黄猄蚁对橡胶盔蚧种群消长的影响

调查西双版纳地区黄猄蚁OecophyllasmaragdinaFabricius对橡胶盔蚧Parasaissetianigra(Nietner)种群数量和寄生蜂的影响。结果表明:黄猄蚁对橡胶盔蚧种群消长及寄生蜂均有影响。"有蚂蚁"枝条上介壳虫种群数量显著高于"无蚂蚁"枝条。"有蚂蚁"枝条介壳虫死亡率和寄生蜂都显著低于"无蚂蚁"枝条。说明黄猄蚁的存在影响了橡胶树介壳虫的种群繁殖率和死亡率。建议在今后综合防治中,充分利用蚂蚁与橡胶树介壳虫关系。通过驱逐橡胶树上的蚂蚁来有效遏制介壳虫的发生。     

A mixed strategy model for the emergence and intensification of social learning in a periodically changing natural environment

Based on a population genetic model of mixed strategies determined by alleles of small effect, we derive conditions for the evolution of social learning in an infinite-state environment that changes periodically over time. Each mixed strategy is defined by the probabilities that an organism will commit itself to individual learning, social learning, or innate behavior. We identify the convergent stable strategies (CSS) by a numerical adaptive dynamics method and then check the evolutionary stability (ESS) of these strategies. A strategy that is simultaneously a CSS and an ESS is called an attractive ESS (AESS). For certain parameter sets, a bifurcation diagram shows that the pure individual learning strategy is the unique AESS for short periods of environmental change, a mixed learning strategy is the unique AESS for intermediate periods, and a mixed learning strategy (with a relatively large social learning component) and the pure innate strategy are both AESS's for long periods. This result entails that, once social learning emerges during a transient era of intermediate environmental periodicity, a subsequent elongation of the period may result in the intensification of social learning, rather than a return to innate behavior.     

五种温带森林土壤微生物生物量碳氮的时空格局

土壤微生物是森林生态系统中的重要分解者,在碳和氮循环中起着重要作用,同时也是对环境变化的敏感指示者。采用氯仿熏蒸浸提法测定了我国东北地区5种温带森林土壤微生物生物量碳(Cmic)和氮(Nmic)的季节动态及其在土壤中的垂直变化。结果表明:林型之间Cmic和Nmic差异显著(P0.01)。落叶松林、红松林、蒙古栎林、杨桦林、硬阔叶林的Cmic的变化范围依次为:278937mgkg-1、2181020mgkg-1、313891mgkg-1、5101092mgkg-1、4401911mgkg-1;其Nmic的变化范围依次为:1872mgkg-1、18103mgkg-1、2495mgkg-1、43125mgkg-1、40208mgkg-1。所有林型的Cmic和Nmic均随土壤深度的增加而下降。Cmic和Nmic基本上呈现出生长季开始之前下降、生长季结束时上升、其中出现12个峰值的季节变化格局,但峰值大小和出现时间随林型和土壤层次而变。010cm土层的Cmic和Nmic季节变化较大。Cmic和Nmic与凋落叶量、土壤有机碳含量和土壤总氮含量呈显著正相关。Cmic与土壤含水量呈正相关,而与土壤温度呈负相关。不同林型凋落物数量和组成、土壤理化性质的差异是导致其土壤微生物生物量时空格局差异的主要因素。     

Molecular dynamics of the FixJ receiver domain: movement of the beta4-alpha4 loop correlates with the in and out flip of Phe101

FixJ is a two-domain response regulator involved in nitrogen fixation in Sinorhizobium meliloti. Recent X-ray characterization of both the native (unphosphorylated) and the active (phosphorylated) states of the protein identify conformational changes of the beta4-alpha4 loop and the conserved residue Phe101 as the key switches in activation. These structures also allowed investigation of the transition between conformations of this two-component regulatory receiver domain by molecular dynamics simulations. The path for the conformational change was studied with a distance constraint directing the system from one state to the other. The simulations provide evidence for a correlation between the conformation of the beta4-alpha4 loop and the orientation of the residue Phe101. A model presenting the sequence of events during the activation/deactivation process is discussed.     

Reduction of protein disulfide isomerase results in open conformations and stimulates dynamic exchange between structural ensembles

Human protein disulfide isomerase (PDI) is an essential redox-regulated enzyme required for oxidative protein folding. It comprises four thioredoxin domains, two catalytically active (a, a’) and two inactive (b, b’), organized to form a flexible abb’a’ U-shape. Snapshots of unbound oxidized and reduced PDI have been obtained by X-ray crystallography. Yet, how PDI’s structure changes in response to the redox environment and inhibitor binding remains controversial. Here, we used multiparameter confocal single-molecule FRET to track the movements of the two catalytic domains with high temporal resolution. We found that at equilibrium, PDI visits three structurally distinct conformational ensembles, two “open” (O₁ and O₂) and one “closed” (C). We show that the redox environment dictates the time spent in each ensemble and the rate at which they exchange. While oxidized PDI samples O₁, O₂, and C more evenly and in a slower fashion, reduced PDI predominantly populates O₁ and O₂ and exchanges between them more rapidly, on the submillisecond timescale. These findings were not expected based on crystallographic data. Using mutational analyses, we further demonstrate that the R300-W396 cation-π interaction and active site cysteines dictate, in unexpected ways, how the catalytic domains relocate. Finally, we show that irreversible inhibitors targeting the active sites of reduced PDI did not abolish these protein dynamics but rather shifted the equilibrium toward the closed ensemble. This work introduces a new structural framework that challenges current views of PDI dynamics, helps rationalize its multifaceted role in biology, and should be considered when designing PDI-targeted therapeutics.     

Setting up and running molecular dynamics simulations of membrane proteins

Molecular dynamics simulations have become a popular and powerful technique to study lipids and membrane proteins. We present some general questions and issues that should be considered prior to embarking on molecular dynamics simulation studies of membrane proteins and review common simulation methods. We suggest a practical approach to setting up and running simulations of membrane proteins, and introduce two new (related) methods to embed a protein in a lipid bilayer. Both methods rely on placing lipids and the protein(s) on a widely spaced grid and then 'shrinking' the grid until the bilayer with the protein has the desired density, with lipids neatly packed around the protein. When starting from a grid based on a single lipid structure, or several potentially different lipid structures (method 1), the bilayer will start well-packed but requires more equilibration. When starting from a pre-equilibrated bilayer, either pure or mixed, most of the structure of the bilayer stays intact, reducing equilibration time (method 2). The main advantages of these methods are that they minimize equilibration time and can be almost completely automated, nearly eliminating one time consuming step in MD simulations of membrane proteins.     

农田周围生态保留带中普通田鼠的种群生态学：种群数量动态及结构

于2003年5月~2004年11月,采用标志重捕法对栖息在生态保留带的普通田鼠种群结构和数量动态进行了跟踪研究。结果表明,两年中种群密度夏季最大分别达到410个体/hm2和641个体/hm2,春季最少分别达到166个体/hm2和153个体/hm2,种群数量从7月份开始增长,8月份种群密度减少并于11月份开始重新增长。种群中雌性个体数量比较多,雌性在种群中的居留时间较长,同时存活率比雄性高,这导致种群数量的季节变化。种群周转率比较高,在两个捕鼠期间种群中的80%个体被更新,这表明普通田鼠在生态保留带中的活动非常频繁,不断与周围的其他种群进行交流,提高了种群对环境的适应能力。种群中雌雄个体的巢区之间没有年间变化,活动巢区比较小,巢区长度2003年平均为11 m,最长为37.5 m,2004年平均为13 m,最长为52 m。Pearson相关指数表明种群数量和生态保留带年龄、覆盖率和高度之间没有相关性。     

Congeneric but still distinct: how closely related trypsin ligands exhibit different thermodynamic and structural properties

A congeneric series of benzamidine-type ligands with a central proline moiety and a terminal cycloalkyl group—linked by a secondary amine, ether, or methylene bridge—was synthesized as trypsin inhibitors. This series of inhibitors was investigated by isothermal titration calorimetry, crystal structure analysis in two crystal forms, and molecular dynamics simulations. Even though all of these congeneric ligands exhibited essentially the same affinity for trypsin, their binding profiles at the structural, dynamic, and thermodynamic levels are very distinct. The ligands display a pronounced enthalpy/entropy compensation that results in a nearly unchanged free energy of binding, even though individual enthalpy and entropy terms change significantly across the series. Crystal structures revealed that the secondary amine-linked analogs scatter over two distinct conformational families of binding modes that occupy either the inside or of the outside the protein's S3/S4 specificity pocket. In contrast, the ether-linked and methylene-linked ligands preferentially occupy the hydrophobic specificity pocket. This also explains why the latter ligands could only be crystallized in the conformationally restricting closed crystal form whereas the derivative with the highest residual mobility in the series escaped our attempts to crystallize it in the closed form; instead, a well-resolved structure could only be achieved in the open form with the ligand in disordered orientation. These distinct binding modes are supported by molecular dynamics simulations and correlate with the shifting enthalpic/entropic signatures of ligand binding. The examples demonstrate that, at the molecular level, binding modes and thermodynamic binding signatures can be very different even for closely related ligands. However, deviating binding profiles provide the opportunity to optimally address a given target.     

基于信息熵的我国日降水量随机性和时空差异性

我国日降水过程呈现明显的随机性与时空差异性,如何准确认识其时空变化规律对洪涝灾害防治等实际工作的影响具有重要意义.本文基于1961—2013年全国520个气象站点的日降水数据,选用信息熵指标研究我国日降水量的随机性.结果表明:研究期间,我国东南地区日降水量的随机性大于西北地区,且不同等级日降水量随机性的空间分布存在差异,小雨(降雨量0.1~10 mm,P_0)等级日降水量随机性较大,差异不明显,中雨(10~25 mm,P₁₀)、大雨(25~50 mm,P₂₅)等级日降水量随机性最大,差异明显,暴雨及以上(≥50 mm,P₅₀)等级日降水量随机性最小,差异最明显.整体上,日降水的信息熵值呈上升趋势,表明全球气候变化下我国大部分地区日降水量的随机性增大,尤其表现为极端暴雨发生的频次明显增大.日降水信息熵的空间分布及其变化趋势可以很好地综合反映我国日降水量随机性的空间分布格局,可为洪涝灾害防治、农业规划布局、生态环境规划等提供科学依据.