How different from random are docking predictions when ranked by scoring functions?

Docking algorithms predict the structure of protein–protein interactions. They sample the orientation of two unbound proteins to produce various predictions about their interactions, followed by a scoring step to rank the predictions. We present a statistical assessment of scoring functions used to rank near‐native orientations, applying our statistical analysis to a benchmark dataset of decoys of protein–protein complexes and assessing the statistical significance of the outcome in the Critical Assessment of PRedicted Interactions (CAPRI) scoring experiment. A P value was assigned that depended on the number of near‐native structures in the sampling. We studied the effect of filtering out redundant structures and tested the use of pair‐potentials derived using ZDock and ZRank. Our results show that for many targets, it is not possible to determine when a successful reranking performed by scoring functions results merely from random choice. This analysis reveals that changes should be made in the design of the CAPRI scoring experiment. We propose including the statistical assessment in this experiment either at the preprocessing or the evaluation step. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

NaCl胁迫对滨藜生长及其根和叶中无机离子含量的影响

用不同浓度的NaCl溶液处理滨藜（Atriplex undulata）植株后发现：100mmol/L NaCl促进滨藜地上部及根部生物量积累,高于100mmol/l NaCl,抑制其生长。各部位的Na^ 和Cl^-含量随着NaCl浓度的升高明显增加。NaCl处理下,叶片的Na^ 和Cl^-含量高于根部,幼叶高于老叶,且叶片的K^ （除500mmol/L NaCl处理的老叶外）,根部的K^ 、Ca^2 和NO3^-无显著变化。叶片的Na/K比随NaCl浓度的升高而增加,但较高浓度时下降（在老叶中）或维持稳定（在幼叶中）。随着处理浓度的增加,各部位对K^ 的选择性（相对于Na^ ）增加,渗透调节能力增强,渗透势降低。另外,还讨论了滨藜对盐渍生境的适应特征。     

混杂试验的多元分析

本文首次提出混杂试验的多元统计分析方法,并以香茅肥料试验为实例,论述平方和与乘积和矩阵的分解及总自由度的裂分方法,各种WilksA统计量的构造及其显著性测验法．最后给出了笔者编制的SAS统计分析程序．     

棉株上烟粉虱若虫种群的垂直分布与统计方法研究

对烟粉虱Bemisiatabaci在棉花植株上的垂直分布调查发现 ,烟粉虱在棉株各部位均有分布 ,且分布极不均匀 ,统计分析表明棉株各部位间烟粉虱的种群数量存在显著的差异。棉花顶部烟粉虱的若虫数量约占全棉株若虫总量的 1 6%,通过对棉株各部位烟粉虱的若虫数量与整株若虫总量的回归分析 ,建立了相应的回归方程式     

Effect of time pressure on attentional shift and anticipatory postural control during unilateral shoulder abduction reactions in an oddball-like paradigm

Background

The effect of time pressure on attentional shift and anticipatory postural control was investigated during unilateral shoulder abduction reactions in an oddball-like paradigm.

Methods

A cue signal (S1) - imperative signal (S2) sequence was repeated with various S2-S1 intervals (1.0, 1.5, and 2.0 s). S2 comprised target and non-target stimuli presented at the position (9° to the left or the right) indicated by S1. Right shoulder abduction was performed only in response to target stimuli, which were presented with a 30% probability. The P1, N1, N2, and P3 components of event-related potentials were analyzed, and onset times of postural muscles (electromyographic activity of erector spinae and gluteus medius) were quantified with respect to middle deltoid activation.

Results

There was no significant effect of S2-S1 interval on the latency or amplitude of P1, N1, or N2. The percentage of subjects with bimodal P3 peaks was significantly smaller and the slope of the P3 waveform in the 100 ms after the first peak was significantly steeper with a 1.0-s S2-S1 interval than with a 1.5- or 2.0-s S2-S1 interval. The onset of postural muscle activity was significantly later in the shorter interval conditions.

Conclusions

These results suggest that with a shorter S2-S1 interval, that is, higher time pressure, attention was allocated to hasten the latter part of cognitive processing that may relate to attentional shift from S2 to next S1, which led to insufficient postural preparation associated with arm movement and anticipatory attention directed to S2.     

Recent novel approaches for population genomics data analysis

Next‐generation sequencing (NGS) technology is revolutionizing the fields of population genetics, molecular ecology and conservation biology. But it can be challenging for researchers to learn the new and rapidly evolving techniques required to use NGS data. A recent workshop entitled ‘Population Genomic Data Analysis’ was held to provide training in conceptual and practical aspects of data production and analysis for population genomics, with an emphasis on NGS data analysis. This workshop brought together 16 instructors who were experts in the field of population genomics and 31 student participants. Instructors provided helpful and often entertaining advice regarding how to choose and use a NGS method for a given research question, and regarding critical aspects of NGS data production and analysis such as library preparation, filtering to remove sequencing errors and outlier loci, and genotype calling. In addition, instructors provided general advice about how to approach population genomics data analysis and how to build a career in science. The overarching messages of the workshop were that NGS data analysis should be approached with a keen understanding of the theoretical models underlying the analyses, and with analyses tailored to each research question and project. When analysed carefully, NGS data provide extremely powerful tools for answering crucial questions in disciplines ranging from evolution and ecology to conservation and agriculture, including questions that could not be answered prior to the development of NGS technology.     

Vertical distribution of bacterial community structure in the sediments of two eutrophic lakes revealed by denaturing gradient gel electrophoresis (DGGE) and multivariate analysis techniques

Vertical distribution of bacterial community structure was investigated in the sediments of two eutrophic lakes of China, Lake Taihu and Lake Xuanwu. Profiles of bacterial communities were generated using a molecular fingerprinting technique, denaturing gradient gel electrophoresis (DGGE) followed by DNA sequence analysis, and the results were interpreted with multivariate statistical analysis. To assess changes in the genetic diversity of bacterial communities with changing depth, DGGE banding patterns were analysed by cluster analysis. Distinct clusters were recognized in different sampling stations of Lake Taihu. Canonical correspondence analysis (CCA) was carried out to infer the relationship between environmental variables and bacterial community structure. DGGE samples collected at the same sampling site clustered together in both lakes. Total phosphorus, organic matter and pH were considered to be the key factors driving the changes in bacterial community composition.     

Influence of ethanol concentration of extraction solvent on metabolite profiling for Salviae Miltiorrhizae Radix et Rhizoma extract by 1H NMR spectroscopy and multivariate data analysis

Salviae Miltiorrhizae Radix et Rhizoma (Danshen in China) and its related preparations are widely used in clinical practice due to its high medicinal value. In recent years, ¹H NMR technology has made great progress and demonstrated its unique advantages in the field of botanical metabolomics. In this study, ¹H NMR-based metabolomics was used to investigate the dissolution of various metabolites in Danshen as a function of ethanol concentration. ¹H NMR spectroscopy of Danshen extract identified 28 metabolites including 6 sugars, 11 amino acids, 3 organic acids, 4 salvianolic acids, and 4 tanshinones. Multivariate statistical analysis was used to classify and compare various Danshen extracts. PCA and HCA were used to obtain a global overview of the similarity in the samples and two-class OPLS-DA models were established for identifying characteristic metabolites. Then, ¹H-qNMR method was used to estimate the concentration of 22 metabolites, which is helpful to further describe the changes in metabolite ratios of various Danshen extracts. The result of this study laid the foundation for further biological activity research, and also provided an important reference for subsequent process research and quality control of Danshen related preparations.     

Fast cortical oscillation after thalamic degeneration: pivotal role of NMDA receptor

We examined electrophysiological and molecular changes of the thalamocortical system after thalamic degeneration in Purkinje cell degeneration (pcd) mice. In pcd mice, neurons in specific thalamic nuclei including the ventral medial geniculate nucleus began to degenerate around postnatal day 50, whereas the visual thalamic nucleus and nonspecific thalamic nuclei remained almost intact. In association with the morphological changes, auditory evoked potentials in the primary auditory cortex (AC) began to decrease gradually. Fast Fourier transform analysis of spontaneous cortical field potentials revealed that fast oscillation (FO) around 25 Hz occurred in the AC but not in the visual cortex. Quantitative mRNA analysis demonstrated that expression of the N-methyl-D-aspartate (NMDA) receptor was up-regulated in the AC but not in the visual cortex. Systemic administration of an NMDA antagonist abolished the FO in the AC. These results indicate that increased NMDA activity may cause the FO in the AC of pcd mice.