Isolation of functional RNA from small amounts of different grape and apple tissues

An efficient, simple, and small-scale procedure for isolating functional ribonucleic acid (RNA) was successfully applied to many different tissues of grape and apple. These woody plants are rich in polyphenolic compounds and polysaccharides that could impair the RNA extraction. The method chosen is based on the use of hot borate buffer at alkaline pH supplemented with several adjuvants and followed by selective precipitations. Starting with only 0.4 g of fresh tissue and working with small tubes (2 mL), we were able to obtain good yields of high-quality RNA suitable for further applications. The procedure can be proposed for many applications, and it is particularly highly recommended when isolating RNA from a large number of samples.     

An evaluation of tyramide signal amplification and archived fixed and frozen tissue in microarray gene expression analysis

Archival formalin-fixed, paraffin-embedded and ethanol-fixed tissues represent a potentially invaluable resource for gene expression analysis, as they are the most widely available material for studies of human disease. Little data are available evaluating whether RNA obtained from fixed (archival) tissues could produce reliable and reproducible microarray expression data. Here we compare the use of RNA isolated from human archival tissues fixed in ethanol and formalin to frozen tissue in cDNA microarray experiments. Since an additional factor that can limit the utility of archival tissue is the often small quantities available, we also evaluate the use of the tyramide signal amplification method (TSA), which allows the use of small amounts of RNA. Detailed analysis indicates that TSA provides a consistent and reproducible signal amplification method for cDNA microarray analysis, across both arrays and the genes tested. Analysis of this method also highlights the importance of performing non-linear channel normalization and dye switching. Furthermore, archived, fixed specimens can perform well, but not surprisingly, produce more variable results than frozen tissues. Consistent results are more easily obtainable using ethanol-fixed tissues, whereas formalin-fixed tissue does not typically provide a useful substrate for cDNA synthesis and labeling.     

Characterization and use of the potent ribonuclease inhibitor aurintricarboxylic acid for the isolation of RNA from animal tissues.

Inclusion of aurintricarboxylic acid (ATA) in extraction buffers for the isolation of RNA from animal tissues resulted in high yields (0.5-2.0 mg/g of tissue) of undegraded material as judged by agarose-gel-electrophoretic analyses and Northern-blotting experiments. However, ATA bound to nucleic acids, forming stable complexes, and so we have established methods for spectrophotometric quantification of RNA in these coloured complexes, and for easy removal of sufficient ATA to leave RNA in a consistently hybridizable condition at the end of a purification. The use and subsequent removal of ATA was straightforward and gave satisfactory results for all rat tissues tested.     

Improved method for the isolation of RNA from plant tissues

A fast and efficient method for the isolation of RNA from plant tissues is described. Tuber tissue is homogenized in a guanidine hydrochloride-containing buffer followed by direct extraction with phenol/chloroform. The RNA is precipitated from the aqueous phase, washed with 3 M sodium acetate and 70% ethanol, and finally dissolved in water. The yield of RNA is up to 500 micrograms/g of tissue and several tests indicate intact and nondegraded RNA. This method can be adapted to a small-scale version by the use of 1.5-ml tubes, allowing rapid isolation of RNA from a larger number of samples. Finally, this method is of particular use for isolating RNA from tissues with a high polysaccharide and nuclease content such as wounded potato tubers.     

Method Optimization for Extracting High-Quality RNA From the Human Pancreas Tissue

Nucleic acid sequencing is frequently used to determine the molecular basis of diseases. Therefore, proper storage of biological specimens is essential to inhibit nucleic acid degradation. RNA isolated from the human pancreas is generally of poor quality because of its high concentration of endogenous RNase. In this study, we optimized the method for extracting high quality RNA from paired tumor and normal pancreatic tissues obtained from eight pancreatic cancer patients post-surgery. RNA integrity number (RIN) was checked to evaluate the integrity of RNA, we tried to extract the RNA with an RIN value of 8 or higher that allows for the latest genetic analysis. The effect of several parameters, including the method used for tissue lysis, RNAlater treatment, tissue weight at storage, and the time to storage after surgical resection, on the quantity and quality of RNA extracted was examined. Data showed that the highest quantity of RNA was isolated using a combination of manual and mechanical methods of tissue lysis. Additionally, sectioning the tissues into small pieces (<100 mg) and treating them with RNAlater solution prior to storage increased RNA stability. Following these guidelines, high quality RNA was obtained from 100% (8/8) of tumor tissues and 75% (6/8) of normal tissues. High-quality RNA was still stable under repeated freezing and thawing. The application of these results during sample handling and storage in clinical settings will facilitate the genetic diagnosis of diseases and their subsequent treatment.     

何首乌总RNA提取方法的比较及改进

目的：探讨不同提取方法对提取何首乌总RNA的质量影响,寻找适于何首乌成熟叶组织RNA的提取方法。方法：以何首乌成熟叶组织为材料,采用SDS／酸酚法、常规CTAB法及改良的TRIzol试剂法分别进行实验,并对所提取RNA的质量进行验证。结果：采用3种方法都能提取出RNA,但质量差异较大。其中改良的TRIzol试剂法能有效抑制次生物质的影响,提取的RNA产量可达70-110μg／g,纯度高于其他2种方法,D260nm／D280nm值为1．85～1．97。结论：改良的TRIzol试剂法操作简便,提取的RNA完整性和纯度较高,可以满足下一步实验的要求。     

Comparison of methods in the recovery of nucleic acids from archival formalin-fixed paraffin-embedded autopsy tissues

Archival formalin-fixed paraffin-embedded (FFPE) human tissue collections are typically in poor states of storage across the developing world. With advances in biomolecular techniques, these extraordinary and virtually untapped resources have become an essential part of retrospective epidemiological studies. To successfully use such tissues in genomic studies, scientists require high nucleic acid yields and purity. In spite of the increasing number of FFPE tissue kits available, few studies have analyzed their applicability in recovering high-quality nucleic acids from archived human autopsy samples. Here we provide a study involving 10 major extraction methods used to isolate total nucleic acid from FFPE tissues ranging in age from 3 to 13 years. Although all 10 methods recovered quantifiable amounts of DNA, only 6 recovered quantifiable RNA, varying considerably and generally yielding lower DNA concentrations. Overall, we show quantitatively that TrimGen’s WaxFree method and our in-house phenol-chloroform extraction method recovered the highest yields of amplifiable DNA, with considerable polymerase chain reaction (PCR) inhibition, whereas Ambion’s RecoverAll method recovered the most amplifiable RNA.     

Using silica particles to isolate total RNA from plant tissues recalcitrant to extraction in guanidine thiocyanate

The most commonly used protocol of the RNA isolation, the guanidine thiocyanate method, was unsuitable for recalcitrant plant tissues containing a large amount of storage proteins and secondary metabolites. We demonstrated that RNA could bind to the silica particles, which have been used successfully in DNA isolation from various sources, under a high concentration of NaCl in the presence of ethanol and sodium acetate. Based on this observation, an efficient, inexpensive, and highly reproducible technique, the acid phenol-silica method, was developed to isolate high-quality RNAs from various plant tissues recalcitrant to extraction in guanidine thiocyanate.     

An efficient method for extraction of RNA from rice leaves at different ages using benzyl chloride.

With a conventional method of RNA extraction using an acid guanidinium thiocyanate-water-saturated phenol-chloroform mixture, extraction efficiency of extractable RNA to total RNA (extractable RNA+ residual RNA) in rice leaves at various ages was 54-69%. With a new method, an improvement of the above, using benzyl chloride instead of water-saturated phenol together with further maceration with a small amount of quartz sand, the efficiency was increased to 81-95%. When RNA fractions obtained with the improved method were subjected to agarose gel electrophoresis, intact bands of 25 S and 17 S rRNAs were detected. With a DNA probe for rice rbcS, only a single band was observed on the blotted membrane. These results indicate that the improved extraction method of RNA with benzyl chloride is useful for quantitative and qualitative analysis of RNA in plant tissues such as stiff leaves of rice.     

Comparison of Fixation Methods for Preservation of Morphology, RNAs, and Proteins From Paraffin-Embedded Human Cancer Cell-Implanted Mouse Models

Xenograft transplantation of human tumor cells into immunodeficient mice is an important method to clarify the roles of specific molecules or chemicals in vivo. Recently, this method has been reported as a definitive examination to identify tumor stem cells. In this study, the authors compared the morphology and the quality and quantity of ribonucleic acid (RNA) and protein in paraffin-embedded tissues of nude mice implanted with human uterine cervical cancer cells, followed by fixation with commonly used fixatives, including 4% paraformaldehyde (PFA), 10% neutral buffered formalin (NBF), 20% NBF, and 99% ethanol (EtOH). The quality of the isolated RNA from PFA- and NBF-fixed paraffin-embedded tissues was high, while EtOH-fixed tissues showed degradation of RNA. NBF-fixed tissues showed excellent quality of morphology, but EtOH-fixed tissues showed contraction of cells. Immunohistochemical results showed differences depending on fixations. The 99% EtOH-fixed samples showed decreases of Ki-67 and VEGF-A immunoreactivities, but improved cytokeratin immunoreactivity. This study indicated that formalin fixation is better than alcohol fixation for RNA preservation in paraffin-embedded cancer cell implantation models. Immunohistochemical results differed markedly depending on fixation materials and antibodies; therefore, suitable fixations are needed to quantify and compare the results of immunohistochemical staining on cancer cell implanted nude mice tissues.     

Use of Sepharose 4B for Preparative Scale Fractionation of Eukaryotic Messenger RNA's

A new technique using Sepharose 4B column chromatography for the partial purification of the total messenger RNA population of several animal tissues is described. The column when eluted with 0.1M sodium acetate, pH 5.0, containing. 001M EDTA, resolves a total nucleic acid extract into four major peaks. DNA is eluted at the void volume, followed successively by peaks of 18S ribosomal RNA, 4S transfer RNA and 28S ribosomal RNA. Ribonucleic acid containing mRNA activities is eluted after the DNA peak but immediately before the 18S rRNA peak. Hence the column enables quantitative removal of DNA, 5S RNA, tRNA and 28S rRNA from the majority of total cellular mRNA's. Partial segregation of mRNA's in the column is also demonstrated. The method does not require the isolation of polysomes as the initial procedure in mRNA isolation and is readily adaptable to large scale preparations. One hundred mg of total nucleic acid extracted from whole tissues can be fractionated on a 5 × 100 cm Sepharose 4B column. Recovery of total mRNA activities ranges between 60–70% and purification with respect to the total cell extract is 7 to 8 fold.     

Isolation of high quality RNA from bilberry (Vaccinium myrtillus L.) fruit

A simple and efficient method is described for isolating high quality RNA from bilberry fruit. The procedure is based on the use of hexadecyltrimethyl ammonium bromide (CTAB), polyvinylpyrrolidone (PVP), and β-mercaptoethanol in an extraction buffer in order to eliminate the polysaccharides and prevent the oxidation of phenolic compounds. This method is a modification of the one described for pine trees, and yields high-quality RNA suitable for cDNA based methodologies. This method is applicable for a variety of plant tissues.     

Tissue-specific expression of four types of rat calmodulin-dependent protein kinase II mRNAs

cDNA clones for a fifth polypeptide of rat brain calmodulin-dependent protein kinase II were isolated and sequenced. The cDNA sequence encoded a polypeptide, designated delta, consisting of 533 amino acid residues with a molecular weight of 60,080. Comparison of amino acid sequences of this and alpha, beta, beta', and gamma polypeptides of calmodulin-dependent protein kinase II reveals marked homology among them. The mRNAs for delta were expressed in rat brain tissues with different regional specificities. The distribution of alpha, beta/beta', gamma, and delta mRNAs in cerebrum, skeletal muscle, diaphragm, heart, small intestine, uterus, aorta, liver, kidney, lung, and testis were examined by RNA blot hybridization analysis with probes specific for the respective mRNAs. A 3.9-kilobase (kb) RNA species hybridizable with a probe for gamma was found in all the tissues examined, and 4.0-4.2-kb RNA species hybridizable with a probe for delta were found in all the tissues examined except for liver, while a 4.8-kb RNA species hybridizable with a probe for alpha and a 4.2-kb RNA species hybridizable with a probe for beta were present in brain but not in the other tissues. With the alpha probe, however, a 4.1- and 2.6-kb RNA species were both detected in skeletal muscle and diaphragm. With the beta probe, a 4.3-kb RNA in skeletal muscle and diaphragm, 2.9-kb RNA in small intestine, and 4.0-kb RNA in testis were detected. With the delta probe, a 3.5-kb RNA in heart and 1.8-kb RNA in testis were detected. Thus, gamma and delta mRNAs were expressed in various tissues, while alpha and beta/beta' mRNAs were primarily, if not exclusively, expressed in brain.