约束线方法在生态学研究中的应用

生态系统格局和过程往往受到多个因子的共同影响, 故此反映两个生态学变量相互关系的散点图常常会表现为有边界的散点云。基于数据均值或中值分析的传统统计方法不适用于散点云数据的分析。散点云所表征的不是两变量之间的相关关系, 而是限制作用关系。约束线(包络)方法为提取散点云边界、理解限制变量对响应变量的作用, 以及预测响应变量的潜在最大值提供了有效手段。该文对应用约束线方法研究生态学问题所取得的成果进行总结与归纳, 介绍了约束线概念的发展历程、提取方法, 从物种分布、种群行为及作物产量优化三个方面总结了约束线方法的优点及适用性, 概述了当前约束线方法应用研究面临的问题与挑战, 指出约束线方法应结合其他统计方法, 实现对生态过程的准确理解, 此外, 还应重视约束线方法的尺度依赖性。最后, 该文展望了约束线方法在研究生态系统服务关系和土地系统优化等方面的应用前景。     

早熟砂梨ISSR-PCR反应体系的建立与优化

以我国南方主栽的早熟砂梨品种‘翠冠’Pyrus pyrifolia ‘Cuiguan’为材料,对ISSR技术体系中的模板DNA浓度、Taq DNA聚合酶用量、引物浓度、dNTP浓度、Mg2+浓度、退火温度、PCR循环数等7个主要因素进行优化和筛选,建立了适合早熟砂梨的ISSR-PCR反应体系。最终反应体系为20 μL体系中10×PCR buffer（不含Mg2+）2 μL,模板DNA浓度60 ng,TaqDNA聚合酶0.75 U,引物浓度1 μmol/L,dNTP浓度90 μmol/L,Mg2+浓度2.25 mmol/L。扩增程序为：预变性94 ℃ 5 min,变性94 ℃ 45 s,退火45 s,72 ℃延伸1 min,共42个循环,然后72 ℃再延伸10 min,4 ℃保存,用1.5%琼脂糖凝胶电泳检测多态性。     

Optimization and elucidation of interactions between ammonium, nitrate and phosphate inCentella asiatica cell culture using response surface methodology

The effects of macronutrients (NO₃ ⁻, NH₄ ⁺ and PO₄ ³⁻) on cell growth and triterpenoids production inCentella asiatica cell suspension cultures were analyzed using the Box-Behnken response surface model experimental design. In screening and optimization experiments, PO₄ ³⁻ as a single factor significantly influenced cell growth where increasing the phosphate level from 0.1 to 2.4 or 2.6 mM, elevated cell growth from 3.9 to 14–16 g/L. The optimum values predicted from the response surface model are 5.05 mM NH₄ ⁺, 15.0 mM NO₃ ⁻ and 2.6 mM PO₄ ³⁻, yielding 16.0 g/L cell dry weight with 99% fitness to the experimental data. While the NH₄ ⁺-NO₃ ⁻ interaction influenced cell growth positively in the optimization experiment, NH₄ ⁺ and NO₃ ⁻ as single factors; and interactions of NO₃ ⁻-PO₄ ³⁻, NH₄ ⁺-PO₄ ³⁻ and NH₄ ⁺-NO₃ ⁻ were all negative in the screening experiment. Cell growth and the final pH level were positively affected by PO₄ ³⁻, but negatively affected by NH₄ ⁺ and NH₄ ⁺-PO₄ ³⁻ interactions. The different effects of factors and their interactions on cell growth and final pH are influenced by a broad or narrow range of macronutrient concentrations. The productions of triterpenoids however were lower than 4 mg/g cell dry weight.     

皮下盘菌属及其近似类群RAPD-PCR反应条件的优化

以悬钩子皮下盘菌等总基因组DNA为皮下盘菌属(Hypodermade Not.)及其近似类群RAPD体系优化的模板,对模板DNA浓度、dNTPs浓度、Mg2+浓度、引物浓度、TaqDNA聚合酶浓度等反应体系以及退火温度和时间、延伸时间、循环次数等扩增程序条件进行优化,寻找出适合此类菌物RAPD-PCR反应的最佳反应体系和最佳扩增程序。     

核酸酶P1催化水解热变性DNA的研究

用桔青霉菌株IM0 2 (PenicilliumcitrinumIM0 2 )发酵制得的核酸酶P1催化水解热变性DNA ,在研究温度、底物浓度、pH、酶加入量等因素对水解结果的影响的实验基础上,通过正交实验获得最佳的工艺条件:温度5 8℃,pH6 5 ,DNA质量浓度4 0g/L ,酶加入量4 % ,脱氧核苷酸的得率92 %。在此基础上推导出其催化米氏常数Km=5 818×10 -2 g/L。     

Diverse metabolic model parameters generate similar methionine cycle dynamics

Parameter estimation constitutes a major challenge in dynamic modeling of metabolic networks. Here we examine, via computational simulations, the influence of system nonlinearity and the nature of available data on the distribution and predictive capability of identified model parameters. Simulated methionine cycle metabolite concentration data (both with and without corresponding flux data) was inverted to identify model parameters consistent with it. Thousands of diverse parameter families were found to be consistent with the data to within moderate error, with most of the parameter values spanning over 1000-fold ranges irrespective of whether flux data was included. Due to strong correlations within the extracted parameter families, model predictions were generally reliable despite the broad ranges found for individual parameters. Inclusion of flux data, by strengthening these correlations, resulted in substantially more reliable flux predictions. These findings suggest that, despite the difficulty of extracting biochemically accurate model parameters from system level data, such data may nevertheless prove adequate for driving the development of predictive dynamic metabolic models.     

Statistical cautions when estimating DEBtox parameters

DEBtox (Dynamic Energy Budget in toxicology) models have been designed to analyse various results from classic tests in ecotoxicology. They consist of a set of mechanistic models describing how organisms manage their energy, when they are exposed to a contaminant. Until now, such a biology-based modeling approach has not been used within the regulatory context. However, these methods have been promoted and discussed in recent guidance documents on the statistical analysis of ecotoxicity data. Indeed, they help us to understand the underlying mechanisms. In this paper, we focused on the 21 day Daphnia magna reproduction test. We first aimed to clarify and detail the model building process leading to DEBtox models. Equations were rederived step by step, and for some of them we obtained results different from the published ones. Then, we statistically evaluated the estimation process quality when using a least squares approach. Using both experimental and simulated data, our analyses highlighted several statistical issues related to the fitting of DEBtox models on OECD-type reproduction data. In this case, particular attention had to be paid to parameter estimates and the interpretation of their confidence intervals.     

Anthraquinones from in vitro root culture of <Emphasis Type="Italic">Morinda royoc</Emphasis> L.

Morinda royoc L. (Rubiaceae) root cultures were established for the production of anthraquinones (AQs). Three independent experiments were performed to evaluate the effects of different levels of indole-3-acetic acid (0–22.8 μM), culture duration (15–75 days) and subculture number (0–4). The following indicators were recorded: root fresh weight per Erlenmeyer and intracellular and extracellular AQ production. The experiments performed in this study allowed an increase of intracellular AQ content up to a maximum of 4.5 mg g⁻¹ of fresh mass, after 30 days of culture in a medium 5.7 μM of IAA. In addition, isolation and identification of seven AQs from M. royoc L. roots is described, one of them being reported for the first time for this species. The structures of isolated compounds were determined from ¹H-NMR data. To the best of our knowledge, this is the first report on AQ production from root culture of this plant.     

High-level expression of a truncated 1,3-1,4-β-<Emphasis Type="SmallCaps">d</Emphasis>-glucanase from <Emphasis Type="Italic">Fibrobacter succinogenes</Emphasis> in <Emphasis Type="Italic">Pichia pastoris</Emphasis> by optimization of codons and fermentation

1,3-1,4-β-d-glucanase is an important endoglycosidase in the brewing and animal feed industries. To achieve high-level expression of recombinant glucanase in Pichia pastoris, we designed sequences encoding the α-factor signal peptide from Saccharomyces cerevisiae and the truncated 1,3-1,4-β-d-glucanase from Fibrobacter succinogenes as a whole. The codons encoding the 52 amino acids of the signal peptide and 106 residues of the glucanase protein were optimized for expression in P. pastoris; 189 nucleotides were changed. The G + C content was adjusted to 48–49%, and AT-rich stretches were eliminated to avoid premature termination. The messenger ribonucleic acid secondary structure near the AUG start codon was also adjusted to ensure efficient translation; the resulting glucanase production was twofold higher compared with that achieved with gene structure optimization alone. We also propose a new fermentation strategy for the induction phase, in which 5/95% glycerol/methanol mixed feed was used in days 1–3 and 100% methanol was used on days 4–6. By comparison with methanol feed and glycerol/methanol-mixed feed alone, the yield of recombinant glucanase increased by 38.5 and 16.5%, respectively. The expressed optimized recombinant 1,3-1,4-β-d-glucanase constituted ~90% of the total secreted protein, reaching up to 3 g l⁻¹ in the medium.