The differential genetic and environmental canalization of fitness components in Drosophila melanogaster

Canalization describes the process by which phenotypic variation is reduced by developmental mechanisms. A trait can be canalized against environmental or genetic perturbations. Stabilizing selelction should favor improved canalization, and the degree of a trait's canalization should be positively correlated with its impact on fitness. Here we report, for Drosophila melanogaster, measurements of environmental canalization for five fitness components. We compare them with measurements of genetic canalization, and we discuss the impact of inbreeding on both. In three experiments we measured the variation of fitness components within lines nested within temperature, treatment, and experiment. Lines differed in the position of a P element insert or in genetic background. Within lines flies were genetically nearly identical. We designated trait variation within lines as environmental canalization. The canalization of the traits increased with their impact on fitness, and the pattern was similar to that found for the canalization of fitness components against genetic differences, measured as the variation among lines nested within temperature, treatment, and experiment. This suggests that developmental mechanisms buffer the phenotype against both genetic and environmental disturbance. The results also suggest, less strongly, that inbreeding weakens canalization.     

Inferring functional relationships of proteins from local sequence and spatial surface patterns

We describe a novel approach for inferring functional relationship of proteins by detecting sequence and spatial patterns of protein surfaces. Well-formed concave surface regions in the form of pockets and voids are examined to identify similarity relationship that might be directly related to protein function. We first exhaustively identify and measure analytically all 910,379 surface pockets and interior voids on 12,177 protein structures from the Protein Data Bank. The similarity of patterns of residues forming pockets and voids are then assessed in sequence, in spatial arrangement, and in orientational arrangement. Statistical significance in the form of E and p-values is then estimated for each of the three types of similarity measurements. Our method is fully automated without human intervention and can be used without input of query patterns. It does not assume any prior knowledge of functional residues of a protein, and can detect similarity based on surface patterns small and large. It also tolerates, to some extent, conformational flexibility of functional sites. We show with examples that this method can detect functional relationship with specificity for members of the same protein family and superfamily, as well as remotely related functional surfaces from proteins of different fold structures. We envision that this method can be used for discovering novel functional relationship of protein surfaces, for functional annotation of protein structures with unknown biological roles, and for further inquiries on evolutionary origins of structural elements important for protein function.     

Molecular modeling of human serum transferrin for rationalizing the changes in its physicochemical properties induced by iron binding. Implication of the mechanism of binding to its receptor

In order to rationalize the physicochemical properties of human serum-transferrin (STf) and the STf-receptor (TfR) recognition process, we have tried to predict the 3D structures of apo- and iron-loaded STf using a homology modeling technique to study the changes in the structural characteristics that take place upon the uptake of iron by STf in solution. The crystal structures of both forms for ovotransferrin were used as templates for the STf modeling. The modeled structure of STf gave a satisfactory interpretation for the typical physicochemical properties such that (1) STf has a negative electrophoretic mobility and its value increases with iron uptake, and (2) the radius of gyration R_g of Tf decreases with iron uptake. It was found that upon iron binding, interdomain closures take place with large movements of the NII and CII subdomains comprising the N- and C-lobes in STf through a hinge-bending motion, accompanied by the opening of the bridge region with a displacement of more than 15 Å. Moreover, in view of the findings from our capillary electrophoresis experiments that the electrostatic interactions significantly contribute to a specific binding of Fe₂-STf with TfR, it is inferred that the connecting (bridge) and its neighboring region associated with a surface exposure of negative charge play an important role in the STf-receptor recognition process.     

Structural analysis and molecular modeling of two antitrichosanthin IgE clones from phage antibody library

Recently we constructed a murine IgE phage surface display library and screened out two IgE (Fab) clones with specific binding activity to Trichosanthin (TCS).In this work,the Vε and Vκ genes of the two clones were sequenced and their putative germline gene usages were studied.On the basis of the known 3D structure of Trichosanthin and antibody,molecular modeling was carried out to study the antigen-antibody interaction.The possible antigenic determinant sites on the surface of TCS recognized by both the clones were analyzed,and the reaction forces between TCS and two Fab fragments were also analyzed respectively.     

Analytic and simulation models predicting positive genetic correlations between traits linked by trade-offs

Summary Using a two-loci multiplicative model of resource allocation, we show how the existence of several levels of resource allocation may affect the sign of the genetic correlations between traits linked by trade-offs. Positive genetic correlations between components of fitness affected by genetic trade-offs may result from different amounts of genetic variability at the pleiotropic loci determining the allocation of resources. Thus positive genetic correlations may be obtained in the absence both of environmental variation and of differences between individuals in resource acquisition. Nevertheless, positive correlations between all components of fitness at the same time cannot be obtained without variability in the acquisition of resources.     

分子表面的计算机表示

提出了一种用于生成分子光滑表面的新算法.该算法从分布在一个包含整个分子表面的椭球上的三角网络开始,逐步收缩网络直到所有的三角形最佳贴近分子表面.所使用的收缩包络椭球的技术只要稍加修改就可用于蛋白质空腔的表示.     

How to distinguish altruism from spite (and why we should bother)

Social behaviour is often described as altruistic, spiteful, selfish or mutually beneficial. These terms are appealing, but it has not always been clear how they are defined and what purpose they serve. Here, I show that the distinctions among them arise from the ways in which fitness is partitioned: none can be drawn when the fitness consequences of an action are wholly aggregated, but they manifest clearly when the consequences are partitioned into primary and secondary (neighbourhood) effects. I argue that the primary interaction is the principal source of adaptive design, because (i) it is this interaction that determines the fit of an adaptation and (ii) it is the actor and primary recipients whom an adaptation foremost affects. The categories of social action are thus instrumental to any account of evolved function.