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Increasing the total quantity of RNA located on 99%-dimethyl sulphoxide gradients profoundly altered the sedimentation pattern of heterogenous RNA and (to a smaller extent) that of rRNA. Aggregation of small quantities of rRNA with fast-sedimenting heterogenous RNA was also found to occur in these gradients.
The need for microgram quantities of RNA for microarray experiments has hindered application of this novel technology in cell types/tissue samples with limited abundance of RNA. In this study, potential application of T7-based linear RNA amplification was investigated for use in gene expression profiling experiments where starting material is limited. Yield and integrity of amplified antisense RNA (aaRNA), microarray hybridization intensities, and fidelity of differential gene expression detected were determined for arrays generated for unamplified versus amplified RNA from the same homogenous starting pools. Total RNA was extracted from bovine spleen and fetal ovary, serially diluted to concentrations ranging from 2 microg to 500 pg and amplified. Quality and quantity of total input RNA and aaRNA were assessed by spectrophotometry, gel electrophoresis and bioanalyzer. In experiment 1, we determined the optimal amounts of aaRNA generated from 20, 40, 200 ng and 2 microg input total RNA for use in cDNA synthesis, labeling and array hybridization that would yield robust and consistent hybridization signals on a bovine oocyte cDNA microarray. In experiment 2, comparison of microarray hybridization intensities and fidelity of differential gene expression between aaRNA generated from 2, 20 and 40 ng input total RNA versus unamplified RNA (uRNA) were conducted. The hybridization intensities for each of the 7000 spots per slide for microarrays conducted using aaRNA versus uRNA were highly correlated (2 ng = 0.84, 20 ng = 0.88, 40 ng = 0.90; P < 0.01). The false positive rate was low and similar (4.0% versus 4.4%) for arrays done with uRNA and aaRNA. Ninety-seven ESTs were detected as differentially expressed in the fetal ovary versus spleen at > 1.5- or < 0.5-fold using uRNA (P < 0.05). However, the number of genes detected in arrays using aaRNA was approximately 1.5-2.5 times greater than with uRNA. Approximately, 65-70% of differentially expressed genes were common between uRNA and aaRNA arrays. Relative fold-expression (Cy3/Cy5 ratios) for 25 overlapping abundant genes was comparable for uRNA versus aaRNA arrays with 2 and 20 ng total RNA as input. Results demonstrate that T7-based linear amplification of small amounts of input RNA and use of aaRNA in microarray experiments retains fidelity of detection of differential gene expression that is relatively comparable to experiments done with uRNA and provides a potentially viable approach to facilitate gene expression profiling using limited amounts of starting material.
BACKGROUND: Nucleic acid preparation from a variety of clinical specimens requires efficient target recovery and amplification inhibitor removal and is critical for successful molecular diagnosis. The QIAamp MinElute Virus kit (Qiagen Inc., Valencia, CA) was compared to the two existing methods currently used in our laboratory, IsoQuick (Orca Research Inc., Bothell, WA) for DNA extraction and RNAzol B (Leedo Laboratories Inc., Houston, TX) for RNA extraction, of viral nucleic acids. STUDY DESIGN: A total of 150 clinical specimens, including cerebrospinal fluid (CSF) and nasopharyngeal swabs (NPS), were used to determine the extraction efficiency of the MinElute compared to the other two methods. Nucleic acid recovery, hands-on time, turn-around-time and cost were compared across all kits. RESULTS: There was complete concordance between the MinElute and IsoQuick/RNAzol kits when herpes simplex virus (HSV), Epstein-Barr virus (EBV), varicella-zoster virus (VZV), influenza A virus or enteroviruses were detected using a colorimetric microtiter plate PCR system. The kits were equivalent in their ability to detect either DNA or RNA with superior ability to recover a high quality and quantity of RNA. With the potential to process larger specimen volumes, the MinElute kit can significantly shorten processing time from 2h to 50-55min. CONCLUSIONS: Although relatively high test kit costs were noted, the MinElute kit provides another rapid and user-friendly specimen processing tool in the diagnostic molecular microbiology laboratory.
Subcellular clustering of ion channels critically affects neuronal function. Coexpression of Eag and Sh channel subunits in Xenopus oocytes leads to accelerated decay of the Sh-like transient K(+) current (Chen, M.-L., T. Hoshi, and C.-F. Wu. 1996. Neuron. 17:535-542). We report that such interaction depends critically on functional expression level (controlled by RNA injection quantities and indicated by current amplitudes) and developmental time after RNA injection. The accelerated decay became apparent 3 days after coinjection and increased thereafter. This was observed in different ionic conditions and at different voltage steps. However, decay was not accelerated at low expression levels, either within 1-2 days after injection or with reduced amounts of RNA. With sequential RNA injection, preformation of either Eag or Sh channels prevented interactions with the other subunit. The carboxyl terminus of Eag was found to be involved in accelerating, and in retarding recovery from, N-type inactivation. The interaction was reduced upon patch excision in macropatch measurements, suggesting involvement of cytosolic factors. We have reproduced the absence of interaction between Eag and Sh reported previously within 2 days after RNA injection and with low levels of current expression (Tang, C.-Y., C. T. Schulteis, R. M. Jiménez, and D. M. Papazian. 1998. Biophys. J. 75:1263-1270). Our findings demonstrate that heterologous expression of channels in Xenopus oocytes is a dynamic process influenced by cell physiology and development. These factors must be considered in interpreting the functional properties of heterologously expressed channels.
The effectiveness of maintaining prokaryotic RNA in Synechococcus and Pseudomonas cells, fixed in 96% ethanol, 4% paraformaldehyde, or suspended in RNAlater, and held in cold storage for 3 months was compared. Fluorometric determination of the RNA extracted from Synechococcus and Pseudomonas cells indicated that the cell storage treatments tested were equally effective at maintaining their total RNA content. There was not any detectable decrease in the quantity of RNA isolated from the preserved samples during storage. Intact mRNA transcripts of the RuBisCO (rbcL) and nir genes were detected by reverse transcriptase-polymerase chain reaction (RT-PCR) from preserved bacterial cells throughout 3 months of storage. In contrast, RT-PCR failed to amplify the mRNA of the rbcL and nitrite reductase genes in unfixed and/or unpreserved bacterial samples, suggesting that bacterial mRNA can be well maintained during a prolonged storage when cells are preserved properly. In addition, RNAlater is a useful reagent for the storage and maintenance of high quality RNA in unfrozen samples.
Protocols for the routine chemical synthesis and purification of milligram quantities of RNA and DNA-RNA chimeras meeting the demands of X-ray crystallography are described. An efficient screening protocol to test the crystallizability of the molecules and the optimization of the crystallization conditions are presented, so as to allow reproduction by others. Essentially the same crystallization conditions as for DNA oligomers can be employed for RNA crystallization. Specific examples involving alternating octamers, G/C-rich decamers, sequences with overhangs, and drug complexes of chimeras are discussed. Success of the methods is attested by the crystals obtained which diffract to high resolution.
OBJECTIVE: To present a brief review of the diagnostic benefits of quantitating viral load for hepatitis C and how the reverse transcriptase polymerase chain reaction is being used as an aid to better diagnose and manage the disease. DATA SOURCE: Research articles about hepatitis C and the reverse transcriptase polymerase chain reaction, as well as data gathered by the authors. STUDY SELECTION: Performed by the authors. DATA EXTRACTION: Performed by the authors. DATA SYNTHESIS: Hepatitis C viral infection is a worldwide health problem, affecting about 100 million people worldwide. Numerous serological tests exist to detect antibodies to hepatitis C antigens, but some affected people fail to generate an immune response. Reactivity in the reverse transcriptase polymerase chain reaction is definitive proof of hepatitis C infection. The titer of RNA indicates patient response to antiviral therapy. Measuring the presence and quantity of RNA by the reverse transcriptase polymerase chain reaction has become an important aid for diagnosis and monitoring of hepatitis C infection. CONCLUSION: The reverse transcriptase polymerase chain reaction method is a highly sensitive and accurate aid in diagnosing or confirming diagnosis of hepatitis C viral infection. This method is widely used to assess likelihood of patient response to therapy, and to monitor efficacy during therapy.
Two analog uridine triphosphates tethering additional functionality, one a primary amino group and the second a mercapto group, were prepared and tested for their compatibility with in vitro RNA selection procedures. 5-(3-Aminopropyl)uridine triphosphate (UNH(2)) as a uridine substitute was a more effective substrate for T7 RNA polymerase than 5-(2-mercaptoethyl)uridine triphosphate (USH). However, both functioned in transcription assays of 100 nt templates to generate RNA transcripts in quantities sufficient to initiate RNA selection procedures. Transcription of RNA pools with T7 RNA polymerase and UNH(2) or USH occurred with efficiencies of 43 and 29%, respectively, of the values obtained for native UTP transcription. In addition, the transcribed RNA containing roughly 25% UNH(2) residues exhibited better substrate properties for SuperScript(TM) II RNase H reverse transcriptase than did RNA transcripts containing approximately 25% of the USH analog. With either analog, both transcription and reverse transcription proceeded with high fidelity for insertion of the analog residue.
Influenza A virus infections are a major cause of morbidity and mortality worldwide. Standard diagnostic methods either are not efficient in identifying infected individuals in a timely manner or lack sensitivity. We developed a PCR-enzyme immunoassay (PCR-EIA) for the detection of influenza A virus RNA in respiratory secretions. A reverse transcription PCR was performed with oligonucleotide primers directed at a highly conserved area of the influenza A matrix gene. Amplified DNA was identified by hybridization in solution to a nested biotinylated RNA probe and quantitated in an EIA. PCR-EIA detected small quantities of RNA from the three prevalent subtypes of human influenza A virus. Influenza B and C, parainfluenza, measles, mumps, and respiratory syncytial viruses tested negative. The potential efficiency of PCR-EIA for use in clinical diagnosis was determined by testing 90 nasal wash specimens obtained daily over a 10-day period from nine human volunteers infected with influenza A virus. Thirty-seven of the postinfection samples had detectable influenza A virus RNA by PCR-EIA, whereas only 26 postinfection samples were positive by culture. PCR-EIA was particularly efficient for the identification of influenza A virus in samples obtained more than 4 days after infection. Seventeen of 45 such samples were positive, whereas virus was cultivated from 4 samples (P < 0.00005). All preinfection samples from volunteers subsequently infected with influenza A virus were negative by PCR-EIA, as were samples from a volunteer infected with parainfluenza virus type 3. Nucleic acid amplification techniques represent important tools for the timely and sensitive diagnosis of influenza A virus infections and, therefore, their management and control.
Plasmid pKYM is a multicopy plasmid isolated from Shigella sonnei and multiples stably in Escherichia coli. The plasmid encodes Rep protein which is essential for its multiplication and synthesizes cop ribonucleic acid (RNA) which is a short RNA complementary to the 5' region of rep m-RNA. This RNA controls the copy number and the incompatibility of the plasmid. The previous analysis located the promoters of rep m-RNA RNA (PR) and cop RNA (PL) in the inc region. This report confirmed the presence of these promoters by analyzing the RNAs isolated from the cells carrying pKYM and those synthesized in vitro. The initiation sites of these transcriptions were also determined. Analysis of in vivo RNA suggested that the quantity of cop RNA whose size was about 90 nucleotides was larger than that of rep m-RNA and these RNAs easily formed RNA-RNA hybrid. The analysis also suggested that the synthesis of rep m-RNA was repressed by cop RNA and Rep protein itself.
Armored Enterovirus RNA was used to standardize a real-time reverse transcription (RT)-PCR for environmental testing. Armored technology is a system to produce a robust and stable RNA standard, trapped into phage proteins, to be used as internal control. The Armored Enterovirus RNA protected sequence includes 263 bp of highly conserved sequences in 5' UTR region. During these tests, Armored RNA has been used to produce a calibration curve, comparing three different fluorogenic chemistry: TaqMan system, Syber Green I and Lux-primers. The effective evaluation of three amplifying commercial reagent kits, in use to carry out real-time RT-PCR, and several extraction procedures of protected viral RNA have been carried out. The highest Armored RNA recovery was obtained by heat treatment while chemical extraction may decrease the quantity of RNA. The best sensitivity and specificity was obtained using the Syber Green I technique since it is a reproducible test, easy to use and the cheapest one. TaqMan and Lux-primer assays provide good RT-PCR efficiency in relationship to the several extraction methods used, since labelled probe or primer request in these chemistry strategies, increases the cost of testing.
Annual seasonal outbreaks of respiratory syncytial virus (RSV) infection occur every winter. Most patients are diagnosed clinically by a rapid detection kit for RSV protein(s) from nasopharyngeal secretion (NPS), but some problems have been reported on the specificity and sensitivity of such rapid detection kits. To ratify these issues, a sensitive, specific, simple, and rapid molecular based diagnostic method is expected to be introduced and we have developed a method to detect the RSV genome of subgroups A and B independently by reverse transcription loop-mediated isothermal amplification (RT-LAMP). We detected the genomic RNA corresponding approximately to 0.1 TCID 50 in the sample by RT-LAMP for both RSV subgroups under isothermal condition within 60 min after extraction of RNA. Specific DNA amplification was monitored by a real-time turbidimeter and the quantity of RNA was calculated. The RSV genome was detected in 47 of 50 NPS by RT-LAMP, and in 42 by nested RT-PCR, whereas virus isolation was positive for 29 and enzyme-linked immunoassay (EIA) for 34. RSV subgroup A was detected in 25 by RSV RT-LAMP A, RSV subgroup B in 23 by RSV RT-LAMP B, and dual infection with RSV subgroups A and B was identified in one case. They were confirmed with digestion with a specific restriction enzyme, Bgl II. The results showed the potential clinical feasibility of RT-LAMP as a useful diagnostic tool for the detection of RSV with high sensitivity similar to nested RT-PCR.
We describe an optimized procedure for protein extraction performed simultaneously with that of DNA and RNA from a single tissue sample that is, unlike the original protocol, suitable for quantitative studies. This optimized protocol is particularly well adapted to studies where gene regulation at DNA, RNA, and protein levels must be examined simultaneously, and when the amount of starting biological material is limited. We applied this procedure to the study of factors affecting both qualitatively and quantitatively the extraction of DNA, RNA, and proteins from lymphocytes of very old individuals, since we observed variability in the recovery of these molecular species with advanced age. Therefore, we investigated the combined effects of age and time delay between blood collection and lymphocyte isolation on the recovery of DNA, RNA, and proteins simultaneously extracted from Danish nonagenarians and centenarians versus younger adult samples. Our results suggest that neither RNA nor DNA nor protein contents of lymphocytes are altered with aging. However, the quantity of RNA and protein recovery is affected by a 24-h delay in blood processing. This effect is more pronounced in the oldest, particularly for RNA, and may affect data interpretation of age-dependent gene expression studies.
1. A method is described for the preparation and purification of the RNA from the RNA coliphage ZIK/1. 2. Some of the physical characteristics and infective properties of coliphage-ZIK/1 RNA were examined. 3. A method is also described for examining the type and quantity of RNA synthesized after bacteriophage infection. 4. Ribosome synthesis was decreased 15min. after bacteriophage adsorption, bacteriophage RNA was synthesized from 15min. to 120min. after adsorption and intracellular bacteriophages appeared 40min. after adsorption. Cell lysis commenced 60min. after adsorption, and was half complete 20min. later and 90-95% complete 120min. after adsorption. 5. Cell division continued until 40min. after bacteriophage adsorption. 6. Bacterial ribosomes were conserved during the infective process. 7. Intracellular bacteriophage RNA has sedimentation coefficient 28s but after cell lysis it has sedimentation coefficient 10-5s.
When treated at pH less than 4.5, yeast nuclei or chromatin lose endogenous RNA synthetic activity. This activity is regained by addition of exogenous RNA polymerases. The specificity of transcription in this system by homologous RNA polymerases I and III has been investigated by gel electrophoresis, hybridization analysis, and RNase T1 mapping. Exogenous RNA polymerase I selectively transcribes rRNA genes. The transcription of these genes by polymerase I is 30- and 8-fold more selective than RNA polymerase III and Escherichia coli polymerase holoenzyme, respectively. Exogenous RNA polymerase III synthesized RNAs similar in size to authentic 5 S RNA, 4.5 S pre-tRNA, and 4 S tRNA. Eleven per cent of this RNA is 5 S RNA as determined by hybridization. Neither polymerase I nor E. coli polymerase synthesizes detectable quantities of RNA in this size range. AT1 ribonuclease digestion of 5 S RNA synthesized by exogenous RNA polymerase III acting on acid-treated chromatin gives a fragment pattern corresponding to that of 5 S RNA. Thus, RNA polymerase III transcribes the entire 5 S gene in this system.
Quantitative estimation of the nucleic acids content in the preparations stained with gallocianine-chromic alum was made in 20 cases of stomach cancer. Coefficients of the ratio of the nucleus section surface and the cytoplasm, the ratio of DNA + RNA of the nucleus to RNA of the cytoplasm, and of DNA of the nucleus to the sum total quantity of RNA in the nucleus and the cytoplasm, the index of DNA accumulation were compared in adenocarcinomas (210 cells) and undifferentiated cancers (390 cells) of the stomach. The ratio of the nucleus surface and the cytoplasm, DNA + RNA of the nucleus to RNA of the cytoplasm was higher (statistically significant value) in adenocarcinomas as compared with undifferentiated cancers of the stomach. This allows to suggest a lower differentiation of adenocarcinoma cells in comparison with tumour cells of undifferentiated forms of stomach cancer.