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At least 1,117 records · Page 62Linked to original sources
PubMed1993

Transcriptional analysis of the virion-sense genes of the geminivirus beet curly top virus.

The genome of the geminivirus beet curly top virus (BCTV) consists of a single circular DNA containing overlapping open reading frames (ORFs) located on both the virion-sense and complementary-sense DNA strands. To investigate the expression of these ORFs, RNA extracted from infected Nicotiana benthamiana and Beta vulgaris has been examined for the presence of viral transcripts. An abundant 1.1-kb virion-sense polyadenylated RNA and four complementary-sense polyadenylated RNAs of 1.7, 1.5, 1.3, and 0.7 kb have been identified by northern blot hybridization, confirming the bidirectional transcription strategy implied by the arrangement of ORFs. We previously demonstrated that two overlapping virion-sense ORFs are involved in coat protein synthesis (ORF V1) and viral single-stranded DNA accumulation (ORF V2). Mutants of a third virion-sense ORF (ORF V3), located upstream and overlapping ORFs V1 and V2, retain the ability to replicate efficiently in N. benthamiana leaf discs but produce an asymptomatic infection in N. benthamiana and B. vulgaris at low frequency, associated with reduced levels of viral DNA compared to wild-type infection. Our data support the recent suggestion that ORF V3 participates in virus movement. The 1.1 kb virion-sense RNA comprises a population of overlapping transcripts with 5' termini suitably positioned for the expression of ORFs V1, V2, and V3. The overlapping arrangement of the transcripts and juxtaposition of putative regulatory elements could provide a means for the temporal control of virion-sense gene expression.

Amino Acid Sequence↗
PubMed1985

Increased type I procollagen mRNA levels and in vitro protein synthesis in the baboon model of chronic alcoholic liver disease.

We have investigated the molecular mechanisms responsible for the histologic changes induced by ethanol in the baboon model of alcoholic liver disease. Eleven ethanol-fed baboons and their pair-fed controls had histology evaluated and RNA extracted from percutaneous liver biopsy specimens. In 6 of the ethanol-fed animals, fatty liver developed, but no significant differences were found when the RNA from the control and ethanol-fed livers was translated in the reticulocyte lysate system or analyzed with specific cDNA probes. Five of the baboons given ethanol, however, developed significant fibrosis. Molecular evaluation revealed that the RNA from these livers was more active in in vitro protein synthesis, and the type I procollagen mRNA content was significantly higher per microgram of liver RNA as determined by hybridization analysis (183% +/- 23% SEM of control, p less than 0.02). In addition, there were higher levels of albumin mRNA content in the livers of ethanol-fed baboons that developed fibrosis (180% +/- 21% SEM of control, p less than 0.05). There was no change, however, in the levels of beta-actin mRNA, a representative constitutive protein. These findings in the baboon model of alcoholic fibrosis show that ethanol consumption increases type I procollagen mRNA, which may foster fibrogenesis; increases albumin mRNA content without causing an increase in serum albumin; and induces no change in levels of beta-actin mRNA. These studies also show that percutaneous needle biopsy can supply sufficient tissue to evaluate molecular changes in human liver disease.

Actins↗
PubMed1990

Reduced DNA topoisomerase II in VP-16 resistant mouse breast cancer cell line.

VP-16 resistant cells, FvprB350 (50B-3), were isolated from mouse breast cancer cell line FM3A. 50B-3 cells showed 84-fold higher resistance than their parent cells. Reduced drug uptake was not found in resistant cells. Quantitative analysis of drug-stimulated DNA cleavage activity using 3'32P end-labeled pBR322 restriction fragments showed that VP-16 stimulated DNA-topoisomerase II cleavable complex forming activity in crude nuclear extract from 50B-3 cells was approximately one-fifth as compared with that of FM3A wild-type cells. Dot-blot analysis of RNA extracted from the two cell lines showed that mRNA levels of topoisomerase II in 50B-3 cells drastically decreased and catalytic activity was also 1/2-1/3 as compared with that of parent cells. 50B-3 cells showed cross resistance to VM-26, m-AMSA, adriamycin. These findings suggest that reduced topoisomerase II activity (cellular levels) and cleavable complex forming activity may be significant factors in the marked drug resistance.

Animals↗
PubMed2005

Optimization of fragmentation conditions for microarray analysis of viral RNA.

An important consideration in microarray analysis of nucleic acids is the efficiency with which the target molecule is captured by, or hybridized to, surface-immobilized oligos. For RNA, secondary and tertiary structure of the target strand can significantly decrease capture efficiency. To overcome this limitation, RNA is often fragmented to reduce structural effects. In this study, the metal ion-catalyzed base hydrolysis fragmentation conditions for viral RNA extracted from influenza viruses were evaluated and the hybridization efficiency of the resulting fragments was determined as a function of fragment length. The amount of RNA captured was evaluated qualitatively by fluorescence intensity normalized to an internal standard. Optimized conditions for influenza RNA were determined to include a fragmentation time of 20-30 min at 75 degrees C. These conditions resulted in a maximum concentration of fragments between 38 and 150 nt in length and a maximum in the capture and label efficiency.

Base Sequence↗
PubMed1988

Direct detection of HIV RNA expression in seropositive subjects.

The polymerase chain reaction (PCR) and reverse transcription were used to assess human immunodeficiency virus type 1 (HIV1) RNA expression in peripheral blood mononuclear cell samples from seropositive subjects. HIV RNA was detected from seropositive subjects who had no symptoms, lymphadenopathy syndrome, and acquired immunodeficiency syndrome. DNA PCR of the samples used for RNA extraction showed that seventeen of eighteen (94%) contained HIV proviral DNA. Eleven (65%) of the seventeen DNA-positive samples were also positive for HIV RNA, including samples from four patients undergoing antiviral drug treatment. Serum HIV antigen assays detected only six (32%) of the nineteen PCR-positive samples. Owing to the speed and high sensitivity of PCR for HIV detection, this technique will be suitable for monitoring antiviral therapy and the virus load of people with HIV infections.

Cells, Cultured↗
PubMed1974

Distribution of repetitive and nonrepetivite sequence transcripts in HeLa mRNA.

Polyadenylated messenger RNA extracted from HeLa cells was hybridized with a mass excess of HeLa DNA. The kinetics of the hybridization reaction demonstrated that most of the messenger RNA is transcribed from nonrepetitive DNA. The amount of messenger RNA hybridized to DNA was measured both with and without prior RNase treatment. Comparison of the results indicates that within the limits of detection, HeLa messenger RNA does not contain repetitive sequence elements covalently linked to nonrepetitive sequence transcripts. However, a small fraction of the HeLa messenger RNA preparation is transcribed entirely from repetitive DNA sequences. This fraction represents about 6% of the total polyadenylated messenger RNA preparation.

Adenosine↗
PubMed1992

DM-20 mRNA is expressed during the embryonic development of the nervous system of the mouse.

We used both the polymerase chain reaction (PCR) and in situ hybridization to search for the presence of proteolipid protein (PLP) gene transcripts in the developing mouse. Total brain RNA extracted from 13-19-day embryos, analyzed by PCR, demonstrated the presence of a single transcript that was unambiguously identified with the DM-20 mRNA. RNA samples from postnatal day 2 animals also showed a signal corresponding to the PLP transcript, in addition to the DM-20 message. By in situ hybridization of 10-day embryos using a DM-20 antisense cRNA probe, we showed that the localization of the DM-20 message was restricted to the diencephalic basal plate. On the same embryo sections, in addition to the brain localization, an intense hybridizing signal was also detected in the trigeminal and spinal ganglia, the vagal glossopharyngeal ganglion, and the sympathetic ganglion chain. The demonstration of transcription of the PLP gene, long before the beginning of the myelination process, suggests that in addition to a structural function in myelin compaction, some of the products of the PLP gene (DM-20) may have a role during the compartmentalization and differentiation of the neural tube.

Animals↗
PubMed2003

Recovery of infectious foot-and-mouth disease virus from suckling mice after direct inoculation with in vitro-transcribed RNA.

We assayed the infectivity of naked foot-and-mouth disease virus (FMDV) RNA by direct inoculation of suckling mice. Our results demonstrate that transcripts generated from full-length cDNA clones were infectious, as was virion-extracted RNA. Interestingly, infectious virus could be recovered from a mutant transcript encoding amino acid substitution L-147-->P in capsid protein VP1, known to be noninfectious for BHK-21 cells. The model described here provides a useful tool for virulence studies in vivo, bypassing possible selection of variants during viral replication in cell culture.

Amino Acid Sequence↗
PubMed1979

[Intercellular information transfer in the process of immunogenesis. VI. The induction of antiphage antibody synthesis in the cells of rat transplantable lymphosarcoma under the influence of splenic RNA from rats and mice immunized with phage T2].

It has been proved that nuclear and cytoplasmic RNAs, isolated from spleens of T2 phage immunized rats and mice, can induce T2 phage antibodies in cells of the transplantable rat lymphosarcoma. With the nuclear RNA from rat spleens, the effect is persisting in a number of subsequent cell generations. The data presented are principally in accord with results of the authors' previous studies in which lymphosarcoma cells were treated with RNA extracted from spleens of rat immunized with sheep red cells. These results well compare with the authors' earlier advanced hypothesis suggesting a possible involvement of RNA in deblockation of genes responsible for the synthesis of the antibodies in question.

Animals↗
PubMed1977

Purification of biologically active globin mRNA using cDNA-cellulose affinity chromatography.

A complementary DNA (cDNA) copy of mouse globin mRNA was synthesized using the RNA-dependent DNA polymerase from avian myeloblastosis virus and the oligo(dT) covalently attached to cellulose as primer. All four deoxyribonucleotide triphosphates, NaCl, the globin mRNA template, and an oligo(dT) primer were required for optimal synthesis of cDNA. By saturating the primer sites using a 3-fold excess of mRNA, sufficient concentrations of immobilized cDNA could be synthesized to allow the hybridization reactions to be performed using an excess of globin cDNA. Conditions which permitted the annealing of globin mRNA to cDNA-cellulose were selected and the sequence specificity for hybridization to cDNA-cellulose was determined using 28 S ribosomal RNA, polyadenylic acid, and mouse L-cell RNA. Both analytical and preparative applications of this chromatographic medium were explored. When radioactively labeled poly(A)-containing 9 S RNA isolated from nucleated erythroid cells was analyzed by affinity chromatography on globin cDNA-cellulose, 46 per cent of the applied radioactivity hybridized to the cDNA-cellulose column. Only 1 per cent of the labeled RNA was retained by the column during reapplication of the unbound fraction, while 96 per cent of the bound RNA reannealed to cDNA-cellulose. Hybridizations utilizing unfractionated RNA extracts from either mouse reticulocytes or nucleated erythroid cells provided a one-step purification method for globin mRNA sequences. The relative purity of the RNA isolated by cDNA-cellulose affinity chromatography was determined by hybridization kinetic analysis. The cDNA-bound fraction obtained from the unfractionated RNA of either cell type was shown to have a Crt1/2 of 2.7 x 10-3. This represents a 60-fold purification of the globin sequences present in reticulocyte polysomal RNA and a 280-fold enrichment of the globin mRNA in nucleated erythroid cells. Hybridization to cDNA-cellulose did not result in any change in the sedimentation rate of globin mRNA. Furthermore, experiments were performed which demonstrated that the globin mRNA isolated by hybridization to cDNA-cellulose retained its biological activity when assayed in a wheat germ cell-free lysate.

Animals↗
PubMed1976

Cell-free translation of influenza virus mRNA.

Cytoplasmic poly (A)-rich RNA extracted from fowl plague virus-infected cells was found to program efficiently the translation of two major peptides in the wheat germ cell-free system. These peptides have the same electrophoretic mobility, on polyacrylamide gels, as the two major virion proteins M and NP. [35S] methionine tryptic peptide analysis by one-dimensionalthin-layer ionophoresis and finger printing by two-dimensional thin-layer ionophoresis and chromatography show a high degree of similarity between the two in vitro products and the authentic viral proteins M and NP. Although virion RNA is devoid of any poly (A) sequence, it is confirmed here that the viral complementary cytoplasmic RNA contains poly (A) stretches of varying lengths. Intact purified virion was found to promote the synthesis of very low amounts of the same NP and M proteins in this cell-free system. Quantitative aspects of data would indicate that this is due to minute amounts of complementary viral RNA associated with the virion or with the virion RNA itself. In conclusion, it is shown diectly by cell-free translation of authentic viral products that the influenza virion is "negative stranded" (Baltimore, 1971), at least for its two major structural proteins.

Cell-Free System↗
PubMed1977

Transformation in Naegleria gruberi: patterns of RNA synthesis examined by polyacrylamide gel electrophoresis.

Naegleria gruberi were grown on bacteria and methods were devised to free the cellular RNA from bacterial RNA contamination. Use of actinomycin D and cycloheximide showed that the transformation of Naegleria from amoeba to flagellate required RNA synthesis for 30 min and protein synthesis for 40 min after the initial stimulus of distilled water. Comparison of the patterns of RNA synthesized during transformation with those during growth indicated a considerable amount of new RNA produced during the phenotypic change. Most marked was the increase in RNA co-migrating on polyacrylamide gels with the small ribosomal sub-unit RNA, together with RNAs between the latter and transfer RNA. These results were compared with other published results using axenically-grown cells cells and sucrose density gradient centrifugation. Cells placed in 80 mM NaCl instead of distilled water fail to transform but the pattern of newly-synthesized RNAs was not significantly different from that seen in transforming cells. This suggested that high salt concentrations inhibit transformation by inhibiting synthesis and/or assembly of certain proteins rather than RNA synthesis. Eluted material from various regions of polyacrylamide gels containing RNA extracted from transforming cells was used in a cell-free system. Incorporation of 3H-glutamic acid but not 3H-tryptophan was stimulated by material extracted from the 18S regions of the gels.

Amoeba↗
PubMed1998

Reverse transcriptase PCR detection of astrovirus, hepatitis A virus, and poliovirus in experimentally contaminated mussels: comparison of several extraction and concentration methods.

Four methods of extraction and three methods of concentration of three enteric viruses from mussels were comparatively evaluated by reverse transcriptase PCR (RT-PCR). Shellfish were experimentally contaminated by immersion in seawater seeded with astrovirus, hepatitis A virus, or poliovirus. Sixty-gram samples of mussel tissues were processed by using borate buffer, glycine solution, saline beef, and saline beef-Freon extraction methods. The viruses were concentrated by precipitation with polyethylene glycol 6000 (PEG 6000) or PEG 8000 or by organic flocculation. RT-PCR was performed with RNA extracts from crude shellfish extracts and concentrates with and without Sephadex LH20 filtration. The glycine solution and borate buffer extraction methods resulted in significantly more RT-PCR-positive samples than the saline beef extraction method. We assessed the efficiency of 20 combinations of extraction and concentration methods. The borate buffer-organic flocculation, borate buffer-PEG 6000, and glycine solution-PEG 6000 combinations gave RT-PCR-positive results for all 27 samples analyzed for the three viruses. Detoxification of the samples by Sephadex LH20 filtration significantly decreased the efficiency of RT-PCR virus detection.

Animals↗
PubMed1990

Molecular phenotype of a pediatric small round cell tumor.

Molecular probes were used to characterize an unusual small round cell abdominal tumor arising from the fallopian tube of a 15-year-old girl. DNA and RNA extracted from the tumor and adjacent normal tissue was subjected to Southern and Northern blot analysis using a variety of different probes. N-myc oncogene RNA was greatly expressed in the tumor, but was not expressed in normal tissue or amplified in chromosomal DNA. Insulin-like growth factor II RNA was similarly overexpressed in the neoplasm, but not in normal tissue. While histopathologic studies could not distinguish between a neuroectodermal neoplasm and Wilms' tumor, electron microscopy and the pattern of gene expression was most consistent with Wilms' tumor.

Adolescent↗
PubMed2004

A one step quantitative RT-PCR for detection of SARS coronavirus with an internal control for PCR inhibitors.

In this study, we report a one step quantitative RT-PCR assay for severe acute respiratory syndrome (SARS) diagnosis. The overall detection rate for clinical samples collected from Days 1 to 9 of disease onset is 86.2% and the specificity of the assay is 100%. To detect false negative results due to PCR inhibitors or faulty RNA extraction, we have further modified this one step RT-PCR assay for simultaneous detection of severe acute respiratory syndrome (SARS) coronavirus (CoV) and 18S ribosomal RNA (rRNA) as an internal positive control.

DNA, Ribosomal↗
PubMed2002

Effects of 60 Hz electromagnetic field exposure on APP695 transcription levels in differentiating human neuroblastoma cells.

Epidemiological studies have suggested that workers with primary occupation that are likely to have resulted in the medium-to-high extremely low frequency (ELF) electromagnetic field (EMF) exposure are at increased risk of Alzheimer's disease (AD) pathogenesis. As a first step in investigating the possibility of an association between the ELF-EMF exposure and AD at the cellular level, we have used the differentiating IMR-32 neuroblastoma cells. In double-blind experiments, IMR-32 cells were exposed to the magnetic field intensities of 50, 100, and 200 microT at a frequency of 60 Hz for a period of 4 h at the three ages of differentiation (2, 10, and 16 days after incubation in differentiation medium). We used a custom-made Helmholtz coil setup driven by a 60-Hz sinusoidal signal from a function generator and an in-house built power amplifier. Total RNA extracted from the exposed cells was separated by the agarose gel electrophoresis and transferred to a nylon membrane for the northern hybridization. Digoxygenin-labeled APP695 RNA probes were used to detect changes in the APP695 mRNA levels in response to the ELF-EMF exposure. The results reported herein provided no support for any relationship between the APP695 gene transcription and IMR-32 differentiation age, as well as the magnetic field exposure. This study constitutes the first step towards investigating the possibility of an association between the ELF-EMF exposure and AD manifestations at the cellular level.

Alzheimer Disease↗
PubMed1983

Discriminatory inhibition of protein synthesis in cell-free systems by vaccinia virus transcripts.

The effect of vaccinia virus early transcripts on cellular (globin, HeLa, Chinese hamster ovary) and viral (vaccinia, encephalomyocarditis) mRNA function was studied in reticulocyte and wheat germ cell-free protein-synthesizing systems. Vaccinia virus transcripts of two size classes (8-10 S and 4-7 S), generated in vitro by viral cores, inhibited function of cellular and encephalomyocarditis virus mRNA but not that of vaccinia virus in reticulocyte lysate systems. Mild alkaline hydrolysis or micrococcal nuclease treatment of vaccinia virus in vitro transcripts resulted in a loss of their ability to inhibit protein synthesis directed by HeLa cell RNA. Vaccinia virus in vitro transcripts also selectively inhibited HeLa cell protein synthesis in wheat germ systems, suggesting that double-stranded RNA is not involved in this inhibition of protein synthesis. The addition, to the reticulocyte translating system, of cytoplasmic RNA obtained from infected cells in conjunction with cellular mRNA (globin, HeLa) resulted in the inhibition of synthesis of the globin or HeLa polypeptides with little or no effect on the translation of the vaccinia virus proteins. RNA extracted from vaccinia virions inhibited cellular but not vaccinia virus mRNA function when added to the reticulocyte lysate systems with uninfected or infected HeLa cell cytoplasmic RNA.

Animals↗
PubMed1975

Variations in hybridization of RNA from different mouse tissues and embryos to endogenous C-type virus DNA transcripts.

Several adult tissues, newborns, and embryos of uninfected BALB/c mice were analysed for RNA complementary to [3H]-DNA transcripts synthesized from an endogenous type-C virus of BALB/c 3T3. The technique of RNA:DNA hybridization was used and the extent of hybridization was measured by the use of a single-strand-specific nuclease (S-I), purified from Aspergillus oryzae. Virus-specific RNA was detected in all adult and embryonic tissues tested. However, the RNA extracted from tissues having higher proliferative activity, such as spleen, small intestine, uterus and embryos, hybridize the [3H]-DNA probe to a greater extent than the RNA from tissues with low proliferative activity, such as kidney and liver. These observations add further support to the view that the repression of the virus genome in normal cells is not complete, and suggest the existence of a correlation between a qualitative or quantitative change in the endogenous C-type virus genome transcription pattern and cell proliferation.

Animals↗