支持向量机在PPⅡ二级结构预测中的应用

PPⅡ二级结构是一种稀有的蛋白质结构类型。目前使用机器学习方法预测此二级结构的工作还比较少见。引入一种新的方法———支持向量机 (SVM)来预测PPII二级结构 ,并与神经网络方法进行了比较 ,结果表明 ,SVM方法在预测PPII结构上表现良好 ,预测精度达到 76 .5 2 %。     

Ab initio prediction of the three-dimensional structure of a de novo designed protein: a double-blind case study

Ab initio structure prediction and de novo protein design are two problems at the forefront of research in the fields of structural biology and chemistry. The goal of ab initio structure prediction of proteins is to correctly characterize the 3D structure of a protein using only the amino acid sequence as input. De novo protein design involves the production of novel protein sequences that adopt a desired fold. In this work, the results of a double-blind study are presented in which a new ab initio method was successfully used to predict the 3D structure of a protein designed through an experimental approach using binary patterned combinatorial libraries of de novo sequences. The predicted structure, which was produced before the experimental structure was known and without consideration of the design goals, and the final NMR analysis both characterize this protein as a 4-helix bundle. The similarity of these structures is evidenced by both small RMSD values between the coordinates of the two structures and a detailed analysis of the helical packing.     

短杆菌肽通道内离子K~＋，Na~＋，Li~＋与水的相关性

基于右手螺旋短杆菌肽Ａ离子通道模型,利用分子动力学计算机模拟方法研究了通道内离子Ｋ＋,Ｎａ＋,Ｌｉ＋与水分子的相关性．     

南亚热带常绿阔叶林林下层植物的生物量及其测定方法的探讨

应用全收割法测定广东省鼎湖山南亚热带常绿阔叶林林下层植物生物量 ,林下植物总生物量为 12 9 58g/m2 ,其中茎、枝、叶、根的生物量占总生物量的比例约为 4 0 % ,9 0 % ,2 2 % ,2 9% .由部分实测数据建立林下植物个体生物量估算模型为W =0 0 0 4 2 ·H1 932 3.应用该模型得到的估算值 ,与收获实测值的相对误差仅为 1 8% ,具有良好的精度 .此外 ,还通过改变取样面积对该模型的适用性进行了探讨 .     

基于相互作用的蛋白质功能预测

蛋白质功能预测是后基因时代研究的热点问题。基于相互作用的蛋白质功能预测方法目前应用比较广泛,但是当"伙伴蛋白质"(interacting partners)数目k较小时,其预测准确率不高。从蛋白质相互作用网络入手,结合"小世界网络"特性,有效解决了k较小时预测准确率不高的问题。对酵母(Saccharomyces cerevisiae)蛋白质的相互作用网络进行预测,当k≤4时其预测准确率比相同条件下的GO(global optimization)方法有一定提高。实验结果表明:该方法能够有效的应用于伙伴蛋白质数目较小时的蛋白质功能预测。     

Genetic diversity and its relationship to hybrid performance in maize as revealed by RFLP and AFLP markers

 The challenge to maize breeders is to identify inbred lines that produce highly heterotic hybrids. In the present study we surveyed genetic divergence among 13 inbred lines of maize using DNA markers and assessed the relationship between genetic distance and hybrid performance in a diallel set of crosses between them. The parental lines were assayed for DNA polymorphism using 135 restriction fragment length polymorphisms (RFLPs) and 209 amplified-fragment polymorphisms (AFLPs). Considerable variation among inbreds was detected with RFLP and AFLP markers. Moreover AFLPs detect polymorphisms more efficiently in comparison to RFLPs, due to the larger number of loci assayed in a single PCR reaction. Genetic distances (GDs), calculated from RFLP and AFLP data, were greater among lines belonging to different heterotic groups compared to those calculated from lines of the same heterotic group. Cluster analysis based on GDs revealed associations among lines which agree with expectations based on pedigree information. The GD values of the 78 F₁ crosses were partioned into general (GGD) and specific (SGD) components. Correlations of GD with F₁ performance for grain yield were positive but too small to be of predictive value. The correlations of SGDs, particularly those based on AFLP data, with specific combining-ability effects for yield may have a practical utility in predicting hybrid performance. Received: 15 August 1997 / Accepted: 19 September 1997     

不同土壤水分和养分条件下喜旱莲子草与同属种生长状况的比较研究

喜旱莲子草(Alternanthera philoxeroides)入侵已在中国造成巨大的生态和经济损失。为揭示喜旱莲子草成功入侵的生态机制并预测其种群扩张趋势及其与环境因子的关系, 作者比较了喜旱莲子草与其同属的外来弱入侵种刺花莲子草(A. pungens)以及土著种莲子草(A. sessilis)在不同土壤水分、养分条件下的生长状况。结果显示: 在高水高肥条件下, 喜旱莲子草的生物量要高于刺花莲子草和莲子草, 而在低水低肥条件下却不如这两个同属种; 弱入侵种刺花莲子草在低水条件下的生物量要高于强入侵种喜旱莲子草和土著种莲子草, 说明植物的入侵性受环境条件的影响。另外, 强入侵种喜旱莲子草形态学性状的可塑性较高, 在各种条件下都具有较高的比叶面积, 暗示这两个指标可作为莲子草属外来植物入侵性的预测指标。     

基于生态位模型的番荔枝实蝇潜在适生性分布预测

番荔枝实蝇Ceratitis artortoe(Graham)是一种重要的外来人侵性检疫害虫.在广东口岸,其幼虫连续从入境旅客所携带的水果中被榆出.目前关于番荔枝实蝇潜在适生性分布的研究进行得很少,但对于我国的生物生态安全却有重要意义.本研究中,我们使用3种牛态位模型(ENFA模型,马氏典型性模型和Maxent模型)对番荔枝实蝇在中斟以及全球范尉内的潜在适生性分布区域进行了预测分析.结果显示:Maxent模型拥有最好的预测精确度,马氏典型件模型次之,而ENFA模型的预测精确度最差;Maxent模型和马氏典型性模型的预测精确度无显著性差异;根据Maxent模型的预测结果,番荔枝实蝇在中国的潜在适生区主要是广西、广东、海南以及云南的少部分地区.分析结果显示,番荔枝实蝇从境外传人中国南部地区并最终在上述地区定殖的风险可能性存在,但风险较小.另外,折刀法(Jackknife)分析显示,6种环境因子,例如地面霜冻频率、年平均降雨量、十月降雨量、四月降雨量、年最低温度以及蒸气压,对于番荔枝实蝇在全球和局部地区的分布模式有显著的影响.     

低等白蚁肠道共生微生物的多样性及其功能

低等白蚁肠道里存在着复杂的微生物区系,包括真核微生物鞭毛虫和原核生物,细菌及古细菌。低等白蚁的后肠以特别膨大的囊形胃及其氢氧浓度的明显梯度分布和丰富的微生物区系为特征,是白蚁进行木质纤维素消化的主要器官。后肠内的鞭毛虫能将纤维素水解并发酵为乙酸,二氧化碳和氢,为白蚁提供营养和能源。系统发育研究表明,低等白蚁肠道共生细菌的主要类群为白蚁菌群1、螺旋体、拟杆菌,低G C mol%含量的革兰氏阳性菌和紫细菌等。而古细菌主要为甲烷短杆菌属的产甲烷菌。共生原核生物与二氧化碳的还原和氮的循环等代谢有关。但肠道共生微生物的具体功能和作用机制还有待进一步的揭示。     

不同酒精度、盐度及酸碱度条件下醉泥螺中副溶血性弧菌的一级生长预测模型

通过分别控制酒精度、盐度、酸碱度三种单一变量腌制醉泥螺,测定醉泥螺中副溶血性弧菌的生长曲线,并采用SGompertz模型进行拟合,建立不同条件下的一级生长预测模型。结果表明酒精可以抑制副溶血性弧菌生长,而pH7.5和盐度3.3%的条件相对适合其生长。本文建立的醉泥螺中副溶血性弧菌在不同条件下的预测模型,可为醉泥螺安全性的预测、副溶血性弧菌的控制、工艺条件的改善提供依据。