群落排表分类的两种数学方法

本文描述两种执行群落排表分类的数学方法:X²分类法和信息熵分类法,并以德国西北部草地数据为例进行了应用和分析。结果表明这两个方法都是有效的群落排表分类方法,它们所排的群落表可直接地反映群落类型和种类组成之间的关系,体现了Braun-Blanquet传统排表法的特点。     

New surface contacts formed upon reductive lysine methylation: Improving the probability of protein crystallization

Surface lysine methylation (SLM) is a technique for improving the rate of success of protein crystallization by chemically methylating lysine residues. The exact mechanism by which SLM enhances crystallization is still not clear. To study these mechanisms, and to analyze the conditions where SLM will provide the optimal benefits for rescuing failed crystallization experiments, we compared 40 protein structures containing N,N-dimethyl-lysine (dmLys) to a nonredundant set of 18,972 nonmethylated structures from the PDB. By measuring the relative frequency of intermolecular contacts (where contacts are defined as interactions between the residues in proximity with a distance of 3.5 Å or less) of basic residues in the methylated versus nonmethylated sets, dmLys-Glu contacts are seen more frequently than Lys-Glu contacts. Based on observation of the 10 proteins with both native and methylated structures, we propose that the increased rate of contact for dmLys-Glu is due to both a slight increase in the number of amine-carboxyl H-bonds and to the formation of methyl C–H···O interactions. By comparing the relative contact frequencies of dmLys with other residues, the mechanism by which methylation of lysines improves the formation of crystal contacts appears to be similar to that of Lys to Arg mutation. Moreover, analysis of methylated structures with the surface entropy reduction (SER) prediction server suggests that in many cases SLM of predicted SER sites may contribute to improved crystallization. Thus, tools that analyze protein sequences and mark residues for SER mutation may identify proteins with good candidate sites for SLM.     

基于最大熵原理的浙江毛竹胸径分布及测量不确定度评定

应用最大熵原理构造了测树因子概率分布的统一模型,这样构造的模型具有明确的解析表达式,并能克服常用方法无法解释测树因子服从某种概率分布的真正原因,从而为测树因子统计分布建模提供了一种有效方法.使用1-3阶样本矩、1-4阶样本矩与1-5阶样本矩,用所构建的概率分布统一模型分别对浙江省域毛竹胸径分布分别作了仿真试验,结果表明当采用1-4阶样本矩时,仿真效果最好,而且比通过假设检验的Weibull分布仿真结果理想:(1)图形非常相似,对实测数据都能很好的模拟;(2)最大熵法的离差平方和为0.00018,Weibull分布的为0.00045[1].由于各种系统与非系统的原因,都会影响测量结果的准确性,对所构建的模型作了不确定度评定,表明结果具有很大的可靠性,测量结果的估计:7.85100,测量结果的标准不确定度:1.82710,置信概率:0.96020.     

基于生态足迹修正模型的江苏省海洋经济可持续发展分析

基于生态足迹的理论和方法,提出海洋生态足迹的概念,并根据江苏省海洋环境的特殊性,构建了渔业用海、交通运输用海、工程建筑用海、能源用海、滩涂5个海洋生态足迹子模型,采用改进熵值法确定5类用海的均衡因子,分析了2000-2008年江苏省海洋生态足迹和生态承载力.结果表明:2000-2008年间,江苏省人均海洋生态足迹增幅近7倍,从36.90 hm2上升到252.94 hm2;人均生态承载力从105.01 hm2增至185.49 hm2,呈平稳增长态势;2000年,江苏省海洋环境处于生态盈余状态,海洋经济呈弱可持续发展状态,2004年,海洋生态环境急剧恶化,生态赤字高达109660.5 hm2,海洋经济可持续能力下降.渔业用海的高生态足迹是造成江苏省海洋生态赤字的主要原因,滩涂是维持江苏省海洋经济可持续发展的重要后备资源.     

细胞寒害的热力学熵理论(Ⅱ)──超熵产生作为寒害稳定性判据的理论研究

本文从物质和能量交换的角度,运用非平衡态热力学超熵产生理论,分析了寒害定态的稳定性,并建立了超熵产生判据．理论分析所得的结论与实验结果基本相符．     

一种新的蛋白质结构类预测方法

基于氨基酸的16种分类模型,给出蛋白质序列的派生序列,进而结合加权拟熵和LZ复杂度构造出34维特征向量来表示蛋白质序列。借助于贝叶斯分类器对同源性不超过25%的640数据集进行蛋白质结构类预测,准确度达到71.28%。     

中国柯属5种资源植物潜在地理分布及其对气候变化的响应

利用最大墒模型和地理信息系统软件对柯属（Lithocarpus）5种资源植物在我国的适宜分布区进行了定量预测,并对未来不同气候情景下其分布区的变化进行了分析。结果显示：木姜叶柯（L.litseifolius（Hance）Chun.）在我国秦岭淮河以南广泛分布,短尾柯（L.brevicaudatus（Skan）Hay.）主要分布在我国亚热带中东部区域;木姜叶柯在未来气候（2061-2080年）RCP2.6、RCP8.5两种情景下适生区面积分别减少了5.1%和3.0%,而短尾柯却分别增加了0.5%和1.5%。白柯（L.dealbatus（Hook.f.et Thoms.ex DC.）Rehd.）适宜区主要分布在云南北部、四川南部,烟斗柯（L.corneus（Lour.）Rehd.）主要分布在两广省份的南亚热带地区。白柯和烟斗柯在RCP2.6情景下适生区面积分别减少了12.1%和17.8%,在RCP8.5情景下分别减少了3.5%和15.9%,这两个种的适宜区面积减少较多。厚斗柯（L.elizabethae（Tutch.）Rehd.）主要分布于广西,在两种情景下适宜区面积分别增加了7.3%和6.3%。研究结果表明,由于分布区存在差异,同属不同物种的未来分布对气候变化的响应不同。     

Toward rational protein crystallization: A Web server for the design of crystallizable protein variants

Growing well-diffracting crystals constitutes a serious bottleneck in structural biology. A recently proposed crystallization methodology for "stubborn crystallizers" is to engineer surface sequence variants designed to form intermolecular contacts that could support a crystal lattice. This approach relies on the concept of surface entropy reduction (SER), i.e., the replacement of clusters of flexible, solvent-exposed residues with residues with lower conformational entropy. This strategy minimizes the loss of conformational entropy upon crystallization and renders crystallization thermodynamically favorable. The method has been successfully used to crystallize more than 15 novel proteins, all stubborn crystallizers. But the choice of suitable sites for mutagenesis is not trivial. Herein, we announce a Web server, the surface entropy reduction prediction server (SERp server), designed to identify mutations that may facilitate crystallization. Suggested mutations are predicted based on an algorithm incorporating a conformational entropy profile, a secondary structure prediction, and sequence conservation. Minor considerations include the nature of flanking residues and gaps between mutation candidates. While designed to be used with default values, the server has many user-controlled parameters allowing for considerable flexibility. Within, we discuss (1) the methodology of the server, (2) how to interpret the results, and (3) factors that must be considered when selecting mutations. We also attempt to benchmark the server by comparing the server's predictions with successful SER structures. In most cases, the structure yielding mutations were easily identified by the SERp server. The server can be accessed at http://www.doe-mbi.ucla.edu/Services/SER.     

Solute complexation degree with human serum albumin: biochromatographic approach

A mathematical model was developed for the study of the D,L-dansylamino acid retention mechanism in reversed-phase liquid chromatography using a C18 column as a stationary phase and human serum albumin (HSA) as an eluent modifier. The solute retention factor is dependent on the HSA concentration in the eluent as well as the binding constant of the guest-HSA complex. A determination of the degree of complexation n(c) (the percent of the complexed guest) could be carried out. Different Van 't Hoff plot shapes of the degree of complexation were observed with different eluent pH, confirming a change in the solute complexation mechanism for physiological pH (between 7-7.5). Enthalpy-entropy compensation was also analysed in relation to this mathematical model to confirm the solute complexation behavior with HSA. These results finally confirmed that at physiological pH and temperature (approximately 35 degrees C) values the HSA was in a favorable structural conformation for its binding with a great majority of drugs.