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Brown TA. Genomes. 2nd edition. Oxford: Wiley-Liss; 2002.
I have tried to make the second edition of Genomes as user friendly as possible. The book therefore includes a number of devices intended to help the reader and to make the book an effective teaching aid.
Organization of the Book
Genomes is divided into four parts:
- Part 1 – Genomes, Transcriptomes and Proteomes introduces the central concepts of modern molecular biology. Chapter 1 begins with DNA and then summarizes the key features of the human genome, with Chapter 2 extending the survey to the genomes of eukaryotes and prokaryotes in general. Chapter 3 then uses the new concepts of the transcriptome and the proteome to introduce the basic steps in genome expression. By the end of Part 1 the reader will have acquired a good working knowledge of the structures and organizations of genomes and will understand, in outline, how the information contained in the genome is released and made available to the cell.
- Part 2 – Studying Genomes begins with an orientation chapter that introduces the reader to the methods, centered on cloning and PCR, that were used in the pre-genome era to examine individual genes. The techniques that are more specifically used for studying genomes are then described in the order in which they would be used in a genome project: methods for constructing genetic and physical maps (Chapter 5); DNA sequencing methodology and the strategies used to assemble a contiguous genome sequence (Chapter 6); and methods for identifying genes in a genome sequence and determining the functions of those genes in the cell (Chapter 7). The Human Genome Project forms a continuous thread throughout Part 2, but this is not to the exclusion of all else and I have tried to give adequate coverage to the strategies that have been used, and are being used, to understand the genomes of other organisms.
- Part 3 – How Genomes Function covers the material that in the past has been described (inadequately in my opinion) as ‘DNA goes to RNA goes to protein’. Chapter 8 addresses the increasingly important issue of how chromatin structure influences genome expression. Chapter 9 then describes the assembly of the transcription initiation complexes of prokaryotes and eukaryotes, and includes a fairly detailed discussion of DNA-binding proteins, these playing the central roles in the initial stages of genome expression. Chapters 10 and 11 give details of the synthesis of RNA and protein, and Chapter 12 surveys the regulation of genome activity. Keeping Chapter 12 to a manageable length was difficult, as many different topics are relevant to genome regulation, but I hope that by using specific examples to illustrate general themes I have managed to achieve a satisfactory balance between conciseness and breadth of coverage.
- Part 4 – How Genomes Replicate and Evolve links DNA replication, mutation and recombination with the gradual evolution of genomes over time. In Chapters 13 and 14 the molecular processes responsible for replication, mutation, repair and recombination are described, and in Chapter 15 the ways in which these processes are thought to have shaped the structures and genetic contents of genomes over evolutionary time are considered. Finally, Chapter 16 is devoted to the increasingly informative use of molecular phylogenetics to infer the evolutionary relationships between DNA sequences.
Organization of Chapters
Learning outcomes
Each chapter starts with a set of learning outcomes. These have been phrased very carefully. They are not merely a series of synopses of the factual content of each chapter, but instead indicate the level and type of knowledge that the student should gain from reading the chapter. Therefore, the learning outcomes state what the student should be able to describe, draw, discuss, explain, evaluate, etc., each verb having been selected to convey precisely what it is that the student is expected to be able to do. The intention is that the student is left in no doubt about what they should get out of each chapter, and hence is in no doubt about whether they have dealt satisfactorily with the material.
Figures
A good diagram is certainly worth a thousand words but a bad one can confuse the reader and a superfluous one is merely distracting. I have therefore tried to ensure that every figure is necessary and fulfils a purpose beyond simply breaking up the text and making the book look pretty. I have also tried to make figures reproducible because in my opinion this makes them much more useful as a learning aid for the student. I have never understood the penchant for making textbook diagrams into works of art because if the student cannot redraw a diagram then it is merely an illustration and does not help the student learn the information that it is designed to convey. The figures in Genomes are as clear, simple and uncluttered as possible.
Boxes, Technical Notes and Research Briefings
The main text in each chapter is supported and extended by additional information, separated into three distinct categories:
- Boxes contain discrete packages of information that I have taken out of the main text, either for emphasis or to avoid disrupting the flow of the text. Some boxes summarize the key points regarding a topic that is described at length in the text, or provide a pointer towards a later topic that has a bearing on the issues being discussed. Other boxes are used to give a more extended coverage of interesting topics, and some describe current speculation regarding areas that have not yet been resolved.
- Each Technical Note is a self-contained description of a technique or a group of techniques important in the study of genomes. The Technical Notes are designed to be read in conjunction with the main text, each one being located at the place in the book where an application of that technique is described for the first time.
- Research Briefings are designed to illustrate some of the strategies that are used to study genomes. Each Briefing is based on one or a few research papers and explains the background and rationale of a research project, describes how the resulting data were analyzed, and summarizes the conclusions that were drawn. The objective is to illustrate the way in which real research is conducted and to show how research into molecular biology has established the ‘facts’ about genomes.
Reading lists
The reading lists at the end of each chapter are divided into two subsect1s:
- References are lists of articles that are cited in the text. Genomes is not itself a research publication and the text is not referenced in the way that would be appropriate for a review or scientific paper. Many points and facts are not referenced at all, and those citations that are given are often review articles rather than the relevant primary research papers. In several cases, for example, I have referred to a Science Perspective or Nature News and Views article, rather than a research paper, because these general articles are usually more helpful in explaining the context and relevance of a piece of work. My intention throughout Genomes has been that the reference lists should be as valuable as possible to students writing extended essays or dissertations on particular topics.
- Further Reading contains books and review articles that are not referred to directly in the main text but which are useful sources of additional material. In most cases I have appended a short summary stating the particular value of each item to help the reader decide which ones he or she wishes to seek out. The lists are not all-inclusive and I encourage readers to spend some time searching the shelves of their own libraries for other books and articles. Browsing is an excellent way to discover interests that you never realized you had!
Study aids
Each set of study aids is divided into three subsect1s: key terms, self study questions and problem-based learning.
Key terms
This is a list of the important words and short phrases that the student will have encountered for the first time when reading the chapter. A short definition is required for each one. All of the terms are highlighted in the text and defined in the Glossary, so the student can check the accuracy of their answers after they have completed the exercise. Short definitions of this kind are a useful type of revision aid: if a student can accurately define every key term then they almost certainly have an excellent knowledge of the factual content of the chapter.
Self study questions
These require 100–500 word answers, or occasionally ask for an annotated diagram or a table. The questions cover the entire content of each chapter in a straightforward manner, and they can be marked simply by checking each answer against the relevant part of the text. A student can use the self study questions to work systematically through a chapter, or can select individual ones in order to evaluate their ability to answer questions on specific topics. The self study questions could also be used in closed-book examinations.
Problem-based learning
This is a student-centered activity in which a group of students research a problem and, through their studies, obtain the information more normally delivered by a teacher-centered activity such as a lecture. Most students and teachers who have adopted this educational tool believe that it is a more effective means of learning than the traditional approaches, and is also more fun. The questions vary in nature and in difficulty. Some are reasonably straightforward and merely require a literature survey, the intention with these problems being that the students take their learning a few stages on from where Genomes leaves off. Some problems require that the students evaluate a statement or a hypothesis, which could be done by reading around the subject but which, hopefully, will engender a certain amount of thought and critical awareness. A few problems are very difficult, to the extent that there is no solid answer to the question posed. These are designed to stimulate debate and speculation, which stretches the knowledge of each student and forces them to think carefully about their statements. Ideally, problem-based learning is conducted as a group exercise, each group comprising 5–10 students, with an exercise lasting 1–2 weeks and being carried out through a series of meetings between the group and a facilitator, interspersed with meetings that the students conduct on their own. The facilitator helps the students to organize their thoughts, steers them away from unproductive lines of research, and points out any serious omissions in their approach. The output from the exercise is a written report, a poster, an oral presentation, or a combination of these things. Most of the problems given in Genomes are suitable for any type of output, and many can also be adapted for use as discussion topics in tutorials. There are no answers at the back of book! To provide answers would defeat the purpose – the intention is that the students discover a solution for themselves.
Appendix – Keeping up to Date
The Appendix gives the reader advice regarding the best way to keep up to date with the latest research discoveries. It is divided into two subsect1s. The first subsect1 covers the various journals and other publications that include reviews and news articles on genome research, and the second subsect1 contains a list of some of the many Internet sites that contain relevant information.
Glossary
I am very much in favor of glossaries as learning aids and I have provided an extensive one for this second edition of Genomes. Every term that is highlighted in bold in the text is defined in the Glossary, along with a number of additional terms that the reader might come across when referring to books or articles in the reading lists. Each term in the Glossary also appears in the index, so the reader can quickly gain access to the relevant pages where the Glossary term is covered in more detail.
- An Introduction to Genomes - GenomesAn Introduction to Genomes - Genomes
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