Genes and Genomics

Genes and Genomics

1st Edition - October 25, 2005

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  • Authors: Dilip K Arora, Randy Berka
  • eBook ISBN: 9780080461328
  • Hardcover ISBN: 9780444518088

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Description

This latest volume addresses the contemporary issues related to recombination in filamentous fungi, EST data mining, fungal intervening sequences, gene silencing, DNA damage response in filamentous fungi, cfp genes of Neurospora, developmental gene sequences, site-specific recombination, heterologous gene expression, hybridization and microarray technology to enumerate biomass. This volume also analyse the current knowledge in the area of hydrophobins and genetic regulation of carotenoid biosynthesis. Over fifty world renowned scientist from both industry and academics provided in-depth information in the field of fungal genes and genomics.

Readership

Students and researchers in the areas of fungal genomics, genetics, biotechnology and bioinformatics.

Table of Contents

  • 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

    A

    B

    C

    D

    E

    F

    G

    H

    I

    K

    L

    M

    N

    O

    P

    R

    S

    T

    U

    V

    W

    X

Product details

  • No. of pages: 444
  • Language: English
  • Copyright: © Elsevier Science 2005
  • Published: October 25, 2005
  • Imprint: Elsevier Science
  • eBook ISBN: 9780080461328
  • Hardcover ISBN: 9780444518088

About the Authors

Dilip K Arora

Affiliations and Expertise

Department of Botany, Banaras Hindu University, Varanasi, India

Randy Berka

Affiliations and Expertise

Novozymes Biotech, Inc., Davis, CA, U.S.A.

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