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161.
In this work, we apply a detailed all‐atom model with a transferable knowledge‐based potential to study the folding kinetics of Formin‐Binding protein, FBP28, which is a canonical three‐stranded β‐sheet WW domain. Replica exchange Monte Carlo simulations starting from random coils find native‐like (Cα RMSD of 2.68 Å) lowest energy structure. We also study the folding kinetics of FBP28 WW domain by performing a large number of ab initio Monte Carlo folding simulations. Using these trajectories, we examine the order of formation of two β‐hairpins, the folding mechanism of each individual β‐hairpin, and transition state ensemble (TSE) of FBP28 WW domain and compare our results with experimental data and previous computational studies. To obtain detailed structural information on the folding dynamics viewed as an ensemble process, we perform a clustering analysis procedure based on graph theory. Further, a rigorous Pfold analysis is used to obtain representative samples of the TSEs showing good quantitative agreement between experimental and simulated Φ values. Our analysis shows that the turn structure between first and second β strands is a partially stable structural motif that gets formed before entering the TSE in FBP28 WW domain and there exist two major pathways for the folding of FBP28 WW domain, which differ in the order and mechanism of hairpin formation. Proteins 2011. © 2011 Wiley‐Liss, Inc. 相似文献
162.
Epistatic miniarray profiling (E-MAP) is a powerful tool for analyzing gene functions and their biological relevance. However, E-MAP data suffers from large proportion of missing values, which often results in misleading and biased analysis results. It is urgent to develop effective missing value estimation methods for E-MAP. Although several independent algorithms can be applied to achieve this goal, their performance varies significantly on different datasets, indicating different algorithms having their own advantages and disadvantages. In this paper, we propose a novel ensemble approach EMDI based on the high-level diversity to impute missing values that consists of two global and four local base estimators. Experimental results on five E-MAP datasets show that EMDI outperforms all single base algorithms, demonstrating an appropriate combination providing complementarity among different methods. Comparison results between several fusion strategies also demonstrate that the proposed high-level diversity scheme is superior to others. EMDI is freely available at www.csbio.sjtu.edu.cn/bioinf/EMDI/. 相似文献
163.
Johnson AW Gallagher M 《Proceedings. Biological sciences / The Royal Society》2011,278(1711):1450-1456
Actions can create preferences, increasing the value ascribed to commodities acquired at greater cost. This behavioural finding has been observed in a variety of species; however, the causal factors underlying the phenomenon are relatively unknown. We sought to develop a behavioural platform to examine the relationship between effort and reinforcer value in mice trained under demanding or lenient schedules of reinforcement to obtain food. In the initial experiment, expenditure of effort enhanced the value of the associated food via relatively lasting changes in its hedonic attributes, promoting an acquired preference for these reinforcers when tested outside of the training environment. Moreover, otherwise neutral cues associated with those reinforcers during training similarly acquired greater reinforcing value, as assessed under conditioned reinforcement. In a separate experiment, expenditure of effort was also capable of enhancing the value of less-preferred low-caloric reinforcers. Analysis of licking microstructure revealed the basis for this increased valuation was, in part, due to increased palatability of the associated reinforcer. This change in the hedonic taste properties of the food can not only serve as a basis for preference, but also guide decision-making and foraging behaviour by coordinating a potentially adaptive repertoire of incentive motivation, goal-directed action and consumption. 相似文献
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2010年3月下旬-7月上旬于浙江富阳市农田采集680只泽陆蛙(Fejervarya limnocharis),研究了泽陆蛙成体和幼体的个体大小和局部形态特征的两性异形;通过解剖雌体获得窝卵数、测量抱对个体获得形态数据,研究了雌体大小与生育力关系以及抱对两性个体体形大小的相关性.结果表明:捕获个体中,雌性和雄性成体的最小体长分别为33mm和30 mm;雄性成体个体数显著超过雌性成体,两性幼体个体数无显著差异;两性成体头部大小、四肢长随体长呈同速增长,眼径和体重随体长呈异速增长,两性幼体所有被检形态特征均随体长呈同速增长;雌性成体平均体长显著大干雄性成体,去除体长差异的影响后发现,除眼径无显著的两性差异外,其余被检形态特征均为雌性大于雄性;幼体除雌性体重大于雄性外,其余被检形态特征均无两性差异;窝卵数与雌体大小(体长和体重)呈显著的正相关;两性抱对个体的体长无显著相关性;泽陆蛙雄性成体体形小于雌性成体的个体大小两性异形模式可能决定于驱使雄性向较大体形发展的进化驱动力相对较弱,雌性增大体形可增加繁殖输出,故向较大体形发展的进化驱动力相对较强;除体重外,其余被检形态特征的两性异形均形成于性成熟之后. 相似文献
167.
祁连山典型林区生态服务功能间接价值估算 总被引:2,自引:1,他引:1
采用常规和替代市场评估技术,对祁连山北坡东段哈溪林区有机质生产、水源涵养、水土保持、固定CO2和净化空气5种生态系统服务功能间接价值进行了估算,并对3种不同植被类型的生态服务功能价值进行了比较。结果表明,哈溪林区5种服务功能总价值为52061.00万元,其中森林、灌丛和草地分别为19510.34万元、25200.01万元和7350.65万元。按有林地面积推算,祁连山森林生态系统提供的服务功能间接经济价值是天祝县国民生产总值的3~5倍,森林生态系统所提供的生态服务功能价值远远超过了当地社会创造的经济价值。就水源涵养和水土保持服务功能而言,灌丛提供的总价值最大。 相似文献
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人工鱼礁构建对海洋生态系统服务价值的影响——以深圳杨梅坑人工鱼礁区为例 总被引:6,自引:0,他引:6
基于深圳杨梅坑人工鱼礁区2008年的研究和统计数据,采用生态系统服务价值方法,系统分析了杨梅坑人工鱼礁建设对海洋生态系统的影响.结果表明:与深圳附近海域相比,杨梅坑人工鱼礁构建后旅游娱乐服务价值所占比例由87%降至42%,食品供给服务价值所占比例由7%升至27%,原材料供给、气候调节、空气质量调节、水质净化调节、有害生物和疾病的生物调节与控制、知识扩展服务价值所占比例少许提高;2008年,深圳杨梅坑人工鱼礁区单位面积服务价值为1714.7万元.km-2,远高于深圳市近海海洋生态系统的平均值和全球近海生态系统的平均值.人工鱼礁生态系统影响并改变了区域海洋生态系统服务价值结构,提高了区域生态系统服务价值,对于合理开发与利用海洋资源、修复受损的海洋生态环境和渔业资源有着重要意义.利用生态系统服务价值方法对人工鱼礁构建区进行评价,可以更好地反映人工鱼礁构建效益,能有效促进我国人工鱼礁建设的发展、提高海洋生态系统管理水平. 相似文献
170.
讨论了带一个参数的非线性四阶狄利克雷边值问题变号解的存在性.在非线性项满足一定条件时,通过利用一些新的概念如O-有界锥和O-正算子,我们得到该边值问题至少存在一个变号解. 相似文献