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At least 433 records · Page 24Linked to original sources
PubMed1975

Bacteriophage SPO1 DNA- and RNA-directed protein synthesis in vitro: comparison with in vivo control.

A cell free protein synthesizing system, derived from E. coli, is shown to be a quantitiative assay system for messenger RNA extracted from B. subtilis infected with bacteriophage SPO1. DNA-directed protein synthesis in this system is shown to be limited mostly to those proteins whose messages are contained in early RNA. A phage induced enzyme, dCMP deaminase, is shown to be dependent on appearance of a class mRNA made in vivo in response to new initiations of transcription dependent on prior synthesis of phage induced protein. Control of the enzyme synthesized in the cell free system is contrasted with in vivo control, and an estimate of "read-through" by RNA polymerase in vitro is presented.

Bacillus subtilis↗
PubMed1980

A facile procedure for purifying maize chloroplast RNA polymerase from whole cell homogenates.

Two DNA-dependent RNA polymerases have been purified from homogenates of maize leaves by a relatively rapid procedure involving Sepharose 4B and DEAE-cellulose chromatography followed by resolution of two RNA polymerasies on phosphocellulose. The RNA polymerase eluting from phosphocellulose at 0.11 M (NH4)2SO4 is inhibited strongly by low levels of alpha-amanitin and possesses catalytic properties and polypeptide subunits like those of maize nuclear RNA polymerase II. The RNA polymerase eluting from phosphocellulose at 0.15 M (NH4)2SO4 resembles the RNA polymerase solubilized from isolated maize chloroplasts in many ways. This enzyme and that isolated from chloroplasts are resistant to alpha-amanitin and rifamycin-SV at high concentrations. Both RNA polymerases have virtually the same Mn2+ and Mg2+ optima, Mg2+/Mn2+ activity ratios, (NH4)2SO4 sensitivity, kinetics of UMP incorporation, and temperature optima. Electrophoresis of this phosphocellulose-purified RNA polymerase on denaturing polyacrylamide slab gels reveals 14 heavily stainable polypeptides that are identical in number and molecular mass to those from chloroplast RNA polymerase. Moreover, two-dimensional tryptic maps of the 14 polypeptides from the phosphocellulose-purified RNA polymerase are very similar to the maps of corresponding polypeptides from chloroplast RNA polymerase. Using this method, relatively large quantities (0.5 mg/kg leaves) of a form of chloroplast RNA polymerase can be prepared in a few days.

Centrifugation, Density Gradient↗
PubMed1975

R17 RNA replicase. VI. A large scale preparation of R17 template RNA.

A new procedure for R17 RNA preparation was devised using a 300 liters fermenter. The key factor in processing such a large quantity is the purification of phage particles prior to RNA extraction. The method involves the preparation of 250 liters of crude lysate, condensation of phage particles by the partition method, purification by DEAE-cellulose column, and removal of adherent proteins by a series of high-salt washes. The method permits preparation of approximately 3 g of phage particles free of ribosomal fragments and RNase. Phage RNA extracted in gram quantities using conventional methods often contain phenol. Thus repeated extraction of R17 RNA with salt-alcohol mixture is required.

Coliphages↗
PubMed1997

Tenosynovial nodulosis in a patient infected with human T cell lymphotropic virus I.

We describe a 45-year-old man who presented with multiple nodules along the tendons of the scapular region, the elbows, wrists, forearms, thighs, and ankles. The patient was a carrier of human T cell lymphotropic virus I (HTLV-I), which was probably transmitted from his mother; his mother also had polyarthritis. Histopathologically, the nodules consisted of numerous, small, fibrinoid masses. The synovium adjacent to the tendon sheath was hyperplastic, with fibrinoid necrosis mimicking rheumatoid synovium. However, synovitis was not present inside the adjacent joint. HTLV-I proviral DNA was detected in the cells of the nodule, in tenosynovial cells, and in peripheral blood lymphocytes, but not in skin fibroblasts. In situ reverse transcription assay showed a high quantity of tax/rex messenger RNA in the proliferating lining cells. Based on these features, we classified this case as an atypical manifestation of HTLV-I-associated arthropathy associated with fibrinoid nodules resulting from chronic tenosynovitis.

Carrier State↗
PubMed1994

A general purification procedure for chemically synthesized oligoribonucleotides.

A general procedure for the purification of chemically synthesized oligoribonucleotides is reported. Purification based on the use of a single reverse-phase HPLC column with buffer systems of differing ion-pairing capacity is described. These methods have been applied to the preparation of a series of RNAs which range in size from 10 to 46 nucleotides. The yields obtained are high, up to 53% (based on isolated product compared to those obtained from final trityl assay). The purity of the isolated material is 96-99%. Thus with this general procedure, milligram quantities of extremely pure RNA can be efficiently obtained.

Base Sequence↗
PubMed1995

Quantitative RNA-polymerase chain reaction-DNA analysis by capillary electrophoresis and laser-induced fluorescence.

Quantitative RNA-polymerase chain reaction (RNA-PCR) is an extremely powerful analytical tool owing to its specificity and high level of sensitivity. Quantitative RNA-PCR is, however, highly labor intensive. No analytical method currently exists that can accurately and rapidly quantitate the small quantities of DNA in RNA-PCR reaction mixtures. We have developed a method using capillary electrophoresis and laser-induced fluorescence to detect YOYO-1 complexes of DNA produced by PCR. RNA-PCR mixtures can be analyzed either directly (without primer and protein removal) or by electrokinetic injection following desalting. Modified competitive and multiplex competitive RNA-PCR assays for glyceraldehyde-3-phosphate dehydrogenase and P4501A1 were tested in a series of mixtures containing equal concentrations, but different proportions, of RNA from untreated (essentially no P4501A1 mRNA) and 2,3,7,8-tetrachlorodibenzo-p-dioxin-treated (high levels of P4501A1 mRNA) HepG2 cells. Twofold differences in concentrations between two P4501A1 mRNA solutions could be detected by competitive RNA-PCR. Glyceraldehyde-3-phosphate dehydrogenase concentrations were constant throughout. Multiplex competitive PCR produced more variable results due to the presence of contaminating peaks, which hindered accurate area integration. These data demonstrate the potential usefulness of capillary electrophoresis in a variety of quantitative PCR applications.

Base Sequence↗
PubMed1988

Nuclear and mitochondrial revertants of a yeast mitochondrial tRNA mutant.

We isolated revertants capable of respiration from the respiratory deficient yeast mutant, FF1210-6C/170, which displays greatly decreased mitochondrial protein synthesis due to a single base substitution at the penultimate base of the tRNAAsp gene on mitochondrial (mt) DNA. Three classical types of revertant were identified: (1) same-site revertants; (2) intragenic revertants which restore the base pairing in the acceptor stem of the mitochondrial tRNAAsp; and (3) extragenic suppressors located in nuclear DNA. In addition a fourth type of revertant was identified in which the mutant tRNAAsp is amplified due to the maintenance of both the original mutant mtDNA and a modified form of the mutant mtDNA in which only a small region around the tRNAAsp gene is retained and amplified. The latter form resembles the mtDNA in vegetative petite (rho-) strains which normally segregates rapidly from the wild-type mtDNA. Each revertant type was characterized genetically and by both DNA sequence analysis of the mitochondrial tRNAAsp gene and analysis of the quantity and size of RNA containing the tRNAAsp sequence. These results indicate that the mitochondrial tRNAAsp of the mutant retains a low level of activity and that the presence of the terminal base pair in tRNAAsp is a determinant of both tRNAAsp function and the maintenance of wild-type levels of tRNAAsp.

Base Sequence↗
PubMed1975

The isolation of large polysomes in high yield from unfractionated tissue homogenates.

It was found that if large quantities of both exogenous RNA and Mg-2+ were present during gentle tissue homogenization, the subsequent addition of deoxycholate to the whole homogenate produced a viscous mass from which polysomes could be isolated in large yields. These polysomes were substantially less degraded than those isolated by previous methods. In the case of rat liver, 15 ribosomes per mRNA was the species present in highest concentration. The parameters of this method were investigated and optimized. About 80 percent of the rRNA in the homogenates was recovered in the polysomes. Omission of deoxycholate permitted the isolation of less-degraded free polysomes as well. In the liver of fed rats these represented one-fourth of the total polysomes, in good agreement with results obtained by an independent approach. Using the method to isolate polysomes from the liver of starving rats, it was found that only about one percent of the large amount of monomers and dimers present resulted from polysome breakdown during isolation. It was further shown that random RNAase hydrolysis of polysomes could not produce the patterns of liver polysomes seen during starvation. Polysomes isolated by this procedure were quite stable in solution and were very active in cell-free protein synthesis. Application of this method without adaptation to eight other tissues also permitted the isolation of large polysomes in high yields.

Animals↗
PubMed1986

Construction of a representative cDNA library from mRNA isolated from mouse oocytes.

A representative cDNA library has been constructed from the small quantities of poly(A)+ RNA present in unfertilised mouse oocytes. The construction of this library has been achieved by use of cow pea mosaic virus RNA as a carrier during isolation of polyadenylated message and during subsequent cloning procedures. This approach may be applicable to any system in which amounts of mRNA are limiting.

Animals↗
PubMed1990

Acetyl-L-carnitine increases cytochrome oxidase subunit I mRNA content in hypothyroid rat liver.

The effect of acetyl-L-carnitine on the quantity of the messenger RNA for the subunit I of cytochrome oxidase in the liver mitochondria of hypothyroid rat was measured by Northern blot and solution hybridization. Three hours after pre-treatment of hypothyroid rat with acetyl-L-carnitine, the level of the transcript increased strongly. This effect was also obtained when acetyl-L-carnitine was administered to T3 pre-treated hypothyroid rats. These results add further evidence to the suggestion that acetyl-L-carnitine is able to stimulate mitochondrial transcription under altered metabolic conditions.

Acetylcarnitine↗
PubMed1990

Selective enrichment of cDNAs from salt-stress-induced genes in the wheatgrass, Lophopyrum elongatum, by the formamide-phenol emulsion reassociation technique.

We present a novel technique for the enrichment of cDNA libraries to enhance the abundance of clones of differentially expressed genes. The technique is relatively simple, requires moderate quantities of poly(A) + RNA and results in preferential enrichment of clones derived from mRNAs that were of low abundance in their original population. This method was used to isolate cDNA clones of salt-stress-induced genes in the roots of Lophopyrum elongatum, a highly salt-tolerant wheatgrass. An excess of sonicated plasmid DNA from a cDNA library from nonstressed roots was hybridized in a formamide-phenol emulsion with inserts from a cDNA library of stressed roots. Clones that were more abundant in, or were unique to, the library of the stressed roots were recovered as double-stranded fragments by virtue of reconstituted restriction-enzyme-digested ends by ligating them to a plasmid vector. The resulting enriched library was screened by differential colony hybridization and clones of eleven different genes that were more strongly expressed in stressed roots than in controls were selected.

Blotting, Northern↗
PubMed2003

Messenger RNA profiling: a prototype method to supplant conventional methods for body fluid identification.

Conventional methods of body fluid identification use a variety of labor-intensive, technologically diverse techniques that are performed in a series, not parallel, manner and are costly in terms of time and sample. Theoretically, the identification of a body fluid may be made by determining a sufficient number of mRNAs that are expressed exclusively in cells that collectively comprise that body fluid. Advantages of an mRNA-based approach, compared to conventional biochemical methods of analysis, include greater specificity, simultaneous and semi-automatic analysis through a common assay format, improved timeliness, decreased sample consumption and compatibility with DNA extraction methodologies. In this report, we demonstrate that RNA is stable in biological stains and can be recovered in sufficient quantity and quality for analysis. Messenger RNA from the housekeeping genes S15, beta-actin and GAPDH was detected in blood, semen and saliva stains using a sensitive reverse transcriptase-polymerase chain reaction assay (RT-PCR). Additionally, we have identified a number of candidate tissue-specific genes, statherin, histatin 3, PRB1, PRB2 and PRB3 that may be useful for the positive identification of saliva. Messenger RNAs from these genes were detectable in saliva stains but not in blood or semen stains. Collectively these findings constitute the basis of a prototype RNA based assay system that may eventually supplant conventional methods for body fluid identification.

Actins↗
PubMed2002

Use of PCR for the diagnosis of herpesvirus infections of the central nervous system.

Polymerase chain reaction (PCR) analysis of cerebrospinal fluid (CSF) has revolutionized the diagnosis of nervous system viral infections, particularly those caused by human herpesviruses (HHV). The PCR technique allows the detection of minute quantities of DNA or RNA in body fluids and tissues. Both fresh-frozen and formalin-fixed tissues may be utilized for PCR assays, with the latter making archival studies possible. CSF PCR has now replaced brain biopsy as the gold standard for the diagnosis of herpes simplex virus (HSV) encephalitis. PCR analysis of both CSF and nervous system tissues has also broadened our understanding of the spectrum of disease caused by HSV-1 and -2, cytomegalovirus (CMV), Epstein-Barr virus (EBV), varicella zoster virus (VZV) and HHV-6. PCR results obtained from tissue specimens must be interpreted cautiously, since this highly sensitive technique may detect portions of viral genomic material that may be present even in the absence of active viral infection. Tissue PCR results in particular must be corroborated with clinical and neuropathologic evidence of central nervous system (CNS) infection. In several neurological diseases, negative PCR results have provided evidence against a role for herpesviruses as the causative agents. This review summarizes the role of CSF PCR in the diagnosis and therapeutic management of herpesvirus infections of the nervous system, particularly those caused by HSV and VZV.

Central Nervous System Viral Diseases↗
PubMed2002

Time course of gene expression in rat experimental autoimmune myocarditis.

Genetic responses that characterize experimental autoimmune myocarditis (EAM) have not yet been determined. To investigate gene expression in the myocardium of EAM, absolute copy numbers of 44 mRNA species [calcium-handling proteins, contractile proteins, natriuretic peptides (NPs), cytokines, chemokines, growth factors, renin-angiotensin-aldosterone (RAA) system, endothelins (ETs) and extracellular matrix] in synthesized cDNA from a fixed quantity of total heart RNA were assessed using real-time reverse-transcriptase PCR at days 0, 14, 21 and 28 after immunization. alpha-Cardiac myosin showed a 26.3-fold decrease and beta-cardiac myosin a 3.75-fold increase at day 14. Atrial NP and brain NP increased 47.7- and 6.35-fold at days 21 and 14 respectively. Angiotensin II type 1 receptor, angiotensin-converting enzyme and ET1 increased 22.3-fold at day 21, 6.30-fold at day 21 and 16.8-fold at day 14 respectively. Aldosterone receptor decreased 2.15-fold at day 14, but aldosterone synthetase was detected only at days 14 and 21. Interleukin (IL)-2, IL-10, interferon-gamma and monocyte chemo-attractant protein-1 increased 9.08-fold at day 14, 398-fold at day 21, 43.1-fold at day 14 and 142-fold at day 14 respectively. Collagen type 3, collagen type 1 and fibronectin increased 34.6-, 1.74- and 44.4-fold respectively at day 21. Interestingly, osteopontin showed a 4540-fold increase and it was the highest mRNA of all at day 14. An isoform of cardiac myosin and NP are dramatically changed in EAM. RAA system and ET expressions are changed differently during the EAM time course. Cytokine, chemokine and extracellular matrix greatly increase and, in particular, large numbers of osteopontin mRNA are expressed in early EAM.

Animals↗
PubMed2001

Degranulation influences heparin-associated inhibition of RT-PCR in human lung mast cells.

BACKGROUND: The study of gene expression from human lung mast cells (HLMC) has been limited by the ability to reliably detect mRNA transcripts from scant quantities of mast cell RNA contaminated with heparin. OBJECTIVE: As heparin is granule-associated within the mast cell, we examined the role of degranulation in altering the intrinsic ability of this proteoglycan to inhibit reverse transcription polymerase chain reaction (RT-PCR) from HLMC RNA. We also explored alternative means of RNA isolation to eliminate primary heparin contamination. METHODS: Purified HLMC (> 90% pure) were challenged for 2 h with buffer, anti-IgE (3 microg/mL) and/or ionophore A23187 (100 ng/mL) or phorbol 12-myristate 13-acetate (50 ng/mL). Histamine release was measured using a spectroflourometric assay. Following challenge, RNA was isolated by either phenol-chloroform extraction or by nitrocellulose spin column. Parallel samples were either treated with heparinase or placed on ice for 2 h prior to reverse transcription. PCR was performed using primers specific for the housekeeping gene, glyceraldehyde-3-phosphate dehydrogenase (GAPDH). RESULTS: In each of five studies, GAPDH bands were detected at greater intensity in total cellular RNA (tcRNA) derived from degranulated than from non-degranulated mast cells. However, when examining heparinase-treated tcRNA from the same mast cell samples, the intensity of GAPDH bands normalized between degranulated and non-degranulated cells. When comparing parallel samples of column-purified tcRNA, subsequent treatment of samples with heparinase had no effect on the detection of GAPDH, indicating that endogenous heparin was effectively removed by the technique. Moreover, no variability was noted in GAPDH signal detected from resting vs. degranulated mast cells (n = 3). CONCLUSIONS: Degranulation influences the degree of heparin-associated inhibition of RT-PCR in HLMC, and that spin column purification of tcRNA is a time-saving, effective alternative to heparinase pre-treatment.

Anticoagulants↗
PubMed2004

Chemical route to the capped RNAs.

Eukaryotic and viral messenger RNAs contain a CAP structure that plays an important role in the initiation of translation and several other cellular processes that involve mRNAs. In this paper, we report a convenient chemical approach to the preparation of milligram quantities of short, capped RNA oligonucleotides, which overcomes some of the limitations of previous approaches. The method is based on the use of a reactive precursor, m7GppQ [P1-7-methylguanosine-5'-O-yl, P2-O-8-(5-chloroquinolyl) pyrophosphate]. The precursor reacts smoothly with 5'-phosphorylated unprotected short RNA in the presence of CuCl2 in organic media. The feasibility of this approach was demonstrated by the synthesis of the capped pentaribonucleotide m7GpppGpApCpU. The synthesized capped oligonucleotide was isolated and purified by reverse phase and ion exchange HPLC with a final yield of 37%. The structure of the m7GpppGpApCpU was confirmed by 31P NMR, mass-spectrometry and enzymatic hydrolysis.

Magnetic Resonance Spectroscopy↗
PubMed1963

The use of bismuth as an electron stain for nucleic acids.

Evidence is presented to show that bismuth combines in vitro with the phosphate of nucleic acids in a manner similar to its reaction with inorganic phosphate. When tested under similar conditions, protein exhibited no attraction for bismuth. The results of the in vitro experiments, which are of interest within themselves, may be indirectly applicable to in vivo staining. Dividing cells of onion root tips were fixed in OsO(4), stained with bismuth, and examined in the electron microscope. The electron opacity of cell structures known to contain nucleic acids was enhanced by bismuth, while organelles known to lack appreciable quantities of DNA or RNA showed little, if any, change. Bismuth is particularly effective as a stain for the chromatin material during interphase and for the chromosomes during division.

Bismuth↗
PubMed2002

Vitamin A supplementation and human immunodeficiency virus type 1 shedding in women: results of a randomized clinical trial.

Observational studies have associated vitamin A deficiency with vaginal shedding of human immunodeficiency virus (HIV) type 1-infected cells and mother-to-child HIV-1 transmission. To assess the effect of vitamin A supplementation on vaginal shedding of HIV-1, a randomized, double-blind, placebo-controlled trial of 6 weeks of daily oral vitamin A (10,000 IU of retinyl palmitate) was conducted among 400 HIV-1-infected women in Mombasa, Kenya. At follow-up, there was no statistically significant difference in the prevalence of HIV-1 DNA (18% vs. 21%, P=.4) or the quantity of HIV-1 RNA (3.12 vs. 3.00 log(10) copies/swab, P=1.0) in vaginal secretions of women receiving vitamin A, compared with women receiving placebo. No significant effect of supplementation on plasma HIV-1 load or CD4 or CD8 cell counts was observed, and no effect was seen among women who were vitamin A deficient at baseline. Vitamin A supplementation is unlikely to decrease the infectivity of women infected with HIV-1.

Acquired Immunodeficiency Syndrome↗