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European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.04753404.
Analysing gene expression, edited by S. Lorkowski and P. Cullen. 2003. Weinheim, Germany: Wiley-VCH. $335.
Researchers studying the regulation of gene expression have developed a range of novel methods to study alterations in cellular RNA and protein content. A new handbook does an excellent job of examining how these procedures work and why they are useful to the biologist.
Tools in science are in constant evolution. So scientists have to update their knowledge and find the best method to answer a question. Nowhere is this more obvious than in the field of molecular biology. To understand a particular disease or to characterize the phenotype of a mutant cell, we need to quantify messenger RNA and protein levels, often at a global level. Likewise, companies in the pursuit of novel drugs have become acutely interested in studying gene expression, both as a means to identify novel targets and to deduce the molecular mechanism (as well as the side effects) of an existing drug. Yet few books provide a comprehensive overview of almost every technique invented for the study of gene expression. The handbook Analysing Gene Expression, by Drs. S. Lorkowski and P. Cullen, is probably the first successful attempt to compile a comprehensive handbook devoted to methods in gene expression.
At the heart of cellular regulation lies the working of tens of thousands of different biological molecules. Proteins regulate each other through posttranslational modifications; compartmentalization into different cellular organelles; and their targeted, controlled degradation, for example. Ultimately, many of these events control gene expression. Here, different mechanisms exist to regulate the production of the active gene product. Whole chromosomal regions or specific genes can be transcriptionally silenced or activated by various enzymes and proteins that lock in the transcriptional state, transcriptional initiation, and elongation can be enhanced in very specific ways; the way genes are spliced together to produce the mature messenger RNA (mRNA) molecule can be influenced; and, finally, translation of mRNAs into proteins can be regulated. Even for a lab studying a single pathway, mechanism, or protein, the sheer complexity of events call for an interdisciplinary approach to study gene and protein function. This need has led molecular biologists to create novel tools on both a conventional lab scale, as well as on a scale (and with a lot of know-how) that originates from the engineering and computer science field. Indeed, modern molecular biology owes a lot to developments in computer technology, robotics, and information management. It is due to these recent efforts that we can speak of functional genomics, proteomics, and systems biology. A small, traditional lab toiling away on their pet gene (or protein) could be forgiven for feeling a little overwhelmed with all this new technology in the gene expression field from time to time. But this need not be so, and the book Analysing Gene Expression proves this point. Despite its considerable length of about 1000 pages, it succeeds at informing the readers who could stand to profit from the book most.
The book is completely up-to-date and provides a compendium of the methods currently used to analyze gene expression. It covers state-of-the-art methods such as DNA microarrays, real-time PCR, differential display, and positron emission tomography. It has required a worldwide joint effort of many leading researchers to achieve this encyclopedia of functional genomics. All the methods and the necessary equipment are presented visually in more than 300—mostly colored—illustrations. Enough details are provided to determine the most suitable technique to address a biological question. Moreover, the concepts are put into perspective by discussing their inherent advantages and drawbacks.
The book has been organized into seven chapters and is divided into two volumes. After an introduction to functional genomics in Chapter 1, the book is divided into six chapters that cover sample preparation, mRNA, and protein analysis, both in basic research and clinical settings, as well as in high throughput, industrial environments. Aware of the new challenges in modern biology, the editors also cover the biocomputing field, dedicating the last chapter to this subject.
The first chapter starts with a general introduction to the basic concepts of gene expression. This is of great interest in that it aims to describe the biology that lies at the heart of current functional genomics efforts. It gives a complete, although sometimes arduous, overview of the mechanisms involved in the regulation of mRNA and protein expression. Quoting the editors, this book is particularly useful to "novice" scientists. This is true. But especially in this chapter, it would be useful to provide a list of definitions for the jargon that is used in gene expression research, as well as for the many acronyms that dot the field. Aside from this omission, the text discusses well the various mechanisms and concepts in biology, with a sound use of schemes and examples. At times, some schemes have no key or are referenced in the text by number when they are actually organized by letter (or to the contrary). Inevitably, this causes some confusion, and can be misleading for someone trying to understand a particular procedure. Overall, while most sections in Chapter 1 are really well-conceived and of great general biology interest, such as the subchapter on housekeeping genes, others are rather terse, and would profit from a few additional schemes. For instance, a better discussion of the differences in translational regulation between prokaryotes and eukaryotes could have followed the nice example set a few pages earlier in the subchapter on the transcriptional regulation.
The fifth chapter of the handbook will catch the attention of scientists thinking about creating their own start-up company or high-throughput functional biology effort. Scaling up from small-scale laboratory use of techniques to industrial applications is no small feat. High-throughput often denotes DNA microarrays and related techniques, which a conventional book would explain at great length. Here, the authors go beyond microarray tools and also deal with high-throughput adaptations of other hybridization-based techniques such as oligonucleotide footprinting or Quantikine mRNA assays. Moreover, they present a whole set of improved PCR-based methods, which nicely complement the picture. Conventional techniques already developed in earlier chapters of the handbook are observed from a different point of view and are found associated with words like automation, robotization, and efficiency. Also in this chapter the authors rightly refer to bioinformatics as a vital requirement to extract meaningful information from the raw data obtained by these high-throughput analyses.
The seventh and last chapter explains how the scientific community is currently facilitating data exchange and database interoperability. Experts (and novices alike) in the biocomputing field will be happy to find an exhaustive and detailed catalog of all the databases and programs that are available. But the chapter does more than that. For example, after reading the section on the "CYTOMER" database (a histological database providing information from the cellular level to that of complete organs), readers will probably be able to employ it readily. Details are provided to facilitate access to and use of the Web pages. The chapter remains concise, but it does provide a comprehensive overview of all gene expression resources. A useful table that recapitulates all the discussed databases is provided at the end of the chapter, serving as a handy index for investigators.
In general, all subchapters in a given chapter follow the same clear progression, highlighting first the aim of a given method, then commenting on the procedure. Finally, most subchapters provide a compendium of advantages and drawbacks related to each technique. The constant use of this implicit pedagogical plan is a great way to help readers focus clearly as they employ a whole set of methods. Every conclusion to a given method provides helpful information on the technique. Still, tables summarizing the strong and weak points for each method would have been valuable. In the current edition, these tables are too infrequent to be useful.
Clearly, the authors did their best to make the book convenient for practitioners. Indeed, a biologist, whose hands are usually busy pipeting, will appreciate not having to deal with a heavy book of 1000 pages, but rather with two lighter volumes. The flip side of this coin is that the index appears only at the end of the second book. This is inconvenient when consulting the first volume. The next edition of this milestone in gene expression reference literature would benefit by having an index also in the first part of the handbook.
One cannot deny the great effort that the authors have made in trying to summarize the experimental bases for each technique without detailing entire protocols. In most cases, the recent and relevant literature is cited, so the reader should be able to easily find all the necessary detail. For example, advanced methods for comparing protein quantities at the level of the whole "proteome," such as ICAT (Isotope-Coded Affinity Tag) or MELK (Multi-Epitope Li-gand-Kartographie), are well presented and referenced. This combination of concise technical presentation and accurate referencing to the bibliography works well.
Several facts show the thought the editors have put into this book to make it a handy and up-to-date tool. Here and there, cross-references to other chapters of the book have been skillfully inserted to avoid unnecessary duplication. This makes each individual paragraph pertinent to the chapter in which it is found, instead of drowning the reader with multiple concepts and examples at the same time. Nevertheless, when using this noticeable, recursive procedure, a precise page number would have been better than the broad chapter names that are usually listed. Another good feature is the number of references to online resources. We cannot ignore the beneficial impact that the Internet has on everyday research. But one of its main disadvantages is its ephemerality. Thus, it would have been convenient to put dates on all the Web links quoted in the text. Information on the Internet evolves so fast that even between the submission of the chapter by an author and the publication of the book, a link may already be out of date.
The writing style of the many different researchers suits this handbook, as they are generally concise and to the point. Moreover, the authors have done a great job at conveying their faith and optimism in future improvements of their techniques, leaving in us all the curiosity that is needed to push for more progress. For its part, the publisher, Wiley-VCH, walks in step with the authors and editors, and has been able to achieve very good copy-editing work. The text contains hardly any first edition pitfalls, like missing articles, repeated words, or incorrect punctuation. The publisher has done an excellent job at honoring the large amount of work achieved both by the authors and by the editors.
We think that many readers will recognize the book’s worth, and be convinced that this is the reference book for gene expression analysis that one should have in the lab. Retailing at $335, the handbook certainly is not cheap. But this is a pittance compared to the cost of at least a few of the powerful techniques described in the book. If your lab can only dream of such research budgets, then at a minimum the book will make for some good bedtime reading.
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