Deoxyribonucleic acid (DNA) was identified 140 years ago by a Swiss physician Friedrich Miescher. His discovery was fundamental for the development of biochemistry, genetics and molecular biology. Contemporary biology, biotechnology and medicine largely depends on our ability to analyze, synthesize and manipulate DNA. We present highlights of the history of DNA research from the very beginning to the sequencing of human genome.
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Specialized software, on-line tools and computational resources are very common in contemporary science. One of the exemplary domain is genomics – a new branch of science that developed rapidly in the last decade. As the genome research is very complex, it must be supported by professional informatics. In a microarray field the following steps cannot be performed without computational work: design of probes, quantitative analysis of hybridization results, post-processing, and finally data storage and management. Here, the general aspects of virtual laboratory systems are presented together with perspectives of their implementation in genomics in order to automate and facilitate this area of research.
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The DNA microarray technology delivers an experimental tool that allows surveying expression of genetic information on a genome-wide scale at the level of single genes - for the new field termed functional genomics. Gene expression profiling - the primary application of DNA microarrays technology - generates monumental amounts of information concerning the functioning of genes, cells and organisms. However, the expression of genetic information is regulated by a number of factors that cannot be directly targeted by standard gene expression profiling. The genetic material of eukaryotic cells is packed into chromatin which provides the compaction and organization of DNA for replication, repair and recombination processes, and is the major epigenetic factor determining the expression of genetic information. Genomic DNA can be methylated and this modification modulates interactions with proteins which change the functional status of genes. Both chromatin structure and transcriptional activity are affected by the processes of replication, recombination and repair. Modified DNA microarray technology could be applied to genome-wide study of epigenetic factors and processes that modulate the expression of genetic information. Attempts to use DNA microarrays in studies of chromatin packing state, chromatin/DNA-binding protein distribution and DNA methylation pattern on a genome-wide scale are briefly reviewed in this paper.
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In contemporary science, virtual laboratories give a chance to improve research by facilitating access to high-throughput technologies and bioinformatics methods. The Genomic Virtual Laboratory (GVL) presented here was developed for automate analysis of data retrieved from a microarray experiment. The system was implemented for R Bioconductor-based analysis of results obtained in the study on human acute myeloid leukaemia (AML). The article extends the theoretical aspects of GVL presented earlier [8] and describes how the particular elements were integrated to establish the advanced system of two-colour microarray data analysis.