异养氨氧化细菌基因组DNA的检测方法比较

氨氧化细菌是参与土壤氮素循环的重要微生物类群之一,其基因组DNA提取质量的准确分析,可直接影响后续分子实验的可行性和精确性。本试验针对3株异养氨氧化细菌的纯培养菌株,应用琼脂糖凝胶电泳、微量紫外分光光度计和Qubit荧光计分别检测不同提取方法获得的基因组DNA的浓度,同时结合细菌通用引物扩增16S r DNA全长来判定提取DNA的质量,进而筛选出可用于检测可培养氨氧化细菌基因组DNA浓度的方法。研究结果表明,针对不同浓度的DNA样品,尽管3种检测方法获得的结果表现出明显差异,但在16S r DNA-PCR中均仍能获得良好的扩增结果。与微量紫外分光光度法相比,Qubit方法对基因组DNA浓度的检测结果更为精确,特别在低浓度DNA检测中,能够较真实的反映基因组DNA的实际情况。     

棉花根际促生菌基因组DNA的提取及其鉴定

植物根际微生物基因组的提取往往因为细胞壁不能完全裂解以及内含物的成分和含量受到影响,获得完整的基因组DNA一直是土壤微生物分子生物学研究的关键。本文以新疆盐碱地棉花根际促生菌为材料,比较了SDS法、CTAB法以及高盐结合的CTAB法提取棉花根际促生菌基因组DNA的效率,结果显示,SDS法和CTAB法在细胞裂解后,由于过多的多糖类物质混于上清液中使其过于粘稠而无法分层,没能得到DNA样品。高盐结合的CTAB法则有效弥补了上述方法的不足,能够获得A260/A280为1.82、A260/A230为2.43的高质量基因组DNA。同时实验还以细菌16SrDNA为内标进行PCR扩增,结果证明所获得的棉花根际促生菌基因组DNA可直接用于PCR等分子生物学进一步研究。     

紫色水稻土水稳性团聚体土壤微生物基因组DNA提取方法探讨

为了找到提取土壤微生物总DNA的最佳方法,通过OD值检验、凝胶电泳、PCR和DGGE分析,比较了Reddy法、基于DNAout kit试剂盒改进的实验方法、以及Kuske修订法、Edgcomb改进法、SDS高盐提取法、Eichner调整法等常用的不同土壤微生物基因组的DNA提取方法在亚热带地区长期免耕紫色水稻土水稳性团聚体0.25～2.0 mm粒径上的提取效果.结果表明,6种方法都可以从团聚体中提取到长度大于23.1 kb的DNA片段,但不同方法提取的DNA的产量存在明显差异,土壤总DNA均不需纯化就可以用于PCR扩增,使用细菌16S rDNA基因V3区的通用引物可扩增得到相应的片段.研究表明,改进的DNAout kit试剂盒法是长期免耕紫色水稻土水稳性团聚体中微生物基因组DNA的最佳提取方法.     

RAPD分析用白花丹参叶片DNA的提取方法

本研究采用改良CTAB法和SDS法提取新鲜白花丹参叶片的基因组DNA,初步筛选RAPD扩增引物。结果表明改良CTAB法提取的DNA较SDS法质量好,随机引物p2扩增条带相对较为清晰。再利用p2随机引物对2种方法提取的DNA进行RAPD检测比较,结果显示仅改良CTAB法能扩增出有效条带,说明改良CTAB法更适合用于白花丹参基因组DNA的RAPD检测分析。本文将为白花丹参叶片DNA的提取提供方法学参考。     

西北地区耕地土壤真菌DNA提取方法比较

由于西北土壤理化性质的复杂性和真菌特殊性,所以从土壤中提取真菌基因组DNA就相对细菌更困难。在2种常用的土壤微生物基因组DNA提取方法与在传统提取方法的基础上,结合了一种专门适用于真菌的提取方法进行了比较,并且利用真菌28SrDNA通用引物U1/U2进行扩增。三种提取方法比较结果表明:SDS法提取的DNA纯度最低,传统CTAB-SDS的DNA产量最低,实验室的提取方法既可以提高DNA产量又可以保证DNA的片段完整性,并且本实验室的提取方法扩增效果最好,可广泛应用于西北地区土壤真菌的分子生物学研究。     

稻米深加工产品基因组提取方法及其对PCR的影响

以4种米粉为原料,每个样品做3个梯度(120、800和2000mg),采用改进的经典酚/仿法、CTAB(十六烷基三乙基溴化铵)沉淀法以及盐酸胍/氯仿法提取基因组,经PCR扩增内标基因(SPS)检测方法的优劣。结果显示,120mg的样品经3种方法提取的基因组均不能扩增出内标基因;800和2000mg的样品只有用CTAB沉淀法提取的基因组(采用相同的模板量)能全部扩增出内标基因。结果表明,CTAB沉淀法提取基因组的效果最好,对PCR的抑制现象最少。     

稻米深加工产品基因组提取方法的研究及其对PCR的影响

本实验以四种米粉为原料，每个样品做三个梯度：120mg, 800mg, 2000mg，采用改进的经典酚/仿法、CTAB沉淀法以及盐酸胍/氯仿法提取基因组，并通过聚合酶链式反应(PCR)通过扩增内标基因(SPS)来检测提取方法的优劣。结果显示：120mg的样品经三种方法提取的基因组均不能扩增出内标基因；800mg的样品和2000mg的样品只有用CTAB沉淀法提取的基因组(采用相同的膜板量)能全部扩增出内标基因。结论：CTAB沉淀法提取基因组的效果最好，对PCR的抑制现象最少。     

短序十大功劳基因组总DNA提取方法研究

以短序大功劳嫩叶为材料,采用CTAB法、CTAB改良法1、CTAB改良法2、SDS法和试剂盒法五种方法提取短序十大功劳基因组总DNA,用分光光度计和琼脂糖凝胶电泳方法检测所得总DNA的纯度和得率,用ISSR-PCR扩增的方法检测所得总DNA的质量。结果表明,五种方法均能从短序大功劳叶片中提取到基因组DNA,但不同方法提取得的基因组DNA的纯度、浓度和得率存在明显的差异。CTAB改良法2和试剂盒法提取的DNA纯度高,可直接用于下游分子生物学实验,CTAB法、CTAB改良法1和SDS法提取的总DNA质量较差,不利于下游的分子生物学实验;五种方法提取的总DNA的得率在10．836-451．709μg/g之间,呈CTAB法〉SDS法〉CTAB改良法1〉CTAB改良法2〉试剂盒法的现象。此实验获得的结果可以为短序十大功劳分子生物学研究提供基础。     

干制羊肉基因组DNA不同提取方法的比较

为了研究干制加工羊肉基因组DNA的最佳提取方法,本试验采用传统酚-氯仿法、磁珠法、改良CTAB法、离心柱法分别提取干制处理后的羊肉基因组DNA,并对4种方法提取的羊肉基因组DNA浓度、纯度、完整性以及提取所需时间、PCR扩增效果等进行比较。结果表明,采用磁珠法提取DNA的效果更好,DNA浓度为118.87 ng·μL^-1,A₂₆₀/A₂₈₀值为1.89,而且此方法具有提取时间短、效率高、污染小等特点。本研究结果为干制加工羊肉基因组DNA的大批量提取和检测提供了参考依据。     

蔺草基因组DNA提取方法的比较研究

以16个蔺草品种实生苗和4个蔺草品种组培苗为材料,探讨了CTAB改良法与DNA试剂盒法对蔺草基因组DNA提取质量的影响。结果发现,对于同一品种而言,CTAB改良法提取获得的DNA A260nm和OD值远低于试剂盒提取法,前者的DNA浓度仅为0.65~4.90μg/ml,而后者则为5.10~32.80μg/ml,后者为前者的1.6~21.2倍。这表明试剂盒提取法更适合于蔺草基因组DNA的提取。试验还发现提取材料对基因组DNA的质量有显著影响,蔺草组培苗优于实生苗。     

Diversity analysis of Central Asia and Caucasian lentil (<Emphasis Type="Italic">Lens</Emphasis><Emphasis Type="Italic">culinaris</Emphasis> Medik.) germplasm using SSR fingerprinting

Diversity analysis was performed among 39 cultivated lentil (Lens culinaris Medik.) accessions of Central Asia and Caucasian origin using five highly polymorphic microsatellite markers. A total of 33 alleles determined ranging from 3 to 8 per locus. Estimated gene diversity value for 33 loci was 0.66. Genetic similarity indices among 39 accessions ranged from 0.24 to 1.0. Cluster analysis using the unweighted pair group method with arithmetic mean method classified accessions into six major groups at 0.5 similarity coefficient. More than half accessions from Tajikistan formed large cluster. On the other hand, a few accessions from each country showed unique genotypes. Overall, most of the accessions, except ones with closely related origin, were distinguished by the present high quality DNA fingerprinting. This molecular diversity information gives important basis for conservation strategy in gene bank and exotic germplasm introduction in breeding programs in Central Asia and Caucasian countries.     

New method of DNA isolation from two food additives suitable for authentication in polymerase chain reaction assays

Locust bean gum and guar gum are galactomannans used as additives (E 410 and E 412, respectively) in the food industry as stabilizing agents. Analytical discrimination between the two additives in gums and foods is now feasible by molecular techniques. However, only complex and time-consuming DNA isolation protocols are available to date. We have developed simple improved protocols to obtain enough DNA suitable for PCR amplification from a few milligrams of commercial E 410 and E 412 additives (containing more than 75% polysaccharides). The suspension of additives in water or 10 mM Tris-HCl, pH 8.5, efficiently recovers DNA suitable for authentication in PCR assays. However, the Tris method was much more efficient for the extraction of DNA from E 410 than for E 412 additives. Conversely, the water method was the most suitable for detecting DNA extracted from E 412 or from E 410/E 412 mixtures. Combined with the use of the two specific ribosomal primer pairs previously designed, our methods are well-suited for a fast and simple high-throughput sample treatment of commercial gums for molecular certification.     

Spectroscopic (IR,NMR) characterization of water-soluble organic substances extracted from straw,straw incubated with Pleurotus ostreatus,and straw compost

Water extracts from fresh wheat and barley straw, straw incubated with Pleurotus ostreatus, and straw compost were studied by IR, ¹H NMR, and ¹³C NMR spectroscopy. During incubation lignin was degraded, water extractability increased, and water extracts were rich in polysaccharides. After composting solubility decreased and the water extracts were rich in aromatic, methoxyl, and carboxyl C, but poor in O-alkyl C indicating that during composting mainly polysaccharides had been mineralized. GPC revealed that water extracts from straw compost contained polysaccharides, peptides, C- and O-substituted aromatics, and alkyl compounds.     

An improved method for purifying genomic DNA from forest leaf litters and soil suitable for PCR

Background, aim and scope  An improving knowledge of bacterial community within natural environments including forest soils and leaf litters requires extraction of nucleic acids directly from environmental samples since molecular approaches provide less biased access to a larger portion of uncultivable microorganisms. However, when DNA was extracted successfully from these samples, it might still have been difficult to apply it as a template for polymerase chain reaction (PCR) amplifications due to the effect of PCR inhibitors. Various compounds from plant tissues including polysaccharides, phenolic compounds and especially humic acids can inhibit PCR amplification. Some of these inhibitors could inhibit PCR amplification by chelating the Mg²⁺ (cofactor for Taq polymerase), or by binding to target DNA, and PCR amplification would consequently be interfered with. Therefore, eliminating the effects of these PCR inhibitors is one of the most important steps for PCR-based molecular techniques. Four different methods were assessed in this study to purify the genomic DNA extracted from F, L layer leaf litters and forest soil in an exotic pine plantation of southeast Queensland, Australia. Materials and methods  Three samples including two leaf litters and one forest soil were collected with a core (25 × 40 cm) from a 22-year-old slash pine plantation in southeast Queensland, Australia. The DNA fragments were extracted directly using the Ultra Clean™ Mega Prep Soil DNA kit (Mo Bio Labs, Solana Beach, CA). Then, four different purification methods were applied and compared to purify the DNA for PCR amplification, which include PVPP, Sephadex ^TM spin column, low-melting agarose gel and a new modified gel purification method. The purified DNA from these four purification methods was detected by agarose gel electrophoresis, and the purity and usefulness of DNA samples were ultimately determined by successful PCR amplifications. Results and discussion  The DNA was extracted from each sample using the Ultra Clean™ Mega Prep Soil DNA kit, and the DNA eluents were dark in colour and sometimes formed compact aggregates. Subsequently, PCR amplification from such samples failed, although a series of dilutions had been made from neat to 1:10³. The DNA purification step could not, therefore, be avoided. It was observed that both the colour of eluent and the DNA concentration decreased gradually after elution. Considering the difficulties of removing PCR inhibitors and the possibility of high DNA losses, 50–200 μl of sample DNA was used for purification. Four DNA purification methods (the PVPP spin column, Sephadex™ spin column, low-melting agarose gel and the modified gel purification method) were applied and compared on leaf litter and soil samples. The DNA purified by the modified gel purification method provided the best PCR products for 16S rRNA gene amplification, but the other methods, PVPP, Sephadex™ spin column and low-melting agarose gel, produced very weak or no products. Thus, in this study, DNA fragments which were purified by the modified gel purification method were amplified efficiently. This may be attributed to running the low-melting agrose gel for a longer time, which could remove substantial humic substances and also some other compounds from the samples and, thus, prevent them from being involved in PCR amplification. Conclusions  A new modified gel purification method which can improve DNA purification and PCR amplification of environmental DNA is first introduced in this study. Comparing PVPP, Sephadex ™ spin column, low-melting agarose gel and modified gel purification method for the effect of DNA purification, the modified gel purification method is more successful in removing the PCR amplification inhibitors and obtaining the highly purified PCR amplifiable high-molecular-weight DNA. The method described here is cheap, fast and easy to operate. It suggests in this study that the method containing less and easier following steps should be widely used to relieve the heavy working load of molecular-biological researchers. Recommendations and perspectives  This study introduces a new modified DNA purification method, and it is found that this modified gel purification method is effective in removing the PCR inhibitors and obtains highly purified DNA from leaf litters for PCR amplification. The modified gel purification method may have wider applications, although it was only assessed on leaf litter and soil samples. The effect of the modified gel purification method on the DNA purification would need to be further investigated on a variety of samples which suffered from PCR inhibitors, such as clinical samples, plant tissues and environmental samples.     

落羽杉属树木基因组总DNA的提取及SRAP反应体系的优化

本文针对落羽杉属植物组织中多糖、多酚等次生物质含量高的特点,对其基因组DNA提取方法进行研究,比较了SDS法、CTAB法提取落羽杉属植物基因组DNA的效果,结果表明：CTAB法提取效果较佳。在此基础上,利用正交设计法,对SRAP反应体系中的各个主要影响因子Mg^2＋．dNTP、引物、TaqDNA聚合酶进行了优化筛选,确立了适合落羽杉属植物SRAP-PCR反应的最佳体系,即10μL体系中含有1μL 10×PCR bufier,Mg^2＋2．0mmol／L,dNTP100μmol／L,引物0-3μmol／L,彻DNA聚合酶0．5U和50ng模板DNA。利用该优化体系,通过48对SRAP引物组合对2个落羽杉属植物（落羽杉和墨杉）及4个杂交后代进行SRAP扩增,结果发现,SRAP引物及优化后的反应体系能够有效地用于落羽杉属植物种质资源鉴定及遗传多样性分析等研究。     

Evaluation of extraction methodologies for corn kernel (Zea mays) DNA for detection of trace amounts of biotechnology-derived DNA

Sensitive and accurate testing for trace amounts of biotechnology-derived DNA from plant material requires pure, high-quality genomic DNA as template for subsequent amplification using the polymerase chain reaction (PCR). Six methodologies were evaluated for extracting DNA from ground corn kernels spiked with 0.1% (m/m) CBH351 (StarLink) corn. DNA preparations were evaluated for purity and fragment size. Extraction efficiency was determined. The alcohol dehydrogenase gene (adh1) and the CBH351 (cry9C, 35S promoter) genes in the genomic DNA were detected using PCR. DNA isolated by two of the methods proved unsuitable for performing PCR amplification. All other methods produced some DNA preparations that gave false negative PCR results. We observed that cornstarch, a primary component of corn kernels, was not an inhibitor of PCR, while acidic polysaccharides were. Our data suggest that amplification of an endogenous positive control gene, as an indicator for the absence of PCR inhibitors, is not always valid. This study points out aspects of DNA isolation that need to be considered when choosing a method for a particular plant/tissue type.     

Effect of flash release and pectinolytic enzyme treatments on wine polysaccharide composition

Various treatments, including flash release and addition of pectic enzymes, have been proposed to enhance degradation of grape berry cell walls and extraction of aroma and phenolic compounds into the wines. The effect of flash release and enzyme treatment used separately or in combination on wine polysaccharide composition was studied. The flash release process increased extraction of polysaccharides originating from grape berry cell walls, that is, polysaccharides rich in arabinose and galactose (PRAGs) and type II rhamnogalacturonan (RG-II), thus yielding enriched wines. Increasing the duration of high-temperature exposure before the flash release treatment further increased extraction of polysaccharides. However, the wine obtained by pressing immediately after flash release and fermenting in the liquid phase contained lower amounts of grape polysaccharides, indicating that their extraction required skin maceration. The use of enzymes without or with flash release modified the composition and the structure of pectic polysaccharides. In particular, it induced the loss of PRAG terminal arabinose residues.     

雅安藏茶茶多糖对~(60)Co-γ射线辐照损伤小鼠抗氧化和造血功能的防护作用

为探究雅安藏茶茶多糖对~(60)Co-γ射线辐射损伤小鼠抗辐射作用的影响,从雅安藏茶中提取茶多糖,用不同浓度(50、100、200 mg·kg-1·d-1)的茶多糖连续15 d灌胃小鼠,在第6天采用5Gy的~(60)Co-γ射线一次性全身辐照各组小鼠,灌胃第16天测定各组小鼠外周血细胞、肝脏组织总抗氧化能力(T-AOC)、总超强氧化物歧化酶(T-SOD)活性和总蛋白(TP)含量等指标。结果表明,与单纯辐照组相比,雅安藏茶茶多糖能显著提高辐照损伤小鼠的外周血细胞数量,极显著提高肝脏组织T-AOC、T-SOD活性和股骨骨髓DNA含量,极显著降低肝脏MDA含量,缓解了免疫器官胸腺的萎缩;且随着茶多糖浓度的增加,其抗辐射作用效果增强。综上,雅安藏茶茶多糖对~(60)Co-γ射线辐照损伤小鼠抗氧化功能和造血功能具有较强的防护作用,且具有一定的剂量效应。本研究结果为进一步深入探究茶多糖防辐射作用机理提供了新参考,也为雅安藏茶辐照保健功效研究提供了一定的理论依据。     

灰枣多糖大孔径树脂提纯工艺优化

新郑灰枣富含各种营养成分,特别是多糖具有抗氧化抗癌等许多生物效应。为研究新郑灰枣多糖的提纯工艺,该文在超声波酶法联合提取、乙醇沉淀、超滤膜过滤得到的粗多糖的基础上,筛选出的AB-8大孔树脂纯化多糖,并对树脂的动态吸附解吸特性进行研究。响应曲面法优化AB-8大孔树脂动态吸附工艺条件,最佳动态吸附条件为:上样速率1.5mL/min,料液浓度2.2mg/mL,pH值5.6,最大动态吸附量为19.52mg/g;正交试验优化AB-8大孔树脂动态解吸的最佳工艺条件为:氯化钠浓度为0.4mol/L,乙醇添加量60%,盐酸浓度0.2mol/L,流速1.5mL/min,最优动态解吸率为85.21%。通过树脂纯化,多糖纯度可达88.87%。该红枣多糖提纯技术是一种非常有效的方法,在医疗及保健行业具有巨大的应用潜力和市场。     

魔芋DNA快速微量提取及其ISSR-PCR扩增

魔芋属天南星科魔芋属草本植物,其组织富含多糖和多酚等次生物质,这类物质的存在不仅使DNA提取变得困难,还会影响下游的分子生物学操作。采用改进的提取方法,主要包括在2mL Eppendorf离心管中液氮研磨,CTAB-SDS裂解细胞,β-巯基乙醇浓度从2％提高到5％和添加PVP抑制多酚氧化,缓冲液去多糖等步骤,成功的提取了魔芋鲜叶的高质量DNA,其A260／A280位于1．80-2．00之间,产率超过470μg／g,ISSR0PCR扩增效果好。该方法具有快速、低廉、微量、稳定等特点,为深入研究魔芋资源遗传多样性、标记辅助育种和种芋纯度的鉴定奠定了基础。