A novel genome-wide fulllength kinesin prediction analysis reveals additional mammalian kinesins

Kinesins are microtubule-based motor proteins that perform diverse functions[1―6], including the transloca- tion of vesicles, organelles, chromosomes, proteincomplexes, RNA-binding proteins (RNPs), etc. They also help to orchestrate microtubule dynamics …     

基因组学领域演进的科学计量研究

该研究分析了当前生命科学中最具理论与应用价值的研究领域基因组学1991 — 2006 年在知识维
度上的演进过程。研究以Web of Science 数据库的论文数据为基础，对基因组学领域高频关键词的共现
矩阵进行了分析：三个不同时间段的多维尺度分析表明，处于不同发展阶段的关键词之间亲疏关系存在规
律性特征，对这些特征的分析进一步可以揭示该领域目前所处的发展阶段；此外，不同阶段共现矩阵的因
子分析展现了研究主题在时间轴上的变迁。数据分析表明：利用科学计量方法对基因组学演进过程进行研
究可以挖掘大量有用的信息。     

Scanning for sisnatures of geosraphically restricted selection based on population genomics analysis

Natural selection, as the driving force of human evolution, has direct impact on population differentiation. However, it is still unclear to what extent the genetic differentiation has been caused by natural selection. To explore this question, we performed a genome-wide scan with single nucleotide polymorphism （SNP） data from the International HapMap Project. Single locus FsTanalysis was applied to assess the frequency difference among populations in autosomes. Based on the empirical distribution of FsT, we identified 12669 SNPs correlating to population differentiation and 1853 candidate genes subjected to geographic restricted natural selection. Further interpretation of gene ontogeny revealed 121 categories of biological process with the enrichments of candidate genes. Our results suggest that natural selection may play an important role in human population differentiation. In addition, our analysis provides new clues as well as research methods for our understanding of population differentiation and natural selection.     

植物功能基因组研究进展

基因组学研究已开始从结构基因组学转向功能基因组学。对功能基因组学研究的重要意义及内容、方法进行了综述，并对植物功能基因的研究进展及应用前景作了介绍。     

Functional genomics in the rice blast fungus to unravel the fungal pathogenicity

A rapidly growing number of successful genome sequencing projects in plant pathogenic fungi greatly increase the demands for tools and methodologies to study fungal pathogenicity at genomic scale. Magnaporthe oryzae is an economically important plant pathogenic fungus whose genome is fully sequenced. Recently we have reported the development and application of functional genomics platform technologies in M. oryzae. This model approach would have many practical ramifications in design and implementation of upcoming functional genomics studies of filamentous fungi aimed at understanding fungal pathogenicity.     

What to Learn from a Comparative Genomic Sequence Analysis of <Emphasis Type="Italic">L</Emphasis>-Carnitine Dehydrogenase

Summary. In contrast to eukaryotic cells certain eubacterial strains have acquired the ability to utilize L-carnitine (R-(–)-3-hydroxy-4-(trimethylamino)butyrate) as sole source of energy, carbon and nitrogen. The first step of the L-carnitine degradation to glycine betaine is catalysed by L-carnitine dehydrogenase (L-CDH, EC 1.1.1.108) and results in the formation of the dehydrocarnitine. During the oxidation of L-carnitine a simultaneous conversion of the cofactor NAD⁺ to NADH takes place. This catabolic reaction has always been of keen interest, because it can be exploited for spectroscopic L-carnitine determination in biological fluids – a quantification method, which is developed in our lab – as well as L-carnitine production.Based on a cloned L-CDH sequence an expedition through the currently available prokaryotic genomic sequence space began to mine relevant information about bacterial L-carnitine metabolism hidden in the enormous amount of data stored in public sequence databases. Thus by means of homology-based and context-based protein function prediction is revealed that L-CDH exists in certain eubacterial genomes either as a protein of approximately 35 kDa or as a homologous fusion protein of approximately 54 kDa with an additional putative domain, which is predicted to possess a thioesterase activity. These two variants of the enzyme are found on one hand in the genome sequence of bacterial species, which were previously reported to decompose L-carnitine, and on the other hand in gram-positive bacteria, which were not known to express L-CDH. Furthermore we could not only discover that L-CDH is located in a conserved genetic entity, which genes are very likely involved in this L-carnitine catabolic pathway, but also pinpoint the exact genomic sequence position of several other enzymes, which play an essential role in the bacterial metabolism of L-carnitine precursors.     

Design of experiments on 135 cloned poplar trees to map environmental influence in greenhouse

To find and ascertain phenotypic differences, minimal variation between biological replicates is always desired. Variation between the replicates can originate from genetic transformation but also from environmental effects in the greenhouse. Design of experiments (DoE) has been used in field trials for many years and proven its value but is underused within functional genomics including greenhouse experiments. We propose a strategy to estimate the effect of environmental factors with the ultimate goal of minimizing variation between biological replicates, based on DoE. DoE can be analyzed in many ways. We present a graphical solution together with solutions based on classical statistics as well as the newly developed OPLS methodology.In this study, we used DoE to evaluate the influence of plant specific factors (plant size, shoot type, plant quality, and amount of fertilizer) and rotation of plant positions on height and section area of 135 cloned wild type poplar trees grown in the greenhouse. Statistical analysis revealed that plant position was the main contributor to variability among biological replicates and applying a plant rotation scheme could reduce this variation.     

Kendall’s tau-type rank statistics in genome data

High-dimensional data models abound in genomics studies, where often inadequately small sample sizes create impasses for incorporation of standard statistical tools. Conventional assumptions of linearity of regression, homoscedasticity and (multi-) normality of errors may not be tenable in many such interdisciplinary setups. In this study, Kendall’s tau-type rank statistics are employed for statistical inference, avoiding most of parametric assumptions to a greater extent. The proposed procedures are compared with Kendall’s tau statistic based ones. Applications in microarray data models are stressed.     

Antibacterial Natural Products in Medicinal Chemistry—Exodus or Revival?

To create a drug, nature's blueprints often have to be improved through semisynthesis or total synthesis (chemical postevolution). Selected contributions from industrial and academic groups highlight the arduous but rewarding path from natural products to drugs. Principle modification types for natural products are discussed herein, such as decoration, substitution, and degradation. The biological, chemical, and socioeconomic environments of antibacterial research are dealt with in context. Natural products, many from soil organisms, have provided the majority of lead structures for marketed anti-infectives. Surprisingly, numerous "old" classes of antibacterial natural products have never been intensively explored by medicinal chemists. Nevertheless, research on antibacterial natural products is flagging. Apparently, the "old fashioned" natural products no longer fit into modern drug discovery. The handling of natural products is cumbersome, requiring nonstandardized workflows and extended timelines. Revisiting natural products with modern chemistry and target-finding tools from biology (reversed genomics) is one option for their revival.