Efficient identification of near‐native conformations in ab initio protein structure prediction using structural profiles

One of the major bottlenecks in many ab initio protein structure prediction methods is currently the selection of a small number of candidate structures for high‐resolution refinement from large sets of low‐resolution decoys. This step often includes a scoring by low‐resolution energy functions and a clustering of conformations by their pairwise root mean square deviations (RMSDs). As an efficient selection is crucial to reduce the overall computational cost of the predictions, any improvement in this direction can increase the overall performance of the predictions and the range of protein structures that can be predicted. We show here that the use of structural profiles, which can be predicted with good accuracy from the amino acid sequences of proteins, provides an efficient means to identify good candidate structures. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Paleoenvironment of Ankilitelo Cave (late Holocene, southwestern Madagascar): implications for the extinction of giant lemurs

Following human arrival, Madagascar suffered well-documented megafaunal extinctions and widespread deforestation. Although humans are widely considered to be the primary cause of the extinctions, the relative contributions of climate change and human activities to this ecological transformation remain uncertain. Reconstructing the habitats of the giant lemurs of Madagascar can provide key information for understanding the evolutionary mechanisms involved in their extinction. In this study, I present a faunal analysis of the subfossil assemblage from Ankilitelo Cave, southwestern Madagascar. This assemblage documents the latest known occurrence of five species of extinct giant lemur, in association with abundant well-preserved small mammal remains. I compared the small mammal fauna at Ankilitelo with 27 extant Malagasy mammal communities spanning the range of Madagascar's habitat types. Similarities in species composition between modern communities and Ankilitelo were assessed using cluster analysis. Ecological similarities were examined by assigning each species to dietary, locomotor, activity pattern, and body size categories. Multiple discriminant analysis was then used to classify Ankilitelo relative to modern habitat types in Madagascar, based on the ecological structure of the subfossil fauna. Results indicate that the habitat surrounding Ankilitelo during the late Holocene was similar to the succulent woodlands of modern southwestern Madagascar. This suggests that approximately 500 yr BP, these semi-arid habitats supported a subfossil lemur community that included the highly-suspensory Palaeopropithecus, and deliberate slow-climber Megaladapis, as well as Archaeolemur, Pachylemur, and Daubentonia robusta. In such environments, these giant lemurs would likely have been highly vulnerable to increasing human pressure in southwestern Madagascar.     

Amino acid 95 causes strong alteration of peptide position PΩ in HLA-B*41 variants

There have been several attempts over the years to identify positions in the peptide-binding region (PBR) of human leukocyte antigens (HLA) that influence the specificity of bound amino acids (AAs) at each position in the peptide. Originally, six pockets (A-F) were defined by calculating the surface area of the PBR on the crystal structure of HLA-A2 molecules. More recent crystallographic analyses of a variety of HLA alleles have led to broader pocket definitions. In this study, we examined the peptide-binding specificity of HLA-B*41 alleles and compared our results with the available pocket definitions. By generating recombinant HLA-B molecules and studying the eluted peptides by mass spectrometry and pool sequencing, we detected two different POmega peptide motifs within the B*41 group: Leu vs Val/Pro. Specificity was dependent on the presence of Leu (B*4102, B*4103, and B*4104) vs Trp (B*4101, B*4105, and B*4106) at AA position 95 in the HLA molecule, whose impact on POmega has been a subject of controversy in current pocket definitions. In contrast, the Arg97Ser mutation did not affect pocket F binding specificity in B*41 subtypes although residue 97 was previously identified as a modulator of peptide binding for several HLA class I alleles. According to most pocket definitions, this study shows that the Asn80Lys substitution in B*4105 impels the peptide's POmega anchor toward more promiscuity. Our sequencing results of peptides eluted from HLA-B*41 variants demonstrate the limitations of current pocket definitions and underline the need for an extended peptide motif database for improved understanding of peptide-major histocompatibility complex interactions.     

鸡骨常山属三个种的核形态

研究了鸡骨常山属（Alstonia）3个种的核形态,其中盆架树（A.rostrata）的核型属首次报道,3个种的体细胞染色体数目均为2n=42,且糖胶树（A.scholaris）和鸡骨常山（A.yunnanensis）的染色体数目同前人报道的2n=44不同。盆架树的间期核和有丝分裂前期染色体分别为棒状前染色体型和中间型,核型公式为2n=42=3M＋21m＋18sm,核型不对称性类型为2A型。糖胶树的间期核和有丝分裂前期染色体分别为球状前染色体型和中间型,核型公式为2n=42=14m＋24sm＋4st,核型不对称性类型为3A型。鸡骨常山的间期核和有丝分裂前期染色体分别为复杂染色体中央粒型和中间型,核型公式为2n=42=5m＋37sm,核型不对称性类型为3B型。根据核形态结果,结合形态学特征和已有的细胞学资料,初步讨论了该属几个种的系统位置及演化趋势。     

Phase-dependent nucleotide substitution in protein-coding sequences

It is well known that due to the degeneracy of genetic code, most of the silent substitutions appear in the third codon position, so the mutation frequency of the third codon position is much higher than that of the first two positions. However, it remains unknown whether the directionality of point mutation in three codon positions is similar or not. In this paper, through analyzing 15 sets of orthologous genes, it is revealed that most of the substitution types are significantly different between any two codon positions, especially between the 2nd and the 3rd phases. Furthermore, the average frequencies of each type of substitution calculated from the fifteen sets of orthologous genes are similar to those identified in single nucleotide polymorphisms (SNPs) of human and mouse genome. The present analyses suggest that the nucleotide substitution in protein-coding sequences is not only context-dependent (so called neighboring-nucleotide effects), but also phase-dependent, which is of significance to improving the prevalent nucleotide-evolution models.     

绢蒿属8种植物果实微形态特征及其分类学意义

为寻找绢蒿属系统学的新证据,应用解剖镜和扫描电镜对我国8种绢蒿属植物的果实微形态特征进行了比较观察。结果表明,绢蒿属8种植物果实形状相似性较高,呈倒卵形或长倒卵形,直或稍弯曲;果脐圆形,常偏向一侧;顶端中央均可见花柱残留物,边缘具衣领状环;果实表面纹饰为搓板状和不规则皱褶纹饰。这些果实微形态特征中,果实的表面纹饰具有一定的差异,特别是次级结构,可作为绢蒿属植物区分种的参考性状之一。     

珍稀濒危植物珙桐超氧化物歧化酶活性

采用比色法测定了不同年龄和部位珙桐叶的超氧化物歧化酶(SOD)活性,以探讨不同年龄级珙桐的生理生态适应性。结果表明:不同年龄同一生长期珙桐叶的SOD活性不同,同年龄级同层珙桐叶的SOD活性随叶位增加大致呈先升后降的变化;同叶位不同层及同层不同叶位的珙桐叶的SOD活性不同。珙桐叶SOD活性对生长期敏感,其活性随叶片的生长、衰老呈先升后降变化。即珙桐叶SOD活性受生物和非生物因子共同影响,且不同年龄级、叶位、层次均存在差异。     

Measuring beta‐diversity from taxonomic similarity

Question: The utility of beta (β‐) diversity measures that incorporate information about the degree of taxonomic (dis)similarity between species plots is becoming increasingly recognized. In this framework, the question for this study is: can we define an ecologically meaningful index of β‐diversity that, besides indicating simple species turnover, is able to account for taxonomic similarity amongst species in plots? Methods: First, the properties of existing measures of taxonomic similarity measures are briefly reviewed. Next, a new measure of plot‐to‐plot taxonomic similarity is presented that is based on the maximal common subgraph of two taxonomic trees. The proposed measure is computed from species presences and absences and include information about the degree of higher‐level taxonomic similarity between species plots. The performance of the proposed measure with respect to existing coefficients of taxonomic similarity and the coefficient of Jaccard is discussed using a small data set of heath plant communities. Finally, a method to quantify β‐diversity from taxonomic dissimilarities is discussed. Results: The proposed measure of taxonomic β‐diversity incorporates not only species richness, but also information about the degree of higher‐order taxonomic structure between species plots. In this view, it comes closer to a modern notion of biological diversity than more traditional measures of β‐di‐versity. From regression analysis between the new coefficient and existing measures of taxonomic similarity it is shown that there is an evident nonlinearity between the coefficients. This nonlinearity demonstrates that the new coefficient measures similarity in a conceptually different way from previous indices. Also, in good agreement with the findings of previous authors, the regression between the new index and the Jaccard coefficient of similarity shows that more than 80% of the variance of the former is explained by the community structure at the species level, while only the residual variance is explained by differences in the higher‐order taxonomic structure of the species plots. This means that a genuine taxonomic approach to the quantification of plot‐to‐plot similarity is only needed if we are interested in the residual system's variation that is related to the higher‐order taxonomic structure of a pair of species plots.