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RNA–Protein Interaction Protocols. Edited by Susan R. Haynes
Analytical Biochemistry 280, 332–333 (2000) All articles available online at http://www.idealibrary.com on
BOOK REVIEWS Environmental Monitoring of Bacteria, Volume 12, Methods in Biotechnology. Edited by Clive Edwards. Humana Press, Totowa, NJ, 1999. 330 pp. This is a rapid survey of the methods that are appropriate for research in environmental biotechnology by some 30 authors largely concentrated in the United Kingdom. The first chapter deals with classical isolation and culture methods; the rest represents methods for recovery of cells, analysis of cells, their biomarkers, and activities. Each chapter describes a method in a short introduction, defines the principles and important limitations, and then describes the materials and instruments. The methods are then described in some cases in sufficient detail with extensive notes on tricks and pitfalls so that a practitioner could gain insight into what is involved, what will be measured, and some helpful suggestions as to how to analyze the data. Each chapter ends with a comprehensive reference list largely through 1995. Twenty methods are described in chapters that are 10
to 15 pages in length and, as expected in a multiauthored book, the quality is somewhat uneven. There are some excellent chapters on molecular methods, particularly the chapter on PCR by I. M. Head who defines the limitations of this kenstone reaction in molecular biology very well. Most of the major methods currently in active use are described in this book. This book would be an ideal introduction to the field for a beginning graduate student contemplating a graduate program in environmental microbiology. I found it particularly useful in explaining to flight engineers methods for sensitively detecting microbial contaminants on spacecraft during assembly. This book provides a concise review of much of what is out there and the references to get started on the pathway to become proficient. David C. White Center for Environmental Biotechnology University of Tennessee/Oak Ridge National Laboratory Knoxville, Tennessee 37932-2575 doi:10.1006/abio.1999.4373
RNA–Protein Interaction Protocols. Edited by Susan R. Haynes. Humana Press, Totowa, NJ, 1999. 481 pp. Any book that offers detailed experimental procedures can be a valuable resource in the laboratory, and this volume of RNA–Protein Interaction Protocols is an example of the best of this genre. This is because the book is both broad in its scope and sufficiently detailed in the protocols. A wide range of topics is covered, starting with procedures for generating and labeling RNA substrates and protocols for crosslinking RNA to RNA-binding proteins. The section on analyzing RNA–protein interactions includes thorough overviews of techniques for RNA footprinting and modification interference and methods for determining equilibrium and kinetic constants of RNA– protein interactions by nitrocellulose filter binding, gel retardation, polyacrylamide coelectrophoresis (PACE), and surface plasmon resonance. Methods for isolating RNA-binding proteins include an Escherichia coli genetic screen, a detailed description of phage display, and techniques for screening expression libraries using proteins immobilized on nitrocellulose or proteins in solution. There are also chapters devoted to methods for isolating RNA targets that bind to proteins, such as identifying targets from libraries of natural RNAs, and for isolating ribonucleoprotein complexes, such as an immunoprecipitation-RNA:random PCR method for identifying low abundance RNPs. Techniques for isolating and analyzing spliceosomes and spliceosome components from Hela and yeast cells comprise about one-third of the volume. The very detailed protocols for preparation of yeast pre-mRNA splicing extracts, splicing assays, and native gel electrophoretic assay of the yeast spliceosome are especially useful. There is also a complete discussion of elements that should be considered
when trying to identify pre-mRNA cis elements that affect splicing and protocols for using the SELEX procedure to identify sequences that enhance alternative splicing. The book ends with techniques for analyzing the processing of the 3⬘ ends of mRNAs and an overview of factors to be considered when investigating mRNA stability. The protocols are concise but sufficiently thorough for someone who previously has not performed the technique. In addition, there are extensive notes and discussions that detail those technical pitfalls that might not be obvious but can derail even the most conscientious researchers. For example, Stephanie Ruby in her chapter on the preparation of yeast pre-mRNA splicing extracts includes a figure that shows both the results of splicing by a competent (“the good”) extract and two incompetent extracts (“the bad and the ugly”). Several authors discuss why one would want to use a particular method and the considerations that go into choosing one method over another. The only major fault of the book is that the half-tone figures are poorly reproduced. However, all the figures are sufficiently clear to illustrate whatever point is being made. In her preface, Susan Haynes, the editor, writes that this book was “written with the novice RNA researcher in mind” and that it provides “an excellent starting point for investigating many types of RNA– protein interactions.” This book definitely meets that assessment and probably will be of use to the more experienced researcher also. Deborah Hinton Laboratory of Molecular and Cellular Biology National Institute of Diabetes and Digestive and Kidney Diseases National Institutes of Health Bethesda, Maryland doi:10.1006/abio.1999.4418
332
0003-2697/00 $35.00 Copyright © 2000 by Academic Press All rights of reproduction in any form reserved.
BOOK REVIEWS Environmental Monitoring of Bacteria, Volume 12, Methods in Biotechnology. Edited by Clive Edwards. Humana Press, Totowa, NJ, 1999. 330 pp. This is a rapid survey of the methods that are appropriate for research in environmental biotechnology by some 30 authors largely concentrated in the United Kingdom. The first chapter deals with classical isolation and culture methods; the rest represents methods for recovery of cells, analysis of cells, their biomarkers, and activities. Each chapter describes a method in a short introduction, defines the principles and important limitations, and then describes the materials and instruments. The methods are then described in some cases in sufficient detail with extensive notes on tricks and pitfalls so that a practitioner could gain insight into what is involved, what will be measured, and some helpful suggestions as to how to analyze the data. Each chapter ends with a comprehensive reference list largely through 1995. Twenty methods are described in chapters that are 10
to 15 pages in length and, as expected in a multiauthored book, the quality is somewhat uneven. There are some excellent chapters on molecular methods, particularly the chapter on PCR by I. M. Head who defines the limitations of this kenstone reaction in molecular biology very well. Most of the major methods currently in active use are described in this book. This book would be an ideal introduction to the field for a beginning graduate student contemplating a graduate program in environmental microbiology. I found it particularly useful in explaining to flight engineers methods for sensitively detecting microbial contaminants on spacecraft during assembly. This book provides a concise review of much of what is out there and the references to get started on the pathway to become proficient. David C. White Center for Environmental Biotechnology University of Tennessee/Oak Ridge National Laboratory Knoxville, Tennessee 37932-2575 doi:10.1006/abio.1999.4373
RNA–Protein Interaction Protocols. Edited by Susan R. Haynes. Humana Press, Totowa, NJ, 1999. 481 pp. Any book that offers detailed experimental procedures can be a valuable resource in the laboratory, and this volume of RNA–Protein Interaction Protocols is an example of the best of this genre. This is because the book is both broad in its scope and sufficiently detailed in the protocols. A wide range of topics is covered, starting with procedures for generating and labeling RNA substrates and protocols for crosslinking RNA to RNA-binding proteins. The section on analyzing RNA–protein interactions includes thorough overviews of techniques for RNA footprinting and modification interference and methods for determining equilibrium and kinetic constants of RNA– protein interactions by nitrocellulose filter binding, gel retardation, polyacrylamide coelectrophoresis (PACE), and surface plasmon resonance. Methods for isolating RNA-binding proteins include an Escherichia coli genetic screen, a detailed description of phage display, and techniques for screening expression libraries using proteins immobilized on nitrocellulose or proteins in solution. There are also chapters devoted to methods for isolating RNA targets that bind to proteins, such as identifying targets from libraries of natural RNAs, and for isolating ribonucleoprotein complexes, such as an immunoprecipitation-RNA:random PCR method for identifying low abundance RNPs. Techniques for isolating and analyzing spliceosomes and spliceosome components from Hela and yeast cells comprise about one-third of the volume. The very detailed protocols for preparation of yeast pre-mRNA splicing extracts, splicing assays, and native gel electrophoretic assay of the yeast spliceosome are especially useful. There is also a complete discussion of elements that should be considered
when trying to identify pre-mRNA cis elements that affect splicing and protocols for using the SELEX procedure to identify sequences that enhance alternative splicing. The book ends with techniques for analyzing the processing of the 3⬘ ends of mRNAs and an overview of factors to be considered when investigating mRNA stability. The protocols are concise but sufficiently thorough for someone who previously has not performed the technique. In addition, there are extensive notes and discussions that detail those technical pitfalls that might not be obvious but can derail even the most conscientious researchers. For example, Stephanie Ruby in her chapter on the preparation of yeast pre-mRNA splicing extracts includes a figure that shows both the results of splicing by a competent (“the good”) extract and two incompetent extracts (“the bad and the ugly”). Several authors discuss why one would want to use a particular method and the considerations that go into choosing one method over another. The only major fault of the book is that the half-tone figures are poorly reproduced. However, all the figures are sufficiently clear to illustrate whatever point is being made. In her preface, Susan Haynes, the editor, writes that this book was “written with the novice RNA researcher in mind” and that it provides “an excellent starting point for investigating many types of RNA– protein interactions.” This book definitely meets that assessment and probably will be of use to the more experienced researcher also. Deborah Hinton Laboratory of Molecular and Cellular Biology National Institute of Diabetes and Digestive and Kidney Diseases National Institutes of Health Bethesda, Maryland doi:10.1006/abio.1999.4418
332
0003-2697/00 $35.00 Copyright © 2000 by Academic Press All rights of reproduction in any form reserved.