Preface |
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xv | |
Acknowledgments |
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xvii | |
Author |
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xix | |
Section I Life and Evolution |
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Chapter 1 Definitions of Life |
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3 | (16) |
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3 | (3) |
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6 | (3) |
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9 | (4) |
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Imagining Cellular and Molecular Dimensions |
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13 | (3) |
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16 | (1) |
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16 | (3) |
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Chapter 2 Earth and Evolution |
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19 | (22) |
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19 | (1) |
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19 | (3) |
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22 | (8) |
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A Short History of the Study of Evolution |
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30 | (5) |
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Earth History as One Year |
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35 | (2) |
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37 | (1) |
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38 | (3) |
Section II Biomolecules |
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Chapter 3 DNA, RNA, and Proteins |
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41 | (16) |
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41 | (1) |
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42 | (9) |
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51 | (1) |
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Amino Acids and Polypeptides |
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52 | (2) |
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54 | (1) |
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55 | (1) |
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56 | (1) |
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56 | (1) |
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Chapter 4 The Central Dogma and Beyond |
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57 | (14) |
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57 | (1) |
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57 | (7) |
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64 | (1) |
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65 | (3) |
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Other Small Noncoding RNA |
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68 | (1) |
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69 | (1) |
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69 | (1) |
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69 | (2) |
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Chapter 5 Ribosomes and Ribosomal RNA |
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71 | (12) |
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71 | (1) |
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71 | (1) |
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72 | (2) |
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74 | (2) |
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How Many rDNA Copies Are Needed? |
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76 | (1) |
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Mechanisms for Increasing rRNA Gene Copy Number |
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77 | (3) |
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80 | (1) |
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81 | (1) |
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81 | (2) |
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Chapter 6 Structure of the Genetic Code |
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83 | (14) |
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83 | (1) |
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Evolution of the Genetic Code |
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83 | (4) |
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87 | (3) |
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90 | (2) |
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92 | (3) |
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95 | (1) |
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96 | (1) |
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Chapter 7 DNA Replication |
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97 | (14) |
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97 | (1) |
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97 | (4) |
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Variations of Replication |
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101 | (5) |
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Topology during Replication |
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106 | (1) |
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Replication of Chromosomes |
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107 | (1) |
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108 | (1) |
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109 | (2) |
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Chapter 8 DNA Segregation |
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111 | (20) |
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111 | (1) |
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Variations on DNA Segregation in Bacteria and Archaea |
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111 | (2) |
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113 | (3) |
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Variations in Mitosis and the Cell Cycle |
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116 | (2) |
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Variations in Chromosome Number |
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118 | (2) |
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Changes in DNA Amount through the Cell Cycle |
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120 | (3) |
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123 | (2) |
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125 | (2) |
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127 | (1) |
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127 | (4) |
Section III Genetics |
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Chapter 9 Mendelian and Non-Mendelian Characters |
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131 | (16) |
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131 | (1) |
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132 | (1) |
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The Basics of Mendelian Inheritance |
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132 | (5) |
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Codominance, Incomplete Dominance, Overdominance, and Underdominance |
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137 | (1) |
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138 | (2) |
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140 | (1) |
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Recombination and Linkage |
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141 | (1) |
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141 | (5) |
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146 | (1) |
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146 | (1) |
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Chapter 10 Population Genetics |
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147 | (12) |
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147 | (1) |
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HardyWeinberg Equilibrium |
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148 | (2) |
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150 | (1) |
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151 | (3) |
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154 | (4) |
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158 | (1) |
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158 | (1) |
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Chapter 11 Alleles through Time |
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159 | (14) |
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159 | (1) |
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160 | (2) |
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162 | (3) |
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165 | (1) |
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166 | (1) |
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167 | (3) |
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Other Factors Affecting Allelic Proportions |
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170 | (1) |
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170 | (1) |
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171 | (2) |
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Chapter 12 Changes to DNA |
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173 | (14) |
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173 | (1) |
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173 | (1) |
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174 | (5) |
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Mutation during Replication |
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179 | (1) |
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180 | (2) |
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182 | (3) |
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185 | (1) |
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185 | (2) |
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Chapter 13 Infectious Changes to DNA: Viruses, Plasmids, Transposons, and Introns |
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187 | (28) |
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187 | (4) |
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Integration into Chromosomes |
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191 | (1) |
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192 | (4) |
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196 | (8) |
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204 | (5) |
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209 | (1) |
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210 | (1) |
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211 | (4) |
Section IV Multicellularity |
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Chapter 14 Multigene Families |
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215 | (14) |
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215 | (2) |
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Ribosomal RNA Gene Family |
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217 | (1) |
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218 | (4) |
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Bacterial Flagella Gene Family |
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222 | (1) |
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223 | (1) |
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223 | (1) |
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224 | (1) |
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Polyploidization and Multigene Family Evolution |
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224 | (3) |
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227 | (1) |
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227 | (2) |
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Chapter 15 Horizontal Gene Transfer |
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229 | (18) |
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229 | (2) |
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231 | (3) |
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234 | (1) |
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235 | (4) |
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239 | (3) |
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Origin of Gram-Negative Bacteria |
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242 | (1) |
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243 | (1) |
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244 | (2) |
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246 | (1) |
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246 | (1) |
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Chapter 16 Development: Part ICooperation among Cells |
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247 | (24) |
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247 | (2) |
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249 | (2) |
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251 | (1) |
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252 | (1) |
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Homeotic Genes and Proteins |
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253 | (8) |
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261 | (3) |
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Development in Vertebrates |
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264 | (2) |
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Hierarchy and Evolution of Homeotic Genes |
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266 | (2) |
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268 | (1) |
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269 | (2) |
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Chapter 17 Development: Part IIPlants |
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271 | (22) |
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271 | (2) |
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273 | (1) |
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274 | (3) |
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Gene Expression during Development |
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277 | (2) |
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Formation of Leaves and Floral Organs |
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279 | (8) |
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287 | (4) |
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291 | (1) |
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292 | (1) |
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293 | (22) |
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293 | (2) |
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295 | (3) |
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298 | (3) |
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301 | (1) |
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Causes of Mutations in Carcinogenesis |
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301 | (10) |
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302 | (1) |
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302 | (3) |
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305 | (1) |
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306 | (3) |
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309 | (2) |
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311 | (1) |
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312 | (1) |
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312 | (3) |
Section V Molecular Biology and Bioinformatic Methods |
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Chapter 19 Extraction and Quantification of Biological Molecules |
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315 | (20) |
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315 | (4) |
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Extraction of Nucleic Acids Using CTAB |
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319 | (2) |
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Purification of Organellar DNA |
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321 | (1) |
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322 | (2) |
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Quantification of Nucleic Acids |
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324 | (1) |
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Agarose Gel Electrophoresis |
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324 | (5) |
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329 | (1) |
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Quantification of Proteins |
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330 | (1) |
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Polyacrylamide Gel Electrophoresis |
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331 | (1) |
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332 | (1) |
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333 | (2) |
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Chapter 20 Recombinant DNA and Characterization of Biological Molecules |
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335 | (22) |
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335 | (1) |
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Polymerase Chain Reaction |
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335 | (3) |
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338 | (5) |
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343 | (6) |
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Determination of Gene Copy Number |
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349 | (2) |
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351 | (2) |
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353 | (2) |
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355 | (1) |
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355 | (2) |
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Chapter 21 Sequencing and Alignment Methods |
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357 | (16) |
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357 | (1) |
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Development of DNA Sequencing Methods |
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357 | (3) |
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High-Throughput Technologies |
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360 | (1) |
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Next-Generation Sequencing |
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361 | (4) |
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365 | (2) |
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Sequence Homology Searches |
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367 | (1) |
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368 | (2) |
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370 | (1) |
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371 | (2) |
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373 | (10) |
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373 | (1) |
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373 | (3) |
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376 | (2) |
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Metagenomics/Metatranscriptomics |
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378 | (1) |
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378 | (3) |
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381 | (1) |
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382 | (1) |
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Chapter 23 Omics: Part II |
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383 | (10) |
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383 | (1) |
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383 | (3) |
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386 | (1) |
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387 | (1) |
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388 | (1) |
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389 | (1) |
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389 | (2) |
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391 | (1) |
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391 | (2) |
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Chapter 24 Species Concepts and Phylogenetics |
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393 | (26) |
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393 | (1) |
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393 | (3) |
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396 | (3) |
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Reconstruction of Evolutionary History |
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399 | (1) |
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400 | (1) |
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401 | (1) |
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Choosing a Genomic Region for Phylogentics |
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402 | (6) |
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Other Considerations When Performing Phylogenetic Analyses |
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408 | (1) |
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409 | (1) |
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Analyzing Aligned Sequences |
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410 | (1) |
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Unweighted Pair Group Method with Arithmetic Mean |
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410 | (1) |
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410 | (1) |
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411 | (3) |
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414 | (1) |
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Bayesian Phylogenetic Analysis |
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415 | (1) |
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415 | (1) |
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Vertical versus Horizontal Evolutionary Events |
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416 | (1) |
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417 | (1) |
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417 | (2) |
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Chapter 25 Phylogenetic Networks and Reticulate Evolution |
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419 | (10) |
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419 | (1) |
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Phylogenetic Analyses of Reticulate Events |
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420 | (1) |
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Advantages of Phylogenetic Networks |
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420 | (2) |
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Horizontal Gene Transfers |
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422 | (1) |
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423 | (1) |
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424 | (1) |
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425 | (1) |
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425 | (1) |
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Examples of Reticulate Evolution Events |
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426 | (1) |
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427 | (1) |
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428 | (1) |
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Chapter 26 Phylogenomics and Comparative Genomics |
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429 | (16) |
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429 | (1) |
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Improvements in Sequencing and Phylogenomics |
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429 | (3) |
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432 | (1) |
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Single-Nucleotide Polymorphisms |
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433 | (1) |
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Microsatellites and Minisatellites |
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433 | (1) |
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434 | (1) |
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434 | (1) |
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434 | (1) |
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435 | (5) |
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440 | (1) |
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441 | (1) |
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442 | (3) |
Section VI Genomes |
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445 | (16) |
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445 | (3) |
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448 | (1) |
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448 | (1) |
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449 | (1) |
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Human Immunodeficiency Virus |
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449 | (4) |
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453 | (4) |
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457 | (1) |
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458 | (1) |
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459 | (2) |
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461 | (14) |
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461 | (1) |
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461 | (2) |
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463 | (5) |
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468 | (3) |
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471 | (3) |
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474 | (1) |
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474 | (1) |
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Chapter 29 Bacteria and Archaea |
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475 | (10) |
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475 | (1) |
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475 | (2) |
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477 | (2) |
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479 | (1) |
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480 | (2) |
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482 | (1) |
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483 | (1) |
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483 | (2) |
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Chapter 30 Mutualists and Pathogens |
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485 | (10) |
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485 | (2) |
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487 | (1) |
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Smallest Bacterial Genome |
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487 | (2) |
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489 | (1) |
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490 | (1) |
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Genome Mixing and Sorting |
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491 | (1) |
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492 | (1) |
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492 | (3) |
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Chapter 31 Endosymbionts and Organelles |
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495 | (20) |
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495 | (1) |
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Intracellular Endosymbionts |
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495 | (1) |
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496 | (7) |
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How Many Genes Make a Functional Mitochondrion? |
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503 | (3) |
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506 | (2) |
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How Many Genes Make a Functional Chloroplast? |
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508 | (2) |
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Differential Development and Function |
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510 | (1) |
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510 | (2) |
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Endosymbioses Leading to Other Organelles |
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512 | (2) |
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514 | (1) |
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514 | (1) |
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Chapter 32 Protein Trafficking |
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515 | (12) |
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515 | (1) |
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Signal Peptides in Bacteria |
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515 | (3) |
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Signal Peptide Systems in Eukarya |
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518 | (2) |
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Protein Trafficking in Mitochondria |
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520 | (1) |
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Protein Trafficking in Chloroplasts |
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520 | (3) |
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Evolution of Protein Trafficking Systems |
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523 | (1) |
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524 | (1) |
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525 | (2) |
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Chapter 33 Eukaryotic Genomes |
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527 | (18) |
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527 | (1) |
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Origin of the Nucleus and Mitochondrion |
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528 | (3) |
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531 | (1) |
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531 | (1) |
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532 | (6) |
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532 | (2) |
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534 | (3) |
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537 | (1) |
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538 | (5) |
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538 | (2) |
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540 | (3) |
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543 | (1) |
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544 | (1) |
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545 | (12) |
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545 | (1) |
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545 | (3) |
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548 | (2) |
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Single-Nucleotide Polymorphisms |
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550 | (1) |
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551 | (1) |
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551 | (3) |
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554 | (1) |
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554 | (3) |
Index |
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557 | |