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。     

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。     

酵母双杂交相关方法的改良及应用

对酵母双杂交实验过程中较为耗时的阳性克隆鉴定过程进行改进,以期建立一种快速有效的鉴定方法。分别采用液氮冻融法、超声破碎法、渗透压破壁法以及煮沸裂解法裂解酵母细胞,获得质粒作为PCR模板,直接测序鉴定筛选到的相互作用蛋白。以液氮冻融法和超声破碎法裂解细胞获得的质粒为模板进行PCR,得到特异的产物,测序鉴定结果明确,与经典的鉴定方法相比效果相当,但更加经济快捷;而渗透压破壁法和煮沸裂解法则效果不好。说明前两种方法可代替常规方法用于阳性克隆的鉴定,从而加快酵母双杂交实验中大量阳性克隆的筛查工作。     

Measurement of penicillin acylase and cephalosporin acylase in fermentation broths

Summary The p-dimethylamino-benzaldehyde method of Bomstein and Evans, the ninhydrin method of Marrelli and the new p-dimethyl-amino-benzaldehyde method of Kornfeld were evaluated for analysis of penicillin-V acylase and cephalosporin-V acylase in fermentation broths. The ninhydrin method was the method of choice for cephalosporin-V acylase, whereas the Kornfeld method had certain advantages with respect to penicillin-V acylase.     

Archaeological Inference and Inductive Confirmation

The limitations of the hypothetico-deductive (H-D) method of inductive confirmation are described, and an alternate method, the hypothetico-analog (H-A) method is described in detail. The H-A method can be characterized as a modified and supplemented form of the simple H-D method, and is proposed as being more appropriate for archaeological inference. Aspects of the H-A method that are given particular attention include the establishment of boundary conditions for reference classes, plausibility considerations, multiple working hypotheses, bridging arguments, and criteria for selecting alternative hypotheses . [scientific method, archaeological inference, hypothetico-analog method, inductive confirmation]     

一种利用Profile-1生物发光仪快速测定土壤中微生物量的改良方法

开发了一种利用Profile-1生物发光仪测定土壤中微生物量的改良方法,并以此方法分别测定了标准大肠杆菌茵液以及3种不同类型的土壤(九段沙湿地土壤,崇明东滩大田土壤和崇明实验地改良土壤)的微生物量,并将结果与Profile-1生物发光仪自带的标准分析方法以及传统的菌落计数法进行比较。结果显示,改良的ATP提取方法(BAB改良分析法)和Profile-1生物发光仪自带的标准分析方法都可用于液体样品中微生物量的测定,其灵敏度和准确度无显著差异(P0.05)。但在测定土壤样品时,菌落计数法测定结果大约占BAB改良分析法测定结果的1%～5%,占Profile-1生物发光仪自带的标准分析方法的测定结果的22%～99%。这表明在分析土壤样品时,BAB改良分析法较Profile-1生物发光仪自带的标准分析方法的ATP提取效率更高,可显著提高仪器检测土壤样品的灵敏度和可靠性,因此可有效应用于各类土壤的微生物量的监测,为土壤环境监控提供微生物量的可靠数据。     

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。     

An improved method of sample preparation on AnchorChip targets for MALDI-MS and MS/MS and its application in the liver proteome project

An improved method for sample preparation for MALDI-MS and MS/MS using AnchorChip targets is presented. The method, termed the SMW method (sample, matrix wash), results in better sensitivity for peptide mass fingerprinting as well as for sequencing by MS/MS than previously published methods. The method allows up-concentration and desalting directly on the mass spectrometric target and should be amenable for automation. A draw back caused by extensive oxidation of methionine and tryptophan in the SMW method can be alleviated by the addition of n-octyl glucopyranoside and DTT to the sample solution. The method was validated for protein identification from a 2-DE based liver proteome study. The SMW method resulted in identification of many more proteins and in most cases with a better score than the previously published methods.     

Analysis of qPCR data by converting exponentially related Ct values into linearly related X0 values

A common method for calculating results from qPCR experiments is the comparative Ct method, also called the 2(-ΔΔCt) method. However, several assumptions are included in the 2(-ΔΔCt) method and standard statistical analyses are not directly applicable. Here, we describe a different method, the X(0) method, for result calculations and statistical analysis from qPCR experiments. The X(0) method differs from the 2(-ΔΔCt) method by introducing a conversion of the exponentially related Ct values into linearly related X(0) values, which represent the amount of starting material in a qPCR experiment. Results calculated by the X(0) method are illustrated for qPCR experiments with technical and biological replicates, including procedures to calculate standard deviations. Incorporation of primer efficiencies in calculations by the X(0) method is also described. Altogether, the X(0) method constitutes a very simple and accurate alternative to the 2(-ΔΔCt) method for result calculations from qPCR data.     

农杆菌质粒DNA的间接酶切鉴定

采用常规手段提酶切鉴定法,与普通大肠杆菌质粒小量抽提试剂盒提取农杆菌质粒酶切鉴定法(简称试剂盒法)和农杆菌质粒反导大肠杆菌间接酶切鉴定法(简称间接法)进行对比,发现本试验创新的试剂盒法和间接法可轻松做酶切鉴定,可为农杆菌质粒DNA提取经验不足者参考.     

Validation of a questionnaire method for estimating extent of menstrual blood loss in young adult women.

The objective of this study was to validate two indirect methods for estimating the extent of menstrual blood loss against a reference method to determine which method would be most appropriate for use in a population of young adult women. Thirty-two women aged 18 to 29 years (mean +/- SD; 22.4 +/- 2.8) were recruited by poster in Dunedin (New Zealand). Data are presented for 29 women. A recall method and a record method for estimating extent of menstrual loss were validated against a weighed reference method. Spearman rank correlation coefficients between blood loss assessed by Weighed Menstrual Loss and Menstrual Record was rs = 0.47 (p = 0.012), and between Weighed Menstrual Loss and Menstrual Recall, was rs = 0.61 (p = 0.001). The Record method correctly classified 66% of participants into the same tertile, grossly misclassifying 14%. The Recall method correctly classified 59% of participants, grossly misclassifying 7%. Reference method menstrual loss calculated for surrogate categories demonstrated a significant difference between the second and third tertiles for the Record method, and between the first and third tertiles for the Recall method. The Menstrual Recall method can differentiate between low and high levels of menstrual blood loss in young adult women, is quick to complete and analyse, and has a low participant burden.     

洗发、护发化妆品微生物检查方法学研究

为提高化妆品潜在微生物的阳性检出率,建立洗发、护发类化妆品微生物限度和控制菌检查方法。采用常规法、培养基稀释法、薄膜过滤法对4种洗发、护发类化妆品进行微生物限度与控制菌方法学研究。结果显示,飘柔长效柔顺滋养洗发露、海飞丝去屑洗发露、飘柔人参滋养润发精华素、力士密集滋养修复-发膜级精华素菌落总数检测方法分别为0.2 m L/皿法、800 m L/膜法、0.5 m L/皿法和300 m L/膜法;霉菌及酵母菌检测方法分别为300 m L/膜法、300 m L/膜法、1 m L/皿法和1 m L/皿法;除海飞丝去屑洗发露采用培养基稀释法,其他均采用常规法进行控制菌检查。建议在化妆品微生物检验前应进行微生物方法研究,从而提高化妆品"潜在"病原菌的检出率。     

A weighted test-area method for calculating surface tension

In this paper, we propose a weighted test-area method to calculate surface tension by incorporating the weighting factor from the Bennett method into the free energy perturbation scheme of the test-area method. This new method was tested by comparing against the results of the Bennett and test-area methods for simulations of square well (SW), Lennard-Jones and point charge fluid models. It is seen that the new method is accurate for all these simulations, giving the same results as the Bennett method, in contrast to the test-area method which cannot calculate the surface tension of a SW fluid. The new method converges as quickly, on the basis of computational time required, as the test-area method and almost twice as quickly as the Bennett method. This combination of speed and accuracy means that the weighted test-area method should be used in preference to the test-area method and Bennett method for surface tension and other macroscopic thermodynamic quantities that can be calculated through perturbation methods.     

4种黑曲霉基因组DNA提取方法的比较

目的:筛选适合提取曲霉DNA的方法.方法:比较2个菌落培养时间段(3d内和10d左右)提取DNA质量的差异;运用氯化苄法、石英砂+CTAB法、Biospin法和微波法分别提取黑曲霉基因组DNA,然后用直接电泳、浓度测定、PCR扩增等方法比较所提DNA的浓度和质量.结果:培养3d内的菌落提取的DNA纯度较高,无需纯化即可用于后续实验;4种方法制备的DNA均可用于PCR等后续实验,其中以石英砂+CTAB法提取的DNA纯度好,产率最高.结论石英砂+CTAB法是一种适用于曲霉DNA提取的简便方法.     

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.     

Evaluation of real-time PCR vs automated ELISA and a conventional culture method using a semi-solid medium for detection of Salmonella

AIMS: Evaluation of iQ-Check PCR Salmonella for Salmonella detection in artificially and naturally contaminated food and environmental field samples. METHODS AND RESULTS: Artificially contaminated samples (poultry meat and ground red meat) subjected to cold- and freeze-stress, and 120 naturally contaminated samples (swabs and meat) were tested for Salmonella using the diagnostic semi-solid Salmonella medium (DIASALM) method, the Vidas assay and the iQ-Check PCR assay after 24 h enrichment in buffered peptone water. CONCLUSIONS: Both the iQ-Check PCR and the Vidas assay provide a rapid and user friendly screening method for detection of Salmonella. False negative samples were obtained for the inoculated samples using both the iQ-Check PCR assay and the Vidas method when Salmonella cells were severely stressed. In total 45 of 120 naturally contaminated field samples showed Salmonella positive using the DIASALM method. The agreement percentage with the DIASALM method was respectively 92% for the iQ-Check PCR and 95% for the Vidas method. SIGNIFICANCE AND IMPACT OF THE STUDY: False-negative samples were obtained for the inoculated samples using both the iQ-Check PCR assay and the Vidas method when Salmonella cells were severely stressed, e.g. freezing at -18 degrees C for 7 days. Of the 120 naturally contaminated field samples 45 showed Salmonella positive using the DIASALM method. The agreement percentage with the DIASALM method was 92% for the iQ-Check PCR and 95% for the Vidas method respectively.     

Rapid high-performance liquid chromatographic method for Vitamin C determination in human milk versus an enzymatic method

Vitamin C is an antioxidant that can be considered a possible biomarker of oxidative stability in human milk. A high-performance liquid chromatographic method was developed and validated for determining the total Vitamin C (ascorbic acid and dehydroascorbic acid) and ascorbic acid levels in human milk. This method was then compared with an enzymatic method (a Colorimetric technique) for quantifying ascorbic acid levels. Repeatability and reproducibility were acceptable for all methods. However, the high-performance liquid chromatography (HPLC) technique provided more satisfactory results than the enzymatic method due to this last method detected 37% less ascorbic acid and does not determine the total Vitamin C because of the enzymatic method cannot reduce the dehydroascorbic acid (DHA) to ascorbic acid. Furthermore, the HPLC method has the added advantages that it requires less reagents and material, and is simpler and less time consuming than the enzymatic method. In conclusion, the drawbacks of this enzymatic method would justify its substitution for a HPLC method.     

药用植物艾纳香基因组DNA提取方法研究

以药用植物艾纳香为研究对象,以-20℃保存、4℃保存、室温自然干燥和硅胶干燥四种样品保存方式,并采用SDS法、CTAB法、SDS-CTAB法和改良CTAB法4种不同的基因组DNA提取方法进行了对比试验,以期建立艾纳香的较好的样品保存方法和基因组DNA提取方法。结果表明,-20℃保存是艾纳香的较理想的样品保存方式;改良CTAB法是艾纳香基因组DNA提取较适宜的方法,该方法提取的DNA经紫外检测,其A_(260)/A_(280)为1.8左右,明显优于SDS法(1.1～1.5)、CTAB法(1.2～1.5)和SDS-CTAB法(1.4～1.6),琼脂糖凝胶电泳、酶切检测和PCR扩增也得出了同样的结论。     

The use of an enzymatic kit to measure plasma creatinine in the mouse and three other species

Plasma creatinine concentrations were determined in mice, rats, dogs and humans using a kinetic alkaline picrate method and an enzymatic method with a centrifugal analyser. Lower creatinine values were obtained for all four species using the enzymatic method, but the differences between methods were greater for mice and rats. Removal of creatininase from the enzymatic method reagents gave proportionally higher values for non-creatinine chromogens in mice and rats. A single enzymatic method was not specific for creatinine when used for these species.