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PubMed1997

Modified Method for Competitive Reverse Transcription Polymerase Chain Reaction for Rapid and Automated Quantitation of Messenger RNA in Multiple Samples.

Background: Competitive reverse transcription polymerase chain reaction (RT-PCR) has been used increasingly to quantitate messenger RNA (mRNA) levels; however, conventional competitive RT-PCR methods require four or five reactions per sample of RNA, employing serial dilutions of an internal competitor sequence, making analysis of multiple samples of tedious process. A modified method is described by which multiple samples and multiple RNA transcripts can be analyzed easily by an automated process. Methods and Results: Transforming growth factor beta-1 (TGF-beta-1) mRNA was assayed in total RNA extracted from cultured human skin fibroblasts. A standard solution of total RNA was first prepared by pooling RNA from several cell lines and stored in aliquots. A 270-bp competitor RNA molecule (RNA mimic) was prepared by in vitro transcription and was added to each reaction. PCR was performed with a fluorescent dye (Hex; Applied Biosystems, Foster City, CA)-labeled sense primer to amplify a 161-bp-long c DNA product of target TGF-beta-1 mRNA sequence and the RNA mimic. The PCR products were analyzed with an automated laser-scanned gel electrophoresis system and the area under the curve (AUC) was used for quantitation. The concentration TGF-beta-1 mRNA in standard RNA was determined by conventional competitive RT-PCR. Subsequently, equal amounts of RNA mimic were mixed with four serial dilutions of standard RNA and 0.1 µg of sample total RNA for RT-PCR. A standard curve was generated using the known dilutions of a standard target RNA solution and ratio of AUC for target to that for mimic for each dilution. The unknown sample was then quantitated by interpolation of its area under the curve ratio on the standard curve. This method had inter- and intra-assay coefficients of variation of less than 10%. Conclusions: This modification is highly reproducible for quantitation of mRNA and significantly reduces the number of PCR reactions required for each assay. It can be used to assay several RNA molecules in a given sample by designing RNA mimics and PCR primers to generate PCR products of different lengths so that they can be analyzed by the laser scanning of a single lane of electrophoretic gel.

Journal Article↗

PubMed1986

Identification of a partial cDNA clone for the C3d/Epstein-Barr virus receptor of human B lymphocytes: homology with the receptor for fragments C3b and C4b of the third and fourth components of complement.

Human complement receptor type 2 (CR2) is the B-lymphocyte receptor both for the C3d fragment of the third component of complement and for the Epstein-Barr virus. Amino acid sequence analysis of tryptic peptides of CR2 revealed a strong degree of homology with the human C3b/C4b receptor, CR1. This homology suggested that CR1 gene sequences could be used to detect the CR2 sequences at conditions of low-stringency hybridization. Upon screening a human tonsillar cDNA library with CR1 cDNA sequences, two clones were identified that hybridized at low, but not at high, stringency. Redundant oligonucleotides specific for CR2 sequences were synthesized and used to establish that the two cDNA clones weakly hybridizing with the CR1 cDNA contained CR2 sequences. One of these CR2 cDNA clones hybridized to oligonucleotides derived from two distinct CR2 tryptic peptides, whereas the other, smaller cDNA clone hybridized to oligonucleotides derived from only one of the CR2 peptides. Nucleotide sequence analysis of the CR2 cDNA confirmed that the site of oligonucleotide hybridization was identical to that predicted from the peptide sequence, including flanking sequences not included within the oligonucleotide probes. The CR2-specific cDNA sequences identified a poly(A)+ RNA species of 5 kilobases in RNA extracted from human B cells but did not hybridize to any RNA obtained from the CR2-negative T-cell line HSB-2, thus confirming the appropriate size and tissue-specific distribution for the CR2 mRNA. The striking peptide sequence homology between CR2 and CR1 and the cross-hybridization of the CR2 cDNA with the CR1-specific sequences allow the placement of CR2 in a recently defined gene family of C3- and C4-binding proteins consisting of CR1, C4-binding protein, factor H, and now, CR2.

Amino Acid Sequence↗

PubMed1994

The physical state of the negative strand of hepatitis C virus RNA in serum of patients with chronic hepatitis C.

Negative strands of the hepatitis C virus (HCV) genome (a positive-stranded RNA virus) have been found in a nuclease-resistant form in the serum of patients with HCV infections. We determined whether a complete negative-strand copy is present in the serum, whether the negative strand is particle-associated, and finally, whether it is virion-associated and encapsidated like the positive (genomic) strand. Isopyknic sucrose and cesium chloride density ultracentrifugation followed by a strand-specific reverse transcription-polymerase chain reaction on the collected fractions was performed to determine whether both positive and negative strands were associated with similar particles. Both strands comigrated to approximately the same density (1.11-1.16 g/cm3) in sucrose. After treatment of the plasma with detergent (0.1% Nonidet P-40) to remove the viral envelope and centrifugation on cesium chloride gradients, the positive strands shifted to a density of 1.35 g/cm3, and the negative strands were not detected. By using antibodies specific for the HCV core or envelope glycoproteins E1 or E2 coated onto the wells of a microtiter plate, it was possible to specifically bind HCV or viral cores to the solid phase. Pelleted virus particles were resuspended in either PBS or PBS with 0.1% Nonidet P-40 to expose the core. These pellets were then incubated in antibody-coated microtiter wells. RNA extracted from the bound and unbound fractions was tested for HCV RNA. The anti-core antibody was able to bind positive strands but not negative strands only in detergent-treated samples. In the nondetergent-treated pellets, the anti-E1 and -E2 bound the positive strand, but only anti-E1 bound the negative strands. These findings indicate that while both strands of HCV RNA can be detected in serum, the positive strand is encapsidated within the enveloped core, and the negative strand appears to be in a membrane particle associated with the viral envelope protein E1 but does not appear to be within the HCV core of circulating virions.

Base Sequence↗

PubMed2003

High quality RNA retrieved from samples obtained by using LMPC (laser microdissection and pressure catapulting) technology.

Isolation of intact RNA in high quality is the first and often the most critical step in performing many fundamental molecular biology experiments, and is essential for many techniques used in gene expression analysis. As many factors influence nucleic acid preservation, RNA isolation should include some important steps before and after the actual RNA extraction. We tested the influence of fixation and staining protocols regarding RNA integrity and concentration. A factor that is often underestimated is the absolute necessity for homogenous starting materials. Application of the LMPC technology allows for a rapidand highly precise procurement of purified cell populations suitable for a variety of downstream analyses.

Animals↗

PubMed1988

Pregnancy-specific beta 1 glycoprotein in rat: tissue distribution of the mRNA and identification of testicular cDNA clones.

A partial cDNA of pregnancy-specific beta 1 glycoprotein isolated from human term placenta was used as probe for slot-blot analysis of total RNA extracted from placental and non-placental tissues in the rat. RNA hybridization with the probe was observed in rat placenta, indicating the presence of mRNA highly homologous to human SP1. The quantity of hybridizing RNA increased with increasing gestational age. In non-pregnant rats, SP1-hybridizing mRNAs were found in uterus, intestine and testis, while no hybridizing material was detected in liver or muscle. The amount of rat SP1 mRNA, based on percentage of total tissue RNA, was greatest in the testis followed by intestine, uterus and placenta. Using the same probe, six clones were obtained by screening a rat testis cDNA library. These clones carried cDNA inserts ranging in size from 1530 to 1983 bp. An internal EcoRI site was present in all cDNA clones. Southern blot analysis confirmed that the cDNA insert of all the clones was homologous to human placental SP1 cDNA. These results suggest a possible origin for the trace quantities of SP1 detected in non-pregnant individuals. It also confirms that the rat is an appropriate model for studying the physiological functions of SP1.

Animals↗

PubMed2006

Proliferative phase endosperm promoters from Arabidopsis thaliana.

Endosperm accounts for a large proportion of human nutrition and is also a major determinant of seed viability and size, not only in cereals, but also in species with ephemeral endosperms, such as soybean and oilseed rape. The extent of endosperm proliferation early in seed development is a crucial component in setting seed size; therefore, a biotechnological approach for the modification of this trait requires promoters active in early endosperm. To find such promoters, we constructed an array based on cDNAs extracted from developing Arabidopsis seeds enriched for proliferating endosperm. Hybridization with RNA extracted from vegetative and reproductive tissues, including endosperm, and subsequent data filtering yielded sets of endosperm-expressed and endosperm-preferred genes, including many hundreds not previously identified in array experiments designed to detect genes expressed in Arabidopsis seeds. Of eight promoters selected for validation, seven were active in early endosperm, three with no detected activity elsewhere in the plant. Therefore, this strategy has yielded proliferative phase endosperm promoters which should be useful in altering seed size.

Arabidopsis↗

PubMed1973

RD 114 virus-specific sequences in feline cellular RNA: detection and characterization.

RNA extracted from cat cells contains sequences homologous to RD-114 viral RNA. The sequences are measured by molecular hybridization with a single-stranded DNA probe synthesized by the virion polymerase using the endogenous viral RNA as template. Viral-specific RNA has been detected in all cells of cat origin tested thus far, but not in cells of other animals, except for the virus-producing human rhabdomyosarcoma cell, RD-114. The extent of hybridization of the DNA probe to cellular RNA was equivalent to that obtained with viral 70S RNA indicating that an equal extent of viral specific sequences is present in all cat cells as well as in RD-114 cells. The amounts of this viral RNA reach approximately 100 copies per cell in cat cells, while virus-producing RD-114 cells contain about 1,000 copies per cell. The viral RNA is present in cat cells in two distinct sizes of about 35S and 18S, whereas in RD-114 cells virus-specific RNA is quite heterogeneous in size.

Animals↗

PubMed1982

Subgenomic mRNA in OK10 defective leukemia virus-transformed cells.

OK10, a defective leukemia virus, is produced as a defective particle by so-called nonproducer transformed quail fibroblasts. OK10 defective viral particles contain an 8-kilobases (kb)-long genomic RNA, lack any detectable reverse transcriptase activity, and are not infectious. We studied the genetic content of OK10 RNA extracted from both virions and infected cells. As shown by RNA-cDNA hybridizations in stringent conditions, about 77% (6.4 kb) of the OK10 8.0kb RNA was related to avian leukosis viruses in the three structural genes gag, pol, and env, as well as in the c region. The remainder of the OK10 genome-encoding capacity (</=1.6 kb) was homologous to the MC29-specific transforming sequence myc(m) and therefore has been named myc(o). EcoRI restriction analysis of the OK10 integrated proviral DNA with different probes indicated the presence of only one provirus in the OK10 QB5 clone, which agreed with the gene order: 5'-gag-Deltapol-myc(o)-Deltaenv-c- 3'. Heteroduplex molecules formed between the viral OK10 8.0-kb RNA and the 6.8-kb SacI DNA fragment of the Prague A strain of Rous sarcoma virus confirmed that structure and indicated that the myc(o) sequence formed a continuous RNA stretch of 1.4 to 1.6 kb long between Deltapol and Deltaenv. We also examined the myc(o)-containing mRNA's transcribed in OK10-transformed cells. OK10-transformed quail fibroblasts (OK10 QB5) transcribed two mRNA species of 8.0 and 3.6 kb containing the myc(o) sequence. The genetic content of the 3.6-kb species made it a possible maturation product of the genome size 8-kb species by splicing out the gag and pol sequences. In OK10-transformed bone marrow cells (OK10 BM), a stable bone marrow-derived cell line producing OK10, the myc(o) sequence was found in four RNA species of 11.0, 8.0, 7.0, and 3.6 kb. Again, the genetic content of these mRNA's indicated that (i) the 3.6-kb species could be spliced out of the 8.0-kb-genome size mRNA and (ii) the 11.0-kb-long mRNA could represent a read-through of the OK10 provirus, the corresponding maturation product being, then, a 7.0-kb mRNA. The 7.0- and 3.6- kb mRNA's both contained the myc(o) sequence, but no sequences related to the gag or pol gene. In conclusion, whereas the myc sequences have been generally thought to be expressed through a gag-onc fusion protein, as for MC29 and CMII viruses, our experiments indicate that they could also be expressed as a non-gag-related product made from a subgenomic mRNA in the OK10-transformed cells.

Animals↗

PubMed1989

In vitro construction of poliovirus defective interfering particles.

To construct poliovirus defective interfering (DI) particles in vitro, we synthesized an RNA from a cloned poliovirus cDNA, pSM1(T7)1, which carried a deletion in the genome region corresponding to nucleotide positions 1663 to 2478 encoding viral capsid proteins, by using bacteriophage T7 RNA polymerase. The RNA was designed to retain the correct reading frame in nucleotide sequence downstream of the deletion. HeLa S3 monolayer cells were transfected with the deletion RNA and then superinfected with standard virus as a helper. The DI RNA was observed in the infected cells after three passages at high multiplicity of infection. The sequence analysis of RNA extracted from the purified DI particle clearly showed that this DI RNA had the same deletion in size and location as that in the RNA used for the transfection. Thus, we succeeded in construction of a poliovirus DI particle in vitro. To gain insight into the mechanism for DI generation, we constructed poliovirus cDNAs pSM1(T7)1a and pSM1(T7)1b that, in addition to the same deletion as that in pSM1(T7)1, had insertion sequences of 4 bases and 12 bases, respectively, at the corresponding nucleotide position, 2978. The RNA transcribed from pSM1(T7)1a was not a template for synthesis of poliovirus nonstructural proteins and therefore was inactive as an RNA replicon. On the other hand, the RNA from pSM1(T7)1b replicated properly in the transfected cells. Superinfection of the transfected cells with standard virus resulted in production of DI particles derived from pSM1(T7)1b and not from pSM1(T7)1a. These observations indicate that deletion RNAs that are inactive replicons have little or no possibility of being genomes of DI particles suggesting the existence of a nonstructural protein(s) that has an inclination to function as a cis-acting protein(s). The method described here will provide a useful technique to investigate genetic information essential for poliovirus replication.

Amino Acid Sequence↗

PubMed1989

Control of beta-interferon expression in murine embryonal carcinoma F9 cells.

Murine embryonal carcinoma F9 cells, a tissue culture model for early embryonic development, do not produce interferon (IFN) in response to poly(I-C), as determined by an antiviral assay. RNase protection analyses were used to examine total RNA extracted from the cells for the presence of beta-IFN RNA. Whereas F9 cells differentiated in vitro with retinoic acid produced a biologically active protein as well as beta-IFN RNA in response to poly(I-C), undifferentiated F9 cells produced no detectable beta-IFN RNA even in the presence of cycloheximide, an IFN-superinducing agent. These results show that undifferentiated embryonal carcinoma cells do not accumulate beta-IFN RNA in response to an IFN-inducing agent, suggesting a transcriptional regulatory mechanism. However, this control mechanism is altered upon differentiation, since the gene can be transcriptionally activated in retinoic acid-differentiated cells.

Animals↗

PubMed2004

Failure to detect enterovirus in the spinal cord of ALS patients using a sensitive RT-PCR method.

OBJECTIVE: To assess the association of enteroviruses (EV) with ALS by applying a sensitive seminested reverse transcription (RT) PCR protocol to the detection of enteroviral RNA in a blinded set of archived tissues from ALS and control cases. METHODS: The specimen set consisted of 24 frozen spinal cord samples from ALS cases, 17 frozen spinal cord samples from negative control (non-ALS) cases, and 5 frozen spinal cord positive control samples. The positive controls were two human spinal cord samples spiked with poliovirus (PV) and three spinal cords from PV-infected transgenic mice. A sensitive, EV-specific, seminested RT-PCR assay was used to detect EV genome in RNA extracted from the specimens and controls. RESULTS: The assay detected EV RNA in a 10(-5) dilution of infected mouse tissue. EV RNA was not detected in the ALS specimens or in specimens from control cases, despite the presence of amplifiable RNA as assessed by amplification with control primers, whereas all of the positive control specimens yielded the expected PV amplification product. CONCLUSION: The reported association between EV infection and ALS was not confirmed by testing this set of specimens with these sensitive methods.

5' Untranslated Regions↗

PubMed1982

Induction of implantation in the rat by intraparametrial injection of uterine RNA from oestrogen-treated animals.

Crude RNA preparations from uteri of oestradiol-treated rats induced the implantation of delayed blastocysts when injected into the parametrium of ovariectomized pregnant rats. Treatment of donor animals with labelled oestradiol showed that this effect could not be due to contamination of the RNA extracts by oestradiol. RNase digestion of these extracts suppressed their capacity to induce implantation. Purified poly (A)-rich RNA from oestrogen-treated uteri failed to elicit implantation although it was capable of increasing epithelial height when repeatedly injected into uterine horns of ovariectomized rats. These results suggest that uterine RNA synthesis might somehow mediate the effects of oestrogen in causing implantation and that RNAs other than messenger RNA might be involved.

Animals↗

PubMed2006

Genome-wide expression profile of human trabecular meshwork cultured cells, nonglaucomatous and primary open angle glaucoma tissue.

PURPOSE: To contrast genome-wide gene expression profiles of cultured human trabecular meshwork (HTM) cells to that of control and primary open angle glaucoma (POAG) HTM tissues. METHODS: Cultured HTM cells, HTM tissue dissected from control donors, and HTM tissue from POAG donors receiving medication for glaucoma were fixed in RNA latertrade mark. Total RNA extracted from these samples was linearly amplified with the Ovation Biotin RNA Amplification and Labeling System and individually hybridized to Affymetrix Human Genome U133 Plus 2.0 high density microarrays. Data analysis was performed using GeneSpring Software 7.0. Selected genes showing significant differential expression were validated by quantitative real-time PCR in nonamplified RNA. RESULTS: Cultured HTM cells retained the expression of some genes characteristic of HTM tissue, including chitinase 3-like 1 and matrix Gla protein, but demonstrated downregulation of physiologically important genes such as myocilin. POAG HTM tissue showed relatively small changes compared to that of control donors. These changes included the statistically significant upregulation of several genes associated with inflammation and acute-phase response, including selectin-E (ELAM-I), as well as the downregulation of the antioxidants paraoxonase 3 and ceruloplasmin. CONCLUSIONS: Downregulation in cultured HTM cells of genes potentially relevant for outflow pathway function highlights the importance of developing new conditions for the culture of TM cells capable of preserving the characteristics of TM cells in vivo. Comparative analysis between control and POAG tissues suggests that the upregulation of inflammation-associated genes might be involved in the progression of glaucoma.

Case-Control Studies↗

PubMed1990

[Virus demonstration and pathologic changes in different phases of coxsackievirus B myocarditis in mice].

A/J mice between 15 days and 10 weeks of age were infected intraperitoneally with Coxsackievirus B3 (CVB3). To search for virus in the myocardium various methods were applied: virus isolation from the myocardium, RNA extraction for dot blot hybridization and in situ hybridization. Two different RNA probes, one specific for CVB3 the other cross-reacting with other enteroviruses, were radioactively labeled with 35S or 32P by in vitro transcription. In paraffin sections histological alterations were assessed semiquantitatively. The animals developed acute myocarditis with myolysis and virus in the myocardium until 14 days after infection. The second stage of the disease was characterized by a persistent inflammatory infiltrate. At this stage no virus could be shown in the myocardium. Antibodies against cardiac myosin appeared 16 days after infection. Autoimmune mechanisms thus seem to be a most relevant factor for persistent inflammation after the acute viral phase of the disease.

Animals↗

PubMed1971

Characterization of ribonucleic acid from visna virus.

A single-stranded ribonucleic acid(s) has been isolated from purified virions of visna virus. It consists of two major components, namely 63S and "4S," under the conditions employed for ribonucleic acid (RNA) extraction. The 63S component can be converted to subunits by heat and dimethylsulfoxide treatments. Analyses by base composition indicate that the "4S" RNA isolated from visna virus is not a random breakdown product of the 63S component as a result of extraction, nor is it randomly derived from cellular RNA.

Animals↗

PubMed1992

RNA analysis from newborn screening dried blood specimens.

We have previously demonstrated that DNA can be extracted from the dried blood specimen of the type used for newborn screening. The technique presented here allows us to extract RNA from newborn screening specimens for cDNA synthesis by reverse transcriptase and amplification by the polymerase chain reaction (PCR). Products of the PCR reaction are then analyzed by restriction enzymes. This method successfully distinguishes beta A and beta S transcripts in unaffected (AA), carrier (AS), and affected (SS) individuals. The value of this approach for identification of a compound heterozygous patient with S/beta-thalassemia, using the original newborn screening specimen, is also demonstrated. This work shows that mRNA is stable in dried blood specimens and that analysis of the mRNA phenotype can be a useful adjunct in the application of molecular genetic technology to newborn screening.

Anemia, Sickle Cell↗

PubMed1977

Biochemical responses of pea root tissue to cytokinin: enhanced rates of RNA synthesis.

Rates of RNA synthesis were studied in cultured pea (Pisum sativum) root segments and cortical explants which require the hormone cytokinin for DNA replication and cell proliferation. Rate calculations were based on the specific radioactivity of the extracted RNA and the specific radioactivity of the extracted ATP pool after a pulse with (3)H-adenosine. The kinetics of RNA synthesis was studied after 24 hours of culture with or without kinetin. We found that kinetin stimulated a 2- to 4-fold enhancement in the rate of RNA synthesis after 24 hours of culture as compared to controls. A similar order of magnitude of stimulation of RNA synthesis was found when RNA was isolated by cesium chloride centrifugation. Pulses during the first 24 hours indicate that kinetin stimulates the rate of RNA synthesis as early as 9 hours after treatment has begun. During the first 24 hours of culture, kinetin did not affect the specific radioactivity of the ATP pool. The ATP pool equilibrated slowly with the exogenous label ((3)H-adenosine) in the presence or absence of kinetin. After 3 days in culture, we found kinetin to cause an expansion of the extractable ATP pool and a corresponding reduction in the ATP pool specific radioactivity. We interpret these results to indicate a stimulation in the rate of RNA synthesis due to kinetin treatment prior to any other known response.

Journal Article↗

PubMed2005

Expression of lexA targeted ribozyme in Escherichia coli BL-21 (DE3) cells.

Coding sequences for a hammerhead ribozyme designed to cleave lexA mRNA in a targeted manner was cloned under phage T7 promoter and expressed in E. coli strain BL-21 (DE3) expressing T7 RNA polymerase under the control of IPTG-inducible lac UV-5 promoter. Ribozyme expression in vivo was demonstrated by RNase protection assay. Also, total RNA extracted from these transformed cells following induction by IPTG, displays site-specific cleavage of labeled lexA RNA in an in vitro reaction. The result demonstrates the active ribozyme in extracts of cell transformed with a recombinant cassette and goes beyond the earlier demonstration of the stability of in vitro synthesized ribozyme in cell extracts. The observed rise in lexA mRNA rules out any role for protease activity or resulting fragments of lexA protein in de-repression of RNA.

Bacterial Proteins↗