E-grāmata: Microbiology

PART I THE MICROBES 1 The Microbial World 2 1.1 The Microbes 4 Mini-Paper: A Focus on the Research THE THREE DOMAINS OF LIFE 10 Toolbox 1.1 POLYMERASE CHAIN REACTION AMPLIFICATION OF rRNA GENES 12 1.2 Microbial Genetics 15 Perspective 1.1 CREATING LIFE IN THE LABORATORY: THE MILLER-UREY EXPERIMENT 18 1.3 Microbial Physiology and Ecology 23 1.4 Microbes and Disease 26 2 Bacteria 34 2.1 Morphology of Bacterial Cells 36 2.2 The Cytoplasm 38 2.3 The Bacterial Cytoskeleton 41 2.4 The Cell Envelope 43 Perspective 2.1 MARVELOUS MAGNETOSOMES! 44 Toolbox 2.1 THE GRAM STAIN 53 Perspective 2.2 THE PROTECTIVE SHELLS OF ENDOSPORES 54 Mini-Paper: A Focus on the Research NEW MICROSCOPY METHODS REVEAL A PERIPLASM IN GRAM POSITIVE BACTERIAL CELLS 58 2.5 The Bacterial Cell Surface 59 2.6 Diversity of Bacteria 66 3 Eukaryal Microorganisms 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 Microorganisms 86 3.3 Replication of Eukaryal Microorganisms 91 3.4 The Origin of Eukaryal Cells 94 Perspective 3.2 SECONDARY ENDOSYMBIOSIS: THE ORIGINS OF AN ORGANELLE WITH FOUR MEMBRANES 97 3.5 Interactions Between Eukaryal Microorganisms and Animals, Plants, and the Environment 98 4 Archaea 106 4.1 Evolution of Archaea 108 4.2 Archaeal Cell Structure 110 Toolbox 4.1 VACCINE DELIVERY STRATEGIES 115 4.3 Diversity of Archaea 118 Perspective 4.1 EXTREMOPHILES AND BIOTECHNOLOGY 120 Mini-Paper: A Focus on the Research THE ROLE OF ARCHAEA IN OUR DIGESTIVE SYSTEM 124 5 Viruses 130 5.1 A Basic Overview of Viruses 132 5.2 Origins of Viruses 140 Perspective 5.1 RIBOZYMES: EVIDENCE FOR AN RNA-BASED WORLD 141 5.3 Cultivation, Purification, and Quantification of Viruses 143 Toolbox 5.1 CELL CULTURE TECHNIQUES 144 Perspective 5.2 MEASUREMENT OF HIV VIRAL LOAD 147 5.4 Diversity of Viruses 150 Toolbox 5.2 REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION (RT-PCR) 154 5.5 Virus-Like Particles 155 5.6 Virology Today 158 Mini-Paper: A Focus on the Research NEW FINDINGS IN THE PACKAGING OF DNA BY THE MODEL BACTERIOPHAGE T4 160 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 MICROORGANISMS 180 6.4 Measuring Microbial Population Growth 181 Mini-Paper: A Focus on the Research BRINGING TO LIFE THE PREVIOUSLY UNCULTURABLE USING THE SOIL SUBSTRATE MEMBRANE SYSTEM (SSMS) 182 Perspective 6.2 MYCOBACTERIUM LEPRAE, AN EXTRAORDINARILY SLOW-GROWING PATHOGEN 189 Perspective 6.3 THE HUMAN INTESTINE-A CONTINUOUS CULTURE 191 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 217 Toolbox 7.1 USING A GEL SHIFT ASSAY TO IDENTIFY DNA-BINDING PROTEINS 219 7.4 Translation 222 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 Perspective 8.1 DNA MICROARRAYS AND THE SARS VIRUS 242 Toolbox 8.1 THE WESTERN BLOT 244 8.2 Viral Entry and Uncoating 246 8.3 Viral Replication 249 Perspective 8.2 PHAGE THERAPY: BIOCONTROL FOR INFECTIONS 256 8.4 Viral Assembly and Egress 258 Mini-Paper: A Focus on the Research THE DISCOVERY OF REVERSE TRANSCRIPTASE 260 9 Bacterial Genetic Analysis and Manipulation 264 9.1 Bacteria as Subjects of Genetic Research 266 9.2 Mutations, Mutants, and Strains 269 Toolbox 9.1 ISOLATING NUTRITIONAL MUTANTS 271 9.3 Restriction Enzymes, Vectors, and Cloning 276 9.4 Recombination and DNA Transfer 283 Perspective 9.1 PLASMIDS THAT PRODUCE PATHOGENS 287 Mini-Paper: A Focus on the Research THE DISCOVERY OF TRANSDUCTION 294 10 Microbial Genomics 300 10.1 Genome Sequencing 302 Perspective 10.1 RATE OF DNA SEQUENCING 306 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 318 Mini-Paper: A Focus on the Research GENOME SEQUENCE OF A KILLER BUG 320 10.4 Metagenomics and Related Analyses 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 345 Toolbox 11.1 USING RNA MOLECULES TO DECREASE GENE EXPRESSION 347 11.5 Quorum Sensing 348 11.6 Two-Component Regulatory Systems 351 11.7 Chemotaxis 354 12 Microbial Biotechnology 360 12.1 Microbes for Biotechnology 362 Perspective 12.1 BIOPROSPECTING: WHO OWNS THE MICROBES? 364 12.2 Molecular Genetic Modification 366 Toolbox 12.1 SITE-DIRECTED MUTAGENESIS 368 Toolbox 12.2 FUSION PROTEIN PURIFICATION 374 Perspective 12.2 THE INTERNATIONAL GENETICALLY ENGINEERED MACHINE (IGEM) COMPETITION, STANDARD BIOLOGICAL PARTS, AND SYNTHETIC BIOLOGY 378 12.3 Red Biotechnology 379 12.4 White Biotechnology 381 Perspective 12.3 BIOFUELS: BIODIESEL AND ALGAE 384 12.5 Green Biotechnology 390 Toolbox 12.3 PLANT TRANSFORMATION USING BACTERIA 392 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 421 Perspective 13.2 ELECTRICIGENIC BACTERIA AND MICROBIAL FUEL CELLS 425 13.5 Metabolism of Non-glucose Carbon Sources 429 Toolbox 13.1 METABOLISM AND RAPID BACTERIAL IDENTIFICATION SYSTEMS 431 13.6 Phototrophy and Photosynthesis 433 13.7 Nitrogen and Sulfur Metabolism 442 Mini-Paper: A Focus on the Research GENOME SEQUENCE OF A DEEP SEA SYMBIONT 443 13.8 Biosynthesis of Cellular Components 448 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 462 Perspective 14.1 CO2 AS A GREENHOUSE GAS AND ITS INFLUENCE ON CLIMATE CHANGE 464 14.3 Cycling Driven by Nitrogen Metabolism 471 Mini-Paper: A Focus on the Research THE FIRST ISOLATION AND CULTIVATION OF A MARINE ARCHAEON 476 14.4 Other Cycles and their Connections 476 Perspective 14.2 LIFE IN A WORLD WITHOUT MICROBES 478 Perspective 14.3 THE MICROBIOLOGY OF ENVIRONMENTALLY TOXIC ACID MINE DRAINAGE 479 Toolbox 14.2 BIOGEOCHEMISTRY IN A BOTTLE: THE WINOGRADSKY COLUMN 481 15 Microbial Ecosystems 486 15.1 Microbes in the Environment 488 15.2 Microbial Community Analysis 493 Toolbox 15.1 FLOW CYTOMETRY 498 Mini-Paper: A Focus on the Research INSIGHTS INTO THE PHYLOGENY AND CODING POTENTIAL OF MICROBIAL DARK MATTER 500 Perspective 15.1 NAMING THE UNCULTURED AND UNCHARACTERIZED 502 15.3 Aquatic Ecosystems 502 Perspective 15.2 DEAD ZONES 503 15.4 Terrestrial Ecosystems 509 15.5 Deep Subsurface and Geothermal Ecosystems 515 Mini-Paper: A Focus on the Research MAKING A SYNTHETIC GENOME 376 16 The Microbiology of Food and Water 524 16.1 Food Spoilage 526 16.2 Food Preservation 530 16.3 Food Fermentation 535 16.4 Foodborne and Waterborne Illness 542 16.5 Microbiological Aspects of Water Quality 545 Perspective 16.1 IMPLICATIONS OF SLUDGE BULKING 550 Toolbox 16.1 MEASURING BIOCHEMICAL OXYGEN DEMAND (BOD) 551 Mini-Paper: A Focus on the Research ENHANCED BIOLOGICAL REMOVAL OF PHOSPHORUS 553 Toolbox 16.2 MOST PROBABLE NUMBER (MPN) METHOD 556 17 Microbial Symbionts 562 17.1 Types of Microbe-Host Interactions 564 17.2 Symbionts of Plants 566 17.3 Symbionts of Humans 571 Toolbox 17.1 GERM-FREE AND GNOTOBIOTIC ANIMALS 575 Perspective 17.1 FOOD PROBIOTICS-DO THEY WORK? 577 Mini-Paper: A Focus on the Research FECAL BACTERIOTHERAPY: "REPOOPULATION" OF THE GUT 580 17.4 Symbionts of Herbivores 582 Perspective 17.2 COWS CONTRIBUTE TO CLIMATE CHANGE 588 17.5 Symbionts of Invertebrates 588 Perspective 17.3 MIDICHLORIANS-NOT JUST FOR JEDI 592 Perspective 17.4 DEATH OF CORAL REEFS 595 PART IV MICROBES AND DISEASE 18 Introduction to Infectious Diseases 600 18.1 Pathogenic Microbes 603 Toolbox 18.1 MEASURING THE VIRULENCE OF PATHOGENS 605 18.2 Microbial Virulence Strategies 607 Perspective 18.1 GENOME EDITING: A POWERFUL AND CONTROVERSIAL NEW TECHNIQUE 613 18.3 The Transmission of Infectious Diseases 614 Mini-Paper: A Focus on the Research EPIDEMIOLOGY OF AN INFECTIOUS DISEASE 622 18.4 Proving Cause and Effect in Microbial Infections 624 Perspective 18.2 THE ARMADILLO-AN IDEAL ANIMAL MODEL? 628 18.5 The Evolution of Pathogens 629 19 Innate Host Defenses Against Microbial Invasion 638 19.1 Immunity 640 19.2 Barriers to Infection 641 Perspective 19.1 MESSY MUCUS 644 19.3 The Inflammatory Response 645 19.4 The Molecules of the Innate System 646 Mini-Paper: A Focus on the Research MAMMALIAN CELLS CAN RECOGNIZE BACTERIAL DNA 650 Toolbox 19.1 THE COMPLEMENT FIXATION TEST 654 19.5 The Cells of Innate Immunity 657 19.6 Invertebrate Defenses 665 Toolbox 19.2 THE LIMULUS AMOEBOCYTE ASSAY FOR LPS 667 20 Adaptive Immunity 672 20.1 Features of Adaptive Immunity 674 20.2 T Cells 677 20.3 Antigen Processing 682 20.4 Antigen-Presenting Cells 684 20.5 Humoral and Cell-Mediated Immune Responses 688 Mini-Paper: A Focus on the Research ATTEMPTING TO ENGINEER A VIRUS TO IMPROVE IMMUNOCONTRACEPTION 690 Perspective 20.1 TOO MUCH OF A GOOD THING? 691 20.6 B Cells and the Production of Antibody 692 Perspective 20.2 VACCINES AGAINST T-INDEPENDENT ANTIGENS 696 Toolbox 20.1 MONOCLONAL ANTIBODY (mAb) PRODUCTION 698 Perspective 20.3 TURNING ANTIBODY UPSIDE DOWN 703 Toolbox 20.2 ENZYME-LINKED IMMUNOSORBENT ASSAY (ELISA) 704 21 Bacterial Pathogenesis 710 21.1 Bacterial Virulence Factors 712 Mini-Paper: A Focus on the Research ESCHERICHIA COLI INJECTS ITS OWN RECEPTOR 718 Perspective 21.1 IRON, VAMPIRES, FASHION, AND THE WHITE PLAGUE 722 21.2 Bacterial Virulence Factors-Toxins 723 Toolbox 21.1 SEROTYPING 724 Perspective 21.2 THE GOOD, THE BAD, AND THE UGLY SIDE OF BOTULINUM TOXIN 732 Perspective 21.3 SUPERABSORBENT TAMPONS AND SUPERANTIGENS 737 21.3 Survival in the Host: Strategies and Consequences 738 Toolbox 21.2 THE TUBERCULIN TEST FOR TUBERCULOSIS 746 21.4 Evolution of Bacterial Pathogens 746 Perspective 21.4 ANTIBIOTICS TRIGGER TOXINS? 750 22 Viral Pathogenesis 756 22.1 Recurring Themes in Viral Pathogenesis 758 Perspective 22.1 VERTICAL TRANSMISSION OF HIV 763 22.2 Interactions with the Host: Strategies and Consequences 765 Perspective 22.2 VIRAL INDUCTION OF APOPTOSIS 767 22.3 Viral Infections and Cancer 770 Toolbox 22.1 IMMUNOPRECIPITATION 773 Mini-Paper: A Focus on the Research VIRUSES THAT CAUSE CANCER BY AFFECTING CELLULAR PROLIFERATION 774 Perspective 22.3 SV40 AND HUMAN CANCERS 776 22.4 Evolution of Viral Pathogens 780 Perspective 22.4 ETHICAL CONCERNS ABOUT AVIAN FLU RESEARCH 784 23 Eukaryal Pathogenesis 788 23.1 Mechanisms of Eukaryal Pathogenesis 790 Mini-Paper: A Focus on the Research AN EXPERIMENTAL SYSTEM FOR THE GENOMIC STUDY OF DUTCH ELM DISEASE 794 Perspective 23.1 PNEUMOCYSTIS JIROVECII OR CARINII : THE EVOLVING FIELD OF TAXONOMY 797 Perspective 23.2 MAGIC MUSHROOMS 802 23.2 Pathogen Study: Plasmodium Falciparum 803 23.3 Macroscopic Eukaryal Pathogens 807 Toolbox 23.1 TESTING FOR MALARIA 808 23.4 Evolution of Eukaryal Pathogens 811 Perspective 23.3 CHYTRID FUNGUS: AN EMERGING FUNGAL PATHOGEN 812 24 Control of Infectious Diseases 818 24.1 Historical Aspects of Infectious Disease Treatment and Control 820 24.2 Antimicrobial Drugs 821 24.3 Antimicrobial Drug Resistance 834 Toolbox 24.1 DRUG SUSCEPTIBILITY TESTING AND MIC 838 Mini-Paper: A Focus on the Research SOIL MICROORGANISMS POSSESS EXTENSIVE RESISTANCE TO ANTIBIOTICS 840 Perspective 24.1 THE PURSUIT OF NEW ANTIBIOTICS: WHY BOTHER? 844 Perspective 24.2 HEALTH CARE-ASSOCIATED INFECTIONS: A RECIPE FOR RESISTANCE 845 24.4 Predicting and Controlling Epidemics 846 24.5 Immunization and Vaccines 848 Perspective 24.3 VARIOLATION: DELIBERATE INFECTION WITH SMALLPOX VIRUS 849 Perspective 24.4 THE WAR AGAINST VACCINES 854 Appendix A Reading and Understanding the Primary Literature A-1 Appendix B Microscopy A-9 Appendix C Taxonomys A-13 Appendix D Origin of Blood Cells A-15 GLOSSARY G-1 INDEX I-1 ONLINE APPENDICES Appendix E Classification of Archaea Appendix F Classification of Viruses Appendix G Origin of Blood Cells

David R. Wessner is a Professor of Biology at Davidson College. David teaches introductory biology and courses on microbiology, genetics, and HIV/AIDS. His research focuses on viral pathogenesis. He is a member of the American Society for Microbiology Committee for K-12 Education. He also is a coauthor of Vision and Change in Undergraduate Education: A Call to Action. Prior to joining the faculty at Davidson, David conducted research at the Navy Medical Center. He earned his Ph.D. in Microbiology and Molecular Genetics from Harvard University and his B.A. in Biology from Franklinand Marshall College. Christine Dupont is a Lecturer in the Department of Biology at the University of Waterloo in southern Ontario, Canada, Christine teaches undergraduate courses in genetics, biotechnology, virology, and bacterial pathogenesis. She earned her Ph.D. from Massey University, Faculty of Veterinary Science, New Zealand; B.Ed. from the University of Windsor, Ontario; and M.Sc. and B.Sc. in Microbiology from the University of Guelph, Ontario. Prior to her Ph.D. studies, Christine taught high school science for several years, developing a passion for teaching and working with students. Trevor C. Charles is a Professor in the Department of Biology, University of Waterloo, Trevor teaches undergraduate courses in microbiology and synthetic biology, and runs a research program that focuses on plant microbe interactions and functional metagenomics. Prior to joining the faculty at Waterloo, he held a faculty position at McGill University and did postdoctoral research at the University of Washington. He earned his Ph.D. from McMaster University, and his B.Sc. in Microbiology from the University of British Columbia. Josh D. Neufeld, as a Professor in the Department of Biology at the University of Waterloo, explores microbiology with undergraduate students in the classroom and both undergraduate and graduate students in his microbial ecology research program. Josh earned his B.Sc. and M.Sc. in Microbiology from McGill University's Macdonald Campus prior to completing a Ph.D. at the University of British Columbia and postdoctoral research at the University of Warwick.