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Book Details
Abstract
Available as an exclusive product with a limited print run, Encyclopedia of Microbiology, 3e, is a comprehensive survey of microbiology, edited by world-class researchers. Each article is written by an expert in that specific domain and includes a glossary, list of abbreviations, defining statement, introduction, further reading and cross-references to other related encyclopedia articles. Written at a level suitable for university undergraduates, the breadth and depth of coverage will appeal beyond undergraduates to professionals and academics in related fields.
- 16 separate areas of microbiology covered for breadth and depth of content
- Extensive use of figures, tables, and color illustrations and photographs
- Language is accessible for undergraduates, depth appropriate for scientists
- Links to original journal articles via Crossref
- 30% NEW articles and 4-color throughout – NEW!
Reviews of the Second Edition
“This is a comprehensive and creative collection of reviews of every imaginable aspect of the microbial world from ABC transport to zoonoses. The scope, detail and organization of this four-volume set is truly remarkable. The editor provides the reader with a limitless supply of reference material for teaching purposes, research, or historical perspective. This encyclopedia is an all-encompassing reference to meet the needs of the diverse number of disciplines dealing with microorganisms, including public health and agricultural and industrial microbiology, to name a few. To this end, the text is a huge success as the editor has provided a balanced compendium of topics in which no discipline is short-changed. The organization of this book is a strong feature. …….. The list of contributors is a veritable who’s who in the field of microbiology, truly reflecting a world-wide consortium of authors. The complexity and array of subject matter covered in this book is (in the current vernacular) awesome! Once the secret is out, this text should find itself on the office shelves of all professional microbiologists and in the library of every academic microbiology department throughout the world.
Wm. Michael Dunner, Jr.m PhD, Case Western University in CHOICE
“As was noted in ARBA 94, entry 1636, about the 1st edition of the Encyclopedia of Microbiology, there “really is nothing else comparable in either coverage or currency on the market. Now with an updated 2nd edition, this “scholarly source of information on microorganisms continues to stand as the major survey of the field for advanced undergraduate and graduate students. …. The 2nd edition appears to meet the basic criteria of an excellent encyclopedia in design, organization, usability and accuracy of data.
Laurel Grotzinger, American Reference Books Annual 2002
Table of Contents
| Section Title | Page | Action | Price |
|---|---|---|---|
| e9780123739391v1 | 1 | ||
| Cover\r | 1 | ||
| Title Page\r | 4 | ||
| Copyright Page\r | 5 | ||
| Dedication | 6 | ||
| Preface | 8 | ||
| Editor in Chief | 10 | ||
| Editors | 12 | ||
| List Of Contributors | 14 | ||
| Contents | 30 | ||
| APPLIED MICROBIOLOGY: AGRO/FOOD | 40 | ||
| Agrobacterium and Plant Cell Transformation | 40 | ||
| Glossary | 40 | ||
| Abbreviations | 41 | ||
| Defining Statement | 41 | ||
| Introduction | 41 | ||
| Overview of Infection Process | 41 | ||
| Ti Plasmid | 42 | ||
| Chromosomally Encoded Virulence Genes | 45 | ||
| T-DNA Processing | 46 | ||
| VirB/D4 System, a Member of the Type IV Secretion Family | 47 | ||
| Substrate Transfer Through the Plant Cell | 51 | ||
| Agrobacterium Host Range and Genetic\rEngineering | 52 | ||
| Conclusions | 54 | ||
| Further Reading | 54 | ||
| Aquaculture | 56 | ||
| Glossary | 56 | ||
| Abbreviations | 56 | ||
| Defining Statement | 56 | ||
| Seafood Farming | 56 | ||
| Bacteria-Covered Surfaces | 57 | ||
| Bacterial Populations of Animals and Plants | 57 | ||
| Microbial Diseases | 57 | ||
| Environmental Factors | 60 | ||
| Recirculating Systems | 60 | ||
| Further Reading | 61 | ||
| Relevant Websites | 61 | ||
| Beer/Brewing | 62 | ||
| Glossary | 62 | ||
| Defining Statement | 62 | ||
| Introduction | 62 | ||
| History of Brewing | 63 | ||
| Brewing | 63 | ||
| Beer Properties | 67 | ||
| Properties of Brewing Yeasts | 67 | ||
| Spoilage Problems of Beer | 68 | ||
| Spoilage Control | 70 | ||
| Other Types of Beer Processing | 71 | ||
| Further Reading | 72 | ||
| Dairy Products | 73 | ||
| Abbreviations | 73 | ||
| Defining Statement | 73 | ||
| Introduction | 73 | ||
| Milk Characteristics, Components, and Properties | 74 | ||
| Microbiology of Milk | 75 | ||
| Fermentation of Dairy Products | 78 | ||
| Fermented Dairy Products | 79 | ||
| Nutritional and Therapeutic Aspects of Fermented Dairy Products | 82 | ||
| Further Reading | 82 | ||
| Fermented Foods | 84 | ||
| Glossary | 84 | ||
| Defining Statement | 84 | ||
| Classification | 84 | ||
| Safety of Fermented Foods | 85 | ||
| Fermentation Processes | 86 | ||
| Nutritional Aspects of Fermented Foods | 90 | ||
| Further Reading | 91 | ||
| Relevant Website | 92 | ||
| Food Spoilage, Preservation and Quality Control | 93 | ||
| Abbreviations | 93 | ||
| Defining Statement | 93 | ||
| Introduction | 93 | ||
| Food Microbiology | 94 | ||
| Methods for Enumeration of Microorganisms in Solid, Liquid, Surface, and Air Samples | 95 | ||
| Sample Preparations and Treatments of Foods | 95 | ||
| Solid Samples | 95 | ||
| Liquid Samples | 96 | ||
| Surface Samples | 97 | ||
| Air Samples | 97 | ||
| Food Spoilage | 102 | ||
| Intrinsic Parameters of Foods | 103 | ||
| Oxidation-Reduction Potential (O/R, Eh) | 104 | ||
| Extrinsic Parameters of Foods | 105 | ||
| Spoilage of Vegetables | 105 | ||
| Spoilage of Fruits | 106 | ||
| Spoilage of Fresh and Processed Meats, Poultry, Egg, and Seafood | 106 | ||
| Fresh Meat | 106 | ||
| Spoilage of Fresh Meat | 107 | ||
| Spoilage of Vacuum-Packaged Meats and Processed Meat | 107 | ||
| Spoilage of Poultry and Egg | 107 | ||
| Spoilage of Fish and Shellfish | 108 | ||
| Microbiology of Food Preservation | 109 | ||
| Food Preservation by Drying and Dehydration | 109 | ||
| Preservation of Food by High Temperatures | 111 | ||
| Pasteurization of Milk and Other Liquid Commodities | 111 | ||
| Organisms Surviving Pasteurization | 111 | ||
| Sterilization of Food by Canning Using Heat | 111 | ||
| Preservation of Food by Radiation | 112 | ||
| Microwave Treatment of Food | 113 | ||
| Quality Control of Foods Related to Microorganisms | 114 | ||
| Degree of Concern Relative to Utility and Health Hazard | 116 | ||
| Conclusions of Applied Food Microbiology | 117 | ||
| Further Reading | 117 | ||
| Forest Products: Biotechnology in Pulp and Paper Processing | 119 | ||
| Abbreviations | 119 | ||
| Defining Statement | 119 | ||
| Introduction | 119 | ||
| Lignocellulosic Components and Their Enzymology | 120 | ||
| Pulping, Bleaching, and Papermaking | 125 | ||
| Biotechnical Applications | 126 | ||
| Conclusion | 133 | ||
| Further Reading | 133 | ||
| Insecticides, Microbial | 134 | ||
| Glossary | 134 | ||
| Abbreviations | 134 | ||
| Defining Statement | 135 | ||
| Introduction | 135 | ||
| Discovery of MIs | 137 | ||
| Bacteria | 137 | ||
| Viruses | 141 | ||
| Fungi | 144 | ||
| Conclusions | 148 | ||
| Further Reading | 148 | ||
| Pesticides, Microbial | 149 | ||
| Glossary | 149 | ||
| Defining Statement | 149 | ||
| The Plant as a Microbial Ecosystem | 149 | ||
| Plant Disease and Biological Control Methods | 150 | ||
| Microorganisms Active in the Biological Control of Plant Pathogens and Their Mechanism of Action | 151 | ||
| Discovery of Microbial Pesticides | 152 | ||
| Production and Formulation | 155 | ||
| Monitoring, Environmental Impact, and Biosafety | 157 | ||
| Registration and Commercialization | 158 | ||
| Further Reading | 159 | ||
| Water, Drinking | 160 | ||
| Glossary | 160 | ||
| Abbreviations | 160 | ||
| Defining Statement | 160 | ||
| Introduction | 160 | ||
| Indicator Organisms in Microbial Monitoring | 161 | ||
| EPA Drinking Water Regulations | 162 | ||
| Sources, Treatment, and Distribution | 164 | ||
| Alternative Water Sources | 173 | ||
| Other Issues Associated with Water Treatment | 174 | ||
| Conclusions | 176 | ||
| Further Reading | 176 | ||
| Relevant Websites | 176 | ||
| Wine | 177 | ||
| Glossary | 177 | ||
| Defining Statement | 177 | ||
| Antiquity of Wine Fermentation | 177 | ||
| Alcoholic Fermentation | 178 | ||
| Yeasts | 178 | ||
| Malolactic Fermentation | 179 | ||
| Nobel Mold | 179 | ||
| Microorganisms Causing Spoilage in Wines | 179 | ||
| Microbiology of Sherry Wines | 179 | ||
| Wine Grapes | 179 | ||
| Wine Classification | 179 | ||
| Steps in Manufacture of Wine | 180 | ||
| Sparkling Wines | 181 | ||
| Fortified Wines | 181 | ||
| Flavor and Acceptability | 181 | ||
| Further Reading | 181 | ||
| Relevant Website | 182 | ||
| APPLIED MICROBIOLOGY: INDUSTRIAL | 183 | ||
| Acetic Acid Production | 184 | ||
| Glossary | 184 | ||
| Abbreviations | 184 | ||
| Introduction | 184 | ||
| Historical Background | 184 | ||
| Acetic Acid Production | 185 | ||
| Fermenter Designs | 187 | ||
| Downstream Processing | 187 | ||
| Further Reading | 188 | ||
| Amino Acid Production | 189 | ||
| Glossary | 189 | ||
| Abbreviations | 189 | ||
| Introduction | 189 | ||
| Microbial Production | 190 | ||
| Enzymatic Production | 196 | ||
| Future Prospects | 197 | ||
| Further Reading | 197 | ||
| Amylases | 198 | ||
| Abbreviations | 198 | ||
| Defining Statement | 198 | ||
| Definition of Amylase | 198 | ||
| Classification of Amylases | 198 | ||
| Catalytic Properties of Amylases | 201 | ||
| Reaction Mechanism of Amylases | 204 | ||
| Structure–Function Relationships of Amylases | 205 | ||
| Industrial Application of Amylases | 209 | ||
| Further Reading | 212 | ||
| Relevant Websites | 212 | ||
| Antibiotic Production | 213 | ||
| Glossary | 213 | ||
| Abbreviations | 213 | ||
| Defining Statement | 213 | ||
| Introduction | 213 | ||
| Discovery of Antibiotics | 215 | ||
| Yield Improvement | 217 | ||
| Engineering Aspects of Process Development and Scale-Up | 225 | ||
| Conclusions | 228 | ||
| Further Reading | 229 | ||
| Relevant Website | 229 | ||
| Biodeterioration – Including Cultural Heritage | 230 | ||
| Glossary | 230 | ||
| Abbreviations | 230 | ||
| Defining Statement | 230 | ||
| Biodeterioration | 230 | ||
| Biodeteriogens | 234 | ||
| Materials Related to Cultural Heritage | 237 | ||
| Methods of Control and Prevention | 242 | ||
| Further Reading | 244 | ||
| Relevant Website | 244 | ||
| Bioreactors | 245 | ||
| Glossary | 245 | ||
| Defining Statement | 245 | ||
| Introduction | 245 | ||
| Classifications of Bioreactors | 246 | ||
| Principles of Bioreactor Analysis and Design | 248 | ||
| Sensors, Instrumentation, and Control | 249 | ||
| Metabolic and Protein Engineering | 249 | ||
| Stability and Sterilization | 250 | ||
| Conclusions | 250 | ||
| Further Reading | 250 | ||
| Biotransformations | 251 | ||
| Glossary | 251 | ||
| Abbreviations | 251 | ||
| Defining Statement | 252 | ||
| General Scope | 252 | ||
| Whole-Cell Factory | 252 | ||
| Immobilization–Stabilization of Whole Cells | 254 | ||
| Applied Biotransformations | 259 | ||
| Conclusion | 289 | ||
| Further Reading | 289 | ||
| Cellulases | 291 | ||
| Glossary | 291 | ||
| Abbreviations | 291 | ||
| Defining Statement | 291 | ||
| Introduction | 291 | ||
| Plant Cell Wall Cellulose | 291 | ||
| Cellulose Turnover | 292 | ||
| Animal Cellulases | 292 | ||
| Plant Cellulases | 292 | ||
| Cellulase Kinetics | 292 | ||
| Cellulase Assays | 292 | ||
| Cellulase Diversity | 293 | ||
| Functional Cellulase Classes | 293 | ||
| Synergism | 294 | ||
| Mechanisms of Cellulose Degradation | 294 | ||
| Carbohydrate-Binding Modules | 295 | ||
| Cellulase Substrate Preference | 296 | ||
| Cellulase Regulation | 296 | ||
| Cellulase Uses | 296 | ||
| Further Reading | 297 | ||
| Relevant Websites | 297 | ||
| Corrosion, Microbial | 298 | ||
| Glossary | 298 | ||
| Defining Statement | 298 | ||
| History and Significance | 298 | ||
| Microbial Biofilms and Corrosion | 299 | ||
| Aerobic Corrosion Processes | 300 | ||
| Anaerobic Corrosion Processes | 302 | ||
| Alternating Aerobic and Anaerobic Conditions | 303 | ||
| Corrosion by Microbial Exopolymers | 304 | ||
| Microbial Hydrogen Embrittlement | 305 | ||
| Corrosion by Other Microbial Metabolites | 305 | ||
| Electron Shuttling in Corrosion | 305 | ||
| Prevention and Control | 306 | ||
| Conclusions | 307 | ||
| Acknowledgments | 308 | ||
| Further Reading | 308 | ||
| Cosmetics Microbiology | 309 | ||
| Glossary | 309 | ||
| Abbreviations | 309 | ||
| Defining Statement | 309 | ||
| Background and Importance of Cosmetic Microbiology | 309 | ||
| Sanitary Manufacture | 311 | ||
| Sanitization | 315 | ||
| Preservation | 316 | ||
| HACCP for Cosmetics | 317 | ||
| Test Methods | 317 | ||
| Further Reading | 319 | ||
| Enzymes, Industrial (overview) | 320 | ||
| Glossary | 320 | ||
| Abbreviations | 320 | ||
| Defining Statement | 320 | ||
| Introduction | 321 | ||
| Classification | 321 | ||
| Starch Conversion | 321 | ||
| Lignocellulosic Biomass Conversion | 325 | ||
| Enzymes in the Production of Functional Oligosaccharides and Other Neutraceuticals | 327 | ||
| Enzymes in the Modification of Fats and Oils | 328 | ||
| Enzymes in the Animal Feed Industry | 328 | ||
| Enzymes in the Pulp and Paper Industry | 329 | ||
| Enzymes in the Fruit Juice Processing Industry | 329 | ||
| Enzymes in the Meat and Fish Processing Industry | 329 | ||
| Enzymes in the Dairy Industry | 330 | ||
| Enzymes in Detergents | 330 | ||
| Enzymes in the Leather Industry | 331 | ||
| Enzymes in the Production of Bulk and Fine Chemicals | 331 | ||
| Analytical Applications of Enzymes | 332 | ||
| Enzyme-Replacement Therapy | 332 | ||
| Further Reading | 333 | ||
| Ethanol | 334 | ||
| Glossary | 334 | ||
| Abbreviations | 334 | ||
| Defining Statement | 334 | ||
| Introduction | 334 | ||
| Engineering E. coli for Ethanol Production | 336 | ||
| Other Engineered Ethanologenic Microbial Biocatalysts | 340 | ||
| Ethanol Production by Z. mobilis | 340 | ||
| Challenges for Cost-Effective Ethanol Production | 341 | ||
| Conclusion | 342 | ||
| Further Reading | 343 | ||
| Relevant Website | 343 | ||
| Flavor Compounds | 344 | ||
| Glossary | 344 | ||
| Defining Statement | 344 | ||
| Introduction | 344 | ||
| Complex Flavors Through de novo Synthesis | 346 | ||
| Bread | 351 | ||
| Other Food-Fermented Products | 351 | ||
| Biotransformations | 352 | ||
| Conclusion | 359 | ||
| Further Reading | 359 | ||
| Heavy Metal Pollutants: Environmental and Biotechnological Aspects | 360 | ||
| Glossary | 360 | ||
| Abbreviations | 360 | ||
| Defining Statement | 360 | ||
| Introduction | 360 | ||
| Environmental Aspects of Heavy Metal Pollution | 361 | ||
| Biotechnological Aspects of Heavy Metal Pollution | 364 | ||
| Further Reading | 372 | ||
| Relevant Website | 373 | ||
| Industrial Biotechnology, (overview) | 374 | ||
| Glossary | 374 | ||
| Abbreviations | 374 | ||
| Defining Statement | 375 | ||
| Introduction | 375 | ||
| Medical Biotechnology | 376 | ||
| Primary Metabolites | 382 | ||
| Enzymes | 382 | ||
| Biopolymers and Bioplastics | 383 | ||
| Biofuels | 384 | ||
| Bioremediation | 386 | ||
| Agricultural Biotechnology | 386 | ||
| Further Reading | 387 | ||
| Industrial Fermentation Processes | 388 | ||
| Glossary | 388 | ||
| Abbreviations | 388 | ||
| Defining Statement | 388 | ||
| Introduction | 389 | ||
| History | 390 | ||
| Culture Selection and Development | 390 | ||
| Process Development and Scale-Up | 392 | ||
| Large-Scale Operation | 394 | ||
| Future Prospects | 399 | ||
| Further Reading | 400 | ||
| Lactic Acid, Microbially Produced | 401 | ||
| Glossary | 401 | ||
| Abbreviations | 401 | ||
| Defining Statement | 401 | ||
| Microorganisms for Production | 401 | ||
| Microbiological Processes | 404 | ||
| Process Control | 409 | ||
| Product Recovery and Purification | 410 | ||
| Commercial Applications | 410 | ||
| Further Reading | 411 | ||
| Lignin, Lignocellulose, Ligninase | 412 | ||
| Glossary | 412 | ||
| Abbreviations | 412 | ||
| Defining Statement | 412 | ||
| Introduction | 412 | ||
| Lignocellulose | 413 | ||
| Microorganisms Involved in the Degradation of Lignocelluloses | 415 | ||
| Expression of Ligninolytic Enzymes – Physiological Demands | 416 | ||
| Low Molecular Weight Compounds Play Role in Expression of Ligninases and/or Lignin Degradation by White-Rot Fungi | 417 | ||
| Ligninases | 417 | ||
| Further Reading | 423 | ||
| Lipases | 424 | ||
| Glossary | 424 | ||
| Abbreviations | 424 | ||
| Defining Statement | 424 | ||
| Introduction | 424 | ||
| Substrate Specificity | 425 | ||
| Industrial Uses of Lipase | 426 | ||
| Conclusion | 431 | ||
| Further Reading | 431 | ||
| Lipids, Production | 432 | ||
| Glossary | 432 | ||
| Abbreviations | 432 | ||
| Defining Statement | 432 | ||
| Introduction | 433 | ||
| Characteristics of Microbial Lipids | 435 | ||
| Single-Cell Oils | 438 | ||
| Valuable Lipid Metabolites | 442 | ||
| Further Reading | 445 | ||
| Metal Extraction and Biomining | 446 | ||
| Glossary | 446 | ||
| Abbreviations | 446 | ||
| Defining Statement | 446 | ||
| Microbial Transformations of Metals | 446 | ||
| Microorganisms that Solubilize Metals | 448 | ||
| Microbial Extraction of Metals from Ores and Biomining | 448 | ||
| Acidiophilic Microorganism–Mineral Interaction | 450 | ||
| Mechanisms Involved in Metal Solubilization by Acidophiles | 452 | ||
| Biomining in the Postgenomic Era | 453 | ||
| Environmental Effects of Metals Solubilization and Bioremediation | 457 | ||
| Conclusions | 458 | ||
| Further Reading | 458 | ||
| Relevant Website | 459 | ||
| Organic and Fatty Acid Production, Microbial | 460 | ||
| Glossary | 460 | ||
| Abbreviations | 460 | ||
| Defining Statement | 461 | ||
| Introduction | 461 | ||
| Organic Acids | 461 | ||
| Fatty Acids | 477 | ||
| Conclusions | 481 | ||
| Further Reading | 481 | ||
| Petroleum Microbiology | 482 | ||
| Glossary | 482 | ||
| Abbreviations | 482 | ||
| Defining Statement | 483 | ||
| Introduction | 483 | ||
| Physiological Mechanisms of Accession and Efflux | 484 | ||
| Metabolism | 486 | ||
| Microorganisms in Oil Recovery | 488 | ||
| Oil Biorefining and Bioprocessing | 491 | ||
| Biodegradation and Bioremediation | 492 | ||
| Concluding Remarks | 495 | ||
| Further Reading | 495 | ||
| Pigments, Microbial | 496 | ||
| Glossary | 496 | ||
| Abbreviations | 496 | ||
| Defining Statement | 496 | ||
| Introduction | 496 | ||
| Monascus Pigments – An Old Story for Asians | 497 | ||
| Arpink Red from P. oxalicum – The New Comer | 500 | ||
| Riboflavin – The Vitamin B2 but also a Yellow Food Colorant | 501 | ||
| Current Carotenoid Production Using Microorganisms | 501 | ||
| Prospects for Carotenoid Production by Genetically Modified Microorganisms | 507 | ||
| Concluding Comments | 509 | ||
| Further Reading | 510 | ||
| Polyketides | 511 | ||
| Glossary | 511 | ||
| Abbreviations | 511 | ||
| Defining Statement | 511 | ||
| Biosynthesis | 512 | ||
| Environmental Roles | 515 | ||
| Human Uses | 516 | ||
| Genomes of Prolific Polyketide Producers | 517 | ||
| Search for New Polyketides | 517 | ||
| Heterologous Expression of Polyketides | 518 | ||
| Engineering of PKSs | 518 | ||
| Conclusions | 519 | ||
| Acknowledgments | 519 | ||
| Further Reading | 519 | ||
| Polysaccharides, Microbial | 521 | ||
| Glossary | 521 | ||
| Abbreviations | 521 | ||
| Defining Statement | 521 | ||
| Introduction | 522 | ||
| Xanthan | 523 | ||
| Xylinan (Acetan) | 525 | ||
| Gellan, XM6, and Curdlan | 526 | ||
| Cyanobacterial Polysaccharides | 527 | ||
| Pullulan | 528 | ||
| Dextrans | 528 | ||
| Scleroglucan and Schizophyllan | 528 | ||
| Bacterial Alginates | 529 | ||
| Bacterial Hyaluronic Acid | 530 | ||
| Polysaccharide Vaccines | 531 | ||
| Conclusion | 532 | ||
| Further Reading | 532 | ||
| Relevant Website | 533 | ||
| Proteases, Production | 534 | ||
| Glossary | 534 | ||
| Abbreviations | 534 | ||
| Defining Statement | 534 | ||
| Introduction | 535 | ||
| Proteases and their Mechanisms of Action | 535 | ||
| Physiological Functions | 538 | ||
| Protease Engineering | 540 | ||
| Industrial Production | 541 | ||
| Industrial Application | 545 | ||
| Proteases in Organic Synthesis | 548 | ||
| Further Reading | 549 | ||
| Solvent Production | 551 | ||
| Glossary | 551 | ||
| Abbreviations | 551 | ||
| Defining Statement | 551 | ||
| Introduction | 551 | ||
| Problems of AB Fermentation | 553 | ||
| Traditional Substrates | 553 | ||
| Novel Substrates | 554 | ||
| Hydrolysis Inhibitors of Agricultural Residues | 555 | ||
| Microbial Cultures and Culture Development | 555 | ||
| Biochemistry and Biochemical Pathways | 556 | ||
| Use of Concentrated Sugar Solutions | 557 | ||
| Bioreactors for Fermentation | 557 | ||
| Novel Product Recovery Technologies | 562 | ||
| Use of Novel Substrates in Combination with Novel Technologies (Efficient Hydrolysis, Fermentation, and Product Recovery Technologies) | 565 | ||
| Solution to the AB Problems: Where are We Now? | 565 | ||
| Economic Scenarios | 565 | ||
| Conclusions | 566 | ||
| Further Reading | 567 | ||
| Sterilization and Disinfection | 568 | ||
| Glossary | 568 | ||
| Abbreviations | 568 | ||
| Defining Statement | 569 | ||
| Introduction | 569 | ||
| General Considerations | 569 | ||
| Physical Disinfection and Sterilization | 572 | ||
| Chemical Disinfection and Sterilization | 575 | ||
| An Introduction to Biocide Resistance | 583 | ||
| Concluding Remarks | 586 | ||
| Further Reading | 587 | ||
| Vitamins and Vitamin-like Compounds: Microbial Production | 588 | ||
| Glossary | 588 | ||
| Abbreviations | 588 | ||
| Defining Statement | 588 | ||
| Applications and Market | 588 | ||
| Fat-Soluble Compounds | 591 | ||
| Water-Soluble Vitamins | 593 | ||
| Conclusions and Outlook | 598 | ||
| Further Reading | 600 | ||
| Wastewater Treatment (not infectious hazards) | 601 | ||
| Glossary | 601 | ||
| Defining Statement | 601 | ||
| Wastewater in Public Water Supplies | 601 | ||
| Chemical Constituents in Untreated Wastewater | 603 | ||
| Impact of Chemical Constituents Remaining after Wastewater Treatment | 604 | ||
| Further Reading | 606 | ||
| Water Treatment, Industrial | 608 | ||
| Glossary | 608 | ||
| Abbreviations | 608 | ||
| Defining Statement | 609 | ||
| Biological Treatment of Industrial Wastewater | 609 | ||
| Characteristics of Industrial Wastewater | 609 | ||
| Aerobic | 611 | ||
| Anaerobic | 617 | ||
| Coupled Anaerobic/Aerobic Treatment Processes | 620 | ||
| Natural Treatment: Wetlands | 620 | ||
| Coupled Biological with Chemical or Physical Treatment | 622 | ||
| Conclusion | 622 | ||
| Further Reading | 625 | ||
| Relevant Websites | 625 | ||
| Water Treatment, Municipal | 626 | ||
| Glossary | 626 | ||
| Abbreviations | 626 | ||
| Defining Statement | 626 | ||
| Introduction | 626 | ||
| Wastewater Treatment | 628 | ||
| Case Studies in Italy and Cyprus: Reuse Practices | 634 | ||
| Further Reading | 637 | ||
| Xylanases | 639 | ||
| Glossary | 639 | ||
| Abbreviations | 639 | ||
| Defining Statement | 639 | ||
| Introduction | 640 | ||
| Structure of Xylan | 640 | ||
| Properties of Xylanases | 640 | ||
| Production of Xylanases | 642 | ||
| Purification of Xylanases | 643 | ||
| Mode of Action of Xylanases | 644 | ||
| Application of Xylanases | 644 | ||
| Conclusions | 650 | ||
| Further Reading | 651 | ||
| e9780123739391v2 | 652 | ||
| Cover | 652 | ||
| Tilte page | 655 | ||
| Copyright page | 656 | ||
| Dedication | 657 | ||
| Preface | 659 | ||
| Editor in Chief | 661 | ||
| Editors | 663 | ||
| List Of Contributors | 665 | ||
| Contents | 681 | ||
| ARCHAEA | 691 | ||
| Archaea (overview) | 691 | ||
| Glossary | 691 | ||
| Abbreviations | 692 | ||
| Defining Statement | 692 | ||
| Introduction | 692 | ||
| Historical Recognition | 692 | ||
| Archaeal Ecology and EnvironmentalBiology | 696 | ||
| Novel Molecular and GeneticCharacteristics of Archaea | 703 | ||
| Archaeal Genomics | 707 | ||
| Biotechnological Applications of Archaea | 711 | ||
| Conclusion | 712 | ||
| Further Reading | 712 | ||
| BACTERIA | 715 | ||
| Actinobacteria | 716 | ||
| Glossary | 716 | ||
| Abbreviations | 716 | ||
| Defining Statement | 716 | ||
| Introduction | 716 | ||
| Systematics of Actinobacteria | 717 | ||
| Phylogeny of Actinobacteria | 722 | ||
| Genome Structure and Evolution | 728 | ||
| Industrially Important Phenotypes of | 731 | ||
| Concluding Remarks | 734 | ||
| Further Reading | 734 | ||
| Relevant Website | 734 | ||
| Bacillus Subtilis | 735 | ||
| Glossary | 735 | ||
| Abbreviations | 735 | ||
| Defining Statement | 735 | ||
| Genetic Analysis | 736 | ||
| Nutrients | 737 | ||
| Regulation | 737 | ||
| Growth and Division | 738 | ||
| The Transition State | 739 | ||
| Spore Formation | 741 | ||
| Germination and Outgrowth | 744 | ||
| Stress Responses | 745 | ||
| Summary | 745 | ||
| Further Reading | 746 | ||
| Relevant Websites | 746 | ||
| Caulobacter | 747 | ||
| Glossary | 747 | ||
| Abbreviation | 747 | ||
| Defining Statement | 747 | ||
| Caulobacter and Caulobacters | 747 | ||
| Development in Caulobacter crescentus | 754 | ||
| Further Reading | 763 | ||
| Chlamydia | 764 | ||
| Glossary | 764 | ||
| Abbreviations | 764 | ||
| Defining Statement | 764 | ||
| Introduction | 765 | ||
| Taxonomy | 765 | ||
| Developmental Cycle | 765 | ||
| Intracellular Survival | 767 | ||
| Secreted Effectors/Virulence Factors | 769 | ||
| Host Tropism | 772 | ||
| Clinical Disease, Diagnosis, andTreatment | 773 | ||
| Conclusion | 775 | ||
| Further Reading | 776 | ||
| Clostridia | 777 | ||
| Glossary | 777 | ||
| Abbreviation | 777 | ||
| Defining Statement | 777 | ||
| Introduction | 777 | ||
| Properties of Clostridia | 779 | ||
| Medical Importance and IndustrialApplications of Clostridia | 781 | ||
| Conclusions | 783 | ||
| Further Reading | 783 | ||
| Corynebacteria (including diphtheria) | 784 | ||
| Glossary | 784 | ||
| Abbreviations | 784 | ||
| Defining Statement | 784 | ||
| Introduction | 784 | ||
| Nonpathogenic Corynebacterium Species | 785 | ||
| Corynebacterium diphtheriae | 786 | ||
| Pathogenic Corynebacteria other than C. diphtheriae | 794 | ||
| Summary | 796 | ||
| Further Reading | 796 | ||
| Cyanobacteria | 797 | ||
| Glossary | 797 | ||
| Abbreviations | 797 | ||
| Defining Statement | 797 | ||
| Introduction | 797 | ||
| Biodiversity: Taxonomy and Phylogeny | 798 | ||
| Cytology and Morphogenesis | 801 | ||
| Physiology and Metabolism | 805 | ||
| Molecular Genetics | 810 | ||
| Ecology and Adaptations | 811 | ||
| Fossil Record and Evolutionary History | 813 | ||
| Commercial Use and Applications | 814 | ||
| Further Reading | 814 | ||
| Escherichia Coli | 815 | ||
| Glossary | 815 | ||
| Abbreviations | 815 | ||
| Defining Statement | 815 | ||
| Introduction | 815 | ||
| Taxonomy | 815 | ||
| Ecology | 816 | ||
| Structure and Function of Cell Parts | 816 | ||
| Metabolism and Growth | 819 | ||
| Pathogenesis | 820 | ||
| Principles of Diagnosis Using Clinical Specimens | 822 | ||
| Further Reading | 822 | ||
| Relevant Website | 822 | ||
| Gram-Negative Cocci, Pathogenic | 823 | ||
| Glossary | 823 | ||
| Abbreviations | 823 | ||
| Defining Statement | 824 | ||
| Infection by Neisseria meningitidisand Neisseria gonorrhoeae | 824 | ||
| Molecular Mechanisms of Infection | 825 | ||
| Antigens | 826 | ||
| Natural Immunity | 831 | ||
| Prevention | 832 | ||
| Conclusion | 834 | ||
| Further Reading | 834 | ||
| Gram-Negative Opportunistic Anaerobes: Friends and Foes | 835 | ||
| Glossary | 835 | ||
| Abbreviations | 835 | ||
| Defining Statement | 835 | ||
| The Complex Relationship Between the Normal Human Microbiota and Human Disease | 835 | ||
| Human Colonic Bacteroides Species in Health and Disease | 838 | ||
| Koch’s Postulates and Microbiota Shift Diseases (Dysbiosis) | 841 | ||
| Common Themes | 841 | ||
| Further Reading | 842 | ||
| Haemophilus Influenzae | 843 | ||
| Glossary | 843 | ||
| Abbreviations | 843 | ||
| Defining Statement | 843 | ||
| Introduction | 843 | ||
| Taxonomy, Morphology, and Cultural Conditions | 843 | ||
| Virulence Factors | 844 | ||
| Antigenic Variation | 847 | ||
| Development of Competence | 849 | ||
| Colonization | 849 | ||
| Biofilm Formation | 850 | ||
| Infections Caused by H. influenzae | 851 | ||
| Further Reading | 852 | ||
| Helicobacter Pylori | 853 | ||
| Glossary | 853 | ||
| Abbreviations | 853 | ||
| Historical Introduction | 854 | ||
| Microbiology | 854 | ||
| Epidemiology | 856 | ||
| Diseases Associated with H. pylori | 857 | ||
| Diagnosis | 858 | ||
| Treatment | 858 | ||
| Vaccine Development | 858 | ||
| Conclusions | 858 | ||
| Further Reading | 858 | ||
| Legionella, Bartonella, Haemophilus | 860 | ||
| Glossary | 860 | ||
| Abbreviations | 860 | ||
| Defining Statement | 860 | ||
| Introduction | 861 | ||
| Legionella | 861 | ||
| Bartonella | 865 | ||
| Haemophilus | 868 | ||
| Conclusion | 871 | ||
| Further Reading | 871 | ||
| Relevant Website | 871 | ||
| Listeria Monocytogenes | 872 | ||
| Abbreviations | 872 | ||
| Defining Statement | 872 | ||
| Listeriology: An Historical Perspective | 872 | ||
| Taxonomy | 872 | ||
| Bacteriological Characterization | 873 | ||
| Listeriosis | 875 | ||
| Infection Cycle of L. monocytogenes and Molecular Mechanisms of Cell Subversion | 878 | ||
| Regulation of Virulence Factors | 884 | ||
| Genomics and Postgenomics | 886 | ||
| Conclusion and Perspectives | 887 | ||
| Further Reading | 888 | ||
| Lyme Disease | 889 | ||
| Glossary | 889 | ||
| Abbreviations | 889 | ||
| Defining Statement | 889 | ||
| History | 889 | ||
| Organisms | 890 | ||
| Ecology | 892 | ||
| Epidemiology | 892 | ||
| Clinical Manifestations | 893 | ||
| Pathogenesis | 894 | ||
| Diagnosis, Treatment, and Prevention | 896 | ||
| Further Reading | 896 | ||
| Mycoplasma and Spiroplasma | 898 | ||
| Glossary | 898 | ||
| Abbreviations | 898 | ||
| Defining Statement | 898 | ||
| Introduction | 898 | ||
| The Systematics of the Mollicutes | 899 | ||
| Biochemistry of the Mollicutes | 902 | ||
| Genetics and Molecular Biology of the Mollicutes | 905 | ||
| Accompanying Feature | 909 | ||
| Further Reading | 909 | ||
| Myxococcus | 910 | ||
| Glossary | 910 | ||
| Abbreviations | 910 | ||
| Defining Statement | 910 | ||
| The Origin of Myxobacteria | 910 | ||
| Predation | 912 | ||
| Cell Movement | 914 | ||
| Responding to Starvation | 924 | ||
| Fruiting Body Morphogenesis | 925 | ||
| Coupling Gene Expression to Morphogenesis | 930 | ||
| Conclusions | 933 | ||
| Further Reading | 933 | ||
| Pseudomonas | 935 | ||
| Glossary | 935 | ||
| Abbreviations | 935 | ||
| Defining Statement | 935 | ||
| Introduction | 936 | ||
| Human Pathogens | 936 | ||
| Plant Pathogens | 943 | ||
| Environmental Aspects of Pseudomonas | 944 | ||
| Genetic and Molecular Tools Used to Study Pseudomonas | 948 | ||
| Biotechnology | 950 | ||
| Further Reading | 950 | ||
| Rhizobia | 951 | ||
| Glossary | 951 | ||
| Abbreviations | 951 | ||
| Defining Statement | 951 | ||
| Nitrogen Fixation in Legumes and Its Global Significance | 951 | ||
| Phylogeny and Taxonomy | 953 | ||
| Rhizobial Host Ranges | 954 | ||
| Development of the Symbiosis | 955 | ||
| Physiology of Rhizobial Symbiotic Nitrogen Fixation | 959 | ||
| Rhizobial Genes and Components Required in Symbiosis | 961 | ||
| Rhizobial Genomes and Genetics | 963 | ||
| Other Properties of the Rhizobia | 965 | ||
| Further Reading | 967 | ||
| Spirochetes | 968 | ||
| Glossary | 968 | ||
| Abbreviations | 968 | ||
| Defining Statement | 968 | ||
| Overview | 968 | ||
| Treponema | 971 | ||
| Borrelia | 974 | ||
| Brachyspira | 976 | ||
| Leptospira | 978 | ||
| Conclusions | 981 | ||
| Further Reading | 981 | ||
| Staphylococcus | 983 | ||
| Glossary | 983 | ||
| Abbreviations | 983 | ||
| Defining Statement | 983 | ||
| Taxonomy | 983 | ||
| Cellular Structure | 984 | ||
| Molecular Structure | 985 | ||
| Coagulase-Negative Versus Coagulase-Positive Staphylococci | 988 | ||
| Pathogenesis and Disease | 989 | ||
| Virulence Factors | 991 | ||
| Further Reading | 993 | ||
| Streptococcus Pneumoniae | 994 | ||
| Abbreviations | 994 | ||
| Defining Statement | 994 | ||
| Guides to the S. pneumoniae Literature | 994 | ||
| Pneumococcus as a Pathogen and as a Model Microbe for Molecular Biology | 994 | ||
| Burden of Pneumococcal Disease | 995 | ||
| The Natural Reservoir of S. pneumoniae | 996 | ||
| Stages in Pneumococcal Pathogenesis: Virulence Factors and Host Defense | 997 | ||
| Human Intervention | 999 | ||
| Impact of the Seven-Valent Pneumococcal Conjugate Vaccine on Pneumococcal Disease and Carriage | 1001 | ||
| Day Care Center Studies | 1003 | ||
| Genetic Exchange In Vivo | 1003 | ||
| Genome Sequencing | 1004 | ||
| Pneumococcal Cell Wall: Composition, Structure and Mechanisms of Replication during Cell Division | 1005 | ||
| PostScript | 1007 | ||
| Acknowledgments | 1007 | ||
| Further Reading | 1007 | ||
| Relevant Website | 1007 | ||
| Streptomyces | 1008 | ||
| Glossary | 1008 | ||
| Abbreviations | 1008 | ||
| Defining Statement | 1008 | ||
| Introduction | 1009 | ||
| The Genome | 1010 | ||
| Cell Biology | 1012 | ||
| Metabolism | 1014 | ||
| Regulation | 1018 | ||
| Conclusion | 1021 | ||
| Further Reading | 1022 | ||
| Relevant Websites | 1022 | ||
| Tuberculosis: Molecular Basis of Pathogenesis | 1023 | ||
| Glossary | 1023 | ||
| Abbreviations | 1023 | ||
| Defining Statement | 1023 | ||
| Overview | 1023 | ||
| TB Pathogenesis | 1024 | ||
| Bacterial Factors Involved in TB Pathogenesis | 1024 | ||
| TB Latency | 1028 | ||
| Drug Resistance and Pathogenesis | 1028 | ||
| Conclusions | 1028 | ||
| Further Reading | 1029 | ||
| CELL STRUCTURE CHEMICAL COMPOSITION | 1031 | ||
| Cell Membrane, Prokaryotic | 1031 | ||
| Glossary | 1031 | ||
| Abbreviations | 1032 | ||
| Defining Statement | 1032 | ||
| Introduction | 1032 | ||
| Membrane Fluidity | 1033 | ||
| Bacterial CMs | 1033 | ||
| Gram-Negative Bacterial OMs | 1036 | ||
| OMs of Acid-Fast Gram-Positive Bacteria | 1039 | ||
| Archaeal Membranes | 1043 | ||
| Conclusions | 1045 | ||
| Further Reading | 1045 | ||
| Cell Structure, Organization, Bacteria and Archaea | 1047 | ||
| Glossary | 1047 | ||
| Abbreviations | 1047 | ||
| Defining Statement | 1048 | ||
| Characteristics of Prokaryotes | 1048 | ||
| Cell Envelope – Appendages | 1050 | ||
| Cell Envelope | 1055 | ||
| Cytoplasm | 1060 | ||
| The Nucleoid | 1062 | ||
| Further Reading | 1064 | ||
| Development, Prokaryotic: Variety and Versatility | 1065 | ||
| Glossary | 1065 | ||
| Abbreviations | 1065 | ||
| Defining Statement | 1065 | ||
| Introduction | 1065 | ||
| Differentiation Leading to Dormancy | 1066 | ||
| Differentiation Leading to Nutrient Acquisition | 1073 | ||
| Differentiation Leading to Cell Dispersal | 1076 | ||
| Conclusion | 1081 | ||
| Further Reading | 1081 | ||
| Flagella, Prokaryotic | 1083 | ||
| Glossary | 1083 | ||
| Abbreviations | 1083 | ||
| Defining Statement | 1083 | ||
| Structure | 1083 | ||
| Function | 1088 | ||
| Genetics | 1089 | ||
| Morphological Pathway | 1091 | ||
| Conclusion | 1093 | ||
| Further Reading | 1093 | ||
| Relevant Website | 1093 | ||
| Intracellular Structures of Prokaryotes: Inclusions, Compartmentsand Assemblages | 1094 | ||
| Glossary | 1094 | ||
| Abbreviations | 1094 | ||
| Defining Statement | 1095 | ||
| Introduction | 1095 | ||
| Structures as Metabolic Machinery | 1095 | ||
| Structures as Contributors to Cell Mobility | 1103 | ||
| Structures as Metabolic Reserves | 1105 | ||
| Further Reading | 1113 | ||
| Localization, Macromolecular, Intracellular | 1115 | ||
| Glossary | 1115 | ||
| Abbreviation | 1115 | ||
| Defining Statement | 1115 | ||
| The First Wave: Midcell and Pole | 1115 | ||
| The Fluorescent Protein Revolution | 1116 | ||
| Cytoskeleton | 1116 | ||
| The Restless Walker A Cytoskeletal ATPases | 1119 | ||
| The Ends Justify the Means | 1121 | ||
| The Division Site | 1123 | ||
| Chromosome Dynamics | 1124 | ||
| Lipid Domains and Spirals | 1126 | ||
| Localization of Metabolic Components | 1126 | ||
| New Imaging Technologies | 1127 | ||
| Conclusions | 1127 | ||
| Further Reading | 1127 | ||
| Outer Membrane, Gram-Negative Bacteria | 1129 | ||
| Glossary | 1129 | ||
| Abbreviations | 1129 | ||
| Defining Statement | 1129 | ||
| Composition, Structure, and Functions of Outer Membrane | 1130 | ||
| Biosynthesis and Assembly of Outer-Membrane Components | 1135 | ||
| Periplasm | 1138 | ||
| Functional Complexes Involving Multiple Components of the Cell Envelope | 1139 | ||
| Mycobacterial Cell Envelope | 1141 | ||
| Further Reading | 1142 | ||
| Peptidoglycan (Murein) | 1143 | ||
| Glossary | 1143 | ||
| Abbreviations | 1143 | ||
| Defining Statement | 1143 | ||
| Introduction | 1143 | ||
| Peptidoglycan Chemical Composition | 1146 | ||
| Biosynthesis of Peptidoglycan Monomer Units | 1148 | ||
| Polymerization of Peptidoglycan | 1151 | ||
| Postinsertional Metabolism of Peptidoglycan | 1155 | ||
| Biophysical Properties of Peptidoglycan Sacculi | 1157 | ||
| Concluding Remarks | 1158 | ||
| Further Reading | 1158 | ||
| Pili, Fimbriae | 1160 | ||
| Glossary | 1160 | ||
| Abbreviations | 1160 | ||
| Defining Statement | 1160 | ||
| Historical Perspective and Classification of Pili | 1161 | ||
| Chaperone/Usher Pathway | 1161 | ||
| Alternate Chaperone Pathway | 1169 | ||
| Type II Secretion Pathway for Type IV Pilus Assembly | 1169 | ||
| Conjugative Pilus Assembly Pathway | 1172 | ||
| Extracellular Nucleation/Precipitation Pathway | 1174 | ||
| Type III Secretion Pathway | 1175 | ||
| Pili in Gram-Positive Bacteria | 1176 | ||
| Regulation of Pilus Biogenesis | 1178 | ||
| Role of Pili in Disease Processes | 1178 | ||
| Further Reading | 1179 | ||
| e9780123739391v3 | 1181 | ||
| Cover | 1181 | ||
| Title page | 1184 | ||
| Copyright page | 1185 | ||
| Dedication | 1186 | ||
| Preface | 1188 | ||
| Editor in Chief | 1190 | ||
| Editors | 1192 | ||
| List Of Contributors | 1194 | ||
| Contents | 1210 | ||
| ENVIRONMENTAL MICROBIOLOGY AND ECOLOGY | 1220 | ||
| Adhesion, Microbial | 1221 | ||
| Glossary | 1221 | ||
| Abbreviations | 1221 | ||
| Defining Statement | 1221 | ||
| Introduction | 1221 | ||
| Biological Significance of Microbial Adhesion | 1222 | ||
| Mechanisms of Microbial Adhesion | 1223 | ||
| Selected Survey of Specific Adhesion Strategies | 1224 | ||
| Consequences of Microbial Adhesion in Human Disease | 1227 | ||
| Targeting Adhesion to Inhibit Bacterial Virulence | 1228 | ||
| Acknowledgments | 1229 | ||
| Further Reading | 1229 | ||
| Aeromicrobiology/Air Quality | 1230 | ||
| Abbreviations | 1230 | ||
| Defining Statement | 1230 | ||
| Introduction | 1230 | ||
| Microbial Sources, and Spatial and Temporal Distributions | 1231 | ||
| Analyses | 1238 | ||
| Meteorology | 1238 | ||
| Atmospheric Microbial Sampler Methods and Sampler Sources | 1239 | ||
| Further Reading | 1245 | ||
| Algal Blooms | 1246 | ||
| Glossary | 1246 | ||
| Abbreviations | 1246 | ||
| Defining Statement | 1246 | ||
| Introduction | 1246 | ||
| Major Contributors to Algal Blooms | 1249 | ||
| Pathogens and Grazers of Algal Blooms | 1253 | ||
| Recurrent and Unusual Algal Blooms | 1254 | ||
| Harmful Algal Blooms | 1257 | ||
| Iron-Fertilized Blooms | 1258 | ||
| Future Research Avenues | 1259 | ||
| Acknowledgments | 1260 | ||
| Further Reading | 1260 | ||
| Relevant Websites | 1260 | ||
| Bacteriophage Ecology | 1261 | ||
| Glossary | 1261 | ||
| Abbreviations | 1262 | ||
| Defining Statement | 1262 | ||
| Introduction | 1262 | ||
| Phage Environmental Microbiology | 1263 | ||
| Phage Population Ecology | 1268 | ||
| Phage Impact on Communities | 1272 | ||
| Phage Impact on Ecosystems | 1275 | ||
| Further Reading | 1276 | ||
| Biofilms, Microbial | 1277 | ||
| Glossary | 1277 | ||
| Abbreviations | 1277 | ||
| Defining Statement | 1277 | ||
| Biofilm Structure and Function | 1277 | ||
| Biofilms in Natural Ecosystems | 1279 | ||
| Biofilms in Industrial Ecosystems | 1280 | ||
| Biofilms in Medical Systems | 1280 | ||
| Postlude | 1281 | ||
| Summary | 1281 | ||
| Further Reading | 1282 | ||
| Deep Sub-Surface | 1283 | ||
| Glossary | 1283 | ||
| Abbreviations | 1283 | ||
| Defining Statement | 1284 | ||
| Introduction and Background | 1284 | ||
| Prokaryotic Cell Concentrations and Distributions in Subseafloor Sediments | 1284 | ||
| Prokaryotic Metabolic Processes and Energy Sources | 1288 | ||
| Deep Biosphere Biodiversity | 1289 | ||
| Deep Biosphere Hot Spots | 1295 | ||
| Significance of the Deep Biosphere | 1297 | ||
| Further Reading | 1298 | ||
| Deep-Sea Hydrothermal Vents | 1299 | ||
| Glossary | 1299 | ||
| Abbreviations | 1299 | ||
| Defining Statement | 1300 | ||
| Mid-Ocean Ridge Hydrothermal Vents | 1300 | ||
| The Chemosynthetic Basis of Life at Hydrothermal Vents | 1301 | ||
| Chemolithoautotrophic Bacteria | 1303 | ||
| Heterotrophic Vent Bacteria | 1304 | ||
| Hyperthermophilic Archaea | 1304 | ||
| Comparison to Terrestrial Hot Springs | 1306 | ||
| Unusual Hydrothermal Vents: Loihi, Guaymas, Lost City | 1307 | ||
| Further Reading | 1309 | ||
| Ecology, Microbial | 1310 | ||
| Glossary | 1310 | ||
| Abbreviations | 1310 | ||
| Defining Statement | 1310 | ||
| What Is Microbial Ecology? | 1310 | ||
| Principles of Microbial Ecology | 1315 | ||
| Strategic Approaches to the Study of Microbial Ecology | 1322 | ||
| Future of Microbial Ecology | 1324 | ||
| Further Reading | 1325 | ||
| Extremophiles: Acidic Environments | 1326 | ||
| Glossary | 1326 | ||
| Abbreviations | 1326 | ||
| Defining Statement | 1326 | ||
| Nature and Origin of Extremely Acidic Environments | 1326 | ||
| Biodiversity of Extreme Acidophiles | 1330 | ||
| Interactions Between Acidophilic Microorganisms | 1335 | ||
| Microbial Ecology of Extremely Acidic Environments | 1338 | ||
| Outlook and Applications | 1344 | ||
| Further Reading | 1345 | ||
| Extremophiles: Hot Environments | 1346 | ||
| Glossary | 1346 | ||
| Abbreviations | 1346 | ||
| Defining Statement | 1346 | ||
| Introduction | 1346 | ||
| Discovery: Life at High Temperatures | 1347 | ||
| Taxonomy | 1347 | ||
| Mechanisms of Thermostability | 1349 | ||
| Upper Temperature Limit of Life | 1350 | ||
| Metabolism and Growth | 1351 | ||
| Relationship between Organisms and their Environment | 1364 | ||
| Further Reading | 1365 | ||
| Extremophiles: Cold Environments | 1366 | ||
| Glossary | 1366 | ||
| Defining Statement | 1366 | ||
| Discovery of Cold-Adapted Microbes | 1366 | ||
| Evolution of Cold Adaptation | 1371 | ||
| Molecular Basis for Cold Adaptation | 1373 | ||
| Conclusion: A Model Habitat for Cold Adaptation | 1376 | ||
| Further Reading | 1376 | ||
| Extremophiles: Dry Environments (including Cryptoendoliths) | 1378 | ||
| Glossary | 1378 | ||
| Abbreviations | 1378 | ||
| Defining Statement | 1378 | ||
| Introduction | 1378 | ||
| Microbial Associations in Arid Regions | 1379 | ||
| Adaptations to the Environment | 1387 | ||
| Further Reading | 1392 | ||
| Food Webs, Microbial | 1393 | ||
| Glossary | 1393 | ||
| Abbreviations | 1393 | ||
| Defining Statement | 1393 | ||
| Introduction | 1393 | ||
| Understanding Microbial Food Webs | 1394 | ||
| Components and Pathways | 1394 | ||
| Microbes in Aquatic Food Webs | 1396 | ||
| Marine Pelagic Habitats | 1399 | ||
| Benthic Habitats | 1399 | ||
| Role of Microbial Food Webs in Biogeochemical Cycling | 1401 | ||
| Food Resource for Metazoans | 1402 | ||
| Modeling Microbial Food Webs | 1403 | ||
| Chemical Interactions between Microbes | 1406 | ||
| Spatial Structure of Microbial Food Webs | 1407 | ||
| Further Reading | 1407 | ||
| Freshwater Habitats | 1409 | ||
| Glossary | 1409 | ||
| Abbreviations | 1409 | ||
| Defining Statement | 1409 | ||
| Overview | 1409 | ||
| Freshwater Wetlands | 1410 | ||
| Lakes | 1413 | ||
| Streams and Rivers | 1417 | ||
| Comparison Among Freshwater Habitats | 1423 | ||
| Further Reading | 1423 | ||
| Heavy Metals Cycle (Arsenic, Mercury, Selenium, others) | 1424 | ||
| Glossary | 1424 | ||
| Abbreviations | 1425 | ||
| Defining Statement | 1425 | ||
| Introduction | 1425 | ||
| 33As75 | 1426 | ||
| 29Cu63 | 1433 | ||
| 25Mn55 | 1435 | ||
| 34Se80 | 1437 | ||
| Acknowledgments | 1437 | ||
| Further Reading | 1438 | ||
| Relevant Website | 1438 | ||
| Heavy Metals, Bacterial Resistance | 1439 | ||
| Glossary | 1439 | ||
| Abbreviations | 1439 | ||
| Defining Statement | 1439 | ||
| Flavors of Arsenic and Its Resistance | 1440 | ||
| Mercury and Organomercurial Resistance | 1442 | ||
| Silver Resistance | 1444 | ||
| Cadmium Resistance | 1445 | ||
| Chromate Resistance | 1445 | ||
| Other Bacterial Toxic Metal Resistance Systems | 1446 | ||
| Further Reading | 1446 | ||
| High-Pressure Habitats | 1447 | ||
| Glossary | 1447 | ||
| Abbreviations | 1447 | ||
| Introduction | 1447 | ||
| Historical and Current Background | 1447 | ||
| Instruments to Survey and Sample Microorganisms in High-Pressure Habitats | 1451 | ||
| High-Pressure Apparatus for Laboratory Studies of Microorganisms | 1452 | ||
| Distribution of Bacteria and Archaea in High-Pressure Habitats | 1453 | ||
| Properties of High-Pressure Inhabitants | 1454 | ||
| Further Reading | 1458 | ||
| Low-Nutrient Environments | 1459 | ||
| Glossary | 1459 | ||
| Abbreviations | 1459 | ||
| Defining Statement | 1459 | ||
| Oligotrophic Aquatic Habitats | 1459 | ||
| Extreme Habitats | 1465 | ||
| Oligotrophic Cultivation | 1467 | ||
| The Niche of Oligotrophic Bacteria in Low-Nutrient-Flux Aquatic Habitats | 1475 | ||
| Further Reading | 1475 | ||
| Marine Habitats | 1477 | ||
| Glossary | 1477 | ||
| Abbreviations | 1477 | ||
| Defining Statement | 1478 | ||
| Introduction | 1478 | ||
| Nature of Marine Microbial Life | 1479 | ||
| Structure and Classification of Marine Macrohabitats | 1480 | ||
| Marine Microbial Inhabitants and Their Growth Requirements | 1484 | ||
| Distribution, Abundance, and Biogeography of Marine Microbes | 1485 | ||
| Sunlight, Nutrients, Turbulence, and the Biological Pump | 1486 | ||
| Time Variability of Marine Habitats and Climate Change | 1488 | ||
| Summary and Prospectus | 1495 | ||
| Acknowledgments | 1495 | ||
| Further Reading | 1495 | ||
| Relevant Websites | 1496 | ||
| Mats, Microbial | 1497 | ||
| Glossary | 1497 | ||
| Abbreviations | 1499 | ||
| Defining Statement | 1499 | ||
| Introduction | 1499 | ||
| Habitat Distribution | 1500 | ||
| Comprehensive Investigations | 1505 | ||
| Case Studies of Selected Microbial Mat Ecosystems | 1505 | ||
| Stresses Experienced by Microbial Mats | 1507 | ||
| Concluding Remarks | 1510 | ||
| Further Reading | 1510 | ||
| Methanotrophy/methane oxidation | 1512 | ||
| Abbreviations | 1512 | ||
| Defining Statement | 1512 | ||
| Introduction | 1512 | ||
| Ecology and Taxonomy of Methanotrophs | 1512 | ||
| Physiology and Biochemistry of Methanotrophs | 1514 | ||
| Methanotrophs in Biotechnology | 1515 | ||
| Postgenomics of Methanotrophs | 1516 | ||
| Further Reading | 1517 | ||
| Nitrogen Cycle | 1518 | ||
| Glossary | 1518 | ||
| Abbreviations | 1518 | ||
| Defining Statement | 1519 | ||
| Introduction | 1519 | ||
| The Biological Nitrogen Cycle | 1519 | ||
| Ammonium Assimilation | 1522 | ||
| Nitrogen Fixation | 1526 | ||
| Nitrate Assimilation | 1528 | ||
| Denitrification | 1531 | ||
| Nitrification | 1534 | ||
| Anammox | 1536 | ||
| Other Processes of the Nitrogen Cycle | 1537 | ||
| Ecological and Environmental Aspects of the Nitrogen Cycle | 1538 | ||
| Evolution of the Nitrogen Cycle | 1539 | ||
| Further Reading | 1540 | ||
| Phosphorus Cycle | 1541 | ||
| Glossary | 1541 | ||
| Abbreviations | 1541 | ||
| Defining Statement | 1541 | ||
| Introduction | 1542 | ||
| Microbially Mediated Processes | 1546 | ||
| Genetic Regulation of Microbially Mediated Processes | 1551 | ||
| Anthropogenic Alteration of the P Cycle: Eutrophication in Aquatic Ecosystems | 1552 | ||
| Conclusion | 1553 | ||
| Further Reading | 1553 | ||
| Rhizosphere | 1554 | ||
| Glossary | 1554 | ||
| Abbreviations | 1554 | ||
| Defining Statement | 1555 | ||
| Historical Description of the Rhizosphere | 1555 | ||
| General Characteristics of the Rhizosphere | 1555 | ||
| Root Exudation and Rhizodeposition in the Rhizosphere | 1557 | ||
| The Volume and Spatial Scale of the Rhizosphere | 1557 | ||
| Direct Microscopy of Microbial Colonization of Roots | 1558 | ||
| Advancements in Rhizosphere Studies Using Modern Technologies | 1559 | ||
| Effects of Microbial Rhizosphere Communities on Plants | 1566 | ||
| Closing Remarks | 1567 | ||
| Acknowledgments | 1568 | ||
| Further Reading | 1568 | ||
| Sediment Habitats, Including Watery | 1569 | ||
| Glossary | 1569 | ||
| Abbreviations | 1569 | ||
| Defining Statement | 1569 | ||
| Introduction | 1569 | ||
| The Diversity of Sediments | 1571 | ||
| Sampling and Description of Sediments | 1571 | ||
| Sediment Properties | 1572 | ||
| Sediments as Habitats for Microbes | 1573 | ||
| Chemical Profiles in Sediments (Layered Microbial Communities) | 1574 | ||
| Nutrient-Poor Sedimentary Environments | 1578 | ||
| Sediments in Shallow Water, and the Impact of Light | 1578 | ||
| Conclusions | 1579 | ||
| Further Reading | 1579 | ||
| Sulfur Cycle | 1580 | ||
| Glossary | 1580 | ||
| Abbreviations | 1580 | ||
| Defining Statement | 1580 | ||
| Planetary Sulfur Fluxes | 1580 | ||
| The Microbial Sulfur Cycle | 1582 | ||
| Sulfur Cycling within the Ecosystems | 1585 | ||
| Environmental Consequences and Technological Applications | 1585 | ||
| Further Reading | 1588 | ||
| EVOLUTION AND SYSTEMATICS | 1589 | ||
| Evolution, Viral | 1589 | ||
| Glossary | 1589 | ||
| Abbreviations | 1589 | ||
| Defining Statement | 1589 | ||
| Introduction | 1589 | ||
| Viral Diversity and the Antiquity of Microbial Viruses | 1590 | ||
| Evolution of Viruses and Their Impact on Cellular Evolution | 1598 | ||
| The Origin of Viruses | 1602 | ||
| DNA Viruses and the Origin of Modern Cells | 1605 | ||
| Conclusion | 1607 | ||
| Further Reading | 1608 | ||
| Paleontology, Microbial | 1609 | ||
| Glossary | 1609 | ||
| Abbreviation | 1609 | ||
| Defining Statement | 1609 | ||
| Fossil Evidence of Ancient Microbes | 1609 | ||
| Stromatolites: Lithified Microbial Mats | 1611 | ||
| Cellular Microbial Fossils | 1611 | ||
| Fossil Evidence of Microbial History | 1618 | ||
| Further Reading | 1618 | ||
| FUNGI | 1620 | ||
| Aspergillus: A Multifaceted Genus | 1620 | ||
| Abbreviations | 1620 | ||
| Defining Statement | 1620 | ||
| Note | 1620 | ||
| What is Aspergillus? | 1620 | ||
| Food Contamination by Aspergilli | 1622 | ||
| Aspergillus as Pathogens | 1622 | ||
| Useful Aspergilli | 1626 | ||
| A. (Emericella) nidulans as a Model\rOrganism | 1627 | ||
| The Genus Aspergillus in the Genomic Era | 1639 | ||
| Further Reading | 1640 | ||
| Relevant Websites | 1640 | ||
| Clavicipitaceae: Free-Living and Saprotrophs to Plant Endophytes | 1641 | ||
| Glossary | 1641 | ||
| Defining Statement | 1642 | ||
| Introduction | 1642 | ||
| Free-Living Saprotrophs and Insect Parasites | 1642 | ||
| Species on Soft-Bodied Scale Insects | 1642 | ||
| Plant Biotrophs | 1642 | ||
| Chemical Diversity in the Clavicipitaceae | 1646 | ||
| Biological Activities of Secondary Metabolites | 1646 | ||
| Economic, Agricultural, and Ecological Importance of Clavicipitacious Endophytes | 1647 | ||
| Origin and Evolution of Ergot Alkaloids | 1647 | ||
| The Proposal of Functionality for Ergot Alkaloids | 1648 | ||
| The Evidence for Defensive Mutualism in the Clavicipitaceae Endophyte/Grass Association | 1648 | ||
| The Defensive Mutualism Controversy: A Debate Regarding Function | 1648 | ||
| Evolution of Defensive Mutualism from Self-Defense to Host Defense | 1649 | ||
| Conclusion | 1649 | ||
| Acknowledgments | 1649 | ||
| Further Reading | 1649 | ||
| Endophytic Microbes | 1650 | ||
| Glossary | 1650 | ||
| Abbreviation | 1650 | ||
| Defining Statement | 1650 | ||
| Introduction | 1650 | ||
| Bacterial Endophytes | 1651 | ||
| Fungal Endophytes | 1652 | ||
| Some Common Endophyte–Grass Associations | 1655 | ||
| Ecological Impacts of Endophytes | 1656 | ||
| Endophytes as Sources of Bioactive Metabolites | 1658 | ||
| Conclusion | 1661 | ||
| Acknowledgments | 1661 | ||
| Further Reading | 1661 | ||
| Entomogenous Fungi | 1662 | ||
| Glossary | 1662 | ||
| Abbreviations | 1663 | ||
| Defining Statement | 1663 | ||
| Introduction | 1663 | ||
| Infection Processes and Pathobiology | 1664 | ||
| Practical Uses of Entomogenous Fungi | 1669 | ||
| A Look Forward for Entomogenous Fungi | 1673 | ||
| Further Reading | 1675 | ||
| Fungi: Plant Pathogenic | 1676 | ||
| Glossary | 1676 | ||
| Abbreviations | 1676 | ||
| Defining Statement | 1676 | ||
| Introduction | 1676 | ||
| Fungal Characteristics | 1677 | ||
| Symptoms of Plant Disease Caused by Fungi | 1682 | ||
| Pathogen Groups | 1684 | ||
| Diagnosis | 1694 | ||
| Control | 1695 | ||
| Further Reading | 1696 | ||
| Yeasts | 1697 | ||
| Glossary | 1697 | ||
| Abbreviations | 1697 | ||
| Defining Statement | 1697 | ||
| Definition and Classification of Yeasts | 1698 | ||
| Yeast Ecology | 1698 | ||
| Yeast Cell Structure | 1699 | ||
| Nutrition, Metabolism, and Growth of Yeasts | 1701 | ||
| Yeast Genetics | 1706 | ||
| Industrial, Agricultural, and Medical Importance of Yeasts | 1707 | ||
| Further Reading | 1710 | ||
| GENETICS, GENOMICS | 1712 | ||
| Chromosome Replication and Segregation | 1712 | ||
| Glossary | 1712 | ||
| Abbreviations | 1713 | ||
| Defining Statement | 1713 | ||
| Introduction | 1713 | ||
| Prokaryotic and Eukaryotic Chromosomes: Replication Origin Placement and Initiation Timing | 1714 | ||
| Features of Microbial Replication Origins and Origin DNA–Protein Complexes | 1715 | ||
| Limiting Initiation to Once per Cell Cycle and Replication Origin Resetting | 1720 | ||
| Chromosome Segregation Systems in Prokaryotic and Eukaryotic Microbes | 1721 | ||
| Further Reading | 1725 | ||
| Chromosome, Bacterial | 1726 | ||
| Glossary | 1726 | ||
| Abbreviations | 1726 | ||
| Defining Statement | 1726 | ||
| Historical Introduction | 1726 | ||
| Chromosome Form and Number | 1727 | ||
| Gene Arrangements | 1728 | ||
| Recombination | 1729 | ||
| DNA Twisting, Folding, and Bending | 1730 | ||
| Chromosome Inactivation | 1732 | ||
| Chromosome Duplication and Segregation | 1733 | ||
| Chromosome Packaging Dynamics | 1734 | ||
| Concluding Remarks | 1735 | ||
| Acknowledgments | 1735 | ||
| Further Reading | 1735 | ||
| Conjugation, Bacterial | 1736 | ||
| Glossary | 1736 | ||
| Abbreviations | 1736 | ||
| Defining Statement | 1736 | ||
| Introduction | 1736 | ||
| Conjugative Process | 1737 | ||
| Physiological Factors | 1738 | ||
| Conjugative Elements | 1738 | ||
| Gram-Negative Conjugation | 1740 | ||
| Gram-Positive Conjugation | 1746 | ||
| Mobilization | 1747 | ||
| Transfer to Plants | 1748 | ||
| Evolutionary Relationships | 1749 | ||
| Conjugation in Natural Environments | 1749 | ||
| Further Reading | 1750 | ||
| DNA Mismatch Repair, Bacterial | 1751 | ||
| Glossary | 1751 | ||
| Abbreviations | 1751 | ||
| Defining Statement | 1751 | ||
| Introduction | 1751 | ||
| Mechanism | 1752 | ||
| Some Roles of Mismatch Repair Systems in Vivo | 1753 | ||
| Fine Structure Recombination | 1753 | ||
| Specificity of One Short-Patch Repair System | 1753 | ||
| Localized Repair of A:G and C:T Mismatches | 1754 | ||
| Localized Repair of A:C and G:T Mismatches | 1755 | ||
| Other Mismatches | 1755 | ||
| Further Reading | 1755 | ||
| DNA Restriction and Modification | 1757 | ||
| Glossary | 1757 | ||
| Abbreviations | 1758 | ||
| Introduction | 1758 | ||
| Detection of Restriction Systems | 1758 | ||
| Nomenclature and Classification | 1759 | ||
| R-M Enzymes as Model Systems | 1762 | ||
| Control and Alleviation of Restriction | 1764 | ||
| Distribution, Diversity, and Evolution | 1765 | ||
| Biological Significance | 1767 | ||
| Applications and Commercial Relevance | 1767 | ||
| Further Reading | 1768 | ||
| Relevant Website | 1768 | ||
| Evolution, Theory and Experiments with Microorganisms | 1769 | ||
| Glossary | 1769 | ||
| Abbreviations | 1769 | ||
| Defining Statement | 1769 | ||
| Review of Evolutionary Theory | 1769 | ||
| Experimental Tests of Fundamental Principles | 1771 | ||
| Genetic and Physiological Bases of Fitness | 1772 | ||
| Genetic Variation within Populations | 1776 | ||
| Coevolution of Interacting Genomes and Species | 1778 | ||
| Evolution of New Metabolic Functions | 1780 | ||
| Evolution of Genetic Systems | 1780 | ||
| Further Reading | 1783 | ||
| Genetically Modified Organisms: Guidelines and Regulations for Research | 1784 | ||
| Glossary | 1784 | ||
| Abbreviations | 1784 | ||
| Defining Statement | 1785 | ||
| Introduction | 1785 | ||
| Concern over GMOs | 1785 | ||
| History of US Guidelines and Regulations Applicable to GMOs | 1786 | ||
| Compliance and Approvals for Contained Research under NIH Guidelines | 1788 | ||
| Compliance and Approvals for Research with Planned Introduction into the Environment | 1789 | ||
| Oversight Mechanisms | 1790 | ||
| Appropriateness of Guidelines and Regulations | 1791 | ||
| Needs, Challenges, and Options | 1794 | ||
| Future Benefits and Concerns | 1795 | ||
| Further Reading | 1795 | ||
| Relevant Website | 1796 | ||
| Genetics, Microbial (general) | 1797 | ||
| Glossary | 1797 | ||
| Abbreviations | 1797 | ||
| Defining Statement | 1797 | ||
| What is Microbial Genetics? | 1797 | ||
| Microbial Genomes on the Earth | 1798 | ||
| Changes in Genomes | 1798 | ||
| Gene Transfer | 1801 | ||
| Evolution | 1801 | ||
| Further Reading | 1805 | ||
| Horizontal Gene Transfer: Uptake of Extracellular DNA by Bacteria | 1806 | ||
| Glossary | 1806 | ||
| Abbreviations | 1806 | ||
| Defining Statement | 1806 | ||
| Process of Natural Uptake of Extracellular DNA in Bacteria | 1806 | ||
| Uptake of Extracellular DNA by Bacteria Present in Various Environments | 1808 | ||
| Some Limitations of the DNA Uptake Model Systems Used | 1811 | ||
| Factors Affecting the Stable Uptake of DNA in Single Bacterial Cells | 1812 | ||
| Considerations of the Long-Term Persistence of Horizontally Acquired DNA in Bacterial Populations | 1813 | ||
| Predictors of DNA Uptake in Bacteria and Implications for the Release of Genetically Modified Microbes | 1814 | ||
| Further Reading | 1815 | ||
| Horizontal Transfer of Genes between Microorganisms | 1816 | ||
| Glossary | 1816 | ||
| Abbreviations | 1816 | ||
| Defining Statement | 1816 | ||
| Thinking about Genes, Not Genotypes | 1817 | ||
| How Genes Reproduce Horizontally | 1818 | ||
| Describing, Predicting, and Understanding HGT | 1820 | ||
| Horizontal Epigenes | 1825 | ||
| Acknowledgments | 1825 | ||
| Further Reading | 1825 | ||
| Metabolic Reconstruction | 1826 | ||
| Glossary | 1826 | ||
| Abbreviations | 1826 | ||
| Defining Statement | 1827 | ||
| Introduction | 1827 | ||
| Metabolic Reconstruction: The Principles | 1827 | ||
| From Genome Sequence to a Draft Biochemical Network | 1828 | ||
| Refinement of a Draft Biochemical Network | 1834 | ||
| Conclusion | 1840 | ||
| Acknowledgments | 1840 | ||
| Further Reading | 1840 | ||
| Relevant Websites | 1840 | ||
| Metagenomics | 1841 | ||
| Glossary | 1841 | ||
| Abbreviations | 1841 | ||
| Defining Statement | 1841 | ||
| Introduction | 1841 | ||
| Building Metagenomic Libraries | 1842 | ||
| Sequence-Based Metagenomic Analysis | 1844 | ||
| Function-Based Metagenomic Analysis | 1847 | ||
| Further Reading | 1851 | ||
| Phylogenomics | 1852 | ||
| Glossary | 1852 | ||
| Abbreviations | 1852 | ||
| Defining Statement | 1852 | ||
| Introduction | 1853 | ||
| Basic Concepts and Principles of Phylogenetic Inference | 1853 | ||
| Phylogenomic Inference Based on Primary Sequences | 1855 | ||
| Supermatrices and Systematic Errors | 1857 | ||
| Phylogenomic Inference Based on Whole Genome Features | 1858 | ||
| Contribution of Phylogenomics to the Microbial Tree | 1860 | ||
| Conclusion | 1862 | ||
| Further Reading | 1862 | ||
| Plasmids, Bacterial | 1863 | ||
| Glossary | 1863 | ||
| Abbreviations | 1863 | ||
| Defining Statement | 1863 | ||
| Impact of Plasmid Research on Molecular Biology | 1863 | ||
| Plasmid Structures and DNA Synthesis | 1864 | ||
| Resolution and Distribution of Newly Replicated Plasmid DNA | 1871 | ||
| Horizontal Plasmid Transfer by Conjugation | 1877 | ||
| Further Reading | 1884 | ||
| Relevant Websites | 1884 | ||
| Transduction: Host DNA Transfer by Bacteriophages | 1885 | ||
| Glossary | 1885 | ||
| Abbreviations | 1885 | ||
| Defining Statement | 1885 | ||
| Introduction | 1885 | ||
| Specialized Transduction | 1886 | ||
| Generalized Transduction | 1889 | ||
| Variations on Transduction | 1894 | ||
| Transduction as a Genetic Tool | 1895 | ||
| Transduction in the Environment | 1897 | ||
| Conclusion | 1898 | ||
| Further Reading | 1898 | ||
| Transposable Elements | 1899 | ||
| Glossary | 1899 | ||
| Abbreviations | 1899 | ||
| Defining Statement | 1899 | ||
| Introduction | 1899 | ||
| The Advent of In Vitro Transposition Systems | 1903 | ||
| Genome-Wide Knockout Analyses | 1903 | ||
| Transposable Element-Based Deletion Studies | 1904 | ||
| Targeting Individual Genes | 1904 | ||
| Conclusion | 1908 | ||
| Further Reading | 1908 | ||
| e9780123739391v4 | 1910 | ||
| Cover\r | 1910 | ||
| Title Page | 1913 | ||
| Copyright Page | 1914 | ||
| Dedication | 1915 | ||
| Preface | 1917 | ||
| Editor in Chief | 1919 | ||
| Editors | 1921 | ||
| List of Contributors | 1923 | ||
| Contents | 1939 | ||
| HISTORY AND CULTURE, (AND BIOGRAPHIES) | 1949 | ||
| AIDS, Historical | 1949 | ||
| Glossary | 1949 | ||
| Abbreviations | 1950 | ||
| Defining Statement | 1950 | ||
| Introduction | 1950 | ||
| Pathophysiology of HIV and AIDS | 1950 | ||
| Origins and Spread of HIV | 1951 | ||
| Emergence and Recognition of AIDS | 1953 | ||
| AIDS Before Effective Treatment: Fear and Blame | 1954 | ||
| The Development of Effective Treatments | 1957 | ||
| The Challenge of Providing Care | 1959 | ||
| Further Reading | 1963 | ||
| Biographies | 1965 | ||
| Glossary | 1965 | ||
| Abbreviations | 1965 | ||
| Defining Statement | 1965 | ||
| Introduction | 1965 | ||
| Genres of Scientific Biography | 1965 | ||
| Standard Biographical Sources | 1967 | ||
| Conclusion | 1967 | ||
| Further Reading | 1971 | ||
| Relevant Websites | 1971 | ||
| Cholera, Historical | 1972 | ||
| Glossary | 1972 | ||
| Defining Statement | 1972 | ||
| Etymological Considerations | 1972 | ||
| Pathogenesis, Signs, and Symptoms | 1973 | ||
| Etiology | 1973 | ||
| The Pandemics | 1974 | ||
| Control, Prevention, and Treatment | 1976 | ||
| Cholera and Society | 1976 | ||
| Further Reading | 1977 | ||
| History of Microbiology | 1978 | ||
| Glossary | 1978 | ||
| Abbreviations | 1979 | ||
| Defining Statement | 1979 | ||
| Introduction | 1979 | ||
| Microscopy in the Seventeenth Century | 1979 | ||
| Spontaneous Generation and Microbes | 1980 | ||
| Classification of Microbes | 1981 | ||
| Contagion | 1982 | ||
| Germ Theories | 1983 | ||
| Applications of the Germ Theories | 1985 | ||
| Antimicrobial Therapies | 1987 | ||
| Public Health | 1987 | ||
| Clinical Microbiology | 1987 | ||
| Agricultural Microbiology | 1988 | ||
| Virology | 1988 | ||
| Microbial Physiology | 1990 | ||
| Microbial Genetics | 1991 | ||
| Bacterial Transformation and DNA | 1993 | ||
| Physiological Genetics | 1994 | ||
| Further Reading | 1995 | ||
| Methods, Philosophy of | 1996 | ||
| Glossary | 1996 | ||
| Abbreviations | 1996 | ||
| Defining Statement | 1996 | ||
| Scientific Method in General | 1996 | ||
| Scientific Method in Biology; Objective Truth and Scientific Progress | 1997 | ||
| Specific but Philosophically General Methods of Experimental Inquiry | 1999 | ||
| Microbiology: Its Scope and Subject Areas; Representative Illustrations of the Philosophy of Method | 2000 | ||
| Further Reading | 2005 | ||
| Plague, Historical | 2006 | ||
| Glossary | 2006 | ||
| Defining Statement | 2006 | ||
| Introduction | 2006 | ||
| Recent Debates about Historical Plagues | 2006 | ||
| Plague in Late Antiquity | 2008 | ||
| Plague in Europe, 1347–c. 1550 | 2009 | ||
| Evolution of Plague Containment and Surveillance Practices, 1400–1900 | 2013 | ||
| Modern Plague, 1894 to the Present | 2017 | ||
| Further Reading | 2020 | ||
| Smallpox, Historical | 2021 | ||
| Glossary | 2021 | ||
| Abbreviations | 2021 | ||
| Defining Statement | 2021 | ||
| Introduction | 2021 | ||
| History | 2022 | ||
| Smallpox, the Disease | 2023 | ||
| The Global Eradication Campaign | 2024 | ||
| Posteradication | 2026 | ||
| Further Reading | 2027 | ||
| Spontaneous Generation | 2028 | ||
| Glossary | 2028 | ||
| Introduction | 2028 | ||
| Early History | 2029 | ||
| The Needham/Spallanzani Controversy | 2030 | ||
| Worms, Molecules, and Evolution | 2033 | ||
| The Role of Louis Pasteur | 2033 | ||
| The British Debate of the 1870s: Darwin, Spontaneous Generation, and the Germ Theory of Disease | 2035 | ||
| Twentieth Century Ideas | 2037 | ||
| Further Reading | 2038 | ||
| Syphilis, Historical | 2039 | ||
| Glossary | 2039 | ||
| Abbreviation | 2039 | ||
| Defining Statement | 2039 | ||
| Introduction | 2039 | ||
| The Origins of Syphilis | 2039 | ||
| The History of a Disease | 2040 | ||
| Managing Syphilis | 2041 | ||
| The Limits of Biomedicine | 2042 | ||
| Further Reading | 2044 | ||
| Typhoid, Historical | 2045 | ||
| Glossary | 2045 | ||
| Defining Statement | 2045 | ||
| Background and History | 2045 | ||
| Taxonomy and Classification | 2046 | ||
| Prevention and Treatment | 2046 | ||
| Epidemiology | 2047 | ||
| Further Reading | 2047 | ||
| Typhus Fevers and Other Rickettsial Diseases, Historical | 2048 | ||
| Abbreviations | 2048 | ||
| Defining Statement | 2048 | ||
| Introduction | 2048 | ||
| Rickettsia and Human Rickettsioses | 2049 | ||
| Epidemic Typhus | 2051 | ||
| Murine Typhus | 2055 | ||
| Rocky Mountain Spotted Fever | 2059 | ||
| Mediterranean Spotted Fever | 2062 | ||
| African Tick Bite Fever | 2065 | ||
| Other Rickettsioses | 2066 | ||
| Conclusion | 2067 | ||
| Further Reading | 2067 | ||
| MUTUALISM AND COMMENSALISM | 2069 | ||
| Behavior Modification of Host by Microbes | 2069 | ||
| Glossary | 2069 | ||
| Abbreviations | 2070 | ||
| Defining Statement | 2070 | ||
| Diversity of Systems | 2070 | ||
| Immune versus Non-immune-Mediated Behavioral Alterations | 2070 | ||
| Nervous System Substrates | 2071 | ||
| Methods for Studying Microbial Effects on Behavior | 2073 | ||
| Methodological Issues | 2074 | ||
| Conclusion | 2074 | ||
| Further Reading | 2075 | ||
| Endosymbionts and Intracellular Parasites | 2076 | ||
| Glossary | 2076 | ||
| Abbreviation | 2076 | ||
| Defining Statement | 2076 | ||
| Chronic Microbial Infections of Eukaryotes | 2076 | ||
| Functional Significance of Endosymbionts | 2077 | ||
| Transmission of Microbial Symbionts and Parasites | 2083 | ||
| Persistence of Associations | 2086 | ||
| Further Reading | 2089 | ||
| Lichens | 2090 | ||
| Glossary | 2090 | ||
| Defining Statement | 2090 | ||
| Further Reading | 2100 | ||
| Mycorrhizae | 2101 | ||
| Glossary | 2101 | ||
| Abbreviation | 2101 | ||
| Defining Statement | 2101 | ||
| Introduction | 2101 | ||
| Types of Mycorrhizae | 2102 | ||
| Mycorrhizal Function | 2104 | ||
| Ecology of Mycorrhizae | 2106 | ||
| Mycorrhizae and Plant Production | 2107 | ||
| Mycorrhizae and Pollution | 2108 | ||
| Further Reading | 2110 | ||
| Relevant Websites | 2110 | ||
| Rumen | 2111 | ||
| Glossary | 2111 | ||
| Abbreviations | 2111 | ||
| Defining Statement | 2111 | ||
| Introduction | 2111 | ||
| Recognition of Ruminal Fermentation | 2112 | ||
| Rumen as a Microbial Habitat | 2112 | ||
| Polymer Degradation | 2113 | ||
| Ruminal Acidosis | 2113 | ||
| Effect of pH on Ruminal Microorganisms | 2113 | ||
| Transport and Phosphorylation | 2114 | ||
| Crossfeeding among Ruminal Microorganisms | 2114 | ||
| Ruminal Fermentation Schemes | 2114 | ||
| Growth, Maintenance, and Energy Spilling | 2115 | ||
| Toxic Compounds | 2116 | ||
| Effects of Ionophores on Ruminal Microorganisms | 2118 | ||
| Genetic Engineering | 2118 | ||
| Rumen Microbial Ecology | 2119 | ||
| Ruminal Bacteria and Nonculturable Bacteria | 2119 | ||
| Genomics | 2119 | ||
| Ruminal Protozoa | 2121 | ||
| Ruminal Fungi | 2121 | ||
| Models of Ruminal Fermentation | 2121 | ||
| Further Reading | 2121 | ||
| Relevant Website | 2122 | ||
| PATHOGENESIS | 2123 | ||
| Airborne Infectious Microorganisms | 2124 | ||
| Glossary | 2124 | ||
| Abbreviations | 2124 | ||
| Defining Statement | 2125 | ||
| Introduction | 2125 | ||
| Bioaerosols | 2125 | ||
| Infectious Airborne Viruses | 2126 | ||
| Infectious Airborne Bacteria | 2128 | ||
| Infectious Airborne Fungi | 2129 | ||
| Airborne Bioterrorism | 2130 | ||
| Further Reading | 2130 | ||
| Aminoglycosides, Bioactive Bacterial Metabolites | 2131 | ||
| Glossary | 2131 | ||
| Abbreviations | 2131 | ||
| Defining Statement | 2131 | ||
| Structural Classes and Sources | 2134 | ||
| Target Sites and General Effects on Cells | 2134 | ||
| Biosynthetic Pathways and Genetics | 2136 | ||
| Clinical Relevance and Resistance | 2139 | ||
| Perspectives | 2140 | ||
| Further Reading | 2140 | ||
| Antibiotic Resistance | 2141 | ||
| Glossary | 2141 | ||
| Abbreviations | 2141 | ||
| Defining Statement | 2142 | ||
| Introduction | 2142 | ||
| Antibiotic Classes | 2142 | ||
| Antibiotic Resistance | 2143 | ||
| Mechanisms of Resistance | 2143 | ||
| Acquisition of Resistance | 2148 | ||
| Biochemistry of Resistance | 2148 | ||
| Genetics of Resistance | 2150 | ||
| Antibiotics Can Act as Pheromones | 2151 | ||
| Biological Cost of Antibiotic Resistance | 2151 | ||
| Conclusion | 2152 | ||
| Further Reading | 2152 | ||
| Antifungal Agents | 2153 | ||
| Glossary | 2153 | ||
| Abbreviations | 2153 | ||
| Defining Statement | 2153 | ||
| Introduction | 2153 | ||
| The Polyenes | 2154 | ||
| Griseofulvin | 2160 | ||
| Cycloheximide | 2160 | ||
| Pyrrolnitrin, Fenpiclonil, and Fludioxonil | 2160 | ||
| The Synthetic Pyrimidines | 2161 | ||
| The Azoles | 2161 | ||
| The Allylamines | 2166 | ||
| The Benzylamines, Thiocarbamates, and Dithiocarbamates | 2166 | ||
| The Benzimidazoles and Methylbenzimidazole Carbamates | 2166 | ||
| The Morpholines | 2167 | ||
| The Pyridines | 2167 | ||
| The Echinocandins, Pneumocandins, and Papulocandins | 2167 | ||
| The Pradimicins and Benanomycins | 2169 | ||
| The Polyoxins and Nikkomycins | 2169 | ||
| The Sordarins | 2170 | ||
| Dimethomorph and Fluazinam | 2170 | ||
| The Phthalimides | 2170 | ||
| Other Antifungal Approaches | 2170 | ||
| Further Reading | 2170 | ||
| Antiviral Agents | 2171 | ||
| Glossary | 2171 | ||
| Abbreviations | 2172 | ||
| Defining Statement | 2172 | ||
| Introduction | 2172 | ||
| Therapeutics for Herpesvirus Infections | 2173 | ||
| Therapeutics for Respiratory Virus Infections | 2181 | ||
| Therapeutics for Hepatitis | 2185 | ||
| Therapeutics for Papillomavirus | 2190 | ||
| Therapeutics for Enteroviral Infections | 2190 | ||
| Anti-HIV Agents | 2191 | ||
| Summary | 2205 | ||
| Acknowledgments | 2205 | ||
| Further Reading | 2205 | ||
| Bacteriophage Therapy: Past and Present | 2206 | ||
| Glossary | 2206 | ||
| Abbreviations | 2206 | ||
| Introduction | 2206 | ||
| Phage Isolation and Selection | 2210 | ||
| Physiological Considerations in Developing Therapeutic Phage Cocktails | 2212 | ||
| Impediments to Broad Implementation of Human Phage Therapy | 2212 | ||
| Further Reading | 2213 | ||
| Bacteriophage Therapy: Potential and Problems | 2215 | ||
| Glossary | 2215 | ||
| Abbreviations | 2215 | ||
| Defining Statement | 2215 | ||
| Potential | 2215 | ||
| Problems | 2217 | ||
| Application | 2219 | ||
| Further Reading | 2221 | ||
| Beta-Lactam Antibiotics | 2222 | ||
| Glossary | 2222 | ||
| Abbreviations | 2222 | ||
| Defining Statement | 2222 | ||
| Classical and Novel Beta-Lactam Families | 2222 | ||
| Clavams | 2228 | ||
| Carbapenems | 2232 | ||
| Monocyclic Beta-Lactams | 2233 | ||
| Resistance Genes in Bacterial beta-Lactam Clusters | 2236 | ||
| Further Reading | 2237 | ||
| Cyanobacterial Toxins | 2238 | ||
| Glossary | 2238 | ||
| Abbreviations | 2238 | ||
| Defining Statement | 2239 | ||
| Cyanobacteria: General Description | 2239 | ||
| Mass Occurrences of Toxic Cyanobacteria | 2239 | ||
| Cyanobacterial Toxins | 2239 | ||
| Toxin Producers | 2246 | ||
| The Biogenesis of Cyanobacterial Toxins | 2248 | ||
| Detection Methods for Cyanotoxins | 2250 | ||
| Factors Influencing Toxin Production | 2251 | ||
| Why Do Cyanobacteria Produce Toxins? | 2253 | ||
| Health Risks Caused by Toxic Cyanobacteria | 2254 | ||
| Prevention of Problems Caused by Toxic Cyanobacteria | 2255 | ||
| Further Reading | 2255 | ||
| Diagnostic Microbiology | 2256 | ||
| Glossary | 2256 | ||
| Abbreviations | 2256 | ||
| Defining Statement | 2257 | ||
| Development of Diagnostic Microbiology | 2257 | ||
| Direct Identification of Microorganisms | 2258 | ||
| Microorganism Culture and Identification | 2260 | ||
| Measurement of Host Responses to Infection | 2262 | ||
| Molecular Techniques in Diagnostic Microbiology | 2263 | ||
| Molecular Diagnosis and Monitoring | 2265 | ||
| Concluding Remarks | 2268 | ||
| Further Reading | 2268 | ||
| Emerging Infections | 2269 | ||
| Glossary | 2269 | ||
| Abbreviations | 2269 | ||
| A 30-Year Perspective | 2269 | ||
| Misplaced Optimism | 2272 | ||
| Public Health Weakness Facilitating Emergence and Reemergence | 2272 | ||
| Globalization | 2274 | ||
| Solutions | 2274 | ||
| Further Reading | 2275 | ||
| Relevant Websites | 2276 | ||
| Enteropathogenic Infections | 2277 | ||
| Glossary | 2277 | ||
| Abbreviations | 2277 | ||
| Defining Statement | 2278 | ||
| Introduction | 2278 | ||
| Infections Caused by Preformed Toxins in the Absence of Bacterial Colonization | 2280 | ||
| Infections Caused by Bacterial Colonization through Attachment | 2281 | ||
| Infections Caused by Bacterial Colonization through Invasion | 2285 | ||
| References | 2290 | ||
| Epidemiological Concepts and Historical Examples | 2292 | ||
| Glossary | 2292 | ||
| Abbreviations | 2292 | ||
| Defining Statement | 2292 | ||
| Introduction | 2292 | ||
| The Scope and Viewpoint of Epidemiology | 2293 | ||
| Bias in Epidemiological Studies | 2294 | ||
| Causation and Epidemiology | 2294 | ||
| Modes of Transmission | 2295 | ||
| Epidemiology and Public Health | 2296 | ||
| Sanitation | 2296 | ||
| Immunization | 2296 | ||
| Epidemiological Models | 2296 | ||
| Historical Examples | 2297 | ||
| Further Reading | 2302 | ||
| Exotoxins | 2303 | ||
| Glossary | 2303 | ||
| Abbreviations | 2303 | ||
| Defining Statement | 2304 | ||
| Classification of Exotoxins | 2304 | ||
| General Properties of Exotoxins | 2306 | ||
| Conversion of Exotoxins into Toxoids | 2309 | ||
| Therapeutic Applications of Exotoxins | 2310 | ||
| Other Classes of Bacterial Toxins | 2311 | ||
| Further Reading | 2312 | ||
| Relevant Websites | 2312 | ||
| Food and Waterborne Illnesses | 2313 | ||
| Abbreviations | 2313 | ||
| Defining Statement | 2313 | ||
| Introduction | 2313 | ||
| Current Foodborne Illnesses Epidemiology | 2314 | ||
| Specific Foodborne Microorganisms | 2317 | ||
| Foodborne Illness due to Preformed Toxins | 2317 | ||
| Natural Toxins | 2318 | ||
| Scombroid | 2318 | ||
| Ciguatera | 2319 | ||
| Shellfish Poisoning | 2319 | ||
| Tetrodotoxin | 2319 | ||
| Aflatoxins | 2319 | ||
| Foodborne Microbes that Produce Toxins following Ingestion | 2320 | ||
| Infant Botulism | 2321 | ||
| Foodborne Infections that Cause Disease by Mechanisms other than Toxin Production | 2321 | ||
| Actions to Prevent Foodborne Illness | 2327 | ||
| Further Reading | 2329 | ||
| Relevant Websites | 2329 | ||
| Fungal Infections, Cutaneous | 2330 | ||
| Glossary | 2330 | ||
| Abbreviations | 2330 | ||
| Defining Statement | 2330 | ||
| Cutaneous Host Defenses | 2330 | ||
| Description of the Diseases | 2332 | ||
| Further Reading | 2336 | ||
| Fungal Infections, Systemic | 2337 | ||
| Glossary | 2337 | ||
| Abbreviations | 2337 | ||
| Defining Statement | 2337 | ||
| Introduction | 2337 | ||
| Classification of Pathogenic Fungi | 2338 | ||
| Host Defenses against Fungal Infections | 2339 | ||
| Molecular Approaches for Studying Fungal Pathogenesis | 2341 | ||
| Common Fungal Diseases | 2344 | ||
| Summary and Conclusion | 2359 | ||
| Further Reading | 2359 | ||
| Fungicides and other Chemical Approaches for use in Plant Disease Control | 2360 | ||
| Glossary | 2360 | ||
| Abbreviations | 2360 | ||
| Defining Statement | 2361 | ||
| Introduction | 2361 | ||
| Multisite Mode-of-Action Fungicides | 2361 | ||
| Single-Site Mode-of-Action Fungicides | 2362 | ||
| Fungicide Resistance | 2363 | ||
| Reduced-Risk and Minimum-Risk Fungicides | 2364 | ||
| Plant Activators | 2365 | ||
| Natural Products and Natural Product–Derived Fungicides | 2366 | ||
| Biopesticides | 2367 | ||
| Fungicides for Organic Crop Production | 2367 | ||
| Chemical Fumigants and Biofumigants | 2367 | ||
| Case History on Chemical Control | 2368 | ||
| Further Reading | 2369 | ||
| Gastrointestinal Microbiology in the Normal Host | 2370 | ||
| Glossary | 2370 | ||
| Abbreviations | 2370 | ||
| Defining Statement | 2370 | ||
| Problems Associated with the Study of Gastrointestinal Flora | 2370 | ||
| Techniques for Study of Gastrointestinal Flora | 2371 | ||
| Normal Flora of Esophagus | 2372 | ||
| Normal Flora of Stomach | 2372 | ||
| Normal Flora of Small Intestine | 2372 | ||
| Normal Flora of Colon | 2373 | ||
| Addendum | 2391 | ||
| Further Reading | 2391 | ||
| Global Burden of Infectious Diseases | 2392 | ||
| Glossary | 2392 | ||
| Abbreviations | 2393 | ||
| Defining Statement | 2393 | ||
| The Global Burden of Disease Study | 2393 | ||
| The Global Burden of Infectious Diseases: Main Findings | 2394 | ||
| Policy Implications | 2400 | ||
| Further Reading | 2402 | ||
| Glycopeptides, Antimicrobial | 2403 | ||
| Glossary | 2403 | ||
| Abbreviations | 2403 | ||
| Defining Statement | 2403 | ||
| Discovery and Uses of Glycopeptides | 2406 | ||
| Mechanism of Action | 2409 | ||
| Mechanism of Resistance | 2410 | ||
| The Producing Strains | 2412 | ||
| Biosynthesis of Glycopeptides | 2412 | ||
| Expanding Chemical Diversity | 2417 | ||
| Further Reading | 2419 | ||
| Immune Suppression | 2420 | ||
| Glossary | 2420 | ||
| Abbreviations | 2420 | ||
| Defining Statement | 2420 | ||
| Historical Perspective | 2420 | ||
| Types of Treg | 2421 | ||
| Suppressor Mechanisms | 2423 | ||
| Role of Treg in Autoimmune Diseases | 2425 | ||
| Control of Tumor and Transplantation Immunity by Treg | 2427 | ||
| Treg and Immunity to Infectious Agents | 2427 | ||
| Manipulation of Treg Function | 2428 | ||
| Further Reading | 2428 | ||
| Immunity | 2429 | ||
| Glossary | 2429 | ||
| Abbreviations | 2430 | ||
| Defining Statement | 2430 | ||
| Introduction | 2430 | ||
| Definitions | 2431 | ||
| Immunocytes (Figure 1) | 2431 | ||
| Trafficking | 2433 | ||
| Fundamentals of Innate Immunity | 2434 | ||
| Acquired Immunity | 2437 | ||
| Antigen Processing and Antigen Presentation | 2439 | ||
| MHC Restriction | 2440 | ||
| B Cell Responses | 2444 | ||
| Complement | 2444 | ||
| Patterns of Regulation in Immunology | 2445 | ||
| Allergy and Autoimmunity | 2446 | ||
| Vaccines | 2446 | ||
| Further Reading | 2447 | ||
| Infectious Waste Management | 2448 | ||
| Glossary | 2448 | ||
| Abbreviations | 2448 | ||
| Defining Statement | 2448 | ||
| Sources of Infectious Waste | 2448 | ||
| Health Risks from Pathogens in BW | 2449 | ||
| Waste Management Strategies | 2452 | ||
| Treatment Options for BW to be Recycled to Arable Land | 2454 | ||
| Biological Treatments | 2455 | ||
| Physical Treatments | 2456 | ||
| Chemical Treatments | 2457 | ||
| Spread and Persistence in the Environment of Infective Agents Originating from BW | 2457 | ||
| Conclusions | 2459 | ||
| Further Reading | 2459 | ||
| Lipopolysaccharides (Endotoxins) | 2461 | ||
| Glossary | 2461 | ||
| Abbreviations | 2461 | ||
| Defining Statement | 2462 | ||
| Lipopolysaccharide Structure | 2462 | ||
| Biosynthesis and Assembly of Lipopolysaccharides | 2465 | ||
| Functions and Biological Activities of Lipopolysaccharides | 2470 | ||
| Further Reading | 2475 | ||
| Relevant Websites | 2476 | ||
| Macrolides | 2477 | ||
| Glossary | 2477 | ||
| Abbreviations | 2477 | ||
| Defining Statement | 2477 | ||
| Nomenclature, Structures, and Classification | 2478 | ||
| Clinical Uses, Pharmacological Properties, and Side Effects of Macrolides | 2480 | ||
| Mechanism of Action | 2483 | ||
| Resistance | 2488 | ||
| Biosynthesis | 2491 | ||
| Rational Approaches to Design and Production of Novel Macrolides | 2499 | ||
| Future Prospects | 2504 | ||
| Further Reading | 2506 | ||
| Mycotoxins | 2507 | ||
| Glossary | 2507 | ||
| Abbreviations | 2507 | ||
| Defining Statement | 2507 | ||
| Poisons and Toxins | 2508 | ||
| A Primer in Toxicology | 2508 | ||
| A Bewildering Diversity of Substrates, Mycotoxin-Producing Fungi, and Physiological Effects | 2509 | ||
| Related Topics in Mycotoxicology | 2510 | ||
| Biosynthesis, Molecular Biology, and Genomics | 2511 | ||
| Mycotoxin Detection, Prevention, and Regulation | 2512 | ||
| Conclusion | 2513 | ||
| Further Reading | 2513 | ||
| Oral Microbiology | 2514 | ||
| Glossary | 2514 | ||
| Abbreviations | 2514 | ||
| Defining Statement | 2514 | ||
| Human Oral Microbiology | 2515 | ||
| Characteristics of the Oral Environment | 2515 | ||
| Microbial Interactions in Oral Biofilms | 2519 | ||
| Oral Diseases | 2527 | ||
| Strategies for Disease Control | 2535 | ||
| Further Reading | 2536 | ||
| Plant Disease Resistance: Natural, Non-Host Innate or Inducible | 2537 | ||
| Glossary | 2537 | ||
| Abbreviations | 2538 | ||
| Defining Statement | 2538 | ||
| Crop Losses | 2538 | ||
| Plant Disease Resistance | 2538 | ||
| Natural Resistance Mechanisms | 2538 | ||
| Vertical Resistance | 2539 | ||
| Horizontal Resistance | 2539 | ||
| Hypersensitivity (Local lesion) | 2539 | ||
| Natural Genetic Resistance | 2540 | ||
| Somaclones | 2541 | ||
| Tolerance | 2541 | ||
| Plant Resistance to Insect Vectors | 2541 | ||
| Pathogen-Derived Resistance | 2542 | ||
| Nonstructural Viral Proteins | 2542 | ||
| Defective Interfering RNA or DNA | 2543 | ||
| Antisense/Ribozyme | 2543 | ||
| Satellite RNA | 2543 | ||
| Other Approaches to Transgenic Resistance | 2544 | ||
| Further Reading | 2544 | ||
| Plant Disease Resistance: Breeding and Transgenic Approaches | 2545 | ||
| Glossary | 2545 | ||
| Defining Statement | 2545 | ||
| General Introduction | 2545 | ||
| Resistance | 2546 | ||
| GM Regulations | 2548 | ||
| Cisgenic Strategy for Late Blight Resistance in Potato | 2553 | ||
| Perspectives | 2559 | ||
| Further Reading | 2560 | ||
| Relevant Websites | 2560 | ||
| Plant Pathogens and Disease: General Introduction | 2561 | ||
| Glossary | 2561 | ||
| Abbreviations | 2561 | ||
| Defining Statement | 2561 | ||
| Introduction: Causes of Disease in Plants | 2561 | ||
| Pathogens that Cause Disease in Plants | 2561 | ||
| Interactions of Pathogens, Plants, and Humans | 2585 | ||
| Conclusion | 2593 | ||
| Further Reading | 2593 | ||
| Plant Pathogens and Disease: Newly Emerging Diseases | 2595 | ||
| Glossary | 2595 | ||
| Defining Statement | 2595 | ||
| Introduction | 2595 | ||
| Where Disease Emergence Stems from Simple Ecological Changes in Distribution | 2596 | ||
| Where Disease Emergence Stems from Genetic Change in Pathogens | 2599 | ||
| Where Disease Emergence Stems from Environmental Change | 2600 | ||
| Can We Predict the Identity of Future Emerging Diseases? | 2601 | ||
| Countering Invasive Plant Diseases | 2601 | ||
| Conclusions | 2602 | ||
| Further Reading | 2602 | ||
| Plant Pathogens, Bacterial | 2603 | ||
| Glossary | 2603 | ||
| Abbreviations | 2604 | ||
| Defining Statement | 2604 | ||
| Introduction | 2604 | ||
| History, Etiology | 2604 | ||
| Symptoms of Bacterial Infection on Plants | 2605 | ||
| Pathogen Identification, Disease Diagnosis, and Management | 2606 | ||
| Taxonomy and Phylogeny | 2606 | ||
| Lifestyles, Nutrition, Habitat, and Dispersal | 2608 | ||
| Plant–Pathogen Interactions | 2609 | ||
| Pathogenicity Mechanisms and Virulence Factors | 2610 | ||
| Genomics of Plant Pathogenic Bacteria and Virulence Factors | 2619 | ||
| Molecular Evolution in Phytopathogenic Bacteria | 2622 | ||
| Concluding Remarks | 2622 | ||
| Acknowledgments | 2624 | ||
| Further Reading | 2624 | ||
| Plant Pathogens, Minor (Phytoplasmas) | 2626 | ||
| Glossary | 2626 | ||
| Abbreviations | 2626 | ||
| Defining Statement | 2627 | ||
| Introduction | 2627 | ||
| Evolutionary History | 2627 | ||
| Ecology | 2629 | ||
| Economic Importance | 2630 | ||
| Association with Plants | 2631 | ||
| Association with Insects | 2632 | ||
| Metabolism | 2632 | ||
| Repeat-Rich Genomes | 2633 | ||
| Virulence | 2634 | ||
| Conclusions | 2635 | ||
| Further Reading | 2636 | ||
| Prions | 2637 | ||
| Glossary | 2637 | ||
| Abbreviations | 2637 | ||
| Defining Statement | 2638 | ||
| Prion Diseases | 2638 | ||
| The Agent | 2641 | ||
| Infectivity and Transmission | 2647 | ||
| Contribution of the Host | 2649 | ||
| Diagnostics | 2651 | ||
| Conclusion | 2653 | ||
| Further Reading | 2654 | ||
| Quinolones | 2655 | ||
| Glossary | 2655 | ||
| Abbreviations | 2655 | ||
| Defining Statement | 2655 | ||
| Introduction | 2655 | ||
| Cleaved Complexes | 2657 | ||
| Quinolone-Mediated Inhibition of DNA Replication | 2659 | ||
| Chromosome Fragmentation | 2660 | ||
| Cleaved Complex Destabilization | 2660 | ||
| Genes Involved in Fluoroquinolone Resistance | 2661 | ||
| Quinolone Concentration and Acquisition of Resistance | 2662 | ||
| Lethal Action and Resistant Mutant Selection | 2663 | ||
| Concluding Remarks | 2664 | ||
| Further Reading | 2664 | ||
| Sexually Transmitted Diseases | 2665 | ||
| Glossary | 2665 | ||
| Abbreviations | 2665 | ||
| Defining Statement | 2665 | ||
| Introduction | 2665 | ||
| Gonorrhea | 2669 | ||
| Chlamydia | 2673 | ||
| Syphilis | 2677 | ||
| Further Reading | 2681 | ||
| Relevant Websites | 2681 | ||
| Skin Microbiology | 2682 | ||
| Glossary | 2682 | ||
| Abbreviations | 2682 | ||
| Defining Statement | 2682 | ||
| Introduction | 2683 | ||
| Skin Structure | 2683 | ||
| Resident and Transient Bacteria | 2683 | ||
| Viral Pathogens | 2688 | ||
| Fungi | 2691 | ||
| Other Skin Microorganisms | 2692 | ||
| Host Defense | 2693 | ||
| Conclusion | 2694 | ||
| Further Reading | 2694 | ||
| Subversion of Host Defences by Microbes | 2696 | ||
| Glossary | 2696 | ||
| Abbreviations | 2696 | ||
| Defining Statement | 2696 | ||
| Introduction | 2696 | ||
| An Overview of Host Defense Strategies | 2697 | ||
| Microbial Subversion of Immune Responses | 2698 | ||
| Further Reading | 2706 | ||
| Surveillance of Infectious Diseases | 2707 | ||
| Glossary | 2707 | ||
| Abbreviations | 2707 | ||
| Defining Statement | 2708 | ||
| Introduction | 2708 | ||
| Elements of Public Health Surveillance of Infectious Diseases | 2709 | ||
| Approaches to Surveillance | 2712 | ||
| Laboratory and Epidemiology Integration as a Critical Element of Infectious Disease Surveillance | 2718 | ||
| Conclusion | 2721 | ||
| Acknowledgment | 2721 | ||
| Further Reading | 2721 | ||
| Vaccine Development: The Development of Avian Influenza Vaccines for Human Use | 2723 | ||
| Glossary | 2723 | ||
| Abbreviations | 2723 | ||
| Defining Statement | 2724 | ||
| Avian Influenza: Background | 2724 | ||
| Public Health Impact of Avian Influenza | 2728 | ||
| Vaccine Immugenicity and Protection | 2729 | ||
| Preclinical Development of Vaccines against Avian Influenza: Animal Models | 2732 | ||
| Vaccine Development | 2734 | ||
| Vaccine Prioritization | 2740 | ||
| Conclusion | 2741 | ||
| Findings and Conclusions | 2742 | ||
| Further Reading | 2742 | ||
| Relevant Websites | 2743 | ||
| Vaccines, Viral | 2744 | ||
| Glossary | 2744 | ||
| Abbreviations | 2744 | ||
| Defining Statement | 2744 | ||
| General Principles | 2744 | ||
| Live Virus Vaccines | 2745 | ||
| Noninfectious Vaccines | 2748 | ||
| Vaccine Immunology | 2749 | ||
| Molecular Approaches to Viral Vaccine Design | 2751 | ||
| Public Health Impact | 2751 | ||
| Further Reading | 2752 | ||
| Viral Pathogens of Domestic Animals and Their Impact on Biology, Medicine and Agriculture | 2753 | ||
| Abbreviations | 2753 | ||
| Defining Statement | 2753 | ||
| Introduction | 2753 | ||
| Historical Perspectives | 2754 | ||
| Studies on Animal Diseases and Their Contribution to Medicine and Pathogen Biology | 2755 | ||
| Major Viral Diseases of Farm Animals | 2758 | ||
| Conclusion | 2767 | ||
| Further Reading | 2767 | ||
| Relevant Website | 2767 | ||
| Zoonoses | 2768 | ||
| Glossary | 2768 | ||
| Abbreviations | 2768 | ||
| Defining Statement | 2768 | ||
| Introduction | 2768 | ||
| Classification and Importance | 2769 | ||
| Orthozoonoses (Direct Zoonoses) | 2772 | ||
| Cyclozoonoses | 2772 | ||
| Pherozoonoses | 2773 | ||
| Saprozoonoses | 2774 | ||
| New and Emerging Zoonoses | 2774 | ||
| Prevention and Control | 2776 | ||
| Further Reading | 2777 | ||
| e9780123739391v5 | 2779 | ||
| Cover | 2779 | ||
| Title Page | 2782 | ||
| Copyright Page | 2783 | ||
| Dedication | 2784 | ||
| Preface | 2786 | ||
| Editor in Chief | 2788 | ||
| Editors | 2790 | ||
| List of Contributors | 2792 | ||
| Contents | 2808 | ||
| PHYSIOLOGY | 2818 | ||
| Amino Acid Synthesis | 2819 | ||
| Glossary | 2819 | ||
| Abbreviations | 2819 | ||
| Defining Statement | 2819 | ||
| Introduction | 2819 | ||
| Nitrogen Sources and Global Regulators of Amino Acid Metabolism | 2820 | ||
| Ammonia Assimilation and the alpha-Ketoglutarate Family: Glutamate, Glutamine, Proline, and Arginine | 2821 | ||
| The Aspartate Family: Asparate, Asparagine, Threonine, Lysine, and Methionine | 2825 | ||
| The Pyruvate Family: Alanine and the Branched-Chain Amino Acids | 2828 | ||
| The 3-Phosphoglycerate Family: Serine, Glycine, and Cysteine | 2829 | ||
| The Aromatic Amino Acids | 2831 | ||
| Histidine | 2833 | ||
| Further Reading | 2834 | ||
| Autotrophic CO2 Metabolism | 2835 | ||
| Glossary | 2835 | ||
| Abbreviations | 2835 | ||
| Defining Statement | 2835 | ||
| Autotrophic Modes of Life | 2835 | ||
| Conversion of Inorganic Carbon to Cell Carbon | 2836 | ||
| Mechanisms for CO2 Assimilation | 2837 | ||
| Assessment of Distribution of the Different Pathways | 2843 | ||
| Regulation | 2846 | ||
| Further Reading | 2847 | ||
| Bacteriocins, Biology, Ecology, and Evolution | 2849 | ||
| Glossary | 2849 | ||
| Abbreviations | 2849 | ||
| Defining Statement | 2849 | ||
| What are Bacteriocins? | 2849 | ||
| Bacteriocins of Gram-Negative Bacteria | 2850 | ||
| Bacteriocins of Gram-Positive Bacteria | 2851 | ||
| Bacteriocins of Archaea | 2852 | ||
| Evolution of Bacteriocin Diversity | 2853 | ||
| Ecological Role of Bacteriocins | 2855 | ||
| Bacteriocin Applications | 2857 | ||
| Conclusions and Future Directions | 2861 | ||
| Further Reading | 2861 | ||
| Bioluminescence, Microbial | 2862 | ||
| Glossary | 2862 | ||
| Abbreviations | 2862 | ||
| Defining Statement | 2862 | ||
| Introduction | 2862 | ||
| Biochemistry of Bacterial Light Production | 2863 | ||
| Species and Systematics of Luminous Bacteria | 2864 | ||
| Habitats and Ecology of Luminous Bacteria | 2865 | ||
| Regulation of Bacterial Luminescence | 2871 | ||
| Functions of Luminescence in Bacteria | 2873 | ||
| Evolution of the Bacterial Luminescence System | 2873 | ||
| Isolation, Storage, and Identification of Luminous Bacteria | 2875 | ||
| Conclusions | 2877 | ||
| Further Reading | 2877 | ||
| Cell Cycles and Division, Bacterial | 2879 | ||
| Glossary | 2879 | ||
| Abbreviations | 2879 | ||
| Defining Statement | 2879 | ||
| Introduction | 2879 | ||
| Terminology and Concepts | 2879 | ||
| The Cell Cycle of E. coli | 2880 | ||
| DNA Replication Cycle | 2882 | ||
| Division Cycle | 2883 | ||
| Cell Cycle Regulation | 2886 | ||
| Further Reading | 2887 | ||
| Chemotaxis | 2888 | ||
| Glossary | 2888 | ||
| Abbreviations | 2888 | ||
| Defining Statement | 2888 | ||
| Response Strategy | 2888 | ||
| Genetics of Bacterial Behavior | 2890 | ||
| Role of Protein Methylation in Adaptation | 2891 | ||
| Mechanism of Signal Transduction in Chemotaxis | 2893 | ||
| Phylogenetic Variations | 2894 | ||
| Social Motility | 2895 | ||
| Further Reading | 2895 | ||
| Coenzyme and Prosthetic Group Biosynthesis | 2896 | ||
| Abbreviations | 2896 | ||
| Defining Statement | 2896 | ||
| Biosynthesis of the Carrier Cofactors | 2896 | ||
| Biosynthesis of Metabolite-Activating Cofactors | 2896 | ||
| Biosynthesis of Redox Cofactors | 2901 | ||
| Further Reading | 2905 | ||
| Crystalline Cell Surface Layers (S Layers) | 2906 | ||
| Glossary | 2906 | ||
| Abbreviations | 2906 | ||
| Defining Statement | 2906 | ||
| Introduction | 2906 | ||
| Location and Ultrastructure | 2906 | ||
| Isolation, Chemical Characterization, and Assembly | 2908 | ||
| Genetics and Biosynthesis | 2911 | ||
| Functional Aspects and Application Potential | 2914 | ||
| Acknowledgments | 2915 | ||
| Further Reading | 2915 | ||
| Relevant Websites | 2915 | ||
| DNA Repair | 2916 | ||
| Glossary | 2916 | ||
| Abbreviations | 2916 | ||
| Defining Statement | 2916 | ||
| Introduction | 2916 | ||
| DNA Damage and Its Outcomes | 2917 | ||
| Direct Reversal | 2919 | ||
| BER | 2920 | ||
| NER | 2922 | ||
| Damage Tolerance | 2923 | ||
| MMR | 2924 | ||
| Double-Strand Break Repair | 2927 | ||
| Future Directions | 2928 | ||
| Further Reading | 2928 | ||
| DNA Replication | 2930 | ||
| Glossary | 2930 | ||
| Abbreviations | 2930 | ||
| Defining Statement | 2930 | ||
| Introduction | 2930 | ||
| Development of the Field | 2930 | ||
| Control of DNA Replication | 2931 | ||
| DNA Strand Synthesis | 2935 | ||
| Termination of Replication | 2937 | ||
| Replication of Linear Chromosomes | 2938 | ||
| Further Reading | 2939 | ||
| Energy Transduction Processes | 2940 | ||
| Glossary | 2940 | ||
| Abbreviations | 2941 | ||
| Defining Statement | 2941 | ||
| Introduction | 2941 | ||
| Mitochondrial Energetics | 2942 | ||
| Bacterial Energetics | 2943 | ||
| Principles of Respiratory Electron- Transport Linked ATP Synthesis in Bacteria | 2944 | ||
| Generation of the Ion Electrochemical Gradient other than by Electron Transport | 2946 | ||
| Photosynthetic Electron Transport | 2947 | ||
| Alkaliphiles | 2948 | ||
| Further Reading | 2948 | ||
| Fermentation | 2949 | ||
| Glossary | 2949 | ||
| Abbreviations | 2949 | ||
| Defining Statement | 2949 | ||
| Introduction | 2949 | ||
| Fermentation Balances | 2950 | ||
| Fermentation of Carbohydrates | 2951 | ||
| Fermentation of Organic Acids, Amino Acids, and Purines | 2953 | ||
| Energy Conservation Reactions in Fermentations | 2956 | ||
| Regulation of Fermentations | 2956 | ||
| Manipulation of Fermentation Pathways in Biotechnology | 2960 | ||
| Further Reading | 2961 | ||
| Glycogen Biosynthesis | 2962 | ||
| Abbreviations | 2962 | ||
| Defining Statement | 2962 | ||
| Introduction | 2962 | ||
| Criteria for Designating an Energy-Storage Function to a Compound | 2962 | ||
| Occurrence of Glycogen in Bacteria | 2962 | ||
| Biological Functions of Bacterial Glycogen | 2963 | ||
| Structural Studies of Glycogen | 2963 | ||
| Enzymatic Reactions Involved in Glycogen Synthesis | 2963 | ||
| Properties of the Glycogen Biosynthetic Enzymes | 2964 | ||
| Genetic Regulation of Glycogen Synthesis in E. coli | 2969 | ||
| Proposed Integrated Model for the Genetic Regulation of the Glycogen Biosynthetics Pathway in E. coli | 2973 | ||
| Further Reading | 2974 | ||
| Glyoxylate Cycle | 2976 | ||
| Glossary | 2976 | ||
| Abbreviations | 2977 | ||
| Defining Statement | 2977 | ||
| Scope | 2977 | ||
| Introduction | 2977 | ||
| The Glyoxylate Cycle in Prokaryotes | 2979 | ||
| The Glyoxylate Cycle in Eukaryotes | 2984 | ||
| The Key Enzymes of the Glyoxylate Cycle | 2991 | ||
| Further Reading | 2996 | ||
| Relevant Website | 2996 | ||
| Growth Kinetics, Bacterial | 2997 | ||
| Glossary | 2997 | ||
| Abbreviation | 2997 | ||
| Defining Statement | 2997 | ||
| History | 2998 | ||
| Unrestricted Growth of Individual Cells and of Populations | 2998 | ||
| Nutrient-Restricted Microbial Growth | 3000 | ||
| Mixed-Substrate-Controlled Growth Kinetics | 3005 | ||
| Growth Kinetics in Competition, Selection, and Evolution of Microbial Cultures | 3008 | ||
| Further Reading | 3010 | ||
| Heme Biosynthesis | 3011 | ||
| Glossary | 3011 | ||
| Abbreviations | 3011 | ||
| Defining Statement | 3011 | ||
| Introduction | 3011 | ||
| Overview of Tetrapyrrole Synthesis | 3012 | ||
| Gene Nomenclature | 3013 | ||
| The Steps in Heme Biosynthesis | 3013 | ||
| Regulation of Heme Biosynthesis | 3022 | ||
| Alternative Heme Biosynthetic Pathways | 3025 | ||
| Further Reading | 3026 | ||
| Relevant Website | 3026 | ||
| Iron Metabolism | 3027 | ||
| Glossary | 3027 | ||
| Abbreviations | 3027 | ||
| Defining Statement | 3027 | ||
| Introduction | 3027 | ||
| Iron Uptake | 3028 | ||
| Iron-Dependent Regulation | 3031 | ||
| Intracellular ‘Free’ and Stored Iron | 3032 | ||
| Iron in Primary Fueling Reactions | 3033 | ||
| Iron and Pathogenicity | 3034 | ||
| Conclusion | 3034 | ||
| Further Reading | 3034 | ||
| Relevant Website | 3035 | ||
| Lipid Biosynthesis | 3036 | ||
| Glossary | 3036 | ||
| Abbreviations | 3036 | ||
| Defining Statement | 3036 | ||
| The Type II Fatty Acid Biosynthetic Pathway | 3037 | ||
| Biosynthesis of UFAs | 3038 | ||
| Phospholipid Synthetic Pathways and Headgroup Diversity | 3040 | ||
| Phospholipid modifications in bacteria | 3041 | ||
| Control of Fatty Acid Biosynthesis | 3043 | ||
| Control of Membrane Fluidity | 3044 | ||
| Fatty Acid Beta-Oxidation | 3044 | ||
| Antibacterial Agents that Target Fatty Acid Biosynthesis | 3045 | ||
| Further Reading | 3045 | ||
| Magnetotaxis | 3046 | ||
| Glossary | 3046 | ||
| Abbreviations | 3046 | ||
| Defining Statement | 3046 | ||
| Introduction | 3046 | ||
| General Features of Magnetotactic Bacteria | 3047 | ||
| Cultivated Magnetotactic Bacteria in Pure Culture | 3048 | ||
| Uncultured Magnetotactic Bacteria | 3049 | ||
| Magnetosomes | 3052 | ||
| Biophysics of Magnetotaxis | 3052 | ||
| Magnetotaxis | 3054 | ||
| Magneto-Aerotaxis | 3054 | ||
| Magnetotactic Eukaryotes | 3055 | ||
| Geochemical, Geophysical, and Astrobiological Aspects of Magnetotactic Bacteria | 3055 | ||
| Biotechnological Applications of Magnetotactic Bacteria, Magnetosomes, and Magnetosome Crystals | 3057 | ||
| Perspectives | 3058 | ||
| Further Reading | 3058 | ||
| Metabolism, Central (Intermediary) | 3059 | ||
| Glossary | 3059 | ||
| Abbreviations | 3059 | ||
| Defining Statement | 3060 | ||
| Introduction | 3060 | ||
| Central Metabolic Pathways | 3060 | ||
| Gluconeogenesis | 3075 | ||
| Utilization of Polysaccharides, Oligosaccharides, and Monosaccharides | 3076 | ||
| Precursor Metabolites for Biosynthesis/ Anabolism | 3079 | ||
| Further Reading | 3081 | ||
| Methanogenesis | 3082 | ||
| Glossary | 3082 | ||
| Abbreviations | 3082 | ||
| Defining Statement | 3082 | ||
| Historical Overview | 3082 | ||
| Diversity and Phylogeny | 3083 | ||
| Habitats | 3088 | ||
| Physiology and Biochemistry | 3093 | ||
| Molecular Genetics | 3098 | ||
| Conclusion | 3102 | ||
| Further Reading | 3102 | ||
| Methylation and other Modifications of Nucleic Acids and Proteins | 3104 | ||
| Glossary | 3104 | ||
| Abbreviations | 3104 | ||
| Defining Statement | 3104 | ||
| Introduction | 3104 | ||
| DNA, RNA, and Protein Methyltransferases | 3104 | ||
| DNA Methylation | 3105 | ||
| RNA Modification | 3110 | ||
| Protein Modification | 3111 | ||
| Concluding Remarks | 3112 | ||
| Further Reading | 3112 | ||
| Nucleotide Metabolism | 3113 | ||
| Glossary | 3113 | ||
| Abbreviations | 3113 | ||
| Defining Statement | 3113 | ||
| Nucleotides: An Overview | 3114 | ||
| Biosynthesis De Novo of Nucleotides | 3115 | ||
| Biosynthesis of Deoxyribonucleotides | 3119 | ||
| Purine and Pyrimidine Salvage | 3120 | ||
| Catabolism of Nucleotides, Nucleosides, and Bases | 3121 | ||
| Selection of Mutants and Use of Analogues | 3122 | ||
| Further Reading | 3123 | ||
| Nutrition, Microbial | 3125 | ||
| Glossary | 3125 | ||
| Abbreviations | 3125 | ||
| Defining Statement | 3125 | ||
| Classification of Microorganisms and Nutrients | 3126 | ||
| Elemental Composition of Biomass | 3128 | ||
| Requirements and Physiological Functions of Principal Elements | 3129 | ||
| Feast and Famine: Unrestricted versus Nutrient-Limited Growth | 3132 | ||
| Design and Analysis of Defined Minimal Growth Media | 3136 | ||
| Further Reading | 3141 | ||
| Photosynthesis: Microbial | 3142 | ||
| Glossary | 3142 | ||
| Abbreviations | 3142 | ||
| Defining Statement | 3142 | ||
| Introduction | 3142 | ||
| Historical Perspective | 3143 | ||
| Classification of Photosynthetic Organisms | 3143 | ||
| The Constituent Processes of Photosynthesis | 3144 | ||
| Absorption and Transfer of Light Energy | 3144 | ||
| The Water-Splitting Complex | 3146 | ||
| Transmembrane Electron Transfer | 3147 | ||
| Calvin–Benson–Bassham Cycle | 3152 | ||
| Anoxygenic Photosynthesis | 3153 | ||
| The Evolution of Photosynthesis | 3156 | ||
| Future Research Directions | 3157 | ||
| Acknowledgments | 3158 | ||
| Further Reading | 3158 | ||
| Posttranscriptional Regulation | 3159 | ||
| Glossary | 3159 | ||
| Abbreviations | 3159 | ||
| Defining Statement | 3159 | ||
| Introduction | 3159 | ||
| Regulation of Premature Termination of Transcription | 3160 | ||
| Regulation of mRNA Stability | 3168 | ||
| Regulation of Translation | 3170 | ||
| Conclusion | 3173 | ||
| Further Reading | 3173 | ||
| Quorum-Sensing in Bacteria | 3174 | ||
| Glossary | 3174 | ||
| Abbreviations | 3174 | ||
| Defining Statement | 3174 | ||
| Introduction | 3174 | ||
| Quorum Signaling in Gram-Positive Bacteria | 3175 | ||
| Acylhomoserine Lactone (AHL) Quorum Signals in Gram-Negative Bacteria | 3179 | ||
| The Study of AHL-Dependent Signal Pathways Demonstrated the Presence of Another Quorum Signal AI-2 | 3183 | ||
| Other Types of Quorum Signals | 3187 | ||
| Extracellular Effectors of Quorum Signaling Systems | 3189 | ||
| Quorum Signal Interaction with the Host | 3189 | ||
| Diffusion Sensing, Efficiency Sensing, and the Future of Quorum Signaling Systems | 3190 | ||
| What’s Next for Quorum Signaling? | 3191 | ||
| Further Reading | 3191 | ||
| Regulation of Carbon Assimilation in Bacteria | 3192 | ||
| Glossary | 3192 | ||
| Abbreviations | 3192 | ||
| Defining Statement | 3193 | ||
| Introduction | 3193 | ||
| Global versus Specific Regulation | 3194 | ||
| Carbon Assimilation Pathways: Central Carbon Metabolism | 3195 | ||
| Uptake of Carbon Sources from the Medium | 3200 | ||
| Catabolite Repression in Gram-Negative Bacteria: Escherichia coli | 3201 | ||
| Catabolite Repression in Firmicutes: Bacillus subtilis | 3204 | ||
| Carbon Regulation and Catabolite Repression in Other Bacteria | 3208 | ||
| Conclusion | 3210 | ||
| Further Reading | 3211 | ||
| RNA Processing | 3212 | ||
| Glossary | 3212 | ||
| Abbreviations | 3212 | ||
| Defining Statement | 3212 | ||
| Introduction | 3212 | ||
| The Players | 3213 | ||
| Messenger RNA Processing | 3213 | ||
| Stable RNA Processing | 3219 | ||
| Future Orientations | 3225 | ||
| Further Reading | 3225 | ||
| RNAs, Small etc. | 3226 | ||
| Glossary | 3226 | ||
| Abbreviations | 3226 | ||
| Defining Statement | 3227 | ||
| Introduction | 3227 | ||
| Small Regulatory RNAs | 3227 | ||
| Sensory RNAs | 3241 | ||
| Other Small RNAs with Diverse Functions | 3245 | ||
| Further Reading | 3254 | ||
| Relevant Website | 3254 | ||
| Secondary Endosymbiosis | 3255 | ||
| Glossary | 3255 | ||
| Abbreviations | 3256 | ||
| Defining Statement | 3256 | ||
| The Origin of Eukaryotic Photosynthesis | 3256 | ||
| Secondary Endosymbiosis | 3258 | ||
| Nucleomorphs and Their Genomes | 3261 | ||
| Further Reading | 3263 | ||
| Sensory Transduction in Bacteria | 3264 | ||
| Glossary | 3264 | ||
| Abbreviations | 3264 | ||
| Defining Statement | 3265 | ||
| General Principles of Signal Transduction | 3265 | ||
| Types of Bacterial Receptors and Signaling Pathways | 3266 | ||
| Structural Organization of Signal Transduction Proteins | 3270 | ||
| Interaction of Signal Transduction Pathways | 3277 | ||
| How E. coli Sees the World? | 3279 | ||
| Further Reading | 3280 | ||
| Stress Responses: Heat | 3281 | ||
| Glossary | 3281 | ||
| Abbreviations | 3281 | ||
| Defining Statement | 3281 | ||
| Introduction | 3281 | ||
| Control of Heat Stress in Bacteria | 3282 | ||
| HS Response in Archaea | 3288 | ||
| Heat Stress in Eukaryotic Microorganisms | 3290 | ||
| Final Remarks | 3293 | ||
| Further Reading | 3293 | ||
| Stress Responses: pH | 3294 | ||
| Glossary | 3294 | ||
| Defining Statement | 3294 | ||
| Range of pH for Growth of Microorganisms | 3295 | ||
| Measurement of Internal pH | 3295 | ||
| pH Homeostasis | 3297 | ||
| pH Stress and Organic Acid Stress | 3298 | ||
| Molecular Responses to pH Stress | 3298 | ||
| Food Microbiology and Other Applications of pH Stress | 3299 | ||
| Environmental Role of pH Stress | 3300 | ||
| Further Reading | 3301 | ||
| Stress, Bacterial: General and Specific | 3302 | ||
| Glossary | 3302 | ||
| Abbreviations | 3302 | ||
| Defining Statement | 3302 | ||
| Introduction | 3302 | ||
| The Stress Response is Two-Pronged | 3303 | ||
| Specific Stress Response | 3303 | ||
| General Stress Response | 3307 | ||
| Regulation of Stress Response | 3310 | ||
| Concluding Remarks | 3317 | ||
| Further Reading | 3317 | ||
| Transcriptional Regulation | 3318 | ||
| Glossary | 3318 | ||
| Abbreviations | 3318 | ||
| Defining Statement | 3318 | ||
| The Transcription Machinery | 3319 | ||
| Template Recognition: Promoters | 3321 | ||
| Transcription Initiation | 3322 | ||
| Transcription Elongation | 3326 | ||
| Transcription Termination | 3329 | ||
| Further Reading | 3333 | ||
| Relevant Websites | 3333 | ||
| Translational Control and Fidelity | 3334 | ||
| Glossary | 3334 | ||
| Abbreviations | 3334 | ||
| Defining Statement | 3334 | ||
| Introduction | 3335 | ||
| Mechanism of Translation | 3335 | ||
| Structural Basis of Translation | 3337 | ||
| Gene-Specific Translational Control of Gene Output | 3337 | ||
| Global Control of Translation | 3340 | ||
| Translational Accuracy | 3341 | ||
| Programmed Alternative Translation | 3344 | ||
| Further Reading | 3345 | ||
| Transport, Solute | 3346 | ||
| Abbreviations | 3346 | ||
| Introduction | 3346 | ||
| Transporter Classification and Annotation | 3347 | ||
| Major Solute Transporter Families | 3351 | ||
| Comparative Studies of Transporter Family Distribution Show Strong Influence of Physiology and the Living Environment | 3358 | ||
| Soil/Plant-Associated Microbes | 3359 | ||
| Autotrophs | 3360 | ||
| Conclusion | 3360 | ||
| Further Reading | 3360 | ||
| Relevant Website | 3361 | ||
| PROTISTS | 3362 | ||
| Amitochondriate Protists (Diplomonads, Parabasalids and Oxymonads) | 3362 | ||
| Glossary | 3362 | ||
| Abbreviations | 3363 | ||
| Defining Statement | 3363 | ||
| Introduction | 3363 | ||
| Amitochondriate Protists and Eukaryote Evolution | 3363 | ||
| Systematics | 3365 | ||
| Habitats | 3367 | ||
| Cell Organization | 3367 | ||
| Hydrogenosomes and Mitosomes | 3371 | ||
| Genetics and Genomics | 3372 | ||
| Important Pathogenic Species | 3373 | ||
| Further Reading | 3374 | ||
| Amoebas, Lobose | 3375 | ||
| Glossary | 3375 | ||
| Abbreviation | 3375 | ||
| Defining Statement | 3375 | ||
| Introduction | 3375 | ||
| Some Noteworthy Dates | 3376 | ||
| Systematics and Phylogeny | 3377 | ||
| Morphology | 3378 | ||
| Morphotypes of Gymnamoebae | 3381 | ||
| Diversity | 3382 | ||
| Amoeboid Movement | 3390 | ||
| Biology and Ecology | 3392 | ||
| Importance | 3393 | ||
| Further Reading | 3394 | ||
| Ciliates | 3395 | ||
| Glossary | 3395 | ||
| Abbreviations | 3395 | ||
| Defining Statement | 3395 | ||
| Introduction | 3395 | ||
| Origin of Ciliates | 3399 | ||
| Major Clades | 3400 | ||
| Diversity at the Class Level | 3403 | ||
| Probing Diversity at the Species Level | 3406 | ||
| Further Reading | 3409 | ||
| Coccolithophores | 3410 | ||
| Glossary | 3410 | ||
| Abbreviations | 3410 | ||
| Defining Statement | 3410 | ||
| Morphology | 3410 | ||
| Taxonomy | 3414 | ||
| Collection Methods | 3415 | ||
| Biogeography and Ecology | 3416 | ||
| Blooms | 3417 | ||
| Evolution | 3420 | ||
| Further Reading | 3422 | ||
| Dictyostelium | 3423 | ||
| Glossary | 3423 | ||
| Abbreviations | 3423 | ||
| Defining Statement | 3424 | ||
| Taxonomy, Evolution, and Ecology | 3424 | ||
| Genomics and Tractability | 3426 | ||
| The Developmental Programme of D. discoideum | 3428 | ||
| Conclusions | 3433 | ||
| Further Reading | 3433 | ||
| Dinoflagellates | 3434 | ||
| Glossary | 3434 | ||
| Abbreviations | 3434 | ||
| Defining Statement | 3434 | ||
| Introduction | 3434 | ||
| Dinoflagellate Evolution | 3435 | ||
| Dinoflagellate Diversity | 3436 | ||
| Evolution of the Mitotic Apparatus | 3442 | ||
| Conclusions | 3446 | ||
| Further Reading | 3449 | ||
| Relevant Website | 3450 | ||
| Euglenozoa | 3451 | ||
| Glossary | 3451 | ||
| Abbreviations | 3451 | ||
| Defining Statement | 3451 | ||
| Taxonomy | 3451 | ||
| Cell Structure | 3452 | ||
| Euglenids | 3454 | ||
| Kinetoplastids | 3457 | ||
| Diplonemids and Other Euglenozoa | 3459 | ||
| Evolutionary Relationships | 3461 | ||
| Further Reading | 3461 | ||
| Foraminifera | 3463 | ||
| Glossary | 3463 | ||
| Abbreviations | 3463 | ||
| Defining Statement | 3463 | ||
| Introduction | 3463 | ||
| Cytological and Morphological Characteristics | 3464 | ||
| Life Cycle and Reproduction | 3466 | ||
| Ecology | 3467 | ||
| Collection and Maintenance | 3469 | ||
| Morphology-Based Classification | 3469 | ||
| Molecular Phylogeny and Diversity | 3470 | ||
| Evolutionary History and Geological Importance | 3478 | ||
| Further Reading | 3478 | ||
| Leishmania | 3480 | ||
| Glossary | 3480 | ||
| Abbreviations | 3480 | ||
| Defining Statement | 3480 | ||
| Classification and Morphology | 3481 | ||
| Life Cycle and Ecology | 3481 | ||
| Cellular Biology | 3482 | ||
| Molecular Biology and Control of Gene Expression | 3484 | ||
| Pathogenesis and Host Response | 3486 | ||
| Epidemiology and Disease | 3487 | ||
| Diagnosis, Treatment, and Control | 3489 | ||
| Further Reading | 3489 | ||
| Picoeukaryotes | 3491 | ||
| Glossary | 3491 | ||
| Abbreviations | 3491 | ||
| Defining Statement | 3491 | ||
| Introduction | 3492 | ||
| Biology of Cultured Marine Picoeukaryotes | 3494 | ||
| Picoeukaryotes in the Marine Environment | 3497 | ||
| Molecular Tools to Study Picoeukaryote Ecology | 3499 | ||
| In Situ Phylogenetic Diversity | 3501 | ||
| The Genomic Era | 3504 | ||
| Concluding Remarks | 3504 | ||
| Further Reading | 3505 | ||
| Relevant Websites | 3505 | ||
| Plant Pathogens: Oomycetes (water mold) | 3506 | ||
| Glossary | 3506 | ||
| Abbreviations | 3506 | ||
| Defining Statement | 3506 | ||
| Impact on Agriculture and Environment | 3506 | ||
| Biology | 3507 | ||
| Pathology | 3509 | ||
| Conclusions | 3511 | ||
| Further Reading | 3512 | ||
| Protozoan, Intestinal | 3513 | ||
| Glossary | 3513 | ||
| Abbreviations | 3513 | ||
| Defining Statement | 3513 | ||
| Introduction | 3514 | ||
| The Apicomplexa: Cryptosporidium Species | 3514 | ||
| The Microsporidia | 3517 | ||
| The Flagellates: Giardia intestinalis | 3518 | ||
| The Amoebae: Entamoeba histolytica | 3519 | ||
| Conclusion | 3521 | ||
| Further Reading | 3522 | ||
| Sleeping Sickness | 3523 | ||
| Glossary | 3523 | ||
| Abbreviations | 3523 | ||
| Defining Statement | 3523 | ||
| Background | 3523 | ||
| Epidemiology of Sleeping Sickness | 3524 | ||
| Causes of Epidemics | 3527 | ||
| Diagnosis | 3528 | ||
| Treatment | 3529 | ||
| Disease Burden | 3530 | ||
| Sleeping Sickness Control | 3531 | ||
| Future Prospects for Controlling Sleeping Sickness | 3534 | ||
| The Future: Control or Eliminate? | 3536 | ||
| Further Reading | 3536 | ||
| Relevant Websites | 3537 | ||
| Stramenopiles | 3538 | ||
| Glossary | 3538 | ||
| Abbreviations | 3538 | ||
| Defining Statement | 3538 | ||
| Evolutionary History of the Stramenopiles | 3538 | ||
| Diversity of the Stramenopiles | 3541 | ||
| Phylogeny and Classification of the Stramenopiles | 3544 | ||
| Conclusion | 3548 | ||
| Further Reading | 3548 | ||
| Relevant Website | 3548 | ||
| Toxoplasmosis | 3549 | ||
| Glossary | 3549 | ||
| Abbreviations | 3549 | ||
| Defining Statement | 3550 | ||
| Introduction | 3550 | ||
| Classification | 3550 | ||
| Life Cycle | 3550 | ||
| Clinical Aspects and Public Health | 3551 | ||
| Population Biology | 3552 | ||
| Molecular Biology and Genetics | 3554 | ||
| Cell Biology | 3554 | ||
| Host Immune Response | 3558 | ||
| Effect on Behavior | 3558 | ||
| Prospects for Future Improvements in Controlling Toxoplasmosis | 3559 | ||
| Further Reading | 3559 | ||
| Relevant Website | 3560 | ||
| Trypanosomes | 3561 | ||
| Glossary | 3561 | ||
| Abbreviations | 3561 | ||
| Defining Statement | 3561 | ||
| Trypanosoma cruzi | 3561 | ||
| Trypanosoma brucei | 3568 | ||
| Further Reading | 3574 | ||
| e9780123739391v6 | 3576 | ||
| Cover\r | 3576 | ||
| Title Page | 3579 | ||
| Copyright Page | 3580 | ||
| Dedication | 3581 | ||
| Preface | 3583 | ||
| Editor in Chief | 3585 | ||
| Editors | 3587 | ||
| List of Contributors | 3589 | ||
| Contents | 3605 | ||
| PUBLIC ISSUES | 3615 | ||
| Biological Warfare | 3615 | ||
| Glossary | 3615 | ||
| Abbreviations | 3615 | ||
| Defining Statement | 3616 | ||
| Introduction | 3616 | ||
| Historical Review | 3616 | ||
| International Treaties | 3619 | ||
| Current Research Programs | 3621 | ||
| Contemporary Issues | 3623 | ||
| Further Reading | 3627 | ||
| Careers in Microbiology | 3628 | ||
| Glossary | 3628 | ||
| Abbreviations | 3628 | ||
| Defining Statement | 3628 | ||
| Perspectives on the Science of Microbiology | 3628 | ||
| Diverse Employment Sectors that Offer Microbiology Positions | 3629 | ||
| Key Features to Consider when Developing a Career Plan | 3631 | ||
| Conclusion | 3634 | ||
| Further Reading | 3634 | ||
| Relevant Websites | 3635 | ||
| Forensic Microbiology | 3636 | ||
| Glossary | 3636 | ||
| Abbreviations | 3636 | ||
| Defining Statement | 3637 | ||
| Introduction | 3637 | ||
| Law Enforcement/Forensic Role | 3639 | ||
| Microbial Forensics Response | 3639 | ||
| Biocrime Investigations | 3644 | ||
| Conclusion | 3647 | ||
| Further Reading | 3647 | ||
| Patenting of Living Organisms and Natural Products | 3649 | ||
| Glossary | 3649 | ||
| Abbreviations | 3649 | ||
| Defining Statement | 3650 | ||
| Introduction | 3650 | ||
| The System of Patenting | 3651 | ||
| Legal Aspects of Microbial Patenting | 3654 | ||
| Components of Microbial Patenting | 3655 | ||
| Mining of Microbial Patents | 3657 | ||
| Conclusion | 3665 | ||
| Further Reading | 3665 | ||
| Space Microbiology: Planetary Protection, Burden, Diversity and Significance of Spacecraft Associated Microbes | 3666 | ||
| Glossary | 3666 | ||
| Abbreviations | 3666 | ||
| Defining Statement | 3667 | ||
| Planetary Protection Policies and Practices | 3667 | ||
| Methodologies Involved in Microbial Diversity Studies | 3669 | ||
| Bioburden and Biodiversity of Spacecraft and Associated Surfaces | 3672 | ||
| Concluding Remarks | 3678 | ||
| Further Reading | 3679 | ||
| Relevant Websites | 3679 | ||
| TECHNIQUES | 3681 | ||
| Antibiotic Susceptibility Testing | 3681 | ||
| Glossary | 3681 | ||
| Abbreviations | 3682 | ||
| Defining Statement | 3682 | ||
| Introduction | 3682 | ||
| Testing for Antimicrobial Resistance in the Modern Era | 3683 | ||
| Antimicrobial Susceptibility Testing Methods | 3683 | ||
| Resistance Phenotypes that Require Specialized Testing | 3687 | ||
| Conclusion | 3691 | ||
| Further Reading | 3691 | ||
| Relevant Websites | 3691 | ||
| Biodegradation Database and Prediction, Microbial | 3692 | ||
| Glossary | 3692 | ||
| Abbreviations | 3692 | ||
| Defining Statement | 3692 | ||
| Introduction | 3692 | ||
| The University of Minnesota Biocatalysis/ Biodegradation Database | 3693 | ||
| Metabolic Pathway Prediction | 3696 | ||
| The Frontiers of Microbial Metabolism and Biodegradation Prediction | 3698 | ||
| Acknowledgments | 3701 | ||
| Further Reading | 3701 | ||
| Biosensors | 3702 | ||
| Glossary | 3702 | ||
| Abbreviations | 3703 | ||
| Defining Statement | 3703 | ||
| Introduction/Limitation of Scope | 3703 | ||
| Biosensor Overview | 3704 | ||
| Biorecognition Elements of Biosensors | 3705 | ||
| Transduction Mechanisms | 3709 | ||
| Applications of Biosensors | 3713 | ||
| Concluding Remarks | 3716 | ||
| Further Reading | 3717 | ||
| Collection and Handling of Clinical Microbiological Specimens | 3718 | ||
| Glossary | 3718 | ||
| Abbreviations | 3718 | ||
| Defining Statement | 3719 | ||
| Introduction | 3719 | ||
| General Considerations for Specimen Handling | 3731 | ||
| Considerations Based on Specimen Source | 3733 | ||
| Special Considerations for Viral Examinations | 3739 | ||
| Special Considerations for Parasite Examinations | 3741 | ||
| Special Considerations for Molecular Detection | 3742 | ||
| Further Reading | 3742 | ||
| Continuous Cultures (Chemostats) | 3744 | ||
| Glossary | 3744 | ||
| Abbreviations | 3745 | ||
| Defining Statement | 3745 | ||
| Introduction | 3745 | ||
| Theory of Continuous Culture | 3745 | ||
| Physiological and Functional Genomic Studies with the Chemostat | 3752 | ||
| Simultaneous Use of Mixed Substrates in Continuous Culture | 3753 | ||
| Ecological Studies in the Chemostat | 3755 | ||
| Industrial Applications of Continuous Culture | 3756 | ||
| Competition and Selection of Mutants in the Chemostat | 3757 | ||
| Essential Equipment in Continuous Culturing | 3759 | ||
| Important Aspects of Continuous Culture | 3760 | ||
| Acknowledgments | 3760 | ||
| Further Reading | 3760 | ||
| DNA Sequencing and Genomics | 3762 | ||
| Glossary | 3762 | ||
| Abbreviations | 3762 | ||
| Defining Statement | 3762 | ||
| Introduction | 3762 | ||
| Benefits of Microbial Genomics | 3763 | ||
| Sequencing Technology | 3765 | ||
| Novel Sequencing Technologies | 3769 | ||
| Future Directions | 3775 | ||
| Further Reading | 3775 | ||
| Relevant Website | 3775 | ||
| Freeze-Drying of Microorganisms | 3776 | ||
| Glossary | 3776 | ||
| Abbreviations | 3776 | ||
| Defining Statement | 3776 | ||
| Introduction | 3776 | ||
| Freeze-Drying Instrumentation | 3777 | ||
| The Freeze-Drying Process | 3777 | ||
| Freezing | 3777 | ||
| Primary Drying | 3778 | ||
| Secondary Drying | 3778 | ||
| Residual Moisture | 3778 | ||
| Stabilizing Effect of Freeze-Drying | 3779 | ||
| Freeze-Drying Containers | 3779 | ||
| Alternative Methods of Drying Microorganisms | 3780 | ||
| The Freeze-Drying Process for Microbial Cells | 3781 | ||
| Growth Phase and Cell Concentration | 3781 | ||
| Growth Media | 3781 | ||
| Freeze-Drying Tolerance | 3782 | ||
| Protective Agents | 3783 | ||
| Sugars as Protective Agents | 3784 | ||
| Proteins as Protective Agents | 3785 | ||
| Rehydration | 3785 | ||
| Biological Safety Hazards with Freeze-Drying | 3785 | ||
| Freeze-Drying of Precise Numbers of Microorganisms | 3786 | ||
| Conclusion | 3786 | ||
| Further Reading | 3787 | ||
| Genome Sequence Databases: Annotation | 3788 | ||
| Glossary | 3788 | ||
| Abbreviations | 3788 | ||
| Defining Statement | 3788 | ||
| Introduction | 3788 | ||
| Genome Sequence Repositories | 3789 | ||
| Genomics and Proteomics Databases | 3792 | ||
| Further Reading | 3798 | ||
| Genome Sequence Databases: Genomic, Construction of Libraries | 3799 | ||
| Glossary | 3799 | ||
| Abbreviations | 3799 | ||
| Defining Statement | 3799 | ||
| Vectors Used in Genomic Library Construction | 3800 | ||
| Genomic DNA Preparation | 3801 | ||
| Agarose Gel Electrophoresis Used in Genomic Library Construction | 3803 | ||
| Quantifying DNA and Determining Quality | 3804 | ||
| Ligation Reactions | 3804 | ||
| Transformation of Library DNA into Bacterial Host Strains | 3804 | ||
| Increasing the Number of Transformants | 3805 | ||
| Determining the Number of Transformants Needed for Coverage of an Entire Genome | 3805 | ||
| Current Strategies to Enhance Genomic Library Production | 3806 | ||
| Sample Protocol to Construct a 4 kb Pseudomonas aeruginosa PAO1 Library with Vector PBTB-1 Within an E. coli Host Strain | 3806 | ||
| Further Reading | 3808 | ||
| Relevant Websites | 3809 | ||
| Genome Sequence Databases: Sequencing and Assembly | 3810 | ||
| Glossary | 3810 | ||
| Abbreviations | 3810 | ||
| Defining Statement | 3810 | ||
| DNA Sequencing | 3811 | ||
| Assembly | 3814 | ||
| Genome Assembly Improvement and Finishing | 3818 | ||
| NCBI Trace and Assembly Archive | 3822 | ||
| Further Reading | 3823 | ||
| Relevant Websites | 3824 | ||
| Genome Sequence Databases: Types of Data and Bioinformatic Tools | 3825 | ||
| Glossary | 3825 | ||
| Abbreviations | 3825 | ||
| Defining Statement | 3826 | ||
| Introduction | 3826 | ||
| Literature Databases | 3827 | ||
| Gateways to Databases and Bioinformatics Tools | 3827 | ||
| Sequence Databases | 3830 | ||
| Searching for Sequence Similarity | 3830 | ||
| Protein Databases | 3833 | ||
| Integrated Databases | 3835 | ||
| Protein Structure | 3835 | ||
| Resources for Genome-Scale Analysis | 3837 | ||
| Metabolomics | 3838 | ||
| Metagenomics | 3838 | ||
| Taxonomy and Phylogeny | 3840 | ||
| Resources for the Analysis of Gene Expression | 3843 | ||
| Resources for Proteomics | 3845 | ||
| Resources for Gene Regulation Analysis | 3845 | ||
| MBDBs and Analysis Programs of RNA Regulatory Elements | 3847 | ||
| Dedicated Integration Systems for Molecular Biology Databases | 3849 | ||
| Future of Biological Databases | 3849 | ||
| Further Reading | 3850 | ||
| Gnotiobiotic and Axenic Animals | 3851 | ||
| Glossary | 3851 | ||
| Abbreviation | 3851 | ||
| Defining Statement | 3851 | ||
| Introduction | 3851 | ||
| Flexible Film Isolators | 3852 | ||
| Microbiological Checks | 3857 | ||
| Experimentation with Germ-Free or Gnotobiotic Animals | 3857 | ||
| Axenic Rederivation | 3858 | ||
| Gnotobiotic Husbandry | 3859 | ||
| Conclusions | 3859 | ||
| Further Reading | 3859 | ||
| Relevant Websites | 3860 | ||
| Phylogenetic Methods | 3861 | ||
| Glossary | 3861 | ||
| Abbreviations | 3861 | ||
| Defining Statement | 3861 | ||
| Introduction | 3861 | ||
| Phylogenetic Analysis of Molecular Sequences | 3862 | ||
| Whole-Genome and Sequence Alignment-Free Approaches | 3870 | ||
| Other Applications of Phylogenetics | 3872 | ||
| Further Reading | 3874 | ||
| Preservation, Storage and Transport: Integrity and Compliance | 3875 | ||
| Glossary | 3875 | ||
| Abbreviations | 3875 | ||
| Defining Statement | 3875 | ||
| Methods of Preservation | 3875 | ||
| Storage | 3876 | ||
| Handling | 3878 | ||
| Transport | 3878 | ||
| Biosafety | 3879 | ||
| Biosecurity | 3881 | ||
| Compliance | 3881 | ||
| Shipping | 3883 | ||
| Further Reading | 3883 | ||
| Recombinant DNA, Basic Procedures | 3885 | ||
| Glossary | 3885 | ||
| Abbreviations | 3885 | ||
| Defining Statement | 3885 | ||
| Cloning Strategies | 3885 | ||
| Cloning Vectors | 3891 | ||
| E. coli Host | 3892 | ||
| Applications | 3893 | ||
| Further Reading | 3894 | ||
| Stable Isotopes in Microbial Ecology | 3895 | ||
| Glossary | 3895 | ||
| Abbreviations | 3895 | ||
| Defining Statement | 3895 | ||
| Introduction | 3895 | ||
| Stable Isotopes and Biogeochemistry | 3897 | ||
| Linking Metabolism to Genetic Identity | 3898 | ||
| Conclusions | 3899 | ||
| Further Reading | 3899 | ||
| Strain Improvement | 3900 | ||
| Glossary | 3900 | ||
| Abbreviations | 3900 | ||
| Defining Statement | 3901 | ||
| Introduction | 3901 | ||
| Attributes of Improved Strains | 3901 | ||
| Significance, Impact, and Benefits | 3902 | ||
| Strategies for Strain Development | 3902 | ||
| Improved Strain Performance Through Engineering Optimization | 3910 | ||
| Further Reading | 3911 | ||
| Teaching Resources, Microbiology | 3913 | ||
| Glossary | 3913 | ||
| Abbreviations | 3913 | ||
| Defining Statement | 3914 | ||
| Introduction | 3914 | ||
| Sources of Material | 3914 | ||
| Diverse Audiences | 3915 | ||
| Categories of Resources | 3916 | ||
| Scholarship of Teaching and Learning | 3917 | ||
| Conclusion | 3918 | ||
| Further Reading | 3919 | ||
| Relevant Websites | 3919 | ||
| Type Culture Collections and their Databases | 3920 | ||
| Glossary | 3920 | ||
| Abbreviations | 3920 | ||
| Defining Statement | 3920 | ||
| Microbial Culture Collections – Applications and History | 3920 | ||
| Types of Culture Collections | 3921 | ||
| Databases and Other Informational Services | 3922 | ||
| Preservation of Cultures | 3923 | ||
| Distribution of Cultures | 3925 | ||
| Conclusions | 3925 | ||
| Further Reading | 3926 | ||
| Relevant Website | 3926 | ||
| VIRUSES | 3927 | ||
| Arboviruses | 3927 | ||
| Glossary | 3927 | ||
| Abbreviations | 3928 | ||
| Defining Statement | 3928 | ||
| Introduction | 3928 | ||
| Arboviral Diseases | 3929 | ||
| Alphaviruses | 3929 | ||
| Bunyaviridae | 3930 | ||
| Flaviviruses | 3932 | ||
| Further Reading | 3935 | ||
| Bacteriophage (overview) | 3936 | ||
| Glossary | 3936 | ||
| Abbreviation | 3936 | ||
| Defining Statement | 3936 | ||
| Introduction | 3936 | ||
| Primer on Phage Biology | 3937 | ||
| Importance of Phage | 3940 | ||
| A Closer Look at Certain Aspects of Phage Biology | 3943 | ||
| Overview of Well-Studied Phage Types | 3946 | ||
| Phage Associated with Different Bacterial Hosts | 3950 | ||
| Further Reading | 3952 | ||
| Hemorrhagic Fever Viruses | 3953 | ||
| Glossary | 3953 | ||
| Abbreviations | 3953 | ||
| Defining Statement | 3953 | ||
| Introduction | 3953 | ||
| Clinical Features and Laboratory Tests | 3955 | ||
| Pathogenesis of Viral Hemorrhagic Fever | 3956 | ||
| Antiviral Therapy | 3959 | ||
| Causative Agents of Viral Hemorrhagic Fever | 3959 | ||
| Conclusion | 3967 | ||
| Further Reading | 3967 | ||
| Hepatitis Viruses | 3968 | ||
| Glossary | 3968 | ||
| Abbreviations | 3970 | ||
| Defining Statement | 3970 | ||
| Introduction | 3970 | ||
| Acute Viral Hepatitis | 3972 | ||
| Chronic Viral Hepatitis | 3974 | ||
| HAV | 3976 | ||
| HBV | 3977 | ||
| HCV | 3981 | ||
| HDV | 3984 | ||
| HEV | 3986 | ||
| ‘New’ Hepatitis Viruses | 3987 | ||
| Further Reading | 3989 | ||
| Relevant Websites | 3989 | ||
| Herpesviruses | 3990 | ||
| Glossary | 3990 | ||
| Abbreviations | 3990 | ||
| Defining Statement | 3991 | ||
| Family Herpesviridae | 3991 | ||
| The Alphaherpesvirinae Subfamily | 3992 | ||
| The Gammaherpesvirinae Subfamily | 3997 | ||
| The Betaherpesvirinae Subfamily | 4001 | ||
| Further Reading | 4004 | ||
| HIV/AIDS | 4005 | ||
| Glossary | 4005 | ||
| Abbreviations | 4005 | ||
| Defining Statement | 4006 | ||
| Introduction | 4006 | ||
| Discovery of the AIDS Virus | 4006 | ||
| The HIV Virion: Structure and Genomic Organization | 4007 | ||
| HIV Genetic Diversity | 4009 | ||
| HIV Transmission | 4010 | ||
| Detection Assays for HIV | 4011 | ||
| HIV Infection and Replication | 4012 | ||
| Effect of HIV on Cells and the Immune System | 4015 | ||
| Host Immune Responses to HIV | 4017 | ||
| Features of HIV Pathogenesis | 4024 | ||
| Future Directions | 4026 | ||
| Further Reading | 4026 | ||
| Relevant Websites | 4027 | ||
| Influenza | 4028 | ||
| Glossary | 4028 | ||
| Abbreviations | 4028 | ||
| Defining Statement | 4028 | ||
| Introduction | 4028 | ||
| Human Influenza | 4028 | ||
| Avian Influenza | 4031 | ||
| Influenza in Nonhuman Mammalian Species | 4033 | ||
| Treatment and Prevention | 4034 | ||
| Further Reading | 4034 | ||
| Oncogenic Viruses | 4035 | ||
| Glossary | 4035 | ||
| Abbreviations | 4035 | ||
| Introduction | 4035 | ||
| General Principles of Virally Induced Cancers | 4036 | ||
| RNA Tumor Viruses | 4036 | ||
| DNA Tumor Viruses | 4037 | ||
| Human Tumor Viruses | 4038 | ||
| Conclusion | 4042 | ||
| Further Reading | 4043 | ||
| Plant Pathogens: DNA viruses | 4044 | ||
| Glossary | 4044 | ||
| Defining Statement | 4044 | ||
| Introduction | 4044 | ||
| Plant ssDNA Viruses | 4045 | ||
| Caulimoviridae | 4051 | ||
| Endogenous Plant DNA Viruses | 4054 | ||
| Silencing and Silencing Suppression of Plant DNA Viruses and Resistance | 4055 | ||
| Acknowledgments | 4056 | ||
| Further Reading | 4056 | ||
| Relevant Website | 4056 | ||
| Plant Pathogens: RNA viruses | 4057 | ||
| Glossary | 4057 | ||
| Abbreviations | 4058 | ||
| Defining Statement | 4058 | ||
| Introduction | 4058 | ||
| General Characteristics of Plant-Infecting RNA Viruses | 4058 | ||
| Double-Stranded RNA Viruses | 4060 | ||
| Negative-Sense Single-Stranded RNA Viruses | 4061 | ||
| Positive-Sense ssRNA Viruses | 4061 | ||
| Replication of Positive-Sense RNA Viruses | 4062 | ||
| Viral Gene Expression | 4065 | ||
| Mechanisms of Pathogenesis | 4067 | ||
| Further Reading | 4072 | ||
| Relevant Websites | 4072 | ||
| Polio | 4073 | ||
| Glossary | 4073 | ||
| Abbreviations | 4073 | ||
| Introduction | 4073 | ||
| Poliovirus | 4073 | ||
| Poliovirus Infectious Cycle | 4075 | ||
| Pathogenesis | 4076 | ||
| Control of Poliomyelitis | 4079 | ||
| Further Reading | 4082 | ||
| Polyomaviruses and Papillomaviruses | 4083 | ||
| Glossary | 4083 | ||
| Abbreviations | 4083 | ||
| Defining Statement | 4084 | ||
| Polyomaviruses | 4084 | ||
| Papillomaviruses | 4092 | ||
| Further Reading | 4097 | ||
| Rabies | 4098 | ||
| Glossary | 4098 | ||
| Abbreviations | 4098 | ||
| Defining Statement | 4099 | ||
| Rabies and Rabies-Related Viruses | 4099 | ||
| Virus Life Cycle | 4103 | ||
| Epidemiology of Animal and Human Rabies | 4105 | ||
| Control and Prevention of Rabies in Domestic and Wildlife Animals | 4106 | ||
| Human Rabies | 4107 | ||
| Rabies Pathogenesis and Histopathology | 4109 | ||
| Rabies Vaccine Prophylaxis | 4111 | ||
| Further Reading | 4113 | ||
| Respiratory Viruses | 4114 | ||
| Abbreviations | 4114 | ||
| Defining Statement | 4114 | ||
| Introduction | 4114 | ||
| Human Respiratory Syncytial Virus | 4115 | ||
| Human Parainfluenza Viruses | 4118 | ||
| Human Metapneumovirus | 4120 | ||
| Rhinovirus | 4121 | ||
| Respiratory Adenoviruses | 4124 | ||
| Human Coronaviruses Unrelated to SARS | 4127 | ||
| SARS Coronavirus | 4129 | ||
| Human Bocavirus | 4131 | ||
| Further Reading | 4132 | ||
| Retroviruses | 4133 | ||
| Glossary | 4133 | ||
| Abbreviations | 4133 | ||
| Defining Statement | 4134 | ||
| Classification | 4134 | ||
| Structure | 4135 | ||
| Retroviral Replication | 4136 | ||
| Retroviruses and Disease | 4140 | ||
| Retroviruses of Humans | 4144 | ||
| Endogenous Retroviruses | 4145 | ||
| Retroviral Vectors | 4146 | ||
| Further Reading | 4148 | ||
| Relevant Websites | 4148 | ||
| Viroids/Virusoids | 4149 | ||
| Glossary | 4149 | ||
| Abbreviations | 4149 | ||
| Defining Statement | 4150 | ||
| Introduction | 4150 | ||
| Viroid Classification and Structure | 4150 | ||
| Host Range of Viroids | 4150 | ||
| Viroid Infection | 4152 | ||
| Viroid Pathogenecity | 4156 | ||
| Virusoids | 4158 | ||
| Conclusion | 4158 | ||
| Further Reading | 4159 | ||
| Relevant Website | 4159 | ||
| Virus Infection | 4160 | ||
| Glossary | 4160 | ||
| Abbreviations | 4160 | ||
| Defining Statement | 4160 | ||
| Virus Life Cycles | 4160 | ||
| Modes of Entry and Transmission of Viruses | 4163 | ||
| Responses to Virus Infections | 4164 | ||
| Outcomes of Virus Infections | 4165 | ||
| Viral Virulence | 4165 | ||
| Antiviral Therapy and Prophylaxis | 4166 | ||
| Further Reading | 4166 | ||
| Viruses, Environmental | 4167 | ||
| Glossary | 4167 | ||
| Abbreviations | 4167 | ||
| Defining Statement | 4168 | ||
| Introduction | 4168 | ||
| Viruses in the Environment | 4168 | ||
| Ecological Importance | 4174 | ||
| Methods for Studying Environmental Viruses | 4177 | ||
| Conclusions | 4180 | ||
| Further Reading | 4180 | ||
| Subject Index | 4183 |