油菜地上部干物质分配与产量形成模拟模型

利用油菜器官生长与发育进程及环境因子之间的定量关系,构建了基于分配指数的油菜地上部器官干物质分配动态模拟模型.各器官干物质分配指数随着生理发育时间而变化,基因型、播期、氮素及水分水平影响各器官干物质在地上部分配的大小.其中,氮素营养水平对绿色叶片干物质分配影响最大,氮素营养水平越高,绿色叶片分配指数越大;播期影响角果分配指数,晚播的角果分配指数高于早播.模型引入氮素营养指数、水分及播期影响因子来定量油菜各器官在实际生产条件下的分配强度,同时考虑了品种遗传特性的影响.通过不同品种氮肥处理试验建立模型,利用不同品种播期试验资料对模型进行了初步检验,表明模型具有较好的预测性和适用性.     

霜冻过程温光因子分析及模拟霜冻条件的建立

近年来霜冻对我国果树产业的影响越来越大, 建立科学的模拟霜冻程序对于加强果树霜冻基础研究十分必要。基于对大田霜冻天气的实际观测, 分析了自然霜冻在降温速度、低温极限、升温速度以及霜后光照条件方面的特点, 建立了用于实验室环境下的霜冻处理程序。结果表明, 霜冻发生时气温的变化主要包括降温、低温维持和升温3个阶段。降温和升温阶段气温的变化近似线性; 霜后一般伴随较强的光照。经研究确定模拟霜冻条件为: 黑暗环境下, 气温在30分钟内从室温(20°C)降到5°C, 在5°C维持30分钟, 之后以0.8°C·h ^-1的速度降到-2°C, 在-2°C维持2小时, 再以4.7°C·h ^-1的速度回升到5°C结束霜冻处理。霜冻处理后的恢复条件为气温16°C及光强800 μmol·m ^-2·s ^-1。     

基于土壤水分平衡的沙地草地最优植被覆盖率的研究

本文从土壤水分平衡出发,用动态仿真模型方法研究我国北方干旱半干旱沙地草地土壤不分平衡与立地条件,如坡度、坡向、土壤物理性状及植被覆盖率之间的关系。有如下初步结论和论点产生：（１）地表因植被的存在而形成的结皮对降水入渗到土壤中的阻滞作用几乎可以忽略。只有在坡度很大,瞬间降水强度很大时,结皮表面才可形成较大的迳流;（２）土壤水分的平衡随植被的覆盖率变化的情况取决于立地条件的差异,笼统地讲“植被覆盖率越     

冬小麦生育期农田尺度下土壤硝态氮淋失动态的数值模拟

在北京通州区永乐店田间试验的基础上 ,假设土壤由一系列不发生相互作用的一维土柱组成 ,根据实测的土壤有机质含量 ,假定土壤有机氮的矿化作用速率常数 (零级动力学 )和有机质含量成正比 ,运用 HYDRUS- 1D软件 ,分别就考虑和不考虑土壤有机氮的矿化速率的空间变异性这两种方案 ,对 2 0 0 0～ 2 0 0 1年冬小麦生长条件下农田尺度土壤氮素转化和硝态氮淋失规律进行了数值分析。两种方案的模拟结果表明 :考虑和不考虑土壤有机氮矿化速率的空间变异性对剖面 2 5 0 cm埋深处硝态氮淋失量的影响很小 ,其差异主要在于前者对土壤氮素的矿化量、固持及反硝化量、作物吸氮量的影响更大 ,其空间变异性高于不考虑矿化速率时的结果。剖面 2 5 0 cm埋深处平均的土壤水渗透量和累积硝态氮淋失量分别为 2 .2 5 mm、0 .0 0 984 m g/cm2 ,变异系数大于 1.4 6 ,属于强变异性。对模拟结果进行地统计学分析 ,结果表明 :剖面 2 5 0 cm埋深处的土壤水渗透量和硝态氮淋失量的半方差函数为纯块金形式 ,在空间上表现为相互独立。考虑有机氮矿化速率空间变异性时的土壤氮素净转化量、吸氮量均可用球状模型描述 ,其变程与土壤有机质含量的变程接近 ,约为 4 .7m;而不考虑有机氮矿化速率空间变异性时的土壤氮素净转化量用线性无基台值     

极低频率（ELF）磁场对细胞生长周期分布谱的影响及其机理的计算机模拟分析

测定在各种温度条件下和在ＥＬＦ（极低频率）磁场作用下细胞生长周期分布谱的变化。实验结果表明温度不仅能使周期分布谱的离散性发生改变,而且也能使谱的峰值产生位移,而ＥＬＦ磁场只能使周期分布谱的离散性发生变化,对谱的峰值没有显著影响。这一差异是由于温度和ＥＬＦ磁场对细胞生长产生影响的机理不同。用计算模拟不同机理对细胞生长周期分布谱的影响与我们早先提出的机理相吻合,即温度影响细胞内各种生长因子、生物离子的     

Dealing with uncertainty in landscape genetic resistance models: a case of three co‐occurring marsupials

Landscape genetics lacks explicit methods for dealing with the uncertainty in landscape resistance estimation, which is particularly problematic when sample sizes of individuals are small. Unless uncertainty can be quantified, valuable but small data sets may be rendered unusable for conservation purposes. We offer a method to quantify uncertainty in landscape resistance estimates using multimodel inference as an improvement over single model‐based inference. We illustrate the approach empirically using co‐occurring, woodland‐preferring Australian marsupials within a common study area: two arboreal gliders (Petaurus breviceps, and Petaurus norfolcensis) and one ground‐dwelling antechinus (Antechinus flavipes). First, we use maximum‐likelihood and a bootstrap procedure to identify the best‐supported isolation‐by‐resistance model out of 56 models defined by linear and non‐linear resistance functions. We then quantify uncertainty in resistance estimates by examining parameter selection probabilities from the bootstrapped data. The selection probabilities provide estimates of uncertainty in the parameters that drive the relationships between landscape features and resistance. We then validate our method for quantifying uncertainty using simulated genetic and landscape data showing that for most parameter combinations it provides sensible estimates of uncertainty. We conclude that small data sets can be informative in landscape genetic analyses provided uncertainty can be explicitly quantified. Being explicit about uncertainty in landscape genetic models will make results more interpretable and useful for conservation decision‐making, where dealing with uncertainty is critical.     

Protein–protein interaction prediction methods: from docking-based to AI-based approaches

Protein–protein interactions (PPIs), such as protein–protein inhibitor, antibody–antigen complex, and supercomplexes play diverse and important roles in cells. Recent advances in structural analysis methods, including cryo-EM, for the determination of protein complex structures are remarkable. Nevertheless, much room remains for improvement and utilization of computational methods to predict PPIs because of the large number and great diversity of unresolved complex structures. This review introduces a wide array of computational methods, including our own, for estimating PPIs including antibody–antigen interactions, offering both historical and forward-looking perspectives.     

Site‐specific inhibition of integrin αvβ3‐vitronectin association by a ser‐asp‐val sequence through an Arg‐Gly‐Asp‐binding site of the integrin

A functional proteomic technology using protein chip and molecular simulation was used to demonstrate a novel biomolecular interaction between P11, a peptide containing the Ser‐Asp‐Val (SDV) sequence and integrin αvβ3. P11 (HSDVHK) is a novel antagonistic peptide of integrin αvβ3 screened from hexapeptide library through protein chip system. An in silico docking study and competitive protein chip assay revealed that the SDV sequence of P11 is able to create a stable inhibitory complex onto the vitronectin‐binding site of integrin αvβ3. The Arg‐Gly‐Asp (RGD)‐binding site recognition by P11 was site specific because the P11 was inactive for the complex formation of a denatured form of integrin–vitronectin. P11 showed a strong antagonism against αvβ3‐GRGDSP interaction with an IC₅₀ value of 25.72±3.34 nM, whereas the value of GRGDSP peptide was 1968.73±444.32 nM. The binding‐free energies calculated from the docking simulations for each P11 and RGD peptide were ?3.99 and ?3.10 kcal/mol, respectively. The free energy difference between P11 and RGD corresponds to approximately a 4.5‐fold lower K_i value for the P11 than the RGD peptide. The binding orientation of the docked P11 was similar to the crystal structure of the RGD in αvβ3. The analyzed docked poses suggest that a divalent metal–ion coordination was a common driving force for the formation of both SDV/αvβ3 and RGD/αvβ3 complexes. This is the first report on the specific recognition of the RGD‐binding site of αvβ3 by a non‐RGD containing peptide using a computer‐assisted proteomic approach.     

Sex and recombination in the Hötzel aging model

Why sex evolved and it prevails in nature remain one of thegreat puzzles of evolution. Most biologists would explain that it promotes genetic variability, however this explanation suffers from several difficulties. What advantages might sex confer? The present communication aims at certain investigations related to this question, in this way we introduce sexual recombination on the Hötzel model (with males and females) and wecompare these results with those from asexual reproduction without recombination.     

An Integrated Study of Tyrosinase Inhibition by Rutin: Progress using a Computational Simulation

Abstract

Tyrosinase inhibition studies have recently gained the attention of researchers due to their potential application values. We simulated docking (binding energies for AutoDock Vina: ?9.1 kcal/mol) and performed a molecular dynamics simulation to verify docking results between tyrosinase and rutin. The docking results suggest that rutin mostly interacts with histidine residues located in the active site. A 10 ns molecular dynamics simulation showed that one copper ion at the tyrosinase active site was responsible for the interaction with rutin. Kinetic analyses showed that rutin-mediated inactivation followed a first-order reaction and mono- and biphasic rate constants occurred with rutin. The inhibition was a typical competitive type with K_i = 1.10 ± 0.25 mM. Measurements of intrinsic and ANS-binding fluorescences showed that rutin showed a relatively strong binding affinity for tyrosinase and one possible binding site that could be a copper was detected accompanying with a hydrophobic exposure of tyrosinase. Cell viability testing with rutin in HaCaT keratinocytes showed that no toxic effects were produced. Taken together, rutin has the potential to be a potent antipigment agent. The strategy of predicting tyrosinase inhibition based on hydroxyl group number and computational simulation may prove useful for the screening of potential tyrosinase inhibitors.