| eTopic and eAppendix Contents |
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xvi | |
| Preface |
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xviii | |
| About the Authors |
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xxxvi | |
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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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1.1 From Germ to Genome: What Is a Microbe? |
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4 | (3) |
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1.2 Microbes Shape Human History |
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7 | (7) |
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14 | (6) |
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1.4 Environment and Ecology |
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20 | (6) |
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Special Topic 1.1 Gut Bacteria Fight Cancer |
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24 | (2) |
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1.5 The Microbial Family Tree |
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26 | (3) |
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1.6 Cell Biology and the DNA Revolution |
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29 | (8) |
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Chapter 2 Observing the Microbial Cell |
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37 | (38) |
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38 | (4) |
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2.2 Optics and Properties of Light |
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42 | (4) |
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2.3 Bright-Field Microscopy |
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46 | (7) |
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2.4 Fluorescence Microscopy, Super-Resolution Imaging, and Chemical Imaging |
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53 | (8) |
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Special Topic 2.1 Biogeography of a Gut Pathogen |
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59 | (2) |
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2.5 Dark-Field and Phase-Contrast Microscopy |
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61 | (2) |
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2.6 Electron Microscopy, Scanning Probe Microscopy, and X-Ray Crystallography |
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63 | (12) |
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Chapter 3 Cell Structure and Function |
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75 | (44) |
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3.1 The Bacterial Cell: An Overview |
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77 | (5) |
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3.2 The Cell Membrane and Transport |
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82 | (5) |
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3.3 The Envelope and Cytoskeleton |
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87 | (10) |
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3.4 Bacterial Cell Division |
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97 | (6) |
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3.5 Cell Polarity, Membrane Vesicles, and Nanotubes |
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103 | (5) |
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Special Topic 3.1 Turrets and Horseshoes: What Are They For? |
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108 | (1) |
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3.6 Specialized Structures |
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108 | (11) |
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Chapter 4 Bacterial Culture, Growth, and Development |
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119 | (40) |
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120 | (4) |
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124 | (6) |
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4.3 Culturing and Counting Bacteria |
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130 | (10) |
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Special Topic 4.1 Antibiotic Hunters Culture the "Unculturable" |
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136 | (4) |
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140 | (7) |
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147 | (4) |
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151 | (8) |
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Chapter 5 Environmental Influences and Control of Microbial Growth |
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159 | (36) |
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5.1 Environmental Limits on Growth: Temperature and Pressure |
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160 | (7) |
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167 | (1) |
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5.3 Hydronium (pH) and Hydroxide Ion Concentrations |
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168 | (5) |
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173 | (3) |
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5.5 Nutrient Deprivation and Starvation |
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176 | (4) |
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5.6 Physical, Chemical, and Biological Control of Microbes |
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180 | (15) |
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Special Topic 5.1 Phage "Smart Bombs" Target Biofilms |
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190 | (5) |
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195 | (44) |
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6.1 Viruses in Ecosystems |
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196 | (6) |
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202 | (6) |
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6.3 Viral Genomes and Classification |
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208 | (7) |
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6.4 Bacteriophages: The Gut Virome |
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215 | (7) |
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Special Topic 6.1 Phages Go Everywhere |
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222 | (1) |
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6.5 Animal and Plant Viruses |
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222 | (11) |
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233 | (6) |
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Chapter 7 Genomes and Chromosomes |
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239 | (38) |
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7.1 DNA: The Genetic Material |
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240 | (1) |
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241 | (10) |
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Special Topic 7.1 DNA as Digital Storage |
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246 | (5) |
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251 | (10) |
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7.4 Plasmids and Secondary Chromosomes |
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261 | (5) |
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7.5 Eukaryotic and Archaeal Chromosomes |
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266 | (2) |
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7.6 Microbiomes and Metagenomes |
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268 | (9) |
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Chapter 8 Transcription, Translation, and Protein Processing |
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277 | (38) |
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8.1 RNA Polymerases and Sigma Factors |
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278 | (3) |
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8.2 Transcription of DNA to RNA |
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281 | (7) |
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8.3 Translation of RNA to Protein |
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288 | (14) |
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Special Topic 8.1 Translocation: EF-G Gets Physical |
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298 | (4) |
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8.4 Protein Modification, Folding, and Degradation |
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302 | (4) |
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8.5 Secretion: Protein Traffic Control |
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306 | (9) |
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Chapter 9 Genetic Change and Genome Evolution |
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315 | (42) |
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316 | (6) |
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322 | (7) |
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Special Topic 9.1 DNA as a Live Wire: Using Electrons to Find DNA Damage |
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324 | (5) |
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9.3 Gene Transfer: Mechanisms and Barriers |
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329 | (14) |
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9.4 Mobile Genetic Elements |
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343 | (5) |
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348 | (9) |
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Chapter 10 Molecular Regulation |
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357 | (44) |
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10.1 Transcription Repressors and Activators |
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358 | (12) |
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10.2 Alternative Sigma Factors and Anti-Sigma Factors |
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370 | (2) |
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372 | (8) |
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380 | (8) |
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10.5 Clocks, Thermometers, and Switches |
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388 | (7) |
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Special Topic 10.1 Inteins, Exteins, and "Spliced-Up" Regulation |
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390 | (5) |
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10.6 Chemotaxis: Posttranslational Regulation of Cell Behavior |
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395 | (6) |
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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 | (10) |
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Special Topic 11.1 Designing a Pandemic Flu |
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418 | (2) |
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11.3 Human Immunodeficiency Virus (HIV): Retrovirus |
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420 | (11) |
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11.4 Endogenous Retroviruses and Gene Therapy |
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431 | (4) |
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11.5 Herpes Simplex Virus: DNA Virus |
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435 | (8) |
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Chapter 12 Biotechniques and Synthetic Biology |
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443 | (42) |
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12.1 DNA Amplification and Sequence Analysis |
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444 | (13) |
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12.2 Genetic Manipulation of Microbes |
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457 | (9) |
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Special Topic 12.1 Constructing the Smallest Genome for Cellular Life |
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462 | (4) |
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12.3 Gene Expression Analysis |
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466 | (6) |
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12.4 Applied Biotechnology |
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472 | (3) |
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12.5 Synthetic Biology: Biology by Design |
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475 | (10) |
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PART 3 Metabolism and Biochemistry |
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Chapter 13 Energetics and Catabolism |
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485 | (48) |
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487 | (6) |
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13.2 Energy Carriers and Electron Transfer |
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493 | (8) |
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13.3 Catabolism: The Microbial Buffet |
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501 | (4) |
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13.4 Glucose Fermentation and Respiration |
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505 | (15) |
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13.5 The Gut Microbiome: Friends with Benefits |
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520 | (3) |
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13.6 Aromatic Catabolism and Syntrophy |
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523 | (10) |
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Special Topic 13.1 Gut Bacteria Rule Host Behavior |
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524 | (9) |
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Chapter 14 Electron Flow in Organotrophy, Lithotrophy, and Phototrophy |
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533 | (48) |
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14.1 Electron Transport Systems and the Proton Motive Force |
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535 | (9) |
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14.2 The Respiratory ETS and ATP Synthase |
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544 | (7) |
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14.3 Anaerobic Respiration |
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551 | (2) |
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14.4 Nanowires, Electron Shuttles, and Fuel Cells |
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553 | (4) |
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14.5 Lithotrophy and Methanogenesis |
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557 | (9) |
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Special Topic 14.1 The Ocean Floor Is a Battery |
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558 | (8) |
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566 | (15) |
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581 | (36) |
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15.1 Overview of Biosynthesis |
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582 | (4) |
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15.2 CO2 Fixation: The Calvin Cycle and Other Pathways |
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586 | (8) |
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15.3 Fatty Acids and Antibiotics |
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594 | (6) |
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15.4 Nitrogen Fixation and Regulation |
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600 | (8) |
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Special Topic 15.1 Mining Bacterial Genomes for Antibiotics |
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602 | (6) |
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15.5 Amino Acids and Nitrogenous Bases |
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608 | (9) |
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Chapter 16 Food and Industrial Microbiology |
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617 | (42) |
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618 | (5) |
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16.2 Acid - and Alkali-Fermented Foods |
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623 | (6) |
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16.3 Ethanolic Fermentation: Bread and Wine |
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629 | (4) |
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16.4 Food Spoilage and Preservation |
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633 | (10) |
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16.5 Industrial Microbiology |
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643 | (9) |
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Special Topic 16.1 Microbial Vitamins for Sale |
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644 | (8) |
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16.6 Microbial Gene Vectors for Plants and Human Gene Therapy |
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652 | (7) |
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PART 4 Microbial Diversity and Ecology |
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Chapter 17 Origins and Evolution |
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659 | (42) |
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660 | (9) |
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17.2 Forming the First Cells |
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669 | (4) |
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17.3 Evolution: Phylogeny and Gene Transfer |
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673 | (8) |
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17.4 Natural Selection and Adaptation |
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681 | (9) |
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Special Topic 17.1 A Giant Petri Dish and the Race to Resistance |
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682 | (8) |
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17.5 Microbial Species and Taxonomy |
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690 | (4) |
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17.6 Symbiosis and the Origin of Mitochondria and Chloroplasts |
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694 | (7) |
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Chapter 18 Bacterial Diversity |
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701 | (46) |
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18.1 Bacterial Diversity at a Glance |
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702 | (6) |
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18.2 Cyanobacteria: Oxygenic Phototrophs |
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708 | (6) |
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18.3 Firmicutes, Tenericutes, and Actinobacteria (Gram-Positive) |
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714 | (12) |
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Special Topic 18.1 Gut Bacterial Hair Balls |
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720 | (6) |
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18.4 Proteobacteria (Gram-Negative) |
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726 | (12) |
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18.5 Spirochetes, Acidobacteria, Bacteroidetes, and Chlorobi (Deep-Branching Gram-Negative) |
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738 | (3) |
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18.6 Planctomycetes, Verrucomicrobia, and Chlamydiae (PVC Superphylum) |
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741 | (6) |
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Chapter 19 Archaeal Diversity |
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747 | (38) |
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19.1 Archaeal Diversity at a Glance |
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748 | (8) |
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19.2 TACK Hyperthermophiles Eat Sulfur |
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756 | (7) |
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19.3 Thaumarchaeota: Ammonia Oxidizers and Animal Symbionts |
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763 | (3) |
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19.4 Euryarchaeota: Methanogens from Gut to Globe |
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766 | (8) |
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Special Topic 19.1 Methanogens for Dinner |
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772 | (2) |
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19.5 Haloarchaea and Other Euryarchaeotes: Underground and Under Ocean |
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774 | (6) |
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19.6 DPANN Symbionts, Altiarchaeales, and Asgard: Branch to Eukaryotes? |
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780 | (5) |
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Chapter 20 Eukaryotic Diversity |
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785 | (42) |
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20.1 Phylogeny of Eukaryotes |
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786 | (7) |
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793 | (12) |
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Special Topic 20.1 Yeast: A Single-Celled Human Brain |
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796 | (9) |
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20.3 Amebas and Slime Molds |
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805 | (3) |
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808 | (7) |
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20.5 Alveolates: Ciliates, Dinoflagellates, and Apicomplexans |
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815 | (6) |
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821 | (6) |
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Chapter 21 Microbial Ecology |
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827 | (56) |
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21.1 Microbial Communities: Metagenomes and Single-Cell Sequencing |
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829 | (9) |
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838 | (7) |
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845 | (6) |
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Special Topic 21.1 Antarctic Lake Mats: Have Ecosystem, Will Travel |
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846 | (5) |
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21.4 Animal Digestive Microbiomes |
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851 | (6) |
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21.5 Marine and Freshwater Microbes |
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857 | (10) |
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21.6 Soil and Plant Microbial Communities |
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867 | (16) |
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Chapter 22 Element Cycles and Environmental Microbiology |
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883 | (38) |
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22.1 The Carbon Cycle and Climate Change |
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885 | (8) |
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22.2 The Hydrologic Cycle and Wastewater Treatment |
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893 | (6) |
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899 | (6) |
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22.4 Sulfur, Phosphorus, and Metals |
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905 | (6) |
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22.5 Our Built Environment |
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911 | (3) |
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Special Topic 22.1 A Microbial Jungle: The Kitchen Sponge |
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914 | (1) |
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914 | (7) |
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PART 5 Medicine and Immunology |
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Chapter 23 The Human Microbiome and Innate Immunity |
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921 | (42) |
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23.1 The Human Microbiome |
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922 | (9) |
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23.2 Benefits and Risks of Microbiota |
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931 | (5) |
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23.3 Overview of the Immune System |
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936 | (9) |
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Special Topic 23.1 Why Do Tattoos Last Forever? |
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940 | (5) |
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23.4 Physical and Chemical Defenses against Infection |
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945 | (4) |
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23.5 Innate Immunity: Surveillance, Cytokines, and Inflammation |
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949 | (8) |
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23.6 Complement and Fever |
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957 | (6) |
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Chapter 24 The Adaptive Immune Response |
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963 | (48) |
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24.1 Overview of Adaptive Immunity |
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964 | (6) |
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24.2 Antibody Structure, Diversity, and Synthesis |
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970 | (12) |
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24.3 T Cells Link Antibody and Cellular Immune Systems |
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982 | (11) |
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24.4 Complement as Part of Adaptive Immunity |
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993 | (1) |
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24.5 Gut Mucosal Immunity and the Microbiome |
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994 | (3) |
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997 | (4) |
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24.7 Hypersensitivity and Autoimmunity |
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1001 | (10) |
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Special Topic 24.1 A Monoclonal Magic Bullet for Ebola? |
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1002 | (9) |
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1011 | (46) |
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25.1 Host-Pathogen Interactions |
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1012 | (8) |
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25.2 Microbial Attachment: First Contact |
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1020 | (5) |
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25.3 Toxins Subvert Host Functions |
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1025 | (11) |
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Special Topic 25.1 Chronic Staph Infections Work with a NET |
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1028 | (8) |
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25.4 Deploying Toxins and Effectors |
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1036 | (4) |
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25.5 Surviving within the Host |
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1040 | (11) |
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25.6 Tools Used to Probe Pathogenesis |
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1051 | (6) |
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Chapter 26 Microbial Diseases |
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1057 | (58) |
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26.1 Skin, Soft-Tissue, and Bone Infections |
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1059 | (5) |
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26.2 Respiratory Tract Infections |
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1064 | (8) |
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26.3 Gastrointestinal Tract Infections |
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1072 | (11) |
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26.4 Genitourinary Tract Infections |
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1083 | (9) |
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26.5 Cardiovascular and Systemic Infections |
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1092 | (12) |
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Special Topic 26.1 How Neutrophils Ambush Staphylococcus aureus in a Lymph Node |
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1094 | (10) |
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26.6 Central Nervous System Infections |
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1104 | (11) |
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Chapter 27 Antimicrobial Therapy and Discovery |
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1115 | (44) |
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27.1 Fundamentals of Antimicrobial Therapy |
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1116 | (7) |
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27.2 Antibiotic Mechanisms of Action |
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1123 | (12) |
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27.3 Challenges of Drug Resistance and Discovery |
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1135 | (12) |
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Special Topic 27.1 Are Designer Antibodies the Next Antibiotics? |
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1146 | (1) |
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1147 | (6) |
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1153 | (6) |
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Chapter 28 Clinical Microbiology and Epidemiology |
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1159 | (1) |
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28.1 Clinical Specimen Collection and Handling |
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1160 | (6) |
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28.2 Pathogen Identification by Culture and Phenotype |
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1166 | (8) |
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28.3 Molecular and Serological Identification of Pathogens |
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1174 | (13) |
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Special Topic 28.1 Next-Generation Diagnostics: CRISPR Launches a "Flare" |
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1180 | (7) |
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1187 | (6) |
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28.5 Detecting Emerging Microbial Diseases |
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1193 | |
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APPENDIX: Reference and Review |
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1 | (1) |
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A.1 A Periodic Table of the Elements |
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2 | (1) |
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A.2 Chemical Functional Groups |
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2 | (2) |
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4 | (1) |
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5 | (1) |
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A.5 Calculating the Standard Free Energy Change, ΔG°, of Chemical Reactions |
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5 | (1) |
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6 | (1) |
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A.7 Semipermeable Membranes |
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6 | (2) |
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A.8 The Eukaryotic Cell Cycle and Cell Division |
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8 | |
| Answers to Thought Questions |
|
1 | (1) |
| Glossary |
|
1 | (1) |
| Credits |
|
1 | (1) |
| Index |
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1 | |
