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PubMed2001

Nucleotide sequence of the coat protein gene of Lettuce big-vein virus.

A sequence of 1425 nt was established that included the complete coat protein (CP) gene of Lettuce big-vein virus (LBVV). The LBVV CP gene encodes a 397 amino acid protein with a predicted M(r) of 44486. Antisera raised against synthetic peptides corresponding to N-terminal or C-terminal parts of the LBVV CP reacted in Western blot analysis with a protein with an M(r) of about 48000. RNA extracted from purified particles of LBVV by using proteinase K, SDS and phenol migrated in gels as two single-stranded RNA species of approximately 7.3 kb (ss-1) and 6.6 kb (ss-2). After denaturation by heat and annealing at room temperature, the RNA migrated as four species, ss-1, ss-2 and two additional double-stranded RNAs (ds-1 and ds-2). The Northern blot hybridization analysis using riboprobes from a full-length clone of the LBVV CP gene indicated that ss-2 has a negative-sense nature and contains the LBVV CP gene. Moreover, ds-2 is a double-stranded form of ss-2. Database searches showed that the LBVV CP most resembled the nucleocapsid proteins of rhabdoviruses. These results indicate that it would be appropriate to classify LBVV as a negative-sense single-stranded RNA virus rather than as a double-stranded RNA virus.

Amino Acid Sequence↗
PubMed2007

The nine C-terminal amino acids of the respiratory syncytial virus protein P are necessary and sufficient for binding to ribonucleoprotein complexes in which six ribonucleotides are contacted per N protein protomer.

The respiratory syncytial virus (RSV) phosphoprotein (P) is a major polymerase co-factor that interacts with both the large polymerase fragment (L) and the nucleoprotein (N). The N-binding domain of RSV P has been investigated by co-expression of RSV P and N proteins in Escherichia coli. Pull-down assays performed with a series of truncated forms of P fused to glutathione S-transferase (GST) revealed that the region comprising the last nine C-terminal amino acid residues of P (233-DNDLSLEDF-241) is sufficient for efficient binding to N. Site-directed mutagenesis shows that the last four residues of this peptide are crucial for binding and must be present at the end of a flexible C-terminal tail. The presence of the P oligomerization domain (residues 100-160) was an important stabilizing factor for the interaction. The tetrameric full-length P fused to GST was able to pull down both helical and ring structures, whereas a monomeric C-terminal fragment of P (residues 161-241) fused to GST pulled down exclusively RNA-N rings. Electron-microscopy analysis of the purified rings showed the presence of two types of complex: undecamers (11N) and decamers (10N). Mass-spectrometry analysis of the RNA extracted from rings after RNase A treatment showed two peaks of 22,900 and 24,820 Da, corresponding to a mean RNA length of 67 and 73 bases, respectively. These results suggest strongly that each N subunit contacts 6 nt, with an extra three or four bases further protected from nuclease digestion by the ring structure at both the 5' and 3' ends.

Amino Acid Substitution↗
PubMed1979

Cell-free cytoplasmic polyadenylation of oogenic RNA.

The products of cell-free ATP incorporation mediated by cytoplasmic fractions prepared from unfertilized sea urchin eggs, anucleate egg halves, nucleate egg halves, emetine-treated fertilized eggs, and four-cell embryos have been characterized to determine to what extent the polymers synthesized are poly(A) and to assess the size distribution of the primers adenylated. As judged by alkaline lability, ribonuclease resistance, and retention on poly(U)-impregnated filters, greater than 92% of the label recovered after RNA extraction is present in poly(A). LiCl fractionation indicates that little, if any, free poly(A) is synthesized or cleaved from RNA primers during the reaction, and that 4S RNA is not an effective initiator. In excess of 85% of the poly(A) is associated with RNA having S-values greater than or equal to 18S. Sedimentation profiles of RNA adenylated in the unfertilized egg and anucleate egg half reactions are identical. Suppression of in vivo protein synthesis by emetine alters the profile of RNA subsequently adenylated in vitro. It is proposed that the apparent constraints on the utilization of cytoplasmic RNA or ribonucleoprotein primers of oogenic origin may be effected by RNA-associated proteins capable of regulating the selection and/or extent of their polyadenylation during early embryogenesis.

Adenosine Triphosphate↗
PubMed1980

Antagonistic action between antibodies directed against 7-methylguanosine and polyamines on translation in vitro of RNA induced by measles virus.

Antibodies directed against N7-methylguanosine (m7Guo) were prepared and added to a wheat germ cell-free protein-synthesizing system programmed with RNA extracted from monkey cells persistently infected with measles virus. A dose-dependent inhibition of [35S]methionine incorporation was observed when RNA was preincubated with anti-m7Guo immunoglobulins. Antibodies preincubated with m7Guo did not show any inhibiting activity. The inhibitory effect of antibodies was abolished when RNA was preincubated with immunoglobulins in the presence of spermine and spermidine. When polyamines were added to the assay programmed with the IgG-RNA complex, no inhibition was observed.

Animals↗
PubMed1996

Introduction of a new hepatitis agent in retrospect: genetic studies of Swedish hepatitis D virus strains.

The supposedly first outbreak of hepatitis D virus (HDV) infection in Sweden occurred among intravenous drug addicts in the Malmö area in the mid-1970s. Stored sera from this outbreak were used for viral RNA extraction and analysis. By sequence comparisons, the HDV genomes from those Swedish patients fell into two separate clusters, within which the RNA sequences were closely related. These two HDV groups genetically resembled the French and US-1 isolates of genotype I, respectively, indicating that there had been at least two separate sources of HDV infection. The genetic alterations of the HDV RNA were investigated by sequence analysis of nine annually drawn serum samples from one patient and paired samples collected between 2 and more than 10 years apart from six patients with chronic HDV infection. Only mutational changes were observed, and no insertion or deletion appeared throughout the periods observed. It was found that the Swedish HDV isolates mutationally evolved at an average rate of 1.1 x 10(-3) substitutions per nucleotide per year over a long time course of chronic HDV infection, which is of the same magnitude as that of other RNA viruses.

Adult↗
PubMed2005

Dynamic range of hepatitis C virus RNA quantification with the Cobas Ampliprep-Cobas Amplicor HCV Monitor v2.0 assay.

Accurate quantification of hepatitis C virus (HCV) RNA is needed in clinical practice to decide whether to continue or stop pegylated interferon-alpha-ribavirin combination therapy at week 12 of treatment for patients with chronic hepatitis C. Currently the HCV RNA quantification assay most widely used worldwide is the Amplicor HCV Monitor v2.0 assay (Roche Molecular Systems, Pleasanton, Calif.). The HCV RNA extraction step can be automated in the Cobas Ampliprep device. In this work, we show that the dynamic range of HCV RNA quantification of the Cobas Ampliprep/Cobas Amplicor HCV Monitor v2.0 procedure is 600 to 200,000 HCV RNA IU/ml (2.8 to 5.3 log IU/ml), which does not cover the full range of HCV RNA levels in infected patients. Any sample containing more than 200,000 IU/ml (5.3 log IU/ml) must thus be retested after dilution for accurate quantification. These results emphasize the need for commercial HCV RNA quantification assays with a broader range of linear quantification, such as real-time PCR-based assays.

Antiviral Agents↗
PubMed1995

Molecular characterization of the 3' terminus of the simian hemorrhagic fever virus genome.

The 3' end of the simian hemorrhagic fever virus (SHFV) single-stranded RNA genome was cloned and sequenced. Adjacent to the 3' poly(A) tract, we identified a 76-nucleotide noncoding region preceded by two overlapping reading frames (ORFs). The ultimate 3' ORF of the viral genome encodes the capsid protein, and the penultimate ORF encodes the smallest SHFV envelope protein. These two ORFs overlap each other by 26 nucleotides. Northern (RNA) blot hybridization analyses of cytoplasmic RNA extracts from SHFV-infected MA-104 cells with gene-specific probes revealed the presence of full-length genomic RNA as well as six subgenomic SHFV-specific mRNA species. The subgenomic mRNAs are 3' coterminal. In its virion morphology and size, genome structure and length, and replication strategy, SHFV is most similar to lactate dehydrogenase-elevating virus, equine arteritis virus, and porcine reproductive and respiratory syndrome virus.

Amino Acid Sequence↗
PubMed2004

Hyperexpression of low-density lipoprotein receptors and hydroxy-methylglutaryl-coenzyme A-reductase in human pinguecula and primary pterygium.

PURPOSE: There is now increasing evidence that pterygium and pinguecula are tumorlike tissues and that cell growth and DNA replication are closely linked to cholesterol metabolism. In this study, the expression of two main genes correlated to cholesterol metabolism--namely, the low-density lipoprotein receptor (LDL-R) gene and the hydroxy-methylglutaryl-coenzyme A-reductase (HMG-CoA-R) gene--were investigated in primary pterygium, pinguecula, and normal conjunctiva. METHODS: Pterygium, pinguecula, and normal conjunctiva samples were obtained from 30 eyes (50% men) at the time of surgery. Total RNA extracted from the specimens was subjected to semiquantitative reverse transcription-polymerase chain reaction (RT-PCR). Equal amounts of total RNA were reverse transcribed into cDNA. The cDNA was subsequently amplified by the PCR in the presence of specific primers for low-density lipoprotein receptor (LDL-R) and for hydroxy-methylglutaryl coenzyme A reductase (HMG-CoA-R). RESULTS: Semiquantitative RT-PCR analysis revealed that the mRNA levels of LDL-R and HMG-CoA-R were increased in pterygia, compared with levels in both pingueculae and normal conjunctivae. Differences were statistically significant (P <0.05), including pingueculae versus normal conjunctivae. CONCLUSIONS: This study indicates that pterygium and pinguecula have an altered metabolism of cholesterol-namely increased LDL-R and HMG-CoA-R mRNAs-as is characteristic of tumorlike tissues, and that the high expression of LDL receptors renders them amenable to be treated by photodynamic therapy with intravenously injected verteporfin.

Cholesterol↗
PubMed1992

Grouping of hantaviruses by small (S) genome segment polymerase chain reaction and amplification of viral RNA from wild-caught rats.

A single pair of consensus primers in the polymerase chain reaction (PCR) amplified a conserved region of the small genome segment of twenty hantavirus isolates. Isolates tested included representatives of the four recognized hantaviruses, Hantaan, Seoul, Puumala and Prospect Hill, as well as isolates from Mus musculus (Leakey), Bandicota indica (Thailand 749), and Suncus murinus (Thottapalayam). Viruses from the Nairovirus and Phlebovirus genera yielded negative results. The amplification products were 281-nucleotide pairs (np) in length, with the exception of Thottapalayam, which had an amplification product of approximately 320 np. Products of all isolates were detected by Southern hybridization with a 32P-labeled Hantaan 76-118 amplicon, while an oligonucleotide probe to a conserved region of the amplified fragment failed to detect some isolates of Seoul and Puumala viruses. Restriction endonuclease analysis allowed three groupings: Hantaan-like viruses, Seoul-like viruses, and a diverse group of patterns for the other viruses. Differences were found within the Seoul-like virus group by this method, whereas the Hantaan-like viruses were shown to be similar. RNA extracted from tissues of seropositive and seronegative rats trapped in Baltimore showed the practical application of the test. Hantavirus-specific RNA was detected in 12 (92%) of 13 seropositive rats, but not in seronegative rats. This simple method for detecting and characterizing hantaviruses has potential for epidemiologic studies and for diagnosing human hantavirus infections.

Animals↗
PubMed1975

Alteratons in RNA synthesis in lymphotoxin-treated target cells.

Lymphotoxin, a cellular mediator produced in vitro by antigen- or mitogen-stimulated lymphocytes, is capable of lysing various types of cells. We have shown that highly purified lymphotoxin preparations both mediate cytolysis and stimulate RNA synthesis in target cells. When RNA extracts from lymphotoxin-treated cells were examined by means of sucrose density gradient centrifugation, we observed a general increase in RNA synthesis, accentuated in species larger than 28S. Analysis on oligo(dT)-cellulose columns revealed a relatively larger increase in adenine-rich m-RNA. In concordance with this finding, we observed a moderate increase in RNA polymerase I (nucleolar) activity and a striking increase in RNA polymerase II (nucleoplasmic) activity in isolated nuclei of lymphotoxin-treated target cells.

Animals↗
PubMed1991

Expression of rat jejunal cystine carrier in Xenopus oocytes.

Functional interactive cystine-lysine carriers have been expressed in Xenopus oocytes following the injection of RNA extracted from rat intestinal mucosa. Lysine-inhibitable cystine uptake was able to be measured 16 h after oocyte injection with RNA. The longer the oocytes were maintained after injection, the more cystine transport capability was induced. Uninjected or water-injected oocytes showed virtually no lysine-inhibitable cystine uptake, and no system developed after the oocytes had been isolated and maintained in vitro. The cystine uptake expressed after RNA injection was selectively inhibited by dibasic amino acids and phenylalanine but not by other amino acids or alpha-methyl-D-glucoside. Expression of the interactive cystine-lysine system was induced only by RNA isolated from intestinal tissue and not by RNA from rat liver. The Km for cystine uptake in RNA-injected oocytes was 0.01 mM and appears identical to the single system found in the RNA source tissue.

Animals↗
PubMed1986

Identification of a bovine enteric syncytial virus as a nongroup A rotavirus.

An atypical or nongroup A rotavirus was identified in feces obtained from gnotobiotic calves in which fecal preparations originally derived during an epizootic of neonatal calf diarrhea had been serially passaged. The epizootic was previously reported to be caused by a noncharacterized viral agent that induced the formation of epithelial syncytia on small intestinal villi of experimentally infected calves. This bovine, nongroup A rotavirus was found to be antigenically related to a described atypical rotavirus of rats by immunofluorescence and by enzyme immunoassay. Complementary DNA derived from the atypical rat rotavirus cross hybridized with RNA obtained from the bovine virus, but not with RNA extracted from group A rotaviruses. Complementary DNA derived from SA-11 group A rotavirus cross hybridized with other group A rotavirus RNA, but not with RNA obtained from either the rat or bovine nongroup A isolates. Additionally, another similar, if not identical, bovine atypical rotavirus was identified in a second epizootic of neonatal calf diarrhea that occurred several hundred kilometers and 8 months apart from the original epizootic.

Animals↗
PubMed1993

Direct extraction and purification of rRNA for ecological studies.

Microgram quantities of rRNA were recovered from natural microbial communities in sediment, soil, and water with a lysozyme-hot phenol direct extraction method. Gel filtration with Sephadex G-75 spun columns readily removed humic-like contaminants without any measurable loss of rRNA and rendered RNA extracts of sufficient quality for molecular procedures.

Bacteria↗
PubMed1996

Myotonic protein kinase expression in human and bovine lenses.

Myotonic dystrophy (DM) is an autosomal dominant trait closely associated with CGT repeat expansions in the same locus on human chromosome 19q13.3. The expansions occur in the 3'untranslated region of a transcription unit encoding a serine-threonine kinase (DM kinase) of a new class based upon structure and function. Lens cataracts are a prominent finding in myotonic dystrophy. DM kinase was shown to be expressed in human and bovine lenses at the RNA level and in human lenses at the protein level. Sequencing of PCR products of RNA extracted from normal human lenses demonstrated an exact match to published genomic and cDNA 3' UTR sequences. Northern blots of bovine lens RNA showed that the transcript is similar in size to the transcript detected in other tissues that are affected in myotonic dystrophy. A polyclonal antibody (DM-2) was produced against recombinant DM protein kinase in rabbits. Development of Western blots with DM-2 showed a single reactive band of 67 kDa. Immunofluorescent studies of formalin-fixed human lens sections detected the DM kinase in the perinuclear cytoplasm of normal human lens epithelial cells and more diffusely in superficial subcapsular cortical fibers. In contrast, the same antibody labeled the nucleus most prominently in a single DM lens.

Animals↗
PubMed1978

In situ hybridization of nuclear and cytoplasmic RNA to locus 2-48BC in Drosophila hydei.

The maximum grain density over the "heat-shock" locus 2-48BC of Drosophila hydei polytene chromosomes obtained after in situ hybridization of nuclear RNA extracted from tissue culture cells labelled during incubation at 37 degrees C is five times higher than that obtainable by using polysomal RNA isolated from the same cells. Furthermore, the addition of a large excess of unlabelled polysomal RNA reduced the amount of in situ hybridization of nuclear RNA by only 20% showing that nuclear 2-48BC RNA contains sequences not present in polysomal 2-48BC RNA.--The polysomal 2-48BC RNA is polyadenylated, as are the RNA sequences present in the polysomes complementary to the other two major "heat shock" loci 2-32A and 2-36A. Polyadenylated RNA, with an apparent size of 15S, complementary to locus 2-48BC is also found in the cytoplasm of D. hydei salivary glands.

Animals↗
PubMed1975

Characterization of inactivation of myxoviruses and paramyxoviruses by hydroxylamine, N-methylhydroxylamine and O-methylhydroxylamine.

A study of the mechanism of myxovirus and paramyxovirus inactivattion by hydroxylamine, O-methylhydroxylamine and N-methylhydroxylamine was conducted. Influenza A (WSN) was used as the sensitive myxovirus and Newcastle disease virus (NDV-L) was used as the relatively resistant paramyxovirus in certain experiments. Inactivation was found to be rapid (15 minutes) and mose effective at high concentrations (2M). All three compounds significantly decreased the hemagglutination titer of WSN treated at pH smaller than or equal to 5.0. There was no detectable change in NDV hemagglutination titer. Adsorption of hydroxylamine (pH 7.0) inactivated WSN appeared normal; however, the rate of adsorption was decreased when virus was inactivated by (pH 5.0) O-methylhydroxylamine. Equilibrium density gradient centrifugation in potassium tartrate showed no density changes in inactivated virus. WSN inactivated virus. WSN inactivated with 14C-O-methylhydroxylamine and subjected to RNA extraction showed greater than or equal to 35 percent of the 14C in the phenol phases and 21 per cent in the RNA. The 14C-O-methylhydroxylamine associated with the RNA of insensitive NDV was about 3 per cent of that associated with sensitive WSN-RNA. Hydroxylamine has no apparent effect on paramyxovirus (NDV) hemagglutination titer and less 14C-O-methylhydroxylamine is associated with the RNA of this virus. The results suggest these compounds may affect both the RNA and the envelope portion of myxoviruses (WSN) to produce inactivation.

Adsorption↗
PubMed1996

Ensuring recovery of intact RNA from rat pancreas.

The isolation of intact RNA from rat pancreas is compromised by autolysis and by the presence of endogenous ribonucleases. In order to ameliorate recovery we systematically investigated available RNA extraction methods and paid particular attention to the influence of frozen storage and ribonuclease inhibition strategies on overall yield and quality of RNA. Modifications to the basic procedure of Chomczynski and Sacchi (1987) are described which allow, reproducibly, to obtain rat pancreatic RNA suitable for Northern blot hybridization, RT-PCR, and differential display analysis.

Animals↗
PubMed1994

Accurate and differential quantitation of HIV-1 tat, rev and nef mRNAs by competitive PCR.

An accurate method is described for measuring the relative abundance of HIV-1 regulatory mRNAs directly in clinical specimens. Specimen RNA is reverse transcribed and coamplified with a common competitor containing tat, rev and nef internal standards using fluorescent primers and a competitive polymerase chain reaction. After amplification, individual products are separated and analyzed on a fluorescent DNA sequencer. Using this approach, it was possible to measure reproducibly two-fold differences in the relative abundance of mRNAs with coding potential for tat, rev and nef from as little as 0.2 ng of total RNA extracted from peripheral blood mononuclear cells of HIV-1 infected persons. The ratio method eliminates the need to account for variability in RNA recovery during sample processing and provides a powerful tool for measuring the differential expression of HIV-1 regulatory genes in vivo.

Acquired Immunodeficiency Syndrome↗