Genes and Genomics

Contributors

Preface

Chapter 1: Recombination in Filamentous Fungi

1. Introduction

2. Historical Background

3. Models of Meiotic Recombination

4. Genes that Regulate Recombination in Specific Locations

5. Polarity

6. The Effect of Genetic Background on Recombination

7. Sequence Heterology and Recombination

8. Recent Contributions of Filamentous Fungi to an Understanding of Meiotic Recombination

9. The Impact of Genomics

10. Putting Recombination to Work

11. Conclusion

Chapter 2: EST Data Mining and Applications in Fungal Genomics

1. Introduction

2. Est Technology

3. Est Data Sources and Data Mining Tools

4. Applications in Fungal Genomics and Comparative Genomics

5. Est Data Quality Management

6. Conclusions

Chapter 3: Fungal Intervening Sequences

1. Introduction

2. Distribution of Intervening Sequences in Fungal Genomes

3. Mobile Introns and Inteins

4. Function and Applications of Fungal Intervening Sequences

5. Conclusion

Chapter 4: Gene Silencing as a Tool for the Identification of Gene Function in Fungi

1. Introduction

2. RNA-Mediated Gene Silencing

3. RNA-Mediated Gene Silencing as a Tool for Functional Genomics

4. Functional Genomics in Fungi

5. Conclusions

Chapter 5: The DNA Damage Response of Filamentous Fungi: Novel Features Associated with a Multicellular Lifestyle

1. Introdution

2. DNA Damage Response Proteins

3. DNA Damage Response in Fungi

4. Programmed Cell Death in Yeast and Filamentous Fungi

5. Nuclear Autonomous Responses to DNA Damage

6. The DNA Damage Response and Hypal Morphogenesis

7. Conclusions

Chapter 6: The cfp Genes (cfp-1 and cfp-2) of Neurospora crassa: A Tale of a Bunch of Filaments, One Enzyme, and Two Genes

1. Introduction

2. The Pre-Genomic Era: Biochemical and Ultrastructural Studies of P59Nc and The 8-10 nm Cytoplasmic Filaments of N. Crassa

3. The Genetics Behind the Cytoplasmic Filaments of N. Crassa

4. The PDC Filaments and the Sexual Cycle: The Cytoskeleton Revisited

5. Regulation of the Expression of the cfp-1 Gene

6. Pyruvate Decarboxylase: An Enzyme with “Moonlighting” Functions?

7. Conclusions

Chapter 7: A Search for Developmental Gene Sequences in the Genomes of Filamentous Fungi

1. Introduction

2. Methods & Materials

3. Results

4. Discussion

5. Conclusion

Chapter 8: Applications of Fungal Site-specific Recombination as a Tool in Biotechnology and Basic Biology

1. Introduction

2. The Flp Recombinase: Its Normal Physiological Function

3. FLP: A Member of the Tyrosine Family of Recombinases

4. Phage Integrases, Tyrosine and Serine Recombinases: Practical Applications

5. Flp Site-Specific Recombination as a Tool in Genetic Engineering

6. Expanding the Target Repertoire of Site-Specific Recombination: Altered Specificity Flp Variants

7. Applications of Flp for Solving Basic Problems in Biology

8. The Geometry of the Flp Recombination Complex

9. Difference Topology Reveals a Three Site, Five Noded DNA Synapse Formed During Phage Mu Transposition

10. Conclusion

Chapter 9: Heterologous Gene Expression in Filamentous Fungi: A Holistic View

1. Introduction

2. Cellular Control Points in Protein Expression

3. Functional Genomics of Productivity

4. Yields and Authenticity of Recombinant Proteins Made in Filamentous Fungi

5. Cell Wall and Physiological Aspects of Productivity

6. Conclusion

Chapter 10: Expression and Engineering of Fungal Hydrophobins

1. Introduction

2. Medical and Technical Application of Hydrophobins

3. Production of Hydrophobin Variants

4. Over-Expression of Hydrophobins in Filamentous Fungi

5. Conclusions

Chapter 11: Genetic Regulation of Carotenoid Biosynthesis in Fungi

1. Introduction

2. Technical Importance

3. Biological Role

4. The Biochemical Pathway

5. Genetic Regulation of Carotenoid Biosynthesis

6. Conclusions

Chapter 12: Combination of Suppression Subtractive Hybridization and Microarray Technologies to Enumerate Biomass-Induced Genes in the Cellulolytic Fungus Trichoderma reesei

1. Introduction

2. Construction of Subtracted and Normalized cDNA Libraries

3. Identification of Differentially Expressed cDNAs Using Microarrays

4. Analysis of Differentially Expressed SSH-cDNAs

5. Conclusions

Chapter 13: Genomics of Some Human Dimorphic Fungus

1. Introduction

2. Candida albicans: The Model Dimorphic Fungus?

3. Few Phase-Specific Genes have been Identified in Dimorphic Fungi.

4. Data Mining in P. Brasiliensis and H. Capsulatum

5. Comparison between Promoter Activity and Genes Specifically Present in Dimorphic Fungi

6. Conclusions

Chapter 14: Phanerochaete chrysosporium Genomics

1. Introduction

2. Microbiology and Physiology of Wood Decay

3. Experimental Systems

4. Extracellular Oxidative Systems

5. Extracellular Carbohydrate Active Enzymes

6. Other Extracellular Enzymes

7. Intracellular Enzymes Related to Lignocellulose Degradation

8. Conclusion

Chapter 15: Genetics of Morphogenesis in Basidiomycetes

1. Introduction

2. Specialized Features

3. Exemplary Model Systems

4. Conclusions

Keyword Index

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