Book Review

Short Protocols in Molecular Biology, 4th ed.

Ausubel et al., eds
Wiley, 1999, ISBN 0-471-32938-X


This is a short and compact (1200 pages, 28 x 21.7 x 5cm) version of the major work, Current Protocols in Molecular Biology, which is currently the preeminent laboratory manual for molecular biological techniques. Unlike some of its competitors, Current Protocols has remained up to date, provides periodic updates, and is available in both print and CD versions; but at $600 a copy, Current Protocols in Molecular Biology is too expensive for individuals and even for most laboratories. Moreover, lab politics in many laboratories prevents Current Protocols from even being considered:
  1. Postdocs would steal it in sections and sneak it back to their home country.
  2. For the CD version, the CDs would turn up having been mysteriously replaced by AOL Version 5.0 CDs.
  3. Government procurement systems allow the purchase of books only from bookstores with between 2 and 19 employees owned by Black female Native-American developmentally-challenged inmates of federal penitentiaries who are blind hearing-impaired war veterans.
These factors may explain why even the NIH library does not keep an up-to-date copy of Current Protocols, and provides a reason for the existence of Short Protocols.

The main competitor to Current Protocols, Molecular Cloning: A Laboratory Manual, widely known in biomedical laboratories simply as Maniatis, seems to have faded away. In its place, Cold Spring Harbor now publishes a 4-volume multi-colored comb-bound work known as Genome Analysis: A Laboratory Manual. This complete set costs about US$400-500, and seems to be much less useful than Maniatis. The procedures are rudimentary and limited, the discussion is not up to the standards of the previous work, and the publisher seems to have used the largest typeface available (with ample amounts of whitespace) to create an oversized, overpriced replacement for what was a highly-regarded work. Despite the large print, one of the four books apparently was still not thick enough, so the publishers included a useless catalog filled with advertisements from equipment vendors.

Rumors are that the long-awaited third edition of Maniatis will be available around the end of December 2000.

The 4th edition of Short Protocols in Molecular Biology, unlike earlier editions, is now a paperback instead of being comb bound, and is printed on cheaper paper. Even so, it is priced at US$120, almost twice that of the 2nd edition (which can be obtained some places now for $17). It has also been hurriedly produced, containing embarrassing spelling errors and extra partial lines of nonsensical text in a few places. Nevertheless, on the whole, it is a definite improvement over the 2nd edition. It contains new sections on the yeast two hybrid system (inexplicably split between chapters 13 and 19), in situ hybridization, baculovirus, protein purification, mutagenesis, differential display, etc., and a little discussion has even been added.

Although most of the chapters describe solid, well-tested methods, there are some chapters that are incomplete, rudimentary, and disorganized. For example, Chapter 18, "Bioinformatics", covers only BLAST searches. "Computer Manipulation of DNA Sequences" is not in Chapter 18, but is hidden in an inadequate 3-page blurb in Chapter 7, "DNA Sequencing". The Appendix to Chapter 7 gives a useful list of some free and commercial sequence analysis software. Unfortunately, the index is so woefully inadequate that many readers will never find this list. There are even sections on basic statistics and a 19-page section of tables, both of which are hopelessly incomplete and in my opinion are out of place in a short protocol manual such as this. For example, in the isotope table, only 3H, 14C, 32P, 35S, 125I, and 131I are mentioned.

The protein methods (2D gel, gel staining, chromatography) are mostly standard, well-tested (i.e., old and obsolete) methods. There is no discussion of immobilized pH gradients (at least that I could find), and (just to give an example) TCA precipitation is covered, but not TCA-deoxycholate precipitation. Readers looking for up-to-date methods currently in use in protein biochemistry labs will need to look elsewhere.

The main value of this book, and the reason to buy it, is for the methods in DNA technology. For example, the chapter "Saccharomyces cerevisiae", while light on discussion, is an excellent introduction to basic yeast techniques. It gives 3 different protocols for yeast transformation, as well as several other basic protocols. If you are starting a new procedure, or just starting out in molecular biology, this book will be invaluable. The main failing of this and similar books, however, in my opinion, is that no descriptions are given of what the samples are supposed to look like at each step. Knowing whether one's sample has the expected appearance is a skill that is as important as knowing how much enzyme to add or what pH to use. Manuals such as Short Protocols would be much more useful if the new practitioner could benefit from the communication of these skills as well.

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