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.     

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。     

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。     

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。     

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.     

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.     

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.     

A centrifugation method for determining the fresh weight of aquatic macrophytes

A centrifugation method to remove the surface water from five species of aquatic macrophytes of various morphologies is described and compared with the standard blotting method. The centrifugation method is up to twice as fast and up to three times more accurate than the blotting method. It works particularly well will plants of complex morphology and is less damaging to delicate plants than the blotting method. Errors in fresh weight determination between workers are also eliminated. Repeated centrifugation of plants, at 3-day intervals, was no more deleterious to their growth than the blotting 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.     

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。     

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.     

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.     

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.     

啮齿动物的巢区面积估算法

巢区(Home range)是动物在其巢附近进行取食、生殖、育幼等日常活动的区域(Burt 1940)。标志流放法是应用最广的调查啮齿动物巢区的方法,尤其是按方格式布笼。但对同一野外调查结果,由于估算方法不同,巢区估算值相差很大,并且至今尚无学者提出一致公认的估算法。1980年5-10月,我们在青海省门源县的高寒草甸生态系统定位站调查根田鼠的巢区,按多种估算法对同一批实际调查结果估计了巢区面积,并对结果进行了分析比较,检查其特点和优缺点,并提出修正平均值法,作为我们今后讨论根田鼠巢区动态的基础。 对方格式布笼的调查结果进行巢区的估算方法,基本上分二大类,图形法和概率性模型法。图形法是按照捕点分布划出巢区,并直接求出巢区面积,如最小面积法,包括或不包括周边地带法,最大距离法和复合散布图法。     

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.     

Modified histogram subtraction technique for analysis of flow cytometry data

Analysis of flow cytometry histogram data by the subjective selection of an integration window can be a tedious and time-consuming task and is often inaccurate. A new method for automated calculation of the percent positive from immunofluorescence histograms is presented. This new method is a modification of the currently used method of channel-by-channel histogram subtraction. Its accuracy is compared to that of the channel-by-channel histogram subtraction method and to another currently used automated method, which selects an integration window by finding the channels that contain the most fluorescent 2% of a control histogram. The new histogram subtraction method is objective, easy to use, and is more accurate than other currently used automated analysis methods. PASCAL source code is given for each method of analysis.     

Utilization of mixtures of carbon compounds by yeasts

As a tool for the classification of yeasts a method is presented for determining the aerobic utilization of each of 28 carbon compounds distributed over 4 mixtures containing respectively 10, 7, 7 and 4 of these compounds. Paper chromatography is used to follow the eventual disappearance of each individual carbon compound from the medium. This method is compared to the well-known standard method where a growth response to singly offered compounds in liquid medium is used for biochemical characterization. The proposed method has two advantages: results are obtained more rapidly and with less work, and the paper-chromatographic method may reveal a time sequence of utilization. Both the new method and the established standard method were applied to eight yeasts. Although the backgrounds are different, the experimental results were similar. The method presented is suitable for the differentiation of species as well as of strains within one species. It should be considered for use in taxonomy.     

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.     

改进的系统发育谱算法在蛋白质功能注释中的应用

系统发育谱方法是目前研究较多的一种基于非同源性的生物大分子功能注释方法。针对现有算法存在的一些缺陷,从两个方面对该方法做了改进：一是构造基于权重的系统发育谱;二是采用改进的聚类算法对发育谱的相似性进行分析。从NCBI上下载100条Escherichia coli K12蛋白质作为实验数据,分别使用改进的算法和经典的层次聚类算法、K均值聚类算法对相似谱进行分析。结果显示,提出的改进算法在对相似谱聚类的精确度上明显优于后两种聚类算法。