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PubMed1992

Intracellular localization of poliovirus RNA by in situ hybridization at the ultrastructural level using single-stranded riboprobes.

Polioviral RNA was localized by electron microscopic in situ hybridization on sections of poliovirus-infected HEp-2 cells. Viral plus-strand RNA was found accumulated in the close surroundings of the membrane-bound replication complex. Two different regions of the viral genome were detected with the same frequency, which indicates the predominant presence of full-length genomic RNA. Viral proteins of the P2 and the P3 genomic region were detected mainly over the core of the replication complex, whereas the hybridization signal was present rather at the peripheral parts of the complex. A more than 100-fold excess of viral plus- over minus-strand RNA was found by strand-specific hybridization to RNA extracted from isolated replication complexes. These findings support the idea of a pool of viral plus-strand RNA set free from the replication complex and accumulating in the close vicinity of the replication complex possibly before encapsidation.

Cells, Cultured↗

PubMed1992

Transcriptional analysis of the isopenicillin N synthase-encoding gene of Streptomyces clavuligerus.

The gene (pcbC) encoding isopenicillin N synthase of Streptomyces clavuligerus is separated from an upstream open reading frame (ORF) by a 31-bp intergenic region. Inspection of the sequence of this intergenic region did not identify a promoter sequence. The promoter probe plasmid, pIJ4083, which contains the promoter-less catechol-2,3-dioxygenase (C23O)-encoding gene (xylE) as a reporter gene, was used to analyze the sequence upstream from the pcbC gene for promoter activity. Introduction of an SphI site at the start codon of pcbC by site-directed mutagenesis allowed the cloning of a 335-bp fragment (-334 to +1 in relation to the pcbC start codon) immediately upstream from xylE in pIJ4083. C23O activity was detected in both Streptomyces lividans and S. clavuligerus cultures that contained the upstream fragment, suggesting the presence of a promoter sequence. Northern analysis of total RNA extracted from S. clavuligerus identified a monocistronic 1.2-kb transcript hybridizing to a pcbC-specific probe. When RNA was isolated at various times during growth in liquid culture, the presence of a transcript was first detected during stationary phase. Analysis of the pcbC transcript by primer extension located the transcription start point to a C residue within the upstream ORF, 91 bp upstream from the pcbC start codon.

Blotting, Northern↗

PubMed1994

A tRNA-like structure is present in 10Sa RNA, a small stable RNA from Escherichia coli.

We have determined that 10Sa RNA (one of the small stable RNAs found in Escherichia coli) has an interesting structural feature: the 5' end and the 3' end of 10Sa RNA can be arranged in a structure that is equivalent to a half-molecule (acceptor stem and TFC stem-loop) of alanine tRNA of E. coli. Primer-extension analysis of 10Sa RNA extracted from a bacterial mutant with temperature-sensitive RNase P function revealed that the precursor to 10Sa RNA (pre-10Sa RNA) is folded into a pre-tRNA-like structure in vivo such that it can be cleaved by RNase P to generate the 5' end of the mature 10Sa RNA. The purified 10Sa RNA can be charged with alanine in vitro. Disruption of the gene encoding 10Sa RNA (ssrA) caused a reduction in the rate of cell growth, which was especially apparent at 45 degrees C, and a reduction in motility on semisolid agar. These phenotypic characteristics of the deletion strain (delta ssrA) allowed us to investigate the effects of some mutations in 10Sa RNA in vivo, although the exact function of 10Sa RNA still remains unclear. When the G.U pair (G3.U357) in 10Sa RNA, which may be equivalent to the determinant G.U pair of alanine tRNA, was changed to a G.A or G.C pair, the ability to complement the phenotypic mutations of the delta ssrA strain was lost. Furthermore, this inability to complement the mutant phenotypes that was caused by the substitution of the determinant bases by a G.A pair could be overcome by the introduction of a gene encoding alanyl-tRNA synthetase (alaS) on a multicopy plasmid. The evidence suggests that the proposed structural features of 10Sa RNA are indeed manifested in vivo.

Base Sequence↗

PubMed1994

Localization of messenger RNA for three distinct alpha 2-adrenergic receptor subtypes in human tissues. Evidence for species heterogeneity and implications for human pharmacology.

BACKGROUND: alpha 2-Adrenergic receptor (alpha 2AR) agonists have become important adjuncts as anesthetic agents. They act by binding to alpha 2ARs on the surface of cell membranes and cause centrally mediated sedation and analgesia. alpha 2ARs also contribute to other aspects of physiologic regulation. Three subtypes of alpha 2ARs (alpha 2-C2, alpha 2-C4, and alpha 2-C10) have been described using molecular and pharmacologic techniques. We recently demonstrated species heterogeneity in the distribution of alpha 1-adrenergic receptor subtypes, therefore making it imperative to analyze the distribution of alpha 2AR subtypes in human tissues. This information may have importance in the understanding of potential side effects of administration of alpha 2AR subtype-selective agonists for anesthesia in humans. METHODS: RNA extracted from human tissues was analyzed by using quantitative ribonuclease protection assays to determine alpha 2AR subtype messenger RNA (mRNA) expression in cardiovascular, central nervous system, and peripheral tissues. RESULTS: alpha 2AR mRNA is present in greatest concentrations in human kidney, followed by aorta > spleen > heart = lung. alpha 2-C4 mRNA predominates in heart, lung, aorta, cerebral cortex, cerebellum, spleen, kidney, and adrenal gland; alpha 2-C2 mRNA in liver; and alpha 2-C10 mRNA in pancreas and small intestine. Hence alpha 2AR subtype mRNA distribution is tissue-selective and differs from that reported for rat. CONCLUSIONS: (1) On comparison with previous research we find possible species heterogeneity in alpha 2AR subtype mRNA distribution (rat vs. human) for all three alpha 2AR subtypes. (2) We demonstrate the presence and subtype heterogeneity of alpha 2AR subtype mRNA in both brain and peripheral tissues. (3) Significant concentrations of alpha 2AR mRNA are present in adult human heart. These findings have important implications for our understanding of human adrenergic physiology, provide a possible explanation for the existence of pharmacologically similar yet distinct alpha 2AR subtypes, and may be important for the rational development of alpha 2AR subtype-selective anesthetics and other therapeutic agents for use in treating human diseases.

Adult↗

PubMed1997

Detection of low HIV-1 RNA levels in plasma.

HIV-1 viremia is a marker of choice for staging, prognosis, and monitoring treatment efficiency in HIV infection. Among the commercial assays, the Amplicor HIV Monitor (Roche, Basel, Switzerland) test has the highest sensitivity for HIV-1 RNA quantitation in plasma with a detection limit of 200 copies per milliliter. To measure HIV-1 viremia below this threshold, boosted versions of the Amplicor assay were developed by adding a centrifugation step prior to RNA extraction and by decreasing dilution factors. In the boosted version, the increase in analytical sensitivity for HIV-1 RNA detection directly correlates with the input of plasma. For 1,500 microl of plasma, the sensitivity of the assay increases by a factor of 30. For routine clinical analysis, we use a boosted assay format with an input plasma volume of 500 microl and a lower detection limit of 20 copies/milliliter. Coefficients of intra- and interassay variation are similar to those reported for the standard assay (approximately 30%). Thirteen (45%) of 29 plasma samples of HIV-infected individuals with undetectable viremia in the standard assay had detectable viremia between 20 and 200 copies/milliliter.

HIV Infections↗

PubMed2004

CTAB-urea method purifies RNA from melanin for cDNA microarray analysis.

Melanin represents a major problem for the study of melanoma by microarrays since it is retained during RNA extraction and inhibits the enzymatic reactions used for probe preparation. Here we report a new method for cleaning RNA from melanin, based on the use of the cationic detergent cetyl-trimethylammonium bromide (CTAB)-urea for RNA precipitation. This method is easy to perform and has a low cost. Purified RNA is recovered with high quality and good yield. CTAB-urea treated RNA from highly pigmented melanoma cells can be successfully reverse transcribed and labeled to obtain probes which can be subsequently used in cDNA microarray experiments, giving consistent and reproducible results.

Biotechnology↗

PubMed1975

RNA synthesis in cells infected with herpes simplex virus. IX. Evidence for accumulation of abundant symmetric transcripts in nuclei.

RNA extracted from nuclei of 8-h infected cells drove approximately 50% of herpes virus DNA into DNA-RNA hybrid. The same RNA, preannealed under conditions which allowed base pairing to take place, drove only 35% of the DNA into DNA-RNA hybrid; further annealing of the RNA did not diminish the amount of RNA sequences remaining available for subsequent hybridization with DNA. Upon denaturation of the preannealed RNA, the RNA sequences sequestered during preannealing became available again for hybridization with DNA. The base pairing that occurred during preincubation of the RNA was inter-molecular, since it was RNA concentration dependent and was not affected by limited alkaline hydrolysis. The nuclear viral transcripts that remained available for hybridization, after preannealing of the RNA, were subset of the RNA sequences that accumulated in the cytoplasm of infected cells. In addition, a small amount (derived from 5% or less of the viral DNA) of complementary transcripts was detected in the cytoplasm.

Base Sequence↗

PubMed2006

BCR-ABL is not an immunodominant antigen in chronic myelogenous leukemia.

In the present study, we analyzed the involvement of the BCR-ABL protein in the induction of antigen-specific CTL in order to develop an immunotherapeutic approach in patients with chronic myelogenous leukemia (CML). To accomplish this, we generated dendritic cells (DC) in vitro and electroporated them with various sources of RNA harboring the chimeric bcr-abl transcript. These genetically engineered DCs were used as antigen-presenting cells for the induction of CTLs. By applying this approach, we found that the CTLs induced by DCs transfected with RNA extracted from bcr-abl-positive K-562 cells or CML blasts lysed DCs transfected with the corresponding RNA, but failed to recognize epitopes derived from the chimeric BCR-ABL fusion protein in (51)Cr-release assays. In contrast, they were able to lyse autologous DCs electroporated with RNA isolated from patients with acute myeloid leukemia, indicating that antigens shared among these malignant cells are involved and recognized by these CTLs. In patients with CML in complete cytogenetic remission during IFN-alpha treatment, we detected some reactivity of CD8(+) T cells against BCR-ABL in IFN-gamma ELISPOT assays, which was weaker as compared with proteinase 3 (PR3)- or prame-directed responses, suggesting that the BCR-ABL protein is less immunogenic as compared with other CML-derived antigens.

CD4-Positive T-Lymphocytes↗

PubMed2006

Transcriptional profiling of degraded RNA in cryopreserved and fixed tissue samples obtained at autopsy.

BACKGROUND: Traditional multiplexed gene expression methods require well preserved, intact RNA. Such specimens are difficult to acquire in clinical practice where formalin fixation is the standard procedure for processing tissue. Even when special handling methods are used to obtain frozen tissue, there may be RNA degradation; for example autopsy samples where degradation occurs both pre-mortem and during the interval between death and cryopreservation. Although specimens with partially degraded RNA can be analyzed by qRT-PCR, these analyses can only be done individually or at low levels of multiplexing and are laborious and expensive to run for large numbers of RNA targets. METHODS: We evaluated the ability of the cDNA-mediated Annealing, Selection, extension, and Ligation (DASL) assay to provide highly multiplexed analyses of cryopreserved and formalin fixed, paraffin embedded (FFPE) tissues obtained at autopsy. Each assay provides data on 1536 targets, and can be performed on specimens with RNA fragments as small as 60 bp. RESULTS: The DASL performed accurately and consistently with cryopreserved RNA obtained at autopsy as well as with RNA extracted from formalin-fixed paraffin embedded tissue that had a cryopreserved mirror image specimen with high quality RNA. In FFPE tissue where the cryopreserved mirror image specimen was of low quality the assay performed reproducibly on some but not all specimens. CONCLUSION: The DASL assay provides reproducible results from cryopreserved specimens and many FFPE specimens obtained at autopsy. Gene expression analyses of these specimens may be especially valuable for the study of non-cancer endpoints, where surgical specimens are rarely available.

Journal Article↗

PubMedDate not supplied

Stimulation of hepatic RNA synthesis by phenobarbital.

Administration of phenobarbital in rats is followed by an in vitro stimulation of hepatic ribosomal protein synthesis. The increase of polyribosomes which is also observed is paralleled by a phenobarbital-dependent enhancement of uridine incorporation into ribonucleic acids. Sedimentation of either ribosomes or ribosomal RNA extracted from ribosomal subunits through sucrose gradients reveals stimulation by phenobarbital of 3H-uridine incorporation into messenger RNA as well as into ribosomal RNA. These experiments together with the findings of stimulation of RNA polymerase activity and blockade of the effects of phenobarbital by the administration of Actinomycin D indicate a primary action of phenobarbital on RNA synthesis.

Animals↗

PubMed2000

Using buffy coat for reverse transcriptase-polymerase chain reaction in the diagnosis of dengue virus infection: preliminary study.

Using reverse transcriptase-polymerase chain reaction (RT-PCR) to detect and type from viremic human serum samples for dengue virus infection is widely used today. However, a few false-negative results were reported due to very low titers of the virus particle in serum samples. As mononuclear cells, macrophages or monocytes are target cells for dengue virus infection, and the replication of virions can be observed in peripheral leukocytes frequently, the amount of virus particle in buffy coat should be higher than those in serum samples. Here, we describe a procedure in which RNA extraction from the buffy coat of a patient with a false-negative serum sample yielded specific viral RNA amplifiable by RT-PCR, thereby providing an alternative choice for the accurate diagnosis of dengue infection.

Dengue↗

PubMed2005

[Study of genes that differentially expressed in eosinophils of patients with asthma by suppression subtractive hybridization technology].

OBJECTIVE: To study genes that differentially expressed in peripheral blood eosinophils of patient with asthmatic. METHODS: Total RNA extracted from eosinophils of patient at the time of exacerbation was taken as the tester and the total RNA from eosinophils of the same patient after improvement as driver. The ds cDNA was synthesized by SMART PCR cDNA Synthesis technology. The differentially expressed genes were obtained by suppression subtractive hybridization (SSH) technology and were further identified by Southern blot. RESULTS: Twelve differentially expressed genes including transformation growth factor beta activated kinase like (TAK1L) protein, cGMP gated channel protein were obtained. CONCLUSION: Increased expression of these genes were involved in the regulation of proinflammatory response, signal transduction, energy metabolism and cell apoptosis, which may help to clarify the molecular mechanism of eosinophils in asthma and may provide the theoretical base for finding out the new medicines towards eosinophils.

Asthma↗

PubMed1984

[Properties of the RNA-component informosome from amphibian oocytes].

RNA synthesis in in vivo ovulated oocytes of Rana temporaria frog was studied. It was shown that RNA synthesised during oocyte maturation is non-mitochondrial and is localized mostly in the ribonucleoprotein fraction; the bulk of the RNA is present in informosomes. The RNA extracted from informosomes shows a heterogeneous sedimentative distribution with predominant components of 19S and 26-27S. This RNA does not adsorb on oligo(dT)-cellulose columns.

Animals↗

PubMedDate not supplied

An RT-PCR assay for the specific detection of classical swine fever virus in clinical samples.

A simple reverse transcriptase-polymerase chain reaction (RT-PCR) assay has been developed for the specific amplification of DNA after reverse transcription of RNA from the classical swine fever virus (CSFV). A pair of oligonucleotides was selected from an area of high homology in the genome of CSFV strains, but which differed from the corresponding sequences in the genome of bovine viral diarrhea virus (BVDV) strains. Using these primers (CSFV1-CSFV2), a CSFV specific DNA band of 174 bp was amplified from the CSFV RNA extracted from four reference strains and 14 field isolates, as well as from 25 organ extracts and eight buffy coats and serum samples of experimentally infected animals. No amplification was observed with the RNA from four BVDV reference and vaccine strains and seven field isolates. This RT-PCR assay made it possible, in a one-step reaction, to detect CSFV rapidly, sensitively and specifically in cell culture supernatants and in clinical specimens.

Animals↗

PubMed1985

The effect of aging on the structure and function of liver messenger RNA.

The size of the poly(A) segment of poly(A)+RNA extracted from hepatocytes isolated from 4- to 30-month-old rats was determined using polyacrylamide-agarose gel electrophoresis. The average size of the poly(A) segment isolated from newly synthesized poly(A)+RNA was 150 nucleotides, and the average size of the poly(A) segment isolated from the steady state pool of cytoplasmic poly(A)+RNA was 70 nucleotides. No significant age related change in either the size or the heterogeneity of the newly synthesized poly(A) segment was found. The translational activity of poly(A)+RNA isolated from livers of 4- to 30-month-old rats was determined using wheat germ extract and rabbit reticulocyte lysate cell-free systems. No age-related change in the translational activity of the poly(A)+RNA was observed. The effect of aging on the cap structure was also studied by measuring the inhibition of cell-free translation by 7-methyl guanosine-5'-monophosphate. No age-related change in the sensitivity of the poly(A)+RNA preparations to inhibition of translation by 7-methyl guanosine-5'-monophosphate was observed. Therefore, the results of this study demonstrate that no major age-related change occurs in the structure of the poly(A) segment, the translational activity, or the cap structure of poly(A)+RNA from rat liver.

Aging↗

PubMedDate not supplied

[DNA synthesis on the heterogeneous nuclear RNA template catalysed by DNA polymerase of avian myeloblastosis virus].

Template activity of nuclear pre-mRNA has been investigated in DNA-polymerase reaction. Active synthesis of DNA was demonstrated on pre-mRNA as a template in the absence of primer. A part of synthetic activity may be attributed to the traces of DNA present in the pre-mRNA preparation. Addition of oligo(dT)10 to the template stimulated the synthesis of DNA product due to transcription of heteropolymeric regions near the poly(A). The rate of DNA synthesis was different depending on the fraction of template used: the RNA extracted by hot phenol at 85 degrees showed higher template activity without adding of primer than the 65 degrees C fraction. On the contrary 65 degrees C pre-mRNA which is known to contain greater quantity of molecules with poly(A) at the 3'-end is more strongly stimulated by addition of oligo(dT). The nuclear RNA corresponding to the precursors of rRNAs extracted at 40 degrees C were not transcribed by the reverse transcriptase. The size of the DNA-product (about 7-8S in alkaline sucrose gradient) did not depend on the size of the template neither on the presence of oligo(dT)10 primer. The inhibition of the second DNA strand synthesis with actinomycin D had also no influence on the size of DNA-product.

Avian Leukosis Virus↗

PubMed1980

Preformed mRNA in Cotyledons of Ungerminated Seeds of Cicer arietinum L.

Polyadenylated RNA was isolated from total RNA extracted from cotyledons of ungerminated or 18-hour-germinated chick-pea seeds by affinity chromatography on oligo(dT)-cellulose. Both poly(A)-containing RNA fractions exhibited a template activity when assayed in two cell-free translation systems, wheat germ extracts, and nuclease-treated reticulocyte lysates. Translation of preformed mRNA from cotyledons of dry seeds was completely abolished in the presence of several inhibitors of polypeptide chain initiation and also in the presence of the two "cap" analogues m(7) GTP and m(7) GMP. The patterns of polypeptides synthesized by translation of poly(A)-containing RNAs from cotyledons of ungerminated or 18-hour-germinated seeds, in the wheat germ system, analyzed by electrophoresis and autoradiography, were similar but not identical. It is concluded that cotyledons of dry Cicer arietinum L. seeds contain preformed mRNA.

Journal Article↗

PubMed1993

Detection of human papillomavirus DNA and mRNA using synthetic, type-specific oligonucleotide probes.

Type-specific 30'mer-36'mer oligonucleotide probes complementary to mRNA transcribed from the E6 and E7 open reading frames of HPV 6b/11, 16, 18 and 33 were designed using the published nucleotide sequences. As oligonucleotides are easily and relatively cheaply synthesized in large amounts and are free of vector DNA, they were assessed for potential use in routine clinical detection and typing of HPV. Multiple Southern and dot blots of cloned HPV 6b, 11, 16, 18, 31 and 33 DNA, and of DNA extracted from cell lines carrying integrated HPV 16 and 18 genomes were prepared. In addition, Northern and dot blots of RNA extracted from the HPV-containing cell lines HeLa, CaSki and SiHa, were also prepared. All filters were first probed with the oligonucleotide and then with the corresponding full-genomic HPV DNA probe and their relative sensitivities and specificities compared: both probe types were labelled with 32P. The oligonucleotide probes were all as specific as the full-genomic probes for Southern, DNA and RNA dot blot hybridisations. The HPV 16 and 18 oligonucleotide probes detected HPV transcripts of the appropriate sizes in the cell line RNA. For DNA detection, oligonucleotide probes were up to 10 times less sensitive than the full-genomic probes, but for RNA detection, they were more sensitive. The sensitivity for both HPV DNA and RNA detection could be improved by using two type-specific oligonucleotide probes in combination, without reducing the specificity. The ease of preparation and handling of oligonucleotide probes, together with their lack of contaminating vector DNA, suggests that they may have some advantages over full-genomic probes for the clinical detection and typing of HPV.

Base Sequence↗