From Genes to Genomes: Concepts and Applications of DNA Technology

From Genes to Genomes: Concepts and Applications of DNA Technology

by Jeremy W. Dale, Malcolm von Schantz, Nicholas Plant

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The latest edition of this highly successful textbook introduces the key techniques and concepts involved in cloning genes and in studying their expression and variation.
The new edition features:

  • Increased coverage of whole-genome sequencing technologies and enhanced treatment of bioinformatics.
  • Clear, two-colour diagrams throughout.
See more details below


The latest edition of this highly successful textbook introduces the key techniques and concepts involved in cloning genes and in studying their expression and variation.
The new edition features:

  • Increased coverage of whole-genome sequencing technologies and enhanced treatment of bioinformatics.
  • Clear, two-colour diagrams throughout.
  • A dedicated website including all figures.

Noted for its outstanding balance between clarity of coverage and level of detail, this book provides an excellent introduction to the fast moving world of molecular genetics.

Editorial Reviews

From the Publisher
"This monograph is excellently organized…. This book would be an outstanding addition to the library of an undergraduate or graduate student and a useful aid for the libraries of mentors of undergraduate studies.” (Biochemistry and Molecular Education, May/June 2003)

"…an introduction to the concept and applications of DNA technologies, and the study of nucleic acids and how this can be used to answer biological questions." (Genetic Engineering News, Vol. 23, No. 13, July 2003)

"...a well-written, short, but comprehensive, introduction...recommended..." (E-Streams, Vol. 6, No. 6)

"...this lucid book provides very nice descriptions of many of the modern methods in molecular biology.." (ASM News, August 2003)

Doody's Review Service
Reviewer: Omer Iqbal, MD, FACC, FESC (Loyola University Medical Center)
Description: This is an update of a 2007 edition of a concise resource on the rapid developments in molecular genetics, including the impact of next generation sequencing.
Purpose: The purpose is to provide an introduction to the concepts and applications of this rapidly advancing field for undergraduate students, researchers, and teachers.
Audience: The intended audience includes undergraduate students in the biological and biomedical sciences who have a basic understanding of molecular biology, researchers and teachers who wish to update their knowledge, and anyone else interested in this field.
Features: After an introductory chapter on genes to genomes, this well-illustrated book presents chapters on how to clone genes, genomic and cDNA libraries, polymerase chain reactions, and sequencing a cloned gene. Other chapters present an analysis of gene expression, products from native and manipulated cloned genes, genomic analysis, analysis of genetic variation, and postgenomic analysis. The concluding chapter on transgenics is directed at the whole organism, and includes an introduction to transgenic animals and plants.
Assessment: This third edition is absolutely necessary to incorporate the recent advances, such as genome sequencing, polymerase chain reaction, and microarray technology, in this field.

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From Genes to Genomes

Concepts and Applications of DNA Technology
By Jeremy W. Dale Malcolm von Schantz

John Wiley & Sons

ISBN: 0-471-49782-7

Chapter One


This book is about the study and manipulation of nucleic acids, and how this can be used to answer biological questions. Although we hear a lot about the commercial applications, in particular (at the moment) the genetic modification of plants, the real revolution lies in the incredible advances in our understanding of how cells work. Until about 30 years ago, genetics was a patient and laborious process of selecting variants (whether of viruses, bacteria, plants or animals), and designing breeding experiments that would provide data on how the genes concerned were inherited. The study of human genetics proceeded even more slowly, because of course you could only study the consequences of what happened naturally. Then, in the 1970s, techniques were discovered that enabled us to cut DNA precisely into specific fragments, and join them together again in different combinations. For the first time it was possible to isolate and study specific genes. Since this applied equally to human genes, the impact on human genetics was particularly marked. In parallel with this, hybridization techniques were developed that enabled the identification of specific DNA sequences, and (somewhat later) methods were introduced for determining the sequence of these bits of DNA. Combining thoseadvances with automated techniques and the concurrent advance in computer power has led to the determination of the full sequence of the human genome.

This revolution does not end with understanding how genes work and how the information is inherited. Genetics, and especially modern molecular genetics, underpins all the biological sciences. By studying, and manipulating, specific genes, we develop our understanding of the way in which the products of those genes interact to give rise to the properties of the organism itself. This could range from, for example, the mechanism of motility in bacteria to the causes of human genetic diseases and the processes that cause a cell to grow uncontrollably giving rise to a tumour. In many cases, we can identify precisely the cause of a specific property. We can say that a change in one single base in the genome of a bacterium will make it resistant to a certain antibiotic, or that a change in one base in human DNA could cause debilitating disease. This only scratches the surface of the power of these techniques, and indeed this book can only provide an introduction to them. Nevertheless, we hope that by the time you have studied it, you will have some appreciation of what can be (and indeed has been) achieved.

Genetic manipulation is traditionally divided into in vitro and in vivo work. Traditionally, investigators will first work in vitro, using enzymes derived from various organisms to create a recombinant DNA molecule in which the DNA they want to study is joined to a vector. This recombinant vector molecule is then processed in vivo inside a host organism, more often than not a strain of the Escherichia coli (E. coli) bacterium. A clone of the host carrying the foreign DNA is grown, producing a great many identical copies of the DNA, and sometimes its products as well. Today, in many cases the in vivo stage is bypassed altogether by the use of PCR (polymerase chain reaction), a method which allows us to produce many copies of our DNA in vitro without the help of a host organism.

In the early days, E. coli strains carrying recombinant DNA molecules were treated with extreme caution. E. coli is a bacterium which lives in its billions within our digestive system, and those of other mammals, and which will survive quite easily in our environment, for instance in our food and on our beaches. So there was a lot of concern that the introduction of foreign DNA into E. coli would generate bacteria with dangerous properties. Fortunately, this is one fear that has been shown to be unfounded. Some natural E. coli strains are pathogenic - in particular the O157:H7 strain which can cause severe disease or death. By contrast, the strains used for genetic manipulation are harmless disabled laboratory strains that will not even survive in the gut. Working with genetically modified E. coli can therefore be done very safely (although work with any bacterium has to follow some basic safety rules). However, the most commonly used type of vector, plasmids, are shared readily between bacteria; the transmission of plasmids between bacteria is behind much of the natural spread of antibiotic resistance. What if our recombinant plasmids were transmitted to other bacterial strains that do survive on their own? This, too, has turned out not to be a worry in the majority of cases. The plasmids themselves have been manipulated so that they cannot be readily transferred to other bacteria. Furthermore, carrying a gene such as that coding for, say, dogfish insulin, or an artificial chromosome carrying 100 000 bases of human genomic DNA is a great burden to an E. coli cell, and carries no reward whatsoever. In fact, in order to make them accept it, we have to create conditions that will kill all bacterial cells not carrying the foreign gene. If you fail to do so when you start your culture in the evening, you can be sure that your bacteria will have dropped the foreign gene the next morning. Evolution in progress!

Whilst nobody today worries about genetically modified E. coli, and indeed diabetics have been injecting genetically modified insulin produced by E. coli for decades, the issue of genetic engineering is back on the public agenda, this time pertaining to higher organisms. It is important to distinguish the genetic modification of plants and animals from cloning plants and animals. The latter simply involves the production of genetically identical individuals; it does not involve any genetic modification whatsoever. (The two technologies can be used in tandem, but that is another matter.) So, we will ignore the cloning of higher organisms here. Although it is conceptually very similar to producing a clone of a genetically modified E. coli, it is really a matter of reproductive cell biology, and frankly relatively uninteresting from the molecular point of view. By contrast, the genetic modification of higher organisms is both conceptually similar to the genetic modification of bacteria, and also very pertinent as it is a potential and, in principle, fairly easy application following the isolation and analysis of a gene.

At the time of writing, the ethical and environmental consequences of this application are still a matter of vivid debate and media attention, and it would be very surprising if this is not still continuing by the time you read this. Just as in the laboratory, the genetic modification as such is not necessarily the biggest risk here. Thus, if a food crop carries a gene that makes it tolerant of herbicides (weedkillers), it would seem reasonable to worry more about increased levels of herbicides in our food than about the genetic modification itself. Equally, the worry about such an organism escaping into the wild may turn out to be exaggerated. Just as, without an evolutionary pressure to keep the genetic modification, our E. coli in the example above died out overnight, it appears quite unlikely that a plant that wastes valuable resources on producing a protein that protects it against herbicides will survive long in the wild in the absence of herbicide use.

Nonetheless, this issue is by no means as clear-cut as that of genetically modified bacteria. We cannot test these organisms in a contained laboratory. They take months or a year to produce each generation, not 20 minutes as E. coli does. And even if they should be harmless in themselves, there are other issues as well, such as the one exemplified above. Thus, this is an important and complicated issue, and to understand it fully you need to know about evolution, ecology, food chemistry, nutrition, and molecular biology. We hope that reading this book will be of some help for the last of these. We also hope that it will convey some of the wonder, excitement, and intellectual stimulation that this science brings to its practitioners. What better way to reverse the boredom of a long journey than to indulge in the immense satisfaction of constructing a clever new screening algorithm? Who needs jigsaw and crossword puzzles when you can figure out a clever way of joining two DNA fragments together? And how can you ever lose the fascination you feel about the fact that the drop of enzyme that you're adding to your test tube is about to manipulate the DNA molecules in it with surgical precision?


Excerpted from From Genes to Genomes by Jeremy W. Dale Malcolm von Schantz Excerpted by permission.
All rights reserved. No part of this excerpt may be reproduced or reprinted without permission in writing from the publisher.
Excerpts are provided by Dial-A-Book Inc. solely for the personal use of visitors to this web site.

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From the Publisher
“This third edition is absolutely necessary to incorporate the recent advances, such as genome sequencing, polymerase chain reaction, and microarray technology, in this field.” (Doody’s, 19 October 2012)

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