模式小鼠总DNA三种提取方法比较

目的：建立简便、快捷、经济的模式小鼠总DNA提取方法,以快速鉴定大批量模式小鼠基因型。方法采用苯酚抽提法、异丙醇沉淀法、鼠耳煮沸法提取同种模式小鼠总DNA,对比DNA纯度、得率、耗费时间,并比较基因型鉴定结果。结果苯酚抽提法得率最高,异丙醇沉淀法最低;而纯度则按照苯酚抽提法、异丙醇沉淀法、鼠耳煮沸法顺序递减;在耗时上鼠耳煮沸法最短。三种方法提取的DNA均可做模版用于基因型鉴定。结论鼠耳煮沸法操作简单、成本最低,快速、基因型鉴定结果可靠,可用于规模化的基因型鉴定实验中。     

Preparation of protein extracts from recalcitrant plant tissues: an evaluation of different methods for two-dimensional gel electrophoresis analysis

This study focuses on the specific problems of protein extraction from recalcitrant plant tissues and evaluates several methods to bypass them. Sample preparation is a critical step in a two-dimensional gel electrophoresis proteome approach and is absolutely essential for good results. We evaluated four methods: the classical trichloroacetic acid (TCA)/acetone precipitation, TCA/acetone precipitation and fractionation, an alternative based on fractionation and without precipitation, and phenol extraction methanol/ammonium acetate precipitation. We optimized the phenol extraction protocol for small amounts of tissue, which is essential when the study material is limited. The protocol was optimized for banana (Musa spp.) and was subsequently applied to two other plant species: apple (Malus domestica L.) and potato (Solanum tuberosum L.). Banana (Musa spp.) is a good representative of a "difficult" plant species since it contains many interfering metabolites. Only classical TCA/acetone precipitation and phenol extraction methods proved useful as standard methods. Both methods are associated with a minor but reproducible loss of proteins. Every extraction method and the subsequent analytical procedure have their physicochemical limitations; both methods should be investigated before selecting an appropriate protocol. The study, which is presented in this paper, is useful for guiding the experimental setup of many other nonmodel species, containing various interfering elements.     

Optimization of a high-throughput CTAB-based protocol for the extraction of qPCR-grade DNA from rumen fluid, plant and bacterial pure cultures

The quality and yield of extracted DNA are critical for the majority of downstream applications in molecular biology. Moreover, molecular techniques such as quantitative real-time PCR (qPCR) are becoming increasingly widespread; thus, validation and cross-laboratory comparison of data require standardization of upstream experimental procedures. DNA extraction methods depend on the type and size of starting material(s) used. As such, the extraction of template DNA is arguably the most significant variable when cross-comparing data from different laboratories. Here, we describe a reliable, inexpensive and rapid method of DNA purification that is equally applicable to small or large scale or high-throughput purification of DNA. The protocol relies on a CTAB-based buffer for cell lysis and further purification of DNA with phenol : chloroform : isoamyl alcohol. The protocol has been used successfully for DNA purification from rumen fluid and plant cells. Moreover, after slight alterations, the same protocol was used for large-scale extraction of DNA from pure cultures of Gram-positive and Gram-negative bacteria. The yield of the DNA obtained with this method exceeded that from the same samples using commercial kits, and the quality was confirmed by successful qPCR applications.     

Contribution of bacterial cell nitrogen to soil humic fractions

Summary Living cells ofSerratia marcescens, uniformly labelled with¹⁵N, were added to samples of maple (Acer saccharum) and black spruce (Picea mariana) forest soils. After different periods of incubation from zero time to 100 days, the soils were subjected to alkali-acid and phenol extraction to provide humic acid, fulvic acid, humin and humoprotein fractions. Significant amounts of the cell nitrogen were recovered in the humic and fulvic acids immediately after addition. After incubation, less cell, nitrogen appeared in the humic acid and more in the fulvic acid. The amount of cell nitrogen recovered in the humin fraction increased with incubation. Roughly 5 to 10 per cent of the added cell nitrogen was found as amino acid nitrogen from humoprotein in a phenol extract of the humic acid. The data are consistent with the occurrence of co-precipitation of biologically labile biomass nitrogen compounds with humic polymers during the alkaline extraction procedure involved in the humic-fulvic fractionation.     

Methods for microbial DNA extraction from soil for PCR amplification

Amplification of DNA from soil is often inhibited by co-purified contaminants. A rapid, inexpensive, large-scale DNA extraction method involving minimal purification has been developed that is applicable to various soil types (1). DNA is also suitable for PCR amplification using various DNA targets. DNA was extracted from 100g of soil using direct lysis with glass beads and SDS followed by potassium acetate precipitation, polyethylene glycol precipitation, phenol extraction and isopropanol precipitation. This method was compared to other DNA extraction methods with regard to DNA purity and size.     

Comparison of strategies for the isolation of PCR-compatible, genomic DNA from a municipal biogas plants

The goal of the project was the extraction of PCR-compatible genomic DNA representative of the entire microbial community from municipal biogas plant samples (mash, bioreactor content, process water, liquid fertilizer). For the initial isolation of representative DNA from the respective lysates, methods were used that employed adsorption, extraction, or precipitation to specifically enrich the DNA. Since no dedicated method for biogas plant samples was available, preference was given to kits/methods suited to samples that resembled either the bioreactor feed, e.g. foodstuffs, or those intended for environmental samples including wastewater. None of the methods succeeded in preparing DNA that was directly PCR-compatible. Instead the DNA was found to still contain considerable amounts of difficult-to-remove enzyme inhibitors (presumably humic acids) that hindered the PCR reaction. Based on the isolation method that gave the highest yield/purity for all sample types, subsequent purification was attempted by agarose gel electrophoresis followed by electroelution, spermine precipitation, or dialysis through nitrocellulose membrane. A combination of phenol/chloroform extraction followed by purification via dialysis constituted the most efficient sample treatment. When such DNA preparations were diluted 1:100 they did no longer inhibit PCR reactions, while they still contained sufficient genomic DNA to allow specific amplification of specific target sequences.     

适用于盐生植物的双向电泳样品制备方法

比较了三氯乙酸,丙酮沉淀法（TCA）、三氯乙酸沉淀法（E-TCA）和酚抽法（Phe）3种方法对盐生植物盐角草（Salicornia europaea L．）总蛋白的提取效果。3种方法分别得到579、343和535个蛋白点;TCA和E-TCA法所得图谱均存在严重的横向纹理,Phe法所得图谱则背景干净,基本上没有纹理。说明Phe法不仅能很好地提取盐角草蛋白,而且能有效去除样品中的盐分。对Phe法的提取液进行了改进,所得图谱背景更加清晰,蛋白点数增加。为其他盐生植物以及嗜盐微生物蛋白质的提取提供了重要参考。     

灵芝子实体原基双向电泳和总蛋白质提取方法的建立

比较了Tris-饱和酚法和三氯乙酸(TCA)/丙酮沉淀法对灵芝子实体原基总蛋白质的提取效果。用Image Master 2D Platinum6.0软件分析两种方法所提蛋白质的双向电泳图谱,分别得到565和273个蛋白质点;(TCA)/丙酮沉淀法在碱性端低分子量区域有些蛋白质斑点存在拖尾现象,Tris-饱和酚法能有效去除样品中的盐分,使蛋白质的聚焦效果更好,蛋白点数增加。Tris-饱和酚法可做为灵芝子实体原基总蛋白质的提取方法并为其他药用真菌总蛋白质的提取提供参考,同时为本实验室后续研究灵芝双向性固体发酵雷公藤的蛋白差异表达奠定了基础。     

THE NUCLEIC ACIDS OF BASAL BODIES ISOLATED FROM TETRAHYMENA PYRIFORMIS

Pellicular fragments were isolated from ethanol-fixed cells of the holotrichous ciliate Tetrahymena pyriformis by the action of digitonin. The isolated pellicles were further fragmented and the basal bodies of the cilia isolated from them by three methods. The preparations, examined in the electron microscope as embedded sections or negatively stained samples, consisted mainly of somewhat deformed pellicular material, the bulk of which was basal body. DNA was determined by the diphenylamine method and by reaction with DNase, and RNA, by the orcinol method. Nucleic acids were isolated by phenol extraction and analyzed spectrophotometrically and by reaction with RNase. The assays indicated 1.2 to 2.6 per cent RNA, similar to previously published work, but only 0.0 to 1.0 per cent DNA, near enough the sensitivity limits to render the presence of DNA in the preparations uncertain. Although the isolation procedure removed nuclear contents and ribosomes, the nucleic acids could still be a residual contaminant bound to the pellicle during the isolation. Hypotheses of basal body self-duplication, moreover, can be constructed both with and without nucleic acids.     

Protein extraction from plant tissues for 2DE and its application in proteomic analysis

Plant tissues contain large amounts of secondary compounds that significantly interfere with protein extraction and 2DE analysis. Thus, sample preparation is a crucial step prior to 2DE in plant proteomics. This tutorial highlights the guidelines that need to be followed to perform an adequate total protein extraction before 2DE in plant proteomics. We briefly describe the history, development, and feature of major sample preparation methods for the 2DE analysis of plant tissues, that is, trichloroacetic acid/acetone precipitation and phenol extraction. We introduce the interfering compounds in plant tissues and the general guidelines for tissue disruption, protein precipitation and resolubilization. We describe in details the advantages, limitations, and application of the trichloroacetic acid/acetone precipitation and phenol extraction methods to enable the readers to select the appropriate method for a specific species, tissue, or cell type. The current applications of the sample preparation methods in plant proteomics in the literature are analyzed. A comparative proteomic analysis between male and female plants of Pistacia chinensis is used as an example to represent the sample preparation methodology in 2DE‐based proteomics. Finally, the current limitations and future development of these sample preparation methods are discussed. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP17).     

非洲山毛豆叶片蛋白组双向电泳样品制备方法的建立

以非洲山毛豆叶片为材料,对非洲山毛豆总蛋白质3种提取方法(TCA/丙酮沉淀法、尿素/硫脲法和酚-甲醇/醋酸铵沉淀法)以及3种蛋白裂解液进行比较分析。结果表明,采用酚-甲醇/醋酸铵沉淀法提取非洲山毛豆叶片总蛋白,用蛋白裂解液(7mol/L尿素,2mol/L硫脲,4%CHAPS,40mmol/LTris-base,1%Bio-LytepH3.5-10,65mmol/LDTT)裂解蛋白1h,2-DE图谱分离到的蛋白点效果最好。此方法适合于色素、多酚及黄酮类次生代谢物含量较多的非洲山毛豆叶片总蛋白制备方法。     

双裂解法提取血清HBV DNA技术的建立

为进行ＰＣＲ实验建立了一种两步裂解血清ＨＢＶ提取其ＤＮＡ的方法。该法首先用ＳＤＳ及蛋白酶消化裂解病毒,随后再进行碱裂解,操作较酚提取法大为简化,而ＰＣＲ实验进行的两法的灵敏性比较,说明双裂解法至少不低于酚法。     

Analysis of grape berry cell wall proteome: a comparative evaluation of extraction methods

Different methods were tested for the extraction of proteins from the cell wall-enriched fraction (CWEf) obtained from a sample formed by skin and seeds of ripe berries of Vitis vinifera L. cv. Cabernet Sauvignon. The CWEf was isolated using a disruptive approach that involves tissue homogenization and precipitation by centrifugation. To extract proteins, the CWEf was treated with CaCl(2) and LiCl in two successive steps or, alternatively, with phenol. The efficiency of the protocols was evaluated by measuring protein yield and by analyzing two-dimensional gel electrophoresis (2-DE) gels for the highest detectable spot number and the greatest spot resolution. The phenol method was also adopted for the extraction of proteins from the cytosolic fraction (CYf). The comparison of 2-DE reference maps of protein extracts from CWEf and CYf indicated the presence of both common traits and unique characteristics. To survey this aspect some spots detected in both fractions or present in only one fraction were analyzed by liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS). Of the 47 spots identified, some were found to be cell wall proteins, while others were proteins not traditionally considered as localized in the apoplastic space. The data presented here provide initial information regarding the apoplastic proteome of grape berry tissues, but also raise the issue of the technical problems that characterize the isolation of cell wall proteins from these very hardy tissues.     

Human Milk MicroRNA and Total RNA Differ Depending on Milk Fractionation

MicroRNA have been recently discovered in human milk signifying potentially important functions for both the lactating breast and the infant. Whilst human milk microRNA have started to be explored, little data exist on the evaluation of sample processing, and analysis to ensure that a full spectrum of microRNA can be obtained. Human milk comprises three main fractions: cells, skim milk, and lipids. Typically, the skim milk fraction has been measured in isolation despite evidence that the lipid fraction may contain more microRNA. This study aimed to standardize isolation of microRNA and total RNA from all three fractions of human milk to determine the most appropriate sampling and analysis procedure for future studies. Three different methods from eight commercially available kits were tested for their efficacy in extracting total RNA and microRNA from the lipid, skim, and cell fractions of human milk. Each fraction yielded different concentrations of RNA and microRNA, with the highest quantities found in the cell and lipid fractions, and the lowest in skim milk. The column‐based phenol‐free method was the most efficient extraction method for all three milk fractions. Two microRNAs were expressed and validated in the three milk fractions by qPCR using the three recommended extraction kits for each fraction. High expression levels were identified in the skim and lipid milk factions for these microRNAs. These results suggest that careful consideration of both the human milk sample preparation and extraction protocols should be made prior to embarking upon research in this area. J. Cell. Biochem. 116: 2397–2407, 2015. © 2015 The Authors. Journal of Cellular Biochemistry Published by Wiley Periodicals, Inc.     

Comparison of rapid methods for the extraction of bacterial DNA from colonic and caecal lumen contents of the pig

AIMS: The increasing uses of DNA methodologies to study the micro flora of the pig gastrointestinal tract requires an efficient recovery of bacterial DNA from the intestinal sample. Thus, the objective of this study was to determine which DNA extraction methods are most effective for luminal samples from pigs. Several routinely used nucleic acid extraction procedures were compared based upon quantity and purity of extracted DNA. METHODS AND RESULTS: DNA was extracted from pig colonic and caecal lumen samples using 19 methods for bacterial DNA extraction. The quantity of total DNA recovered by each extraction method was determined and compared. Two methods using extraction with polyvinylpolypyrrolidone (PVPP) or phenol and two methods involving bead mill homogenization were found to provide the greatest quantity of extracted DNA for both colonic and caecal lumen. Extracted DNA from these four methods was further analysed for purity based upon the presence of PCR inhibitors, which was ascertained by determining the efficiency of amplification of a segment of the 16S rDNA. PCR amplification could be readily achieved with DNA extracted by each of these four methods, but efficiency of amplification tended to be higher with DNA from two of the methods (one extracted with PVPP and one with bead mill homogenization). CONCLUSIONS: Four extraction methods proved to be significantly superior in quantity of DNA extracted from luminal samples. Of these four, no strong inhibitors of PCR amplification were detected in any of the extracted DNA. However, the efficiency of amplification tended to be lower in DNA samples from two of the methods, suggesting the presence of low levels of PCR inhibitors. SIGNIFICANCE AND IMPACT OF THE STUDY: Results of this study provide a basis for choosing which DNA extraction procedures are most effective for use with samples of pig lumen.     

Physicochemical properties of fowlpox virus deoxyribonucleic acid and its anomalous infectious behavior

Randall, Charles C. (University of Mississippi, Jackson), Lanelle G. Gafford, Richard L. Soehner, and James M. Hyde. Physicochemical properties of fowlpox virus deoxyribonucleic acid and its anomalous infectious behavior. J. Bacteriol. 91:95-100. 1966.-Deoxyribonucleic acid (DNA) was extracted from fowlpox virus-infected tissue, purified inclusions, and purified virus by five variations of detergent and phenol methods. Phenol methods gave a poor yield, whereas detergent techniques extracted up to 78% of the DNA. The buoyant density was 1.695 g/ml, and the melting temperature in 7.2 m NaClO(4) was 39 C, both approximately equivalent to a guanine plus cytosine content of 35 moles per cent. Further proof of the double-stranded nature of the DNA was shown by the characteristic behavior toward deoxyribonuclease, formaldehyde, and heat. Infectious DNA was obtained by the various methods described, but this manifestation of biological activity was capricious and for unknown reasons was often not evident. The infectivity could not be related quantitatively to the amount of DNA employed. Furthermore, the infectious nature of fowlpox virus DNA was demonstrable only when the route of infection was the chorioallantoic membrane. In contrast, whole virus infected both membrane and chick skin with equal efficiency.     

A novel method for the two-dimensional analysis of proteins.

Nuclei from hamster embryo fibroblasts treated with radioactive benzo(a)pyrene were lysed in 6 m guanidine, and nuclear macromolecules were separated by isopycnic centrifugation in Cs₂SO₄. Control experiments showed that cross-contamination of the RNA, DNA, and protein fractions was less than 2% of the total recovery of each macromolecular class. When compared to previous techniques utilizing phenol extraction, similar specific activities of bound hydrocarbon (pmol benzo[a]pyrene/mg protein or nucleic acid) were obtained. However, overall recoveries of macromolecular components were higher with the present method. In addition, recovery of undegraded histones in the density gradient preparation of nuclear protein was demonstrated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and recovery of native DNA was demonstrated by thermal denaturation studies. Although developed specifically for work with carcinogenic hydrocarbons, the Cs₂SO₄ technique should be generally useful in cases where it is necessary to prepare all three classes of macromolecules from one batch of nuclei.     

Accumulative phases for heavy metals in limnic sediments

Data from mechanical concentrates of recent sediments indicate that clay minerals, clay-rich aggregates and heavy minerals are the major carriers of heavy metals in detrital sediment fractions. Hydrous Fe/Mn oxides and carbonates and sulfides, in their specific environments, are the predominant accumulative phases for heavy metals in autochthonous fractions. Sequential chemical extraction techniques permit the estimation of characteristic heavy metal bonding forms: exchangeable metal cations, easily reducible, moderately reducible, organic and residual metal fractions, whereby both diagenetic processes and the potential availability of toxic compounds can be studied. The data from lakes affected by acid precipitation indicate that zinc, cobalt and nickel are mainly released from the easily reducible sediment fractions and cadmium from organic phases. In contrast at pH 4.4, neither lead nor copper seem to be remobilized to any significant extent. Immobilization by carbonate precipitation seems to provide an effective mechanism for the reduction of dissolved inputs 9f metals such as zinc and cadmium in pH-buffered, hard water systems.     

A comparison of methods for extracting DNA from Coxiella burnetii as measured by a duplex qPCR assay

Aims: To determine the optimal DNA extraction method for the detection of Coxiella burnetii including the small‐cell variant (SCV) by real‐time PCR (qPCR) in clinical samples. Methods and Results: A duplex qPCR detecting two Coxiella burnetii gene targets (com1 and IS1111a genes) was developed. Each target in this PCR had a sensitivity of one copy number per reaction. DNA extraction methods were compared on spiked negative samples and included a silica column kit, a chloroform separation prior to a silica column method and a chloroform/phenol separation and DNA precipitation method. Conclusions: The silica column extraction method was more efficient at recovering C. burnetii DNA, from large‐cell and small‐cell variants, than a chloroform or chloroform/phenol method. The silica column method was useful on spiked human samples including serum, buffy coat and bone marrow samples. Significance and impact of study: This study demonstrated that a simple column kit method is efficient to use for the detection of C. burnetii in clinical samples including the SCV.     

14型肺炎链球菌荚膜多糖纯化工艺中两种去除蛋白方法的比较

目的苯酚抽提法和脱氧胆酸钠沉淀法去除14型肺炎链球菌荚膜多糖中蛋白质的效果比较。方法将3批次14型肺炎链球菌发酵培养液经超滤、乙醇沉淀等方法初步纯化后,平分成两份,分别采用苯酚抽提法和脱氧胆酸钠沉淀法去除蛋白,通过比较多糖收获量、多糖组分检定结果、多糖分子质量、多糖抗原活性、多糖核磁共振图谱,以此评价这两种蛋白去除方法的效果。结果与苯酚抽提法相比,脱氧胆酸钠沉淀法制备的14型肺炎链球菌纯化荚膜多糖除收获量较高,蛋白和核酸杂质含量较低外,氨基己糖含量、多糖分子质量、抗原活性和多糖核磁共振图谱的检定分析结果无显著性差异(P>0.1)。结论作为14型肺炎链球菌荚膜多糖纯化工艺中的除蛋白方法,脱氧胆酸钠沉淀法优于苯酚抽提法。