PART I THE MICROBES 1
The Microbial World 2
1.1 The Microbes 4
Toolbox 1.1 POLYMERASE CHAIN REACTION AMPLIFICATION OF rRNA GENES 12
Mini-Paper: A Focus on the Research THE THREE DOMAINS OF LIFE 14
1.2 Microbial Genetics 16
Perspective 1.1 CREATING LIFE IN THE LABORATORY: THE MILLER–UREY EXPERIMENT 18
Perspective 1.2 RIBOZYMES: EVIDENCE FOR AN RNA-BASED WORLD 19
1.3 Microbial Metabolism and Ecology 24
1.4 Microbes and Disease 27
2 Bacteria 36
2.1 Morphology of Bacterial Cells 38
2.2 The Cytoplasm 41
2.3 The Bacterial Cytoskeleton 44
2.4 The Cell Envelope 45
Perspective 2.1 MARVELOUS MAGNETOSOMES! 46
Toolbox 2.1 THE GRAM STAIN 55
Perspective 2.2 THE PROTECTIVE SHELLS OF ENDOSPORES 57
Mini-Paper: A Focus on the Research NEW MICROSCOPY METHODS REVEAL A PERIPLASM IN GRAM-POSITIVE BACTERIAL CELLS 60
2.5 The Bacterial Cell Surface 62
2.6 Bacterial Taxonomy 68
3 Eukaryal Microbes 72
3.1 The Morphology of Typical Eukaryal Cells 74
Mini-Paper: A Focus on the Research LIPID RAFTS: ORGANIZED CLUSTERING OF LIPIDS WITHIN A MEMBRANE 80
Toolbox 3.1 USING MICROSCOPY TO EXAMINE CELL STRUCTURE 82
Perspective 3.1 HIJACKING THE CYTOSKELETON 86
3.2 Diversity of Eukaryal Microbes 87
3.3 Replication of Eukaryal Microbes 92
3.4 The Origin of Eukaryal Cells 95
Perspective 3.2 EXPLOITING A SHARED EVOLUTIONARY HISTORY WITH PLANTS IN THE TREATMENT OF MALARIA 99
3.5 Interactions Between Eukaryal Microbes and Animals, Plants, and the Environment 100
4 Archaea 106
4.1 Distinctive Properites of Archaea 108
4.2 Archaeal Cell Structure 110
Toolbox 4.1 VACCINE DELIVERY STRATEGIES 115
4.3 Diversity of Archaea 119
Perspective 4.1 EXTREMOPHILES AND BIOTECHNOLOGY 121
Mini-Paper: A Focus on the Research THE ROLE OF ARCHAEONS IN OUR DIGESTIVE SYSTEM 126
5 Viruses 130
5.1 A Basic Overview of Viruses 132
5.2 Origins of Viruses 140
5.3 Cultivation, Purification, and Quantification of Viruses 142
Toolbox 5.1 CELL CULTURE TECHNIQUES 143
Perspective 5.1 MEASUREMENT OF HIV VIRAL LOAD 147
5.4 Diversity of Viruses 149
Toolbox 5.2 REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION (RT-PCR) 154
5.5 Virus-Like Particles 155
5.6 Virology Today 157
Mini-Paper: A Focus on the Research NEW FINDINGS IN THE PACKAGING OF DNA BY THE MODEL BACTERIOPHAGE T4 158
6 Cultivating Microorganisms 164
6.1 Nutritional Requirements of Microorganisms 166
6.2 Factors Affecting Microbial Growth 168
Toolbox 6.1 PHENOTYPE MICROARRAYS FOR EXAMINING MICROBIAL GROWTH 169
6.3 Growing Microorganisms in the Laboratory 173
Perspective 6.1 THE DISCOVERY OF HELICOBACTER PYLORI 178
Toolbox 6.2 FISHING FOR UNCULTIVATED MICROBES 180
Mini-Paper: A Focus on the Research BRINGING TO LIFE THE PREVIOUSLY UNCULTURABLE USING THE SOIL SUBSTRATE MEMBRANE SYSTEM (SSMS) 182
6.4 Measuring Microbial Population Growth 184
Perspective 6.2 MYCOBACTERIUM LEPRAE, AN EXTRAORDINARILY SLOW-GROWING PATHOGEN 190
Perspective 6.3 THE HUMAN INTESTINE—A CONTINUOUS CULTURE 192
6.5 Eliminating Microbes and Preventing Their Growth 192
PART II MICROBIAL GENETICS
7 DNA Replication and Gene Expression 202
7.1 The Role of DNA 204
7.2 DNA Replication 210
7.3 Transcription 216
Toolbox 7.1 USING A GEL SHIFT ASSAY TO IDENTIFY DNA-BINDING PROTEINS 219
7.4 Translation 233
7.5 The Effects of Mutations 229
Mini-Paper: A Focus on the Research TELOMERES WITH PROMOTER ACTIVITY 232
Perspective 7.1 USING MUTATIONS TO CONTROL VIRAL INFECTIONS 234
8 Viral Replication Strategies 238
8.1 Recognition of Host Cells 240
Toolbox 8.1 THE WESTERN BLOT 242
8.2 Viral Entry and Uncoating 244
8.3 Viral Replication 248
8.4 Viral Assembly and Egress 256
8.5 Antiviral Drugs 258
Perspective 8.1 DNA MICROARRAYS AND THE SARS VIRUS 258
Mini-Paper: A Focus on the Research THE DISCOVERY OF REVERSE TRANSCRIPTASE 262
9 Bacterial Genetic Analysis 266
9.1 Bacteria as Subjects of Genetic Research 268
9.2 Mutations, Mutants, and Strains 271
Toolbox 9.1 ISOLATING NUTRITIONAL MUTANTS 274
9.3 Restriction Enzymes, Vectors, and Cloning 278
9.4 Recombination and DNA Transfer 285
Perspective 9.1 PLASMIDS THAT PRODUCE PATHOGENS 290
Mini-Paper: A Focus on the Research THE DISCOVERY OF TRANSDUCTION 299
10 Microbial Genomics 302
10.1 Genome Sequencing 304
Perspective 10.1 RATE OF DNA SEQUENCING 307
Toolbox 10.1 GENOME DATABASES 310
10.2 Genomic Analysis of Gene Expression 312
10.3 Comparative Genomics 318
Perspective 10.2 THE MINIMAL GENOME 319
Mini-Paper: A Focus on the Research GENOME SEQUENCE OF A KILLER BUG 320
10.4 Metagenomics 323
11 Regulation of Gene Expression 328
11.1 Differential Gene Expression 330
11.2 The Operon 332
11.3 Global Gene Regulation 337
Mini-Paper: A Focus on the Research TUNING PROMOTERS FOR USE IN SYNTHETIC BIOLOGY 338
Perspective 11.1 THE USE OF LACTOSE ANALOGS IN GENE EXPRESSION STUDIES 342
11.4 Post-initiation Control of Gene Expression 346
Toolbox 11.1 USING RNA MOLECULES TO DECREASE GENE EXPRESSION 347
11.5 Quorum Sensing 350
11.6 Two-Component Regulatory Systems 352
11.7 Chemotaxis 355
12 Microbial Biotechnology 362
12.1 Microbes for Biotechnology 365
Perspective 12.1 BIOPROSPECTING: WHO OWNS THE MICROBES? 366
12.2 Molecular Genetic Modification 368
Toolbox 12.1 SITE-DIRECTED MUTAGENESIS 370
Toolbox 12.2 FUSION PROTEIN PURIFICATION 375
Mini-Paper: A Focus on the Research MAKING A SYNTHETIC GENOME 378
Perspective 12.2 THE INTERNATIONAL GENETICALLY ENGINEERED MACHINE (IGEM) COMPETITION, STANDARD BIOLOGICAL PARTS, AND SYNTHETIC BIOLOGY 380
12.3 Red Biotechnology 381
12.4 White Biotechnology 382
Perspective 12.3 BIOFUELS: BIODIESEL AND ALGAE 386
12.5 Green Biotechnology 391
Toolbox 12.3 PLANT TRANSFORMATION USING BACTERIA 394
PART III MICROBIAL PHYSIOLOGY AND ECOLOGY
13 Metabolism 400
13.1 Energy, Enzymes, and ATP 402
Perspective 13.1 WHO NEEDS VITAMINS? 405
13.2 Central Processes in ATP Synthesis 406
13.3 Carbon Utilization in Microorganisms 412
13.4 Respiration and the Electron Transport System 422
Perspective 13.2 ELECTRICIGENIC BACTERIA AND MICROBIAL FUEL CELLS 426
13.5 Metabolism of Non-glucose Carbon Sources 429
Toolbox 13.1 METABOLISM AND RAPID BACTERIAL IDENTIFICATION SYSTEMS 432
13.6 Phototrophy and Photosynthesis 433
13.7 Nitrogen and Sulfur Metabolism 443
13.8 Biosynthesis of Cellular Components 447
Mini-Paper: A Focus on the Research GENOME SEQUENCE OF A DEEP SEA SYMBIONT 450
14 Biogeochemical Cycles 456
14.1 Nutrient Cycling 459
Toolbox 14.1 USING MICROARRAYS TO EXAMINE MICROBIAL COMMUNITIES: THE GeoCHIP 461
14.2 Cycling Driven by Carbon Metabolism 463
Perspective 14.1 CO2 AS A GREENHOUSE GAS AND ITS INFLUENCE ON CLIMATE CHANGE 464
14.3 Cycling Driven by Nitrogen Metabolism 472
Mini-Paper: A Focus on the Research THE FIRST ISOLATION AND CULTIVATION OF A MARINE ARCHAEON 476
14.4 The Interconnectedness of Cycles 478
Perspective 14.2 THE MICROBIOLOGY OF ENVIRONMENTALLY TOXIC ACID MINE DRAINAGE 479
15 Microbial Ecosystems 484
15.1 Microbes in the Environment 486
15.2 Microbial Community Structure 490
Toolbox 15.1 FLOW CYTOMETRY 494
Mini-Paper: A Focus on the Research A METHOD FOR THE IDENTIFICATION OF CATABOLIC GENES FROM METAGENOMIC LIBRARIES BASED ON THEIR GENE EXPRESSION CHARACTERISTICS 496
Perspective 15.1 NAMING THE UNCULTURABLE AND UNCHARACTERIZED 498
15.3 Aquatic Ecosystems 498
Perspective 15.2 DEAD ZONES 499
15.4 Terrestrial Ecosystems 506
15.5 Deep Subsurface and Geothermal Ecosystems 512
16 The Microbiology of Food and Water 522
16.1 Food Spoilage 524
16.2 Food Preservation 528
16.3 Food Fermentation 534
PART IV MICROBES AND DISEASE
18 Introduction to Infectious Diseases 600
18.1 Pathogenic Microbes 603
Toolbox 18.1 MEASURING THE VIRULENCE OF PATHOGENS 606
18.2 Microbial Virulence Strategies 608
Perspective 18.1 HOST DEFENSES IN BACTERIA 612
18.3 The Transmission of Infectious Diseases 613
18.4 Proving Cause and Effect in Microbial Infections 621
Perspective 18.2 THE ARMADILLO—AN IDEAL ANIMAL MODEL? 624
18.5 The Evolution of Pathogens 625
Mini-Paper: A Focus on the Research EPIDEMIOLOGY OF AN INFECTIOUS DISEASE 626
19 Innate Host Defenses Against Microbial Invasion 636
19.1 Immunity 638
19.2 Barriers to Infection 639
Perspective 19.1 MESSY MUCUS 642
19.3 The Inflammatory Response 643
19.4 The Molecules of the Innate System 644
Toolbox 19.1 THE COMPLEMENT FIXATION TEST 650
19.5 The Cells of Innate Immunity 653
Perspective 19.2 NATURAL BORN KILLERS 659
19.6 Invertebrate Defenses 663
Mini-Paper: A Focus on the Research MAMMALIAN CELLS CAN RECOGNIZE BACTERIAL DNA 664
Toolbox 19.2 THE LIMULUS AMOEBOCYTE ASSAY FOR LPS 667
16.4 Foodborne and Waterborne Illness 541
16.5 Microbiological Aspects of Water Quality 543
Perspective 16.1 IMPLICATIONS OF SLUDGE BULKING 549
Toolbox 16.1 MEASURING BIOCHEMICAL OXYGEN DEMAND (BOD) 550
Mini-Paper: A Focus on the Research ENHANCED BIOLOGICAL REMOVAL OF PHOSPHORUS 552
17 Microbial Symbionts 560
17.1 Types of Microbe–Host Interactions 563
17.2 Symbionts of Plants 564
17.3 Lichens 569
17.4 Symbionts of Vertebrates 571
Toolbox 17.1 GERMFREE AND GNOTOBIOTIC ANIMALS 571
Perspective 17.1 PROBIOTICS—DO THEY WORK? 577
Mini-Paper: A Focus on the Research DO MICROBES CAUSE OBESITY? 579
Perspective 17.2 COWS CONTRIBUTE TO CLIMATE CHANGE 586
17.5 Symbionts of Invertebrates 587
Perspective 17.3 MIDICHLORIANS—NOT JUST FOR JEDI 592
Perspective 17.4 DEATH OF CORAL REEFS 595
21.2 Survival in the Host: Strategies and Consequences 743
Toolbox 21.2 THE TUBERCULIN TEST FOR TUBERCULOSIS 750
21.3 Evolution of Bacterial Pathogens 751
Perspective 21.4 ANTIBIOTICS TRIGGER TOXINS? 754
22 Viral Pathogenesis 760
22.1 Recurring Themes in Viral Pathogenesis 762
Perspective 22.1 VERTICAL TRANSMISSION OF HIV 767
22.2 Interactions with the Host: Strategies and Consequences 770
Perspective 22.2 VIRAL INDUCTION OF APOPTOSIS 772
22.3 Viral Infections and Cancer 775
Toolbox 22.1 IMMUNOPRECIPITATION 778
Perspective 22.3 SV40 AND HUMAN CANCERS 779
Mini-Paper: A Focus on the Research VIRUSES THAT CAUSE CANCER BY AFFECTING CELLULAR PROLIFERATION 782
22.4 Evolution of Viral Pathogens 785
Perspective 22.4 ETHICAL CONCERNS ABOUT AVIAN FLU RESEARCH 789
23 Eukaryal Microbe Pathogenesis 792
23.1 Mechanisms of Eukaryal Microbe Pathogenesis 794
Mini-Paper: A Focus on the Research AN EXPERIMENTAL SYSTEM FOR THE GENOMIC STUDY OF DUTCH ELM DISEASE 798
Perspective 23.1 PNEUMOCYSTIS JIROVECII OR CARINII: THE EVOLVING FIELD OF TAXONOMY 801
Perspective 23.2 MAGIC MUSHROOMS 807
20 Adaptive Immunity 672
20.1 Features of Adaptive Immunity 674
20.2 T Cells 677
20.3 Antigen Processing 681
20.4 Antigen-Presenting Cells 686
20.5 Humoral and Cell-Mediated Immune Responses 690
Perspective 20.1 TOO MUCH OF A GOOD THING 693
Mini-Paper: A Focus on the Research ATTEMPTING TO ENGINEER A VIRUS TO IMPROVE IMMUNOCONTRACEPTION 694
20.6 B Cells and the Production of Antibody 694
Perspective 20.2 VACCINES AGAINST T-INDEPENDENT ANTIGENS 699
Toolbox 20.1 MONOCLONAL ANTIBODY (mAb) PRODUCTION 702
Toolbox 20.2 ENZYME-LINKED IMMUNOSORBENT ASSAY (ELISA) 706
Perspective 20.3 TURNING ANTIBODY UPSIDE DOWN 708
21 Bacterial Pathogenesis 714
21.1 Bacterial Virulence Factors 716
Mini-Paper: A Focus on the Research E. COLI INJECTS ITS OWN RECEPTOR 722
Toolbox 21.1 SEROTYPING 724
Perspective 21.1 THE GOOD, THE BAD, AND THE UGLY SIDE OF BOTULINUM TOXIN 730
Perspective 21.2 SUPERABSORBENT TAMPONS AND SUPERANTIGENS 736
Perspective 21.3 IRON, VAMPIRES, FASHION, AND THE WHITE PLAGUE 742
Perspective 24.1 THE PURSUIT OF NEW ANTIBIOTICS: WHY BOTHER? 847
Perspective 24.2 HEALTH CARE-ASSOCIATED INFECTIONS: A RECIPE FOR RESISTANCE 848
Perspective 24.3 PHAGE THERAPY: BIOCONTROL FOR INFECTIONS 849
24.4 Predicting and Controlling Epidemics 850
Perspective 24.4 VARIOLATION: DELIBERATE INFECTION WITH SMALLPOX VIRUS 853
24.5 Immunization and Vaccines 853
Appendix A Reading and Understanding the Primary Literature A-1
Appendix B Microscopy A-9
Appendix C Classification of Bacteria A-13
Appendix D Classification of Eukarya A-14
Appendix E Classification of Archaea A-15
Appendix F Classification of Viruses A-16
Appendix G Origin of Blood Cells A-17
GLOSSARY G-1
INDEX I-1
23.2 Pathogen Study: Plasmodium falciparum 808
Toolbox 23.1 TESTING FOR MALARIA 812
23.3 Macroscopic Eukaryal Pathogens 814
23.4 Evolution of Eukaryal Pathogens 816
Perspective 23.3 CHYTRID FUNGUS: AN EMERGING FUNGAL PATHOGEN 817
24 Control of Infectious Diseases 822
24.1 Historical Aspects of Infectious Disease Treatment and Control 824
24.2 Antimicrobial Drugs 825
24.3 Antimicrobial Drug Resistance 836
Toolbox 24.1 DRUG SUSCEPTIBILITY TESTING AND MIC 842
Mini-Paper: A Focus on the Research SOIL MICROBES POSSESS EXTENSIVE RESISTANCE TO ANTIBIOTICS 844
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