| Preface |
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xix | |
| About the Authors |
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xxxiv | |
| Part 1 The Microbial Cell |
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Chapter 1 Microbial Life: Origin and Discovery |
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1 | (36) |
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Special Topic 1.1: How Did Life Originate? |
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4 | (2) |
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1.1 From Germ to Genome: What Is a Microbe? |
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6 | (3) |
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1.2 Microbes Shape Human History |
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9 | (6) |
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15 | (7) |
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22 | (3) |
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1.5 The Microbial Family Tree |
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25 | (3) |
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1.6 Cell Biology and the DNA Revolution |
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28 | (9) |
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Chapter 2 Observing the Microbial Cell |
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37 | (40) |
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38 | (4) |
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2.2 Optics and Properties of Light |
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42 | (6) |
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Special Topic 2.1: Catch Your Bacteria Snacking |
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44 | (4) |
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2.3 Bright-Field Microscopy |
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48 | (7) |
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2.4 Fluorescence Microscopy and Super-Resolution Imaging |
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55 | (6) |
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2.5 Dark-Field and Phase-Contrast Microscopy |
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61 | (4) |
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2.6 Electron Microscopy, Scanning Probe Microscopy, and X-Ray Crystallography |
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65 | (12) |
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Chapter 3 Cell Structure and Function |
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77 | (40) |
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3.1 The Bacterial Cell: An Overview |
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79 | (5) |
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3.2 The Cell Membrane and Transport |
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84 | (6) |
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3.3 The Cell Wall and Outer Layers |
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90 | (10) |
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3.4 The Nucleoid and Cell Division |
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100 | (4) |
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3.5 Cell Polarity and Aging |
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104 | (3) |
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3.6 Specialized Structures |
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107 | (10) |
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Special Topic 3.1: Senior Cells Make Drug-Resistant Tuberculosis |
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108 | (9) |
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Chapter 4 Bacterial Culture, Growth, and Development |
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117 | (40) |
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118 | (5) |
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123 | (6) |
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4.3 Culturing and Counting Bacteria |
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129 | (10) |
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Special Topic 4.1: Antibiotic Hunters Culture the "Unculturable" |
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134 | (5) |
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139 | (6) |
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145 | (3) |
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148 | (9) |
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Chapter 5 Environmental Influences and Control of Microbial Growth |
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157 | (36) |
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5.1 Environmental Limits on Growth |
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158 | (1) |
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5.2 Temperature and Pressure |
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159 | (5) |
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164 | (2) |
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5.4 Hydronium (pH) and Hydroxide Ion Concentrations |
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166 | (5) |
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171 | (4) |
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5.6 Nutrient Deprivation and Starvation |
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175 | (3) |
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5.7 Physical, Chemical, and Biological Control of Microbes |
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178 | (15) |
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Special Topic 5.1: Phage "Smart Bombs" Target Biofilms |
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188 | (5) |
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193 | (42) |
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6.1 Viruses in Ecosystems |
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195 | (4) |
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199 | (6) |
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6.3 Viral Genomes and Classification |
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205 | (7) |
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6.4 Bacteriophages: The Gut Virome |
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212 | (8) |
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Special Topic 6.1: Virus to the Rescue |
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216 | (4) |
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6.5 Animal and Plant Viruses |
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220 | (8) |
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228 | (7) |
| Part 2 Genes and Genomes |
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Chapter 7 Genomes and Chromosomes |
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235 | (38) |
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7.1 DNA: The Genetic Material |
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236 | (2) |
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238 | (8) |
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246 | (9) |
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255 | (5) |
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Special Topic 7.1: Nucleoid Occlusion Factors and the Septal "Guillotine" |
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256 | (4) |
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7.5 Eukaryotic and Archaeal Chromosomes |
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260 | (2) |
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7.6 DNA Sequence Analysis |
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262 | (11) |
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Chapter 8 Transcription, Translation, and Bioinformatics |
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273 | (42) |
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8.1 RNA Polymerases and Sigma Factors |
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274 | (4) |
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8.2 Transcription of DNA to RNA |
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278 | (5) |
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8.3 Translation of RNA to Protein |
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283 | (14) |
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Special Topic 8.1: Translocation: EF-G Gets Physical |
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293 | (4) |
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8.4 Protein Modification, Folding, and Degradation |
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297 | (3) |
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8.5 Secretion: Protein Traffic Control |
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300 | (5) |
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8.6 Bioinformatics: Mining the Genomes |
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305 | (10) |
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Chapter 9 Gene Transfer, Mutations, and Genome Evolution |
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315 | (42) |
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9.1 Mosaic Genomes and Gene Transfer |
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316 | (14) |
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330 | (2) |
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332 | (6) |
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338 | (8) |
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Special Topic 9.1: DNA as a Live Wire: Using Electrons to Find DNA Damage |
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340 | (6) |
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9.5 Mobile Genetic Elements |
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346 | (3) |
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349 | (8) |
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Chapter 10 Molecular Regulation |
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357 | (44) |
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10.1 Gene Expression: Levels of Control |
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358 | (6) |
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364 | (10) |
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10.3 Sigma Factors and Regulatory RNAs |
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374 | (9) |
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10.4 Integrated Control Circuits |
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383 | (5) |
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10.5 Quorum Sensing: Chemical Conversations |
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388 | (6) |
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Special Topic 10.1: Networking with Nanotubes |
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392 | (2) |
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10.6 Transcriptomics and Proteomics |
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394 | (7) |
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Chapter 11 Viral Molecular Biology |
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401 | (42) |
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11.1 Phage Lambda: Enteric Bacteriophage |
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402 | (8) |
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11.2 Influenza Virus: (-) Strand RNA Virus |
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410 | (8) |
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11.3 Human Immunodeficiency Virus (HIV): Retrovirus |
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418 | (11) |
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11.4 Endogenous Retroviruses and Gene Therapy |
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429 | (4) |
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11.5 Herpes Simplex Virus: DNA Virus |
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433 | (10) |
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Special Topic 11.1: Cytomegalovirus |
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438 | (5) |
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Chapter 12 Biotechniques and Synthetic Biology |
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443 | (34) |
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444 | (6) |
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12.2 Molecular Techniques |
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450 | (8) |
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12.3 Visualizing the Interactions and Movements of Proteins |
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458 | (3) |
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12.4 Applied Biotechnology |
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461 | (4) |
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12.5 Synthetic Biology: Biology by Design |
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465 | (12) |
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Special Topic 12.1: Bacteria "Learn" to Keep Time and Signal Danger |
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466 | (11) |
| Part 3 Metabolism and Biochemistry |
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Chapter 13 Energetics and Catabolism |
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477 | (46) |
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13.1 Energy and Entropy for Life |
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478 | (5) |
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13.2 Energy in Biochemical Reactions |
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483 | (6) |
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Special Topic 13.1: Microbial Syntrophy Cleans Up Oil |
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486 | (3) |
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13.3 Energy Carriers and Electron Transfer |
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489 | (6) |
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13.4 Catabolism: The Microbial Buffet |
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495 | (6) |
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13.5 Glucose Breakdown and Fermentation |
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501 | (10) |
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13.6 The TCA Cycle and Aromatic Catabolism |
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511 | (12) |
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Chapter 14 Electron Flow in Organotrophy, Lithotrophy, and Phototrophy |
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523 | (44) |
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14.1 Electron Transport Systems |
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525 | (5) |
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14.2 The Proton Motive Force |
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530 | (4) |
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14.3 The Respiratory ETS and ATP Synthase |
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534 | (7) |
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14.4 Anaerobic Respiration |
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541 | (4) |
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Special Topic 14.1: Bacterial Electric Power |
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544 | (1) |
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14.5 Lithotrophy and Methanogenesis |
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545 | (8) |
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553 | (14) |
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567 | (38) |
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15.1 Overview of Biosynthesis |
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568 | (4) |
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15.2 CO2 Fixation: The Calvin Cycle |
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572 | (7) |
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15.3 CO2 Fixation: Diverse Pathways |
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579 | (4) |
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15.4 Biosynthesis of Fatty Acids and Polyketides |
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583 | (4) |
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15.5 Nitrogen Fixation and Regulation |
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587 | (7) |
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Special Topic 15.1: Mining a Bacterial Genome for Peptide Antibiotics |
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588 | (6) |
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15.6 Biosynthesis of Amino Acids and Nitrogenous Bases |
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594 | (11) |
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Chapter 16 Food and Industrial Microbiology |
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605 | (40) |
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606 | (2) |
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16.2 Fermented Foods: An Overview |
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608 | (3) |
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16.3 Acid- and Alkali-Fermented Foods |
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611 | (7) |
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16.4 Ethanolic Fermentation: Bread and Wine |
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618 | (4) |
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16.5 Food Spoilage and Preservation |
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622 | (10) |
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16.6 Industrial Microbiology |
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632 | (13) |
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Special Topic 16.1: Microbial Enzymes Make Money |
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638 | (7) |
| Part 4 Microbial Diversity and Ecology |
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Chapter 17 Origins and Evolution |
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645 | (44) |
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646 | (10) |
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656 | (5) |
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17.3 Microbial Phylogeny and Gene Transfer |
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661 | (9) |
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670 | (4) |
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17.5 Microbial Species and Taxonomy |
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674 | (7) |
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Special Topic 17.1: Jump-Starting Evolution of a Hyperthermophilic Enzyme |
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676 | (5) |
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17.6 Symbiosis and the Origin of Mitochondria and Chloroplasts |
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681 | (8) |
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Chapter 18 Bacterial Diversity |
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689 | (46) |
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18.1 Bacterial Diversity at a Glance |
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690 | (6) |
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18.2 Cyanobacteria: Oxygenic Phototrophs |
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696 | (6) |
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18.3 Firmicutes and Actinobacteria (Gram-Positive) |
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702 | (12) |
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Special Topic 18.1: Gut Bacterial Hair Balls |
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708 | (6) |
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18.4 Proteobacteria (Gram-Negative) |
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714 | (11) |
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18.5 Deep-Branching Gram-Negative Phyla |
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725 | (2) |
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18.6 Spirochetes: Sheathed Spiral Cells with Internalized Flagella |
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727 | (2) |
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18.7 Chlamydiae, Planctomycetes, and Verrucomicrobia: Irregular Cells |
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729 | (6) |
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Chapter 19 Archaeal Diversity |
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735 | (38) |
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19.1 Archaeal Traits and Phylogeny |
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736 | (8) |
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19.2 Crenarchaeota across the Temperature Range |
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744 | (7) |
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19.3 Thaumarchaeota: Symbionts and Ammonia Oxidizers |
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751 | (2) |
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19.4 Methanogenic Euryarchaeota |
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753 | (9) |
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Special Topic 19.1: Methanogens for Dinner |
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758 | (4) |
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19.5 Halophilic Euryarchaeota |
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762 | (5) |
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19.6 Extremophilic Euryarchaeota and Deeply Branching Divisions |
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767 | (6) |
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Chapter 20 Eukaryotic Diversity |
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773 | (42) |
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20.1 Phylogeny of Eukaryotes |
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774 | (8) |
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782 | (12) |
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Special Topic 20.1: Yeast: A Single-Celled Human Brain? |
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786 | (8) |
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794 | (6) |
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20.4 Amebas and Slime Molds |
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800 | (3) |
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20.5 Alveolates: Ciliates, Dinoflagellates, and Apicomplexans |
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803 | (6) |
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809 | (6) |
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Chapter 21 Microbial Ecology |
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815 | (52) |
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21.1 Metagenomes-and Beyond |
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817 | (9) |
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826 | (5) |
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831 | (6) |
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Special Topic 21.1: Antarctic Cyano Mats: Have Ecosystem, Will Travel |
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832 | (5) |
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21.4 Animal Digestive Microbiomes |
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837 | (5) |
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21.5 Marine and Freshwater Microbes |
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842 | (10) |
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21.6 Soil and Plant Microbial Communities |
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852 | (15) |
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Chapter 22 Microbes in Global Elemental Cycles |
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867 | (34) |
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22.1 Biogeochemical Cycles |
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868 | (3) |
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22.2 The Carbon Cycle and Bioremediation |
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871 | (5) |
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Special Topic 22.1: An Underground River in Antarctica |
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872 | (4) |
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22.3 The Hydrologic Cycle and Wastewater Treatment |
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876 | (6) |
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882 | (5) |
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22.5 Sulfur, Phosphorus, and Metals |
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887 | (7) |
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894 | (7) |
| Part 5 Medicine and Immunology |
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Chapter 23 Human Microbiota and Innate Immunity |
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901 | (40) |
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902 | (7) |
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23.2 Benefits and Risks of Microbiota |
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909 | (6) |
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23.3 Overview of the Immune System |
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915 | (8) |
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Special Topic 23.1: Are NETS a Cause of Lupus? |
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|
918 | (5) |
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23.4 Physical and Chemical Defenses against Infection |
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|
923 | (4) |
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23.5 Innate Immunity: Surveillance, Cytokines, and Inflammation |
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927 | (7) |
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23.6 Complement and Fever |
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934 | (7) |
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Chapter 24 The Adaptive Immune Response |
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941 | (48) |
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24.1 Overview of Adaptive Immunity |
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942 | (6) |
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24.2 Antibody Structure, Diversity, and Synthesis |
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948 | (14) |
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Special Topic 24.1: Can Retroviruses Help B Cells? |
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956 | (6) |
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24.3 T Cells Link Antibody and Cellular Immune Systems |
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962 | (11) |
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24.4 Complement as Part of Adaptive Immunity |
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|
973 | (1) |
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24.5 Gut Mucosal Immunity and the Microbiome |
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974 | (3) |
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977 | (3) |
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24.7 Hypersensitivity and Autoimmunity |
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980 | (9) |
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Chapter 25 Microbial Pathogenesis |
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989 | (48) |
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25.1 Host-Pathogen Interactions |
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990 | (5) |
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25.2 Virulence Factors and Pathogenicity Islands |
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995 | (3) |
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25.3 Microbial Attachment: First Contact |
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998 | (5) |
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25.4 Toxins Subvert Host Function |
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1003 | (11) |
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25.5 Deploying Toxins and Effectors |
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1014 | (5) |
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25.6 Surviving within the Host |
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1019 | (11) |
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Special Topic 25.1: Type VI Secretion: Poison Darts |
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1020 | (10) |
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25.7 Experimental Tools That Probe Pathogenesis |
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1030 | (7) |
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Chapter 26 Microbial Diseases |
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1037 | (54) |
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26.1 Diagnosing Microbial Diseases |
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1038 | (2) |
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26.2 Skin, Soft-Tissue, and Bone Infections |
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1040 | (4) |
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26.3 Respiratory Tract Infections |
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1044 | (6) |
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26.4 Gastrointestinal Tract Infections |
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1050 | (12) |
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Special Topic 26.1: Sprouts and an Emerging Escherichia coli |
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1054 | (8) |
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26.5 Genitourinary Tract Infections |
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1062 | (8) |
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26.6 Cardiovascular and Systemic Infections |
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1070 | (11) |
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26.7 Central Nervous System Infections |
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1081 | (10) |
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Chapter 27 Antimicrobial Therapy |
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|
1091 | (42) |
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27.1 Fundamentals of Antimicrobial Therapy |
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|
1092 | (7) |
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27.2 Antibiotic Mechanisms of Action |
|
|
1099 | (11) |
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27.3 Challenges of Drug Resistance and Discovery |
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|
1110 | (11) |
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Special Topic 27.1: Are Designer Antibodies the Next Antibiotics? |
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|
1118 | (3) |
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1121 | (6) |
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1127 | (6) |
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Chapter 28 Clinical Microbiology and Epidemiology |
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|
1133 | |
|
28.1 Clinical Microbiology: Specimen Collection and Handling |
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|
1134 | (6) |
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28.2 Approaches to Pathogen Identification |
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1140 | (18) |
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28.3 Principles of Epidemiology |
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|
1158 | (7) |
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28.4 Detecting Emerging Microbial Diseases |
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|
1165 | |
|
Special Topic 28.1: What's Blowing in the Wind? |
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|
1166 | |
| Appendix 1 Reference and Review |
|
A-1 | |
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A1.1 A Periodic Table of the Elements |
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A-2 | |
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A1.2 Chemical Functional Groups |
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A-2 | |
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A-4 | |
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A-4 | |
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A1.5 Calculating the Standard Free Energy Change, ΔG, of Chemical Reactions |
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|
A-5 | |
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A-6 | |
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A1.7 Semipermeable Membranes |
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|
A-6 | |
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A1.8 The Eukaryotic Cell Cycle and Cell Division |
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|
A-8 | |
| Appendix 2 Taxonomy |
|
A-11 | |
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A-12 | |
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A-14 | |
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A-18 | |
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A-20 | |
| Answers to Thought Questions |
|
AQ-1 | |
| Glossary |
|
G-1 | |
| Figure Credits |
|
FC-1 | |
| Index |
|
I-1 | |
