"Frontmatter". In: Plant Genomics and Proteomics
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Christopher A. Cullis - Plant Genomics and Proteomics-J. Wiley & Sons (2004)
CHAPTER
2 T H E B A S I C T O O L B O X — A C Q U I R I N G F U N C T I O N A L G E N O M I C D ATA O VERVIEW “If the only tool you have is a hammer, then everything looks like a nail.” This old adage really does apply to many scientific situations and has shaped the historical investigations of plant form and function. When the tools were ruler and microscope, growth studies and detailed structural descriptions were all that were possible. As the molecular technology developed both the range of studies and the way that questions can be framed have been greatly expanded. As the technology improves old questions can be revisited and new explanations can be suggested. The new tools that are available for investigating gene structure and function have been steadily developed over the past 30 years. The molecu- lar biology revolution for the characterization of genomes began with the development of recombinant DNA techniques. Today the molecular tools include various cloning vectors, the incorporation of robotics into high- throughput methodologies, for example, in the area of DNA sequencing, and mass spectroscopy for the detailed characterization of proteins. The application of these methodologies results in the generation of very large amounts of data that need to be processed. Whereas in the past the actual accumulation of the data was the rate-limiting step, the bottleneck is now the ability to analyze all the data. The wealth of data generated by high-throughput methodologies will advance our understanding of gene structure and function by the molecu- Plant Genomics and Proteomics, by Christopher A. Cullis ISBN 0-471-37314-1 Copyright © 2004 John Wiley & Sons, Inc. 2 3 lar characterization of already existing variants. In addition, the ability to change gene expression in vivo, by using insertional mutagenesis, RNA interference, or other silencing mechanisms, will be crucial in determining the specific function of a particular gene. Therefore, at the present time, techniques are available to identify gene expression at various stages of development and/or in response to biotic or abiotic stresses and then to develop the biological material to determine which of these observations or structural entities are causal of the changes seen and which are simply the downstream result of some earlier modulation of gene expression. This chapter considers the various techniques used in the acquisition of genomic data. Broadly speaking, they cover the following main areas: 1. Methods of isolating and fractionating genomes into manageable- sized pieces, with the associated automation and tracking systems that are necessary to manage the experiments and to interpret the results. Genome fractionation must occur at both the DNA and RNA levels so that the actual expressed genomic regions can be deter- mined. The cloning of both genomic DNAs and expressed RNAs is therefore necessary. 2. The development of microarray technology has opened up the pos- sibilities of expression profiling, the visualization of the expression of many genes simultaneously. 3. The downstream processing of the RNAs into proteins and the modification of these proteins and their abundances can also be determined so that the effective contribution of any expressed RNAs can be more directly demonstrated. The development of metabolic profiling will continue to open up new avenues for understanding the function and contribution each of these proteins to the phenotype. 4. The informatics tools to analyze this wealth of molecular data. 5. The ability to select a particular gene or suite of genes and to selec- tively interfere with their expression, to directly test whether the con- clusions drawn from the molecular data actually hold up in practice. Download 1.13 Mb. Do'stlaringiz bilan baham: |
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