Preface |
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xix | |
About the Authors |
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xxi | |
Study Aids |
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xxiii | |
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section I microbial activity |
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1 | (16) |
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2 | (15) |
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3 | (1) |
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3 | (2) |
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5 | (1) |
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6 | (2) |
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8 | (1) |
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8 | (1) |
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Colonizing every niche and making Earth inhabitable |
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9 | (2) |
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11 | (1) |
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12 | (1) |
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Cooperating for complex endeavors |
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13 | (2) |
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15 | (1) |
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15 | (2) |
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section II structure and function |
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17 | (32) |
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prokaryotic cell structure and function: envelopes and appendages |
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18 | (20) |
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19 | (1) |
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20 | (2) |
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21 | (1) |
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Scanned-proximity probe microscopes |
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21 | (1) |
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21 | (1) |
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Prokaryotes have complex envelopes and appendages |
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22 | (1) |
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22 | (1) |
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How the cell membrane is protected |
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23 | (8) |
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The gram-positive solution |
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23 | (3) |
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The gram-negative solution |
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26 | (2) |
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28 | (1) |
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Crystalline surface layers |
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29 | (1) |
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Bacteria without cell walls: the mycoplasmas |
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30 | (1) |
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Cell envelopes of the Archaea |
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30 | (1) |
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Capsules, flagella, and pili: how prokaryotes cope in certain environments |
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31 | (6) |
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Capsules and slime layers |
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31 | (1) |
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32 | (3) |
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35 | (2) |
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37 | (1) |
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prokaryotic cell structure and function: the cell interior |
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38 | (11) |
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39 | (1) |
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39 | (5) |
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44 | (1) |
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45 | (2) |
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45 | (1) |
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Organelles for photosynthesis and chemosynthesis |
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46 | (1) |
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46 | (1) |
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47 | (1) |
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Storage granules and others |
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47 | (1) |
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47 | (1) |
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48 | (1) |
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49 | (134) |
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growth of microbial populations |
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50 | (20) |
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51 | (2) |
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How to measure growth of a bacterial culture |
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53 | (1) |
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When should the growth rate be determined? |
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54 | (1) |
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55 | (2) |
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57 | (1) |
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58 | (1) |
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How is the physiology of the cells affected by the growth rate? |
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59 | (2) |
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Effects of temperature, hydrostatic pressure, osmotic strength, and pH |
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61 | (7) |
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62 | (1) |
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62 | (1) |
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Classifying the temperature responses of microbes |
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63 | (1) |
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Growth limits at temperature extremes |
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63 | (3) |
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66 | (1) |
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67 | (1) |
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67 | (1) |
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68 | (1) |
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68 | (1) |
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69 | (1) |
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70 | (12) |
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71 | (1) |
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Growth metabolism: making life from nonlife |
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71 | (2) |
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Framework of growth metabolism |
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73 | (7) |
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74 | (1) |
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Assembling cell structures |
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75 | (1) |
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76 | (1) |
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Synthesizing building blocks |
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76 | (1) |
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77 | (3) |
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Global effects of growth metabolism |
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80 | (1) |
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80 | (1) |
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80 | (1) |
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81 | (1) |
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81 | (1) |
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82 | (30) |
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Overview of fueling reactions |
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83 | (1) |
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Getting energy and reducing power |
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84 | (14) |
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Driving force and its generation |
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84 | (3) |
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Substrate level phosphorylation and fermentation |
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87 | (3) |
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Transmembrane ion gradients |
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90 | (1) |
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90 | (4) |
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94 | (2) |
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96 | (1) |
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96 | (2) |
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98 | (1) |
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Making precursor metabolites: heterotrophy |
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98 | (11) |
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98 | (1) |
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Transport through the OM of gram-negative bacteria |
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99 | (1) |
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Transport through the cell membrane |
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100 | (3) |
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103 | (1) |
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104 | (1) |
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Common pathways of central metabolism |
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104 | (2) |
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Auxiliary pathways of central metabolism |
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106 | (1) |
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Diversity and flexibility of central metabolism |
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107 | (2) |
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Making precursor metabolites: autotrophy |
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109 | (1) |
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109 | (1) |
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109 | (1) |
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110 | (1) |
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111 | (1) |
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112 | (18) |
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Some general observations |
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113 | (5) |
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Biosynthesis and nutrition |
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113 | (1) |
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Bacterial studies and biosynthetic pathways |
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113 | (1) |
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The concept of a biosynthetic pathway |
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114 | (4) |
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118 | (4) |
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Central actors: glutamate and glutamine |
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118 | (2) |
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Synthesis of glutamate and glutamine |
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120 | (1) |
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121 | (1) |
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122 | (1) |
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122 | (2) |
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Assimilation of phosphorus |
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124 | (1) |
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Pathways to building blocks |
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124 | (3) |
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124 | (1) |
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125 | (1) |
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Sugars and sugar-like derivatives |
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126 | (1) |
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126 | (1) |
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127 | (1) |
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127 | (3) |
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130 | (38) |
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131 | (1) |
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132 | (9) |
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132 | (1) |
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Initiation of replication |
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133 | (2) |
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135 | (1) |
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Repair of errors in replication |
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136 | (2) |
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Termination of replication |
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138 | (1) |
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139 | (1) |
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140 | (1) |
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141 | (8) |
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Overview of transcription |
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141 | (1) |
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141 | (1) |
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Products of transcription |
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142 | (1) |
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Initiation of transcription |
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142 | (1) |
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143 | (2) |
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145 | (1) |
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145 | (1) |
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Termination of transcription |
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146 | (1) |
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146 | (1) |
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147 | (1) |
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Modification and assembly of stable RNA |
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147 | (1) |
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Polymerase collision and genome organization |
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148 | (1) |
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149 | (13) |
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Special tempo and mode of protein synthesis |
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149 | (2) |
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151 | (1) |
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Initiation of protein synthesis |
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151 | (2) |
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Polypeptide chain elongation |
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153 | (2) |
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Termination of translation |
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155 | (1) |
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156 | (1) |
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156 | (1) |
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157 | (1) |
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Translocation of proteins |
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158 | (4) |
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162 | (4) |
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Challenges of envelope formation |
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162 | (1) |
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163 | (1) |
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164 | (1) |
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165 | (1) |
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165 | (1) |
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166 | (1) |
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166 | (1) |
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166 | (2) |
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168 | (15) |
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169 | (1) |
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Strategies for studying the bacterial cell cycle |
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169 | (2) |
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DNA replication during the cell cycle |
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171 | (1) |
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How is DNA replication regulated? |
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172 | (2) |
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174 | (4) |
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Morphological considerations |
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174 | (1) |
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How is the septum formed? |
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175 | (2) |
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How does a bacterium find its middle? |
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177 | (1) |
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The connection between cell division and DNA replication |
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178 | (2) |
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Cell division and plasmid replication |
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180 | (1) |
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The prokaryotic equivalent of mitosis |
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181 | (1) |
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182 | (1) |
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183 | (36) |
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184 | (20) |
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185 | (1) |
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Exchange of DNA among prokaryotes |
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185 | (10) |
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186 | (1) |
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Artificial transformation |
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187 | (1) |
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187 | (2) |
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189 | (1) |
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190 | (1) |
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191 | (1) |
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192 | (1) |
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193 | (1) |
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Conjugation among gram-negative bacteria |
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193 | (2) |
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Conjugation among gram-positive bacteria |
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195 | (1) |
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Mutation and sources of genetic variation among prokaryotes |
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195 | (5) |
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196 | (1) |
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197 | (1) |
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198 | (2) |
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Site-directed mutagenesis |
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200 | (1) |
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200 | (2) |
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201 | (1) |
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202 | (1) |
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202 | (1) |
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203 | (1) |
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204 | (15) |
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205 | (1) |
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Sequence of bases in macromolecules |
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206 | (4) |
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Small-subunit ribosomal RNA |
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206 | (2) |
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Proteins as markers of evolution |
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208 | (2) |
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210 | (1) |
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211 | (1) |
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Mechanisms of bacterial evolution |
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212 | (2) |
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212 | (1) |
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213 | (1) |
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Early eukaryotes and endosymbiosis |
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214 | (2) |
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216 | (1) |
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217 | (1) |
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217 | (2) |
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219 | (70) |
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coordination and regulation |
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220 | (28) |
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221 | (1) |
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Evidence for coordination of metabolic reactions |
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221 | (2) |
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Coordination in biosynthesis |
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221 | (1) |
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222 | (1) |
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Coordination in polymerization |
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223 | (1) |
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223 | (2) |
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Controlling enzyme activity |
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224 | (1) |
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Controlling enzyme amounts |
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224 | (1) |
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Why two modes of regulation? |
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224 | (1) |
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Modulation of protein activity |
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225 | (3) |
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225 | (1) |
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Allostery in biosynthesis |
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226 | (1) |
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227 | (1) |
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228 | (1) |
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Modulation of protein amounts |
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228 | (17) |
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Regulation of operon expression |
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229 | (3) |
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Mechanisms at site 1: promoter recognition |
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232 | (1) |
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Mechanisms at sites 2, 3, and 4: transcriptional repression, activation, and enhancement |
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232 | (1) |
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Mechanisms at site 5: targeting by sRNAs |
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233 | (1) |
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Mechanisms at site 6: DNA supercoiling |
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233 | (1) |
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Mechanisms at site 7: translational repression |
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234 | (1) |
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Mechanisms at site 8: attenuation |
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234 | (4) |
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Mechanisms at site 9: mRNA stability |
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238 | (1) |
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Mechanisms at site 10: proteolysis |
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238 | (1) |
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Regulation beyond the operon |
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238 | (1) |
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Regulatory units above the operon |
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239 | (3) |
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Examples of global regulatory systems |
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242 | (3) |
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Cooperative interaction of regulatory devices |
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245 | (1) |
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Summary and conclusions: networks for coordination and response |
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245 | (1) |
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246 | (2) |
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succeeding in the environment |
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248 | (26) |
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Microbes in their habitat |
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249 | (1) |
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Coping with stress as individual cells |
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250 | (18) |
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250 | (1) |
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Overview of stress responses |
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251 | (1) |
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251 | (1) |
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Complex circuitry for complex responses |
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252 | (1) |
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253 | (4) |
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Major stress response networks |
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257 | (1) |
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257 | (2) |
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The ultimate stress response: stationary phase |
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259 | (3) |
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Stress responses and microbial diversity |
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262 | (1) |
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Stress responses and safety in numbers |
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263 | (1) |
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Coping with stress by escaping |
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263 | (1) |
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264 | (3) |
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267 | (1) |
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267 | (1) |
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268 | (1) |
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Coping with stress by community effort |
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268 | (3) |
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268 | (2) |
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Formation of organized communities |
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270 | (1) |
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Quorum sensing, motility, and biofilm formation |
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271 | (1) |
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271 | (1) |
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272 | (2) |
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differentiation and development |
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274 | (15) |
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275 | (2) |
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277 | (5) |
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277 | (1) |
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Phylogenetic distribution |
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277 | (1) |
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278 | (2) |
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Programming and regulation |
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280 | (1) |
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280 | (1) |
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281 | (1) |
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Sporulation: a group activity |
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281 | (1) |
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Development of Caulobacter crescentus |
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282 | (2) |
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282 | (1) |
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Genetic control of development |
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283 | (1) |
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Development of myxobacteria |
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284 | (2) |
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Regulation of development |
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285 | (1) |
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Other bacteria that undergo differentiation and development |
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286 | (1) |
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287 | (1) |
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287 | (2) |
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289 | (64) |
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290 | (22) |
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291 | (1) |
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Making order of prokaryotic diversity |
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291 | (2) |
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293 | (1) |
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Extent of prokaryotic diversity |
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294 | (3) |
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Higher taxa of prokaryotes |
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297 | (1) |
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297 | (5) |
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299 | (1) |
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299 | (1) |
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300 | (1) |
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301 | (1) |
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302 | (8) |
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Phylum B4: Deinococcus-Thermus |
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303 | (3) |
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Phylum B10: Cyanobacteria |
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306 | (1) |
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Phylum B12: Proteobacteria |
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307 | (1) |
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307 | (2) |
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Betaproteobacteria and Gammaproteobacteria |
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309 | (1) |
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Phylum B14: Actinobacteria |
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309 | (1) |
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310 | (1) |
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310 | (2) |
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312 | (18) |
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313 | (1) |
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314 | (5) |
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315 | (1) |
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316 | (2) |
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Why is yeast such a popular genetic tool? |
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318 | (1) |
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319 | (9) |
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319 | (3) |
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Plasmodium, the parasite that causes malaria |
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322 | (3) |
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325 | (3) |
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328 | (1) |
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328 | (2) |
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viruses, viroids, and prions |
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330 | (23) |
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331 | (1) |
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331 | (3) |
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Ecology and classification |
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334 | (1) |
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335 | (6) |
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Attachment and penetration |
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335 | (2) |
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Viral nucleic acid synthesis: a theme with variations |
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337 | (1) |
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338 | (2) |
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Virion assembly and release from the host cell |
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340 | (1) |
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Visualizing and quantitating viral growth |
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341 | (1) |
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Lysogeny and integration into the host genome |
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341 | (6) |
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341 | (2) |
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How does the genome of a temperate phage become integrated into that of a host cell? |
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343 | (1) |
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How does the integrated viral genome remain quiescent? |
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344 | (1) |
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What causes viral induction? |
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345 | (1) |
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Deciding between lysogeny and lysis |
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345 | (1) |
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What are the genetic consequences of lysogeny? |
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346 | (1) |
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What is the effect of lysogeny in evolution? |
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347 | (1) |
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347 | (3) |
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348 | (1) |
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349 | (1) |
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350 | (1) |
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351 | (2) |
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353 | (120) |
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354 | (22) |
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355 | (2) |
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Methods of microbial ecology |
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357 | (4) |
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358 | (1) |
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Studying microbes in the laboratory and in their natural environments |
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358 | (3) |
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361 | (8) |
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361 | (3) |
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364 | (3) |
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367 | (1) |
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368 | (1) |
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369 | (1) |
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370 | (3) |
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370 | (1) |
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370 | (2) |
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Microbes, climates, and weather |
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372 | (1) |
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The future of microbial ecology |
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373 | (1) |
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374 | (1) |
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374 | (2) |
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symbiosis, predation, and antibiosis |
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376 | (26) |
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377 | (16) |
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377 | (1) |
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Mitochondria, chloroplasts, and the origin of eukaryotic cells |
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378 | (3) |
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Bacterial endosymbionts of insects: organelles in the making? |
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381 | (4) |
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Nitrogen-fixing bacteria and the legumes |
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385 | (3) |
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The rumen and its microbes |
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388 | (2) |
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Feeding via a murderous partnership: bacteria and nematodes |
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390 | (1) |
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Leaf-cutting ants, fungi, and bacteria |
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391 | (2) |
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Behavioral changes due to parasitism |
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393 | (2) |
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Reckless rats and fatal attraction |
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393 | (1) |
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394 | (1) |
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When is a flower not a flower? |
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394 | (1) |
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|
395 | (3) |
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Antibiotics and bacteriocins |
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398 | (1) |
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|
399 | (1) |
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|
400 | (2) |
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infection: the vertebrate host |
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402 | (22) |
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403 | (4) |
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404 | (1) |
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405 | (1) |
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405 | (1) |
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406 | (1) |
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407 | (15) |
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408 | (1) |
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|
408 | (1) |
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|
408 | (6) |
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How do microbes evade the innate defenses? |
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|
414 | (2) |
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416 | (1) |
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416 | (1) |
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416 | (2) |
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|
418 | (2) |
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|
420 | (1) |
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How do microbes defend themselves against adaptive immunity? |
|
|
421 | (1) |
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Integration of the defense mechanisms |
|
|
422 | (1) |
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422 | (1) |
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|
422 | (2) |
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|
424 | (20) |
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|
425 | (1) |
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|
426 | (16) |
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Tetanus, a relatively ``simple'' infectious disease |
|
|
426 | (2) |
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An outbreak of hemorrhagic colitis, a complicated infection caused by E. coli strain O157:H7 |
|
|
428 | (4) |
|
TB, a disease caused mainly by the host response |
|
|
432 | (3) |
|
Infectious mononucleosis: the ``kissing disease'' |
|
|
435 | (2) |
|
How does EBV cause infectious mono? |
|
|
437 | (1) |
|
How does EBV persist in the body? |
|
|
437 | (1) |
|
How does EBV contribute to cancer? |
|
|
438 | (1) |
|
|
438 | (4) |
|
|
442 | (1) |
|
|
442 | (2) |
|
microbes and human history |
|
|
444 | (12) |
|
|
445 | (2) |
|
How infectious diseases change |
|
|
447 | (2) |
|
Microbial agents of warfare |
|
|
449 | (4) |
|
|
449 | (1) |
|
|
450 | (2) |
|
|
452 | (1) |
|
|
452 | (1) |
|
Coping with danger in a microbial world |
|
|
453 | (1) |
|
|
453 | (1) |
|
|
453 | (1) |
|
|
454 | (1) |
|
|
454 | (1) |
|
|
455 | (1) |
|
|
455 | (1) |
|
|
456 | (17) |
|
|
457 | (1) |
|
|
457 | (1) |
|
Making better wines: the malolactic fermentation |
|
|
458 | (2) |
|
Protecting plants and making snow: ice-minus bacteria |
|
|
460 | (2) |
|
Using microbes to make protein drugs: insulin and human growth hormone (hGH) |
|
|
462 | (2) |
|
Microbial enzymes: sweeteners from corn |
|
|
464 | (3) |
|
Biological insecticides: Bt |
|
|
467 | (1) |
|
Undoing pollution: bioremediation |
|
|
468 | (3) |
|
|
471 | (1) |
|
|
471 | (2) |
Coda |
|
473 | (2) |
Glossary |
|
475 | (20) |
Answers to Study Questions |
|
495 | (14) |
Figure and Table Credits |
|
509 | (4) |
Index |
|
513 | |