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Most analyses assume that genomes are to be read as linear text, much as a sequence of nucleotides can be translated into a sequence of amino acids by looking in a table. However, information can evolve in genomes with distinct forms of representation, such as in the structure of DNA or RNA and/or the relationship between nucleotide sequences. Such information has importance to biology yet is largely unexpected and unexplored. As described in this volume, much of this information, through mechanisms ranging from alternative splicing of RNA to the generation of bacterial coat protein diversity, affects the probability of distinct types of alterations in the nucleic acid sequence. Some genomic DNA sequences affect genome stability, handling and organization, with implications for the robustness of lineages over evolutionary time. The examples reviewed in this volume, taken from a broad range of biological organisms, both extend our view of the nature of information encoded within genomes, and can deepen our appreciation of the power of natural selection, through which this information, in its various forms, has emerged.
目录
Contributors p. ix
An Overview of the Implicit Genome Lynn Helena Caporale p. 3
1 Sequence-Dependent Properties of DNA and Their Role in Function Donald M. Crothers p. 23
2 Mutation as a Phenotype Errol C. Friedberg p. 39
3 Repeats and Variation in Pathogen Selection Christopher D. Bayliss and E. Richard Moxon p. 54
4 Tuning Knobs in the Genome: Evolution of Simple Sequence Repeats by Indirect Selection David G. King and Edward N. Trifonov and Yechezkel Kashi p. 77
5 Implicit Information in Eukaryotic Pathogens as the Basis of Antigenic Variation J. David Barry p. 91
6 The Role of Repeat Sequences in Bacterial Genetic Adaptation to Stress Eduardo P. C. Rocha p. 107
7 The Role of Mobile DNA in the Evolution of Prokaryotic Genomes Garry Myers and Ian Paulsen and Claire Eraser p. 121
8 Eukaryotic Transposable Elements: Teaching Old Genomes New Tricks Susan R. Wessler p. 138
9 Immunoglobulin Recombination Signal Sequences: Somatic and Evolutionary Functions Ellen Hsu p. 163
10 Somatic Evolution of Antibody Genes Rupert Beale and Dagmar Iber p. 177
11 Regulated and Unregulated Recombination of G-rich Genomic Regions Nancy Maizels p. 191
12 The Role of the Genome in the Initiation of Meiotic Recombination Rhona H. Borts and David T. Kirkpatrick p. 208
13 Nuclear Duality and the Genesis of Unusual Genomes in Ciliated Protozoa Carolyn L. Jahn p. 225
14 Editing informational Content of Expressed DNA Sequences and Their Transcripts Harold C. Smith p. 248
15 Alternative Splicing: One Gene, Many Products Brenton R. Graveley p. 266
16 Imprinting: The Hidden Genome Alyson Ashe and Emma Whitelaw p. 282
Epilogue: An Engineering Perspective: The Implicit Protocols John Doyle and Marie Csete and Lynn Caporale p. 294
References p. 299
List of Acronyms p. 363
Index p. 365
An Overview of the Implicit Genome Lynn Helena Caporale p. 3
1 Sequence-Dependent Properties of DNA and Their Role in Function Donald M. Crothers p. 23
2 Mutation as a Phenotype Errol C. Friedberg p. 39
3 Repeats and Variation in Pathogen Selection Christopher D. Bayliss and E. Richard Moxon p. 54
4 Tuning Knobs in the Genome: Evolution of Simple Sequence Repeats by Indirect Selection David G. King and Edward N. Trifonov and Yechezkel Kashi p. 77
5 Implicit Information in Eukaryotic Pathogens as the Basis of Antigenic Variation J. David Barry p. 91
6 The Role of Repeat Sequences in Bacterial Genetic Adaptation to Stress Eduardo P. C. Rocha p. 107
7 The Role of Mobile DNA in the Evolution of Prokaryotic Genomes Garry Myers and Ian Paulsen and Claire Eraser p. 121
8 Eukaryotic Transposable Elements: Teaching Old Genomes New Tricks Susan R. Wessler p. 138
9 Immunoglobulin Recombination Signal Sequences: Somatic and Evolutionary Functions Ellen Hsu p. 163
10 Somatic Evolution of Antibody Genes Rupert Beale and Dagmar Iber p. 177
11 Regulated and Unregulated Recombination of G-rich Genomic Regions Nancy Maizels p. 191
12 The Role of the Genome in the Initiation of Meiotic Recombination Rhona H. Borts and David T. Kirkpatrick p. 208
13 Nuclear Duality and the Genesis of Unusual Genomes in Ciliated Protozoa Carolyn L. Jahn p. 225
14 Editing informational Content of Expressed DNA Sequences and Their Transcripts Harold C. Smith p. 248
15 Alternative Splicing: One Gene, Many Products Brenton R. Graveley p. 266
16 Imprinting: The Hidden Genome Alyson Ashe and Emma Whitelaw p. 282
Epilogue: An Engineering Perspective: The Implicit Protocols John Doyle and Marie Csete and Lynn Caporale p. 294
References p. 299
List of Acronyms p. 363
Index p. 365
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