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At least 721 records · Page 40Linked to original sources
PubMed1985

Characterization of dihydrofolate reductase-related DNA and RNA from human KB cell subclones containing different amounts of enzyme.

The present study was aimed to characterize dihydrofolate reductase (DHFR)-related DNA and RNA in a series of human KB cell sublines and to further understand the mechanisms of DHFR regulation. We used two probes, one which could recognize the 5' flanking sequence (p5') of the human DHFR gene and one derived from mouse complementary DNA (pDHFR 26) which contains the coding sequence for DHFR, to identify the DHFR-related DNA and RNA. Our results revealed no major differences in DNA gene structure as the copy number increases. The recognizable fragments of DHFR gene were similar including the 5' flanking sequence upstream from the first exon. We observed that all DHFR mRNA species identified were present in the subclones. The content of cytoplasmic DHFR mRNA does not always correlate with the relative gene copy number in these cell lines. Furthermore, we were able to detect high-molecular-weight RNA related to DHFR which might be the precursors of the DHFR mRNAs. Finally, using different RNA extraction procedures, we observed that different patterns of cytoplasmic DHFR mRNA can be obtained, which is probably due to differential breakdown of RNA species during extraction procedures.

Base Sequence↗
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↗
PubMedDate not supplied

Quantitative reverse transcription-PCR-HPLC for nerve growth factor mRNA using a deletion RNA as an internal standard.

We have developed a convenient method for the routine measurement of the absolute amount of nerve growth factor (NGF) mRNA in tissue samples. The method consists of RNA extraction, amplification by reverse transcription-PCR and detection by high-performance liquid chromatography. The addition of a deletion mutant RNA to tissue samples as an internal standard enabled correction for RNA recovery during extraction, and the target mRNA and the internal standard were both amplified with the same PCR primers. The conditions were optimized so that the procedure was conducted in the region where the calibration curve was linear, thereby allowing high reproducibility and reliability. The method was applied to the measurement of NGF mRNA in tissues such as skin and skeletal muscle, where the levels are too low to be easily detected by Northern blotting analysis: skin, 14.1 +/- 4.6 fg/mg tissue and skeletal muscle, 11.0 +/- 2.2 fg/mg tissue (mean +/- SD, n = 10). The coefficient of variation of this method was less than 2.8%. This approach should also be applicable to the routine assay of the absolute amount of other mRNAs present at low levels in tissues.

Animals↗
PubMed1995

Detection of HIV-1 RNA in plasma and serum samples using the NASBA amplification system compared to RNA-PCR.

The presence of HIV-1 RNA in the plasma and serum of European and African patients was monitored using RNA-polymerase chain reaction (RNA-PCR) and the new isothermal NASBA nucleic acid amplification system encompassing a gel-based detection assay (ELGA). Identical RNA extraction procedures, provided by the NASBA amplification system, were used for both methods. The detection limit for HIV-1 RNA, measured on a 10-fold dilution series of spiked HIVIIIB in negative plasma, was about 0.05 CCID50 per test for both methods. Both NASBA and RNA-PCR were more sensitive than a p24 assay for the detection of circulating HIV-1 virus in blood: 17 of the 34 (50%) p24 antigen-tested seropositives were p24-positive while 32 (94%) were positive by NASBA and 30 (88%) by RNA-PCR. Among the 45 seropositives, 34 of which were tested for p24 antigen, 43 (96%) were positive by NASBA and 41 (91%) by RNA-PCR. Almost all seropositives had a detectable viral load in 100 microliters plasma. Lower viral loads were only encountered in some healthy seropositives with a higher CD4 count. There was no cross-reactivity with HIV-2 or HIV-I with both the RNA-PCR and NASBA. The extraction method used permitted the detection of HIV-1 RNA equally well in serum and in plasma with heparin or EDTA.

Africa↗
PubMed1985

No evidence for increased incidence of common cellular antigens recognized by Crohn's disease antisera.

Autoimmunity has been implicated in the pathogenesis of Crohn's disease. However, the molecular nature of the antigens involved is unknown. This study was undertaken to determine whether Crohn's disease antisera contain antibodies directed against any common cellular antigens. Antigenic proteins were investigated by immunoblotting after gel electrophoresis of cell extracts. RNA containing antigens were detected by in vivo labelling of cells and immunoprecipitation of cell extracts. No protein or RNA species specifically recognized by Crohn's disease antisera was detected. These results suggest that antibody mediated cell injury due to antisera containing antibodies to common cellular proteins does not occur in Crohn's disease.

Antigens↗
PubMed2003

[Molecular detection of yellow fever virus in human sera and mice brains].

A molecular method for the diagnosis of yellow fever virus infection was developed based on reverse transcription (RT) followed by polymerase chain reaction (PCR) amplification. Examinations were conducted on lyophilized sera from 3 fatal yellow fever cases and 4 fresh sera from 3 fatal cases and one from a symptomatic patient (positive IgM against yellow fever virus). Sera were extracted with TRIZOL-LS to isolate viral RNA for RT treatment and the PCR reaction included 2 primers sets designed specifically for yellow fever virus: sense, JM2104 (5'-CGTTGGGAGAGGAGATTC-3') y JM2249 (5'-TTCTTCACTTCGGTTGGG-3'), and antisense, JM2673 (5'-TCATCTGCCCTGCTTCTC-3') y JM2751 (5'-CCTCTCTGGTAAACATTCT-3'). The technique for demonstrating the yellow fever virus in tissue samples was used in infected mice brains treated with lysis buffer before RNA extraction. PCR reactions were evaluated in agarose gels where single bands of the expected size for each primers pair (569 bp and 502 bp) were observed for all serum samples. In addition, the results for 2 fresh positive sera were supported by histopathologic finding of yellow fever virus. The RT-PCR method permits a rapid and specific demonstration of the presence of yellow fever virus.

Animals↗
PubMed1975

Abundant species of poly(A)-containing RNA from Saccharomyces cerevisiae.

Hybridization experiments using uniformly labeled poly(A) RNA derived from Saccharomyces cerevisiae strains carrying the "killer character" showed that (1) these molecules appear to be transcribed from repetitive DNA sequences. (2) there are approximately 35 DNA template sequences that are transcribed into poly(A) RNA. It is concluded that under the RNA extraction procedure used, most of the poly (A) RNA represents killer-RNA as judged by the dependence of the kinetic complexity of poly(A) RNA on the genomic complexity of killer-RNA.

Formamides↗
PubMed1985

Polytranscripts of Sendai virus do not contain intervening polyadenylate sequences.

Discrete high-molecular-weight RNA species with the properties of polytranscripts were observed in poly(A)-rich RNA extracted from Sendai virus-infected cells. These RNA species were virus specific, being synthesized in the presence of actinomycin D, but not seen in uninfected cells. They were not genome or antigenome fragments, since they were not encapsidated, as shown by their destruction when ribonuclease was added to cell homogenates and by their absence from the RNA fractions that did not bind to oligo(dT)-cellulose. Two lines of evidence indicated that the gene-specific regions of these polytranscripts were not linked by poly(A) sequences, but were faithful copies of virus genomic RNA sequences at gene boundaries. First, a small cDNA clone obtained by reverse transcription of poly(A)-rich RNA species from infected cells contained 90 bases from the 5' terminus of the gene for the P protein and about 600 bases from the 3' end of the downstream gene, which specifies the M protein, the entire cloned sequence being an accurate complement of the genomic RNA. Second, dideoxynucleotide sequencing of poly(A)-rich RNA species primed by virus gene-specific oligodeoxynucleotides revealed read-through products of transcription containing no detectable poly(A). If Sendai virus polytranscripts are intermediates in the production of monocistronic viral mRNAs by a cleavage process, and poly(A) sequences do not link the mRNAs, polyadenylation would have to follow the cleavage step; it seems more likely that these polytranscipts are aberrant transcription products generated by occasional termination failure in a stop-start mechanism of transcription.

Base Sequence↗
PubMed1990

Analysis of genetic variability in human respiratory syncytial virus by the RNase A mismatch cleavage method: subtype divergence and heterogeneity.

We have applied the RNase A mismatch cleavage method to the analysis of genetic variability among human Respiratory Syncytial (RS) viruses. Antisense RNA probes of the Long strain were hybridized to total RNA extracted from cells infected with other strains. The RNA:RNA heteroduplexes were digested with RNase A and the resistant products analyzed by gel electrophoresis. Each virus generated characteristic band patterns with the different probes. Comparative analyses of the cleavage patterns indicate that antigenic subtypes correlate with genetically distinct viral groups. Viruses within each subtype, however, show substantial genetic heterogeneity and progressive accumulation of genetic changes with time. This heterogeneity is also observed among viruses of the same epidemic outbreak which cannot be distinguished with a panel of monoclonal antibodies. Different genes and gene regions also differ in their rates of change. These results are discussed in terms of RS virus evolution.

Cell Line↗
PubMed1989

Rapid isolation of morbillivirus nucleocapsid for genomic RNA cDNA cloning and the production of specific core protein antisera.

A procedure is described for the rapid isolation of canine distemper virus nucleocapsid, free from contaminating viral non-core and host cellular proteins. Nucleocapsid isolated in this manner is amenable to ultrastructural evaluation, protein isolation for the production of monospecific hyperimmune serum, and genomic RNA isolation for cDNA cloning. Nucleocapsid (NC) and a defective NC variant (Df-NC) isolated from 5.5 x 10(7) Vero cells infected with Ond-CDV is readily visualized on cesium gradients. The calculated density for NC is 1.2976 +/- 0.0033 g/ml and 1.2458 +/- 0.0056 g/ml for Df-NC. Ultrastructurally, NC appears as long uninterrupted strands, 1.6 +/- 0.1 microns in length, 21.2 +/- 1.7 nm in diameter, with well defined capsid subunits. Df-NC are truncated with a uniform length of 85.8 +/- 7.1 nm and a 24.5 +/- 1.3 nm diameter. A total of 2.1 +/- 0.2 mu of NC protein is obtained for every 1 x 10(6) cells infected; 89.7% of this mass is represented by a 61 kDa protein (N), 8.4% by a 75 kDa protein (P), and 1.9% by a 160-200 kDa protein (L), which is in agreement with the NC constituency of other paramyxoviruses. Viral N and P proteins, purified by 7.5% SDS-PAGE, were used in the production of hyperimmune serum. Specificity was demonstrated by Western blot analysis. Both antisera were capable of detecting viral antigen in persistently and lytically CDV infected cells by indirect immunofluorescence. A single high molecular weight species of nucleic acid was isolated from purified nucleocapsids compatible with a 14.6 kb morbillivirus genome. Although the efficiency of RNA extraction from purified NC was low (14.2%), sufficient RNA was obtained for gel analysis and the establishment of genomic RNA cDNA clones.

Antibodies, Viral↗
PubMed2006

A simple method for detection of rabies viral sequences in 16-year old archival brain specimens with one-week fixation in formalin.

Archival formalin-fixed and paraffin-embedded brain tissues are important source for diagnosis and molecular analysis. However, nucleic acids are particularly vulnerable to degradation during tissue processing. The brain cutting process usually is performed after 1 week of brain storage in formalin followed by embedding of each particular neuro-anatomical specimen in paraffin. A simple method of deparaffinization, proteinase K digestion and RNA extraction using the Boom technique to obtain rabies RNA in unbuffered, formalin-fixed and paraffin-embedded brain tissues kept at 30 degrees C for 16 years is described. Reverse transcription-polymerase chain reaction (RT-PCR) can be used to identify rabies viral N gene sequences of 150 bases in length in all patients, but not from every immunohistochemical (IHC)-positive specimen. Direct sequencing of 301bp of N gene was achieved in 4 of 7 patients. Results of sequencing a single sample of 1432 bases of N gene from a 24h processed formalin-fixed and paraffin-embedded rabies infected brain tissue after 1 month storage were in accord with those from frozen specimen analysis. It is strongly suggested that for further molecular analysis, a piece of fresh brain tissue should be saved prior to the brain sectioning process and stored no longer than 24h in formalin before embedding.

Animals↗
PubMed2006

Rapid and efficient purification of Cowpea chlorotic mottle virus by sucrose cushion ultracentrifugation.

A simple, economical and efficient method for isolation of Cowpea chlorotic mottle virus (CCMV) particles was developed. Abundant viral particles could be obtained with three steps of 10 min duration each of conventional differential centrifugations and one sucrose cushion ultracentrifugation step of 2 h. Characterization of purified virus assessed by transmission electron microscopy, polyacrylamide gel electrophoresis (PAGE) and Western blot revealed the typical isometric particles of CCMV without any visible contamination or degradation. RNA extracted from purified CCMV particles showed all four RNA components by agarose gel electrophoresis. Both purified virus particles and RNA were biologically active and initiated successful infection upon inoculation to cowpea.

Blotting, Western↗
PubMed1991

Expression of alpha B-crystallin in the developing rat kidney.

The expression and cellular localization of alpha B-crystallin during rat renal development was studied by Northern blot analysis and by immunocytochemistry. Northern blotting of total RNA extracted from whole kidneys revealed that the messenger RNA for alpha B-crystallin rapidly increased after birth to reach adult levels by 20 days. At the same time, immunohistochemistry for alpha B-crystallin demonstrated that the prominent elongation of Henle's loop during the first 10 days of life was accompanied by increased alpha B-crystallin expression. Thus, the development of alpha B-crystallin expression is correlated temporally with the acquisition of tubule function in early post-natal life.

Animals↗
PubMed1998

Simple competitive two-step RT-PCR assay to monitor minimal residual disease in CML patients after bone marrow transplantation.

Quantitative reverse transcription-polymerase chain reaction (Q-RT-PCR) assessing the amount of transcripts of the BCR/ABL gene, the molecular marker of chronic myeloid leukemia (CML), is the only method sensitive enough for monitoring of minimal residual disease (MRD) in CML patients after bone marrow transplantation (BMT). In this study we present a simple modification of competitive Q-RT-PCR using natural competitors from cell lines K562 and BV173. The competitors were used in the form of unpurified RNA in cell lysates which ensured their high stability. Mixing competitors and samples before RNA extraction eliminated problems with quantification of cDNA or RNA entering the competitive reaction and with checking for the RNA quality and reverse transcription (RT) efficiency. The bulk of the malignant clone was expressed as the number of leukemic cells in 10(6) leukocytes when the overproduction of the BCR/ABL mRNA in the cell lines we used as competitors was taken into account. It was found to be 82-fold and 14-fold in K562 and BV173, respectively, in comparison with 100% Ph-positive CML standard. The assay reliability was verified by comparison of results with the mathematical model of competitive PCR. The assay is highly reproducible and sensitive (10(-5)). Its accuracy was proved to be excellent in a wide range of malignant cell concentrations. The method is demonstrated on three CML patients suffering from MRD after BMT. In conclusion, this method fulfills all criteria of competitive Q-RT-PCR. Because of its simplicity it is suitable for clinical laboratories and due to the high stability of the lysates used it may serve in the standardization of results between different laboratories.

Binding, Competitive↗
PubMed1976

Viral factors required for interferon induction by Newcastle disease virus in mouse macrophages and chicken embryo cells.

The triggering mechanism for interferon synthesis in mouse peritoneal macrophages and chick embryo (CE) cells by Newcastle disease virus (NDV) exposed to hydroxylamine or homologous antiserum was investigated in relation to the intracellular fate of these agents. Inactivation of NDV at 22 degrees C by I M-hydroxylamine proceeded with first-order kinetics, whereas the interferon-inducing capacity of hydroxylamine-treated virus in macrophages was unimpaired. In contrast to infective NDV, hydroxylamine-inactivated virus produced interferon in CE cells, and such a virus still had partial RNA-dependent RNA polymerase activity. Hydroxylamine-inactivated NDV was adsorbed to and uncoated in both normal and chloroquine diphosphate treated cells, but no viral double-stranded RNA was detected. Hydroxylamine treatment of virion-extracted RNA and neutralization of intact virions by antibody abolished the capacity of the virus to induce interferon. Infective as well as neutralized NDV interacted with macrophages to the same degree, but association between NDV and CE cells was prevented by antibody-coating. In macrophages, the RNA of neutralized NDV became more sensitive to RNase than RNA of infective NDV, but this process was inhibited in chloroquine diphosphate-treated cells. These results suggest that interferon induction by NDV involves components of the virion which are present up to the regular uncoating process.

Animals↗
PubMed1977

Aminoacylation of encephalomyocarditis virus RNA.

RNA extracted from purified encephalomyocarditis (EMC) virus (EMC-RNA) can be aminoacylated with synthetase praparations from Escherichia coli, beef and rabbit liver. The extent of aminoacylation is between 0-024 and 0-080 moles per mole EMC-RNA and occurs only with serine. Either removal of possible low mol. wt. contaminants with 3 M-sodium acetate nor periodate oxidation of the virus RNA affects its aminoacylation capacity.

Amino Acids↗
PubMed1980

Rabies virus-induced RNA synthesis in BHK21 cells.

Rabies virus polysomes contained two sizes of messenger RNAs, one of which had a sedimentation value of 30S and another which sedimented at 12 to 16S. RNA extracted from infected cultures contained virion-size RNA, 42S, as well as 30S and 12 to 16S RNA species. Hybridization studies indicated that the 30S and 12 to 16S RNAs had nucleotide sequences which were complementary to virion RNA. RNA. RNA isolated from virus polysomes contained adenylate-rich sequences which were heterogeneous in size and were determined to be about 100 to 250 nucleotides in length on the basis of their migration rates in polyacrylamide gels. Acid-urea agarose gel electrophoresis established that the 30S RNA material was composed of a single RNA species (mol. wt. greater than or equal to 1.65 X 10(6)), whereas the 12 to 16S material could be resolved into at least four distinct species whose mol. wt. ranged from 0.28 to 0.87 X 10(6). When labelled rabies-infected cell RNAs, which were purified by oligo(dT)-cellulose chromatography, were annealed to excess unlabelled virus RNA, digested with ribonuclease T2 and the RNA duplex molecules analysed by polyacrylamide gel electrophoresis, five duplexes could be separated. The mol. wt. of these duplexes were estimated to be 3.2, 1.4, 0.96, 0.55 and 0.39 X 10(6), when compared to the known mol. wt. of vesicular stomatitis virus (VSV) RNA duplexes. This study suggests that the replicative processes of rabies virus are very similar to VSV and that rabies virus proteins are probably translated from smaller than virion-size RNAs.

Animals↗
PubMed2000

Isolation of Hendra virus from pteropid bats: a natural reservoir of Hendra virus.

Since it was first described in Australia in 1994, Hendra virus (HeV) has caused two outbreaks of fatal disease in horses and humans, and an isolated fatal horse case. Our preliminary studies revealed a high prevalence of neutralizing antibodies to HeV in bats of the genus PTEROPUS:, but it was unclear whether this was due to infection with HeV or a related virus. We developed the hypothesis that HeV excretion from bats might be related to the birthing process and we targeted the reproductive tract for virus isolation. Three virus isolates were obtained from the uterine fluid and a pool of foetal lung and liver from one grey-headed flying-fox (Pteropus poliocephalus), and from the foetal lung of one black flying-fox (P. alecto). Antigenically, these isolates appeared to be closely related to HeV, returning positive results on immunofluorescent antibody staining and constant-serum varying-virus neutralization tests. Using an HeV-specific oligonucleotide primer pair, genomic sequences of the isolates were amplified. Sequencing of 200 nucleotides in the matrix gene identified that these three isolates were identical to HeV. Isolations were confirmed after RNA extracted from original material was positive for HeV RNA when screened on an HeV Taqman assay. The isolation of HeV from pteropid bats corroborates our earlier serological and epidemiological evidence that they are a natural reservoir host of the virus.

Animals↗