Fungi Experimental Methods In Biology

Fungi Experimental Methods In Biology
 
Author:
Ramesh Maheshwari
Publisher: CRC Press
ISBN No:
978-1-4398-3904-1
Release at: 2012
Pages: 354
Edition:
Second Edition
File Size: 13 MB
File Type: pdf
Language: English



Content of Fungi Experimental Methods In Biology



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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