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Book Review Bioinformatics and Genome Analysis.

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Angewandte
Books
Chemie
Bioinformatics and Genome
Analysis
Edited by HansWerner Mewes,
Bertram Weiss,
and Henrik Seidel.
Springer-Verlag,
Heidelberg 2002.
296 pp., hardcover E 80.20.—
ISBN 3-54042893-3
As a compilation of articles by the
invited speakers at a workshop with
the same title (Ernst Schering Foundation Workshop No. 38, Berlin 2001), this
book is not intended to be a textbook—
quite a few of those have also recently
appeared on the market, if that is what
you are looking for. Instead, the editors
are addressing “scientists and researchers working in bioinformatics and
genome analysis world-wide” with this
volume, and it is packed full with really
hot topics.
The editors have brought together a
remarkably diverse set of recognized
researchers from different specialist
areas, ranging from purely wet-experimental functional genomics to the—at
least at present—extremely theoretical
realm of systems biology (which could
be very roughly described as the
endeavor to extend kinetic modeling to
entire organisms). The biological/biomedical context of the articles in the
book ranges from identifying cancer
genes to determining protein interactions and to drug discovery. The editors
are to be complimented for looking
ahead and thus not missing out on
some of the currently less well
researched topics, such as membranes,
Angew. Chem. Int. Ed. 2003, 42, 3715 – 3717
metabolic networks, and glycosylation.
Probably because of the present lack of
a clear concept of how these areas could
be investigated experimentally on a
large enough scale to feed the data
into our post-genomic big picture, they
are often overlooked in compendia of
this kind. Scarcity of data also means
that the reliability of predictive bioinformatic approaches cannot be easily
assessed—all the more reason to raise
awareness of these “next” challenges.
The editors2 aim towards diversity in the
selection of speakers for the workshop is
reflected in the different backgrounds of
the authors, who include biologists of
various kinds, computer scientists, mathematicians/statisticians, and all flavors in
between.
As I mentioned above, the book on
the whole is not for beginners. However,
some of the chapters are very instructive
overviews in which the authors address a
broad audience and describe the special
features of their respective fields. Chapter 1 by A. Reis, which explains positional cloning in a simple way, appeals
especially in this regard. Other topics on
which the reader will gain a good overview are membrane proteins and current methodology for predicting transmembrane protein features from
sequence (Chap. 2, G. van Heijne), the
role of gene promoter sequences and
methodology for predicting these
(Chap. 4, T. Werner), and considerations
pertaining to protein glycosylation
(Chap. 13, R. Gupta, L. J. Jensen, S.
Brunak). The overview about efforts
towards representing, and querying,
metabolic pathways by graphical theoretical means (Chap. 12, J. van Helden,
L. Wernisch, D. Gilbert, S. J. Wodak) is
different in that the topic discussed is
very narrow, new, and still in progress,
but here also there is a clear attempt to
keep a wider audience interested.
Finally, the outline of how protein
modeling can assist at different stages
of the drug discovery process (Chap. 8,
L. Brive, R. Abagyan) seems to pay a
little less attention than the aforementioned chapters to reviewing methods of
others besides those of the authors.
However, this is understandable given
the breadth of scope the authors have
chosen for their contribution, and this
chapter too belongs in the category of
easily accessible overview articles—
www.angewandte.org
albeit with a potentially confusing title
(“Computational Structural Proteomics”).
It is symptomatic of the differences
in terminology (or misunderstandings?)
between scientific disciplines—especially where buzz-words are involved—
that the word “proteomics” is used with
no less than three different meanings in
Chapters 8 – 10. In one case it is a
derivative of the classic experimental
definition of the “proteome” as the
complement of expressed proteins in a
cell under particular conditions (Chap.
9). Secondly it is extended to include
any protein whose expression can be
induced in vitro, disregarding its natural
subcellular location and potentially mispredicted gene termini, in the case of
eukaryotes (Chap. 10). Thirdly (Chap. 8)
it represents the entirety of predicted
proteins in a genome (a priori, without
experimental verification of whether the
putative gene sequences in question are
ever really expressed). Only the authors
of Chapter 9 took the time to explicitly
define their use of the term, which is
unfortunate since this would have
seemed a good forum to clarify issues
like the precise usage of common terms.
A few other chapters in the book can
be categorized as specialist reviews of
current research in specific areas or
techniques. These articles will be very
valuable to experts in the respective
fields, but require advanced knowledge
and understanding of technical language
in one or several fields. The thorough
review of the latest developments in
experimental proteomics technology by
M. Gentzel, T. KBcher, and M. Wilm
(Chap. 9) should come as a welcome
break to non-bioinformaticians, since
this is the only chapter in which there
is no reliance, in one way or another, on
computational interpretation or prediction—only solid experimental techniques. Unfortunately, the technical language used might pose a problem for the
many bioinformaticians who would
greatly benefit from understanding this
technology in more detail when
attempting to analyze the data emerging
from it. Two further chapters apply
interesting combinations of wet-experimental and theoretical perspectives.
One of them (Chap. 6, N. Friedman, N.
Kaminski) describes methods used to
extract information from recent micro-
' 2003 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
3715
Books
array studies (including the associated
difficulties) and is specifically focused
on cancer research. The other one
reviews current experimental strategies
for investigating on a large scale
whether two proteins interact with
each other, and includes a discussion of
prediction methodology (Chap. 10, V.
SchFchter).
The remaining chapters in the book
should be read as research articles in
which the authors describe and discuss
novel computational/theoretical methods of their own. In some cases the
techniques seem to be quite well established, and some validation is included;
others contain interesting proposals and
ideas for future work. A novice reader
should be aware that much research into
the practical value and applicability of
these methods still remains to be done,
but for the specialist these chapters
make interesting reading and starting
points for discussion amongst colleagues. The problems addressed range
from finding functionally connected
genes from sequence (Chap. 3, G. Kolesov, H.-W. Mewes, D. Frishman) or from
gene expression data (Chap. 5, R.
Sharan, R. Elkon, R. Shamir; a particularly well-structured chapter discussing
the authors2 clustering method), to comparing protein structures (Chap. 7, W. R.
Taylor), and to modeling entire cells
(Chap. 11, H. V. Westerhoff, W. M.
Getz, H. W. van Verseveld, J.-H. S. Hofmeyr, J. L. Snoep).
With such a colorful variety of topics
and authors, holding the contributors to
stricter guidelines with respect to the
breadth, style, and extent of specialist
technical language used in their articles
would most certainly have opened up
this book to a broader audience. Viewed
as an entity, this collection of articles
clearly lacks coherence in these aspects.
Admittedly, this is probably painting
quite a realistic portrait of one of the
greatest challenges (besides the scientific ones) that must be overcome to
make interface research more effective:
communication difficulties. All in all,
however, experienced readers who
come from within the multidisciplinary
scene or are familiar with it will thoroughly enjoy the articles as individual
pieces (I did). The workshop itself must
have been a delight for speakers and
other participants alike, featuring such
3716
variety in such an active scientific area.
These are exciting times for all of us,
with teams of scientists from all fields
and affiliations joining up to tackle
whole genomes/organisms and (hopefully one day) to understand what is
going on inside.
Dietlind L. Gerloff
Institute of Cell & Molecular Biology
University of Edinburgh (UK)
Industrial Dyes
Chemistry, Properties, Applications. Edited by
Klaus Hunger.
Wiley-VCH, Weinheim 2003. 660
pp., hardcover
E 199.00.—ISBN
3-527-30426-6
Comprehensive surveys of industrially
important dyes appear only rarely. Without such up-to-date surveys one has
usually had to rely on “Ullmann” to
find information about important
classes of dyes arranged under key
headings. Therefore the publication of
a monograph on dyes of technological
importance is very welcome. The aim of
this book is to give an up-to-date overview of the subject and to provide
convenient access to the patent literature, which is often difficult to find one2s
way around. Here the editor, Klaus
Hunger, who is best known as one of
the authors of Industrial Organic Pigments, has set out, together with 18
co-authors who are mainly industrial
dye chemists, to give a survey of the
current state of knowledge in color
chemistry from an industrial standpoint.
The result is a substantial book of 660
pages divided into eight chapters.
Chapter 1 consists of a short overview describing the classification of
dyes, their economic importance
(although unfortunately without sufficiently up-to-date numerical data), and
aspects of their production (which are
treated too briefly and unspecifically).
' 2003 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
www.angewandte.org
In Chapter 2, which amounts to about
100 pages, the various authors in the
team describe the most important types
of chromophores in turn. This form of
treatment is appropriate, because it
gives a thorough picture of how the
enormous variety of commercially interesting dyes all depend on a limited
number of basic chromophores. However, the different authors do not all
cover their subjects with the same
degree of success. In some of the contributions the variety is simply catalogued in full and the reader is overloaded with too many details. Also the
classification of the chromophores is
puzzling in some cases; for example,
cationic dye chromophores and arylmethane dyes are treated as two different
classes of chromophores, which inevitably results in some overlapping.
In Chapter 3 the most important
classes of dyes are described, grouped
according to their applications and
modes of use: reactive dyes, disperse
dyes, acid dyes, direct dyes, and sulfur
dyes. The chemistry relating to each
type is explained, including synthetic
routes, and also the most important
commercial dyes of that type are listed
with their structures and CI numbers,
which is very useful. This enables the
reader to find the desired information
very quickly, including details of commercially available dyes for particular
areas of application. Unfortunately,
however, the above classification is not
always followed consistently. As well as
the classification of dyes according to
their uses, the same chapter also
includes articles relating to particular
chromophores, for example, grouping
together dyes based on anthraquinone,
metal complex, or naphthoquinone
chromophores. This leads to some
unnecessary overlapping and repetition;
for example, anthraquinone disperse
dyes are covered twice. Vat dyes are
not treated in a separate article but are
included along with anthraquinone dyes.
The technology of using textile dyes is
described in a separate chapter, and thus
the chemistry of these dyes and their use
are treated in different places. One
consequence of splitting the discussion
in this way is that the relationships
between the structures of the dyes and
their technological properties cannot be
brought out as clearly as they should be.
Angew. Chem. Int. Ed. 2003, 42, 3715 – 3717
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