中国现代植物区系(地理)学的学派形成和展望

简要回顾了中国近代植物区系 (地理 )学的历史。记述了吴征镒的植物区系的热带亲缘理论和张宏达的华夏植物区系理论的形成和主要特点 ,比较异同 ,以期通过他们及其研究群体联手协作 ,形成具有中国特色的植物区系学新学派     

The role of pattern databases in sequence analysis

In the wake of the numerous now-fruitful genome projects, we are entering an era rich in biological data. The field of bioinformatics is poised to exploit this information in increasingly powerful ways, but the abundance and growing complexity both of the data and of the tools and resources required to analyse them are threatening to overwhelm us. Databases and their search tools are now an essential part of the research environment. However, the rate of sequence generation and the haphazard proliferation of databases have made it difficult to keep pace with developments. In an age of information overload, researchers want rapid, easy-to-use, reliable tools for functional characterisation of newly determined sequences. But what are those tools? How do we access them? Which should we use? This review focuses on a particular type of database that is increasingly used in the task of routine sequence analysis--the so-called pattern database. The paper aims to provide an overview of the current status of pattern databases in common use, outlining the methods behind them and giving pointers on their diagnostic strengths and weaknesses.     

Fold prediction by a hierarchy of sequence, threading, and modeling methods.

Several fold recognition algorithms are compared to each other in terms of prediction accuracy and significance. It is shown that on standard benchmarks, hybrid methods, which combine scoring based on sequence-sequence and sequence-structure matching, surpass both sequence and threading methods in the number of accurate predictions. However, the sequence similarity contributes most to the prediction accuracy. This strongly argues that most examples of apparently nonhomologous proteins with similar folds are actually related by evolution. While disappointing from the perspective of the fundamental understanding of protein folding, this adds a new significance to fold recognition methods as a possible first step in function prediction. Despite hybrid methods being more accurate at fold prediction than either the sequence or threading methods, each of the methods is correct in some cases where others have failed. This partly reflects a different perspective on sequence/structure relationship embedded in various methods. To combine predictions from different methods, estimates of significance of predictions are made for all methods. With the help of such estimates, it is possible to develop a "jury" method, which has accuracy higher than any of the single methods. Finally, building full three-dimensional models for all top predictions helps to eliminate possible false positives where alignments, which are optimal in the one-dimensional sequences, lead to unsolvable sterical conflicts for the full three-dimensional models.     

银鲫复合种外源遗传物质整入的RAPD分析

在优化ＲＡＤＰＤ检测条件的基础上,采用４０对随机引物,比较分析了银复合物,异育银鲫和兴国红鲤相互间扩增ＤＮＡ片段的异同性。总的来说,银鲫复合种和异育银鲫具有基本一致的扩增产物,而与兴国红鲤的扩增产物多数不同,相似率分析表明,银鲫复合种与兴国红鲤之间的相似率为３１．６％,异育银鲫与兴国红鲤之间的相似率为２８．６％。在分析中,除发现银鲫复合种,异育银鲫与兴国红鲤间共有扩增片段外,还发现了银鲫复合种与兴     

广西姑婆山及邻近地区大型真菌物种多样性

姑婆山紧邻南岭生物多样性保护优先区，孕育了丰富的生物资源。为了解该区域大型真菌物种多样性，该文采用随机踏查法对广西姑婆山自治区级自然保护区(以下简称姑婆山)及邻近地区大型真菌资源进行调查采集，并结合形态学和分子生物学方法进行物种鉴定。结果表明：(1)共发现348种大型真菌，隶属于2门6纲17目69科175属，其中包含食用菌40种、药用菌42种、毒菌7种。(2)对该区的物种组成分析表明，优势科为蘑菇科(Agaricaceae)、牛肝菌科(Boletaceae)、粉褶蕈科(Entolomataceae)和锈革菌科(Hymenochaetaceae)等9科；优势属为鹅膏属(Amanita)、靴耳属(Crepidotus)、毛皮伞属(Crinipellis)和粉褶蕈属(Entoloma)等11属。(3)共发现2个中国特有属，即脆孔菌属(Fragiliporia)和臧氏牛肝菌属(Zangia);11个中国特有种，即厚集毛菌(Coltricia crassa)、魏氏集毛菌(C.weii)、丛生粉褶蕈(Entoloma caespitosum)、极细粉褶蕈(E.praegracile)、近薄囊粉褶蕈...     

Biogeographical patterns in endoparasite communities of a marine fish (Sebastes capensis Gmelin) with extended range in the Southern Hemisphere

Aim The endoparasites of Sebastes capensis Gmelin are examined over most of its geographical range (coasts of Peru, Chile, Argentina and South Africa) to determine: (1) whether the endoparasite communities of this fish show zoogeographical patterns; and (2) if so, whether there are any relationships between spatial variations in the endoparasite fauna and known zoogeographical patterns for marine free‐living organisms (e.g. prey that are included in the life cycles of endoparasites). Location Fish were captured at nine localities along the Pacific coast of South America, from 11° S in the centre of the Peruvian coast, to 52° S in southern Chile, and also at two localities in the Atlantic Ocean, at 43° S in Argentina, and 34° S in South Africa. Methods From April to September 2003 and April to August 2004, 626 fish were captured. Endoparasites and diet were examined following traditional methods. Cluster analyses were used to evaluate the distribution patterns of the endoparasite communities, and to evaluate similarities in the prey composition per locality. Results The endoparasite fauna of S. capensis consisted of four species widely distributed along the Pacific coast: Ascarophis cf. sebastodis, Anisakis sp., Corynosoma australe, and Pseudopecoelus sp. Other parasites were distributed only in some geographical areas. The species richness of the parasite communities increased with latitude along the Pacific coast, while parasite communities from Argentina and South Africa showed low species richness. Cluster analyses based on endoparasite composition and on prey composition grouped localities in a way consistent with known biogeographical areas for marine free‐living organisms. Main conclusions The endoparasites of S. capensis exhibit a pattern associated with known biogeographical areas for free‐living organisms. The latitudinal increase in endoparasite community richness is associated with changes in prey composition (intermediate hosts) and also possibly with the presence of definitive hosts. Therefore, the biogeographical patterns of prey are considered key determinants of the endoparasite community structure of the host.     

Prediction of protein targets of kinetin using in silico and in vitro methods: a case study on spinach seed germination mechanism

Kinetin, a cytokinin which promotes seed germination by inhibiting the action of abscisic acid, is an important molecule known to trigger various molecular mechanisms by interacting with an array of proteins shown from experimental observations in various model organisms. We report here the prediction of most probable protein targets of kinetin from spinach proteome using in silico approaches. Inverse docking and ligand-based similarity search was performed using kinetin as molecule. The former method prioritized six spinach proteins, whereas the latter method provided a list of protein targets retrieved from several model organisms. The most probable protein targets were selected by comparing the rank list of docking and ligand similarity methods. Both of these methods prioritized chitinase as the most probable protein target (ΔG_pred = 5.064 kcal/mol) supported by the experimental structure of yeast chitinase 1 complex with kinetin (PDB: 2UY5) and Gliocladium roseum chitinase complex with 3,7-dihydro-1,3,7-trimethyl-1H-purine-2,6-dione (caffeine; 3G6M) which bears a 3D similarity of 0.43 with kinetin. An in vitro study to evaluate the effect of kinetin on spinach seed germination indicated that a very low concentration of kinetin (0.5 mg/l) did not show a significant effect compared to control in inducing seed germination process. Further, higher levels of kinetin (>0.5 mg/l) constituted an antagonist effect on spinach seed germination. It is anticipated that kinetin may have a molecular interaction with prioritized protein targets synthesized during the seed germination process and reduces growth. Thus, it appears that kinetin may not be a suitable hormone for enhancing spinach seed germination in vitro.

Electronic supplementary material

The online version of this article (doi:10.1007/s12154-015-0135-3) contains supplementary material, which is available to authorized users.     

Kinship and similarity in residency status structure female social networks in black‐and‐white colobus monkeys (colobus vellerosus)

Kinship shapes female social networks in many primate populations in which females remain in their natal group to breed. In contrast, it is unclear to which extent kinship affects the social networks in populations with female dispersal. Female Colobus vellerosus show routine facultative dispersal (i.e., some females remain philopatric and others disperse). This dispersal pattern allowed us to evaluate if facultative dispersed females form social networks shaped by an attraction to kin, to social partners with a high resource holding potential, or to similar social partners in terms of maturational stage, dominance rank, and residency status. During 2008 and 2009, we collected behavioral data via focal and ad libitum sampling of 61 females residing in eight groups at Boabeng‐Fiema, Ghana. We determined kinship based on partial pedigrees and genotypes at 17 short tandem repeat loci. Kinship influenced coalition and affiliation networks in three groups consisting of long‐term resident females with access to a relatively high number of female kin. In contrast, similar residency status was more important than kinship in structuring the affiliation network in one of two groups that contained recent female immigrants. In populations with female dispersal, the occurrence of kin structured social networks may not only depend on the kin composition of groups but also on how long the female kin have resided together. We found no consistent support for females biasing affiliation toward partners with high resource holding potential, possibly due to low levels of contest competition and small inter‐individual differences in resource holding potential. Am J Phys Anthropol 153:365–376, 2014. © 2013 Wiley Periodicals, Inc.     

SRAP Technique Efficiently Generates Polymorphisms in Puccinia striiformis Isolates

Wheat stripe rust, caused by the fungal pathogen Puccinia striiformis f.sp. tritici (PST), is a major disease of wheat in temperate‐cold climates. The identification of new markers would ease the procedure for evaluating the ongoing pathogen evolution. Twelve single pustule isolates were generated from samples of PST obtained in UK during 1987–2001. They were evaluated for their pathogenic behaviour on a set of differential cultivars and were analysed by sequence‐related amplified polymorphisms (SRAP) technique, to identify polymorphisms useful to evaluate variability among isolates. This is the first report of the application of SRAP technique to Uredinales order.     

Fast and automated functional classification with MED‐SuMo: An application on purine‐binding proteins

Ligand–protein interactions are essential for biological processes, and precise characterization of protein binding sites is crucial to understand protein functions. MED‐SuMo is a powerful technology to localize similar local regions on protein surfaces. Its heuristic is based on a 3D representation of macromolecules using specific surface chemical features associating chemical characteristics with geometrical properties. MED‐SMA is an automated and fast method to classify binding sites. It is based on MED‐SuMo technology, which builds a similarity graph, and it uses the Markov Clustering algorithm. Purine binding sites are well studied as drug targets. Here, purine binding sites of the Protein DataBank (PDB) are classified. Proteins potentially inhibited or activated through the same mechanism are gathered. Results are analyzed according to PROSITE annotations and to carefully refined functional annotations extracted from the PDB. As expected, binding sites associated with related mechanisms are gathered, for example, the Small GTPases. Nevertheless, protein kinases from different Kinome families are also found together, for example, Aurora‐A and CDK2 proteins which are inhibited by the same drugs. Representative examples of different clusters are presented. The effectiveness of the MED‐SMA approach is demonstrated as it gathers binding sites of proteins with similar structure‐activity relationships. Moreover, an efficient new protocol associates structures absent of cocrystallized ligands to the purine clusters enabling those structures to be associated with a specific binding mechanism. Applications of this classification by binding mode similarity include target‐based drug design and prediction of cross‐reactivity and therefore potential toxic side effects.