Microbes Concepts and Applications
Buku ini pertama kali diterbitkan Tahun 2012 oleh Willey-Blackwell A John Wiley & Sons, Inc., Publication.
Judul: Microbes Concepts and Applications
Pengarang: Prakas S. Bisen
Penerbit: Willey-Blackwell A John Wiley & Sons, Inc., Publication
Tahun: 2012
Jumlah Halaman: 717 hal.
Author:
Prakash S. Bisen
Emeritus Scientist Defence Research Development Establishment
Defence Research Development Organization Ministry of Defence, Government of India
Gwalior, India
Mousumi Debnath
Associate Professor Department of Biotechnology Central University of Rajasthan City Road, Kishangargh Ajmer, India
Godavarthi B. K. S. Prasad
Professor School of Studies in Biochemistry and Biotechnology
Jiwaji University Gwalior, India
Lingkup Pembahasan:
Buku ini terdiri atas 7 Bagian Utama, yaitu: 1) Manusia dan Dunia Mikroba, 2) Gene Teknologi: Aplikasi dan Teknik, 3) Mikrobiologi Media dan Diagnostik Molekuler, 4) Identifikasi dan Klasifikasi Mikroba, 5) Keragaman Mikro Organisme, 6) Mikroba di Bidang Pertanian, dan 7) Mikroba sebagai Alat untuk Industri dan Penelitian. Masing-masing Bagian Utama ini mencakup secara rinci lagi.
Daftar Isi:
PREFACE xiii
ACKNOWLEDGMENTS xv
1 HUMAN AND MICROBIAL WORLD 1
1.1 Prologue 1
1.2 Innovations in Microbiology for Human Welfare 1
1.2.1 Impact of Microbes on the Human Genome Project, 2
1.2.2 Microbial Biosensors, 5
1.2.3 Molecular Diagnostics, 7
1.2.4 Nanomedicine, 13
1.2.5 Personalized Medicine, 16
1.2.6 Biowarfare, 21
1.3 The Microbial World 24
1.3.1 Classification System, 25
1.3.2 Viruses, Viroids, and Prions, 26
1.3.3 Bacteria, 32
1.3.4 Eucarya, 35
1.3.5 Algae, 39
1.3.6 Fungi, 44
1.3.7 Protozoa, 47
1.3.8 Microscopic Invertebrates, 51
1.3.9 Microbial Interrelationships, 54
1.3.10 Probiotic Microbes, 56
1.4 Future Challenges: Metagenomics 57
References 60
2 GENE TECHNOLOGY: APPLICATIONS AND TECHNIQUES 65
2.1 Prologue 65
2.2 Introduction to Gene Technology 65
2.2.1 Genes and Bacteria, 67
2.2.2 Reporter Genes, 68
2.2.3 Recombinant DNA Pharmaceuticals, 69
2.2.4 In vitro DNA Selection, 73
2.3 Nucleic Acid Hybridization 75
2.3.1 Colony Blot and Southern Blot, 76
2.3.2 Dot Blot and Zoo Blot, 77
2.3.3 In situ Hybridization, 79
2.3.4 Microarray Technology, 83
2.3.5 Molecular Diagnostic Research, 87
2.4 DNA Sequencing 88
2.4.1 Dideoxychain Termination Method, 89
2.4.2 Automated DNA Sequencing, 90
2.4.3 Maxam and Gilbert Method, 92
2.4.4 Primer Walking, 96
2.4.5 Contig Sequencing, 97
2.4.6 Shotgun Sequencing, 97
2.4.7 Importance of Sequencing, 99
2.5 Polymerase Chain Reaction 99
2.6 Omics Technology and Microbes 103
2.6.1 Genomics: A Tool for Understanding Genes, 104
2.6.2 Transcriptomics: A Tool for Deciphering Gene Function, 108
2.6.3 Proteomics: A Tool to Unravel the Mysteries of Protein, 112
2.6.4 Metabolomics: A Tool to Ultimately Understand the Whole Metabolome, 116
2.6.5 Integration of Omics, 121
2.7 Bioinformatics in Microbial Technology 124
2.8 Future Challenges: The Biochips 126
References 137
3 MEDICAL MICROBIOLOGY AND MOLECULAR DIAGNOSTICS 151
3.1 Prologue 151
3.2 Microbial Biology 152
3.2.1 Morphology and Nature of Microorganisms, 152
3.2.2 Use of Bergey’s Manual and Identibacter Interactus, 154
3.2.3 Bacterial Growth and Physiology, 154
3.2.4 Antimicrobial Agents, 156
3.2.5 Bacterial Genetic Variations, 158
3.2.6 Bacterial Pathogenecity, 158
3.2.7 Virus–Cell Interaction, 159
3.3 Infection and Immunity 160
3.3.1 Overview of the Immune System, 160
3.3.2 The Organs of the Immune System, 161
3.3.3 Cells of the Immune System, 162
3.3.4 Innate Immunity, 164
3.3.5 Adaptive Immunity, 165
3.3.6 Hypersensitivity, 180
3.3.7 Immunity in Viral Infections, 183
3.4 Bacterial Pathogens and Associated Diseases 185
3.4.1 Airborne Bacterial Infections, 186
3.4.2 Foodborne and Waterborne Diseases, 190
3.4.3 Soilborne Bacterial Infections, 198
3.4.4 Arthropodborne Bacterial Infections, 200
3.4.5 Sexually Transmitted Bacterial Infections, 201
3.4.6 Other Important Bacterial Diseases, 203
3.4.7 Actinomycetes Mycetoma, 204
3.5 Viral Pathogens and Associated Diseases 209
3.5.1 Herpes Simplex Viruses, 210
3.5.2 Varicella Zoster Virus, 210
3.5.3 Cytomegalovirus, 210
3.5.4 Epstein–Barr Virus, 211
3.5.5 Human Herpes Virus, 211
3.5.6 Hepatitis, 211
3.5.7 Respiratory Syncytial Virus, 213
3.5.8 Influenza Viruses, 214
3.5.9 Parainfluenza Viruses, 215
3.5.10 Adenoviruses, 215
3.5.11 Rhinoviruses, 215
3.5.12 Coronaviruses, 216
3.5.13 SARS Virus, 216
3.5.14 Diarrheal Viruses, 216
3.5.15 Calicivirus (Sapovirus), 217
3.5.16 Enterovirus, 217
3.5.17 Poliomyelitis, 217
3.5.18 Coxsackie, 217
3.5.19 Echoviruses, 218
3.5.20 Mumps, 218
3.5.21 Measles Virus, 218
3.5.22 Rubella, 219
3.5.23 Parvovirus B, 219
3.5.24 Human Immunodeficiency Viruses, 220
3.5.25 Human T Cell Lymphotropic Viruses (HTLV), 222
3.5.26 Papillomaviruses, 222
3.5.27 Polyomaviruses, 223
3.5.28 Rabies, 223
3.5.29 Smallpox, 223
3.5.30 Monkeypox, 224
3.5.31 Vaccinia, 224
3.5.32 Cowpox, 224
3.5.33 Arthropodborne Viruses, 224
3.5.34 Lymphocytic Choriomenigitis Virus, 226
3.5.35 Filovirus, 226
3.5.36 Hantaviruses, 227
3.6 Prions 227
3.6.1 Kuru, 227
3.6.2 Creutzfeldt–Jacob Disease (CJD), 227
3.6.3 Gerstmann–Straussler Syndrome (GSS), 228
3.7 Parasitic Infections 228
3.7.1 Nematoda, 229
3.7.2 Trematoda, 232
3.7.3 Cestoda, 234
3.7.4 Protozoan Parasites, 236
3.7.5 Skin Parasites, 248
3.8 Fungal Pathogen 249
3.8.1 Superficial Fungal Infections, 249
3.8.2 Systemic Fungal Infections, 250
3.9 Microbial Diagnostics 253
3.9.1 Immunodiagnostic Methods, 253
3.9.2 Molecular Diagnostic Approaches, 258
3.10 Future Challenges: Promises of Pharmacogenomics 265
References 267
4 IDENTIFICATION AND CLASSIFICATION OF MICROBES 275
4.1 Prologue 275
4.2 Principles of Taxonomy 276
4.2.1 Strategies Used to Identify Microbes, 280
4.2.2 Methods for Bacterial Identification, 281
4.3 Using Phenotypic Characteristics to Identify Microbes 281
4.3.1 Microscopic Morphology, 283
4.3.2 Metabolic Differences, 288
4.3.3 Serology, 295
4.3.4 Fatty Acid Analysis (FAME), 298
4.4 Using Genotypic Character to Identify Microbes 299
4.4.1 Nucleic Acid Probes to Detect Specific Nucleotide Sequence, 300
4.4.2 Amplifying Specific DNA Sequences Using PCR, 301
4.4.3 Sequencing Ribosomal RNA Genes, 302
4.5 Characterizing Strain Differences 306
4.5.1 Phenotypic Typing Methods, 306
4.5.2 Molecular Typing Methods, 315
4.6 Classification of Microbes on the Basis of Phenotypic Characteristics 319
4.6.1 Carbohydrate Utilization, 322
4.6.2 Enzyme Production, 322
4.6.3 Mode of Growth, 323
4.6.4 Motility, 323
4.6.5 Antigen and Phage Susceptibility, 324
4.7 Classification of Microbes on the Basis of Genotypic Characters 324
4.7.1 DNA Base Ratio (G + C Ratio), 325
4.7.2 DNA Hybridization, 326
4.7.3 Nucleotide Sequence Analysis, 330
4.7.4 Comparing the Sequence of 16S Ribosomal Nucleic Acid, 331
4.8 Future Challenges: Aptamers for Detection of Pathogens 333
References 334
5 DIVERSITY OF MICROORGANISMS 339
5.1 Prologue 339
5.2 Physiological Diversity of Microorganisms 339
5.2.1 Anaerobic Chemotrophs, 340
5.2.2 Anoxygenic Phototrophs, 340
5.2.3 Oxygenic Phototrophs, 342
5.2.4 Aerobic Chemolithotrophs, 343
5.2.5 Aerobic Chemoorganotrophs, 344
5.3 Thriving in Terrestrial Environment 345
5.3.1 Microbial Population Counts in Soil, 346
5.3.2 Bacteria that Form a Resting Stage, 348
5.3.3 Bacteria that Associate with Plants, 349
5.3.4 Isolation of Antibiotic-Producing Bacteria from Soil, 351
5.4 Aquatic Environment 353
5.4.1 Sheathed Bacteria, 353
5.4.2 Prosthecated Bacteria, 354
5.4.3 Bacteria that Derive their Nutrients from Other Organisms, 357
5.4.4 Bacteria that Move by Unusual Mechanisms, 358
5.4.5 Bacteria that Form Storage Granules, 359
5.4.6 Bacteriological Examination of Water—Qualitative Tests, 360
5.4.7 Membrane Filter Method, 361
5.4.8 Standard Plate Count—Quantitative Test, 363
5.5 Animals as Habitat 364
5.5.1 Bacteria that Inhabit the Skin, 365
5.5.2 Bacteria that Inhabit the Mucous Membrane, 366
5.5.3 Obligate Intracellular Parasites, 367
5.6 Archaea in Extreme Environments 368
5.6.1 Extreme Halophiles, 369
5.6.2 Extreme Thermophiles, 371
5.6.3 Thermophilic Extreme Acidophiles, 372
5.7 Biogeochemical Cycles 373
5.7.1 Various Cycles, 376
5.7.2 Consequences of Biogeochemical Cycles Gone Wild, 376
5.8 Environmental Influence and Control of Microbial Growth 377
5.8.1 Temperature, 378
5.8.2 Osmotic Pressure, 379
5.8.3 UV Light, 381
5.8.4 pH, 382
5.8.5 Oligodynamic Action, 384
5.9 Microorganisms and Organic Pollutants 385
5.9.1 Environmental Law, 386
5.9.2 Process of Biodegradation, 387
5.9.3 Relationship between Contaminant Structure, Toxicity, and Biodegradability, 389
5.9.4 Environmental Factors, 391
5.9.5 Biodegradation of Organic Pollutants, 392
5.9.6 Bioremediation, 394
5.10 Microorganisms and Metal Pollutants 396
5.10.1 Metals Defined, 398
5.10.2 Metal Toxicity Effect on Microbial Cells, 399
5.10.3 Mechanism of Microbial Metal Resistance and Detoxification, 400
5.10.4 Metal–Microbe Interaction, 402
5.10.5 Microbial Approaches in Remediation of Metal-Contaminated Soil and Sediments, 403
5.11 Environmentally Transmitted Pathogens 405
5.11.1 Transmission of Pathogen, 405
5.11.2 Indicator Organisms in Polluted Water, 431
5.11.3 Microbiology of Sewage Treatment, 449
5.12 Microorganisms as Friends of Man 453
5.12.1 Microbes to Join the Oil Industry, 454
5.12.2 Microbes and Biodiesel: Production and Feedstocks, 455
5.12.3 Genetic Modification of Lignin Biosynthesis for Improved Biofuel Production, 457
5.12.4 Microbes and Biogas Production, 459
5.12.5 Biosensors for Environmental Monitoring, 460
5.12.6 Microbes as Mining Agents, 462
5.12.7 Microbial Fuel Cells, 464
5.12.8 Microbes as a Source of Bioenergy, 466
5.13 Microbes as a Disastrous Enemy 468
5.13.1 Microbes as Biowarfare Agents, 470
5.14 Future Challenges: Microbes in the Space 472
References 475
6 MICROBES IN AGRICULTURE 481
6.1 Prologue 481
6.2 The Soil Plant Microorganisms 482
6.2.1 Soil Fertility, 483
6.2.2 Rhizosphere Environment, 488
6.2.3 Ammonification in Soil, 491
6.2.4 Nitrification in Soil, 493
6.2.5 Organic Compounds Released by Plants, 495
6.2.6 Nitrogen-Fixing Bacteria, 495
6.3 Root Microbial Interaction 500
6.3.1 Biological Dinitrogen Fixation, 504
6.3.2 Free-Living Dinitrogen Fixation, 505
6.3.3 Associative Nitrogen Fixation, 506
6.3.4 Legume–Rhizobia Symbioses, 507
6.3.5 Mycorrhizal Association, 507
6.4 Pathogenic Microbes in Agriculture 508
6.4.1 Microbes and Agriculture, 510
6.4.2 Biopesticides, 512
6.4.3 Commercial Microbial Pesticides, 514
6.4.4 Bioweedicides, 518
6.4.5 Diseases Caused by Bacteria, 519
6.4.6 Diseases Caused by Virus, 525
6.4.7 Soil Biological Control and Plant Diseases, 528
6.5 Microbes as a Tool of Genetic Engineering 535
6.5.1 Agrobacterium: The Friendly Bacteria, 536
6.5.2 Transformation Technology: Refined Tools for Genetic Transformation, 537
6.5.3 Transgenic Cellulosic Biofuel Crops, 541
6.5.4 Expression of Microbial Enzymes in Crops, 545
6.5.5 Genetic Transformation for Crop Improvement: Biotic Stress Tolerance, 547
6.5.6 Genetic Transformation for Crop Improvement: Altering Plant Development, 552
6.5.7 Genomics: Gene Mining and Gene Expression Profiling, 554
6.6 Future Challenges: Functional Genomics Approach for Improvement of Crops 557
References 560
7 MICROBES AS A TOOL FOR INDUSTRY AND RESEARCH 567
7.1 Prologue 567
7.2 Historical Development 567
7.2.1 Era of Pasteur and Fermentation, 568
7.2.2 Discovery of Antibiotics, 572
7.2.3 Growth of Industrial Fermentation, 573
7.2.4 Production of Strains, 576
7.2.5 Strain Development, 577
7.3 Clinical Diagnostics in a New Era 578
7.3.1 Genes and Diseases, 579
7.3.2 Biomedical Research in the Postgenomic Era, 582
7.3.3 Molecular Diagnostics Technology and Health Care Industries, 586
7.3.4 Therapeutic Applications of rDNA Pharmaceuticals, 593
7.3.5 Aptamers as Therapeutics, 595
7.3.6 Immunodiagnostics, 599
7.3.7 Reporter Genes in Molecular Diagnostics, 602
7.3.8 Human Genome Project and Health Services, 604
7.3.9 Prognostics, Diagnostics, and Therapeutics of Disease-Causing Pathogens, 607
7.3.10 Promise of Pharmacogenomics, 611
7.4 Industrial Microorganisms and Product Formation 615
7.4.1 Microorganisms and Their Products, 616
7.4.2 Primary and Secondary Metabolites, 617
7.4.3 Characteristics of Large-Scale Fermentation, 619
7.4.4 Fermentation Scale-Up, 621
7.5 Major Industrial Products for Health and Industry 622
7.5.1 Immobilized Enzymes, 623
7.5.2 Antibiotics, 626
7.5.3 Organic Acids, 632
7.5.4 Enzymes, 635
7.5.5 Solvents, 637
7.5.6 Amino Acids, 638
7.5.7 Vitamins, 640
7.5.8 Yeast, 641
7.5.9 Single Cell Protein, 643
7.5.10 Fermented Food, 645
7.5.11 Mushroom, 647
7.5.12 Beverages, 647
7.6 Food Diagnostics, Food Preservation, and Foodborne Microbial Diseases 649
7.6.1 Food Preservation and Microbial Growth, 650
7.6.2 Microbial Sampling and Food Poisoning, 662
7.6.3 Food Diagnostics, 666
7.7 Future Challenges: Next Generation Diagnostics Industry 680
References 681
INDEX 685
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