures by sensitive techniques such as RT-PCR may be indicated.

Equipment Reuse↗
PubMed2003

Rapid detection of human pathogenic orthobunyaviruses.

Modern detection and identification tools can help to provide answers to urgent questions about the incidence, prevalence, and epidemiology of currently emerging diseases. We developed highly sensitive one-step TaqMan reverse transcription-PCR assays with sensitivities ranging from 10(4) to 10(1) molecules for 11 human pathogens of the orthobunyaviruses. We compared the performances of these assays on three currently available cyclers (ABI-PRISM 7700, LightCycler, and SmartCycler). The assay for Oropouche virus (OROV) was tested using sera collected from days 1 to 5 after onset of OROV disease and was found to be greatly superior to an established nested PCR system. A mean copy number of 1.31 x 10(7) OROV RNA/ml of serum was detected. Diagnostic RNA detection can be used as early as day 1 after onset of OROV disease. The use of a mobile SmartCycler and a hands-on time of less than 3 h could help to intensify outbreak surveillance and control, especially in field studies.

Animals↗
PubMed1992

New data concerning the functional organization of the mammalian cell nucleolus: detection of RNA and rRNA by in situ molecular immunocytochemistry.

We have investigated the fine spatial distribution of RNA and rRNA within the Ehrlich tumor cell nucleolus by in situ hybridization with a biotin-labeled probe and by two new strategies, the polyadenylate nucleotidyl transferase-immunogold technique and immuno-labeling with anti-RNA antibodies. Besides the presence, as expected, of RNA and rRNA in the granular component and the dense fibrillar component, we show, for the first time, significant label over all the fibrillar centers of the nucleoli. When RNA and DNA were detected simultaneously on the same sections, only the fibrillar centers were positive for both. These results throw light on the controversial subject of the precise location of transcribing rRNA genes within the nucleolus. The fibrillar centers, and not the dense fibrillar component, should thus be the site of rRNA synthesis.

Animals↗
PubMed2003

Increased hepatitis C virus load among injection drug users infected with human immunodeficiency virus and human T lymphotropic virus type II.

Coinfection of hepatitis C virus (HCV) and human immunodeficiency virus (HIV) and/or human T-lymphotropic virus type II (HTLV-II) is common among drug users. We compared HCV RNA detection and load in a cohort of 6570 injection drug users from 9 US cities during 1987-1991. Of 385 subjects selected from 16 strata by sex, race (black or nonblack), and HIV/HTLV-II group (HIV positive [HIV(+)]/HTLV-II(+), HIV(+)/HTLV-II negative [HTLV-II(-)], HIV(-)/HTLV-II(+), and HIV(-)/HTLV-II(-)), 376 had HCV antibodies, of whom 305 had detectable HCV load. HCV RNA detection was unrelated to sex, race, and virus groups, but differed by study site. The mean HCV load was 5.4 log(10) IU/mL and was 0.24 log(10) higher in men than in women. Virus load increment with HIV or HTLV-II infection was higher among white subjects than among other subjects. Compared with HIV(-)/HTLV-II(-) subjects, virus load was 0.50, 0.22, and 0.56 log(10) higher in HIV(+)/HTLV-II(-), HIV(-)/HTLV-II(+), and HIV(+)/HTLV-II(+) subjects, respectively. HTLV-II infection significantly increased HCV load in white subjects but not in other racial groups.

Adult↗
PubMed1995

Expression of VL30 vectors in human cells that are targets for gene therapy.

Novel vectors made from mouse VL30 retrotransposons were tested in cell types that are targets for gene therapy, including normal human cells (skeletal muscle epithelium, bronchial epithelium, mammary epithelium), Epstein-Barr virus-transformed peripheral blood lymphocytes (PBLs), and various tumor cell lines. The long terminal repeat (LTR) transcriptional promoter, derived from the retroelement NVL-3, expressed abundant mRNA containing the bacterial neomycin resistance gene (neo) in all cell types tested. The amounts of neo RNA detected on RNA blots from normal vs. transformed cells were similar, although relatively less RNA was expressed in PBLs than in other cell types. Vector RNA expression in PBLs persisted during six months of continuous culture. Transcription was regulated by fibroblast growth factor (bFGF) and insulin, with the effects of each being cell-type-dependent. Thus, VL30 vectors introduced and expressed transgenes at significant levels in a number of cell types that are of interest for human gene therapy of metabolic and neoplastic diseases.

Cell Transformation, Neoplastic↗
PubMed2002

Triplex-forming DNAs in the human interphase nucleus visualized in situ by polypurine/polypyrimidine DNA probes and antitriplex antibodies.

The polypurine/polypyrimidine (PuPy) tracts present in the human genome are known to be scattered among and within chromosomes. In PuPy tract sequences, triplex formation occurs readily under physiological conditions, leaving single-stranded DNAs capable of hybridization with complementary single-stranded DNAs and RNAs. The formation of single-strands and transmolecular triplexes is thought to enable sequences spaced distantly along the genome to associate with each other and organize nuclear DNA into ordered configurations. Triplex-forming DNAs in the human interphase nucleus were analyzed by combining fluorescence in situ "nondenaturing" hybridization employing PuPy tract probes and immunodetection by antitriplex antibodies. The nondenaturing hybridization technique, which has been used to detect RNA, may detect single-stranded DNAs in nondenatured nuclei, if present. Probes such as (GA/TC)(n) and (GAA/TTC)(n) sequences gave sequence-specific signals that overlapped with or were closely associated with triplexes immunolocalized by using known antitriplex antibodies. Pretreatment of nuclei with antitriplex antibodies blocked probe signal formation. Signal formation was resistant to pretreatment of nuclei with RNases but sensitive to single strand-specific nucleases. Triplexes visualized differentially with distinct PuPy tract probes were associated spatially with centromeric sequences in the interphase nucleus in a sequence-specific manner.

Cell Line↗
PubMed1994

Isolation and purification of U7 snRNP particles.

1. A procedure has been developed for the isolation of U7 small nuclear ribo-protein particles involved in the processing of histone pre-mRNAs. They were fractionated from the rest of the snRNPs through a series of gel filtration and affinity chromatography steps. 2. The isolated assembly of U7 snRNP particles appeared to be intact and pure as judged by the gel electrophoresis of their RNA. No detectable RNA species were monitored other than U7 RNA.

Chromatography, Gel↗