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2003 The Royal Microscopical Society

Journal of Microscopy, Vol. 210, Pt 2 May 2003, pp. 187189

BlackwellPublishingLtd.

Book reviews

In situ Hybridization in Light Microscopy By Grard Moreland Annie Cavalier. Published by CRC Press, New York, 2001.

327 pages. ISBN 0-84930-044-4.

Practical information for the novice in RNA in situ

hybridisation

In situ hybridization (ISH) refers to a set of techniques devel-

oped during the final three decades of the last century. They

permit visualization of specific nucleic acid sequences in mor-

phologically preserved biological structures and bridge the

gap that existed for a long time between the histo- and cyto-

morphological and molecular biological sciences. Particularly

with the introduction of non-radioactive labelling and detec-

tion methods for nucleic acids in the early 1980s, the devel-

opment and application of ISH methodology has gained

momentum as it fundamentally eliminated safety, resolution

and multiplexing limitations associated with the radioactive

ISH variants. An avalanche of methodological ISH papers

resulted in the 1980s and 1990s. Todays molecular genetic,

cell biological and pathological papers indeed frequently fea-

ture microscopic ISH images that pinpoint the location of

genes and gene transcripts within normal or diseased cells.

Authors of such papers often refer to the ISH methods stating

in the Experimental section: ISH was according to .

A new student in the lab with the assignment to set up agiven ISH technique may find the way to the library to read the

ISH-method papers or spend time at the PC to surf the web to

collect relevant protocols, but for him or her to complete the

chore proficiently, a methodological book written by special-

ists who have gathered the requisite theoretical and practical

information will be a great help. With their book In situ hybrid-

ization in light microscopy in the Series Methods in visualization,

Grard Morel and Annie Cavalier aim at such a readership.

It has over 326 pages of theoretical and technical information

on ISH methods with a strong focus on mapping RNA gene

expression by ISH to tissue sections with visualization protocols

for bright-field microscopy. While that branch of ISH is complexand important enough to be dealt with in a single method-

orientated book, it would have been useful to have that focus of

the book reflected in the title or a subtitle. Indeed, if the students

assignment is to develop and apply multicolour fluorescence

ISH technology for cytogenetic analysis I would not recommend

this book.

The book will guide the novice in RNA-ISH to some extent

in making the choices for the experimental procedure that has

the greatest chance of success, but its true value will becomeapparent when it comes to the actual hands-on work. The

Appendices give excellent information on the trick-of-the trade

of making and storing the many solutions involved in RNA-

ISH, while the many Protocol Sections describe and illustrate

with simple, but instructive graphics how to use them in probe

preparation, tissue fixation and pretreatments, probe hybridiza-

tion and visualization. The book is surely worth buying for this

technical reason.

But does it have additional value? Not much. As said, it will

to some extent guide in selecting protocols, but not more than

that. General as well as straightforward recommendations

and specifications are lacking. Answers cannot be found to

such obvious questions as Which protocols should I pursue

for detecting low abundant RNAs?, How many mRNA copies

per cell can one reliably detect with a given protocol in cells of

a given tissue type? and What positive procedural controls

would be useful for me to set up the technique. I miss a con-

cluding chapter in which the authors take distance from the

detailed information they provided and put it all in a broader

application-orientated perspective with illustrative examples

of what can and what cannot be achieved. Also I find the

theoretical part rather weak. One would welcome a more

vivid explanation of the essentials of reaction mechanisms

and molecular structures, instead of the dry excerption of

textbooks that now dominate the theoretical part of the book.The part on microscopy is rudimentary and guidelines for

use of the microscope so essential for the procedure in its

entirety are absent.

The quality of the part dealing with the wet technical

details compensate these negative aspects of the book to a very

large extent. And, of course, the ambitious student with the

task of setting up the technique can spend some extra time in

learning more of the ISH methods and associated microscop-

ies when he or she goes to the (electronic) library to read the

latest articles dealing with the biomedical question he/she is

addressing. But then an unscientific aspect of the book soon

becomes apparent: it does not have a single literature citation!In summary: if you are a newcomer in the field with no

practical experience in RNA-ISH buy this book and take

advantage in your practical work of the detailed technical

information provided, but rely on other sources to get more

theoretical insights and a broader view on the ISH field.

Ton Raap

Leiden University Medical Centre

January20032091OriginalArticleBOOKREVIEWBOOKREVIEWBookreview

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BOOK REVIEWS

2003 The Royal Microscopical Society,Journal of Microscopy

, 210

, 187189

Green Fluorescent Protein Applications and Protocols.

Methods in Molecular Biology Series, Vol. 183. Edited by B. W.

Hicks. Published by Humana Press Inc., Totowa, New Jersey,

2002. Hardback. ISBN 0-89603-905-6.

Green Fluorescent Protein

Applications and Protocols is a

unique guide to the uses of the green fluorescent protein (GFP)

and its spectral variants in a vast number of biological applica-

tions. The essence of this manual is to illustrate numerous

techniques in which GFP finds applications, and is not exclu-

sive to subcellular imaging.

The book comprises 29 chapters, well organized into six

sections, and supplementary material for many of the chap-

ters is provided on an attached CD. The first part of the manual

is dedicated to the manipulation of the fluorescent protein

structure at genetic level. Extensive coverage of imaging tech-

niques with conventional and cutting-edge microscopy appli-

cations such as BRET, FRET and FLIM follow. Examples for the

use of GFP in monitoring protein distribution and traffickingin the cell and in whole organisms are presented and the vol-

ume concludes with application of GFPs as biosensors and in

viral biology. Amazingly, the material does not overlap

between chapters, making every chapter unique.

This book is a pleasant and stimulating manual to read. The

authors convey their reports in such a clear and simple man-

ner that even a novice researcher with only a limited knowl-

edge of fluorescent protein technology will appreciate the

potential use of GFP, not simply as a bioimaging tool but also

for wider applications. In this respect, the book is very

advanced as it shows how far the GFP discipline has developed

in the last few years and the myriad of biological applications itmay support.

A real strength of the book is the simplicity of presentation

and the coherence in the layout of chapters. The manual is

impressive in terms of clarity and the undemanding style by

which theoretical and practical approaches are delivered to

the reader. Each chapter is self-contained and complete for the

subject to which it is dedicated. The chapters have a good bal-

ance between introduction and methodological explanation.

These are integrated by an exhaustive list of materials and

well-described, fully detailed, procedures. An excellent note

section, in which the authors introduce the reader to useful

practical hints and technical insights, integrates all of this.

Moreover, each chapter is complemented with an excellent

and up-to-date list of references. These features make this

book both a very useful manual and reference.

More importantly, an overall comment on this book might

be: Finally a manual like this!. This book is,per se

, a novelty in

its field as it aims to deliver the latest insights of a large number

of potential applications of GFPs to a rapidly growing public.

These finally go beyond the standard description on subcellu-

lar imaging.

Another peculiarity that emerges from reading this book

is that this manual manages to support a sound basis for

the application of GFP to biological questions covering a

variety of applications, beyond those just described in the text.

In this respect, this manual is aimed not only at novices in

the field but it also encourages experienced researchers to

explore applications of GFP beyond the standard reported

applications.

In conclusion, this book succeeds in covering a very wide

range of topics inherent to GFP technology. A unique mixture

of high quality text, power in delivering the message, up-to-

date examples of GFP applications, integrated by a solid sup-

port offered in the methodology section of each chapter, offers

biologists an invaluable source of essential information

needed to create novel GFP-based, powerful but easy-to-han-

dle, tools to answer basic biological questions.

F. Brandizzi

Oxford Brookes University, UK

209BookReviewBOOKREVIEWBookreview

Fractals in Biology and Medicine Volume III.

Edited by G. Losa,

D. Merlini, T. F. Nonnenmacher & E. R. Weibel. Published by

Birkhuser Verlag, Basel, 2002. Hardcover, 362 pages. ISBN

3-76436-474-2.

Understanding and explaining biological phenomena are by

no means straightforward tasks. Some of the difficulties that

arise in characterizing complex biological structures and

processes are a reflection of the lack of suitable statistical or

mechanical models. However, and perhaps unexpectedly, a

variety of exploratory tools and concepts useful to tackle someof those problems originated from the work of B. Mandelbrot

on fractal geometry. There is no doubt that Mandelbrots ideas

have prompted innovative ways of understanding and quanti-

fying complex hierarchical processes and systems from a new

perspective. For example, scale invariance and self-similarity

are concepts that have attracted a great deal of interest in

biology regarding possible algorithmic mechanisms in mor-

phogenesis. At the same time, fractal geometry provides ways

of measuring hierarchical complexity, and so a myriad of qual-

itatively assessed morphology problems can now be better

described in numerical terms using formal methods. As a

direct consequence of this, fractals have found their way into

many diverse areas of biomedicine.

This book is a compilation of the presentations given at the

Third International Symposium on Fractals in Biology and

Medicine held in Ascona, Switzerland on 811 March 2000.

The symposium was the third of a series that originated back

in 1992, always held at Ascona. The author of this review had

the fortune to attend the three conferences in which research-

ers from a wide range of specialities presented their work

under the unifying theme of fractals.

The volume consists of a Foreword by the editors and 33

contributions organized under four sections:

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2003 The Royal Microscopical Society,Journal of Microscopy

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(1) Fractal design of biological structures and functions

(eight papers)

(2) Fractal structures in tumours and diseases (14 papers)

(3) Organization and evolution of living systems (five papers)

and

(4) Modelling (six papers).

The layout of the contributions follows standard journal

style format. The subjects covered are varied and include mor-

phometrical analyses of tumour growth, chromatin texture

patterns in cell nuclei, quantification of trabecular bone, anal-

ysis of voice sounds, cardiac and EEG series, complexity of evo-

lutionary trees, and X-ray texture quantification. Some of the

papers do not strictly deal with fractals (for example, on the

use of neural networks for cancer diagnosis), but nevertheless

involve interesting mathematical and analytical techniques.

There are a small number of presentations on fractals in

non-biomedical subjects (for example in architecture) that

still should be of interest to a multidisciplinary audience.

Below are some examples of the subjects covered in eachpart of the book.

(1) Fractal design of biological structures and functions

One of the classic examples of biological fractal structures is

the respiratory system. This is perhaps one of the areas where

a lot of innovative research has been undertaken using con-

cepts of fractal geometry. There are several interesting papers

in this section; however, two are of particular interest: Sapoval

et al

. on modelling diffusion and screening in the alveolar

space of the lung, and Kitaoka on 3D computer modelling

of the bronchial tree using a branching algorithm which rep-roduced the geometry of foetal to adult airway trees.

(2) Fractal structures in tumours and diseases

Nielsen et al

. introduced a method to analyse the complexity

and lacunarity of chromatin patterns in electron micrographs

of normal and premalignant hepatocytes nuclei. Rigaut &

Sharif-Salamatian used an asymptotic fractal model and

geostatistics-derived sampling methods to characterize heter-

ogeneity distribution of MIB-1 stained cells in breast cancer

samples.

(3) Organization and evolution of living systems

Wests paper on fractional calculus and memory in biophysi-

cal time series extended the random walk model to include

long-term memory and showed examples. These include

fractal random fluctuations in time series from the intervals

between heart beats in neonates, the number of births to teen-

agers and fluctuations in stride intervals.

(4) Modelling

Nekka presented a review of the previously proposed

methods to measure lacunarity (a parameter that is stillnot formally defined and which is intended to quantify

textural characteristics of fractal sets). Baumannet al

. developed

a dynamical model of DNA packing in an attempt to explain

the Levinthal paradox. This paradox shows that the time

that it would take to randomly sample DNA for correct

folding configurations, even for a relatively small number of

nucleotides, is extremely large, although DNA folds in time

scales of minutes.

As shown here, fractal geometry has a wide range of

applications in biomedicine, and the diverse subjects dealt

with in this volume are a clear reflection of this. Although

this book is not a reference book on fractals, it would be ofinterest to a large audience interested in quantitative analysis

in biomedicine.

G. L

andini

The University of Birmingham, UK