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.     

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.     

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     

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.     

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。     

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.     

Discovering high mobility group A molecular partners in tumour cells

DNA-based activities rely on an extremely coordinated sequence of events performed by several chromatin-associated proteins which act in concert. High Mobility Group A (HMGA) proteins are non-histone architectural nuclear factors that participate in the regulation of specific genes but they are also believed to have a more general role in chromatin dynamics. The peculiarity of these proteins is their flexibility, both in terms of DNA-binding and in protein-protein interactions. Since these proteins act as core elements in the assembly of multiprotein complexes called enhanceosomes, and have already displayed the ability to interact with several different proteins, we started a proteomic approach for the systematic identification of their molecular partners. By a combination of affinity chromatography, two-dimensional gel electrophoresis and mass spectrometry we have identified about twenty putative HMGA interactors which could be roughly assigned to three different classes: mRNA processing proteins, chromatin remodelling related factors and structural proteins. Direct HMGA interaction with some of these proteins was confirmed by glutathione-S-transferase pull-down assays and the HMGA domain involved was mapped. Blot-overlay experiments reveal that members of the HMGA family share most of their molecular partners but, interestingly, it seems that there are some cell-type specific partners. Taken together, these experimental data indicate that HMGA proteins are highly connected nodes in the chromatin protein network. Since these proteins are strongly implicated with cancer development, the identification of molecules able to perturb the HMGA molecular network could be a possible tool to interfere with their oncogenic activity.