The intelligence in developing systems for molecular biology

A report on the 14th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Fortaleza, Brazil, 6-10 August 2006.     

Discovering novel biology by in silico archaeology

Archaea are prokaryotes that evolved in parallel with bacteria. Since the discovery of the distinct status of the Archaea, extensive physiological and biochemical research has been conducted to elucidate the molecular basis of their remarkable lifestyle and their unique biology. Here, we discuss how in-depth comparative genomics has been used to improve the annotation of archaeal genomes. Combined with experimental verification, bioinformatic analysis contributes to the ongoing discovery of novel metabolic conversions and control mechanisms, and as such to a better understanding of the intriguing biology of the Archaea.     

Discovering the targets of drugs via computational systems biology

Computational systems biology is empowering the study of drug action. Studies on biological effects of chemical compounds have increased in scale and accessibility, allowing integration with other large-scale experimental data types. Here, we review computational approaches for elucidating the mechanisms of both intended and undesirable effects of drugs, with the collective potential to change the nature of drug discovery and pharmacological therapy.     

Prospects for the biology of human intelligence

Despite the ubiquitous nature of Spearman's g in mental test performance, the charge «intelligence is what intelligence tests test» has not been countered in a satisfactory way. It is proposed that there are two ways to answer this complaint. The first concerns the new hypothesis testing models in factor analysis. The second involves studying the ‘biology of intelligence’. The biology of intelligence has various meanings and four are discussed: biology as theory; biology as race and genetics; biology as neurobiology; and biology as basic psychological processes. The last of these is considered in some detail and it is found that reaction time, evoked potentials and inspection time offer bright prospects for further research on the biology of psychometric intelligence.     

Techniques in molecular biology

Book Review

Techniques in molecular biologyJ.M. Walker and W. Gaastra (Eds.), vol. 2. London: Croom Helm, 1987. iv + 332 pages. £14.95. ISBN 0-7099-3673-7     

Phosphorothioates in molecular biology

The observation that phosphorothioate analogues of the nucleoside triphosphates are substrates for DNA- and RNA-polymerases has proven a boon for the molecular biologist. As these phosphorothioate-containing polymers are stable to degradation by nucleases and the sulfur atom confers many favourable chemical properties, several applications in molecular biology have been developed, including new methods for site-directed mutagenesis and DNA sequencing.     

Reconstructionist molecular biology

In the editorial inaugurating this journal, Levine (1989) pointed to a new reductionism in biology, which--unlike the old reductionism that led to specialization and isolation of areas concerned with different aspects of a complex biological problem--is providing a renewed sense of unity. This development is the result of widespread use of common experimental methodology and the emergence of signal transmission and differential gene expression as themes that are central to many areas of modern biology. I describe here a set of complementary developments in molecular biology that focus attention on the problems of complexity and organization. Simple examples are given that illustrate the difficulty of relating systemic behavior to the properties of the underlying molecular determinants, and the outlines of a general approach to this problem are presented. These developments, together with those highlighted by Levine, are leading us to a new, more integrative intellectual paradigm whose fruits will be the elucidation of fundamental issues concerning network function, design, and evolution that cannot be addressed by the current paradigm.     

Discovering regulatory and signalling circuits in molecular interaction networks

MOTIVATION: In model organisms such as yeast, large databases of protein-protein and protein-DNA interactions have become an extremely important resource for the study of protein function, evolution, and gene regulatory dynamics. In this paper we demonstrate that by integrating these interactions with widely-available mRNA expression data, it is possible to generate concrete hypotheses for the underlying mechanisms governing the observed changes in gene expression. To perform this integration systematically and at large scale, we introduce an approach for screening a molecular interaction network to identify active subnetworks, i.e., connected regions of the network that show significant changes in expression over particular subsets of conditions. The method we present here combines a rigorous statistical measure for scoring subnetworks with a search algorithm for identifying subnetworks with high score. RESULTS: We evaluated our procedure on a small network of 332 genes and 362 interactions and a large network of 4160 genes containing all 7462 protein-protein and protein-DNA interactions in the yeast public databases. In the case of the small network, we identified five significant subnetworks that covered 41 out of 77 (53%) of all significant changes in expression. Both network analyses returned several top-scoring subnetworks with good correspondence to known regulatory mechanisms in the literature. These results demonstrate how large-scale genomic approaches may be used to uncover signalling and regulatory pathways in a systematic, integrative fashion.     

白蚁的分子生物学研究进展

白蚁是危险性社会昆虫,建立安全有效的白蚁防治方法有赖多学科的参与,分子生物学已经成为白蚁研究的重要工具。目前,DNA序列分析方法已应用于白蚁鉴定和分类,其中线粒体基因是最通用的分子标记;基因工程技术成功构建了可用于白蚁防治的白蚁肠道工程菌;Hexamerin、COX Ⅲ、纤维素酶等白蚁功能基因以及白蚁品级分化相关的若干蛋白相继得到了分离和鉴定。文章从白蚁分类、防治、功能基因、品级分化4个方面综述白蚁分子生物学的研究进展,为白蚁的防治提供新的方法和思路。     

Data warehousing in molecular biology

In the business and healthcare sectors data warehousing has provided effective solutions for information usage and knowledge discovery from databases. However, data warehousing applications in the biological research and development (R&D) sector are lagging far behind. The fuzziness and complexity of biological data represent a major challenge in data warehousing for molecular biology. By combining experiences in other domains with our findings from building a model database, we have defined the requirements for data warehousing in molecular biology.     

苔藓植物的分子生物学研究

苔藓植物是一类较低等的陆生植物,但由于它生存环境的特殊性及物种本身的特性,在多种领域均具有重要的应用价值。主要从苔藓植物分子生物学的角度介绍国际和我国研究概况．以期为进一步加强认识、提高其利用价值提供帮助。