reading

Cover
Title Page
List of Contributors
Preface
1 Introduction to Fungal Physiology
1. 1.1 Introduction
2. 1.2 Morphology of Yeasts and Fungi
3. 1.3 Ultrastructure and Function of Fungal Cells
4. 1.4 Fungal Nutrition and Cellular Biosyntheses
5. 1.5 Fungal Metabolism
6. 1.6 Fungal Growth and Reproduction
7. 1.7 Conclusion
8. Further Reading
2 Fungal Genetics
1. 2.1 Introduction
2. 2.2 Fungal Lifecycles
3. 2.3 Sexual Analysis: Regulation of Mating
4. 2.4 Unique Characteristics of Filamentous Fungi that Are Advantageous for Genetic Analysis
5. 2.5 Genetics as a Tool
6. 2.6 Conclusion
7. Acknowledgment
8. Further Reading
3 Fungal Genomics
1. 3.1 Introduction
2. 3.2 Genome Sequencing
3. 3.3 Bioinformatics Tools
4. 3.4 Comparative Genomics
5. 3.5 Genomics and the Fungal Tree of Life
6. 3.6 Online Fungal Genomic Resources
7. 3.7 Conclusion
8. Further Reading
4 Fungal Genetics: A Post‐Genomic Perspective
1. 4.1 Introduction
2. 4.2 The Yeast Saccharomyces cerevisiae: A Cornerstone of Post‐Genomic Research
3. 4.3 Of ‐omics and Systems Biology
4. 4.4 Genomics
5. 4.5 Transcriptomics and Proteomics
6. 4.6 Systems Biology
7. 4.7 Conclusion
8. Further Reading
5 Fungal Proteomics
1. 5.1 Introduction
2. 5.2 Protein Isolation and Purification
3. 5.3 Electrophoretic Techniques
4. 5.4 Protein Mass Spectrometry
5. 5.5 Fungal Proteomics
6. 5.6 Label‐Free Quantitative Proteomic Applications
7. 5.7 Specialized Proteomics Applications in Fungal Research
8. 5.8 Conclusion
9. Acknowledgments
10. Further Reading
6 Fungi as Food
1. 6.1 Introduction
2. 6.2 The Main Cultivated Mushroom Species
3. 6.3 The Main Species of Mushroom Collected in Nature
4. 6.4 Nutritional Value of Mushrooms
5. 6.5 Potential Medicinal Properties of Mushrooms
6. 6.6 Conclusion
7. Further Reading
8. Useful Websites
7 Pharmaceutical and Chemical Commodities from Fungi
1. 7.1 Introduction
2. 7.2 Fungal Metabolism
3. 7.4 Pharmacologically Active Compounds
4. 7.5 Chemical Commodities
5. 7.6 Yeast Extracts
6. 7.7 Enriched Yeast
7. 7.8 Conclusion
8. Further Reading
8 Biotechnological Use of Fungal Enzymes
1. 8.1 Introduction
2. 8.2 Enzymes in Industry
3. 8.3 Current Enzyme Applications
4. 8.4 Enzymes and Sustainability
5. 8.5 Future Direction of Industrial Enzymes
6. 8.6 Applications of Specific Fungal Enzymes
7. 8.7 Enzyme Production Strategies
8. 8.8 Conclusion
9. Further Reading
9 Biotechnological Exploitation of Heterologous Protein Production in Fungi
1. 9.1 Introduction
2. 9.2 Heterologous Protein Expression in Fungi
3. 9.3 Use of Saccharomyces cerevisiaefor Heterologous Protein Production
4. 9.4 Use of Pichia pastoris for Heterologous Protein Production
5. 9.5 Case Study: Hepatitis B Vaccine – A Billion‐Dollar Heterologous Protein from Yeast
6. 9.6 Further Biotechnological Applications of Expression Technology
7. 9.7 Conclusion
8. Further Reading
10 Fungal Infections of Humans
1. 10.1 Introduction
2. 10.2 Superficial Mycoses
3. 10.3 Opportunistic Mycoses
4. 10.4 Endemic Systemic Mycoses
5. 10.5 Mycotoxicoses
6. 10.6 Conclusion
7. Further Reading
8. Useful Websites
11 Immunity to Human Fungal Infections
1. 11.1 Introduction
2. 11.2 Compromised Immunity Increases Host Susceptibility to Fungal Infections
3. 11.3 Shaping of the Antifungal Immune Response
4. 11.4 Paradigm Shifts in Antifungal Immunity
5. 11.5 Anatomy of the Antifungal Immune Response
6. 11.6 The Role of DCs in Antifungal Immunity
7. 11.7 Adaptive Immunity to Fungal Infections
8. 11.8 Immunity to Dermatophytes
9. 11.9 Evasion of Host Immunity by Fungal Pathogens
10. 11.10 Conclusion
11. Further Reading
12 Antifungal Agents for Use in Human Therapy
1. 12.1 Introduction
2. 12.2 Drugs Targeting the Plasma Membrane
3. 12.3 Drugs Targeting the Cell Wall
4. 12.4 Drugs Targeting Nucleic Acid and Protein Synthesis
5. 12.5 Novel Therapies
6. 12.6 Conclusion
7. Further Reading
13 Fungi in the Environment
1. 13.1 Introduction
2. 13.2 Macrofungi, Mushrooms, and Sporocarps
3. 13.3 Symbiotic Fungi
4. 13.4 Saprobic Fungi
5. 13.5 Parasitic Fungi
6. 13.6 Fungi in Food Webs
7. 13.7 Fungi and Nutrient Cycling
8. 13.8 Quantifying Fungi in the Environment
9. 13.9 Conclusion
10. Further Reading
14 Fungal Pathogens of Plants
1. 14.1 Introduction
2. 14.2 Disease Symptoms
3. 14.3 Factors Influencing Disease Development
4. 14.4 The Disease Cycle
5. 14.5 Genetics of the Plant–Fungal Pathogen Interaction
6. 14.6 Mechanisms of Fungal Plant Parasitism
7. 14.7 Mechanisms of Host Defense
8. 14.8 Disease Control
9. 14.9 Disease Detection and Diagnosis
10. 14.10 Vascular Wilt Diseases
11. 14.11 Blights
12. 14.12 Rots and Damping‐Off Diseases
13. 14.13 Leaf and Stem Spots, Anthracnose, and Scabs
14. 14.14 Rusts, Smuts, and Powdery Mildew Diseases
15. 14.15 Global Repercussions of Fungal Diseases of Plants
16. 14.16 Conclusion
17. Acknowledgments
18. Further Reading
Supplemental Images
Index
End User License Agreement

List of Tables

Chapter 01
1. Table 1.1 Diversity of yeast cell shapes.
2. Table 1.2 Major polymers found in different taxonomic groups of fungi and fungus‐like organisms, together with presence of perforate septa in these groups.
3. Table 1.3 Functional components of an idealized fungal cell.
4. Table 1.4 Elemental requirements of fungal cells.
5. Table 1.5 Diversity of carbon sources for yeast and filamentous fungal growth.
6. Table 1.6 Yeast and fungal metabolism based on responses to oxygen availability.
7. Table 1.7 Metals required for fungal growth and metabolic functions.
8. Table 1.8 Principal ingredients of selected industrial media for yeasts and fungi.
9. Table 1.9 Modes of nutrient transport in fungi.
10. Table 1.10 Respiratory chain characteristics of yeasts and fungi.
11. Table 1.11 Modes of vegetative reproduction in yeasts.
Chapter 03
1. Table 3.1 Useful online resources.
Chapter 04
1. Table 4.1 Details of the 19 completed fungal genomes.
2. Table 4.2 Genome topology of model fungi.
3. Table 4.3 Evolutionary history of model fungal genomes.
4. Table 4.4 Post‐genomic vocabulary.
5. Table 4.5 Proteomics is much more challenging than transcriptomics or genomics.
Chapter 05
1. Table 5.1 Advantages and disadvantages of alternative chromatographic techniques for fungal protein isolation.
2. Table 5.2 Genomic, proteomic, and general fungal websites.
3. Table 5.3 Features of various MS‐based methods of quantitative proteomic analysis.
Chapter 06
1. Table 6.1 Amounts of mushrooms and truffles^* produced by the top 10 producers in the world.
2. Table 6.2 Proximate composition per 100 g of fresh weight of raw fresh mushrooms compared to other foods.
3. Table 6.3 Contents of vitamins in 100 g of raw fresh mushrooms.
4. Table 6.4 Contents of minerals in 100 g of raw fresh mushrooms and other raw foods.
Chapter 07
1. Table 7.1 Fungal products of economic importance.
2. Table 7.2 Examples of primary and secondary metabolites.
3. Table 7.3 Isolated endophytic fungi and their bioactive products.
4. Table 7.4 Industrial production of vitamins.
Chapter 08
1. Table 8.1 Sources and applications of industrial enzymes.
2. Table 8.2 Enzyme activities and associated supplementational effects on animal performance.
3. Table 8.3 Classification of proteases.
4. Table 8.4 Components of aerobic fungal cellulases and their mode of action on the cellulose chain.
Chapter 09
1. Table 9.1 Representative selection of heterologous proteins produced in filamentous fungi.
2. Table 9.2 Representative selection of heterologous proteins produced in yeast.
3. Table 9.3 Promoters used to direct heterologous gene expression in S. cerevisiae.
4. Table 9.4 Signal sequences used to direct secretion of heterologous proteins from S. cerevisiae.
5. Table 9.5 Heterologous proteins of therapeutic use produced in yeasts.
Chapter 10
1. Table 10.1 Examples of superficial mycoses.
2. Table 10.2 Examples of risk factors for opportunistic fungal infection.
3. Table 10.3 Examples of opportunistic mycoses.
4. Table 10.4 Candida species most commonly associated with human disease.
5. Table 10.5 Virulence factors of C. albicans.
6. Table 10.6 Examples of endemic systemic mycoses.
Chapter 11
1. Table 11.1 Commonly encountered opportunistic fungal infections in patients with impaired immunity.
2. Table 11.2 Commonly used transgenic and knockout mouse models in antifungal immunity research.
3. Table 11.3 Tentative summary of the role of various immune cells and mediators in antifungal immunity.
Chapter 12
1. Table 12.1 Nature, target, mode of action, and fungal resistance mechanisms of the major antifungal drugs used in human therapy.
2. Table 12.2 Tolerability and drug interactions of membrane‐targeting antifungals.
3. Table 12.3 Biochemical basis of azole resistance.
4. Table 12.4 Tentative list of promising alternative approaches to prevent and/or treat fungal infections.
Chapter 13
1. Table 13.1 Notable macrofungal species frequently grown or collected worldwide.
2. Table 13.2 Sampling methods for the collection of fungi in the environment.
3. Table 13.3 Identification methods for quantifying fungi in an environmental sample.
Chapter 14
1. Table 14.1 Examples of economically significant fungal diseases, causal organisms, hosts, and associated symptoms^*.
2. Table 14.2 Gene‐for‐gene interaction between fungal pathogens and plants^*.
3. Table 14.3 Examples of fungal toxins, their specificity, producer fungi, and associated diseases.
4. Table 14.4 Pre‐formed and induced defense strategies used by plants to combat fungal diseases.

List of Illustrations

Chapter 01
1. Figure 1.1 Scanning electron micrograph of a typical yeast cell (×10,000). BS, Bud scar; BirS, birth scar.
2. Figure 1.2 Transmission electron microscopy of ultrathin sections of a hyphal tip of Fusarium reveals intracellular fine structure. Layers of cell wall are shown in greater detail in lower image. M, Mitochondrion; V, vesicles; P, plasma membrane; MT, microtubules; SC, smooth Golgi cisternae; 1, 2, 3, 4, four layers of the cell wall. The Spitzenkörper appears as a region surrounded by vesicles containing many small particles (rectangle).
3. Figure 1.3 Cell envelope structure of the yeast S. cerevisiae.
4. Figure 1.4 Electron micrograph of a typical yeast cell. CW, Cell wall; CM, cell membrane; CMI, cell membrane invagination; BS, bud scar; M, mitochondrion, N, nucleus; V, vacuole; ER, endoplasmic reticulum.
Chapter 02
1. Figure 2.1 Lifecycle of Saccharomyces cerevisiae.
2. Figure 2.2 Lifecycle of Aspergillus nidulans.
3. Figure 2.3 Lifecycle of Neurospora crassa.
4. Figure 2.4 Lifecycle of Coprinus cinerus.
5. Figure 2.5 Lifecycle of Cryptococcus neoformans.
6. Figure 2.6 (a) Developing conidiophore composed of a vesicle giving rise to phialides and conidia in the filamentous fungus A. nidulans. Released conidia are indicated by an arrow. (b) Hyphae growing from yeast cells of the dimorphic fungus C. albicans. (c) Various stages in the lifecycle of the yeast S. cerevisiae. The first panel demonstrates vegetatively growing yeast, the second shows a zygote, and the third asci (arrows). Bars: 10 µm.
7. Figure 2.7 Chromosome assortment in N. crassa.
8. Figure 2.8 Genetic screen identifying metabolic mutants in N. crassa.
9. Figure 2.9 Selected genetic screens identifying cell cycle mutants in A. nidulans.
10. Figure 2.10 CRISPR/Cas9 for gene editing. (a) CRISPR components sgRNA and Cas9, and the target gene of interest containing a PAM sequence. (b) Cas9 interaction with the sgRNA and target locus, resulting in double‐strand (DS) DNA breaks and introduction of mutation during repair.
Chapter 03
1. Figure 3.1 Schematic of the current consensus on fungal phylogeny. Fungal phylogenetics is currently in flux and the relationships between particular phyla are still unknown. (Phylogeny redrawn from the Tree of Life web project (Table 1).)
2. Figure 3.2 Schematic of the Sanger sequencing method. (a) Four separate DNA extension reactions are carried out. Materials required include single‐stranded DNA, DNA polymerase, DNA primers, and all four dNTPs. One of the dNTPs is radioactively labeled to enable visualization in part c). (b) Each of the four reactions contains a different dideoxynucleoside triphosphate (ddNTP). Synthesis continues until a ddNTP is incorporated, terminating extension reaction. (c) Products are separated based on size on a polyacrylamide gel and the sequence can be determined.
3. Figure 3.3 Schematic of the Illumina genome analyzer sequencing technology. (a) DNA is fragmented and adapters are ligated to both ends of the fragments. (b) Single‐stranded fragments bind randomly to the surface of the flow cell (see main text). (c) Sequencing by synthesis (see main text).
4. Figure 3.4 Steps taken by the BLAST algorithm when searching a database. (a) The query sequence is compared to a scoring matrix (b), and scores for query words of a given length (three in this case) are calculated (c); query words greater than a certain threshold (T) are used to search the database. (d) The algorithm attempts to extend the alignment either side of the query word that has a hit in the target database. (e) Extension continues until the alignment score falls off more than the allowable significance decay, X.
5. Figure 3.5 Steps taken by the FASTA algorithm when searching a database. (a) Words common to the query and target sequence are located. FASTA connects words close to one another and these are represented by diagonal lines. (b) The top 10 diagonals are selected for further analysis. (c) Diagonals are aligned optimally using a local alignment strategy.
6. Figure 3.6 Synteny of eight orthologs in five Candida species. Genes A, D, and F are syntenic in all species; this is represented by conservation of color between them. Genes B, C, G, and H are syntenic in C. albicans, C. dubliniensis, and C. tropicalis. Orthologs of B, C, G, and H are present in C. parapsilosis and L. elongisporus and are syntenic with one another, although they are located in different genomic locations relative to the first three species. The degree of synteny between the five species closely matches the phylogeny of these species.
7. Figure 3.7 Representation of supertree reconstruction. Supertree methods take individual gene trees and express them as a single representative phylogeny. Thousands of trees (expressed as n) can be used as input for supertree techniques.
Chapter 04
1. Figure 4.1 Finding an ORF. Finding the ATG methionine codon requires a computer search of six different reading frames. An ORF continues for a further 99 codons before hitting a nonsense codon.
2. Figure 4.2 Sequence of the H1 gene in the S. cerevisiae database. Using an appropriate search, the bases encoding the H1 gene (blocked in above) were found as part of the sequence of chromosome 16.
3. Figure 4.3 ORF knockout in the yeast S. cerevisiae. Appropriate PCR primers are used to generate hybrid DNA molecules consisting of the KanR selectable marker flanked by blocks of DNA consisting of the 5′ and 3′ ends of the ORF of interest. Homologous recombination in transformants knocks out the ORF of interest.
4. Figure 4.4 Using comparative genomics to assign biological significance to ORFs. BLAST searches of all the Schiz. pombe ORFs revealed that 681 ORFs (14%) were uniquely present in Schiz. pombe, 769 (16%) were homologous to S. cerevisiae ORFs, and approximately 3,300 Schiz. pombe ORFs (70%) had homologs in common with both S. cerevisiae and C. elegans.
5. Figure 4.5 Creating a fluorescently labeled protein. PCR was used to create a hybrid DNA consisting of a selectable marker (His 3) and the coding sequence for GFP fused in‐frame with the two adjacent sequences of DNA from the 3′ end of the coding sequence of the target ORF. Homologous recombination was then used to target each hybrid molecule back into the correct chromosomal locus, thereby creating a GFP tagged gene sequence.
6. Figure 4.6 Meta‐network consisting of 32 functions (and their 70 or so associated interlinking connections) in place of the 1,548 individual proteins and their 2,700 links which constitute the yeast interactome.
7. Figure 4.7 Overview of high‐throughput systems designed to capture information on protein–protein interactions. (a) A yeast two hybrid (Y2H) detects interactions between proteins X and Y, where X is linked to a DNA binding domain which binds to upstream activating sequence (UAS) of a promoter. (b) MS identifies polypeptide sequence. (c) TAP purifies proteins associated with the target (x). (d) Gene co‐expression analysis produces the correlation matrix, where dark areas show high correlation between expression levels of corresponding genes. (e) Protein microarrays (protein chips) can detect interactions between actual proteins rather than genes: target proteins immobilized on solid support are probed with a fluorescently labeled protein. (f) Synthetic lethality method describes the genetic interaction when two individual, nonlethal mutations result in lethality when administered together (a⁻ b⁻).
8. Figure 4.8 This low‐resolution map of the Biological Process ontology is built by drawing up a carefully controlled vocabulary of terms about biological processes and then linking them with logical statements. This ontology is read from bottom to top. (See http://www.geneontology.org/GO.ontology.relations.shtml for a full description of logical nomenclature for all three ontologies.
9. Figure 4.9 Using a subset of Molecular Function ontology to illustrate the difference between annotation and ontology. Biological terms populating nodes, and arrows between nodes, constitute the ontology. Gene designations for the three model organisms, linked to keyword databases such as GenBank, EMBL, and MIPS, are the annotations. In the case of the single ontological term “chromatin binding” there are 16 separate annotations arising from three different databases.
10. Figure 4.10 System analysis reveals new levels of regulation in a basic fungal metabolic pathway. Dotted interactions denote model refinements to galactose metabolism in yeast following a post‐genomic global analysis of the yeast genome sequence, microarray‐based mRNA analysis, databases of protein–protein interactions, and rapid MS analysis of proteins.
Chapter 05
1. Figure 5.1 Schematic representation of SDS‐PAGE and 2D‐PAGE. (a) SDS‐PAGE separation of proteins by molecular mass. Lane 1 illustrates proteins of known molecular mass (“marker proteins”), lane 2 contains a protein extract containing proteins of different molecular mass, and lane 3 contains a purified protein preparation (single band). (b) 2D‐PAGE consists of two distinct steps: isoelectric focussing (IEF) followed by PAGE. In step 1, native proteins are separated according to charge on an IEF strip. This strip is then placed on top of a PAGE gel and step 2 involves the additional separation of proteins by molecular mass to yield protein “spots.” These can be excised and digested with trypsin for mass spectrometric analysis.
2. Figure 5.2 Immunoproteomics. (a) Duplicate 2D‐PAGE analysis is performed and gel‐1 is stained with Coomassie brilliant blue dye, while gel‐2 is subjected to electrotransfer onto a suitable membrane. This membrane is subsequently probed with antisera using an immunoblot procedure as shown in (b) to detect immunoreactive proteins (2D‐immunoblot). The corresponding protein (circled) in gel‐1 can then be excised and identified by protein MS.
3. Figure 5.3 2D‐PAGE of a mycelial extract from an ascomycete stained with Coomassie Brilliant Blue protein stain. IEF was carried out over a pH range 4–7 and 10% PAGE was employed for molecular mass separation. Each “spot” corresponds to an individual protein monomer from the organism. In general, different protein spot intensity corresponds to different relative amounts.
4. Figure 5.4 Schematic diagram of the overall process involved in fungal proteomics. Fungal cultures are initially separated into mycelia and culture supernatants. Protein fractionation can then be carried out using gel‐based electrophoresis (SDS‐PAGE or 2D‐PAGE), or chromatography (not shown). Alternatively, whole cell lysates can be trypsin‐digested without prior fractionation. Ultimately, peptide mixtures derived from either individual proteins (following purification) or protein mixtures (shotgun proteomics) are analyzed by LC‐MS/MS to generate mass or sequence information. These data are then used to interrogate publicly available or local genomic/cDNA databases to facilitate protein identification.
5. Figure 5.5 Gradient profile for reverse phase LC‐MS and total ion chromatogram, respectively. (a) Typical gradient profile used in qualitative or quantitative MS‐based proteomics. A polar solvent (Solvent A: 0.1 % (v/v) formic acid in water) is used initially for peptide loading to the column. Peptides bound to the column are eluted by increasing concentration of the nonpolar solvent (Solvent B: 0.1 % (v/v) formic acid in acetonitrile) across a 2‐hour gradient. Most peptides typically elute by 30–40% B, and this is followed by a nonpolar wash step to remove any tightly bound molecules, before re‐equilibration into a low % B for loading of the next sample. (b) MS‐based proteomics: this total ion chromatogram (TIC: ion intensity versus time (min)) shows separation of peptides by nanoLC, with peptide detection and identification by MS/MS (via electrospray ionization), following trypsin digestion of a total fungal protein lysate (Figure 5.4). Sample amount used for analysis is generally 0.7 µg peptide and an LC gradient time of 120 min is necessary to enable optimal peptide fractionation. Instrument software (primarily) and operator expertise then matches peptide mass/sequence data to translated DNA/cDNA sequences in in silico databases to enable multiple protein identification. Thousands of individual proteins in a single sample can be confidently identified using this approach.
6. Figure 5.6 Quantitative MS‐based proteomics methods. In label‐free workflows, proteins from distinct samples are extracted, processed, and analyzed separately. MS spectra from each sample are compared within specific windows of time, and relative peptide abundance is calculated based on the “intensities” of precursor ions (area under the curve or spectral counts). Isotopic or isobaric labeling allows samples possessing different labels to be combined once the label/tag has been introduced (metabolically or chemically). In the case of isotopic labels, each type of label will add a distinct mass upon incorporation into the peptide. “Heavy” peptides can be differentiated from their “light” counterparts based on a defined increase in the m/z value. Relative abundance of a peptide originating from comparator samples is calculated by comparing the MS spectra for each isotope. In contrast, each isobaric label adds the same mass to the labeled peptides, and so no distinction can be made from MS spectra following multiplexing. Fragmentation of the precursor peptide ions prior to MS² leads to release of reporter ions of a specific m/z. By comparing the intensities of reporter ions, the relative abundance of the peptide can be determined for each sample.
7. Figure 5.7 The role of protein MS in confirming in silico splice site identification in fungal genes. Following fungal genome sequencing, in silico analysis had predicted the presence of two introns (I1 and I2), and a stop codon in exon 3 (E3), in the gene of interest. LC‐MS/MS analysis of tryptic peptides from the protein revealed the presence of four peptides (A–D). Peptide A was originally encoded by exon 1. Peptides B and C could only have been detected if I1 and I2, respectively, had been present in DNA and subsequently excised during mRNA synthesis. Peptide D did not contain a C‐terminal K or R residue and so its detection by LC‐MS/MS strongly indicates correct stop codon (*) annotation in genomic DNA.
Chapter 06
1. Figure 6.1 Development of world mushroom production.
Chapter 07
1. Figure 7.1 Structures of the core β‐lactam ring and β‐lactam antibiotics.
2. Figure 7.2 Natural and semisynthetic penicillins.
3. Figure 7.3 Cephalosporin structures.
4. Figure 7.4 Chemical structure of paclitaxel.
5. Figure 7.5 Types of reactor for citric acid production.
6. Figure 7.6 Citric acid biosynthetic pathway.
7. Figure 7.7 Vitamin D biosynthesis.
8. Figure 7.8 Yeast extract manufacturing process.
9. Figure 7.9 Selenium compounds in selenium yeast.
10. Figure 7.10 Selenium yeast production.
Chapter 08
1. Figure 8.1 Flow diagram of fungal enzyme production.
Chapter 09
1. Figure 9.1 A generalized expression vector for use in S. cerevisiae.
2. Figure 9.2 Structure (a) and integration (b) of a P. pastoris expression vector.
3. Figure 9.3 A secretion vector for use in S. cerevisiae.
4. Figure 9.4 Cleavage of a secretory signal sequence from a heterologous protein.
5. Figure 9.5 Hepatitis B virus.
6. Figure 9.6 Proof of principle (a) and scale‐up (b) plasmids.
7. Figure 9.7 Analysis of oestrogen receptor proteins.
8. Figure 9.8 Heterologous receptor analysis using a re‐engineered yeast pathway.
9. Figure 9.9 The two‐hybrid system – only when “X” interacts with “Y” can the reporter gene get activated.
Chapter 10
1. Figure 10.1 Candida albicans yeast cells (blastospores) producing (a) hyphae and (b) chlamydospores.
2. Figure 10.2 Aspergillus fumigatus (a) conidiophore and (b) germinating conidia.
3. Figure 10.3 Chemical structure of aflatoxin B₁.
Chapter 11
1. Figure 11.1 General overview of cell‐mediated antifungal immunity.
2. Figure 11.2 Differentiation and production of pro‐ and anti‐inflammatory cytokines.
3. Figure 11.3 Balancing inflammation vs. tolerance: following interaction with fungal antigens, DCs and Tregs produce cytokines like IL‐1 and IL‐10 to influence the activity of downstream T cells that regulate the pro‐inflammatory activity of Th1 (and perhaps Th17) cells and those that regulate the activity of Th2 cells. Subsequently, Th1 inflammatory response is subdued during the early phase of the T cell response while that of Th2 is subdued during the late phase of the Th2 response.
Chapter 12
1. Figure 12.1 Sites of action and mechanisms of systemic antifungal agents. CW, Cell wall; BS, bud scar; CM, cell membrane; ER, enodplasmic reticulum; CMI, cell membrane invagination; M, mitochondrion; N, nucleus; V, vacuole.
2. Figure 12.2 Chemical structure of polyene antifungal agents.
3. Figure 12.3 Chemical structure of imidazole and triazole antifungal agents.
4. Figure 12.4 Inhibition of ergosterol synthesis by 14‐α demethylase by miconazole.
5. Figure 12.5 Ergosterol biosynthetic pathways and inhibition sites of clinically important antifungal agents.
6. Figure 12.6 Chemical structure of allylamines (naftifine and terbinafine), pirtenidine, octenidine, and chlorhexidine.
7. Figure 12.7 Chemical structure of two sordarin derivatives (GM193663 and GM531920) in addition to some promising antifungal compounds under development.
8. Figure 12.8 Chemical structure of three echinocandins.
9. Figure 12.9 (a) Chemical structure of 5‐fluorocytosine and (b) the metabolic action of 5‐FC.
Chapter 13
1. Figure 13.1 Schematic of abiotic and biotic filters that affect the establishment of fungi in a habitat.
2. Figure 13.2 Illustrative molecular phylogeny of several macrofungal taxonomic orders from fungal phyla Glomeromycota, Ascomycota, and Basidiomycota, showing the polyphyletic nature of mode of nutrition arbuscular mycorrhizal (AM), (saprobic (SAP), ectomycorrhizal (ECM), parasitic (PAR)) in fungal orders.
3. Figure 13.3 Illustrative representation of one of the hypotheses to explain the source‐sink mechanism in distributing nitrogen between trees of different size in a common mycorrhizal network. Arrow indicates direction of resource transfer; width of arrow indicates magnitude of transfer.
4. Figure 13.4 Species accumulation curve for macrofungi collected in nine spruce forests in Ireland over 3 years.
Chapter 14
1. Figure 14.1 The disease triangle.
2. Figure 14.2 Generalized fungal disease cycle.
3. Figure 14.3 Fungal penetration of a host plant by means of a specialized appresorium and penetration peg.
4. Figure 14.4 Means by which biological control agents can inhibit development of a fungal disease.
5. Figure 14.5 Fusarium wilt disease cycle.
Supplemental Images
1. Plate 1.1 Radiating circular pattern of (a) Chlorophyllum molybdites fruit bodies forming a fairy ring in grassland, and (b) Tinea corporis infection of the skin; (c) fruiting bodies of Agaricus bitorquis; (d) scanning electron micrograph of Agaricus bisporus gill surface (P.T. Atkey); (e) light micrograph of basidium bearing two spores (T.J. Elliott); (f) spore print from underside of fruit body (M.P. Callen); (g) germ tubes emerging from spores (T.J. Elliott; published by John Wiley & Sons Ltd); (h) branching hyphae growing on agar plate (T.J. Elliott) (all from Carlile, Watkinson, & Gooday (2001) Academic Press). Dry‐rot fungus Serpula lacrymans (i) colony decaying timbers in a wall void and forming red‐brown fruiting structure; (j) close‐up of underside of a basidiocarp (from Ingold & Hudson printed by Chapman & Hall); (k) exploratory fan‐shaped mycelium with connected rhizomorphs; (l) fast‐growing and (m) slow‐growing colonies on agar media.
2. Plate 4.1 Two‐color microarray technology of 6,400 distinct ORFs, arrayed on slide (only 36 are shown here). Two separate cDNA samples, one from yeast growing in glucose at beginning of fermentation labeled with green fluorescent dye, the other from later in the fermentation labeled with red dye. Red color indicates gene expression increased relative to the reference, green indicates gene expression decreased relative to reference, and yellow indicates no change in expression level. Three ORFs are shown in detail here.
3. Plate 4.2 Pattern interpretation of microarray (after de Risi (1997)). This shows how expression levels of genes known to be stress‐induced via STREs in their promoters were identical to one another. (Promoter sequences of other genes with the same profile but not previously identified as stress‐inducible were than examined – many contain one or more recognizable STRE sites.)
4. Plate 6.1 Button mushroom (Agaricus bisporus).
5. Plate 6.2 Interior of a composting tunnel. Compost is filled in a layer about 2.5 m deep on top of a mat. Air is blown in underneath the compost to allow an aerobic composting process.
6. Plate 6.3 Cross‐section of a mushroom bed. On top of the compost (brown layer), a black layer of casing soil can be seen, on top of which mushrooms develop.
7. Plate 6.4 Three species of oyster mushroom. From left to right: Pleurotus ostreatus, Pleurotus citrinopileatus, and Pleurotus flabellatus.
8. Plate 6.5 Example of log cultivation of shiitake mushroom (Lentinula edodes).
9. Plate 6.6 Example of bag cultivation of shiitake mushroom (Lentinula edodes).
10. Plate 10.1 Different forms of oral candidiasis: pseudomembranous candidiasis of the palate (a) and oral mucosa (b), erythematous candidiasis of the palate (c), and angular cheilitis (d).
11. Plate 10.2 Colonies of Candida spp. grown from a clinical sample taken from the oral cavity of a patient with oral candidiasis and grown on CHROMagar Candida^TM plate. Most Candida spp. can be identified on the basis of color of colonies produced (e.g. C. albicans colonies are green/blue, C. glabrata pink, and C. parapsilosis pale cream).
12. Plate 10.3 Schematic diagrams indicating stages of candidal infection. (1) Candida cells (black) come into contact with host epithelium (blue). (2) Candida cells, particularly germ tubes and hyphae, adhere to epithelial cell surface via specific interactions between candidal adhesins (e.g. Hwp1) and host ligands. (3) Once they have bound to the tissue, Candida cells begin to proliferate and produce hyphae. (4) Growth continues by budding and production of extensive levels of hyphae (growth is often associated with formation of biofilm). (5) Fungal hyphae and yeast cells eventually penetrate through the epithelial layer to tissues below, ultimately reaching the bloodstream (red), via which they disseminate throughout the body to cause disseminated candidiasis. (6) Photograph of reconstituted human epithelial tissue infected with C. albicans.
13. 13.1a Laccaria amethystina – an ectomycorrhizal basidiomycete.
14. 13.1b Lycoperdon perlatum – a saprobic basidiomycete with the puffball‐type sporocarp.
15. 13.1c Piptoporus betulinus – a parasitic basidiomycete with a shelf‐type sporocarp.
16. 13.1d An unidentified Rhizopogon sp. – an ectomycorrhizal basidiomycete with a hypogeous truffle‐type sporocarp.
17. 13.1e An unidentified Clavulinopsis sp. – a saprobic basidiomycete with a coral‐type sporocarp.
18. 13.1f Tolypocladium longisegmentum – a parasitic ascomycete with a club‐type sporocarp that only grows on sporocarps of the hypogeous fungal genus Elaphomyces.
19. 13.1g Tremella mesenterica – a saprobic basidiomycete with a jelly‐type sporocarp.
20. 13.1h An unidentified Cyathus sp. – a saprobic basidiomycete with a bird’s‐nest‐type sporocarp.
21. 13.1i Phallus impudicus – a saprobic basidiomycete with a stinkhorn‐type sporocarp.
22. 13.1j Daldinia concentrica – a parasitic ascomycete composed of a glebal mass of perithecia on a large stromata.
23. 13.1k Pullchericium cearullium – a saprobic basidiomycete with a resuprinate crust‐like fruiting mass.
24. Plate 13.1 Some fungal species that represent the more common fungal sporocarp types. The types include mushroom (Laccaria amethystina), puffball (Lycoperdon pyriforme), bracket (Piptoporus betulinus), truffle (Rhizopogon sp.), coral (Clavulinopsis sp.), club (Tolypocladium longisegmentum), jelly (Tremella mesenterica), bird’s-nest (Cyathus sp.), stinkhorn (Phallus impudicus), glebal (Daldinia concentrica), and resuprinate crust (Pullchericium cearullium).
25. Plate 13.2 A lichen growing on a tree branch.
26. Plate 13.3 Ectomycorrhizal root tips and mycelium on roots of a potted spruce plant.
27. Plate 14.1 Variation in head blight susceptibility of two barley cultivars to Fusarium head blight disease. Both heads were inoculated with Fusarium culmorum, but only the cultivar on the left shows disease symptoms (premature bleaching of head spikelets).
28. Plate 14.2 Effect of deoxynivalenol, a non‐host‐specific fungal trichothecene toxin, on germination of wheat seedlings. Seeds germinated on toxin solution (a) show reduced root and coleoptile growth compared to those germinated on water (b).
29. Plate 14.3 Club‐root of brassicas caused by Plasmodiophora brassicae. Roots swell and develop tumors due to increased hormone (e.g. cytokinin) production.
30. Plate 14.4 Means by which biological control agents can inhibit development of a fungal disease.
31. Plate 14.5 Biological control of net blotch disease of barley (caused by Perenophora teres) by a bacteria (Bacillus spp.) originating from a cereal field. Blotch disease symptom severity caused by this pathogen on inoculated leaves in the absence (a) and presence (b) of the biocontrol agent.
32. Plate 14.6 Fusarium wilt. Microscopic analysis of typical asexual macroconidia (a) and mycelial growth on potato dextrose agar (b) of Fusarium sp. (F. oxysporum also produces microconidia and chlamydospores). (c) Fusarium oxysporum f. sp. lycopersici wilt of tomato: symptoms range from healthy (left) to severe wilting and stunting (right).
33. Plate 14.7 Yellowing/browning of leaves of an elm branch due to Dutch elm disease. The entire tree subsequently wilted and died.
34. Plate 14.8 Phytophthora infestans late blight of potatoes. Microscopic analysis of asexual sporangia containing zoospores (a) and sexual oospore (b). Disease symptoms: water‐soaked dark lesions on leaves (c) and diseased tubers exhibit brown/black blotches on their surface, and internally they exhibit water‐soaked dark brown rotted tissue (d).
35. Plate 14.9 Pythium damping‐off disease. (a) Asexual sporangia containing zoospores; (b) sexually produced oospore formed on the surface of a tomato seedling; (c) seedlings of cress that are healthy (above) and others exhibiting damping‐off symptoms (below).
36. Plate 14.10 Septoria leaf blotch of wheat caused by Mycosphaerella graminicola. (a) Oval disease lesions (surrounded by chlorotic halo) on an infected leaf, running parallel to leaf blade; (b) black pycnidia develop on mature lesions and cirri may form on lesions if weather is dry for prolonged periods.
37. Plate 14.11 Sunken lesions on broad bean pod due to anthracnose disease caused by Colletotrichum lindemuthianum.
38. Plate 14.12 Black stem rust of mature wheat stems caused by Puccinia graminis f. sp. tritici. The three stems possess black pustules of teliospores; these pustules arise from red urediospore pustules that erupt through the stem epidermis earlier in the growing season.
39. Plate 14.13 Smut diseases of cereals. Covered smut of oats caused by Ustilago hordei (a) and covered smut or “bunt” of wheat caused by Tilletia sp. (b). Grains are replaced with black spore masses and hence destroyed.
40. Plate 14.14 Powdery mildew disease of wheat caused by Blumeria (= Erysiphe) graminis.