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PubMed2006

Efficient extraction of high-quality total RNA from various hop tissues (Humulus lupulus L.).

The isolation of high-quality RNA is a prerequisite for gene expression studies. RNA quality is of special relevance if PCR-based strategies such as cDNA-AFLP or RT-PCR are followed. Our molecular investigations of hop (Humulus lupulus L.) focus on genes that determine the biosynthesis of prenylflavonoids with interesting biological activities which accumulate in the lupulin glands. However, optimized protocols for RNA extraction from hop cones are not available. In this study, the RNeasy midi kit protocol was modified to isolate high amounts of total RNA from fresh and freeze-dried hop tissues, specifically leaves, female inflorescences, and lupulin-enriched hop cone fractions. The main difficulties in obtaining high RNA yields were related to specific features of hop, including the abundance of secondary metabolites and their accumulation in the sticky lupulin glands. The introduction of a number of modifications into the RNeasy midi kit protocol resulted in RNA of high quality, as assessed by spectrophotometry and electrophoresis in agarose gels. The protocol developed is currently being used to produce cDNA-AFLP fingerprints of hop cones and leaves for genetic screening. Furthermore, the method could provide RNA for further molecular studies, including Northern blot hybridizations and reverse transcription-polymerase chain reactions.

Blotting, Northern↗
PubMed2003

An improved method for constructing a full-length enriched cDNA library using small amounts of total RNA as a starting material.

We have developed an improved method for constructing a full-length cDNA library using small quantity of material by modifying the original oligo-capping method. In our devised method, total RNAs are used in sequential oligo-capping steps directly without preliminary mRNA purification. Using this method, we constructed full- length cDNA libraries from 100 mg of total RNA. These libraries contained 8x10(5) to 8x10(6) independent clones with average insert sizes of 2.0 kb. Moreover, the number of full-length cDNAs containing the translation initiation codon ATG in the constructed libraries was estimated to 60-70%. In addition, 54% of the known cDNAs had a longer 5' end than the corresponding genes in the public database. Our results show that the method can be effectively used to construct full-length enriched cDNA libraries, especially, if starting material is limited.

Base Sequence↗
PubMed2001

Efficient isolation of total RNA from Clostridium without DNA contamination.

Several molecular techniques require high-quality RNA, free from DNA. Various methods have been described to obtain RNA to be used in expression studies or as starting material in differential display-reverse transcriptase (dd-RT-PCR), for which high-quality RNA free from DNA is an essential requirement. In this report, we compare three different methods to isolate RNA from Gram-positive bacteria: (1) An acid-phenol extraction protocol. (2) The "RNeasy mini kit" from QIAGEN (Valencia, CA, USA). (3) The "SV Total RNA Isolation System" from Promega (Madison, WI, USA).The QIAGEN-kit delivers the highest amount of RNA with the highest purity. Slot blot analysis and dd-RT-PCR confirm the absence of DNA contamination and Northern blot analysis and dd-RT-PCR show high quality of the extracted RNA. This RNA extraction method thus addresses current problems by permitting rapid and safe isolation with high yields of intact RNA for subsequent analysis.

Blotting, Northern↗
PubMed2002

[Introduction of a simple and effective method for plant total RNA isolation].

Wheat leaf and seeds at different development stages had been squashed in liquid nitrogen, then lysed by urea buffer which contains 0.1% SDS and 0.1% LDS, denatured protein had been removed by NaAc and chloroform precipitation, total RNA was further purified by LiCl. The RNA we obtained had sharp bands of 28S and 18S after agarose gel electrophoresis, 23S and 16S RNA bands can also be seen clearly in leaf RNA extract, the value of OD260/OD280 of RNA was 2.05-2.105 mg RNA can been isolated from 10 g leaf of wheat. This method can also been used in high molecular weight DNA isolation but the concentration of SDS and LDS must be increased to 1%.

English Abstract↗
PubMed1981

[Changes in the concentrations of total RNA and DNA in the cerebral cortex and internal organs (liver and heart) after prolonged hypovolemic hypotension and in the post-resuscitation period].

It was shown in experiments on dogs that after 4-hour hypovolemic hypotension the content of total RNA in brain cortex and myocardium homogenates decreased. In the liver, there was a significant decrease both in RNA and DNA content. In the postresuscitation period, the content of nucleic acids in the myocardium returned to normal after 14--21 days, and that in the liver after 3--4 months. The gray matter of the brain manifested a delayed lowering of DNA content (after 14--21 days), and the level of nucleic acid did not return ot normal over 3--4 months after resuscitation.

Animals↗
PubMed2000

miniSAGE: gene expression profiling using serial analysis of gene expression from 1 microg total RNA.

The use of serial analysis of gene expression (SAGE) to determine gene expression profiles is increasing because the technique can provide absolute transcript numbers in a digital format and identify new genes. We developed a miniSAGE technique, which uses only 1 microg total RNA and reduces the amount of the starting material by 250- to 500-fold. Unlike the other modified SAGE methods, the miniSAGE technique does not require the additional PCR amplifications. The additional PCR amplifications potentially introduce bias and compromise the quantitative aspects of the SAGE method. Three key modifications in the miniSAGE technique are: (i) using the phase lock gel (PLG, Eppendorf) to increase the recovery and the purity of DNA material after each phenol extraction step; (ii) reducing the amount of linkers in the ligation, thereby minimizing their interference with SAGE ditag amplification and increasing the SAGE ditag yield; and (iii) employing the mRNA capture kit (Boehringer Mannheim) to allow the first five steps: mRNA isolation, cDNA synthesis, enzyme cleavage of cDNA, binding of the cleaved biotin-cDNA to the streptavidin-magnetic beads, ligating linkers to the bound cDNA, and the release of cDNA tags to occur within one tube to significantly reduce the loss of material between successive steps. Two fibroblast SAGE libraries have been successfully prepared. The preliminary analysis of 3838 tags from one library demonstrated a typical fibroblast gene expression pattern. This miniSAGE technique will permit a broader application of SAGE.

Biopsy↗
PubMed2005

A rapid and efficient method for purifying high quality total RNA from peaches (Prunus persica) for functional genomics analyses.

Prunus persica has been proposed as a genomic model for deciduous trees and the Rosaceae family. Optimized protocols for RNA isolation are necessary to further advance studies in this model species such that functional genomics analyses may be performed. Here we present an optimized protocol to rapidly and efficiently purify high quality total RNA from peach fruits (Prunus persica). Isolating high-quality RNA from fruit tissue is often difficult due to large quantities of polysaccharides and polyphenolic compounds that accumulate in this tissue and co-purify with the RNA. Here we demonstrate that a modified version of the method used to isolate RNA from pine trees and the woody plant Cinnamomun tenuipilum is ideal for isolating high quality RNA from the fruits of Prunus persica. This RNA may be used for many functional genomic based experiments such as RT-PCR and the construction of large-insert cDNA libraries.

DNA, Complementary↗
PubMed2004

Evaluation of vector-primed cDNA library production from microgram quantities of total RNA.

cDNA sequences are important for defining the coding region of genes, and full-length cDNA clones have proven to be useful for investigation of the function of gene products. We produced cDNA libraries containing 3.5-5 x 10(5) primary transformants, starting with 5 mug of total RNA prepared from mouse pituitary, adrenal, thymus, and pineal tissue, using a vector-primed cDNA synthesis method. Of approximately 1000 clones sequenced, approximately 20% contained the full open reading frames (ORFs) of known transcripts, based on the presence of the initiating methionine residue codon. The libraries were complex, with 94, 91, 83 and 55% of the clones from the thymus, adrenal, pineal and pituitary libraries, respectively, represented only once. Twenty-five full-length clones, not yet represented in the Mammalian Gene Collection, were identified. Thus, we have produced useful cDNA libraries for the isolation of full-length cDNA clones that are not yet available in the public domain, and demonstrated the utility of a simple method for making high-quality libraries from small amounts of starting material.

Animals↗
PubMed1990

Total RNA content of brain cells of inbred mice reared under different conditions.

AB/Jena, DBA/2Jena, C57B1/6 Jena inbred mice and ABD2F1- and B6D2F4-hybrid mice either were reared communally and weaned at day 30 or were reared by isolated mothers and weaned at day 21 (I21). On day 50 the total RNA content of pyramidal brain cells of male offspring was determined by cytophotometry. The studied brain areas were the frontal pole of cerebral cortex (FCC) and the CA1 region of the dorsal hippocampus (DHI). The DBA, C57 and ABD2 mice had a reduced FCC and DHI RNA-content under I21-rearing. Under these conditions the AB strain has the highest RNA-content in both substrates. The results call for the awareness of possible genetic influences when studying the effects of environmental enrichment/impoverishing.

Animals↗
PubMed1995

Expression of Ca(2+)-ion permeable alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionate (AMPA) receptors in Xenopus oocytes injected with total RNA from human epileptic temporal lobe.

By using the Xenopus oocyte as an expression system, we have performed a series of experiments in order to examine the divalent cation-permeability of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionate (AMPA) receptors from the human epileptic temporal lobe. Xenopus oocytes, injected with total RNA from the epileptic temporal lobe, were tested for expression of receptors by a conventional two electrode voltage-clamp technique. Administration of glutamate and AMPA gave small or no clear current responses, whereas kainate produced large inward non-desensitizing currents. The current responses evoked by kainate were concentration dependent. Experimental data gave a Hill coefficient of 1.06 and an EC50 value of 87 microM. The current to voltage relationship showed an inward rectification and when the concentration of divalent cations were enhanced, there was a shift in the reversal potential from -11 mV (2 mM Ca2+) to 12 mV (60 mM Ba2+). This yielded a pBa2+/pK+ permeability ratio of 1.6 when the constant field equation was used. The amplitude of the currents evoked by 600 microM kainate in solutions containing higher Ba(2+)-ion concentrations was markedly diminished (46% in 10 mM Ba(2+)- and 75% in 60 mM Ba(2+)-solution), when compared to those obtained in normal Ringer's solution, suggesting interactions between different cation species and/or screening of surface charges.

Animals↗
PubMed2006

Direct and sensitive miRNA profiling from low-input total RNA.

We have developed a sensitive, accurate, and multiplexed microRNA (miRNA) profiling assay that is based on a highly efficient labeling method and novel microarray probe design. The probes provide both sequence and size discrimination, yielding in most cases highly specific detection of closely related mature miRNAs. Using a simple, single-vial experimental protocol, 120 ng of total RNA is directly labeled using Cy3 or Cy5, without fractionation or amplification, to produce precise and accurate measurements that span a linear dynamic range from 0.2 amol to 2 fmol of input miRNA. The results can provide quantitative estimates of the miRNA content for the tissues studied. The assay is also suitable for use with formalin-fixed paraffin-embedded clinical samples. Our method allows rapid design and validation of probes for simultaneous quantitative measurements of all human miRNA sequences in the public databases and to new miRNA sequences as they are reported.

Animals↗
PubMed1989

Point mutation analysis in a mammalian gene: rapid preparation of total RNA, PCR amplification of cDNA, and Taq sequencing by a novel method.

We have developed a very rapid procedure for DNA sequence analysis of induced mutations in a typically large mammalian gene. We are able to determine the nature of chemical carcinogen-induced point mutations in the 25 kb Chinese hamster ovary (CHO) cell dihydrofolate reductase gene within two days starting with 5 to 10 x 10(6) cells. The approach is based on the use of rapidly prepared total RNA from which a 730 bp dhfr cDNA is synthesized by reverse transcriptase and amplified by the polymerase chain reaction (PCR) procedure. Genomic DNA can simultaneously be prepared from the same cells. The amplified double-stranded cDNA is then sequenced directly by the dideoxy method using Taq polymerase in the Thermal Cycler (Perkin Elmer/Cetus). We have previously shown that nonsense codons in the dhfr coding sequence often result in greatly reduced steady-state levels of dhfr mRNA (2). The methods described are suitable for mutants of this type which contain only 1 to 2 copies of mRNA per cell. This approach is readily adaptable to other selectable genes and other cell types provided the necessary primers can be prepared.

Animals↗
PubMed2004

Microarray-based comparison of three amplification methods for nanogram amounts of total RNA.

Gene expression profiling using microarrays requires microgram amounts of RNA, which limits its direct application for the study of nanogram RNA samples obtained using microdissection, laser capture microscopy, or needle biopsy. A novel system based on Ribo-SPIA technology (RS, Ovation-Biotin amplification and labeling system) was recently introduced. The utility of the RS system, an optimized prototype system for picogram RNA samples (pRS), and two T7-based systems involving one or two rounds of amplification (One RA, Standard Protocol, or Two RA, Small Sample Prototcol, version II) were evaluated in the present study. Mouse kidney (MK) and mouse universal reference (MUR) RNA samples, 0.3 ng to 10 mug, were analyzed using high-density Affymetrix Mouse Genome 430 2.0 GeneChip arrays. Call concordance between replicates, correlations of signal intensity, signal intensity ratios, and minimal fold increase necessary for significance were determined. All systems amplified partially overlapping sets of genes with similar signal intensity correlations. pRS amplified the highest number of genes from 10-ng RNA samples. We detected 24 of 26 genes verified by RT-PCR in samples prepared using pRS. Two RA yielded somewhat higher call concordances than did RS and pRS (91.8% vs. 89.3% and 88.1%, respectively). Although all target preparation methods were suitable, pRS amplified the highest number of targets and was found to be suitable for amplification of as little as 0.3 ng of total RNA. In addition, RS and pRS were faster and simpler to use than the T7-based methods and resulted in the generation of cDNA, which is more stable than cRNA.

Animals↗
PubMed2003

Selective labeling and detection of specific mRNA in a total-RNA sample.

We report a unique approach to selectively label and detect specific RNA using its internal sequence, without separation, reverse transcription, and/or polymerase chain reaction. This approach is especially useful for individual mRNA labeling and detection. To expose mRNA internal sequence for selective labeling and detection, RNase H digestion is used to remove the 3(')-common sequences. We have designed a DNA-2(')-O-Me-RNA hybrid as the template for both RNase H digestion and Klenow extension and have found buffer conditions for both enzymes. Sharing the same template and buffer by these two enzymes largely simplifies experimental procedures. Using this approach, lacZ mRNA was selectively labeled and detected in the presence of thousands of mRNAs. We have successfully demonstrated for the first time the direct labeling and detection of an individual mRNA in a total-RNA sample. The detection sensitivity can reach up to attomole level (5 x 10(-18)mole). This method has great potential in RNA decay and metabolic regulation studies via individual mRNA labeling and in methodology of mRNA direct detection on microchip and direct gene expression profiling, without reverse transcription and polymerase chain reactions.

Biochemistry↗
PubMed1996

Differential display RT PCR of total RNA from human foreskin fibroblasts for investigation of androgen-dependent gene expression.

Male sexual differentiation is a process that involves androgen action via the androgen receptor. Defects in the androgen receptor, many resulting from point mutations in the androgen receptor gene, lead to varying degrees of impaired masculinization in chromosomally male individuals. To date no specific androgen regulated morphogens involved in this process have been identified and no marker genes are known that would help to predict further virilization in infants with partial androgen insensitivity. In the present study we first show data on androgen regulated gene expression investigated by differential display reverse transcription PCR (dd RT PCR) on total RNA from human neonatal genital skin fibroblasts cultured in the presence or absence of 100 nM testosterone. Using three different primer combinations, 54 cDNAs appeared to be regulated by androgens. Most of these sequences show the characteristics of expressed mRNAs but showed no homology to sequences in the database. However 15 clones with significant homology to previously cloned sequences were identified. Seven cDNAs appear to be induced by androgen withdrawal. Of these, five are similar to ETS (expression tagged sequences) from unknown genes; the other two show significant homology to the cDNAs of ubiquitin and human guanylate binding protein 2 (GBP-2). In addition, we have identified 8 cDNA clones which show homologies to other sequences in the database and appear to be upregulated in the presence of testosterone. Four of these clones again are similar to ETS from unknown genes. Three differential expressed sequences that appear to be upregulated in the presence of testosterone show significant homology to the cDNAs of L-plastin and one to the cDNA of testican. This latter gene codes for a proteoglycan involved in cell social behavior and therefore of special interest in this context. The results of this study are of interest in further investigation of normal and disturbed androgen-dependent gene expression.

Base Sequence↗
PubMed1985

Interstrain differences in the total RNA content in brain cells of the laboratory rat.

Total content of the ribosomal RNA in the cells of the frontal cerebral cortex (FCC), the septum (S), the dorsal hippocampus (DHI) and the lateral and medial hypothalamus (LHY, MHY) in adult males of the laboratory rat was determined cytophotometrically in two albino strains (i.e. in the Wistar strain (W) and in a strain with spontaneous hypertension (SHR) derived from the former) and in two pigmented strains (i.e. in the Long Evans strain (LE) and in the Brattleboro strain with spontaneous diabetes insipidus (DI) derived from the latter). The used quantitative histochemical method turned out to be very sensitive and demonstrated considerable differences in all brain structures examined. The LE strain showed higher values than the W strain in the FCC, S, DHI and LHY cells and lower ones in the MHY cells. The SHR strain was identical with the W strain from which it originated only in the FCC cells; in the S, DHI, and LHY cells it exhibited higher values, in the MHY cells lower ones. In the DI strain all values agreed with those of its original LE strain in all the areas evaluated except in the S and MHY cells where the values were lower. The data evaluated by stepwise discriminant analysis were found to be exceptional in the W strain. The data for the SHR strain were closer to the LE and DI strains, the data for the LE and DI strains intermingled.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2005

Isolation of Brucella abortus total RNA from B. abortus-infected murine RAW macrophages.

Brucella is a Gram-negative facultative bacterium that persists intracellularly in macrophages. However, the intracellular survival mechanisms used by Brucella are not fully understood. Isolation of Brucella RNA from infected macrophages has been challenging, and the inability to isolate sufficient Brucella RNA from infected macrophages has contributed to the failure in understanding bacterial transcriptional events. We describe the isolation of sufficient Brucella abortus RNA from its infective host cell environment using osmotic lysis and RNase and DNase digestion. This method takes advantage of the B. abortus cell envelope that protects bacterial RNA and DNA. The cell envelope of B. abortus was digested using SDS/proteinase K (PK) that, importantly, inhibits any residual RNase after digesting macrophage RNA permitting the extraction of B. abortus RNA. In our experiments, 4.5 microg of RNA was routinely isolated from 1 ml bacterial culture and 2-9 microg of bacterial RNA from infected macrophages without detectable host cell RNA or DNA contamination. The method is rapid and uses inexpensive, commonly available reagents. Total bacterial RNA was isolated in quantities sufficient for RT-PCR and microarray analysis.

Animals↗
PubMed1983

Concerning the thermal stability of E. coli 23S ribosomal RNA.

Total RNA prepared from E. coli by several extraction procedures behaves as a mixture of covalently continuous heat stable 23S, 16S and 4-5S components. 16S rRNA remains heat stable after isolation from such preparations, whereas isolated 23S rRNA is heat labile but becomes heat stable after EDTA treatment. This and other evidence leads to the conclusion that heat lability of purified 23S rRNA is due, not to nuclease contamination of the type observed in earlier studies of the stability of this RNA, but to polyvalent cation catalyzed temperature-dependent scission of phosphodiester bonds. Heat stability of 23S rRNA in total RNA is due to the presence in these preparations of a contaminant which appears to act as a chelator of polyvalent cations. This material is similar or identical to the pyrogenic E. coli lipopolysaccharide described by Westphal and coll.

Edetic Acid↗