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PubMed2005

Assessment of fixatives, fixation, and tissue processing on morphology and RNA integrity.

Molecular characterization of morphologic change requires exquisite tissue morphology and RNA preservation; however, traditional fixatives usually result in fragmented RNA. To optimize molecular analyses on fixed tissues, we assessed morphologic and RNA integrity in rat liver when sections were fixed in 70% neutral-buffered formalin, modified Davidson's II, 70% ethanol, UMFIX, modified Carnoy's, modified methacarn, Bouin's, phosphate-buffered saline, or 30% sucrose. Each sample was subjected to standard or microwave fixation and standard or microwave processing, and sections were evaluated microscopically. RNA was extracted and assessed for preservation of quality and quantity. Modified methacarn, 70% ethanol, and modified Carnoy's solution each resulted in tissue morphology representing a reasonable alternative to formalin. Modified methacarn and UMFIX best preserved RNA quality. Neither microwave fixation nor processing affected RNA integrity relative to standard methods, although morphology was modestly improved. We conclude that modified methacarn, 70% ethanol, and modified Carnoy's solution provided acceptable preservation of tissue morphology and RNA quality using both standard and microwave fixation and processing methods. Of these three fixatives, modified methacarn provided the best results and can be considered a fixative of choice where tissue morphology and RNA integrity are being assessed in the same specimens.

Animals↗
PubMed1982

A critical evaluation of Bernhard's EDTA regressive staining technique for RNA.

The EDTA regressive staining procedure to detect RNA (Bernhard's technique) is based on the proposition that after staining ultrathin sections with uranyl the stain is preferentially removed from DNA rather than RNA by the action of the chelating agent EDTA. Whilst attempting to use the EDTA regressive staining procedure to detect the presence of RNA in the large granule complexes of chicken erythrocyte nuclei, certain anomalous staining patterns were observed in the chromatin of these nuclei. Essentially, these were that the edges of condensed chromatin bodies stained positively for RNA even though this molecule is known not to be present there in significant quantities. The staining patterns suggested that chromatin was retaining its stain in a manner expected of RNA but not DNA as a consequence of EDTA-containing species failing to pass freely through the section. This hypothesis was tested by carrying out the EDTA procedure on embedded specimens of a DNA-containing virus, simian virus 40 (SV40), small enough not to be exposed at the surface of the section. In this way it has been shown that virus particles completely surrounded by resin destain so much more slowly than chromatin, which is accessible at the surface of the section, that without any other information it would be concluded that the viruses contained RNA, not DNA. This apparently anomalous result arises because the difficulties encountered by stain or EDTA molecules in passing through a plastic section were not appreciated at the time of the initial publication of the technique. The observations are discussed in the light of recent knowledge that has been gained on the kinetics of staining by measuring the electron-scattering densities of stained sections, similar measurements having been made on sections stained by Bernhard's technique. A model for the mechanism of the EDTA regressive staining technique consistent with the experimental observations is proposed and the conditions under which Bernhard's staining procedure retains its specificity are defined. Briefly, these conditions are that: (a) the sections be stained for only a short period with uranyl before treating them with EDTA even though such brief staining is undesirable for quantitative measurements of stain uptake into biological material; and (b) that sections stained in lead only be compared as controls with sections stained by Bernhard's technique so that any specificity of lead for sub-cellular components is not confused with a positive indication of the presence of RNA. Unless these conditions are fulfilled, results obtained by the use of the regressive staining technique may be highly misleading.

Animals↗
PubMed1989

Formation of large, sedimentable transcription complexes with VARNA genes and other related genes.

We have used an Eppendorf centrifuge for isolation of transcription complexes assembled on VARNA genes and other related genes with NTP-depleted cell-free extracts. Similar to the 5 S rRNA gene, sedimentable, stable transcription preinitiation complexes could be assembled from two VARNA genes, two EB virus-specific EBER genes, four human tRNA genes, and one human Alu-family RNA gene, suggesting that the 5 S rRNA-specific transcription factor, TFIIIA, was not required for formation of these sedimentable, stable preinitiation complexes. Parameters affecting assembly of these complexes were sequences in circular DNA templates, sizes and sequences of linear DNA templates, temperature and incubation time. These complexes were stable at from 4 to 37 degrees C, and somewhat stable to salt wash. From results of effects of various mutations on assembly of these sedimentable complexes, we concluded that they were transcription machineries. Addition of the supernatant and partially purified factors to salt-washed complexes stimulated their transcription, we concluded that these sedimentable complexes were minimal transcription machineries containing suboptimal quantities of loosely bound transcription factors, TFIIIB, and RNA polymerase III. DNase 1 footprints of these sedimentable preinitiation complexes showed that two regions were protected, from +34 to +80 including the B block promoter element, and from +98 to +105. Similar DNase 1 footprints were also obtained from salt-washed complexes and stable preinitiation complexes isolated by molecular sieve column chromatography.

Adenoviridae↗
PubMed1997

Increased hippocampal 5-lipoxygenase mRNA content in melatonin-deficient, pinealectomized rats.

Melatonin is neuroprotective because of its antioxidative action, but it also can modify neuronal vulnerability by altering gene expression. 5-Lipoxygenase (5-LO) gene expression is suppressed by the binding of melatonin to its high-affinity nuclear receptors. Recently, we reported that in rats the melatonin deficiency elicited by pinealectomy increases hippocampal susceptibility to excitotoxic injury. Here we have hypothesized that pinealectomy may increase hippocampal vulnerability by eliminating the tonic inhibitory action of melatonin on 5-LO gene expression. Sham-pinealectomized controls and pinealectomized rats were killed 15 days after surgery. Their hippocampi were dissected, and total RNA was extracted and processed for quantitative reverse transcription-polymerase chain reaction assay of 5-LO and cyclophilin mRNAs. Mutated primers were used as internal standards to assay attomole quantities of these two specific mRNAs per microgram of total RNA; the ratio 5-LO/cycophilin was used to compare samples from control and pinealectomized rats. Pinealectomy increased hippocampal 5-LO mRNA content by about threefold. These results support our hypothesis that melatonin deficiency may abate the tonic inhibition of 5-LO mRNA expression and thereby up-regulate 5-LO gene expression, which in turn would increase the brain's synthesis rate of potentially harmful eicosanoids, leukotrienes.

Animals↗
PubMed1983

A population-kinetical approach to RNA formation and degradation in growing and in resting cells.

Labelled RNA was extracted from growing and stationary cultures of the ciliate Tetrahymena and was separated chromatographically into poly(A)- and no poly(A)-containing fractions. A new method was used to derive from the data (cpm/A260, and tD, doubling time of RNA) absolute values of three growth terms which fully describe the population kinetics of RNA molecules: the rates of transcription, decay, and net growth. At all times the messenger RNA (mRNA) content of Tetrahymena was the result of a self-regulating equilibrium between synthesis and decay. The rates of transcription and of degradation of mRNA and ribosomal RNA (rRNA) were found to be controlled independently, but decay was dominant in establishing the growth-specific quantities per cell. In the stationary phase about 94% of all poly(A)-RNA molecules and about 50% of all mRNA molecules were kinetically silent. The remaining portions were transcribed with high rates, but also degraded immediately. During the culture growth cycle the rate of rRNA net growth responded positively to the cellular rRNA content suggesting an autocatalytic effect of rRNA on the rate of its accumulation.

Animals↗
PubMed1993

Photochemical sterilization of 3SR reactions.

The self-sustained sequence replication (3SR) reaction is an extremely efficient method for amplifying target DNA and RNA sequences that may be present in minute quantities. A serious problem often encountered in its practice is carryover contamination from products of previous 3SR reactions. A postamplification treatment of 3SR reaction products with the photoactive agent 4'-aminomethyl-4,5-dimethylisopsoralen (IP-10) was investigated as an approach for preventing carryover contamination by 3SR amplicons. Initially, inhibition of the amplification reaction by high concentrations of the reagent was observed. This problem was circumvented by developing a gel-based delivery of IP-10, and the method was found to provide highly efficient sterilization (approximately 10(6)-fold) of 3SR amplicons. Evaluation of this strategy on a number of 3SR targets has indicated that the degree of sterilization is dependent on the length of the amplified region and on the concentration of IP-10. It appears that the sterilization effect is caused by covalent modification of the pyrimidine bases of RNA and DNA, which renders them unusable as templates for the 3SR reaction. Modification of a purified RNA transcript with IP-10 was shown to prevent effectively reverse transcription by avian myeloblastosis virus reverse transcriptase (AMV RT). Similarly, treatment of a T7 RNA polymerase promoter-containing DNA template with IP-10 eliminated full-length transcription by T7 RNA polymerase. This isopsoralen method may be used to sterilize multiple 3SR reactions in a clinical assay with a convenient UV irradiation step.

Base Sequence↗
PubMed2002

Effects of quantity and quality of dietary protein on the brain polysome profile in aged rats.

The purpose of this study was to determine whether the quantity and quality of dietary protein affected the polysome profile of the brain in aged rats. Two experiments were done on three groups of aged rats (30 wk) given the diets containing 20% casein, 5% casein, or 0% casein (experiment 1), and 20% casein, 20% gluten, or 20% gelatin (experiment 2) for 10 d. The aggregation in brain ribosomes declined with a decrease of quantity and quality of dietary protein except in the hippocampus. The RNA concentration (mg RNA/g protein) did not differ among the three groups varying the dietary protein in any brain regions. The results suggest that the higher quantity and quality of dietary protein improves the polysome profile in the brain of aged rats, and that the polysome profile is at least partly related to the mechanism by which the dietary protein affects brain protein synthesis in aged rats.

Animals↗
PubMed1979

In vivo transcription and protein synthesis capabilities of bunyaviruses: wild-type snowshoe hare virus and its temperature-sensitive group I, group II, and group I/II mutants.

The in vivo primary and secondary transcription capabilities of wild-type snowshoe hare (SSH) virus and certain of its temperature-sensitive (ts) mutants have been analyzed. The results obtained agree with in vitro studies (Bouloy et al., C.R. Acad. Sci. Paris 280:213-215, 1975; M. Bouloy and C. Hannoun, Virology 69:258-264, 1976; M. Ranki and R. Pettersson, J. Virol. 16:1420-1425, 1975) which have shown that bunyaviruses are negative-stranded RNA viruses with a virion RNA-directed RNA polymerase. The in vivo transcription studies have demonstrated that in the presence of protein synthesis inhibitors (puromycin or cycloheximide) SSH virus can synthesize viral complementary RNA (primary transcription) throughout the infection cycle. The increased levels of viral complementary RNA obtained in the absence of protein synthesis inhibitors (secondary transcription) were not markedly reduced if cells were pretreated with actinomycin D (5 mug/ml), alpha-amanitin (25 mug/ml), or rifampin (100 mug/ml), although progeny virus yields were reduced by up to 80% in the actinomycin D- and rifampin-treated cells. The in vivo transcription capabilities of SSH group I ts mutants at temperatures which were nonpermissive (40 degrees C) for virus replication gave values comparable to those obtained at permissive temperatures (33 degrees C). The SSH group I mutants appear, therefore, to be RNA-positive mutant types. When compared with their transcription capabilities at 33 degrees C, the in vivo transcription abilities of four SSH group II ts mutants (and one double group I/II ts mutant) were found to be more impaired at 40 degrees C than those of the SSH group I ts mutants or wild-type SSH virus at 40 degrees C, although the viral complementary RNA synthetic capabilities of these group II (and group I/II) mutants at 40 degrees C were significantly higher than their primary transcription capabilities (as measured at 33 degrees C in the presence of puromycin or cycloheximide). It was concluded, therefore, that these SSH group II (and double group I/II) ts mutants have an intermediate RNA phenotype. Hybridization studies using (32)P-labeled individual L, M, and S viral RNA species of SSH virus have demonstrated the presence of viral complementary RNA to all three species in extracts of cells infected with SSH ts II-30 and incubated at 33 degrees C (primary and secondary transcription) or 40 degrees C, a nonpermissive temperature for its replication. The results of pulse-labeled in vivo protein analyses indicated that greater quantities of intracellular N protein (coded for by S RNA [J. R. Gentsch and D. H. L. Bishop, J. Virol. 28:417-419, 1978]) than G1 and G2 polypeptides (coded for by M RNA [J. R. Gentsch and D. H. L. Bishop, J. Virol. 30:767-776, 1979]) were present in extracts of cells infected with wild-type SSH virus. In extracts of SSH group I, II, or I/II ts mutant-infected cells incubated at 33 degrees C, N and G1, and for the group II mutant-infected cells, G2, viral polypeptides were detected, whereas in extracts obtained from group I or II mutant virus-infected cells incubated at 40 degrees C, low levels of N and G1 polypeptides were evident.

Animals↗
PubMed1998

Early upregulation of hippocampal 5-lipoxygenase following systemic administration of kainate to rats.

5-Lipoxygenase (5-LO; arachidonate:oxygen 5-oxidoreductase, EC 1.13.11.34) is the enzyme responsible for the first step in the formation of inflammatory leukotrienes from arachidonic acid. 5-LO is expressed in hippocampal neurons. Increased formation of leukotrienes was found in the hippocampus of rats in which seizures were induced by a glutamate receptor agonist, kainate. Expression of the 5-LO gene can be stimulated by vitamin D3 and suppressed by the pineal hormone melatonin. Here we hypothesize that kainate also stimulates 5-LO expression in the hippocampus. Kainate was injected intraperitoneally (10 mg/kg). Rats were sacrificed 3 hr later and their hippocampi were dissected and total RNA was extracted and processed for quantitative reverse transcription/polymerase chain reaction (RT-PCR) assay of 5-LO and cyclophilin (cyc) mRNAs. Mutated primers were used as internal standards to assay attomol quantities of these two specific mRNAs per microgram of total RNA. Fixed hippocampal slices were processed for 5-LO immunostaining and Nissl staining (assay of cell damage). Kainate induced about a 2.5-fold increase in 5-LO mRNA and triggered a redistribution of 5-LO like immunoreactivity from the pyramidal cell bodies into the dendrites of these neurons, particularly in the CA3 area. The results suggest that glutamate receptor-mediated signaling may modify the expression of neuronal 5-LO and that this enzyme might be involved in glutamate receptor-mediated neuronal plasticity and/or degeneration.

Journal Article↗
PubMed2003

Long-term mitochondrial toxicity in HIV-uninfected infants born to HIV-infected mothers.

Although children born to HIV-infected (HIV+) women receiving antiretroviral therapy during pregnancy show virtually no adverse clinical effects at birth, the antiretroviral nucleoside analog drugs are known to damage nuclear and mitochondrial DNA. In this study, biomarkers of mitochondrial toxicity and genotoxicity have been examined in a well-characterized sample set consisting of infants born to HIV-uninfected (HIV-) mothers (n = 30), and HIV- infants (n = 20) born to HIV-infected (HIV+) mothers who received either no antiretroviral therapy (n = 10) or zidovudine (3'-azido-3'-deoxythymidine [AZT]) during pregnancy (n = 10). DNA from cord blood leukocytes and peripheral blood leukocytes taken at 1 and 2 years of age was examined for loss of mitochondrial DNA (mtDNA) and telomere integrity. Telomere length, a measure of nuclear DNA damage, was the same in all infants at birth and at age 1 year. The quantity of mtDNA was assessed relative to nuclear DNA using a polymerase chain reaction-based chemiluminescence detection (PCR-CID) method that determined mitochondrial D Loop gene copies relative to nuclear 18S RNA gene copies by comparison with a standard curve. MtDNA quantity was expressed as a ratio of gene copy numbers. In infants of uninfected mothers (AZT-/HIV-) at the three time points, the ratios were 442 to 515, whereas in infants of untreated AZT-/HIV+ mothers the ratios were 261 to 297, and in infants of AZT-treated (AZT+/HIV+) mothers the ratios were 146 to 203. At all three time points, differences between the AZT-/HIV- group and the two HIV+ groups were statistically significant (p <.05), and differences between the AZT-/HIV+ and AZT+/HIV+ groups were also statistically significant (p <.05), demonstrating that AZT exposure causes a persistent depletion of mtDNA. The study shows that children of HIV+ mothers are at risk for mitochondrial damage that is further increased in infants of mothers receiving AZT during pregnancy.

Adult↗
PubMedDate not supplied

Simultaneous isolation of high molecular weight RNA and DNA from limited amounts of tissues and cells.

A simple method is described for the simultaneous isolation of both DNA and RNA from tissues and cultured cells obtainable in limited quantities only. The method is based on a suitable combination of steps designed for preparations of high molecular weight nucleic acids in cases when restricted amounts of tissues like small-sized and unique biopsies of tumors are available for studies of gene organization and expression. Using this protocol, undegraded total RNA suitable for Northern blot analysis and high molecular weight DNA for Southern blots was obtained from various sources (mammary and colon carcinomas, meningiomas, colonic and placental tissue, and several cell cultures).

Blotting, Southern↗
PubMed1983

Characterization of messenger RNA by direct translation from agarose gels.

A method for characterizing nanogram quantities of poly(A)-containing messenger RNAs that have been fractionated according to size by electrophoresis through agarose gels has been developed. The mRNAs from Friend leukemia cells were identified by the protein products they encode, as determined by slicing the agarose gel and directly translating the enclosed mRNA with an extract from rabbit reticulocytes that had been treated with micrococcal nuclease. A number of parameters which affect the efficiency of translation in this system have been examined. These include the sensitivity of the in vitro translational system to RNA, the agarose concentration, the incubation temperature, and the addition of either exogeneous tRNA or RNasin. The procedure is rapid, simple, reproducible, and applicable for the fractionation and characterization of mRNAs from any source.

Animals↗
PubMed2003

Discovery of aminoglycoside mimetics by NMR-based screening of Escherichia coli A-site RNA.

A method is described for the NMR-based screening for the discovery of aminoglycoside mimetics that bind to Escherichia coli A-site RNA. Although aminoglycosides are clinically useful, they exhibit high nephrotoxicity and ototoxicity, and their overuse has led to the development of resistance to important microbial pathogens. To identify a new series of aminoglycoside mimetics that could potentially overcome the problems associated with toxicities and resistance development observed with the aminoglycosides, we have prepared large quantities of E. coli 16 S A-site RNA and conducted an NMR-based screening of our compound library in search for small-molecule RNA binders against this RNA target. From these studies, several classes of compounds were identified as initial hits with binding affinities in the range of 70 microM to 3 mM. Lead optimization through synthetic modifications of these initial hits led to the discovery of several small-molecule aminoglycoside mimetics that are structurally very different from the known aminoglycosides. Structural models of the A-site RNA/ligand complexes were prepared and compared to the three-dimensional structures of the RNA/aminoglycoside complexes.

Aminoglycosides↗
PubMed1998

Characterizations of coronavirus cis-acting RNA elements and the transcription step affecting its transcription efficiency.

Seven to eight species of viral subgenomic mRNAs are produced in coronavirus-infected cells. These mRNAs are produced in different quantities, and their molar ratios remain constant during viral replication. We studied RNA elements that affect coronavirus transcription efficiency by characterizing a series of cloned coronavirus mouse hepatitis virus (MHV) defective interfering (DI) RNAs containing an inserted intergenic sequence, from which subgenomic DI RNA is transcribed in MHV-infected cells. Certain combinations of upstream and downstream flanking sequences of the intergenic sequence suppressed subgenomic DI RNA transcription, yet changing one of the flanking sequences to a different sequence eliminated transcription suppression. The suppressive effect of certain combinations of flanking sequences, but not all combinations, could be counteracted by altering the intergenic sequence. Thus, the combination of intergenic sequence and flanking sequence affected transcription efficiency. We also characterized another set of DI RNAs designed to clarify which transcription step determines the relative molar ratios of coronavirus mRNAs. Our study indicated that if subgenomic mRNAs were exclusively synthesized from negative-strand genomic RNA, then the relative molar ratios of coronavirus mRNAs were most likely determined after synthesis of the genomic-sized template RNA. If negative-strand subgenomic RNAs were templates for subgenomic mRNAs, then the relative molar ratios of coronavirus mRNAs probably were determined after synthesis of the genomic-sized template RNA used for subgenomic-sized RNA transcription but prior to the completion of the synthesis of subgenomic-sized RNAs containing the leader sequence. The relative molar ratios of coronavirus mRNAs, therefore, seem to have been established prior to a putative replicon-type amplification of subgenomic mRNAs.

Animals↗
PubMed1997

A bacterial group II intron encoding reverse transcriptase, maturase, and DNA endonuclease activities: biochemical demonstration of maturase activity and insertion of new genetic information within the intron.

The Lactococcus lactis group II intron Ll.ltrB is similar to mobile yeast mtDNA group II introns, which encode reverse transcriptase, RNA maturase, and DNA endonuclease activities for site-specific DNA insertion. Here, we show that the Lactococcal intron can be expressed and spliced efficiently in Escherichia coli. The intron-encoded protein LtrA has reverse transcriptase and RNA maturase activities, with the latter activity shown both in vivo and in vitro, a first for any group II intron-encoded protein. As for the yeast mtDNA introns, the DNA endonuclease activity of the Lactococcal intron is associated with RNP particles containing both the intron-encoded protein and the excised intron RNA. Also, the intron RNA cleaves the sense-strand of the recipient DNA by a reverse splicing reaction, whereas the intron-encoded protein cleaves the antisense strand. The Lactococcal intron endonuclease can be obtained in large quantities by coexpression of the LtrA protein with the intron RNA in E. coli or reconstituted in vitro by incubating the expressed LtrA protein with in vitro-synthesized intron RNA. Furthermore, the specificity of the endonuclease and reverse splicing reactions can be changed predictably by modifying the RNA component. Expression in E. coli facilitates the use of group II introns for the targeting of specific foreign sequences to a desired site in DNA.

Bacterial Proteins↗
PubMed1976

Counting the genes for stabel RNA in the nucleus and chloroplasts of Euglena.

Improved procedures for counting the genes for ribosomal and 4 S RNA in the nucleus and chloroplasts of Euglena are described. These procedures exploit (a) the chloroplast-free strain ZHB, (b) the flotation method for purifying chloroplasts, (c) Hg2+/Cs2SO4 density gradients to fractionate large quantities of DNA and (d) more efficient conditions of DNA - RNA hybridization particularly for 4 S RNA. We find that the average Euglena cell in an exponentially growing culture contains 800 nuclear genes for each cytoplasmic rRNA and 800-880 chloroplast genes for chloroplast rRNA. Each chloroplast chromosome of molecular weight 92 - 10(6) contains two genes for each rRNA. The number of nuclear genes for 4 S RNA is approx. 760. The total number of chloroplast genes for 4S RNA is approx. 10 000, or 22-25 on each chloroplast chromosome.

Animals↗
PubMed2000

Transcription termination by RNA polymerase III in fission yeast. A genetic and biochemically tractable model system.

In order for RNA polymerase (pol) III to produce a sufficient quantity of RNAs of appropriate structure, initiation, termination, and reinitiation must be accurate and efficient. Termination-associated factors have been shown to facilitate reinitiation and regulate transcription in some species. Suppressor tRNA genes that differ in the dT(n) termination signal were examined for function in Schizosaccharomyces pombe. We also developed an S. pombe extract that is active for tRNA transcription that is described here for the first time. The ability of this tRNA gene to be transcribed in extracts from different species allowed us to compare termination in three model systems. Although human pol III terminates efficiently at 4 dTs and S. pombe at 5 dTs, Saccharomyces cerevisiae pol III requires 6 dTs to direct comparable but lower termination efficiency and also appears qualitatively distinct. Interestingly, this pattern of sensitivity to a minimal dT(n) termination signal was found to correlate with the sensitivity to alpha-amanitin, as S. pombe was intermediate between human and S. cerevisiae pols III. The results establish that the pols III of S. cerevisiae, S. pombe, and human exhibit distinctive properties and that termination occurs in S. pombe in a manner that is functionally more similar to human than is S. cerevisiae.

Amanitins↗
PubMed2006

A simple, rapid and effective method for total RNA extraction from Lentinula edodes.

A rapid, inexpensive and reliable method for total RNA extraction from fruiting bodies of Lentinula edodes containing large quantities of polysaccharides and secondary metabolites is described. An initial extraction step using saturated NaCl solution facilitates the separation of nucleic acids from contaminants and, after further extraction with organic solvents and precipitation with 2-propanol, total RNA of high purity and suitable for applications such as cDNA synthesis, RT-PCR and Northern blot hybridization was obtained. The procedure may also have wider applicability for total RNA extraction from the tissues of other mushrooms.

Blotting, Northern↗