利用Excel电子数据表计算遗传相似系数的方法

利用分子标记技术对生物物种群进行类群分类时,一般需要通过分析电泳图谱获得0/1矩阵,通过统计计算来得到其遗传相似系数和遗传距离指数。科学工作者常借助计算器徒手计算,容易出错,速度又慢。本文介绍一种以MicrosoftExcel电子数据表为平台,能较轻松又准确地根据0/1矩阵实现遗传相似系数和遗传距离指数计算的操作方法。     

FS2M01．pl，转换片段大小表为0／0矩阵的Perl脚本

用Perl语言编写了一个脚本——FS2M01．pl来实现片段大小表向0／1矩阵的转换,解决了由人工方法将遗传图谱的位点信息转换成0／1矩阵的问题。     

苍白秤钩风(Diploclisia Glaucescens)中的木脂素——左旋丁香脂素的晶体结构研究

通过X 射线单晶衍射法测定了标题化合物的晶体结构。结果表明 :晶体属正交晶系 ,P2 12 12 1空间群 ,a =8 6 0 10 (3) ,b =13 0 830 (9) ,c =18 1130 (11) ,V =2 0 38 2 0 (2 0 ) 3 ,Z =4 ,Mr =4 18 4 9,Dx =1 36 9g/cm3 ,λ(MoKα) =0 710 73 ,μ(MoKα) =1 12cm-1,F(0 0 0 ) =888。在 0 <2θ <5 0°范围内共收集了 1988个独立衍射点 ,其中可观测衍射点 196 3个 [Ⅰ≥ 8σ(Ⅰ ) ]。晶体结构用直接法解出 ,经全矩阵最小二乘法修正 ,最终偏离因子Rf=0 0 6 2 ,Rw=0 0 5 5。     

菌根共生网络嵌套性判定的零模型选择

零模型是判定网络嵌套性的重要依据, 菌根共生关系网络经常出现高度非对称性, 该文通过探究矩阵非对称变化对基于不同零模型构建方法的网络嵌套性的影响, 试图为非对称网络零模型的选择提供依据。结果表明: 不同零模型保守性不同, 增加限定条件减少零模型构建过程中的自由空间, 高度限定条件易导致第II类错误。高度非对称网络会增加基于完全随机(r00)零模型的矩阵温度(NT)偏离、降低配对重叠度(NODF)偏离, 标准化指数z-score值显示网络非对称增加后有助于NT和NODF显著性判定。行或列限定对非对称网络嵌套性判定的影响存在差异, 列限定(c0)的网络嵌套性判定对网络非对称性变化的响应规律与r00零模型的响应趋势基本一致, 具有更低的嵌套性偏离和标准差值。行限定(r0, 包括行列限定(backtrack))零模型NT值和NT偏移随矩阵非对称性的变化保持稳定, 较之c0零模型在高度非对称网络中呈现更低的NODF偏离值。选用完全随机和限定零模型相结合的方法, 有助于更加准确判断非对称网络是否具有嵌套结构。高度非对称网络嵌套性判定中对行属性特征比较敏感, 不同非对称性网络间嵌套性水平相比较时选用r0零模型要优于r00和c0零模型。     

马可波罗百合的组织培养和离体快繁

以马可波罗百合的鳞片、茎段和茎尖为外植体 ,成功建立了快速无性繁殖系。诱导鳞片产生丛芽的最佳培养基为 :MS +0 .3～ 0 .8mg/LBA +0 .0 5mg/LNAA ;茎尖的最佳诱导培养基为 :MS +2mg/LBA +0 .0 5mg/LNAA ;茎段的最佳诱导培养基为 :MS +0 .8mg/LBA +0 .1mg/LNAA。丛芽增殖培养基 :MS +0 .2mg/LBA +0 .1mg/LNAA和MS +0 .2mg/LBA +0 .1mg/LIAA。生根诱导最佳培养基为 1 /2MS +0 .2mg/LKT +0 .0 5～ 0 .5mg/LNAA。     

鸡传染性支气管炎病毒两个地方分离株S1基因的扩增克隆与序列分析

对IBV肾型毒株JS/95 /0 3和呼吸型毒株SD/97/0 1的S1全基因进行了扩增、克隆和序列测定 ,将两毒株的S1基因序列与 10个参考毒株进行了比较。结果表明 ,JS/95 /0 3和SD/97/0 1分别与M41和H12 0株亲缘关系最近 ,它们可能是疫苗毒株的变异株。JS/95 /0 3和SD/97/0 1间的亲缘关系也较近 ,两者S1蛋白中只有 2 4个氨基酸的差异 ,其中有 15个位于前 130个氨基酸中 ,第 116位氨基酸可能与毒株的致病性有关。对两毒株S1蛋白的二级结构进行了预测和比较 ,结果发现 ,一个或极少数氨基酸的差异即可导致S1蛋白二级结构和抗原性的改变     

滇牡丹自然种群数量动态

运用种群静态生命表、存活曲线、生殖力表和Leslie矩阵模型研究了中国西南特有濒危植物滇牡丹(Paeonia delavayi)种群数量动态过程。静态生命表和种群存活曲线表明: 滇牡丹在株龄3-6 a之间经历了较强的环境筛, 其单株生理寿命为15 a左右, 平均周期为8 a, 种群的净增殖率(R₀ = 0.985 7)、内禀增长率(r_m = -0.001 7)和周限增长率(λ = 0.998 3)表明其为衰退型种群; 滇牡丹种群存活表现为台阶型曲线(B1型), 分别在6 a和12 a阶段种群消亡率(K_x)较高。Leslie矩阵模型的模拟结果表明, 在未来30 a内种群数量呈现出下降趋势, 大约下降了50%, 其种群数量靠自身根系的萌蘖和种子繁殖共同维持。野生滇牡丹种群数量下降与其自身繁殖特性有关, 但主要原因是人为采挖和生态环境的破坏。     

葡萄色顶枝瑚菌中矿质元素及氨基酸含量的测定

采用原子吸收分光光度法和FDBN柱前衍生高效液相色谱等方法测定了葡萄色顶枝瑚菌中的矿质元素、氨基酸和蛋白质的含量。矿质元素K、Ca、Mg、Cu、Zn、Fe的含量分别是 :4 2 .5 0 0 0mg/g、0 .90 0 0mg/g、0 .4 1 3 0mg/g、0 .0 1 1 2mg/g、0 .0 64 3mg/g、0 .0 3 1 7mg/g、0 .0 73 7mg/g;蛋白质含量为 2 8.1 7% ;氨基酸总量为 2 2 6.91mg/g,其中七种必需氨基酸含量占氨基酸总量的 4 9.2 5 %     

蔷薇属38个野生种果实的维生素含量及其与分组的关系

对蔷薇属 (Rosa) 38个野生种果实 (以下简称蔷薇果 )的经济性状进行了分析 ,并测定了 VC、VE 和胡萝卜素等重要维生素的含量。蔷薇果 VC 含量在该属种间差异很大 ,以秦岭蔷薇 (R.tsinglingensis)的含量为最高 (2 576mg/ 1 0 0 g) ,德钦蔷薇 (R.deqenensis)的含量为最低 (49mg/ 1 0 0 g)。胡萝卜素含量种间差异明显 ,以软条七蔷薇 (R.henryi)的含量为最高 (1 9.2 4 mg / 1 0 0 g) ,黄刺玫 (R.xanthina)的含量为最低 (0 .0 6 mg/ 1 0 0 g)。 VE 含量种间差异较小 ,在 1 .34 mg/ 1 0 0 g(黄刺玫 )至 3.86 mg/ 1 0 0 g(硕苞蔷薇R.bracteata)之间。对蔷薇亚属 54种野生种果实重要维生素含量的统计分析表明 ,维生素含量与分组具有一定相关性 ,尤以 VC 含量与分组的相关性最为明显 ,桂味组和小叶组 Vc含量很高 (均值都高于 1 80 0mg/ 1 0 0 g) ;合柱组、月季组、木香组和硕苞组含量很低 (均值都在 30 0 mg/ 1 0 0 g以下 ) ,芹叶组除宽刺蔷薇 (R.platyacantha) VC含量很高外 ,其余种类含量都很低 (均值为 1 90 mg/ 1 0 0 g)。胡萝卜素含量与分组也具有一定相关性 ,桂味组、芹叶组、合柱组和硕苞组的胡萝卜素含量较高 ,均值在 6 mg/ 1 0 0 g以上 ;月季组、小叶组和木香组含量较低 ,均值在 0 .4mg/ 1 0 0 g以下。V     

植物激素在小球藻异养培养中的作用

本文研究了几种植物激素对小球藻异养培养的影响。结果表明 ,IAA、IBA及 6_BA三种植物激素均不同程度地促进了小球藻的异养生长 ,培养≤ 36h时 ,IAA或IBA以 2 0mg/L的促进小球藻异养生长的效应最大 ,1 0 0mg/LIAA或IBA则抑制了藻的生长 ;>36h时 ,1 0 0mg/LIAA或IBA表现出促进小球藻生长的效应 ,并最终获最大净A540 增长量 ;6_BA以 0 1mg/L的促进作用最大。IBA与 6_BA组合同样表现出促进小球藻异养生长的效应 ,但并非IBA和 6_BA简单的加合效应 ,5mg/LIBA与 6_BA组合的效应维持 6_BA单因子的作用趋势 ,2 0mg/LIBA与 1mg/L 6_BA组合的效应大于与 0 .1mg/L 6_BA组合的 ,1 0 0mg/LIBA与 0 .1mg/L 6_BA组合的效应在≤ 36h时大于与 1mg/L 6_BA组合的 ,>36h时则相反。另外 ,高浓度IBA(≥ 2 0mg/L)与 6_BA组合抑制了前中期异养藻对葡萄糖的吸收 ,但加速了中后期葡萄的吸收。再者 ,IBA与 6_BA组合加速了异养小球藻对NO_3 的吸收。     

Large DNA fragment sizing by flow cytometry: application to the characterization of P1 artificial chromosome (PAC) clones.

A flow cytometry-based, ultrasensitive fluorescence detection technique is used to size individual DNA fragments up to 167 kb in length. Application of this technology to the sizing of P1 artificial chromosomes (PACs) in both linear and supercoiled forms is described. It is demonstrated that this method is well suited to characterizing PAC/BAC clones and will be very useful for the analysis of large insert libraries. Fluorescence bursts are recorded as individual, dye stained DNA fragments pass through a low power, focused, continuous laser beam. The magnitudes of the fluorescence bursts are linearly proportional to the lengths of the DNA fragments. The histograms of the burst sizes are generated in <3 min with <1 pg of DNA. Results on linear fragments are consistent with those obtained by pulsed-field gel electrophoresis. In comparison with pulsed-field gel electrophoresis, sizing of large DNA fragments by this approach is more accurate, much faster, requires much less DNA, and is independent of the DNA conformation.     

Bacteria genome fingerprinting by flow cytometry.

BACKGROUND: A flow cytometry-based, ultrasensitive fluorescence detection technique has been developed that demonstrates unique advantages in the analysis of large DNA fragments over the currently most widely used technology, pulsed-field gel electrophoresis (PFGE). The technique described herein is used to characterize the restriction fingerprints of the bacteria genome Staphylococcus aureus in this study. METHODS: The isolation of the bacterial genomic DNA and the subsequent complete digestion by a restriction endonuclease were performed inside an agarose plug. Electroelution was used to move the DNA fragments out-of the agarose plug into a solution containing low concentrations of spermine and spermidine, added to stabilize the large DNA fragments. DNA was stained with the bisintercalating dye thiazole orange homodimer (TOTO-1) and subsequently introduced into our ultrasensitive flow cytometer from a capillary. RESULTS: Individual DNA fragments up to 351 kbp were successfully handled and sized. The histograms of the burst sizes were generated from signals associated with individual fragments in <7 min with <2 pg of DNA. The sizing accuracy was better than 98%. In contrast, standard PFGE takes approximately 20 h and requires approximately 1 microg of DNA with a sizing accuracy of approximately 90%. CONCLUSIONS: With the demonstrated success and advantages, our approach has the potential of being applied to fast, accurate bacteria species and strain identification.     

Improved single-strand DNA sizing accuracy in capillary electrophoresis.

Interpolation algorithms can be developed to size unknown single-stranded (ss) DNA fragments based on their electrophoretic mobilities, when they are compared with the mobilities of standard fragments of known sizes; however, sequence-specific anomalous electrophoretic migration can affect the accuracy and precision of the called sizes of the fragments. We used the anomalous migration of ssDNA fragments to optimize denaturation conditions for capillary electrophoresis. The capillary electrophoretic system uses a refillable polymer that both coats the capillary wall to suppress electro-osmotic flow and acts as the sieving matrix. The addition of 8 M urea to the polymer solution, as in slab gel electrophoresis, is insufficient to fully denature some anomalously migrating ssDNA fragments in this capillary electrophoresis system. The sizing accuracy of these fragments is significantly improved by the addition of 2-pyrrolidinone, or increased capillary temperature (60 degrees C). the effect of these two denaturing strategies is additive, and the best accuracy and precision in sizing results are obtained with a combination of chemical and thermal denaturation.     

Interaction of cationic bilayer fragments with a model oligonucleotide

The interaction between cationic bilayer fragments and a model oligonucleotide was investigated by differential scanning calorimetry, turbidimetry, determination of excimer to monomer ratio of 2-(10-(1-pyrene)-decanoyl)-phosphatidyl-choline in bilayer fragment dispersions and dynamic light scattering for sizing and zeta-potential analysis. Salt (Na?HPO?), mononucleotide (2'-deoxyadenosine-5'-monophosphate) or poly (dA) oligonucleotide (3'-AAA AAA AAA A-5') affected structure and stability of dioctadecyldimethylammonium bromide bilayer fragments. Oligonucleotide and salt increased bilayer packing due to bilayer fragment fusion. Mononucleotide did not reduce colloid stability or did not cause bilayer fragment fusion. Charge neutralization of bilayer fragments by poly (dA) at 1:10 poly (dA):dioctadecyldimethylammonium bromide molar ratio caused extensive aggregation, maximal size and zero of zeta-potential for the assemblies. Above charge neutralization, assemblies recovered colloid stability due to charge overcompensation. For bilayer fragments/poly (dA), the nonmonotonic behavior of colloid stability as a function of poly (dA) concentration was unique for the oligonucleotide and was not observed for Na?HPO? or 2'-deoxyadenosine-5'-monophosphate. For the first time, such interactions between cationic bilayer fragments and mono- or oligonucleotide were described in the literature. Bilayer fragments/oligonucleotide assemblies may find interesting applications in drug delivery.     

Usefulness of microchip electrophoresis for reliable analyses of nonstandard DNA samples and subsequent on-chip enzymatic digestion.

The Hitachi SV1100 utilizes capillary electrophoresis on a microchip that is capable of rapidly sizing DNA fragments. Reproducibility of electrophoresis in different channels was shown by comparing the migration times of the internal controls, DNA fragments of 100 and 800 bp. The range of DNA sizing for this microchip is between 100 and 800 bp, and accuracy in sizing of a 322 bp DNA fragment of a pUC118 PvuII digest was observed, independent of DNA concentration. Although relatively good quantification of this fragment was observed with a DNA concentration of 1.83 ng.microL(-1), error increased in a dose-dependent manner. Furthermore, the feasibility of sequential analysis with this microchip was shown by the reproducibility of successive electrophoreses of the internal control in one channel. When the pUC118 PvuII digest was treated with endonuclease KpnI on the microchip for 10 min, sequential analysis showed that the 322 bp fragment completely disappeared and two peaks corresponding to the 130 and 192 bp fragments appeared. This analysis was performed within 4 min, and the peaks were estimated as 127 and 183 bp, respectively. These results indicate the potential of on-microchip endonuclease treatment of plasmid DNA with sequential analysis, offering high resolution in a short time.     

Rapid sizing of individual fluorescently stained DNA fragments by flow cytometry.

Large, fluorescently stained restriction fragments of lambda phage DNA are sized by passing individual fragments through a focused continuous wave laser beam in an ultrasensitive flow cytometer at a rate of 60 fragments per second. The size of the fluorescence burst emitted by each stained DNA fragment, as it passes through the laser beam, is measured in one millisecond. One hundred sixty four seconds of fluorescence burst data allow linear sizing of DNA with an accuracy of better than two percent over a range of 10 to 50 kbp. This corresponds to analyzing less than 1 pg of DNA. Sizing of DNA fragments by this approach is much faster, requires much less DNA, and can potentially analyze large fragments with better resolution and accuracy than with gel-based electrophoresis.     

A normalization strategy applied to HiCEP (an AFLP-based expression profiling) analysis: Toward the strict alignment of valid fragments across electrophoretic patterns

Background  

Gene expression analysis based on comparison of electrophoretic patterns is strongly dependent on the accuracy of DNA fragment sizing. The current normalization strategy based on molecular weight markers has limited accuracy because marker peaks are often masked by intense peaks nearby. Cumulative errors in fragment lengths cause problems in the alignment of same-length fragments across different electropherograms, especially for small fragments (< 100 bp). For accurate comparison of electrophoretic patterns, further inspection and normalization of electrophoretic data after fragment sizing by conventional strategies is needed.     

Rapid DNA fingerprinting of pathogens by flow cytometry

BACKGROUND: A new method for rapid discrimination among bacterial strains based on DNA fragment sizing by flow cytometry is presented. This revolutionary approach combines the reproducibility and reliability of restriction fragment length polymorphism (RFLP) analysis with the speed and sensitivity of flow cytometry. METHODS: Bacterial genomic DNA was isolated and digested with a rare-cutting restriction endonuclease. The resulting fragments were stained stoichiometrically with PicoGreen dye and introduced into an ultrasensitive flow cytometer. A histogram of burst sizes from the restriction fragments (linearly related to fragment length in base pairs) resulted in a DNA fingerprint that was used to distinguish among different bacterial strains. RESULTS: Five different strains of gram-negative Escherichia coli and six different strains of gram-positive Staphylococcus aureus were distinguished by analyzing their restriction fragments with DNA fragment sizing by flow cytometry. Fragment distribution analyses of extracted DNA were approximately 100 times faster and approximately 200,000 times more sensitive than pulsed-field gel electrophoresis (PFGE). When sample preparation time is included, the total DNA fragment analysis time was approximately 8 h by flow cytometry and approximately 24 h by PFGE. CONCLUSIONS: DNA fragment sizing by flow cytometry is a fast and reliable technique that can be applied to the discrimination among species and strains of human pathogens. Unlike some polymerase chain reaction (PCR)-based methods, sequence information about the bacterial strains is not required, allowing the detection of unknown, newly emerged, or unanticipated strains.     

Development and validation of a PCR-based marker assay for negative selection of the HMW glutenin allele <Emphasis Type="Italic">Glu-B1-1d</Emphasis> (<Emphasis Type="Italic">Bx-6</Emphasis>) in wheat

Polymorphisms between the coding sequences of high-molecular-weight (HMW) glutenin x-type genes at the Glu-1 locus were used to amplify Glu-1B x-type-specific PCR fragments. PCR analysis in a wheat cultivar subset carrying different Glu-1B x-type alleles resulted in PCR fragments that differed in size for Glu-B1-1d (B-x6) and non-Glu-B1-1d (B-x6) genotypes. Subsequent sequencing analysis revealed a 15-bp in-frame insertion in the coding regions of all Glu-B1-1d (B-x6) genotypes which allowed the development of a B-x6-specific PCR assay for high-throughput allele sizing by ion-pair reversed-phase high-performance liquid chromatography. The assay was validated in a set of 86 German wheat cultivars, and genotyping data unequivocally verified the presence of HMW glutenin subunits GLU-B1-1D (Bx-6) + GLU-B1-2A (By-8) by means of sodium dodecyl sulphate-polyacrylamide gel electrophoresis. These results demonstrate that the PCR assay can be applied for the detection and negative selection of the poor breadmaking quality Glu-B1-1d (B-x6) alleles in wheat breeding programs.