Editorial
The final issue of Briefings in Functional Genomics and Proteomics this year contains a broad mix of articles covering microscopy, microarrays, HPLC for proteomics, transcriptional silencing and data integration. In our first article, Goran Mitulovic reviews recent advances in chromatographic techniques for proteomic analysis. One of the difficulties associated with the proteome is the separation of complex protein mixtures, and the subsequent identification of the individual components. One approach is to use two-dimensional gel electrophoresis to separate protein spots followed by detection using mass spectrometry. However, HPLC methods have developed considerably in the last few years, and provide a versatile alternative. Mitulovic discusses the use of HPLC to analyse post-translational modifications and goes on to review immobilized metal-ion affinity chromatography for HPLC. In the second half of the article, Mitulovic looks at multi-dimensional separation techniques such as MudPIT, and provides an insightful outlook at technologies that are in development.
Katrina Waters and colleagues follow this with a discussion of some of the issues surrounding data merging for integrated microarray and proteomic analysis. This is not a trivial task, given the fundamental differences between technology platforms for generating expression and proteome data. Yet, this is a problem that needs to be reconciled if we are to understand the real differences between the transcriptome and proteome at any given time point and in any sample, and as a consequence begin to understand the dynamics of complex biological systems. The authors tackle this considerable task by identifying potential sources of error in protein and transcript abundance, and examining methods to reduce these. They next look at disparity among databases, a worrying trend in an age when large-scale biology both generates, and relies on, many different data sources with varying degrees of confidence. The use of biological process or functional annotation, the authors suggest, would be of great benefit in cross-referencing databases and merging data sets. Ontologies have the potential to be extremely useful, if they are comprehensive and universal, but comparison of different ontologies often provides inconsistent results, and clearly more work is needed in this area, including most probably a great deal of intensive manual annotation. The authors remain optimistic, with the hope that as the sensitivity of quantitation improves in both expression and proteome analyses, together with improvements in database consistency, accurate merging of diverse data will be possible, providing invaluable information on biological processes.
We stay with microarrays for the third review as Michael Allen and William Wilson inform us about the Coccolithovirus microarray, and how it has been utilized in a variety of applications. Indeed, this is a nice example of how microarrays may be made not only to model organisms with known genomes, but to little known ones too. The Coccolithoviridae is in fact a family of giant viruses that infect the super-abundant species Emiliania huxleyi, a marine alga that generates beautifully sculpted calcium carbonate cell coverings known as coccoliths. E. huxleyi plays a significant role in the Earth's climate through both coccolith formation and gas emission, yet the molecular biology of this alga and the viruses that infect it is poorly understood.
The Coccolithovirus EhV-86 is a large virus, with a genome size of over 400 kb which has been completely sequenced. With a large number of predicted open reading frames with little or no database similarity, a modest microarray was fabricated covering the majority of the predicted genes in the genome. This, it turns out, was an insightful decision, as the array has subsequently been used for a number of different experiments, enriching our knowledge of the molecular biology of this large and important viral family.
The penultimate review in this volume is bought to us by Lu Gao and David Gross, and focuses on mechanisms of transcriptional silencing in yeast. Using Saccharomyces cerevisiae as their model, the authors describe how genomics and proteomics are being used to help understand how chromatin in budding yeast is silenced by silent information regulator (SIR) proteins in association with modified histones at nucelosomes. Silencing involves regions of the chromosome rather than individual genes and mediates a change in topography of the chromatin. How these regions are defined and controlled forms the basis of this review, together with a discussion of how SIR heterochromatin might act to repress transcription. Future proteomic approaches show a great deal of promise in this area.
The issue closes with Rainer Heintzmann and Gabriella Ficz reviewing recent developments and future perspectives in breaking the resolution limit in light microscopy. Microscopy has always been an essential tool for biologists, but it is becoming increasingly attractive to be able to use real time and live imaging to provide functional readout at the cellular and whole organism levels. The authors discuss how increasing resolution is being achieved for fluorescence-based approaches using either non-linear illumination or molecular/particle tracking methods. So we draw to a close for another year; a year in which Briefings in Functional Genomics and Proteomics has seen considerable change. We now look forward to a productive and insightful future with Oxford University Press.
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