VPMCD: variable interaction modeling approach for class discrimination in biological systems

Data classification algorithms applied for class prediction in computational biology literature are data specific and have shown varying degrees of performance. Different classes cannot be distinguished solely based on interclass distances or decision boundaries. We propose that inter-relations among the features be exploited for separating observations into specific classes. A new variable predictive model based class discrimination (VPMCD) method is described here. Three well established and proven data sets of varying statistical and biological significance are utilized as benchmark. The performance of the new method is compared with advanced classification algorithms. The new method performs better during different tests and shows higher stability and robustness. The VPMCD is observed to be a potentially strong classification approach and can be effectively extended to other data mining applications involving biological systems.     

Altered resource allocation during seed development in Arabidopsis caused by the abi3 mutation

The regulation of whole-plant resource allocation during seed development in Arabidopsis thaliana was investigated by examining growth rate and partitioning of ¹⁴CO₂ in wild-type plants and those carrying the abi3 mutation. Plants carrying the abi3 mutation partitioned more resources into seed development than the wild type. The extra resources were available as a result of delayed senescence of the cauline leaves in the mutant. After supply of ¹⁴CO₂ at later stages of reproductive development differences in patterns of ¹⁴C distribution between mutant and wild type were consistent with long-term changes in growth and allocation. The role of long-distance signals in the regulation of seed yield in Arabidopsis is discussed.     

广东黑石顶南亚热带常绿阔叶林树木生长研究(英文)

用测树器和年轮解析法 ,测定了广东黑石顶南亚热带常绿阔叶林的立木和幼树的径向生长和高生长。年轮解析法测得立木的年直径生长量在 0 .1～ 0 .5cm之间 ,一些立木的直径生长呈现出生长快的年份 ( 1～ 3a)和生长慢的年份 ( 1～ 3a)交替的节律。测树器测得立木 5a的年平均直径生长量为0 .0 74cm,5年期间测得有 1 7.6%的个体直径为零增长或负增长。立木的年高增长量为 1 0～ 50 cm,高生长高峰期通常在 1 0～ 30年龄。在树木生长的早期 ,高度的生长优于直径的生长 ,而在树木生长的中、后期 ,直径的生长逐渐优于高度的生长。用游标卡尺和卷尺测得幼树 (通常 1～ 3m高 )的直径和高度 5a的平均生长量分别为 0 .1 0 7cm和 4.76cm。 5a间没有幼树的直径生长为零增长或负增长 ,但约有 9%的个体的高度生长为零增长或负增长。     

香菇亲本菌株及其杂交后代的RAPD分析*

运用随机扩增多态性DNA（RandomamplifiedpolymorphicDNA,RAPD）技术对源于两个香菇（Lentinulaedodes）双核菌株的孢子单核体、原生质体单核体及其杂交后代进行了基因组DNA多态性分析。用9个随机引物共扩增出116条DNA片段,其中82．5％具有多态性。综合分析9个随机引物的扩增谱带,可将所有供试亲本单核体清楚地分开,且早核体聚类分析的结果与其来源及遗传背景相吻合。此外,用两个双核亲本菌株的各4个不同交配型的孢子单核体两两支配所得的所有杂交组合,也均可与双核亲本菌株明确地区分开来。因此,在杂交育种中,RAPD分析可为亲本的选配及杂种的鉴定提供可靠依据。     

Genome-wide survey of prokaryotic O-protein phosphatases

Complex and diverse signal transduction circuits are responsible for the efficient functioning of cellular network. Protein kinases and O-protein phosphatases are primarily responsible for propagating such stimuli within a eukaryotic cell. However, there is limited understanding of O-protein phosphatases in the prokaryotic genomes. The availability of complete genome sequence information for several prokaryotes permits a genome-wide survey of O-protein phosphatases. The distribution of the various protein phosphatase families has been observed to be mosaic, with the exception of the members of the phospho protein family P (PPP), which is consistent with previous studies. The PPP family is ubiquitous in the prokaryotic world and undergoes the highest sequence divergence within a genome amongst phosphatases studied. The co-occurrence of low molecular mass tyrosine phosphatase (LMWPc) and PPP domain in a single polypeptide suggests that the protein present in Archaeoglobus fulgidus might represent the progenitor for all protein phosphatases. The curation of data on prokaryotic protein phosphatases provides a convenient framework for the analysis of domain architectures and for characterising structural and functional properties of this important family of signalling proteins.     

Conditional likelihood score functions for mixed models in linkage analysis

In this paper, we develop a general strategy for linkage analysis, applicable for arbitrary pedigree structures and genetic models with one major gene, polygenes and shared environmental effects. Extending work of Whittemore (1996), McPeek (1999) and Hossjer (2003d), the efficient score statistic is computed from a conditional likelihood of marker data given phenotypes. The resulting semiparametric linkage analysis is very similar to nonparametric linkage based on affected individuals. The efficient score S depends not only on identical-by-descent sharing and phenotypes, but also on a few parameters chosen by the user. We focus on (1) weak penetrance models, where the major gene has a small effect and (2) rare disease models, where the major gene has a possibly strong effect but the disease causing allele is rare. We illustrate our results for a large class of genetic models with a multivariate Gaussian liability. This class incorporates one major gene, polygenes and shared environmental effects in the liability, and allows e.g. binary, Gaussian, Poisson distributed and life-length phenotypes. A detailed simulation study is conducted for Gaussian phenotypes. The performance of the two optimal score functions S(wpairs) and S(normdom) are investigated. The conclusion is that (i) inclusion of polygenic effects into the score function increases overall performance for a wide range of genetic models and (ii) score functions based on the rare disease assumption are slightly more powerful.     

Mountain summer farms in Røldal,western Norway –; vegetation classification and patterns in species turnover and richness

This paper discusses vegetation types and diversity patterns in relation to environment and land-use at summer farms, a characteristic cultural landscape in the Norwegian mountains. Floristic data (189 taxa) were collected in 130 4-m² sample plots within 12 summer farms in Røldal, western Norway. The study was designed to sample as fully as possible the range of floristic, environmental, and land-use conditions. Vegetation types delimited by two-way indicator species analysis were consistent with results from earlier phytosociological studies. Detrended correspondence analysis and canonical correspondence analysis show that rather than being distinct vegetation types, the major floristic variation is structured along a spatial gradient from summer farm to the surrounding heathland vegetation. Species richness (alpha diversity) was modelled against environmental variables by generalized linear modelling and compositional turnover (beta diversity) by canonical correspondence analysis. Most environmental factors made significant contributions, but the spatial distance-to-farm gradient was the best predictor of both species richness and turnover. While summer farms reduce mean species richness at the plot scale, the compositional heterogeneity of the upland landscapes is increased, thereby creating ‘ecological room’ for additional vegetation types and species. Within an overall similarity across scales, soil variables (pH, base saturation, LOI, phosphate and nitrogen) differed considerably in their explanatory power for richness and turnover. A difference between ‘productivity limiting’ factors and ‘environmental sieves’ is proposed as an explanation. Species turnover with altitude is relatively low in grasslands as compared to heaths.     

Exploring structural features of the interaction between the scorpion toxinCnErg1 and ERG K+ channels

The gamma-KTx-type scorpion toxins specific for K+ channels were found to interact with ERG channels on the turret region, while alpha-KTx3.2 Agitoxin-2 binds to the pore region of the Shaker K+ channel, and alpha-KTx5.3 BmP05 binds to the intermediate region of the small-conductance calcium-activated K-channel (SK(Ca)). In order to explore the critical residues for gamma-KTx binding, we determined the NMR structure of native gamma-KTx1.1 (CnErg1), a 42 amino acid residues scorpion toxin isolated from the venom of the Mexican scorpion Centruro?des noxius Hoffmann, and we used computational evolutionary trace (ET) analysis to predict possible structural and functional features of interacting surfaces. The 1H-NMR three-dimensional solution structure of native ergtoxin (CnErg1) was solved using a total of 452 distance constraints, 13 3J(NH-Halpha) and 10 hydrogen bonds. The structure is characterized by 2 segments of alpha-helices and a triple-stranded antiparallel beta-sheet stabilized by 4 disulfide bridges. The ET and structural analysis provided indication of the presence of two important amino acid residue clusters, one hydrophobic and the other hydrophilic, that should be involved in the surface contact between the toxin and the channel. Some features of the proposed interacting surface are discussed.