Forsdyke Evolutionary Bioinformatics

2. Auflage 2011
ISBN: 978-1-4419-7771-7
Verlag: Springer US
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, 509 Seiten

Books on bioinformatics which began appearing in the mid 80s primarily served gene-hunters, and biologists who wished to construct family trees showing tidy lines of descent. Given the great pharmaceutical industry interest in genes, this trend has continued in most subsequent texts. These deal extensively with the exciting topic of gene discovery and searching databases, but hardly consider genomes as information channels through which multiple forms and levels of information, including genic information, have passed through the generations.

Autoren/Hrsg.

Forsdyke, Donald R.

Inhaltsverzeichnis

1;Contents;8
2;Note on the Second Edition;10
3;Abbreviations;11
4;Prologue;12
4.1;To Select is Not To Preserve;12
4.1.1;That Sort of Clearness;13
4.1.2;A Buck or Two;14
4.1.3;The Dawn;15
4.1.3.1;Homo bioinformaticus;15
4.1.4;Further Veils?;16
4.1.5;Scope;17
4.1.6;Goals;21
5;Part 1 Information and DNA;24
5.1;Chapter 1;25
5.1.1;Memory – A Phenomenon of Arrangement;25
5.1.1.1;Priorities;25
5.1.1.2;Textual and Hereditary Information;27
5.1.1.3;Mental Information;29
5.1.1.4;Periodical Rhythms;32
5.1.1.5;Food;35
5.1.1.6;Informational Macromolecules;36
5.1.1.7;Translation;40
5.1.1.8;Variation;43
5.1.1.9;Latency;46
5.1.1.10;Summary;47
5.2;Chapter 2;49
5.2.1;Chargaff's First Parity Rule;49
5.2.1.1;Error-Detection;49
5.2.1.2;In-Parallel Redundancy;50
5.2.1.3;DNA Structure;50
5.2.1.4;Turnover;58
5.2.1.5;Promiscuous DNA;59
5.2.1.6;Haploidy and Diploidy;60
5.2.1.7;In-Series Redundancy;61
5.2.1.8;Bits and Bats;62
5.2.1.9;Accidents and Non-Accidents;65
5.2.1.10;Summary;67
5.3;Chapter 3;68
5.3.1;Information Levels and Barriers;68
5.3.1.1;Symbols and Code;68
5.3.1.2;Primary and Secondary Information;69
5.3.1.3;Primary Information for Protein;70
5.3.1.4;Information Barriers;72
5.3.1.5;Barriers Preserve Discontinuity;73
5.3.1.6;To Select is Not to Preserve;77
5.3.1.7;Another Order of Variation;79
5.3.1.8;Context as Barrier;81
5.3.1.9;Not a Palimpsest;83
5.3.1.10;Hybrid Disciplines and Hybrid Sterility;85
5.3.1.11;Summary;87
6;Part 2 Parity and Non-Parity;88
6.1;Chapter 4;89
6.1.1;Chargaff’s Second Parity Rule;89
6.1.1.1;Information Conflict;89
6.1.1.2;Prose, Poetry and Palindromes;90
6.1.1.3;Intrastand Parity;92
6.1.1.4;Polarity and Complementarity;93
6.1.1.5;Duplets and Triplets;97
6.1.1.6;Species Specificity of Tuple Frequencies;101
6.1.1.7;Metagenomics;103
6.1.1.8;Introns Obey Better Than Exons;103
6.1.1.9;Level of Selection?;105
6.1.1.10;Inter-chromosomal Accounting;108
6.1.1.11;Summary;110
6.2;Chapter 5;111
6.2.1;Stems and Loops;111
6.2.1.1;Transfer RNA;111
6.2.1.2;The Bacteriophage Paradox;114
6.2.1.3;Genome-Level Selection;115
6.2.1.4;Calculation from Single Base Pairs;116
6.2.1.5;Role of Base Composition;120
6.2.1.6;Calculation from Dinucleotide Pairs;121
6.2.1.7;RNA Structure and Conflict;123
6.2.1.8;PR2 Revisited;126
6.2.1.9;Symmetrical Extrusions;127
6.2.1.10;DNA as Substrate;128
6.2.1.11;Summary;129
6.3;Chapter 6;130
6.3.1;Chargaff’s Cluster Rule;130
6.3.1.1;Base Clusters;130
6.3.1.2;Clusters of Clusters;131
6.3.1.3;Polarity;134
6.3.1.4;Origin of Replication;135
6.3.1.5;Gene Movements;138
6.3.1.6;Leading and Lagging Strands;139
6.3.1.7;Purine loading;141
6.3.1.8;Pyrimidine-Loading in Mitochondria;144
6.3.1.9;Summary.;146
7;Part 3 Variation and Speciation;147
7.1;Chapter 7;148
7.1.1;Mutation;148
7.1.1.1;The Genetic Code;150
7.1.1.2;One Base at a Time;151
7.1.1.3;RNY Rule;153
7.1.1.4;Negative and Positive Selection;155
7.1.1.5;Neutral Mutations;157
7.1.1.6;Genome Phenotype;158
7.1.1.7;Compensatory Mutations;161
7.1.1.8;Were First Mutations Synonymous?;163
7.1.1.9;Phylogenetic Trees;165
7.1.1.10;Limits of Natural Selection;166
7.1.1.11;Summary;168
7.2;Chapter 8;169
7.2.1;Species Survival and Arrival;169
7.2.1.1;Blending or Discrete Inheritance?;170
7.2.1.2;Mendelism;172
7.2.1.3;Multigenic Characters;174
7.2.1.4;Reproductive Isolation;175
7.2.1.5;Cycling through the Generations;177
7.2.1.6;Jurrasic Park;178
7.2.1.7;Branching Evolution;180
7.2.1.8;Dobzhansky and Muller;182
7.2.1.9;Pattern Change;183
7.2.1.10;Summary;185
7.3;Chapter 9;186
7.3.1;The Weak Point;186
7.3.1.1;Cryptic Variability of the Reproductive System;187
7.3.1.2;Collective Variation of a Population Subset;189
7.3.1.3;Sporadic and Regular Sterilities;189
7.3.1.4;Chromosomes and the Residue or Irresoluble Base;193
7.3.1.5;Two Factors must Complement to Produce Sterility;194
7.3.1.6;Complementation like Sword and Scabbard;197
7.3.1.7;Modern Chromosomal Views;199
7.3.1.8;Darwin’s Difficulties;201
7.3.1.9;Species Selection;202
7.3.1.10;Summary;203
7.4;Chapter 10;204
7.4.1;Chargaff’s GC rule;204
7.4.1.1;Uniformity of (G+C)%;205
7.4.1.2;The Holy Grail;205
7.4.1.3;Language;206
7.4.1.4;Crick’s Unpairing Postulate;209
7.4.1.5;Structure-Mediated Homology Recognition;210
7.4.1.6;(G+C)% Controls Pairing;213
7.4.1.7;Mutational Meltdown;215
7.4.1.8;Coinfecting Viruses;216
7.4.1.9;Protein Pressure Reinforces;217
7.4.1.10;Polyploidy;217
7.4.1.11;Saltum?;218
7.4.1.12;Summary;219
7.5;Chapter 11;220
7.5.1;Homostability;220
7.5.1.1;Gene Duplication and Isochores;221
7.5.1.2;Isochores Early;226
7.5.1.3;The Gene as a Unit of Recombination;228
7.5.1.4;The Boundary Problem;230
7.5.1.5;Thermophiles;231
7.5.1.6;Summary;233
8;Part 4 Conflict within Genomes;234
8.1;Chapter 12;235
8.1.1;Conflict Resolution;235
8.1.1.1;Two Levels of Information;236
8.1.1.2;Codon Bias;237
8.1.1.3;GC-Pressure versus Protein-Pressure;240
8.1.1.4;Species Barcode in Mitochondria;242
8.1.1.5;Species versus Genes;244
8.1.1.6;Species Win at (G+C)% extremes;247
8.1.1.7;Intermediate (G+C)% Allows Compromise;250
8.1.1.8;Levels of Selection;251
8.1.1.9;Dog Wags Tail;252
8.1.1.10;AG-Pressure versus Protein-Pressure;253
8.1.1.11;GC-Pressure versus AG-Pressure;255
8.1.1.12;AG-Pressure and ‘Placeholder’ Amino Acids;257
8.1.1.13;Thermophiles;259
8.1.1.14;Summary;261
8.2;Chapter 13;262
8.2.1;Exons and Introns;262
8.2.1.1;Introns Interrupt Information;263
8.2.1.2;Protein versus DNA;267
8.2.1.3;Achilles Heels;272
8.2.1.4;Mirror Repeats;272
8.2.1.5;RNA versus DNA;273
8.2.1.6;Overlapping Genes;274
8.2.1.7;Simple Sequences;274
8.2.1.8;Multiple Pressures;277
8.2.1.9;Summary;279
8.3;Chapter 14;280
8.3.1;Complexity;280
8.3.1.1;Scoring Information Potential;280
8.3.1.2;The New Bioinformatics;281
8.3.1.3;Protein or Nucleic Acid Level Function?;282
8.3.1.4;Base Pair Pressures;284
8.3.1.5;Epstein-Barr Virus;286
8.3.1.6;Malaria;291
8.3.1.7;Conflict with Fold Potential;295
8.3.1.8;Roles of Low Complexity Segments;297
8.3.1.9;Short Tandem Repeats;298
8.3.1.10;AC-Pressure and Asymmetric Fold Potential;301
8.3.1.11;Repetitive Sequences and Speciation;302
8.3.1.12;Long-Range Periodicities;303
8.3.1.13;Summary;304
9;Part 5 Conflict between Genomes;305
9.1;Chapter 15;306
9.1.1;Self/Not-Self?;306
9.1.1.1;Homology Search;307
9.1.1.2;Antibody Response;309
9.1.1.3;Antibody Variable Genes;310
9.1.1.4;Prototypic Immune Systems;311
9.1.1.5;Polymorphism Creates Host Unpredictability;315
9.1.1.6;Junk DNA;316
9.1.1.7;Repetitive Elements;317
9.1.1.8;All Hands on Deck!;320
9.1.1.9;The Double-Stranded RNA Alarm;321
9.1.1.10;Purine-Loading to Self-Discriminate;323
9.1.1.11;Entropy;324
9.1.1.12;The Hidden Transcriptome;326
9.1.1.13;CRISPR;328
9.1.1.14;Summary;329
9.2;Chapter 16;330
9.2.1;The Crowded Cytosol;330
9.2.1.1;Piles of Coins;331
9.2.1.2;Homoaggregates;333
9.2.1.3;Collective Pressure;334
9.2.1.4;Concentration Fine-Tuning;335
9.2.1.5;Heteroaggregates;336
9.2.1.6;Protein ‘Immune Receptors’;337
9.2.1.7;Phenotypic Plasticity;338
9.2.1.8;Polymorphism Makes You Individual;339
9.2.1.9;Polymorphism Also Makes You Vulnerable;341
9.2.1.10;Death at Home or in Exile;342
9.2.1.11;Selfish Genes and the Menopause;343
9.2.1.12;Molecular Chaperones;343
9.2.1.13;Positive Repertoire Selection;346
9.2.1.14;Summary;347
10;Part 6 Sex and Error-Correction;349
10.1;Chapter 17;350
10.1.1;Rebooting the Genome;350
10.1.1.1;Redundancy;351
10.1.1.2;Recombination Repair;352
10.1.1.3;Strand Guidance;354
10.1.1.4;DNA Damage;356
10.1.1.5;Piano Tuning;358
10.1.1.6;Spot Your Reprotype?;358
10.1.1.7;Haldane’s Rule;359
10.1.1.8;Sex Chromosomes;360
10.1.1.9;Sex and Speciation;363
10.1.1.10;Sex Chromosome Dosage Compensation;366
10.1.1.11;Summary;369
10.2;Chapter 18;371
10.2.1;The Fifth Letter;371
10.2.2;Editing of DNA;371
10.2.3;Restriction Enzymes;372
10.2.4;CpG Islands;375
10.2.5;CpG Suppression;376
10.2.6;Methylation Differences in Twins;378
10.2.7;Imprinting;378
10.2.8;Transgenerational Inheritance;380
10.2.9;Editing of RNA;381
10.2.10;Summary;382
11;Part 7 Information and Mind;383
11.1;Chapter 19;384
11.1.1;Memory – What is Arranged and Where?;384
11.1.1.1;The Organ Par Excellence;384
11.1.1.2;The Cupboard is Bare;385
11.1.1.3;The Conventional Wisdom;386
11.1.1.4;Tomorrow;387
11.1.1.5;Savants and Information Measurement;388
11.1.1.6;Internal Signal Detection and Emission;389
11.1.1.7;Cloud Computing;390
11.1.1.8;The Physics of Space;391
11.1.1.9;Syntax;392
11.1.1.10;Argument from Incredulity;393
11.1.1.11;A Hilbertian List;394
11.1.1.12;Summary;396
12;Epilogue;397
12.1;To Preserve is Not To Select;397
12.1.1;Percepts;397
12.1.2;Torch Passed;398
12.1.3;Voting with Facts;400
12.1.4;False Leads?;402
12.1.5;Marketing;404
12.1.6;Joining the Dots;405
12.1.7;Cogito Ergo …?;407
13;Appendices;408
13.1;Appendix 1;409
13.1.1;What the Graph Says;409
13.1.1.1;Horizontal Lines;409
13.1.1.2;Tilted Lines;412
13.1.1.3;Curved Lines;413
13.1.1.4;No Lines;414
13.1.1.5;A Caution;414
13.2;Appendix 2;415
13.2.1;Scoring Information Potential;415
13.2.1.1;Two Units;415
13.2.1.2;Four Units;416
13.2.1.3;Twenty Units;416
13.2.1.4;Meaning;417
13.3;Appendix 3;419
13.3.1;No Line?;419
13.3.1.1;Setting the Stage;419
13.3.1.2;Rules of Thumb;421
13.3.1.3;Probabilities;422
13.3.1.4;No Beginning?;423
13.3.1.5;Can Intermediate States Exist?;425
13.3.1.6;Contradiction Shall Reign!;427
14;Acknowledgements;429
15;References and Notes;432
15.1;Prologue – To Select is Not To Preserve;432
15.1.1;Chapter 1 – Memory: A Phenomenon of Arrangement;433
15.1.2;Chapter 2 – Chargaff’s First Parity Rule;437
15.1.3;Chapter 3 – Information Levels and Barriers;438
15.1.4;Chapter 4 – Chargaff’s Second Parity Rule;439
15.1.5;Chapter 5 – Stems and Loops;441
15.1.6;Chapter 6 – Chargaff’s Cluster Rule;442
15.1.7;Chapter 7 – Mutation;445
15.1.8;Chapter 8 – Species Survival and Arrival;446
15.1.9;Chapter 9 – The Weak Point;448
15.1.10;Chapter 10 – Chargaff’s GC Rule;448
15.1.11;Chapter 11 – Homostability;451
15.1.12;Chapter 12 – Conflict Resolution;453
15.1.13;Chapter 13 – Exons and Introns;454
15.1.14;Chapter 14 – Complexity;457
15.1.15;Chapter 15 – Self/Not-Self?;459
15.1.16;Chapter 16 – The Crowded Cytosol;461
15.1.17;Chapter 17 – Rebooting the Genome;463
15.1.18;Chapter 18 – The Fifth Letter;465
15.1.19;Chapter 19 Memory – What is Arranged and Where?;467
15.2;Epilogue – To Preserve in Not To Select;470
15.3;Appendix 3 – No Line?;473
16;Index;475