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ویرایش: [1 ed.]
نویسندگان: Oscar Zaragoza (editor). Arturo Casadevall (editor)
سری:
ISBN (شابک) : 0128199903, 9780128199909
ناشر: Elsevier
سال نشر: 2021
تعداد صفحات: 1626
[1628]
زبان: English
فرمت فایل : PDF (درصورت درخواست کاربر به PDF، EPUB یا AZW3 تبدیل می شود)
حجم فایل: 55 Mb
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در صورت تبدیل فایل کتاب Encyclopedia of Mycology به فرمت های PDF، EPUB، AZW3، MOBI و یا DJVU می توانید به پشتیبان اطلاع دهید تا فایل مورد نظر را تبدیل نمایند.
توجه داشته باشید کتاب دائر ycl المعارف قارچ شناسی نسخه زبان اصلی می باشد و کتاب ترجمه شده به فارسی نمی باشد. وبسایت اینترنشنال لایبرری ارائه دهنده کتاب های زبان اصلی می باشد و هیچ گونه کتاب ترجمه شده یا نوشته شده به فارسی را ارائه نمی دهد.
Cover ENCYCLOPEDIA OF MYCOLOGY CONTENT OF VOLUME 1 LIST OF CONTRIBUTORS FOR VOLUME 1 CONTENT OF ALL VOLUMES EDITOR BIOGRAPHIES PREFACE Next Generation Sequencing: Transcriptomics The Rise of NGS Transcriptomics in Fungi Transcriptomics Through RNA-Seq NGS Transcriptomics to Identify Changes During Development and Growth Under Different Environmental Conditions NGS Transcriptomics to Decipher the Molecular Mechanism of Interactions With Other Organisms Perspectives of NGS Transcriptomics in Fungi Conclusions References Further Reading Relevant Websites The Cell Wall of Medically Relevant Yeasts and Molds Introduction The Candida albicans Cell Wall Chitin Synthesis beta-Glucans Synthesis Glycoproteins Synthesis The Candida albicans Cell Wall Proteome The Cell Wall Composition in Other Candida Species The Aspergillus Cell Wall The Fungal Cell Wall and the Development of Antifungal Drugs Immune Sensing and the Fungal Cell Wall References The Fungal Chitinases Introduction Group A Chitinases Group B Chitinases Group C Chitinases Concluding Remarks References GTPases in Hyphal Growth Hyphal Growth in Filamentous Fungi Cell Wall Synthesis The Spitzenkrper and Vesicles Pathway Structure and Action Mechanism of Small GTPases Structure Action Mechanism Classification Ras Rho Rab Arf Ran Function of Small GTPase in Hyphal Growth Ras Rho subfamily Rho Cdc42 Rac Rab Arf References Membrane Transporters, an Overview of the Arbuscular Mycorrhizal Fungal Transportome Introduction Types of Transport Processes Simple Diffusion Facilitated Diffusion Channels Transporters or carriers Active Transport Primary active transporters P-type ATPases V-ATPases F-type ATPases ABC (ATP binding cassette) transporters Secondary transporters Antiporters Symporters Why Arbuscular Mycorrhizal Fungi? AM Fungal Transportome Primary Active Transporters P-type ATPases ABC transporters Transporters of Macronutrient Ions Phosphate transporters Ammonium transporters Nitrate transporters Other transporters of inorganic ions Metal Transporters Zinc transporters Copper transporters Iron transporters Arsenite efflux pump Transporters of Organic Compounds Organic nitrogen transporters Sugar transporters Water Channels Concluding Remarks Acknowledgments References Further Reading Relevant Websites Fungal Secondary Metabolism Introduction Biochemistry and Biological Impact of Fungal Secondary Metabolites Main Classes of Fungal Secondary Metabolites Polyketides Non-ribosomal peptides Terpenes and terpenoids Indole alkaloids Biological Functions and Ecological Roles of Fungal Secondary Metabolites Fungal Genes Involved in Secondary Metabolite Biosynthesis Regulation of Fungal Secondary Metabolism Pathway-Specific Regulators Regulation of Secondary Metabolism by Nutritional and/or Environmental Conditions pH regulation Regulation by carbon and nitrogen sources Redox status and iron levels Regulation Mediated by Chromatin Modifications Histone methylation Histone acetylation References Further Reading Mycotoxins and Mycotoxigenic Fungi: Risk and Management. A Challenge for Future Global Food Safety and Security Introduction Social and Economic Impact of Mycotoxins Regulated Mycotoxins and Associated Fungi Aflatoxins Ergot Alkaloids Fumonisins Ochratoxin A Patulin Trichothecenes Zearalenone Co-Occurrence of Mycotoxins Modified (Masked) Mycotoxins Emerging Mycotoxins Emerging Fusarium Mycotoxins Enniatins and beauvericin Fusaproliferin Moniliformin Emerging Aspergillus and Penicillium Mycotoxins Emerging Alternaria Mycotoxins Control and Management of Mycotoxins Pre-Harvest Interventions Post-Harvest Interventions Dietary Interventions Mycotoxins in a Global Warming Scenario Biosynthesis and Genetic Regulation of Mycotoxins Aflatoxins Trichothecenes Fumonisins Ochratoxins References Relevant Website RNA Interference in Fungi The Discovery of RNA Interference The Core of RNAi Machinery: DCL, AGO and RdRp Different Classes of sRNAs are Involved in RNAi An Overview on RNAi and sRNAs in Fungi Defense-related RNAi Pathways Defense against mobile elements and transgenes Defense against viruses Endogenous Regulatory RNAi Pathways Loss of RNAi in Some Fungi The Role of sRNAs and RNAi in Inter-kingdom Interactions References The MAP Kinase Network As the Nervous System of Fungi Introduction to Candida albicans Biology Morphological Transitions Fungal Recognition by Immune Cells and Activation of Host Defenses Fungal Adaptation Through MAPKs-Mediated Signaling HOG Pathway: Sensing Environmental Stress Mkc1-Mediated Pathway: Maintaining Cell Integrity Cek1-Mediated Pathway: The SVG Pathway Cek2: The Pheromone Response Conclusions Acknowledgments References Communication With Plants Interaction of Fungi With the host Necrotrophic Fungi Biotrophic Fungi Hemibiotrophic Fungi Host Sensing How do Fungi Perceive the Host? Plant Surface Detection Cell Detection Root Detection Fungal Chemotropism How Plants and Fungi Communicate By-Passing Plant Defenses Lipid Signaling Fatty Acids Oxidized Fatty Acids: The Oxylipins Sphingolipids Sphingolipids Main Component of Lipid Rafts How Fungus-Host Communication can Influence the Virulence and the Secondary Metabolism References Further Readings Genome Evolution of Fungal Plant Pathogens Introduction to Filamentous Plant Pathogens Large-Scale Genome Dynamics: Evolution of Size Genome Contraction Genome Expansion Transposable elements (TEs) and effector evolution Whole genome duplication (WGD) and polyploidy Lateral DNA transfer and hybridization: Mechanisms of gene exchange between species Horizontal gene transfer (HGT) and horizontal chromosome transfer (HCT) Hybridization through sexual mating and by vegetative fusion of fungal hyphae Rapid Evolution of Virulence Associated Genes: One, Two, Multi-Speed Genomes Mechanisms of mutations Introduction of Alien Pests in New Environments: Phytophthora Ramorum, as Example of Genetic Diversification in... Conclusions References Further Readings Mycoviruses: A Hidden World Within Fungi Introduction Distribution and Phylogeny Evolutionary Theories Impact on Fungal Behavior Mycoviruses as Triggers and Target of RNA Silencing Machinery Biotechnological Applications and Future Perspectives References Transposable Elements in Fungi: Coevolution With the Host Genome Shapes, Genome Architecture, Plasticity and Adaptation Introduction: The Extensive Diversity of Repetitive DNA in Fungal Genomes The Fine-Tuned Regulation of Transposable Elements Proliferation Epigenetic Silencing due to Histone Methylation DNA Methylation Small RNA Silencing Host Population Dynamics Impact Transposable Element Landscapes in Fungi The TE Burst and Decay Model New Transposable Element Insertions are Influenced by Selection and Genetic Drift How can Population Dynamics Lead to Differences in TE Content Among Species? Are Transposable Elements Essential for Rapid Adaptation? Transposable Element and Host Genome Compartmentalization Transposable Elements are Activated Under Stress Locus-Specific Effects of Transposable Elements Insertions Perspectives References Aspergilli, More Than Just Fungi: Shaping the Last Decades of Model Systems Introduction What Aspergillus Taught us About Eukaryotic Genome Regulation and Maintenance Drug Resistance Runs Rampant What About the Contribution of Aspergillus in the Comprehension of Cell Biology and Eukaryotes Development? The Evolutionary Dynamics Explained Spilling the Beans on the Antioxidant Potential of Bioactives A Stairway to System Biology References Relevant Websites Proteomics in Mycorrhizal and Plant Pathogenic Fungi Introduction Ectomycorrhizal and Endomycorrhizal Fungi Proteomics of Plant Pathogens Fungi Botrytis cinerea Sclerotinia sclerotiorum Fusarium graminearum Magnaporthe oryzae Concluding Remarks References Further Reading Host-Induced Stress Response in Human Pathogenic Fungi Introduction Response to Nutrient Limitation in Human Host Environments Carbon Limitation Iron Limitation Oxygen Limitation Oxidative Stress Response Nitrosative Stress Response pH Stress Response Weak Acid Stress Response Response to Stress During Phagocytosis Biofilm Formation as a Stress Response Conclusions Acknowledgments References Biodegradation of Aromatic Toxic Pollutants by White Rot Fungi Introduction White Rot Fungi: The Lignin-Degrading Fungi Phanerochaete chrysosporium Burdsall Trametes (Coriolus) versicolor (L.) Lloyd (“Turkey Tail”) Pleurotus ostreatus (“Fries”) Kummer (“Oyster Mushroom”) Degradation of Major Groups of Organic Pollutants Polychlorinated Biphenyls (PCBs) Polycyclic Aromatic Hydrocarbons (PAHs) Textile Dyes Pharmaceuticals and Personal Care Products Can the Knowledge Accumulated on Biodegradation Lead to Mycoremediation? References Fungal Chitin and Chitosan Introduction Fungal Cell Wall Physiological Function of Fungal Chitin and Chitosan Fungal Cell Wall Composition and Architecture Biosynthesis of Cell Wall Polysaccharides Chitin Synthases and Synthesis Biosynthesis of Chitin and Chitosan Physicochemical Properties Solubility Molecular Weight Degree of Deacetylation Occurrence and Biological Functions in Nature Industrial Production of Chitin and Chitosan Features of Fungal Chitin and Chitosan Production Chitin and Chitosan-Producing Fungi Applications of Chitin and Chitosan Biological Properties Industrial Applications Agricultural Applications Biomedical and Pharmaceutical Applications Fermentation Systems of Fungal Chitin and Chitosan Conclusion References Chitin Synthases in Fungi Introduction Classification of Fungal Chitin Synthases Evolution of Fungal Chitin Synthases Functions of Chitin Synthases References Glucose Metabolism and Use of Alternative Carbon Sources in Medically-Important Fungi Introduction Glucose Metabolism in Medically-Important Fungi Alternative Carbon Metabolism in Medically-Important Fungi Pathways for Alternative Carbon Metabolism and Their Roles in Fungal Pathogenicity Beta Oxidation of Fatty Acids The Glyoxylate Cycle Gluconeogenesis Glucose and Alternative Carbon Metabolism: A Prospective Therapeutic Target for Fungal Diseases Conclusion and Future Prospects References Ergosterol Synthesis Introduction Physiological Function of Ergosterol Ergosterol Biosynthesis Subcellular Localization of Ergosterol Enzymes Regulation of Ergosterol Synthesis Post-Translational Feedback Regulation Transcriptional Regulation Inhibitors of Ergosterol Synthesis and Ergosterol Target Conclusion References Fungal Volatile Organic Compounds Introduction Volatilome and Volatome Chemical Analysis Fungal VOCs as Odorants Foods and Flavors Biotechnology VOCs for Indirect Detection of Fungal Growth Chemical Ecology VOCs as Antimicrobial Agents Eight Carbon VOCs Summary Acknowledgments References Further Reading Relevant Website Outline of Ascomycota Introduction Introduction to Ascomycota Life Modes and Habitats Species Number Attempts of Higher-Level Classification of Ascomycota One Fungus, One Name Current Status Orphaned Genera Novel Lineages Within the Phylum Future Perspectives and Conclusion Acknowledgments References Further Reading Relevant Websites Structure and Development of Ascomata Introduction Morphology of Ascomata Ascomata Development in Model Systems Factors Affecting the Development of Ascomata Regulatory Networks Involved in the Development of Ascomata Concluding Remarks References Laboulbeniomycetes, Enigmatic Fungi With a Turbulent Taxonomic History From Roland Thaxter to the Present: Synergy Among Mycologists, Entomologists, Parasitologists The Winding Road to Molecular Phylogenetics: Progress in the Study of Laboulbeniomycetes Thallus-Forming Ectoparasites Laboulbeniales First sightings Current versus estimated species diversity Museum collections, citizen science projects, and social media Classification of the order Notes on ecology Thallus morphology Receptacle Perithecium Appendage and antheridia Ascospores Herpomycetales Pyxidiophorales, Hyphal Mycoparasites Taxonomy and Phylogeny Morphology of Pyxidiophorales Life Cycle States Perithecial morphs Phialidic conidial hyphal morphs Ascospore-derived conidial morphs Fine-Tuned Life Histories Expanding Diversity Laboulbeniopsis Clade Chantransiopsis Clade Filling Knowledge Gaps Epilogue Acknowledgments References Relevant Websites Phylogenetic Advances in Leotiomycetes, an Understudied Clade of Taxonomically and Ecologically Diverse Fungi Introduction Morphological and Ecological Diversity of Leotiomycetes Morphology Ecology Current Understanding of Evolutionary Relationships Challenges of Leotiomycetes Systematics Chaetomellales Cyttariales Helotiales Lahmiales Lauriomycetales Leotiales Lichinodiales Marthamycetales Medeolariales Micraspidales Phacidiales Rhytismatales Thelebolales Biases in Sampling of Leotiomycetes Distributional Unevenness Helotiales, a Mega-Order in Disarray Understudied Ecological Niches Future Research Perspectives Acknowledgements References Further Reading Pezizomycetes Introduction Distribution and Ecology Morphological Features Ascomata The Hymenium The Ascus Ascospores Paraphyses Septal Structures Anamorphic States Genomes, Microbiomes, and Model Organisms Classification and Phylogenetic Studies Families Acknowledgments References Outline of Basidiomycota Brief Introduction of Basidiomycota Advances on Phylogeny of Basidiomycota The Taxonomic System of Basidiomycota Outline of Basidiomycota References Cantharellales Gäum Overview Phylogenetic Incongruences, Family Classification and The Polyphyly of Sistotrema Diversity, Current Knowledge and Issues in Species Delimitation Trophic Strategies Synopsis Families Previously Included in Cantharellales and Excluded Here References Boletales Introduction Morphological Framework, Chemical and Ecological Features, Taxonomic Limits Brief Historical Overview and Current State of Knowledge Origins, Diversification and Historical Evolutionary Dynamics Symbiotic Partners, Mutualistic Interactions, Paleoecological Processes and Evolutionary Ecology Historical Biogeography, Paleo-biogeographical Dynamics and Distribution Patterns Notes on the Edibility, Toxicity and Poisonings, Therapeutic Properties, Ethnomycological Traditions, Cultivation,... Conclusions Acknowledgments References Functional Traits of Stipitate Basidiomycetes The Rationale The Mycelium Morphological Traits Mycelial coverage, mycelial biomass Vertical distribution Hyphal cords and rhizomorphs Ectomycorrhizal mantles Extramatrical mycelia, exploration types Common mycorrhizal networks (CMN) Hyphal wall thickness Clamp connections Mitospores Mycelial cysts and cystidia Sclerotia and pseudosclerotia Physiological Traits Behavior Aerotropism Autotropism Chemotropism Phototropism Thigmotropism Mycelial persistence Host specificity The Basidiome Basidiome Size and Number Basidiome Architecture Hymenophores Basidiome Physiology Pigments Volatile organic compounds (VOCs) Taste compounds Toxins Latex Texture Luminescence Basidiome Behavior Gravitropism (geotropism) Phototropism Thigmotropism Dwarfing Fairy rings Phenology The Spore Spores Size Discharge Wind dispersal Impaction Desiccation resistance Dormancy Germinability Spore Shape Discharge Wind dispersal Impaction, substrate attachment Dormancy Production (numbers) The Spore Wall Ornamentation Pigmentation Appendages Hydrophobicity Germ pore Wall thickness Plage (suprahilar depression) Guild-Specific Trait Syndromes Morphological Differences Physiological Differences Behavioral Differences Future Directions References Fossil Ascomycota and Basidiomycota, With Notes on Fossil Lichens and Nematophytes Introduction Fungal Evolution Modes of Fossil Preservation Amber Impressions and Compressions Petrifactions and Permineralizations Indirect Evidence Fossils of Ascomycota and Basidiomycota Ascomycota Basidiomycota Lichens Nematophytes Future directions Permissions Acknowledgments Appendix 1 Citations for Appendix 2 Citations for References Further Reading The Cultivation of Macrofungi Introduction Cultivation of Saprotrophic Species Main Steps Isolation Substrate, inoculum and incubation Cultivation and harvest Pests and Adversities of Cultivated Saprotrophic Mushrooms Cultivation of Ectomycorrhizal Species Ectomycorrhizal Plant Production Spore suspension inoculum Radical proximity Mycelium-based inoculum Adversities of Cultivation of ECM Mushrooms The Cultivation of Macrofungi for New Biotechnology Conclusions References Macrofungi as Food Introduction Types of Edible Macrofungi Wild Macrofungi Cultivated Macrofungi Health and Nutritional Benefits Provided by Macrofungi Economic Value and Social Perspectives of Edible Macrofungi Seasonal Availability and Preservation Socio-Cultural Aspects of Macrofungi as Food Food Safety Conclusion References Overview: Human Fungal Pathogens Acknowledgments References Polyenes and Amphotericin B Introduction to Fungal Pathogens and Antifungal Drugs Amphotericin B. An Old Drug, But Still With Many Secrets Behind Mechanisms of Action Pore Formation at the Membrane Ergosterol Sequestration Beyond the Membrane: Oxidative Burst and Intracellular Damage Spectrum of Action and Resistance Amphotericin B Toxicity and Lipidic Formulations Clinical Uses of AmB Conclusions References Azole Antifungal Drugs: Mode of Action and Resistance Glossary Introduction Antifungals in Clinical Use Definition of Resistance How Resistance is Determined? Antifungal Susceptibility Testing Azoles: Mode of Action Azole Drug Resistance Mechanisms Azole Resistance Mechanisms in Candida Spp. Azole Resistance Mechanisms in Aspergillus Spp. Conclusions References Echinocandins Background and Structure Mechanism of Action, Spectrum of Activity, and Susceptibility Testing Resistance to Echinocandins Pharmacokinetics and Pharmacodynamics Pharmacologic Properties Pharmacodynamics Clinical Use of Echinocandins Echinocandins in Special Populations Pediatrics Geriatric Pregnancy/Lactation Drug-Drug Interactions References Allylamines, Morpholine Derivatives, Fluoropyrimidines, and Griseofulvin Introduction Allylamines Morpholine Derivatives Fluoropyrimidines Griseofulvin Acknowledgments References Further Reading New Targets for the Development of Antifungal Agents Introduction Cell Wall GPI Anchor Chitin Synthase Lipids Acetyl-CoA Synthetase Ergosterol Biosynthesis Squalene synthase (SQS) Sterol methyltransferase (SMT) Sphingolipid Biosynthesis Inositol phosphorylceramide synthase (IPCs) GlcCer synthase Efflux Pump Proton Pump Protein Synthesis Elongation Factor 2 (EF2) Transfer RNA Synthetase Folate Biosynthesis Dihydropteroate Synthase (DHPS) Dihydrofolate Reductase (DHFR) Cell Stress Regulators Calcineurin Heat Shock Protein 90 (Hsp90) Drug Repositioning Miltefosine (MFS) Sertraline Tamoxifen Verapamil Benzimidazoles Acknowledgments References Immunotherapy of Fungal Infections Glossary Introductory Concepts Host-Microbe Interaction, Infection, Disease, Damage Host-Fungal Interaction and Virulence Factors Management of Fungal Diseases Current antifungal chemotherapy Rationale for immunotherapy Host immunity and antifungal defense Antifungal Immunotherapy Active Immunotherapeutic Modalities Fungal vaccines Specific challenges to fungal vaccine development Passive Immunotherapeutic Modalities Passive antibody therapy for fungal diseases Immunotherapy with mAbs Protective mAbs against fungal antigens Radioimmunotherapy Immunomodulation via mAb Specific challenges to development of mAb-based immunotherapies AMPs Killer toxins and killer peptides: A functionally different mAb and AMP-based approach Immunotherapy via nonspecific immunomodulation Cytokine therapy Immunotherapy of rare mold infections via immunomodulation The importance of negative immunomodulation as therapy for fungal infections Adoptive cell transfer Fungal allergy and immunotherapy Concluding Remarks References Diagnosis of Fungal Infections Glossary Introduction Conventional Diagnostic Methods Culture Direct Visualization and Histopathology New Diagnostic Methods Antibody Detection Antigen Detection Detection of 1,3-beta-D-glucan (BDG) for diagnosis of fungal infection Detection of galactomannan (GM) and glycoproteins for diagnosis of IA Detection of capsular polysaccharide antigen (CPA) for the diagnosis of cryptococcosis Detection of mannan (MNN) for diagnosis of invasive candidiasis Detection of endemic fungal antigens (EFA) for the diagnosis of endemic fungal infections DNA-Based Methods/Molecular Methods PCR-based methods Non-PCR based methods Future Directions and Conclusion References Further Reading Relevant Websites Commensal to Pathogen Transition of Candida albicans Glossary Introduction: Candida albicans as Commensal and Pathogen Candida albicans as a Commensal: Living with the Host and Microbial Neighbors Fungal Factors That Contribute to C. albicans Survival in the Human Gut Morphology of C. albicans in the Gut Animal Models Used to Investigate C. albicans Commensalism in the Gut Candida albicans as Part of the Microbiota Features That Contribute to the Success of C. albicans as Pathogen Interaction of Candida albicans with Epithelial Cells Interaction of Candida albicans with the Immune System The Cell Wall as a Dynamic Factor in Candida-Host Interactions The Influence of Macronutrients on Candida-Host Interaction Acquisition of Micronutrients by C. albicans C. albicans Morphology - Does it Determine the Difference Between Commensalism and Infection? References Candida psilosis Complex Glossary Candida parapsilosis Sensu Lato - General Introduction Candida parapsilosis Sensu Lato Complex - History Candida parapsilosis Sensu Lato - Epidemiology Candida parapsilosis Sensu Lato - Diagnostics and Treatment Candida parapsilosis Sensu Lato - Phylogeny Candida parapsilosis Sensu Lato - Genomics Candida parapsilosis Sensu Stricto - The Single Candida orthopsilosis - Keep on Hybridizing Candida metapsilosis - The Virulent Hybrid Candida parapsilosis Sensu Lato - Genetic Manipulation Candida parapsilosis Sensu Lato - Virulence Morphology Adherence and Biofilm Formation Secreted Enzymes Host Interaction Acknowledgement References Candida auris: A New, Threatening Yeast Introduction Microbiological Characteristics Biology and Morphology Phylogenetic Colony morphology Cellular morphology Biochemical features Virulence Identification Antifungal Resistance Persistence on Hospital Environment Resistance to Disinfectant and Antiseptic Compounds Epidemiology Clinical Features Colonization Clinical Presentation Outcome Treatment Infection Prevention and Control Conclusion References Further Reading Relevant Websites Immune Response to Candida albicans Infection Glossary Introduction: Candida albicans, an Opportunistic Fungal Pathogen Initial Recognition of C. albicans, Innate Immune Responses PRRs Involved in C. albicans Detection Innate Immune Responses to C. albicans Epithelial Cells: The First Barrier Against Candida Invasion Killing of C. albicans Cells by Phagocytes: Macrophages and Neutrophils Innate Lymphoid and ϒδ T Cells Microbiome and Anti-C. albicans Defense Mechanisms Adaptive Immune Responses to C. albicans Dendritic Cells: Driving CD4plus T Helper Subset Differentiation CD8plus T Cells Humoral Responses: Antibodies Evasion of Host Defenses by C. albicans Emergency Myelopoiesis and Trained Immunity Final Comments References Further Reading Relevant Websites Infections by Cryptococcus species Glossary Cryptococcus Neoformans and Cryptococcus Gattii: Main Features Classification of Cryptococcus Neoformans/Gattii Life Cycle Epidemiology of Cryptococcosis Cryptococcus in the Environment Virulence Factors Cryptococcal Capsule Melanin Cryptococcus as a Facultative Intracellular Pathogen Formation of Titan Cells Diagnosis and Treatment Conclusions References Further Reading Relevant Websites Epidemiology of Infections Caused by Molds Aspergillosis Invasive Aspergillosis Azole-Resistant Aspergillus Infections Chronic Pulmonary Aspergillosis (CPA) Critical Care and Post-Influenza Aspergillosis Mucormycosis Fusariosis Other Hyaline Molds Conclusions References Diseases Caused by Aspergillus fumigatus Glossary Introduction Clinical Manifestations of Aspergillus fumigatus Infections Allergic Bronchopulmonary Aspergillosis (ABPA) Allergic Aspergillus Sinusitis Aspergilloma Chronic Pulmonary Aspergillosis Invasive Aspergillosis Invasive pulmonary aspergillosis Other aspergillosis invasive syndromes Molecular Bases of Aspergillus fumigatus Virulence Conclusions References Relevant Websites Mucormycoses Introduction Epidemiology and Burden of Disease Pathogenesis and Host Immune Response Molecular Pathogenesis of Mucorales Role of Morphogenesis Role of Iron uptake CotH Proteins and Angioinvasion Diagnosis Molecular diagnostics Treatment of Mucormycosis Surgery Currently Approved Antifungal Drugs Investigational Antifungal Drugs Adjunctive Therapies Conclusions and Future Perspectives Disclosures References Epidemiology of Dimorphic Fungi Glossary Introduction Coccidioides immitis and C. posadasii Histoplasma capsulatum Sporothrix schenckii Species Complex Paracoccidioides spp. Blastomyces dermatitidis Talaromyces marneffei Emergomyces spp. References Histoplasma Introduction Epidemiology Pathogenesis Clinical Features Acute Histoplasmosis Disseminated Histoplasmosis Chronic Pulmonary Histoplasmosis Diagnosis Treatment Acute Pulmonary Histoplasmosis Moderately Severe to Severe Acute Pulmonary Histoplasmosis Chronic Cavitary Histoplasmosis Disseminated Histoplasmosis References Coccidioidomycosis: The Valley Fever Introduction History Early History: A Mistaken Identity Ecology and Life Cycle of the Desert Dust Fungus Emergence of Coccidioidomycosis as a Growing Threat Coccidioidomycosis is a Threat to Public Health in the Western Hemisphere Risk Factors Clinical Manifestations Coccidioides in the US Southwest Coccidioides in Latin America Virulence and Pathogenesis Treatment and Prevention Therapeutics Prophylaxis and Vaccination Authorship Conflict of Interest Acknowledgements References Blastomyces and Blastomycosis Overview Historical Perspective Mycology and Phylogenetics Geography and Ecology of Blastomyces Epidemiology Pathogenesis, Virulence, and Host Defense Overview Molecular Regulation of the Phase Transition to Yeast Virulence Factors Molecular Regulation of the Phase Transition to Hyphae Immunology & Vaccine Development Clinical Manifestations of Blastomycosis Overview Human Blastomycosis Pulmonary Blastomycosis Disseminated Blastomycosis Blastomycosis in Pregnancy Blastomycosis in Immunocompromised Persons Diagnosis of Blastomycosis Treatment of Blastomycosis Outcomes and Mortality References Relevant Website Paracoccidioidomycosis Introduction Morphological Aspects Epidemiological Aspects Laboratorial Diagnosis Pathogenesis and Histopathology Clinical Manifestations Treatment Prognosis Vaccine Development DNA Vaccine Antibodies Acknowledgments References Further Reading Sporotrichosis Introduction The Genus Sporothrix The Human Pathogenic Sporothrix Species Morphology and Dimorphism Fungal Biology and Ecology Putative Virulence Factors The Disease Epidemiology Clinical Presentations Pathogenesis Diagnosis Treatment Conclusions and Perspectives References Advances in Genomics Research of Pneumocystis Species Introduction Pneumocystis Genomes Ploidy Comparative Genomics Genes Absent From the Genome Select Genomic Features of Pneumocystis Sexual replication Major surface glycoprotein superfamily Drug Targets, Gene Polymorphism and Drug Resistance Drug Resistance New Drug Targets and Therapies Conclusions and Future Directions References Subcutaneous Fungal Infections Introduction Chromoblastomycosis Epidemiology Pathophysiology Clinical Features Differential Diagnosis Diagnosis Treatment Lobomycosis Etiology and Transmission Epidemiology Pathophysiology Clinical Features Diagnosis Treatment Mycetoma Epidemiology Pathophysiology Clinical Features Differential Diagnosis Diagnosis Treatment Subcutaneous Phaeohyphomycosis Epidemiology Pathophysiology Clinical Features Differential Diagnosis Diagnosis Treatment Entomophthoramycosis Epidemiology Pathophysiology Clinical Features Differential Diagnosis Diagnosis Treatment Prevention References Superficial Infections of the Skin and Nails Introduction Superficial Mycoses Pityriasis Versicolor Tinea Nigra White Piedra Black Piedra Cutaneous Mycoses Dermatophytosis Candidiasis Dermatomycoses References Genitourinary Fungal Infections (Other Than Vaginal Candidiasis) Introduction Definition and Diagnosis of Urinary Tract Diseases Caused by Fungi Epidemiology of Candiduria Microbiology Pathogenesis Clinical Presentation and Diagnosis Treatment Other Fungal Infection of Genitourinary Tract Acknowledgment References Oropharyngeal and Vulvovaginal Candidiasis Introduction Epidemiology Pathogenesis Clinical Manifestations Oral Candidiasis Esophageal Candidiasis Vulvovaginal Candidiasis Syndromes Involving Candidiasis Diagnosis Treatment References Fungal Infections of Human Mammary Gland During Lactation Breastfeeding Structure of the Mammary Gland Pathogenesis of Fungal Breast Infections Candida albicans Symptoms of Fungal Breast Infections Diagnosis of Breast Fungal Infections Treatment Prevention of Fungal Breast Infections Conclusions References Further Readings Fungal Infections of the Central Nervous System Central Nervous System Fungal Infections The Cryptococcus Genus Cryptococcosis Epidemiology Cryptococcus “Travels” to the Brain Trojan Horse Model Paracellular Model Transcellular Model Cryptococcus “Passport” to Brain Travel Inositol Urease Phospholipase B1 Laccase Metalloprotease 1 (Mrp1) Antifungal Alternatives for Treating Cryptococcal Meningitis References Further Reading Relevant Websites Fungal Cardiac Infections Candida Species Pathogenesis Endocarditis Myocarditis Aspergillus Species Overview Pathogenesis Endocarditis Myocarditis Histoplasma Capsulatum Pathogenesis Endocarditis Myocarditis Blastomyces Dermatitidis Pathogenesis Coccidioides Pathogenesis Endocarditis Myocarditis Cryptococcus Neoformans Pathogenesis Endocarditis Myocarditis Zygomycetes (Phycomycetes) Miscellaneous Fungi References Further Reading Fungal Ophthalmological Infections Introduction Fungal Keratitis Overview Epidemiology and Risk Factors Signs and Symptoms Diagnostic Workup Treatment Fungal Endophthalmitis Overview Epidemiology Signs and Symptoms Diagnostic Workup Treatment References Further Reading AIDS-Related Mycoses Candidiasis Epidemiology Clinical Presentation Diagnosis Management Prophylaxis Treatment Cryptococcosis Epidemiology Clinical Presentation Diagnosis Management Drug therapy Raised intracranial pressure (ICP) Cryptococcal antigen screening Immune restoration and ART timing Histoplasmosis Epidemiology Clinical Presentation Diagnosis Treatment Pneumocystis Pneumonia (PCP) Epidemiology Pathophysiology and Clinical Presentation Diagnosis Management Antimicrobial therapy Adjunctive therapy Antiretroviral therapy Ventilatory support Emergomycosis Epidemiology Clinical Presentation Diagnosis Management Talaromycosis Epidemiology Clinical Presentation Diagnosis Management Treating disease Primary and secondary prophylaxis Timing of ART References Further Readings Fungal Infections in Transplant Recipients Introduction Candidiasis Diagnosis Treatment Prophylaxis Aspergillosis Diagnosis Treatment Prophylaxis Mucormycosis Diagnosis Treatment Cryptococcosis Diagnosis Treatment Endemic Fungal Infections Histoplasmosis Blastomycosis Coccidioidomycosis Pneumocystis Pneumonia Diagnosis Treatment Prophylaxis References Fungal Infections in Cancer Patients Introduction Effects of Cancer Treatment on Immune Response to Fungal Infection Opportunistic Fungal Infections Endemic Fungal Infections Prevention of Fungal Infections in Cancer Patients Mycobiome Future Directions References Fungal Infections in the Setting of Biological Therapies (in the Non-Transplant Host) Introduction Immune Cells and Signaling Pathways That Promote Fungus-Specific Host Defense Mucosal Candidiasis IFIs by Candida and Inhaled Molds Infections by Intracellular Fungi (Cryptococcus, Endemic Dimorphic Fungi and PJP) Fungal Infections in the Setting of Biological Therapies Lymphocyte-Depleting Mabs Biologics That Target Cytokine-Mediated Pathways Biologics that target IL-1 receptor (IL-1R) and IL-6 receptor (IL-6R) signaling mAbs that target IL-17R signaling TNF-alpha-targeting biologics IFN-gamma-targeting mAb GM-CSF receptor (GM-CSFR)-targeting mAb Complement-Targeting Biologics mAbs That Target Checkpoint Pathways SMKI SMKIs targeting BTK signaling SMKIs targeting JAK-STAT signaling SMKIs targeting CLR-Spleen tyrosine kinase (Syk)-CARD9 signaling SMKIs targeting MAPK and other intracellular pathways Conclusion Acknowledgments References Relevant Website Uncommon Yeasts and Molds Causing Human Disease Uncommon Yeast-Like Pathogens Malassezia Species Introduction Clinical presentation Diagnosis and identification Treatment and outcomes Pseudozyma Species Introduction Clinical presentation Diagnosis and identification Therapy and outcomes Rhodotorula Species Introduction Clinical presentation Diagnosis and identification Therapy and outcomes Saccharomyces Cerevisiae (Var Boulardii) Introduction Clinical presentation Diagnosis and identification Therapy and outcomes Saprochaete Species Introduction Clinical presentation Diagnosis and identification Therapy and outcomes Trichosporon and Cutaneotrichosporon Species Introduction Clinical presentation Diagnosis and identification Therapy and outcomes Phaeohyphomycosis Introduction Clinical Manifestations Cutaneous phaeohyphomycosis Subcutaneous phaeohyphomycosis Keratitis Fungal sinusitis Disseminated phaeohyphomycosis Common Species Causing Phaeohyphomycosis Alternaria species Bipolaris species Cladophialophora species Curvularia species Exophiala species Exserohilum rostratum Lomentospora prolificans Hyalohyphomycoses Fusarium Scedosporium Paecilomyces Scopulariopsis Emergomyces References Fungal Infections in Children Introduction Candida Infections Neonates Invasive candidiasis Epidemiology Host Pathogen Disease manifestations and outcome Mucocutaneous candidiasis Epidemiology Pathogen and host Primary Immunodeficiency and Candida Infection Invasive candidiasis Chronic mucocutaneous candidiasis Diagnosis Culture Fungal antigen and molecular testing Aspergillus Infections Invasive Aspergillosis Epidemiology Organism Pathogenesis Clinical Diagnosis Radiologic features Culture Fungal antigen and molecular studies Antifungal Treatment in Children With IFD References e9780128199909v2_WEB Cover ENCYCLOPEDIA OF MYCOLOGY CONTENTS OF VOLUME 2 LIST OF CONTRIBUTORS FOR VOLUME 2 CONTENT OF ALL VOLUMES Elderly Exposure to Fungi: A Review Study Introduction Methodology First Step Second Step Third Step Results and Discussion Conclusion Appendix A Supplementary Material References Further Reading Exposure to Fungi in Health Care Facilities Epidemiology of Nosocomial Fungal Infections Candida Aspergillus Mucorales Fusarium Other Fungi Associated With Hospital Infections Novel Methods and Future Perspectives Final Remarks References Further Reading Relevant Websites Integrating Fungi in the Drinking Water Regulation and in Guidelines for Materials in Contact With Drinking Water. Is... Introduction Why are Fungi in Drinking Water a Present and a Future Legislation Problem? Regulation and Legislation The Lack of Knowledge on the “Core Fungal Species” Connected to the General Water Quality and/or Human Diseases Setting Equivalent Methods for Enumeration or Cultivation of Fungi Correct and Uniform Identification of Fungi Exploring Fungi in Water Distribution Systems “Core Species” and Diversity of Fungal Communities Depend on the Main Raw Water Source The Most Common Fungi Isolated From European End-Point Drinking Water Fungal Effect on Used Building Materials in Water Distribution Networks Colonization and Biodegradation of Materials in Contact With Drinking Water Induced by Water-Related Fungi How Big is the Health Risk Due to Fungal Presence in Tap Water for End-Point Users? Development of Fungal Disease due to Contaminated Water Indirect Health Effects Due to the Secretion of Fungal Secondary Metabolites Conclusions Lowering the Effect of Water-Borne Fungi on Construction of Water Networks Lowering Effect of Water-Borne Fungi on Human Health Funding References Mycological Studies in Cultural Heritage Biodeterioration, Fungi and Cultural Heritage Fungal Biodeterioration Mechanisms and Impact on Cultural Heritage Organic Supports: Paper Based Objects Organic Supports: Photographic Collections Inorganic Supports: Stone Artefacts and Monuments Inorganic Supports: Ceramics and Glazed Tiles Treatment and Preventive Measures for Fungal Contamination in Cultural Heritage References How to Asses Fungal Contamination in School Environments Introduction Materials and Methods Results Discussion References Airborne Fungi in Workplace Atmospheres: Overview of Active Sampling and Offline Analysis Methods Used in 2009-2019 Introduction General Presentation of the Reviewed Articles Overview of Active Samplers Used for Airborne Fungi Characterization in the Workplace Atmospheres Inertial Impactors Filtration Samplers Liquid Samplers/Impingers Static Versus Personal Sampling Overview of Downstream Analyses Used for Airborne Fungi Characterization in the Workplace Atmospheres Culture-Based Methods/Overview Culture-Based Methods/Enumeration of Culturable Fungi Culture-Based Methods/Identification of Culturable Fungi Culture-Independent Methods/Generality Culture-Independent Methods/Microscopic Analysis Culture-Independent Methods/Molecular Methods Culture-Independent Methods/Metabolites Analysis Conclusion Appendix A Supplementary Information References Fungal Contamination of Sawmills Introduction Fungi as Occupational Health Risks at Sawmills Fungal Exposure in Sawmills Exposure Measurements and Identification by Cultivation of Aerosol Samples From Sawmills Exposure Assessment of Both Live and Dead Fungi by Microscopy Fungal Fragments - A Large Part of Fungal Aerosol in Sawmills Revelation of the Sawmill Mycobiome by Metabarcoding Bioactive Fungal Components in Sawmill Aerosol Sawmills as Potential Reservoirs of Azole Resistant Fungi Determinants of Fungal Exposure in Sawmills Wood Type Departments Seasons Other Factors That Impact Fungal Exposures at Sawmills Reducing the Exposure to Fungi Health Effects of Fungal Aerosol Inhalation in Sawmills Hypersensitivity Pneumonitis (HP) Other Inflammatory Airway Responses Among Sawmill Workers Immune Modulating or Positive Effects of Fungal Diversity Conclusions and Future Perspectives Appendix A Supplementary Material References Relevant Websites Next-Generation Sequencing in Environmental Mycology. A Useful Tool? Introduction Environmental Exposure to Fungi Cultivating Fungi High-Throughput Sequencing High-Throughput Sequencing Platforms Bioinformatics Conclusion References Relevant Websites Fungal Contamination of Swimming Pools and Fitness Centers Introduction Materials and methods Results Discussion Conclusions References Occupational Fungal Exposure and Assessment on Animal Production Introduction Materials and methods Results Discussion Conclusions Acknowledgments References Further Reading Fungal Prevalence on Waste Industry - Literature Review Introduction Materials and Methods Results Discussion Conclusions References Aspergillus in Indoor Environments Sources of Mold and Mold-Derived Fragments or Metabolites and Elevated Mold Exposure What is Aspergillosis? Is Aspergillosis Community Acquired or a Hospital-Associated Infection? Investigation of Indoor Biotic Fungal Communities General Considerations of Aspergillus Growth and Proliferation Nutrients Water pH Oxygen Temperature Light Where Does Aspergillus Proliferate? Soil Water Water-Damaged Building Materials Colonization of Buildings and Building Fabric Is Dust a Biotic Environment That Supports the Survival of Aspergillus? Aspergillus Spore Dispersal in Indoor Air Numbers of Inhaled Conidia Diversity of Molds in Social Housing Does the Presence of Aspergillus in Home Environments Present a Risk Factor for Invasive Aspergillosis? Aspergillus Mycotoxins in Indoor Environments Aspergillus and Hospital Environments Is the Presence of Aspergillus Fumigatus in Indoor Environments Reflected in the Mycobiome of the Respiratory Tract? References Further Reading Relevant Websites Fungal Exposure in Agricultural Environments - A Review Introduction Materials and Methods Results Discussion Conclusions References Further Reading Fungal Contamination of Beaches Introduction The Fungal Flora in Beaches The Ecosystem Human and Animal Impact on Beach Contamination The Relevance of Beach Contamination on Human Health Guidelines/Recommendations Summary References Relevant Websites Fungal Exposure and Relevant Recreational Settings Fungi and Recreational Water Environments Exposure Swimming Pools Sunbathing Water Sports Cave Exploration Gardening and Camping Sandboxes Climate Change - The Game Changer Quantitative Microbial Risk Assessment (QMRA) Conclusion References Further Reading Assessment of Aspergillus Section Fumigati in Occupational Environments - A Bibliographic Review Introduction Materials and methods Results Discussion Conclusion Acknowledgments References Further Reading Screening of Fungal Azole Resistance in Different Environmental Samples Introduction Materials and Methods Results Discussion References Further Readings Assessment of Azole Resistance in Healthcare Facilities Introduction Materials and methods Results Discussion References Climate Change and Aflatoxins Contamination in the Iberian Peninsula Introduction Are Aflatoxins a Current Concern in the Iberian Peninsula? Climate Change and the Impact on Aflatoxins Contamination and the Risk of Human Exposure Conclusions and Future Perspectives References The Usefulness of Human Biomonitoring in the Case of Mycotoxins Exposure Assessment Human Biomonitoring - What it is? Biomonitoring as an Exposure and Risk Assessment Tool Biomonitoring Data to Support Risk Management Measures and Regulatory Actions What is a Mycotoxin and How We Can be Exposed? The Usefulness of HBM in the Case of Mycotoxins Exposure Assessment References Further Reading Mycotoxins as Endocrine Disruptors - An Emerging Threat Introduction Zearalenone Main Characteristics Metabolism of Zearalenone Mode of Action and Toxicity Occurrence of Zearalenone in Food Alternaria Toxins Main Characteristics Mode of Action and Toxicity Occurrence of Alternaria Toxins in Food Metabolism of Alternaria Toxins Biomonitoring and Toxicokinetic Studies Conclusions and Future Perspectives References Fungi in Milk and in Dairy Products Introduction Fungi and Yeasts in Milk Fungi and Yeasts in Dairy Products Conclusions References Profile of Fungi in Dietary Supplement, Based on Plant Raw Material Introduction Occurrence of Fungi in Plants and Dietary Supplements - A Global Problem Conclusions References Further Reading Molds in Food Spoilage Introduction Diversity of Spoilage Fungi Xerophilic Fungi Heat-Resistant Molds (HRM) Preservative-Resistant Molds (PRM) Anaerobic Fungi Psychrophilic and Psychrotolerant Fungi Mold Spoilage Assessment Conclusion References Mycobiota Causing Diseases in Pets Do Fungi Need to Be Pathogenic? Ecology of Pathogenic Fungi Microscopic Mycobiota Able to Cause Diseases in Pets, Incl. Captive Animals Macroorganism Histopatological Responses to Subcutaneous and Systemic (Deep) Mycoses Human Health Risks When Working With Medically Important Fungi Serological Methods to Diagnose Systemic Mycoses (; Seyedmousavi, 2019; Barrs et al., 2015) Antifungal Therapy Applicable in Pets’ Treatment Conclusion Potential Conflict of Interest References Production of Native and Recombinant Enzymes by Fungi for IndustrialApplications Introduction Fungal Hosts for Industrial Enzyme Production Aspergillus Trichoderma Fermentation Technologies for Fungal Enzymes Production Solid-State Fermentation Submerged Fermentation Application of Fungal Enzymes Commercial Native Enzymes From Fungi Amylases Proteases Xylanases Pectinases Glucose Oxidase and Catalase Cellulases Glucoamylase Commercial Heterologous Enzymes From Fungi Genetic Strain Improvement for Native and Heterologous Enzyme Production Enzyme Discovery Genome Mining and Functional Metagenomics Protein Engineering Approaches Conclusion References Fungal Laccases as Biocatalysts for Wide Range Applications General Aspects of Laccases Catalytic Site and Reaction Mechanism of Laccases Laccase Mediator Systems Heterologous Expression of Fungal Laccases Biotechnological Applications Pulp and Paper Industry Textile Industry Waste Treatment Food and Beverages Biosensors Laccases in Organic Synthesis Oxidative coupling and polymerization reactions catalyzed by laccase Synthesis of polyaniline catalyzed by laccase Conclusions References Fungal Lignin-Modifying Peroxidases and H2O2-Producing Enzymes Plant Cell Wall Structure and Composition Lignin Plant Cell Wall Carbohydrates Lignin-Modifying Fungi White-Rot Fungi Brown-Rot Fungi Grey-Rot Fungi Soft-Rot Fungi Class II Fungal Heme Peroxidases Manganese Peroxidase Lignin Peroxidase Versatile Peroxidase Structural Properties of Class II Peroxidases Evolutionary Background of Class II Peroxidases H2O2-Producing Enzymes Glucose-Methanol-Choline Oxidoreductases Copper Radical Oxidases Glucooligosaccharide Oxidases Potential Applications of Fungal Lignin-Modifying Peroxidases and H2O2-Producing Enzymes Concluding Remarks Acknowledgments References Relevant Websites Fungal Peroxygenases - A Versatile Tool for Biocatalysis Introduction General Aspects Phylogeny Reaction Cycle Structural Insights Applicability of UPOs Wild-Type UPOs Recombinant UPOs pH and Temperature Stability UPO Inactivation by Peroxide Peroxide Supply Immobilization Reactions Catalyzed by UPOs Carbon Oxygenations Hydroxylations (sp3) Epoxidations (sp2) Alkynes (sp1) Limitations Oxygenation of Heteroatoms Halogenations Conclusions and Outlook Acknowledgments References Fungal Lytic Polysaccharide Monooxygenases (LPMOs): Biological Importance and Applications Introduction The Discovery of LPMOs and Basic Structural and Functional Information Occurrence of LPMOs and LPMO-Like Proteins in Fungi Assaying LPMO Catalysis Interplay With Other Fungal Redox Enzymes Applications: Cellulose Saccharification and Fibrillation Future Perspectives References Applications of Fungal Cellulases Introduction Cellulose Cellulose Hydrolyzing Enzymes Biotechnological Applications of Fungal Cellulases Fungal Cellulases in Food, Feed and Beverage Industries Textile and Detergent Industries Pulp and Paper Industry Biorefineries Agriculture Improvement of Fungal Cellulases and Their Production Forward Genetics Protein Engineering Overexpression and Promoter Engineering Manipulation of Transcriptional Regulators Epigenetic Engineering and CRISPR/Cas9 Concluding Remarks References Further Reading Relevant Website Applications of Fungal Hemicellulases Introduction Applications of Hemicellulases Bio-Bleaching Bio-Scouring Biorefining Wine and Fruit Juice Clarification Oligosaccharide Generation Detergent Additives Bakery Animal Feed Up-Gradation Conclusions and Future Perspectives Acknowledgments References Further Readings Relevant Websites Applications of Fungal Pectinases Introduction Pectin Structure and Depolymerization Pectinase Production Biotechnological Applications Juice Production Wine Production Olive Oil Extraction Tea and Coffee Production Extraction of Phytopigments Bio-Scouring of Cotton Biofuel Production References Further Reading Relevant Website Fungal Biotechnology: Fungal Amylases and Their Applications Introduction Starch, the Natural Substrate for Amylases Role of Amylases in Starch Hydrolysis alpha-Amylases Glucoamylases Starch Binding Domain (SBD) Application of Amylases Production of High-Fructose Corn Syrups Biofuel Production From Starch Food and Beverage Markets Amylase in Animal Feeds Detergent Industries Textile and Paper-and-Pulp Industries Clinical and Medicinal Applications Production of Industrial Amylases Recombinant Production of Amylases Amylolytic Strains for Biofuel Production Searching for Novel Amylases Future Outlook References Further Reading Relevant Websites Applications of Fungal Inulinases Introduction Inulin: General Introduction, Distribution, Annual Production and Availability Inulinases: Characteristics, Production and Heterologous Expression Applications of Inulinases High Fructose Syrup Production Production of Prebiotic Fructooligosaccharides Bioethanol Generation Single Cell Oil (SCO) Production Citric Acid and Lactic Acid Production Single Cell Protein and Tequila Production Immobilized Inulinases Conclusion References Relevant Websites Fungal Proteases: Current and Potential Industrial Applications Introduction Fungal Proteases Fungal Proteases in Industry Proteases for the Food Industry Dairy Baking Brewing Protein hydrolysate production Proteases for the Pharmaceutical Industry Proteases for Leather and Fabric Processing Other Applications of Fungal Proteases Conclusion and Future Prospective References Multifarious Applications of Fungal Phytases Introduction Applications of Phytases Applications in Foods and Animal Feed Foods Animal feeds Phytases from transgenic plants and animals Applications in Aquaculture and Fish Farming Phytases in Plant Growth Promotion and Soil Amendment Utility of Phytases in Environmental Pollution Mitigation Use of Phytases in Generating Specific Inositol Phosphates With Therapeutic Applications Virtual Peroxidases Derived From Phytases and Their Uses Other Applications Commercially Available Phytases Conclusions References Further Reading Relevant Website Modification of Plant Carbohydrates Using Fungal Enzymes Introduction Carbohydrate Active Enzyme Classification Fungal Plant Carbohydrate Degrading Enzymes and Their Substrates Starch and Inulin Degrading Glycoside Hydrolases Cellulose Degrading Glycoside Hydrolases Xyloglucan Degrading Glycoside Hydrolases Pectin Degrading Glycoside Hydrolases and Polysaccharide Lyases Xylan Degrading Glycoside Hydrolases Mannan Degrading Glycoside Hydrolases Lytic polysaccharide monooxygenases (LPMOs) Relevance for Industry References Further Reading Relevant Websites Production of Oligosaccharides by Fungi or Fungal Enzymes Introduction Fructooligosaccharides Xylooligosaccharides Chito-Oligosaccharides Galacto-Oligosaccharides Final Considerations References Further Reading Metabolic Modeling of Fungi Introduction Reconstruction of a Genome-Scale Network Automated Draft Reconstruction Manual Curation of the Draft Biomass Formation and Energy Requirements Approaches to Analyze Genome-Scale Metabolic Reconstructions Other Commonly Used Approaches to Study GEMs Dynamic flux balance analysis (dFBA) Flux variability analysis (FVA) Reduced cost analysis Integration of transcriptomics Integration of proteomics Integration of metabolomics Multi-omics integration Metabolic engineering Applications of Fungal Models Prediction of Phenotypes Metabolic Engineering Future of Metabolic Modeling of Fungi Conclusions Funding References Relevant Websites Production of Organic Acids by Fungi Introduction Why Do Fungi Accumulate Organic Acids? Biochemical Aspects of Organic Acid Accumulation by Fungi Description of the Production of Organic Acid Monocarboxylic Acids L-lactic acid Dicarboxylic Acids Oxalic acid L-Malic acid Fumaric acid Succinic acid Trans-2,3-epoxysuccinic acid (ESA) Tricarboxylic Acids Citric acid Itaconic acid Sugar Acids Gluconic acid Engineering Aspects of Fungal Organic Acid Production Acknowledgment References Relevant Website Biotechnological Advancements, Innovations and Challenges for Sustainable Xylitol Production by Yeast Introduction Biotechnological Production of Xylitol: The Yeast’s Role Xylitol Production by Native Xylose Utilizing Yeasts Exploiting Saccharomyces cerevisiae as Cell Factory for the Biotechnological Production of Xylitol Xylitol Production From Renewable Resources by Yeast Conclusions Acknowledgments References Further Reading Biotechnology of Wine Yeasts A Taste of Biotechnological History The Rising Power of Wine Yeast The Essence of Winemaking The Dominant Role of Saccharomyces Cerevisiae Genomics of Saccharomyces Cerevisiae Genetic Modification of Wine Yeast The Role of Non-Saccharomyces Yeast Concluding Remarks Acknowledgments References Ethanol Tolerance and Production by Yeasts Introduction Ethanol Production by Yeasts During the Fermentation Process Ethanol Fermentation by Saccharomyces Yeasts Fermentation by Non-Saccharomyces Yeasts Industrial Process for Bioethanol Production Molecular Basis of Fermentation-Associated Stress Ethanol Stress and Tolerance Yeast Improvement for Higher Ethanol Production and Tolerance Classical (Non-GMO) Optimization of Yeasts Evolutionary engineering UV and chemical mutagenesis Protoplast fusion Genome shuffling Genetic Engineering of Yeasts Conclusions and Future Perspectives References The Biosynthesis of Fungal Secondary Metabolites: From Fundamentals to Biotechnological Applications Introduction Fungi Produce Bioactive Secondary Metabolites That Impact Human Societies Fungal Secondary Metabolites in Human Daily Life Fungal Secondary Metabolites in Fungal Daily Life The Fundamentals of Secondary Metabolite Production in Fungi A Diversity of Biosynthetic Enzymes The Gene Cluster Organization Tight Regulation of Secondary Metabolite Production Genomics of Fungal Secondary Metabolism Abundance of Biosynthetic Pathways in Fungal Genomes In Silico Prediction of Biosynthetic Gene Clusters Motif-dependent detection Motif-independent detection Strategies for Prioritizing the Study of Biosynthetic Gene Clusters Phylogeny-informed prediction Comparative genomics and gene cluster families Function-guided prioritization Linking Compounds to Biosynthetic Genes Activation of Silent Biosynthetic Pathways Modification of Culture Conditions Co-Cultivation of Microorganisms Genetic Modifications Pathway-specific activation Genetic manipulation of the global regulation Heterologous Expression of Biosynthetic Gene Clusters Engineering Biosynthetic Pathways: Chimeric Enzymes, Pathway Refactoring, Combinatorial Biosynthesis, Artificial Pathways Fungal Secondary Metabolite Production: Future Perspectives Acknowledgments References Relevant Websites Degradation of Homocyclic Aromatic Compounds by Fungi Introduction Names of Aromatic Compounds Plant Derived Aromatic Compounds Lignin Plant Derived Monomeric Aromatic Compounds Allelopathy Lignin Degradation Degradation of Aromatic Compounds by Fungi Hazardous Aromatic Compounds Benzene Ethylbenzene Toluene Xylenes Phenol Plant Derived and Food Related Aromatic Compounds Salicylic acid Vanillin Benzoic acid Cinnamic acid Conclusions and Future Prospects References Genetic Engineering for Strain Improvement in Filamentous Fungi Introduction Classical Genetic Engineering Approaches Genetically Modified Strains (GMOs) Genetic Engineering of Filamentous Fungi Protoplast-mediated transformation Agrobacterium tumefaciens-mediated transformation Electroporation-mediated transformation Biolistic transformation Shock wave-mediated transformation technology Non-GMO Genetic Engineering Approaches UV mutagenesis Chemical mutagenesis Combined use of mutagenesis approaches Adaptive evolution Novel Strain Engineering Approaches CRISPR/Cas Technology Other Novel Strain Engineering Approaches Applications of Strain Improvement Gene Overexpression Replacing the promoter Increasing the gene copy number Gene Downregulation Gene deletion Point mutations RNA interference (RNAi) Conclusions and Future Prospects References Strain Improvement and Genetic Engineering of Trichoderma for Industrial Applications Introduction Untargeted Genetic Recombination by Classical Mutagenesis Forced Random Mutagenesis Resulted in the Creation of the Industrial Hypercellulolytic Strains of T. reesei In Vitro Sexual Crossing, the Dedicated Gift for T. reesei Protoplast Fusion and Parasexuality, the Cloud of Trichoderma Strain Improvement Targeted Genetic Recombination Recombination Based on Selective Markers Recombination Based on Markerless Systems Methods for Introducing Recombinant DNA Into Trichoderma Agrobacterium tumefaciens-mediated transformation PEG-mediated protoplast transformation RNA Interference Promoter Engineering Approaches CRISPR/Cas9, the Next-Generation Genome Editing Revolution and Its Application in Trichoderma Acknowledgments References Further Reading Relevant Website Expression of Recombinant Fungal Proteins in Pichia Pastoris Introduction Construction of Expression Strains Vectors and Type of Induction System Strains Using Functional Host Strains Vectors Transformation Cultivation Medium and General Conditions Cultivation in a Jar Fermenter Post Cultivation and Purification Conclusion References Transcriptional Regulation: How Saprobic Fungi Tune the Production of Plant Cell Wall Degrading Enzymes Introduction The Molecular Basis of PCWDE Production Transcriptional Regulation of PCWDEs in Fungi Environmental Inducers and Their Corresponding Transcription Factors Sugars or their metabolic conversion products are the major inducers of genes encoding plant biomass degrading enzymes Other environmental inducers of genes encoding plant biomass degrading enzymes Environmental Repressors and Their Corresponding Transcription Factors Regulation of Transcription Factor Activity Methods for Discovery of Transcription Factors and Identification of Their Regulons Manipulation of Transcriptional Regulation of PCWDEs in Biotechnology Research Technologies and Approaches for Future Research Acknowledgments References Bioinformatics Approaches for Fungal Biotechnology Introduction Current Status of Fungal Genomic Analysis Bioinformatics Workflow and Tools for Genomics Analysis Examples of Fungal Genomic Studies Current States of Fungal Post-Genomics Analysis Transcriptomics Bioinformatics Workflow and Tools for Transcriptomics Analysis Examples of Fungal Transcriptomics Studies Proteomics Bioinformatics Workflow and Tools for Proteomics Analysis Peptide and Protein Identification Data Analysis of Quantitative Proteomics Biological Interpretation of Proteomics Results Examples of Fungal Proteomics Studies Metabolomics Bioinformatics Workflow and Tools for Metabolomic Analysis Examples of Fungal Metabolomics Studies Integrative Analysis of Multiple Omics Challenges and Perspectives for Future Bioinformatics Analysis References Further Reading Relevant Websites Production of Biofuels From Biomass by Fungi The Demand for Biofuels How do Plants Store Energy? How do Fungi Break Down Plant Polysaccharides? Transcription Factors Fungi in the Biofuel Industry Ethanol as a Biofuel First Generation Feedstocks Deconstruction of Lignocellulosic Material Breaking Down Cellulose Phanerochaete chrysosporium and Lignin Degradation Starch Degradation Lignocellulose Degrading Specialists Fermentation Processes First Generation Ethanol Fermentation Heterologous Xylose Degradation in S. cerevisiae Heterologous Starch Degradation in S. cerevisiae Biodiesel Conclusion References Oleaginous Fungi in Biorefineries Introduction Oleaginous Fungi and Their Advantages for SCO Production Limiting Factors of Large-Scale SCO Production Lipid Synthesis Mechanism of Oleaginous Fungi Biochemistry of Lipid Accumulation Lipid Profiles in Oleaginous Fungi Different Substrates for Microbial Lipids Production Conventional Carbon Substrates Lignocellulosic Biomass The Main Applications of Microbial Lipids From Oleaginous Fungi Biodiesel Functional Oils gamma -linolenic acid Arachidonic acid Eicosapentaenoic acid Docosahexaenoic acid Future Strategies for Productive Oleaginous Fungi Conclusions and Perspectives References Role of Fungi in Fermented Foods Introduction Foods Fermented With Filamentous Fungi Koji Soy Sauce Miso Tempeh Angkak Oncom Sufu Cheese Meat Fungi as Alternative Protein Sources Quorn Other Types of Mycoprotein Yeasts in Fermented Foods Injera Bread Cacao Beverages Wine and Fruit-Based Alcoholic Fermented Beverages Sake Beer Kombucha Beverages Produced Using Basidiomycetes Conclusion References The Application of Fungal Biomass as Feed Introduction Feed Market Prospects Compound Feed: Composition and Requirements Filamentous Fungi Fungal Cultivation Process Filamentous Fungal Biomass Composition Protein and Amino Acid Profile Fat and Fatty Acid Content Cell Wall Components Other Compounds Feed Applications Conclusions and Perspectives Acknowledgments References Applications of Fungal Polysaccharides Introduction Medicine and Pharmacy Medical Properties of Fungal Polysaccharides Antibacterial and antiviral effect Anticancer effect Antioxidant potential of polysaccharides Anti-diabetes polysaccharides Hepatoprotective effect of polysaccharides Immunomodulating activity Pharmaceutical Application Fungal Polysaccharides in Food Industry Food Additives Edible and/or Biodegradable Films Functional Foods and Nutraceuticals Animal Feed Cosmetics Environment and Agriculture Other Industrial Applications References Further Reading Development of Mycoherbicides Introduction What is Mycoherbicide Important Stages of Mycoherbicide Development General Considerations Selection of Appropriate Biocontrol Agent Biology and Ecology of Weed Pathogens Production, Formulation and Application Safety and Registration Alternaria or Colletotrichum? Potential Use of Fungal Secondary Metabolites Future Prospects References Biofungicides: An Eco-Friendly Approach for Plant Disease Management Introduction Biofungicide Agents Screening for Novel Biofungicides Biocontrol Mechanisms Against Fungal Plant Pathogens Plant Extracts as Potential Biofungicides Biofungicides in the Post-Genomic Era References Further Reading Degradation of Plastics by Fungi Introduction Plastics in the Environment Fungal Degradation of Polymers Polymers Containing Ester Bonds Polyethylene terephthalate (PET) Polyurethanes (PU) Polylactid acid (PLA) Polycaprolactone (PCL) Polyhydroxyalkanoates (PHA) Polyamides (PA) Non-Hydrolysable Synthetic Polymers Polyolefins (polyethylene and polypropylene) Polystyrene (PS) Polyvinyl chloride (PVC) Conclusions References Treatment of Industrial Wastewaters and Liquid Waste by Fungi Introduction The Role of Fungi in Industrial Wastewater and Liquid Waste Treatment Removal of Recalcitrant Organic Pollutants Mechanisms responsible for removal of recalcitrant organic pollutants Removal of Heavy Metals by Fungi Mechanisms of heavy metals removal Benefits of Fungal Consortia Emerging Trends in Fungal Wastewater Treatment Research Technical Aspects of Fungal Wastewater Treatment Principles of Microbial Wastewater Treatment Possible Technical Solutions Bioreactors Key Monitoring Parameters Challenges and Opportunities Conclusions References Antitumor and Immunomodulatory Compounds from Fungi Introduction Interrelations Between Immunomodulatory and Antitumor Properties Finding Fungi Producing Antitumor and Immunomodulatory Drugs Chemodiversity of Antitumor and Immunomodulatory Products from Fungi Mechanisms of Action of Antitumor and Immunomodulatory Compounds Antimitotic Agents and Cell Cycle Regulators Diverse Enzyme Inhibitory Properties Angiogenesis Inhibitors Antimetastatic Products Future Perspectives Acknowledgment References Further Reading Mycelium Materials A Non-Sustainable Economy Composite and Pure Mycelium Materials Pure Mycelium Materials Composite Materials Cell Wall Composition and Materials of Cell Wall Components Conclusions References Subject Index