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PubMed2001

Increased AST and GGT activity as marker of RT-PCR inhibition in RNA extracts from peripheral blood.

The presence of HCV RNA in PMBC, with simultaneous absence of the virus in the plasma (7.8%), suggests that blood is better material for HCV RNA detection than plasma or serum in the diagnostic procedures of patients with chronic hepatitis C as well as in monitoring the antiviral therapy. We studied 111 patients with chronic hepatitis C (anti-HCV+) and elevated level of at least one biochemical marker: AST, ALAT, GGT, AP and bilirubin. Inhibition of amplification was 2% in plasma and 34% in whole blood samples. We applied modification of extraction to reduce the inhibitory effect on PCR, by introducing additional purification of the RNA extract in the Chomczyński method. After our modification of extraction was applied, inhibition was reduced to 1%. In attempt to identify such inhibitory markers that would label the samples, in which additional RNA extract purification should be applied, we analysed the activity of AST and ALAT enzymes, the key markers for parenchymal liver damage; GGT and AP, the markers for cholestatic hepatitis as well as bilirubin. We observed that the increased GGT and AST activities were correlated with the inhibition of RT-PCR. This correlation was statistically significant; for AST (Mann-Whitney test p = 0.09654 and Kolmogorow-Smirnow test p = 0.01543) and for GGT (Mann-Whitney test p = 0.02419 and Kolmogorow-Smirnow test p = 0.01921).

Alanine Transaminase↗

PubMed1994

Recovery of a rare clone from a population of unstable retroviral vector-expressing mammalian cells using a new RNA extraction and slot-blot protocol.

Although a useful and important method of gene transfer, retroviral vectors can be genetically unstable. In the course of experiments using DOEJS, a retroviral vector able to confer expression of a H-ras oncogene and a neomycin resistance gene (neo) on mammalian cells (Compere et al., 1989), it was found that the vast majority of infected rat embryo fibroblasts, recovered on the basis of neo activity (i.e., G418 resistance), did not express ras mRNA. It was subsequently observed that most cells in the psi 2 cell line used to propagate DOEJS failed to produce virus capable of expressing both ras and neo in primary rat embryo fibroblasts. A simplified RNA extraction and slot-blot technique was developed to screen mRNA from several hundred fibroblast clones and, in doing so, infected fibroblast clones producing both neo and ras mRNA were identified at low frequency. The DOEJS/psi 2 packaging line was subsequently subcloned and individual clones screened for their ability to confer appropriate gene expression on target cells. Subclone DOEJS/psi 2-B6 was eventually isolated after screening 24 DOEJS subclones and 240 infected rat embryo fibroblast colonies. DOEJS/psi 2-B6 was shown to induce reliably phenotypic transformation, G418 resistance, and ras and neo mRNA expression in primary rat embryo fibroblasts. The RNA extraction and screening procedure was thus useful for recovering an infrequent subclone producing a retrovirus with the original properties.

Animals↗

PubMed1999

Optimisation of DNA and RNA extraction from archival formalin-fixed tissue.

Archival, formalin-fixed, paraffin-embedded tissue is an invaluable resource for molecular genetic studies but the extraction of high quality nucleic acid may be problematic. We have optimised DNA extraction by comparing 10 protocols, including a commercially available kit and a novel method that utilises a thermal cycler. The thermal cycler and Chelex-100 extraction method yielded DNA capable of amplification by PCR from every block and 61% of sections versus 54% using microwave and Chelex-100, 15% with classical xylene-based extraction and 60% of sections using the kit. Successful RNA extraction was observed, by beta-actin amplification, in 83.7% sections for samples treated by the thermal cycler and Chelex-100 method. Thermal cycler and Chelex-100 extraction of nucleic acid is reliable, quick and inexpensive.

Archives↗

PubMed2006

Evaluation of microbial RNA extractions from Streptococcus pneumoniae.

The mechanisms that control Streptococcus pneumoniae's ability to colonize the nasopharynx or to invade the middle ear and cause acute otitis media are not understood. Focused study of these mechanisms requires efficient methods for the extraction of microbial RNA from minute clinical samples. Several lysis/extraction methods were tested and compared to determine the optimal conditions for isolating intact total RNA from pneumococcal cells. The sensitivity and efficiency of the extractions were evaluated by reverse transcription polymerase chain reaction (RT-PCR). Compared to other methods, mechanical homogenization in TRIZOL was the most efficient for releasing microbial RNA, and addition of polyinosinic acid (Poly I) as an RNA carrier increased the assay sensitivity to 10(2) colony forming units when detected by RT-PCR amplification of 16S ribosomal RNA or messenger RNA for penicillin binding protein 2b. Quantitative results were confirmed using a ribonuclease protection assay. Penicillin binding protein 2b was also detected in rat middle ear mucosa recovered 5 weeks after middle ear challenge with S. pneumoniae. This study describes a useful core methodology for use in identifying pneumococcal virulence genes from small titer samples and has promising applications in clinical studies of pneumococcal nasopharyngeal colonization and otitis media pathogenesis.

Animals↗

PubMed2006

Successful RNA extraction from various human postmortem tissues.

Recently, several authors described the observation that RNA degradation does not correlate with the postmortem interval (PMI), but rather with other parameters like environmental impact and the circumstances of death. Therefore, the question arose if the analysis of gene expression could be a valuable tool in forensic genetics to contribute to the determination of the cause of death. In our study, six human tissues obtained from six individuals with PMI varying between 15 and 118 h were used for total RNA extraction. Quantification was performed using a GAPDH real-time assay, and the quality of mRNA was checked by amplification of different fragment lengths of the GAPDH transcript. In our set of samples, nearly all tissues in all PMI revealed satisfactory results, while skeletal muscle, followed by brain and heart, gave the best results. No correlation between PMI and RNA degradation could be detected, as very good results were observed for all tissues from the individual with the longest PMI. The highly promising results obtained in this study raise hopes that in the near future several fields of forensic investigation may profit from additional information about gene expression patterns and their correlation with pathological findings.

Autopsy↗

PubMed1976

Study of messenger-like RNA extracted from HeLa cells polysomes. II. Identification of the types of RNA eluted from methylated albumin kieselguhr columns.

Together with the elution pattern of pure messenger RNA molecules of various origin, the labelling kinetics of rapidly labelled heterogeneously sedimenting RNA (HSRNA) extracted from polysomes of HeLa cells have been studied by chromatogrphy on columns made of methylated bovine serum albumin adsorbed on kieselguhr. HSRNA is eluted within three peaks-IP, Q2P and TDP-following in that order the increase of NaC1 concentration in the eluting buffer. Besides peak TDP which results from an experimental artefact, our data suggest that the appearance of peaks IP and Q2P reflects the absence and presence respectively of polyadenylic acid stretches in these molecules. Within peak Q2P, the critical factor affecting the order of elution is the size of the polyadenylic acid stretch.

HeLa Cells↗

PubMed2003

Modifications and substitutions of the RNA extraction module in the ViroSeq HIV-1 genotyping system version 2: effects on sensitivity and complexity of the assay.

Genotypic testing for HIV-1 resistance to anti-retroviral drugs has become accepted widely as a routine method to guide anti-retroviral therapy. However, implementation into routine high-throughput laboratory diagnosis is difficult due to the complexity of the assay. A commercially available assay is the ViroSeq HIV-1 Genotyping System (Applied Biosystems, Weiterstadt, Germany). We modified and substituted the RNA extraction module to optimize the proportion of samples amplified successfully as follows: 1 ml plasma was concentrated by ultracentrifugation and extracted according to the manufacturer's instructions (Kit), by substituting the lysis buffer (Roche, Roche Diagnostics GmbH, Mannheim, Germany), and by using the QIAamp Viral RNA Kit (Qiagen GmbH, Hilden, Germany) with elution volumes of 60 (Q60) or 50 micro l (Q50). Overall Q50 showed a higher success rate (97%) than the other extraction modules used (range 88-91%). In samples with a viral load range of 1,000-4,999 copies/ml, Q50 was superior (95 vs. 65% to 83%), while in samples with a viral load range of 5,000-9,999 copies/ml or those with 10,000 or more copies/ml, the success rate of the extraction procedures showed no significant differences. In 18 samples, which were negative using the Kit or Roche extraction, Q60 resulted in 7/18 positive results; in addition the Q50 was successful in amplifying 7/10 of the Q60 negative samples. When investigating samples with a measurable viral load of less than 1,000 copies/ml or lower, Q50 had the highest success rate with 80% compared to the other procedures (33-63%). A statistically significant new cut-off could be defined for Q50 at a value of 250 copies/ml. The results showed clearly that the ViroSeq System is suitable for analyzing the HIV-1 genotype over a wide range of viral loads but could be improved significantly when substituting the RNA extraction module with Q50 without using a nested PCR protocol. This is of great importance as it avoids further time- and cost-intensive steps.

Drug Resistance, Viral↗

PubMed2000

Evaluation of automated RNA-extraction technology and a qualitative HCV assay for sensitivity and detection of HCV RNA in pool-screening systems.

BACKGROUND: The objective of this study was the evaluation of NAT technology for the detection of HCV RNA in plasma pools according to the recommendations of the Paul Ehrlich Institute (5000 IU/mL/donation) and the Committee for Proprietary Medical Products (100 IU/mL/manufacturing pool). STUDY DESIGN AND METHODS: Serial dilutions of both the EUROHEP standard (3,800 genome equivalents [geq]/mL; HCV genotype 1) and the World Health Organization (WHO) international standard (100,000 IU/mL; HCV genotype 1) were made in S/D plasma (ESPEP plasma, OctaPharma), which was nonreactive in serologic tests. Serial dilutions of plasma (2 mL) were used for extraction of HCV RNA with an automated version of a nucleic acid isolation method (NucliSens Extractor, Organon Teknika). HCV RNA was co-extracted from 2 mL of plasma, together with 84 copies of an in vitro-synthesized single-strand RNA serving as internal extraction control (IC) to monitor the efficiency of extraction and PCR. Amplification and detection of both HCV RNA and IC RNA were performed with an automated PCR system and a qualitative HCV assay (COBAS Amplicor 2.0 HCV, Roche Diagnostics). RESULTS: A cutoff value of 16 geq per mL (10/10 runs [100% hit rate]) was found by using the EUROHEP standard, whereas the WHO international standard had a cutoff value of approximately 12 IU per mL (10/10 runs [100% hit rate]). The IC had a cutoff value of approximately 17.5 copies per mL (6/6 runs [100% hit rate]). Forty-two copies per mL of IC RNA were found in 282 of 284 runs (99% hit rate). The negative controls (ESDEP plasma) were negative in all experiments. Experiments with pool sizes of 12, 24, 48, and 96 using serial dilutions of the WHO international standard revealed a cutoff value of 8 IU per mL (100% hit rate). The EUROHEP standard and the WHO international standard were detected with a 50 percent detection endpoint of 5.2 geq per mL and 1.5 IU per mL, respectively. CONCLUSION: This test system (NucliSens Extractor, and the COBAS Amplicor 2.0 HCV assay) revealed a high sensitivity for HCV RNA; considering the proposed requirements for sensitivity of NAT assays for the detection of HCV RNA in donor plasma, pool sizes of about 400 donors are possible. These endpoint results indicated that 1 IU is equal to about 3.4 geq.

Autoanalysis↗

PubMed1995

Rapid detection of bovine viral diarrhea virus by using RNA extracted directly from assorted specimens and a one-tube reverse transcription PCR assay.

We describe a simple method for the rapid detection of bovine viral diarrhea virus (BVDV) that uses a one-tube reverse transcription PCR (RT-PCR) and total RNA extracted directly from a variety of bovine specimens, including whole blood and tissues. Reagents for both RT and PCR were combined in a one-tube, single-buffer system, and amplification was performed with a single uninterrupted thermal cycling program. Using the novel cationic surfactant tetradecyltrimethylammonium oxalate (Catrimox-14), we consistently extracted RT-PCR-quality RNA from specimens containing blood. Amplification with primers derived from conserved sequences within the BVDV 5'-untranslated region yielded a 244-bp product. Assay specificity was confirmed by ethidium bromide-stained gel electrophoresis and by chemiluminescence-assayed Southern blot hybridizations involving BVDV 5'-untranslated region-specific digoxigenin-labelled cDNA probes. The assay detection level was 0.1 50% tissue culture infectious dose of BVDV when ethidium bromide-stained gel electrophoresis was used and 0.01 50% tissue culture infectious dose of BVDV when Southern blot hybridization was used. Our method is an alternative to the conventional cell culture assays used in a diagnostic laboratory and is an improvement over existing RT-PCR assays for BVDV.

Animals↗

PubMed2000

Improved RNA extraction and one-tube RT-PCR assay for simultaneous detection of control plant RNA plus several viruses in plant extracts.

A procedure was developed for simultaneous detection of plant RNA viruses and of plant RNA, as a control. RT-PCR amplification with primers designed for the detection of the plant mRNAs encoding malate dehydrogenase (MDH) and the large subunit of ribulose bisphosphate carboxylase oxygenase (RubiscoL) was used for the development of a plant extraction procedure that consistently yields extracts that can be amplified. The control amplification was used successfully on extracts from cane, leaf and/or bud tissues from grapevine, apple, raspberry, strawberry, peach, apricot, plum and wheat. Multiplex RT-PCR conditions were established for the simultaneous detection in grapevine extracts of either arabis mosaic virus, rupestris stem pitting associated virus and malate dehydrogenase mRNA, or grapevine virus A, grapevine virus B, grapevine leafroll associated virus-3, and RubiscoL mRNA.

Malate Dehydrogenase↗

PubMed2005

Optimization of the PAXgene blood RNA extraction system for gene expression analysis of clinical samples.

One major problem associated with collecting whole blood from patients for use as a source of RNA in gene expression studies is that the RNA degrades during collection and storage. Preservation of RNA quality is vital in such studies because the stability of the RNA ultimately affects analysis of gene expression. In this study the PAXgene blood collection system was compared with a standard erythrocyte lysis method for isolating RNA from blood samples. The methods were compared in terms of RNA yield, RNA stabilization, and DNA contamination. The study also included the downstream application to RT-PCR analysis for relative mRNA expression levels of the ribonucleotide reductase subunits R1 and R2. The results show that blood collection in conventional collection tubes, and leukocyte isolation by erythrocyte lysis lead to significant degradation of RNA. Our findings confirm the ability of PAXgene to stabilize RNA in whole blood; however, RNA extracted by the PAXgene method contained significant DNA contamination. Given the low basal expression of the target genes analyzed in this study, contaminating DNA could potentially affect accurate interpretation of RT-PCR data. As a result, the PAXgene protocol was optimized to include off-column DNase treatments, which yielded high-quality RNA suitable for gene expression studies. Furthermore, the results suggest that RNA isolation with PAXgene is advantageous compared to traditional extraction methods for RT-PCR analysis of large or different-sized amplicons.

Actins↗

PubMed2001

Substitution of a commercially available, RNA extraction procedure in an HIV-1 genotyping system improves sensitivity and allows reduced sample volume.

The use is described of a commercially available, silica-based extraction procedure for HIV-1 RNA that can be substituted for the extraction procedure supplied with a commercially available, PCR-based genotyping kit for HIV-1. The advantages of using this alternative, commercially available extraction procedure include the following: (1) reduced safety concerns, due to inactivation of virus in the initial step of the extraction procedure; (2) enhanced sensitivity, allowing the use of plasma with HIV-1 RNA levels of less than 2000 copies/ml; (3) improved yield, allowing a 60% reduction in plasma volume; and (4) convenience and improved reproducibility, with a single extraction providing RNA suitable for PCR-based sequencing and for quantitation of HIV-1 RNA levels.

Genotype↗

PubMed1997

Comparison of four RNA extraction methods for the detection of porcine reproductive and respiratory syndrome virus by RT-PCR.

We compared four commercial RNA isolation methods for the extraction of RNA from porcine reproductive and respiratory syndrome virus (PRRSV). The sensitivity of the methods was determined by extraction of RNA from serial 10-fold dilutions of PRRSV diluted in PRRSV-negative porcine serum or in Eagle's minimal essential medium (EMEM) followed by amplification of extracted nucleic acids by RT-PCR. The PCR products were detected in ethidium bromide-stained agarose gels. The QIAamp viral kit, which is based on binding of RNA to silica particles, was the most sensitive, allowing the detection of an equivalent of 10 TCID50 of virus in 100 microliters of serum or EMEM. The QIAamp-tissue and the TRIzol LS kits detected 100 TCID50 per 100 microliters in both diluents whereas Ultraspec-3 detected 100 TCID50 of virus in EMEM and 1000 TCID50 in serum. These results indicate that QIAamp viral kit has a higher sensitivity for RT-PCR analysis of PRRSV.

Animals↗

PubMed1991

RNA extracted from paraffin-embedded human tissues is amenable to analysis by PCR amplification.

Fixed and paraffin-embedded tissues from pathology department archives can be available for RNA expression analysis. In this report, we show that RNA isolated from surgical or autopsy tissues, routinely processed by fixation and paraffin embedding, is not completely degraded. RNA fragments around 100-200 bases in length are still present even in organs late fixed and very rich in RNase, such as the pancreas. Here we describe a general protocol to obtain RNA from single 6-8-microns tissue sections. The RNA extracted can be analyzed for the presence of specific sequences by reverse transcription and amplification with the PCR. We studied the retinoblastoma gene expression in 38 human pancreas specimens from surgical or autopsy origin.

Animals↗

PubMed2003

Cytoplasmic expression of EGFP in dendritic cells transfected with in vitro transcribed mRNA or cellular total RNA extracted from EGFP expressing leukemia cells.

The present study was designed for identifying the protein synthesis in cytoplasm of dendritic cells transfected with in vitro transcribed mRNA and cellular total RNA extracted from tumor cells. Dendritic cells were generated from cord blood-CD34+ cells by culture with GM-CSF, SCF, and TNF-alpha, or from peripheral blood adherent cells or CD14+ cells by culture with GM-CSF and IL-4. Dendritic cells were transfected with in vitro transcribed EGFP mRNA or cellular total RNA, which was isolated from EGFP expressing K562, by electroporation using a square-wave pulse. Optimal in vitro transcribed EGFP mRNA transfection efficiency (>90%) was observed in a single electroporation of 1.75 kV/cm (electric field strength) with a pulse width of 250 micros. Although the intensity of EGFP expression in dendritic cells transfected with cellular total RNA was less compared with that in dendritic cells transfected with in vitro transcribed EGFP mRNA, a definite cytoplasmic synthesis of EGFP was demonstrated in dendritic cells transfected with cellular total RNA. The visual identification of cytoplasmic expression of cellular total RNA in dendritic cells revealed that electroporation of tumor cell-derived RNA could be a useful tool to load dendritic cells with tumor antigens for establishing an efficient dendritic cell-based tumor immunotherapy.

Dendritic Cells↗

PubMed1991

Application of two RNA extraction methods prior to amplification of hepatitis E virus nucleic acid by the polymerase chain reaction.

Amplification of the enterically-transmitted non-A, non-B hepatitis virus (HEV) RNA using conventional reverse transcriptase reactions followed by the polymerase chain reaction (PCR) of the cDNA has not been successful. However, after application of two different RNA capture/extraction methods we were able to amplify HEV nucleic acid from clinical samples and specimens from experimentally infected animals. The first procedure, adapted from an immune electron microscopy (IEM) technique, incorporated an immunocapture step with concentration of the virus-antibody complexes by pelleting in a Beckman airfuge. In the second method, glass powder (or size-fractionated silicon dioxide) was used to capture the RNA from its surrounding milieu by adsorption of the nucleic acid to the silicate particles. Since conventional immunoassays for HEV antigen or antibody are not currently available, the use of these RNA extraction methods, coupled with PCR techniques, will be valuable in screening clinical specimens and in further defining the course of disease using animal infectivity studies.

Adsorption↗

PubMed2002

Comparison of DNA and RNA extraction methods for mummified tissues.

Nucleic acids extracted from mummified tissues are valuable materials for the study of ancient human beings. Significant difficulty in extracting nucleic acids from mummified tissues has been reported due to chemical modification and degradation. The goal of this study was to determine a method that is more efficient for DNA and RNA extraction from mummified tissues. Twelve mummy specimens were analyzed with 9 different nucleic acid extraction methods, including guanidium thiocyanate (GTC) and proteinase K/detergent based methods prepared in our laboratory or purchased. Glyceraldehyde 3-phosphate dehydrogenase DNA and beta-actin RNA were used as markers for the presence of adequate DNA and RNA, respectively, for PCR and RT-PCR amplification. Our results show that 5 M GTC is more efficient of releasing nucleic acids from mummified tissue than proteinase K/detergent, and phenol/chloroform extraction with an additional chloroform step is more efficient than phenol/chloroform along. We were able to isolate DNAs from all 12 specimens and RNAs from 8 of 12 specimens, and the nucleic acids were sufficient for PCR and RT-PCR analysis. We further tested hepatitis viruses including hepatitis B virus, hepatitis C virus, hepatitis G virus, and TT virus DNA, and fail to detect these viruses in all 12 specimens.

Chloroform↗

PubMed1991

An automated RNA extraction procedure and application for 16S rRNA sequencing of Leuconostoc amelobiosum.

The determination of 16S ribosomal ribonucleic acid (16S rRNA) primary structures by in vitro reverse transcription requires the extraction of rRNA in pure form. Although a number of high reliable techniques have been developed for the purpose most are fairly complex, involving numerous steps and the wasting of large volumes. It describes here a RNA extraction and purification method, suitable for automatic extractors, which consistently yields reasonable amounts of pure total RNA from prokaryotes, free of DNA and RNases. The rRNA from the type strain Leuconostoc amelobiosum was isolated using this procedure. Its 16S rRNA sequence was determined and a comparative analysis with those from all currently described leuconostocs, including several atypical lactobacilli, revealed very high sequence homology with Leuconostoc citreum confirming Leuconostoc amelobiosum is phylogenetically a member of the genus Leuconostoc sensu stricto.

Base Sequence↗