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Professor and Chair, Pharmacogenomics Department and Associate Dean for Academic Affairs, Bernard J Dunn School of Pharmacy, Shenandoah University, Winchester, VA
Published Online, February 27, 2007. www.theannals.com, DOI 10.1345/aph.1H575
Audience: Integrated Genomics is based on a laboratory course taught at The University of Alabama. It was developed with the support of a Howard Hughes Medical Institute Undergraduate Biological Sciences Education Program Grant and subsequent funding from the National Sciences Foundation CAREER program. Although initially designed as an undergraduate course, the discovery-based format of the course would provide an excellent education experience for students pursuing careers in the biomedical sciences, biotechnology, medicine, and pharmacy.
Purpose: Integrated Genomics provides a framework for an instructor to present a discovery-based experience for students enrolled in contemporary molecular biology and genomics. The experiments are designed to be adaptable to allow the instructor to substitute other genes and proteins that may be of interest. Alternative experiments provide flexibility for determining the timing or goal of the experiments, as well as for working within limited resources.
Content: The text uses 3 different model organism systems including bacteria, yeast, and nematodes. Concepts of basic microbiology, genetics, molecular biology, genomics, proteomics and bioinformatics are presented in an integrated framework of experiments for which the results are not predetermined. The first chapter introduces Caenorhabditis elegans, which serves as a whole animal system for the study of gene expression in Chapter 2. In Chapters 3 and 4, the yeast Saccharomyces cerevisiae is employed in a 2 hybrid system in an in vivo method for assaying protein-protein interactions by reporter gene expression. Chapter 5 addresses isolation and identification of interacting proteins. Chapter 6 provides hands-on experience with bioinformatics by using both experimental results and online databases. Chapter 7 involves detailed analysis of a few selected targets for functional analysis by RNA interference. C. elegans is again used as an example in Chapter 8 to study RNA-mediated interference by bacterial feeding. The appendices provide a tremendous amount of additional useful information, including discussion of recombinational cloning, recipes and media preparation, sterile techniques and worm protocols, vector maps, and a compilation of C. elegans phenotypes.
Usability: The laboratory experiments and exercises are well thought out and extensive information is provided that allows for modification and adaptation.
Highlights: The authors' enthusiasm and excitement for the topic and teaching are readily apparent. Although the experiments are complex and require a great deal of attention to detail, the discovery-based framework is the antithesis of a "cookbook" style of laboratory experiences. The continuum of exercises really does provide integrated coverage of the modern principles of molecular biology, genomics, proteomics, and bioinformatics. The experimental design and concepts are readily adaptable to other genes and proteins with discovery-based methodology.
Limitations: Although the manual provides a wealth of techniques and approaches, many of the experiments would require a substantial laboratory infrastructure and legions of technically skilled graduate students. For example, adequate facilities, time, and knowledgeable personnel are needed for proper maintenance of worm colonies and skill in handling worms while teaching the concepts of the laboratory text. Many research-intensive institutions could substitute similar types of activities while maintaining the discovery-based nature of the experiments. However, for smaller institutions that are not primarily research based, these requirements may be overwhelming. Activities such as DNA sequencing that are routine at research-based institutions can represent substantial obstacles elsewhere.
Comparison with Other Related Books or Products: Although there are a few university courses that cover similar content, I am not aware of any other published laboratory manuals that are comparable in content, design, or scope.
Reviewer's Summary: Integrated Genomics: A Discovery-Based Laboratory Course is an excellent tool for introducing a wide range of students to modern concepts in molecular biology, genomics, proteomics, and bioinformatics in an integrated discovery-based format. It is written with enthusiasm and clarity and presents principles that can be easily adapted.
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