Fungi: Biology and Applications, 3rd Edition
December 2017, Wiley-Blackwell
This newly updated edition covers a wide range of topics relevant to fungal biology, appealing to academia and industry
Fungi are extremely important microorganisms in relation to human and animal wellbeing, the environment, and in industry. The latest edition of the highly successful Fungi: Biology and Applications teaches the basic information required to understand the place of fungi in the world while adding three new chapters that take the study of fungi to the next level. Due to the number of recent developments in fungal biology, expert author Kevin Kavanagh found it necessary to not only update the book as a whole, but to also provide new chapters covering Fungi as Food, Fungi and the Immune Response, and Fungi in the Environment.
Proteomics and genomics are revolutionizing our understanding of fungi and their interaction with the environment and/or the host. Antifungal drug resistance is emerging as a major problem in the treatment of fungal infections. New fungal pathogens of plants are emerging as problems in temperate parts of the world due to the effect of climate change. Fungi: Biology and Applications, Third Edition offers in-depth chapter coverage of these new developments and moreultimately exposing readers to a wider range of topics than any other existing book on the subject.
- Includes three new chapters, which widen the scope of fungi biology for readers
- Takes account of recent developments in a wide range of areas including proteomics and genomics, antifungal drug resistance, medical mycology, physiology, genetics, and plant pathology
- Provides extra reading at the end of each chapter to facilitate the learning process
Fungi: Biology and Applications is designed for undergraduate students, researchers, and those working with fungi for the first time (postgraduates, industrial scientists).
LIST OF CONTRIBUTORS:
Dr. Khaled H. Abu-Elteen, Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates.
Dr. Catherine Bachewich, Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montreal, QC, Canada H4P 2R2.
Dr. Johan Baars, Plant Research International, Droevendaalsesteeg 1 6708PB, Wageningen, The Netherlands
Dr. Virginia Bugeja, School of Natural Sciences, University of Hertfordshire, College Lane, Hatfield, Hertfordshire AL109AB, England.
Prof. David Coleman, Microbiology Research Laboratory, Dublin Dental Hospital, Trinity College, Dublin 2, Ireland
Dr. Brendan Curran. School of Biological Science, Queen Mary, University of London, Mile End Road, London E1 4NS, England.
Dr. Fiona Doohan, Department of Plant Pathology, University College Dublin, Belfield, Dublin 4, Ireland.
Prof. Sean Doyle, Department of Biology, Maynooth University, Co. Kildare, Ireland.
Dr. David Fitzpatrick, Department of Biology, Maynooth University, Co. Kildare, Ireland.
Dr. Mawieh Hamad, Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates.
Dr. Karina A. Horgan, Alltech Biotechnology Centre, Summerhill Road, Dunboyne, Co. Meath, Ireland.
Dr. Kevin Kavanagh, Department of Biology, Maynooth University, Co. Kildare, Ireland.
Dr. Mohammad G. Mohammad, Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates.
Dr. Gary Moran, Microbiology Research Laboratory, Dublin Dental Hospital, Trinity College, Dublin 2, Ireland.
Dr. Richard A. Murphy, Alltech Biotechnology Centre, Summerhill Road, Dunboyne, Co. Meath, Ireland.
Dr. Richard O’Hanlon, Department of Agriculture, Food and Marine, Backweston, Celbridge, Co. Kildare, Ireland.
Dr. Rebecca Owens, Department of Biology, Maynooth University, Co. Kildare, Ireland
Dr. Derek Sullivan, Microbiology Research Unit, Dublin Dental School & Hospital, Trinity College, Dublin 2, Ireland.
Dr. Graeme M. Walker, Biotechnology & Forensic Sciences, School of Contemporary Sciences, University of Abertay Dundee, Kydd Building Dundee DD1 1HG, Scotland.
Dr. Nia A. White, Biotechnology & Forensic Sciences, School of Contemporary Sciences, University of Abertay Dundee, Kydd Building Dundee DD1 1HG, Scotland.
Dr. Malcolm Whiteway, Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montreal, QC, Canada H4P 2R2.
CONTENTS OF THIRD EDITION
1. INTRODUCTION TO FUNGAL PHYSIOLOGY
Graeme M. Walker & Nia A. White
Fungi are extremely important microorganisms in relation to human and animal wellbeing, the environment and in industry. This Chapter will cover the nutrition, metabolism, growth, reproduction and death of yeast and fungal cells – all topics that pertain to Fungal Physiology. The topics in question will be revised and updated from the second edition of the textbook. Some aspects will be expanded upon to reflect more recent developments in areas such as fungal cell death, modelling of fungal growth and modern methods for studying fungal physiology. The coverage will be at an introductory level but will include up-to-date references for further reading.
1.2. Morphology of yeasts and fungi
1.4. Fungal nutrition and cellular biosyntheses
1.5. Fungal metabolism
1.6 Fungal growth and reproduction
1.8 Further Reading
1.9 Revision Questions
2. FUNGAL GENETICS (To be updated and revised)
Malcolm Whiteway & Catherine Bachewich
2.2 Life cycles
2.3 Sexual analysis: regulation of mating
2.4 Unique Characteristics of filamentous fungi that are advantageous for genetic analysis
2.5. Genetics as a tool
2.7 Further reading
2.8 Revision Questions.
3. FUNGAL GENOMICS (To be updated and revised)
David Fitzpatrick and Edgar Medina
3.1 Genome sequencing
3.2 Bioinformatics tools
3.3 Comparative Genomics
3.4 Genomics and the Fungal tree of life
3.5 Online Fungal Genomic Resources
3.7 Further Reading
3.8 Revision questions
4. Fungal Genetics : A post-genomic perspective. To be updated and revised
Brendan Curran & Virginia Bugeja
4.3 Transcriptomics and Proteomics
4.5 Systems Biology
4.7 Further Reading.
4.8 Revision Questions
5. FUNGAL FERMENTATION SYSTEMS AND PRODUCTS - To be updated and revised
5.1 Fungal Fermentation Systems
5.2 Fungal fermentation products
5.4 Further Reading
5.5 Revision Questions
6 FUNGI AS FOOD
New Chapter in third edition
The chapter will describe the main species of basidiomycetes that are cultivated for food on a commercial scale; Oyster mushroom (Pleurotus ostreatus), shiitake (Lentinula edodes), button mushroom/champignon de Paris (Agaricus bisporus), wood ear (Auricularia auricula), rice straw mushroom (Volvariella volvacea) and winter mushroom (Flammulina velutipes). For each of the species, the method of commercial cultivation will briefly be discussed.
Next to this a section will be attributed to fungi collected in nature (chanterelle, morels, truffles). Next to this, nutritional value of the cultivated mushrooms will be discussed. This will mainly focus on energy content, protein content (and if possible protein quality from a nutritional point of view), the content of the soluble carbohydrates, fiber content and composition. Next to this mushrooms are known for their contents of vitamin B. The last few year there is also a lot of attention for the ergosterol/vitamin D2 content. Finally, in this section attention will be paid to mineral content (for instance, basidiomycete fungi are known to accumulate cadmium etc.).
The last decade there is an increased interest in medicinal properties of mushrooms. In the last section a review will be given of potential medicinal aspects of the main cultivated mushrooms. In this review also fungi that are usually not eaten for food, but mainly for medicinal purposes will be discussed.
7. ANTIBIOTIC AND CHEMICAL COMMODITIES FROM FUNGI- to be update and revised.
Karina A. Horgan & Richard A. Murphy
Will include discussion of problem of antibiotic resistance.
7.0 Introduction to Pharmaceutical and Chemical Commodities
7.1 Fungal Metabolism
7.2 Antibiotic Production
7.3 Pharmacologically Active Compounds
7.4 Chemical Commodities
7.5 Yeast Extracts
7.6 Enriched Yeast
7.8 Further Reading
7.9 Revision Questions
8. BIOTECHNOLOGICAL USE OF FUNGAL ENZYMES- To be update and revised.
Shauna M. McKelvey and Richard Murphy
8.1 Introduction to Enzymes
8.2 Enzymes in Industry
8.3 Current Enzyme Applications
8.4 Future Direction of Industrial enzymes
8.5 Specific Enzymes
8.6 Enzyme production strategies
8.8 Further Reading
8.9 Revision questions
9. The biotechnological exploitation of heterologous protein production in fungi - To be update and revised.
Brendan Curran & Virginia Bugeja.
9.2 Heterologous protein expression in fungi
9.3 Case Study: Hepatitis B vaccine – A billion dollar heterologous protein from yeast.
9.4 Further biotechnological applications of expression technology.
9.6 Further Reading
9.7 Revision questions
10. FUNGAL PROTEOMICS
Sean Doyle & Rebecca Owens
The term proteomics is used to describe the techniques used to identify the total protein content of a cell or organism. In addition, it can be further defined in terms of either the study of protein modifications or protein-protein interactions. Fungal proteomics, that is the study of the proteome of fungi, has emerged as an important area whereby modern proteomic techniques allow rapid identification of fungal proteins of biomedical or biotechnological importance. This chapter will describe methods used for protein extraction and isolation, subcellular fractionation and electrophoretic techniques used for protein purification prior to identification by protein mass spectrometry. In particular, recent developments in label-free quantitative proteomics will be explained and discussed. Finally, selected examples of the uses of proteomics in the study of fungal virulence and commercial potential.
Fungi as ‘black boxes’.
Fungi as reservoirs of valuable protein products.
2. Protein isolation and purification.
Cell lysis strategies.
3. Electrophoretic techniques.
4. Protein mass spectrometry
5. Shotgun and Quantitative proteomics.
6. Uses of proteomics
Studying fungal virulence.
Fungal secretome to identify enzymes of commercial importance.
Assignment of function to ‘hypothetical proteins’ or ‘proteins of unknown function’ derived from fungi.
Applications of proteomics in food biotechnology.
11. FUNGAL DISEASES OF HUMANS - To be updated and revised with new material on novel diagnostic methods.
Derek Sullivan, Gary Moran & David Coleman
11.0 Introduction to Human Fungal Infections
11.1 Superficial Mycoses
11.2 Opportunistic Mycoses
11.3 Endemic Systemic Mycoses
11.5 Concluding Remarks
11.6 Further Reading
11.7 Revision Questions
12. IMMUNITY TO HUMAN FUNGAL INFECTIONS
Mawieh Hamad,Mohammad G. Mohammad, and Khaled H. Abu-Elteen.
New Chapter in Third edition
- Innate Immunity to human fungal infections
1.1 Physiological and biochemical barriers
1.2 Antifungal peptides and other soluble mediators
1.3 Recognition of fungal pathogens
1.3.1 PAMPs and PRRS
1.3.2 Phagocytosis and the oxidative burst
1.3.3 The role of neutrophil extracellular traps (NETs) in fungal immunity
1.3.4 C-type lectin receptors and signal transduction pathways
1.3.5 Activation of dendritic cells
1.3.6 Cellular effector responses
- Adaptive immunity to fungi
2.1 At the crossroads between innate and adaptive antifungal immunity (Dendritic cells)
2.2 Th responses
2.3 Cytotoxic and killer cells
2.4 Antibody responses
- Regulation of antifungal immunity
3.1 Inflammation vs. tolerance: a balancing act
3.2 Cytokines and Th polarization
3.3 IDO and tryptophan metabolism
- Controversies and outstanding issues
4.1 Antifungal overdosing and host immunity
4.2 Reshaping immunity by immunotherapy
4.3 The role of iron metabolism in fungal immunity
- Concluding remarks
- Review questions
- Suggested readings
13. ANTIFUNGAL AGENTS FOR USE IN HUMAN THERAPY
Khaled H Abu Elteen and Mawieh Hamad
13.0 Introduction (to be revised in the light of the new scope the edited chapter, inclusion of one or more new figures; update previous figures and enhance their quality to look more appealing)
13.1 Drugs Targeting the Plasma Membrane
184.108.40.206 General Properties
220.127.116.11 Mechanism(S) of Action (Adding more information about other formulations of AMB)
18.104.22.168 Spectrum of Activity
22.214.171.124 Administration and Dosage
126.96.36.199 Adverse Effects
188.8.131.52 Resistance to Polyenes
184.108.40.206 General Properties (More information about newer generations of triazoles: Isavuconazole, Ravuconazole, Efinaconazole, Luliconazole and Albaconazole)
220.127.116.11 Mechanism of Action
18.104.22.168 Spectrum of Activity
22.214.171.124 Adverse Effects
126.96.36.199 Resistance to Azoles
13.1.3 Allylamines and Thiocarbamates
13.1.4 Octenidine and Pirtenidine
13.1.5 Morpholines and Other Agents
13.2 Drugs Targeting the Cell Wall
13.2.1 Echinocandins and Aminocandin
13.2.2 Nikkomycin and Chitin Synthesis
13.3 Drugs Targeting Nucleic Acid and Protein Synthesis
13.3.1 Sordarin and its derivatives
188.8.131.52 Mechanism of Action
184.108.40.206 Spectrum of Activity
220.127.116.11 Pharmacokinetics and Dosage
18.104.22.168 Adverse Effects
22.214.171.124 Resistance to 5-FC
13.4 Novel Therapies (to be revised in light of recent developments in antifungal immunotherapy, new antifungal peptides, advances in probiotic therapy)
13.5 Conclusion [to be re-focused]
13.6 Revision Questions [to be revisited]
13.7 Further Reading [to be updated]
14. FUNGAL PATHOGENS OF PLANTS - To be updated and revised
14.1 Fungal pathogens of plants
14.2 Disease symptoms
14.3 Factors influencing disease development
14.4 The disease cycle
14.5 Genetics of the plant-fungal pathogen interaction.
14.6 Mechanisms of fungal plant parasitism
14.7 Mechanisms of host defence
14.8 Disease control
14.9 Disease detection and diagnosis
14.10 Vascular wilt diseases
14.12 Rots and damping off diseases
14.13 Leaf and stem spots, anthracnose and scabs
14.14 Rusts, smuts and powdery mildew diseases
14.15 Global repercussions of fungal diseases of plants
14.18 Revision questions
15. FUNGI IN THE ENVIRONMENT
New Chapter in Third edition
Fungi are ubiquitous in the natural environment. There are an estimated 1.5 million species of fungi, and these can be roughly divided into symbiotic, saprobic or pathogenic lifestyles depending on how they gain their primary food source. Symbiotic fungi exist in a close association with an other organism, and include mycorrhizal and lichen forming fungi. Saprobic fungi play a large part in recycling important nutrients (e.g. N, P, K) back into the environment. Pathogenic fungi are responsible for economic losses in agriculture and forestry, but like saprobic fungi, also play an important role in recycling nutrients back into ecosystems. Fungi also provide a food source for other organisms in natural environments, their fruit bodies (e.g. mushrooms, truffles) being eaten by a wide range of insects and animals. Fungal surveys use a wide range of techniques to detect and measure fungal diversity and biomass in the environment.
15.2 Symbiotic fungi
15.3 Saprobic fungi
15.4 Pathogenic fungi
15.5 Fungi in food webs
15.6 Fungi and nutrient cycling
15.7 Quantifying fungi in the environment
15.9 Further reading
15.10 Revision questions
Answers to Revision Questions.