演化极端结合分支分类方法

从生物演化的逆方向考虑,提出一种聚合的分支分类运算方法,称为演化极端结合分支分类法。文章阐明其设计思路、演算步骤,并以实例具体说明其演算过程。最后以演化长度系数、合理解与合理方法等概念,对演化极端结合法进行评价。     

酵母表达重组人血清白蛋白检测方法的比较

应用生化法、电泳扫描结合Bradford法、竞争ELISA等3种方法检测酵母表达重组人血清白蛋白(rHSA)的表达量。结果表明,3种方法检测结果近似。比较而言,生化法灵敏度较低,但操作简便,价格低廉;竞争ELISA法灵敏度最高,但需要特异的抗体;电泳扫描结合Bradford法需要特殊仪器,操作繁琐,花费时间长,灵敏度介于生化法和竞争ELISA法之间。综合利弊,生化法可作为检测酵母表达rHSA的首选方法,如条件允许,可考虑采用电泳扫描结合Bradford法或竞争EUSA。     

Genotyping of single nucleotide polymorphism using model-based clustering

MOTIVATION: Single nucleotide polymorphisms have been investigated as biological markers and the representative high-throughput genotyping method is a combination of the Invader assay and a statistical clustering method. A typical statistical clustering method is the k-means method, but it often fails because of the lack of flexibility. An alternative fast and reliable method is therefore desirable. RESULTS: This paper proposes a model-based clustering method using a normal mixture model and a well-conceived penalized likelihood. The proposed method can judge unclear genotypings to be re-examined and also work well even when the number of clusters is unknown. Some results are illustrated and then satisfactory genotypings are shown. Even when the conventional maximum likelihood method and the typical k-means clustering method failed, the proposed method succeeded.     

不同取样方式在稻田节肢动物采集中的效率评估

水稻是我国主要粮食作物,每年都会因虫害造成大量的经济损失,为了挽回害虫造成的损失,必须对害虫进行防治。田间节肢动物群落调查是评价害虫防治效果的重要依据,取样方式对节肢动物群落调查的准确性具有重要的影响。另外,对转基因作物对稻田生物多样性安全性进行评价时,取样方式对多样性评价的准确性也具有重要的影响。本文采用吸虫器法、盆拍法和马氏网诱集法3种取样方式进行稻田节肢动物调查,并评估不同取样方式的采集效率。得到的结果有:1.采集到的节肢动物物种数:马氏网诱集法吸虫器法盆拍法;2.采集的节肢动物数量:盆拍法吸虫器法马氏网诱集法;3.吸虫器取样法在调查叶蝉科、秆蝇科、茧蜂科、姬蜂科、金小蜂科、缘腹细蜂科、蕈蚋科时,取样效率较高;4.盆拍取样法在调查叶蝉科、瘿蚊科、微蛛亚科、跳蛛科、狼蛛科、猫蛛科、弹尾虫目、飞虱科时,取样效率较高;5.马氏网诱集法在调查缟蝇科和毛蠓科时取样效率较高。马氏网诱集法善于采集具有飞行能力的节肢动物;吸虫器法对不同习性的节肢动物采集效果均较高;盆拍法适合采集活动于水稻基部的节肢动物。     

Method for rapid screening of pesticide mineralization in soil

A method has been developed for the analysis of (14)CO(2) evolution from the mineralization of (14)C-labelled organic compounds in soil samples. The new method is less space demanding and substantially cuts down laborious manual work compared to the traditional incubation bottle method used. Furthermore, the use of scintillation cocktail is largely reduced with the new method. In the new method, (14)CO(2) is trapped in filter paper held in the lid of a 20 ml glass vial by surface tension. The trapping solution used is Ca(OH)(2), which fixates CO(2) in the filter paper and the analysis of trapped (14)CO(2) is done using the Cyclone trade mark Storage Phosphor system. The lids are placed in a 32 well holder and exposed to a phosphor screen prior to scanning in a Cyclone trade mark scanner. The new filter method has been tested and compared to results obtained using the traditional method. The results show good agreement but due to a smaller capacity for CO(2) with the filter method compared to the traditional method, the interval between sampling has to be shorter using the filter method when the CO(2) development is high. The detection limits for the filter method is higher compared to the traditional method. With the filter method, the level of radioactivity has to exceed 300 dpm before detection is possible, while the same limit for the traditional method is around 30 dpm. On the other hand, the gas trapping faster and the efficiency is higher with the filter method.     

Analysis of exponential decay curves: a three-step scheme for computing exponents

A study of four techniques is examined to determine which method has the greater overall utility. An iterative least-squares error minimization method provides the greatest accuracy, while a linear algebraic method is accurate only for two-exponential data with small error. Consequently, a three-method sequential identification scheme is devised utilizing a graphical method, a transform method, and an iterative method. This scheme is successfully applied to physiological data containing three and four exponents.     

深圳地区参考作物蒸散量计算方法适用性分析

根据深圳1998~2007日值气象资料,以4种方法计算参考作物蒸散量,并以FAO Penman-Monteith公式计算结果为标准,评价其他各公式在深圳的适用性。结果表明:Irmark-Allen公式的月平均参考作物蒸散量及年参考作物蒸散量与Penman-Monteith公式结果没有显著差异,与Hargreaves公式和Pristley-Taylor公式计算结果差异显著,Hargreaves最大,Pristley-Taylor最小;Irmark-Allen公式、Pristley-Taylor公式与Penman-Monteith公式的相关性较高,而Hargreaves相关性较低。Irmark-Allen法可作为深圳地区缺少相关气象资料条件下计算ET0较理想的替代方法。     

A simple graphic method for reconstructing phylogenetic trees from molecular data

A simple graphic method is proposed for reconstructing phylogenetic trees from molecular data. This method is similar to the unweighted pair-group method with arithmetic mean, but the process of computation of average distances and reconstruction of new matrices, required in the latter method, is eliminated from this new method, so that one can reconstruct a phylogenetic tree without using a computer, unless the number of operational taxonomic units is very large. Furthermore, this method allows a phylogenetic tree to have multifurcating branches whenever there is ambiguity with bifurcation.     

Mapping quantitative trait loci by an extension of the Haley-Knott regression method using estimating equations

The Haley-Knott (HK) regression method continues to be a popular approximation to standard interval mapping (IM) of quantitative trait loci (QTL) in experimental crosses. The HK method is favored for its dramatic reduction in computation time compared to the IM method, something that is particularly important in simultaneous searches for multiple interacting QTL. While the HK method often approximates the IM method well in estimating QTL effects and in power to detect QTL, it may perform poorly if, for example, there is strong epistasis between QTL or if QTL are linked. Also, it is well known that the estimation of the residual variance by the HK method is biased. Here, we present an extension of the HK method that uses estimating equations based on both means and variances. For normally distributed phenotypes this estimating equation (EE) method is more efficient than the HK method. Furthermore, computer simulations show that the EE method performs well for very different genetic models and data set structures, including nonnormal phenotype distributions, nonrandom missing data patterns, varying degrees of epistasis, and varying degrees of linkage between QTL. The EE method retains key qualities of the HK method such as computational speed and robustness against nonnormal phenotype distributions, while approximating the IM method better in terms of accuracy and precision of parameter estimates and power to detect QTL.     

Condition Number Estimation of Preconditioned Matrices

The present paper introduces a condition number estimation method for preconditioned matrices. The newly developed method provides reasonable results, while the conventional method which is based on the Lanczos connection gives meaningless results. The Lanczos connection based method provides the condition numbers of coefficient matrices of systems of linear equations with information obtained through the preconditioned conjugate gradient method. Estimating the condition number of preconditioned matrices is sometimes important when describing the effectiveness of new preconditionerers or selecting adequate preconditioners. Operating a preconditioner on a coefficient matrix is the simplest method of estimation. However, this is not possible for large-scale computing, especially if computation is performed on distributed memory parallel computers. This is because, the preconditioned matrices become dense, even if the original matrices are sparse. Although the Lanczos connection method can be used to calculate the condition number of preconditioned matrices, it is not considered to be applicable to large-scale problems because of its weakness with respect to numerical errors. Therefore, we have developed a robust and parallelizable method based on Hager’s method. The feasibility studies are curried out for the diagonal scaling preconditioner and the SSOR preconditioner with a diagonal matrix, a tri-daigonal matrix and Pei’s matrix. As a result, the Lanczos connection method contains around 10% error in the results even with a simple problem. On the other hand, the new method contains negligible errors. In addition, the newly developed method returns reasonable solutions when the Lanczos connection method fails with Pei’s matrix, and matrices generated with the finite element method.     

Measurement of DNA with an automatic spectrophotometer

A method that uses an automated spectrophotometer to read microtiter plates in a modification of the diphenylamine method of DNA determination in tissue extracts, is presented. The micromethod saves technician time, and reduces exposure to acetic acid fumes. The reproducibility of the method is superior to the manual method. Fewer pipetting steps are required, and the method is suited to large batches of samples.     

电化学法快速检测微生物的发展现状及趋势

自1898年Stewart提出利用电化学法检测微生物,电化学法已发展成为一种微生物快速检测的方法。根据检测的参数不同,电化学微生物检测法可以分为阻抗微生物法和介电常数法。阻抗法主要用于食品工业中微生物的快速检测(≤10⁷ cfu/mL),尤其用于易腐食品的微生物快速检测,以期实现在其发生明显腐败之前得到检测结果。而介电常数则用于生物发酵过程中的微生物数量的快速测定,可以实现在线监测微生物数量及生物发酵过程的实时控制。电化学法由于其检测迅速、可以实现自动化检测,在工业化生产中具有广阔的应用前景。     

改进的SDS-CTAB法提取濒危植物连香树总DNA

对珍稀濒危植物连香树(Cercidiphyllum japonicum)的6种总DNA提取方法进行了对比试验,结果表明改进的SDS-CTAB法更适合于连香树总DNA提取。该方法提取的DNA经紫外消光值检测,其A260/A280为1.8532,优于CTAB法(1.4872)、SDS法(1.3552)、PVP法(1.5079)、尿素法(1.1858)和高盐低pH法(1.4534)。琼脂糖凝胶电泳和PCR扩增结果也得出同样的结论。     

用气相色谱-质谱联用比较牛耳草代谢物的提取方法

通过比较不同的提取方法对牛耳草新鲜和脱水叶片中代谢物的提取效率,旨在建立一种可以有效鉴定并分析牛耳草脱水过程中关键小分子代谢物的种类和含量变化的方法,为研究植物耐脱水分子机制提供技术方法。本研究以气相色谱-质谱联用(GC-MS)为分析方法,对复苏植物牛耳草代谢物提取方法进行比较。从提取总色谱峰数目、提取效率、代谢物保留时间和提取效率稳定性等方面比较甲醇溶液(A法)和甲醇-氯仿-水溶液(B法)两种提取方法的提取效果。对牛耳草新鲜样品提取结果表明,B法提取的总色谱峰数目多于A法;对9种共有代谢物的提取效率比较结果表明,B法的提取效率高于A法;对10种色谱峰的保留时间和提取效率的方法学考察结果表明,两者保留时间RSD(相对标准偏差)值均小于1%,A法提取效率的RSD值≤10%的比例为50%,B法的为100%。A法对干样的提取色谱峰数目远少于鲜样,而B法对干样的提取色谱峰数目和鲜样没有显著差异,保留时间RSD值均小于1%,提取效率的RSD值与鲜样没有差异,稳定性良好。     

A new semiparametric estimation method for accelerated hazard model

The accelerated hazard model has been proposed for more than a decade. However, its application is still very limited, partly due to the complexity of the existing semiparametric estimation method. We propose a new semiparametric estimation method based on a kernel-smoothed approximation to the limit of a profile likelihood function of the model. The method leads to smooth estimating equations and is easy to use. The estimates from the method are proved to be consistent and asymptotically normal. Our numerical study shows that the new method is more efficient than the existing method. The proposed method is employed to reanalyze the data from a brain tumor treatment study.     

A simple method for classifying genes and a bootstrap test for classifications

A new simple method for classifying genes is proposed based on Klastorin's method. This method classifies genes into monophyletic groups which are made distinct from each other by evolutionary changes. The method is applicable as long as the phylogenetic tree of genes is obtained. There is a fast algorithm for obtaining the classification. A bootstrap test of a classification is also presented. As an example, we classified opsin genes. The classification obtained by this method is the same as the previous classification based on the function of opsins.     

Evaluating a new method to estimate the rate of leaf respiration in the light by analysis of combined gas exchange and chlorophyll fluorescence measurements

Day respiration (R(d)) is an important parameter in leaf ecophysiology. It is difficult to measure directly and is indirectly estimated from gas exchange (GE) measurements of the net photosynthetic rate (A), commonly using the Laisk method or the Kok method. Recently a new method was proposed to estimate R(d) indirectly from combined GE and chlorophyll fluorescence (CF) measurements across a range of low irradiances. Here this method is tested for estimating R(d) in five C(3) and one C(4) crop species. Values estimated by this new method agreed with those by the Laisk method for the C(3) species. The Laisk method, however, is only valid for C(3) species and requires measurements at very low CO(2) levels. In contrast, the new method can be applied to both C(3) and C(4) plants and at any CO(2) level. The R(d) estimates by the new method were consistently somewhat higher than those by the Kok method, because using CF data corrects for errors due to any non-linearity between A and irradiance of the used data range. Like the Kok and Laisk methods, the new method is based on the assumption that R(d) varies little with light intensity, which is still subject to debate. Theoretically, the new method, like the Kok method, works best for non-photorespiratory conditions. As CF information is required, data for the new method are usually collected using a small leaf chamber, whereas the Kok and Laisk methods use only GE data, allowing the use of a larger chamber to reduce the noise-to-signal ratio of GE measurements.     

A new colorimetric determination of D-amino acid oxidase and urate oxidase activity.

A new method of colorimetric determination of d-amino acid oxidase and urate oxidase using catalase and 4-amino-3-hydrazino-5-mercapto-1,2,4-triazole is reported. This method is based on the combination of two steps of enzyme reactions and colorimetric procedure. The values obtained by this method are satisfactorily correlated with those obtained by the dinitrophenylhydrazine method for d-amino acid oxidase activity and the ultraviolet method for urate oxidase activity and showed good reproducibility and accuracy. It is considered that the method can be useful as a method of activity determination for studying enzyme kinetics and the reaction mechanism.     

A new method for isolation of polyamines from animal tissues

A new method for isolation of polyamines from tissues was developed and compared with the butanol extraction method which has been widely used for quantitative determination of polyamines. In the new method protein-free tissue extracts are applied to a small Dowex-50 column. The column is washed with appropriate buffers to remove ninhydrin-positive contaminants and the polyamines are eluted. With this method, the overall recovery of polyamines, after separation by paper electrophoresis and subsequent colorimetric determination with ninhydrin, is always over 90% (average 95%). This method is much better than the butanol method, which gives variable recoveries of 70–90%. The new method also has the advantages over the butanol method that the isolated polyamines are purer and the procedure is simpler.