slings and arrows
TRANSCRIPT
book reviews
E234 NATURE CELL BIOLOGY VOL 4 OCTOBER 2002 www.nature.com/naturecellbiology
Slings and arrows
In situ detection of DNA damageedited by Vladimir V. Didenko
Human Press • 2002
Hardback £/$89.50
William M. Bonner
Our genomes are subject to the slingsand arrows of outrageous fortune. Ineach of us, cosmic radiation is inflict-
ing a DNA double-stranded break (DSB) in105 cells every second. To add insult toinjury, we are self-destructive. In 1955,Isaac Asimov published a proposal that lifeonly became possible as 40K decayed(Asimov, I. “The Radioactivity of theHuman Body”. J. Chem. Edu., February1955). 40K has a half-life of 1.26 × 109 years,with the result that 8.4% of the amount inthe big bang is still around, and enough ofit is in us to cause a DNA DSB in 2 × 104
cells every second. Even ‘getting some sun’damages our DNA. In addition, DNA canbe broken or otherwise damaged by whatwe eat, and our metabolism makes mis-takes that result in DNA damage. In con-trast, programmed DNA breaks occur inrecombination during development of theimmune system and germ cell develop-ment — processes essential for our exis-tence. Programmed cell death also causesextensive DNA fragmentation. DNA conti-nuity is important for replication and tran-scription, and essential for normal mitosis.Fortunately for us, our cells contain a hostof systems to restore, repair and rejoinDNA. It is defects in these systems that typ-ically result in sensitivity to radiation and apropensity towards cancer.
Many techniques are used in the studyof DNA damage. Volume 203 of Methods inMolecular Biology is devoted to methodsand protocols for in situ detection of DNAdamage. Although the title suggests a broadcoverage, the main biological applicationdiscussed is apoptosis (programmed celldeath) and most of the techniques dis-cussed are limited by their sensitivity toanalysing the extensive DNA fragmenta-tion that occurs during apoptosis. The firstthree parts of the book contain chapters onend-labelling DNA fragments with termi-nal transferase, DNA polymerase I and lig-ase, respectively. Each part begins with oneor two chapters that provide a usefuloverview of techniques and a discussion of
their applicability, specificity and limita-tions. Part I concentrates on the terminaluridine nucleotide end labelling (TUNEL)and in situ end labeling (ISEL) assays.Techniques starting with cells and tissuesections and finishing with flow cytometry,and light, confocal, and electronmicroscopy are presented in detail.
The fourth part contains chapters onthe comet assay, in which single cells aresubjected to gel electrophoresis and the sizeand shape of the resulting comet-shapedDNA distribution are analysed by a varietyof detection methods. The last two partscontain chapters covering the detection ofmodified DNA bases and some othermethods for detecting DNA damage.
There is a great deal of useful informa-tion in this manual, but in spite of its titleand claim to be state-of-the-art, the bookdoes not include all known techniques inthe area. Indeed, it would have benefitedgreatly from an overview of all known insitu methods for detecting DNA damage tohelp researchers decide what is the bestmethod for their application. In particular,there is no mention of the use of antibod-ies to proteins such as γ-H2AX and otherDNA DSB repair proteins to detect focithat form at DNA DSB sites, techniquesthat are used widely. These foci detectionmethods cover non-apoptotic applications,such as V(D)J recombination and exposureto ionizing radiation, applications in whichcells contain DNA DSBs in small numbers.
Researchers also need to be aware ofother limitations of this book. Readers areconfronted with a format that often obfus-cates rather than clarifies in the name of sty-listic uniformity. Most chapters include mul-tiple related techniques that are dismem-bered and sorted into ‘Materials, Methodsand Notes’. Thus, researchers must endureconstant cross-referencing to get a completedepiction of any technique. Simply subdi-viding each chapter primarily by techniquewould have eliminated this difficulty.
To make this process of matching rele-vant material across irrelevant paragraphs
more challenging, the cross-referencing issometimes compromised by damaged links.For example, in the methods section of eachchapter, researchers are sometimes referredto various parts of the materials sectionsonly to come up empty-handed. Sometimesthe misreferenced item is located in aneighbouring materials list. In at least onecase, it took a whole body search of thechapter to find the desired item buried inone of the notes. I wonder if some of theauthors may have experienced similar frus-trations in trying to present their methodsin this format.
Unfortunately, the index of the book isalso found wanting. Researchers cannotrely on it to find where, or even if, a topicof interest is discussed in the book. Forexample, references to DNA DSBs duringV(D)J recombination and a PCR methodof detecting DNA DSBs were found bybrowsing, but are absent from the index.The index also assumes a high degree ofknowledge about the field. Mentions oftechniques by their acronyms and nick-names in the text are indexed as discreteitems. Mentions of SCGE are indexed onlyunder “single cell gel electrophoresis”, andmentions of comet assay, another namefor SCGE, are indexed separately as if thetwo were unrelated. A similar situationexists for AP and apurinic/apyrimidinicsites.
Clearly, this book would work better as aCD-ROM so that researchers could use asearch program to bypass the poor indexingand cross-referencing. Most researchers lackthe time for patient browsing and deserve aclear presentation of methods and protocols— at least clearer than the one offered by thisbook. While this book may be useful forresearchers interested in apoptosis, thoseinterested in DNA DSB detection techniquesin areas other than apoptosis must still con-sult the original research literature.William M. Bonner is in the NationalInstitute of Health, Bldg 37 Rm 5050A, 9000Rockville Pike, Bethesda, MD, 20892, USAemail: [email protected]
© 2002 Nature Publishing Group