南亚热带森林片断化对厚壳桂种群遗传结构的影响

森林片断化是造成全球生物多样性丧失的主要原因,但从种群遗传学角度开展的研究还远远不够。因此,本文采用ISSR(inter-simplesequencerepeat)方法对广东省鼎湖山、黑石顶、大雾岭、古田、萝岗和饶平6个地点的南亚热带片断化森林中的厚壳桂(Cryptocaryachinensis)种群的遗传多样性进行了研究。每个种群分成体、小树和幼苗3个年龄级采样,共采集厚壳桂样品448个。7个ISSR引物共扩增出209条多态性带。研究结果表明,6个厚壳桂种群的总遗传多样性为0.1529,种群平均遗传多样性为0.0537。和保护较好的厚壳桂种群相比,萝岗和饶平的两个村边林种群的遗传多样性较低。6个厚壳桂种群间的遗传分化系数(GST)为0.6489。AMOVA分析结果表明,总的遗传变异中,67.97%(P<0.0002)的遗传变异存在于种群间,2.06%(P<0.01)的遗传变异存在于不同年龄级之间,29.96%(P<0.0002)的遗传变异存在于种群内。基于遗传距离的UPGMA分析结果表明,6个厚壳桂种群大致分成两支:一支包括大雾岭和黑石顶2个种群,另一支包括其他4个种群。鼎湖山、古田、大雾岭和黑石顶不同年龄级均各自聚合在一起。可以看出,森林的破碎化导致了南亚热带厚壳桂种群遗传多样性降低,种群间基因流受阻,提示我们对于同一地区的易危物种,这种威胁将很大,急需开展相关的保护研究。     

Ordered conformational change in the protein backbone: prediction of conformationally variable positions from sequence and low-resolution structural data

Ordered conformational changes are an important structural property of proteins and are involved in a variety of fundamental biological activities. Large-scale analyses of the implications of such changes for protein function and dysfunction require efficient methods for automated recognition of conformationally variable residue positions. The goal of this work was to study sequence and low-resolution structural properties of residue positions that change backbone conformation upon changes in protein environment and the utility of these properties for automated recognition of such conformationally variable positions. This study was performed using a large nonredundant set of experimentally characterized proteins that undergo ordered conformational transitions obtained from the Database of Macromolecular Movements. The results of this study show that ordered changes in backbone conformation are not limited to solvent accessible loop regions. A considerable fraction of conformationally variable positions is observed in helices and strands, and in buried positions. Conformationally variable positions are less conserved in evolution. Local patterns of (a) sequence neighbors, (b) evolutionary conservation, and (c) solvent accessibility can be used to predict conformationally variable positions with balanced sensitivity and specificity, albeit with large variance at the level of individual proteins. However, including a pattern of secondary structure into the prediction scheme results in a highly unbalanced performance when all conformationally variable positions located in regular secondary structure are misclassified. Application of the present methodology to the prion protein (PrP) shows that conformationally variable positions predicted in its ordered C-terminal domain are located within segments presumed to be involved in refolding of PrP.     

Comparative lca of industrial objects part 1: lca data quality assurance — sensitivity analysis and pedigree matrix

Goal, Scope and Background  The main aim of this paper is to present some methodological considerations concerning existing methods used to assess quality of the LCA study. It relates mainly to the quality of data and the uncertainty of the LCA results. The first paper is strictly devoted to methodological aspects whereas, the second is presented in a separate article (Part II) and devoted mainly to a case study. Methods  The presented analysis is based on two well-known concepts: the Data Quality Indicators (DQIs) and the Pedigree Matrix. In the first phase, the Sensitivity Indicators are created on the basis of the sensitivity analysis and then linked with the DQIs and the Quality Classes. These parameters indicate the relative importance of input data and their theoretical quality levels. Next, the Weidema’s Pedigree Matrix (slightly modified) is used to establish the values of the new parameter called the Data Quality Distance (DQD) and to link them with the DQIs and Quality Classes. This way the information about the “real” quality levels is provided. Further analysis is performed using the probabilistic distributions and Monte Carlo simulations. Results and Discussion  Thanks to this approach it is possible to make a comparison between two types of the quality factors. On the one hand, the sensitivity analysis allows one to check the importance of input data and to determine their required quality. It is done according to the following relation: the higher the sensitivity indicator, the higher the importance of input data and the higher quality should be demanded. On the other hand the data have a certain real quality, not always in accord with the demanded one. To make possible a comparison between these two types of quality, it is necessary to find and develop a common denominator for them. Here, for this purpose the DQIs and Quality Classes are used. Conclusions  In the further stage of the assessment the DQIs are used to perform the uncertainty analysis of the LCA results. The results could be additionally analysed by using other techniques of interpretation: the sensitivity-, the contribution-, the comparative-, the discernability- and the uncertainty analysis. Recommendations and Outlook  The presented approach is put into practice to conduct the comparative LCA study for the industrial pumps by using the Ecoindicator99 method. Thanks to this, complex analysis of the credibility of the results is carried out. As a consequence, uncertainty ranges for the LCA results of every product system can be determined [1].     

Annual and seasonal space use of different age classes of female wild boar Sus scrofa L.

In a radiotelemetric study, we analysed space use of 24 female specimens (14 family groups and 14 nonreproductive yearling females) out of 23 wild boar groups for periods between 3 and 39 months. Generally, wild boar used relatively small areas, showed high site fidelity but also a strong individual variation of home ranges, indicating a high flexibility in space use. Although age-specific differences were not statistically significant, female yearlings tended to have larger mean annual home ranges (1,185 ha MCP) than animals ranging in family groups (771 ha). Yearlings also showed a stronger shifting from spring to summer home ranges (2,345 m) and a tendency towards larger home range sizes in summer (791 ha MCP), compared to family groups (shift 1,766 m, MCP 461 ha). Yearlings displayed a dislocation of about 1 km of the annual centre in the first year after dividing from the mother. In contrast, in adults older than 2 years, the dislocation of the annual center was only 240 m.     

Relationship quality affects fission decisions in wild spider monkeys (Ateles geoffroyi)

Fission–fusion dynamics are thought to be mainly a response to differential availability of food resources. However, social factors may also play a role. Here, we examined whether the quality of social relationships between group members affects fission decisions. During 21 months, we collected data on social interactions and fission events of 22 spider monkeys (Ateles geoffroyi) living in a community in the protected area of Otoch Ma'ax Yetel Kooh, Yucatan, Mexico. By entering seven indexes of social interactions into a principal component analysis, we obtained three components of relationship quality, which we labelled “compatibility,” “value” and “insecurity” given the relative loadings of the indexes. Our results showed that individuals were more likely to fission into the same subgroup with community members with whom they shared higher levels of compatibility and value and lower levels of insecurity. In addition, individuals preferred to fission into the same subgroup with same‐sex group members, as expected based on what is known for the species. Our findings highlight the role of social factors in fission decisions. Adjustments in subgroup size are based on multifaceted social preferences, incorporating previously unexamined aspects of relationship quality, which are independent from overall levels of affiliative interactions.     

从非同源蛋白质的一级序列预测其结构类

对基于氨基酸组成、自相关函数和自协方差函数提取特征的蛋白质结构类预测算法进行分析比较,对氨基酸组成和自相关函数相结合的方法,以及氨基酸组成和自协放差函数相结合的方法的预测算法进行了研究。结果表明：对非同源蛋白质,因氨基酸和自相关函数相结合的方法中,采用Miyazawa和Jernigan的疏水值时,训练的自检验的总精度为95．34％,其Jackknife检验的总精度为81．92％,检验加的他检验的总精工为86．61％。在氨基酸组成和自协方差函数相结合的方法中,采用Wold等的疏水值时,训练库的自检验的总精度为96．71％,其Jackknife检验的总精度为82．18％,检验加的他检验的总精工为86．88％。这说明氨基酸组成和自相关函数相结合的方法,以及氨基酸组成和自协方差函数相结合的方法可有效提高结构类预测精度,表明提取更多有效的序列信息是提高分类精度的关键。     

A land cover map of South America

A digital land cover map of South America has been produced using remotely sensed satellite data acquired between 1995 and the year 2000. The mapping scale is defined by the 1 km spatial resolution of the map grid‐cell. In order to realize the product, different sources of satellite data were used, each source providing either a particular parameter of land cover characteristic required by the legend, or mapping a particular land cover class. The map legend is designed both to fit requirements for regional climate modelling and for studies on land cover change. The legend is also compatible with a wider, global, land cover mapping exercise, which seeks to characterize the world's land surface for the year 2000. As a first step, the humid forest domain has been validated using a sample of high‐resolution satellite images. The map demonstrates both the major incursions of agriculture into the remaining forest domains and the extensive areas of agriculture, which now dominate South America's grasslands.     

GO功能类与基因差异表达的关联规则挖掘算法

针对基因功能分类体系Gene Ontology的层次结构特点,修改关联规则挖掘算法Apriori,开发“挖掘与基因差异表达关联的GO功能组合”软件(RuleGO).RuleGO以基因表达谱上的差异表达基因集合和不差异表达基因集合为输入,输出组合特征功能类与基因差异表达现象的关联规则,有助于解释基因差异表达现象的本质原因,如疾病发病机制、药物作用机理等.将RuleGO 和OntoExpress应用在结肠癌和腺癌表达谱数据集上,结果显示,RuleGO比OntoExpress能发现更多的与差异表达现象关联的特征功能类,更能看到在OntoExpress上不能发现的组合特征功能类.另外,结果显示,将规则的置信度和支持度要求设置较高时,一般只有组合功能类才能满足要求,这提示在基因表达谱分析中不宜采用单个角度的单个功能分类单元,考虑功能分类单元的组合可能更有意义.     

四种结构类型的蛋白质设计方法

给出了以疏水一亲水模型为基础的蛋白质设计方法,该方法以物理学原理为基础,以相对熵作为优化的目标函数。对四种不同结构类型的天然结构的真实蛋白质进行了检测,分析了影响检测成功率的主要因素,结果表明,该方法是普适的,可用于对不同结构类型的蛋白质设计序列。     

杭州午潮山天然次生林木本幼苗组成及其时空分布格局

木本植物幼苗是森林生态系统的重要的组成部分,其定居、存活、生长的生态学过程对于森林植被的更新具有潜在指示和筛选作用。为探究浙江杭州午潮山亚热带常绿阔叶次生林群落更新和演替机制,基于样方法对150 m²样地内天然更新幼苗的物种组成、数量特征和基径结构进行统计,在此基础上采用最近邻分析和Ripley''s K函数的点格局方法,分析其中主要优势树种的更新动态及其时空分布格局。结果表明:(1)样地内乔木幼苗树种组成丰富,共调查到幼苗811株,隶属12科20属27种,其中樟科Lauraceae、壳斗科Fagaceae、山茶科Theaceae和山矾科Symplocaceae为主要优势科。(2)红楠Machilus thunbergii、薄叶润楠M. leptophylla、毛柄连蕊茶Camellia fraterna和刨花润楠M. spauhoi在所有调查物种重要值排序前4,因而被确定为优势林下植物,绘制的基径结构小提琴图(violin plot)进一步显示它们的种群分属快速增长型、稳定增长型、缓慢增长型和稳定型。(3)红楠、薄叶润楠和刨花润楠在小径级和小尺度上多呈聚集分布,随生长发育和空间尺度的增加,聚集强度呈现先增高后降低趋势,最终向离散分布或随机分布转变,可视为群落演替的早期树种;同时,三者在聚集强度上有所差异,排序为红楠＞薄叶润楠＞刨花润楠。毛柄连蕊茶Camellia fraterna种群密度较低,在小径级和小尺度上呈随机分布,随生长发育和空间尺度的增加,聚集强度呈波动趋势,最终向离散分布转变,可视为演替的中期树种。本研究在小尺度上初步揭了午潮山木本幼苗种群的演替过程中的种群结构和分布格局,可以为亚热带森林管理与植被恢复提供理论依据。