Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “RNA extraction”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,279 records · Page 71Linked to original sources
PubMed1977

Immunochemical isolation of gamma-globulin mRNA and estimation of immunoglobulin gene reiteration.

The polyribosomes synthesizing gamma-globulin have been isolated by the achievement of specific precipitation using bentonite-treated anti-IgG antibody. The RNA extracted from the immunochemically precipitated polysomes was tested for its ability to direct the synthesis of proteins in a cell-free system. The specific gamma-globulin-synthesizing activity (cpm of gamma-globulin synthesized/microgram RNA) of this RNA was 10-fold greater than that from total polysomes. gamma-globulin mRNA (messenger RNA) isolated by immunoprecipitation was more than 89% pure with respect to contamination by other species of mRNA. The products synthesized by the cell-free system were also analyzed by sodium dodecyl sulphate(SDS)-polyacrylamide gel electrophoresis. This RNA has been hybridized with mouse myeloma DNA. The estimation of immunoglobulin gene reiteration was carried out using hybridization kinetics with consideration given to the DNA/RNA ratio since the estimation from the "half Cot value" is not accurate. The results suggest that in the mouse there are about 20 copies per subgroup of genes coding for the variable region of the H and L chains.

Alleles↗
PubMed1976

Influence of immune stimulators on viral leukemogenesis.

Injection of RNA, extracted from statolon by the SDS-phenol method, into FLV-infected mice 24 hours before SRBC immunization restored the immune response to SRBC to normal levels. Leukemosuppression was observed in 50% of the RNA-treated FLV-infected mice. These RNA-treated mice were clinically normal 25 days after infection, whereas all untreated infected mice developed erythroleukemia. Furthermore, all RNA-treated mice with suppressed erythroleukemia produced antibody which was cytotoxic for Friend leukemia cells. Our studies, and studies by others, indicate that the immunostimulatory and leukemosuppressive principle in statolon appears to be a dsRNA.

Animals↗
PubMed2004

Microdissected region-specific gene expression analysis with methacarn-fixed, paraffin-embedded tissues by real-time RT-PCR.

We have previously shown methacarn to be a versatile fixative for analysis of proteins, DNA, and RNA in paraffin-embedded tissues (PETs). In this study we analyzed its suitability for quantitative mRNA expression analysis of microdissected PET specimens using a real-time RT-PCR technique. Fidelity of expression in the methacarn-fixed PET sections, with reference to dose-dependent induction of cytochrome P450 2B1 in the phenobarbital-treated rat liver, was high in comparison with the unfixed frozen tissue case, even after hematoxylin staining. RNA yield from methacarn-fixed PET sections was equivalent to that in unfixed cryosections and was also not significantly affected by hematoxylin staining. Correlations between the expression levels of target genes and input amounts of extracted RNA in the range of 1-1000 pg were very high (correlation coefficients >0.98), the regression curves being similar to those with unfixed cryosections. Although cell numbers should be optimized for each target gene/tissue, >/=200 cells were necessary for accurate measurement in 10-microm-thick rat liver sections judging from the variation of measured value in small microdissected areas. These results indicate high performance with methacarn, close to that of unfixed tissues, regarding quantitative expression analysis of mRNAs in microdissected PET-specimens.

Acetic Acid↗
PubMed1977

[Compared expression of murine plasmacytoma associated virus in tumor cells and in mouse embryo cells].

A DNA complementary to the viral genome of C-type particles produced by a Mouse myeloma derived cell line (MF2 cell line) was synthesized. This cDNA was used as a probe to study the viral genome expression among the total RNA and the poly (A)-rich RNA extracted from the MF2 and Balb/c embryonic cells. As evidenced by molecular hybridization experiments, the presence of at least one endogenous Balb/c virus in the MF2 virus stocks is suggested. In the productive cells, the viral RNA sequences are expressed in the poly (A)-rich RNA fraction.

Animals↗
PubMed1980

The therapy of renal adenocarcinoma with immune RNA.

Twenty-five patients with metastatic renal cell carcinoma and ten patients with minimum residual disease, but at high risk of recurrence after surgery, received weekly intradermal injections of purified RNA extracted from lymphoid organs of sheep immunized with human renal cell carcinoma. A retrospective control group consisted of 86 consecutive patients with metastatic renal cell carcinoma from the same institution. Group survival was notable in RNA-treated patients who had multiple metastases limited to the lungs when compared with matched controls. Therapy did not influence the survival of patients with metastases to other sites or with multiple organ involvement. Eight of ten patients with minimum residual disease remained free of recurrence from 16 to 36 months after the initiation of therapy. Toxicity of RNA therapy was minimal. Changes in skin test response to dinitrochlorobenzene and common antigens, and levels of lymphocyte-mediated cytotoxicity and complement-fixing antibody, were primarily related to changes in tumor burden. Immune RNA therapy may be of value in selected patients with metastatic renal cell carcinoma and as adjunctive therapy after definitive surgery.

Adenocarcinoma↗
PubMed2000

Morphofunctional plasticity in the adult hypothalamus induces regulation of polysialic acid-neural cell adhesion molecule through changing activity and expression levels of polysialyltransferases.

Polysialic acid-neural cell adhesion molecule (PSA-NCAM) expression in the adult nervous system is restricted to regions retaining a capacity for morphological plasticity. For the female rat hypothalamoneurohypophysial system (HNS), we have previously shown that lactation induces a dramatic decrease in PSA-NCAM, while leaving the level of total NCAM protein unchanged. Here, we wanted to elucidate the molecular mechanisms leading to a downregulation of PSA, thereby stabilizing newly established synapses and neurohemal contacts that accompany the increased activity of oxytocinergic neurons. First, we show that the overall specific activity of polysialyltransferases present in tissue extracts from supraoptic nuclei decreases by approximately 50% during lactation. So far, two polysialyltransferase enzymes, STX and PST, have been characterized for their capacity to transfer PSA onto NCAM in vitro. Using a competitive RT-PCR on RNA extracts from the HNS, we demonstrate furthermore a significant decrease in the expression levels of both STX and PST mRNAs in lactating versus virgin animals. Interestingly, this downregulation of NCAM polysialylation is not correlated with the post-transcriptional regulation of variable alternative spliced exon splicing, in contrast to neural development. The control of polysialylation via a regulation of both enzyme activity and expression underlines the important role of this post-translational modification of NCAM in morphofunctional plasticity in adult brain.

Animals↗
PubMed1984

In vitro and in vivo analysis of the control of dihydrofolate reductase gene transcription in serum-stimulated mouse fibroblasts.

We have studied the rate of transcription of the gene for dihydrofolate reductase (DHFR) in mouse 3T6 fibroblasts during serum-induced transitions between the resting (G0) and growing states. As a model system, we have used a methotrexate-resistant 3T6 cell line that overproduces DHFR and its mRNA about 300-fold, yet regulates the expression of the DHFR gene in the same manner as normal 3T6 cells. In previous studies, we showed that the rate of production of cytoplasmic DHFR mRNA relative to total mRNA is about 4 times lower in resting than in exponentially growing cells. The rate increases to the growing value by about 15 hr following serum stimulation of the resting cells. This increase appeared to be controlled by regulating the rate of synthesis of DHFR hnRNA. In this study, we analyze the transcription of the DHFR gene in more detail. We use a variety of labeling times and RNA extraction procedures to measure the rate of synthesis of DHFR hnRNA relative to total hnRNA in pulse-labeled cells or in nuclei isolated from cells at various times following serum stimulation. The amount of labeled DHFR RNA is determined by DNA-excess filter hybridization. In all cases, the relative rate of synthesis of DHFR hnRNA increases at the same time, and to the same extent, as the rate of production of DHFR mRNA, suggesting that the increase in DHFR mRNA production is due to a corresponding increase in the rate of transcription of the DHFR gene. The increase in DHFR gene transcription is not blocked by cytosine arabinoside, showing that the increase does not depend on gene duplication. In isolated nuclei, DHFR RNA synthesis is inhibited by alpha-amanitin (1 microgram/ml), indicating that the DHFR gene is transcribed by RNA polymerase II. Others have shown that when stationary phase cells are stimulated to proliferate, the increase in DHFR mRNA content is controlled primarily at the post-transcriptional level. Therefore, it appears that the rate of production of DHFR mRNA is controlled by different biochemical mechanisms when cells are in different physiological states.

Animals↗
PubMed1975

Characterization of bovine viral diarrhea virus RNA.

RNA extracted from isopycnically banded [3-H]uridine-labeled bovine viral diarrhea virus with sodium dodecyl sulfate was resolved into one major and two minor components by both sedimentation analysis and electrophoresis in polyacrylamide gels. The major RNA component was estimated to have a 38S sedimentation coefficient. The minor RNA components were estimated to have S values of 31 and 24. The approximate colecular weights were calculated to be 3.22 times 10-6 (38S), 2.09 times 10-6 (31S), and 1.22 times 10-6 (24S). A single broad peak of radioactivity, maximum at 24S, was obtained when sedimentation was conducted under conditions of low ionic strength. All three RNA components were found to be susceptible to digestion with RNase. The presence of multiple RNA components in heterogeneous populations of infectious virus is discussed.

Animals↗
PubMed2005

Analysis of nucleotide sequences and multimeric forms of a novel satellite RNA associated with beet black scorch virus.

The full-length sequence of a satellite RNA (sat-RNA) of Beet black scorch virus isolate X (BBSV-X) was determined. This agent is 615 nucleotides long and lacks extensive sequence homology with its helper virus or with other reported viruses. Purified virus particles contained abundant single-stranded plus-sense monomers and smaller amounts of dimers. Single-stranded RNAs from total plant RNA extracts also included primarily monomers and smaller amounts of dimers that could be revealed by hybridization, and preparations of purified double-stranded RNAs also contained monomers and dimers. Coinoculation of in vitro transcripts of sat-RNA to Chenopodium amaranticolor with BBSV RNAs was used to assess the replication and accumulation of various forms of sat-RNA, including monomers, dimers, and tetramers. Dimeric sat-RNAs with 5- or 10-base deletions or 15-base insertions within the junction regions accumulated preferentially. In contrast, the replication of monomeric sat-RNA was severely inhibited by five-nucleotide deletions in either the 5' or the 3' termini. Therefore, sequences at both the 5' and the 3' ends of the monomers or the presence of intact juxtaposed multimers is essential for the replication of sat-RNA and for the predomination of monomeric progeny. Comparisons of the time courses of replication initiated by in vitro-synthesized monomeric or multimeric sat-RNAs raised the possibility that the dimeric form has an intermediate role in replication. We propose that replication primarily involves multimers, possibly as dimeric forms. These forms may revert to monomers by a termination of replication at 5' end sequences and/or by internal initiation at the 3' ends of multimeric junctions.

Base Sequence↗
PubMed1996

An improved method for the detection of Tospoviruses using the polymerase chain reaction.

A reverse transcription-polymerase chain reaction (RT-PCR)-based assay for the detection of tomato spotted wilt virus (TSWV) has been improved and extended to enable the detection of additional Tospoviruses. In addition to TSWV-specific primers, two further pairs of primers have been designed, one pair which specifically detects impatiens necrotic spot virus (INSV) and another which detects all Tospoviruses tested, including TSWV, INSV, tomato chlorotic spot virus and groundnut ringspot virus. An improved, rapid RNA extraction method is also described.

Base Sequence↗
PubMed1972

Cell-mediated tumor allograft immunity: in vitro transfer with RNA.

Specific inhibition of migration of spleen cells from C57B1/6J mice, which had rejected A/J sarcoma-1 tumors, occurred in the presence of A/J lymph mode antigens. The migration inhibitory effect was transferable to normal C57B1/6J spleen cells by RNA extracted from lymph nodes and spleens of immunized animals.

Animals↗
PubMed1994

Tissue specificity of rat mitochondrial dimethylglycine dehydrogenase expression.

Expression of mitochondrial dimethylglycine dehydrogenase (Me2GlyDH) was analysed in various tissues, liver cell types and developmental stages of the rat. Total RNA extracted from liver, spleen, brain, kidney, lung and heart was reverse-transcribed into cDNA and amplified with Me2GlyDH cDNA-specific oligonucleotides by PCR. Expression of the enzyme was observed mainly in liver and kidney. In addition, Me2GlyDH mRNA could be demonstrated in total RNA samples of lung, heart and brain but was barely detectable in spleen total RNA. In RNA prepared from 14-day rat embryos, Me2GlyDH-specific mRNA was clearly present. Among various liver cell types, besides hepatocytes, endothelial cells showed a high level of Me2GlyDH mRNA expression. There was no amplification product detectable in liver macrophages (Kupffer cells) and only a very faint one in fat-storing cells (Ito cells). Western blots confirmed at the protein level the predominant expression of the enzyme in liver and kidney, but Me2GlyDH protein was also present in the protein extract of lung, heart, spleen and brain. Immunohistochemical staining of liver slices with Me2GlyDH-specific antiserum revealed that expression of this enzyme is evenly distributed throughout the liver tissue. In the kidney, expression of the enzyme was located in the proximal tubule cells. Our results demonstrate that, contrary to the previously assumed liver-restricted expression, this enzyme is specifically expressed predominantly in the liver and kidney, but, in addition, it is detectable in many other tissues of the rat.

Aging↗
PubMed2005

Potential for quantifying expression of the Geobacteraceae citrate synthase gene to assess the activity of Geobacteraceae in the subsurface and on current-harvesting electrodes.

The Geobacteraceae citrate synthase is phylogenetically distinct from those of other prokaryotes and is a key enzyme in the central metabolism of Geobacteraceae. Therefore, the potential for using levels of citrate synthase mRNA to estimate rates of Geobacter metabolism was evaluated in pure culture studies and in four different Geobacteraceae-dominated environments. Quantitative reverse transcription-PCR studies with mRNA extracted from cultures of Geobacter sulfurreducens grown in chemostats with Fe(III) as the electron acceptor or in batch with electrodes as the electron acceptor indicated that transcript levels of the citrate synthase gene, gltA, increased with increased rates of growth/Fe(III) reduction or current production, whereas the expression of the constitutively expressed housekeeping genes recA, rpoD, and proC remained relatively constant. Analysis of mRNA extracted from groundwater collected from a U(VI)-contaminated site undergoing in situ uranium bioremediation revealed a remarkable correspondence between acetate levels in the groundwater and levels of transcripts of gltA. The expression of gltA was also significantly greater in RNA extracted from groundwater beneath a highway runoff recharge pool that was exposed to calcium magnesium acetate in June, when acetate concentrations were high, than in October, when the levels had significantly decreased. It was also possible to detect gltA transcripts on current-harvesting anodes deployed in freshwater sediments. These results suggest that it is possible to monitor the in situ metabolic rate of Geobacteraceae by tracking the expression of the citrate synthase gene.

Acetates↗
PubMed2004

The farnesoid X receptor induces very low density lipoprotein receptor gene expression.

The farnesoid X receptor (FXR) is a nuclear receptor activated by bile acids (BAs). In response to ligand-binding, FXR regulates many genes involved in BA, lipid, and lipoprotein metabolism. To identify new FXR target genes, microarray technology was used to profile total RNA extracted from HepG2 cells treated with the natural FXR agonist chenodeoxycholic acid (CDCA). Interestingly, a significant increase of transcript level of the very low density lipoprotein receptor (VLDLR) was observed. Our data, resulting from selective FXR activation, FXR RNA silencing and FXR-deficient mice, clearly demonstrate that BAs up-regulate VLDLR transcript levels via a FXR-dependent mechanism in vitro in human and in vivo in mouse liver cells.

Animals↗
PubMed1987

A study of viral genomes and antigens in brains of patients with Alzheimer's disease.

The presence of viral nucleic acid sequences and antigens from a variety of conventional viruses in selected brain regions of cases of Alzheimer's disease (AD), diagnosed pathologically, was investigated using molecular hybridization and immunocytochemical techniques. Seven DNA and 4 RNA viruses were used as probes in 18 AD and 5 control brains. With Southern blot hybridization, no viral DNA sequences could be detected in the cerebral cortex. With dot blot hybridization, results were also negative, except for 2 cases, 1 a control brain, the other an AD brain, which gave a positive signal in the RNA extracted from the substantia innominata when c-DNA from measles virus was used as a probe. Four specific brain areas from each of 8 AD brains and 5 controls tested with viral probes (3 DNA and 5 RNA viruses), using immunocytochemical techniques for viral antigens, showed no positive reproducible specific reactions. These results, although negative, do not totally exclude the possibility that conventional viruses may play a role in the aetiology and pathogenesis of AD.

Alzheimer Disease↗
PubMed1977

Effects of pyrimidine derivatives on RNA-dependent RNA polymerase of mengovirus-infected Fogh and Lund (FL) cells.

Two newly synthesized pyrimidine derivatives were found to possess antiviral activity against Mengovirus in Fogh and Lund (FL) cells and in a cell-free system. The inhibitory effect on RNA-dependent RNA polymerase of Mengovirus-infected FL cells was assayed using 14C-UTP as precursor. Addition of 50 or 100 muM of the inhibitors in a cell-free system of crude enzyme and nucleoside triphosphate medium for 60 min incubation at 37 degrees C resulted in about 40 to 60% lower counting rates for drug-treated reaction mixtures. The analysis of the polymerase synthesis product (virus RNA extracted from the cell-free reaction mixture and deproteinized by the phenol-SDS method) was carried out by means of agarose-acrylamide gel electrophoresis. The main finding was a reduction of single-stranded Mengovirus RNA (RNase-sensitive and LiCl-precipitable). The rates of synthesis of the replicative intermediate (LiCl-precipitable) and the replicative form of RNA (LiCl-soluble) were not significantly influenced.

Antiviral Agents↗
PubMed1997

Signal amplification in the detection of single-copy DNA and RNA by enzyme-catalyzed deposition (CARD) of the novel fluorescent reporter substrate Cy3.29-tyramide.

We demonstrate that the CAtalyzed Reporter Deposition method (CARD), utilizing the novel fluorescent reporter Cy3.29-tyramide, is successful in the Fluorescent in Situ Hybridization (FISH) detection of RNA and single-copy DNA. Histone 4 expression is detected in RNA extracts of 5-phase, synchronized HeLa cells by dot-blot analysis. Gene expression of histone 4 in HeLa cells is demonstrated by FISH via CARD, utilizing oligonucleotide probes. Fluorescence intensity measurements on CARD-amplified histone 4 RNA detection showed (a) a 25-fold amplification of the signal brightness by biotinylated oligonucleotide probes and (b) a sixfold amplification of the signal brightness by horseradish peroxidase (HRP)-labeled histone 4 probes vs the directly stained control. The sensitivity of the CARD method is demonstrated by the FISH detection of single-copy DNA on human corneal fibroblast and HeLa S5 interphase nuclei. Chromosomal localization of the single copy DNA is demonstrated on HeLa S3 metaphase chromosome spreads.

Avidin↗
PubMedDate not supplied

Microbial community structures in foaming and nonfoaming full-scale wastewater treatment plants.

A survey of full-scale activated-sludge plants in Illinois revealed that filamentous foaming is a widespread problem in the state, and that the causes and consequences of foaming control strategies are not fully understood. To link microbial community structure to foam occurrence, microbial populations in eight foaming and nine nonfoaming full-scale activated-sludge systems were quantified using oligonucleotide hybridization probes targeting the ribosomal RNA (rRNA) of the mycolata; Gordonia spp.; Gordonia amarae; "Candidatus Microthrix parvicella"; the alpha-, beta-, and gamma-subclasses of the Proteobacteria, and members of the Cytophaga-Flavobacteria. Parallel measurements of microbial population abundance using hybridization of extracted RNA and fluorescence in situ hybridization (FISH) showed that the levels of mycolata, particularly Gordonia spp., were higher in most foaming systems compared with nonfoaming systems. Fluorescence in situ hybridization and microscopy suggested the involvement of "Candidatus Microthrix parvicella" and Skermania piniformis in foam formation in other plants. Finally, high numbers of "Candidatus Microthrix parvicella" were detected by FISH in foam and mixed liquor samples of one plant, whereas the corresponding levels of rRNA were low. This finding implies that inactive "Candidatus Microthrix parvicella" cells (i.e., cells with low rRNA levels) can cause foaming.

Bacteria↗