| Author: |
Ramesh Maheshwari
|
| Release at: | 2012 |
| Pages: | 354 |
| Edition: |
Second Edition
|
| File Size: | 13 MB |
| File Type: | |
| Language: | English |
Description of Fungi Experimental Methods In Biology 2nd Edition (PDF)
Fungi Experimental Methods In Biology 2nd Edition by Ramesh Maheshwari is a great book for research related to Mycology available in (eBook) PDF download. The ease with which yeasts and molds can be cultivated in simple nutritive media has made these eukaryotic organisms the choice material for basic and applied research. Fungi: Experimental Methods in Biology (FEMIB) gives an account of real experiments that have been carried out on the diverse lifestyles of these organisms. The subject matter here is grouped in six sections. In addition to recent information, each chapter includes a historical perspective and illustrations that enable the reader to progress from elementary concepts to advanced research. The summary of each chapter focuses on unsolved problems. A glossary of mycological and interdisciplinary terms serves as a compilation of the concepts introduced in the chapters.
Fungi are organisms generally composed of tubes that are invisible to the naked eye. The cells of these tubes are multinucleate and in cytoplasmic continuity. Fungi are among the oldest and largest living organisms, rivaling the mass of a California redwood tree or a blue whale. As the chief agents of decomposition of organic matter, fungi contribute to the sustenance of the carbon cycle. As mycorrhizal partners of roots, they provide the primary mechanism for the capture of nutrients used by plants, thereby contributing to the green cover on earth. Some fungi occur as endophytes in plants or as symbiotic partners with algae, allowing the mutualistic partners to tolerate and grow in harsh conditions that they could not do otherwise. As virulent pathogens of plants, fungi are a constant threat in agriculture and forestry. Since antiquity, fungus has been exploited either unwittingly or intentionally for the conversion of grape juice into ethanol in wine. As producers of antibacterial compounds, fungi are sources of life-saving drugs.
This book on fungi is an outcome of my association with graduate students in biochemistry. The majority of these students had little or no previous exposure to fungi and a few not even to biology. I found that students became interested in fungi if an attempt was made to demonstrate fungi in natural situations and how they could be used to understand complex biological questions, in particular if the design of the experiments that were done to obtain information were described. Today’s accelerated pace of research, aided by new instruments and techniques combining the approaches of genetics, biochemistry, and cell biology, has changed the character of mycology, necessitating a new approach for the organization of the subject matter and learning about the fungi.
Content of Fungi Experimental Methods In Biology 2nd Edition (PDF)
Part I The Unique Features of Fungi
Chapter 1 The Hyphal Mode of Life 3
1.1 Features of Hyphae .3
1.1.1 Apical Extension3
1.1.2 Spread and Longevity 4
1.1.3 Large Surface Area6
1.2 Hyphal Structure.8
1.2.1 Cell Wall 8
1.2.2 Glucan9
1.2.3 Hydrophobin 11
1.3 Internal Structure 12
1.3.1 Microtubules and Actin Filaments 12
1.3.2 Spitzenkörper and Polarisome . 16
1.3.3 Calcium 17
1.3.4 Vacuole. 18
1.3.5 Septa and Woronin Body . 18
1.4 Networking 18
1.4.1 Branching. 18
1.4.2 Hyphal Fusion 19
1.5 Main Functions .20
1.5.1 Nutrient Uptake20
1.5.2 Protein Secretion20
1.6 Morphogenesis 21
1.6.1 Hyphal Differentiation.22
1.6.2 Rhizomorph .23
1.6.3 Mushroom Fruiting Body 23
1.7 Autophagy.24
1.8 Concluding Remarks.24
References24
Chapter 2 The Multinuclear Condition.29
2.1 Nuclear Number and Hyphal Growth Rate.29
2.2 Chromosome Numbers .29
2.2.1 Classical Methods29
2.2.2 New Methods.30
2.3 Multiple Genomes in Individual Nuclei 32
2.4 Nuclear Division Cycle . 33
2.4.1 Temperature-Sensitive Mutants.34
2.4.2 Stages in Nuclear Division Cycle.34
2.5 Asynchronous Nuclear Divisions 35
2.6 Nuclear Migration .36
2.7 Nuclear Positioning and Gene Regulation 36
2.8 Heterokaryosis 38
2.8.1 Sheltering of Lethal Mutation39
2.8.2 Change in Nuclear Ratio40
2.8.3 Nuclear Competence 42
2.9 Parasexual Recombination 43
2.10 Are All Nuclei Active Simultaneously? 43
2.11 Concluding Remarks.44
References44
Chapter 3 Spores: Their Dormancy, Germination, and Uses. 47
3.1 Models for Cellular Processes. 47
3.2 Pleomorphism .48
3.3 Dissemination .50
3.4 Longevity 50
3.5 Structure50
3.5.1 Topography 50
3.5.2 Wall Structure 52
3.6 Water Relations. 53
3.7 Endogenous Substrates 53
3.7.1 Lipids . 53
3.7.2 Polyols54
3.7.3 Trehalose 55
3.8 Link between Sporulation and Secondary Metabolism 55
3.9 Self-Reconditioning of Substratum. 55
3.10 Germination Triggers56
3.10.1 Adhesion 56
3.10.2 Heat 57
3.10.3 Light. 57
3.10.4 Chemicals 57
3.11 Material for Probing Fungal Physiology.58
3.11.1 Prerequisites for Development.58
3.11.2 Release of Self-Inhibitors and Efflux of Carbon Compounds.58
3.11.3 Cold Dormancy59
3.11.4 Genome Activation 59
3.11.5 Dark Fixation of CO2 .60
3.11.6 Respiratory Increase 60
3.11.7 Regeneration of Reducing Power. 62
3.11.8 Synthetic Pathways 62
3.11.9 Sensing, Signaling, and Transcriptional Changes .63
3.12 Applications 64
3.12.1 Biocatalysis64
3.12.2 Biocontrol.64
3.13 Concluding Remarks.65
References65
Part II Fungi in Biosphere and Human Health
Chapter 4 Fungi as Scavengers. 71
4.1 Decay of Wood and Litter. 71
4.2 Clues from Microscopy.72
4.3 White- and Brown-Rot Fungi .73
4.4 Litter Decomposers. 74
4.5 Degradation of Cell Wall Polymers 75
4.5.1 Lignin. 75
4.5.2 Cellulose 84
4.5.3 Hemicellulose 86
4.6 Reactive Oxygen Species86
4.7 Unsolved Problems87
4.8 Clues from Genome Sequence87
4.9 Physiological Processes.88
4.10 Concluding Remarks.88
References89
Chapter 5 Fungi as Symbiotic Partners 91
5.1 Mycorrhiza 91
5.1.1 Types of Mycorrhiza 91
5.1.2 Identification 93
5.1.3 Development 93
5.1.4 Carbohydrate Transfer .94
5.1.5 Phosphorus Transfer 95
5.1.6 Nitrogen Transfer.95
5.1.7 Decomposition of Plant Residues 96
5.1.8 Mycorrhiza as Conduits of Photosynthetically Fixed Carbon Compounds 96
5.1.9 Cheating in Plant-Fungus Marriages.99
5.1.10 Genome Sequence100
5.2 Endophytic Fungi100
5.3 Lichens 101
5.3.1 Mycobiont and Photobiont . 102
5.3.2 In Situ Study. 102
5.3.3 Synthesis 102
5.3.4 Movement of Carbohydrate . 103
5.4 Concluding Remarks. 103
References 103
Chapter 6 Fungi as Plant Pathogens. 107
6.1 The Rust Fungi 107
6.1.1 Thigmotropism and Thigmomorphogenesis 108
6.1.2 Haustorium. 110
6.2 Host Resistance and Pathogen Avirulence 112
6.3 Dual Role for Haustorium. 115
6.4 Effector Molecules 115
6.5 Concluding Remarks. 117
References 118
Chapter 7 Fungi as Chemical Factories 121
7.1 Fungal Factories 121
7.1.1 Penicillin 121
7.1.2 Cephalosporin126
7.1.3 Statins.126
7.1.4 Anticancer Drugs. 127
7.1.5 Defensins 127
7.2 Attractions. 128
7.3 Yield Improvement 130
7.4 Heterologous Protein Production 131
7.4.1 Chymosin . 131
7.4.2 Lipases. 131
7.4.3 Lactoferrin . 132
7.4.4 Human Vaccine 132
7.5 Methylotrophic Yeasts. 132
7.6 New Methods of Yield Improvement 133
7.6.1 Increase in Gene Copy Number. 133
7.6.2 Manipulation of Morphology. 133
7.6.3 Hyperbranching Mutants. 134
7.6.4 Modification of Cell Wall 135
7.6.5 Other Molecular Manipulations. 135
7.6.6 New Expression Hosts . 135
7.7 Biofuel Ethanol . 136
7.8 Agrochemicals 138
7.9 Concluding Remarks. 138
References 139
Part III Gene Silencing
Chapter 8 Transformation and Discovery of Gene-Silencing Phenomena. 145
8.1 Transformation Procedure 145
8.2 Homologous vs. Ectopic Integration of Transgene . 146
8.3 Purification of Transformant. 146
8.4 Gene-Silencing Phenomena 147
8.4.1 Silencing by Mutation 147
8.4.2 Meiotic Silencing by Unpaired DNA (MSUD) 149
8.4.3 Silencing by DNA Methylation (MIP). 152
8.4.4 Quelling . 152
8.5 RNA Silencing 155
8.6 Concluding Remarks. 156
References 157
Part IV Model Organisms
Chapter 9 Yeast: A Unicellular Paradigm for Complex Biological Processes. 161
Amitabha Chaudhuri
9.1 Molecular Mechanisms of DNA Replication and Cell Division. 162
9.2 Bud Growth and Polarity 165
9.3 Mating and Signal Transduction Cascade. 168
9.4 Protein Targeting. 172
9.5 Mitochondrial Biogenesis . 172
9.6 Functional Genomics 176
9.6.1 Evolution of the Yeast Genome 176
9.6.2 Functional Analysis of the Yeast Genome. 177
9.6.3 Expression Pattern of Genes Using DNA Microarray. 179
9.6.4 Mapping Transcription Network 180
9.7 Proteomics and System Biology Modeling. 181
9.8 Concluding Remarks. 183
References 184
Chapter 10 Neurospora: A Gateway to Biology. 187
10.1 Habitat and Life Cycle 187
10.2 Life History. 191
10.3 One Gene—One Enzyme . 192
10.4 Mutational Analysis of Conidia Development 193
10.5 Meiotic Events. 195
10.6 Gene Maps 196
10.7 Chromosome Morphology and Gene Expression . 201
10.8 Ascus Development Biology . 201
10.9 Molecular Revolution202
10.10 Genome Sequence.203
10.11 Concluding Remarks.204
References204
Chapter 11 Aspergillus nidulans: A Model for Study of Form and Asexual Reproduction 207
11.1 Conidiophore Structure.207
11.2 Conidiation Genes.208
11.3 Conidiation Trigger.209
11.4 Developmental Competence . 210
11.5 Regulatory Pathway 211
11.6 Master Regulatory Genes 211
11.7 Microcycle Conidiation. 212
11.8 Concluding Remarks. 212
References 214
Chapter 12 Ustilago maydis and Other Fungi as Models of Sexual Reproduction 217
12.1 Heterothallism vs. Homothallism . 217
12.2 Cell–Cell Recognition. 219
12.2.1 Mating Types . 219
12.2.2 Assay for Mating Compatibility 222
12.3 Extracellular Recognition .222
12.3.1 The a Locus .222
12.3.2 Pheromone and Receptor.223
12.4 Intracellular Recognition 224
12.5 Genetic Engineering for Sex.225
12.6 Concluding Remarks.227
References227
Part V Adaptations
Chapter 13 Photoresponses and Circadian Rhythm. 231
13.1 Photoresponse Phenomena 231
13.1.1 Pigmentation 231
13.1.2 Zonations . 232
13.1.3 Reproduction 232
13.1.4 Periodicity of Spore Discharge 233
13.1.5 Phototropic Curvature234
13.1.5.1 Pilobolus spp. .234
13.1.5.2 Phycomyces blakesleeanus 236
13.2 Morphogenesis of Fruiting Bodies238
13.2.1 Development of Fruit Bodies.238
13.2.2 Other Fungi238
13.3 Circadian Rhythm in Neurospora. 239
13.3.1 Clock Gene.240
13.3.2 Feedback Loops. 241
13.4 Light-Responsive Genes243
13.5 Entrainment.244
13.6 Possible Role of Circadian Rhythm in Neurospora245
13.7 Concluding Remarks.245
References245
Chapter 14 Thermophilic Fungi: Eukaryotic Life at High Temperature .249
14.1 Discovery 249
14.1.1 Guayule Rets250
14.1.2 Composts 251
14.1.3 Soil . 252
14.2 Physiology .254
14.2.1 Nutrition.254
14.2.2 Respiration .254
14.2.3 Utilization of Carbon Sources . 255
14.2.4 Transport of Nutrients256
14.2.5 Protein Turnover 256
14.3 Extracellular Enzymes 257
14.3.1 Protease 257
14.3.2 Lipase. 257
14.3.3 Amylase .258
14.3.4 Cellulase.258
14.3.5 Xylanase.259
14.4 Intracellular Enzymes.259
14.4.1 Trehalase 259
14.4.2 Invertase.259
14.5 Thermotolerance Gene 261
14.6 Heat-Shock Proteins 261
14.7 Intracellular Solutes262
14.8 Concluding Remarks.262
References263
Part VI Populations
Chapter 15 Species: Their Diversity and Populations 267
15.1 Number of Fungal Species269
15.2 Value of Studying Population Structure and Diversity.269
15.2.1 Basic Research . 270
15.2.2 Applied Research. 271
15.3 Species Recognition 271
15.4 Discovery of Intraspecies Variability . 272
15.4.1 Physiological Races . 272
15.4.2 Vegetative Compatibility . 273
15.5 Generation of Variation. 273
15.5.1 Mutation and Heterokaryosis. 273
15.5.2 Transposable Elements. 273
15.6 Detection of Genetic Variation in Populations . 274
15.6.1 Isozyme Electrophoresis 274
15.6.2 Restriction Fragment Length Polymorphism. 275
15.6.3 Random Amplified Polymorphic DNA . 276
15.6.4 Ribosomal DNA.277
15.6.5 Mitochondrial DNA and Mitochondrial Plasmids 277
15.6.6 Karyotype Polymorphism 278
15.6.7 Spore Killer Elements 278
15.6.8 Multilocus Strain Typing . 278
15.6.9 Microcycle Conidiation 279
15.7 Speciation 279
15.8 Concluding Remarks. 281
References 281
Chapter 16 Senescence .283
16.1 Discovery 283
16.2 Terminology of Senescence 284
16.3 Nucleus- or Mitochondria-Based Senescence.284
16.3.1 Genetic Cross.286
16.3.2 Heterokaryon Test286
16.4 Senescence and Other Death Phenomena.287
16.5 Cytoplasmic Mutants287
16.6 Preservation of Senescing Strains.287
16.7 Instability of Mitochondrial DNA 288
16.8 Senescence-Inducing Plasmids. 291
16.8.1 Variant Plasmids292
16.8.2 Spread of Plasmids.292
16.9 Nuclear Gene Mutants 293
16.9.1 Natural Death.293
16.9.2 Senescent293
16.10 Link with Aerobic Respiration296
16.11 Concluding Remarks.297
References298
A Glossary of Mycological and Interdisciplinary Terms 301
Appendix: Naming, Defining, and Broadly Classifying Fungi. 319
General References 328
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