Fundamental laboratory approaches for biochemistry and biotechnology, 2nd edition

Authors


A.J. Ninfa, D.P. Ballou, and Marilee Benore, John Wiley & Sons,Hoboken, NJ, 2010, 457 pp., ISBN 978-0-470-08766-4, $70.95.

John Markwell*, * Beadle Centre, Department of Biochemistry, Lincoln, NE 68588-0664.

I generally have mixed feelings when I see that a new book has been published for the biochemistry teaching labs. On the one hand, it would be nice to have some new ideas because we tend to get locked into a set of exercises that we use year after year. However, most of us teaching in the labs have to contend with the reality of what equipment and resources are available at our institution, don't have colleagues begging us to let them come into the labs and try something new, and are only too aware that the teaching laboratory already consumes more of an instructor's time than the lecture hall. To attempt to be objective, I put off looking at this 457 page paperback until Saturday so that I could give it a full perusal.

This book attempts to provide a textbook for undergraduate and graduate students that gives an in-depth background and perspective related to the analytical techniques used in the exercises and provides 30 exercises intended to be appropriate for a 3-hour laboratory period. I feel that the intent to provide a textbook works much better than the attempt to provide a manual for specific exercises. The chapters describe the basic elements of scientific research and functioning in the laboratory, spectroscopy, quantitative determination of protein concentration, chromatography, electrophoresis, protein purification, subcellular fractionation, direct enzyme assay, coupled assay of enzymes, enzyme purification, ligand binding, recombinant DNA techniques, PCR, and internet resources for biochemical research. I enjoyed reading many of these sections of the book because they not only attempted to cover the basic principles behind common laboratory techniques but also provided practical information about the ins and outs of the analyses. These “tricks of the trade” should be quite valuable to graduate students who understand the difference between completing an assay and doing science. I was pleasantly surprised at the depth of the material in some of the sections and will recommend this book to some of the mastery-motivated undergraduate students who really want to understand how things work in the laboratory. Resources were included on techniques such as mass spectrometry, NMR, and EPR even though they were not included in the exercises.

I was less impressed with the 30 exercises that were presented. I have struggled with how to express this and still be fair to the authors and their honest attempt to provide a valuable resource. The analogy that comes to mind is recalling when my son moved out of the dormitory after the first undergraduate year and lived in a room with a very small refrigerator, a toaster oven, and a hot plate. In spite of almost 20 years training in eating a balanced diet, he resorted to living on pizza and ramen noodles for 9 months. I was somewhat surprised to open the book to page 39 and see an analog Spectronic 20® and find that the exercises are designed to be carried out with this venerable instrument. The problem is not only the analog nature of the instrument but also in the use of test tubes, rather than cuvettes with no fixed path length and the 20-nm bandpass of the measuring beam. Herein, lies the dilemma for teaching laboratories. We expose students to exercises permitted by the equipment in our teaching labs, regardless of whether this equipment is still being used in industrial or research labs in the digital real world. The reality for those of us who instruct in teaching labs is that the curriculum is dictated by the available equipment. The lecture courses are kept current by continuous revision of textbooks, but there is no revision of teaching lab infrastructure every 5 or 10 years to keep their curriculum current. This appears to be as true at the authors' institution as it is at mine, and I see no signs of improvement.

Moving on to the described exercises, the initial ones tend to have no degrees of freedom, whereas there are suggestions toward the latter exercises for open-ended explorations by the students. The reagents and supplies necessary for the exercises are listed along with suppliers and catalog numbers. In some places the volumes per number of students are provided, whereas for other exercise it is not. The exercises use several different enzymes to expose students to simple chromogenic assays and enzyme-coupled assays. The description of kinetic analysis is particularly thorough and should give students an understanding of the different graphical methods and the strengths of each. One of the suggested PCR exercises involves analysis of pseudo-forensic evidence to determine the likely suspect in a “murder.” The final chapter on internet resources is a survey and does not provide specific exercises.

While reading the book, I did find several minor issues that I would change, but no more than I find in my own lab manual when I force myself to give it a thorough perusal. One area in which I feel there could be improvement is environmental health and safety. The text on page 163 appears to advocate putting unpolymerized acrylamide down the drain, and, although the need to avoid contact with ethidium bromide is emphasized, there are no instructions on how to dispose of used gels or buffer. Similarly, there is adequate coverage of most elements of laboratory safety, but no mention of hazardous material placards. I presume that most of us would find a similar lack of comprehensive coverage of topics in our own lab manuals and accept that these materials continually evolve and improve.

In summary, I found the text portion of the book useful and worth having on my bookshelf as a reference and to loan to students. The portion of the book with exercises has the same limitations as every compendium of laboratory exercises. The reality is that most of us instructing in teaching laboratories are forced to use exercises suitable for the equipment in place and our budgets. Most of us may be able to use or adapt some of the exercises presented in this book, but few of us are likely to be able to use all of them and adopt this as a textbook for our laboratory course.

Ancillary