Оглавление
Группа авторов. Biomolecular Engineering Solutions for Renewable Specialty Chemicals
Table of Contents
List of Tables
List of Illustrations
Guide
Pages
Biomolecular Engineering Solutions for Renewable Specialty Chemicals. Microorganisms, Products, and Processes
Preface. Biocommodity Engineering
List of Contributors
1 Engineered Microorganisms for Production of Biocommodities
1.1 Introduction
1.2 Fundamentals of Genetic Engineering
1.2.1 DNA‐altering Enzymes
1.2.1.1 DNA Polymerases
1.2.1.2 Nucleases
1.2.1.3 Ligases
1.2.1.3.1 Mechanism of Action
1.2.1.4 DNA‐modifying Enzymes. 1.2.1.4.1 Alkaline Phosphatase
1.2.1.4.2 T4 Poly Nucleotide Kinase
1.2.1.4.3 Terminal Transferase
1.2.1.4.4 Topoisomerases
1.2.2 Vectors
1.2.3 Incorporation of Modified DNA into Host
1.2.3.1 Introducing Recombinants into Prokaryotes
1.2.3.1.1 Transformation
1.2.3.1.2 Transduction
1.2.3.1.3 Conjugation
1.2.3.2 Introducing Recombinants into Eukaryotic Hosts
1.2.3.2.1 Transfection
1.2.3.2.2 Electroporation
1.2.3.2.3 Microinjection
1.2.3.2.4 Biolistics
1.2.4 Selection of Transformants
1.2.4.1 Direct Selection
1.2.4.1.1 Direct Antibiotic Resistance Screening
1.2.4.1.2 Blue–White Color Screening
1.2.4.2 Identification of the Clone from a Gene Library
1.2.4.2.1 Nucleic Acid Hybridization
1.2.4.2.2 Functional Screening
1.2.4.2.3 Chromosome Walking
1.3 Beneficial Biocommodities Produced Through Engineered Microbial Factories
1.3.1 Biopolymers
1.3.1.1 Cellulose
1.3.1.2 Poly‐ϒ‐glutamic Acid
1.3.1.3 Hyaluronic Acid
1.3.1.4 Polyhydroxyalkoate
1.3.2 Organic Acids
1.3.2.1 Citric Acid
1.3.2.2 Lactic Acid
1.3.2.3 Succinic Acid
1.3.2.4 Fumaric Acid
1.3.3 Therapeutic Proteins
1.4 Photosynthetic Production of Biofuels
1.4.1 Biohydrogen
1.4.2 Biodiesel
1.4.3 Bioethanol
1.4.4 Terpenoids
1.5 Conclusion
References
2 Microbial Cell Factories for the Biosynthesis of Vanillin and Its Applications
2.1 Introduction
2.2 Natural Sources of Vanilla and Its Production
2.3 Biotechnological Production of Vanillin
2.3.1 Enzymatic Synthesis of Vanillin
2.3.2 Microbial Biotransformation of Ferulic Acid to Vanillin
2.3.3 Agro‐wastes as a Source for Biovanillin Production
2.4 Strain Development for Improved Production of Vanillin. 2.4.1 Metabolic and Genetic Engineering
2.5 Bioactive Properties of Vanillin. 2.5.1 Antimicrobial Activity
2.5.2 Antioxidant Activity
2.5.3 Anticancer Activity. 2.5.3.1 Apoptosis Pathway
2.5.3.2 Tumor Necrosis Factor‐induced Apoptosis
2.5.3.3 Cell Cycle Arrest
2.5.3.4 Nuclear Factor κB (NF‐κB) Pathway
2.5.4 Anti‐sickling Activity
2.5.5 Hypolipidemic Activity
2.6 Conclusion
Acknowledgments
References
3 Antimicrobials : Targets, Functions, and Resistance
3.1 Introduction
3.2 Classification of Antibiotics
3.2.1 Classification of Antibiotics Based on Mode of Action: Bactericidal and Bacteriostatic
3.2.2 Classification of Antibiotics Based on the Spectrum of Action: Broad‐ and Narrow‐spectrum Antibiotics
3.3 Antibacterial Agents
3.3.1 Penicillins
3.3.1.1 Mechanism of Action
3.3.1.2 Clinical Implications. 3.3.1.2.1 Penicillin
3.3.1.2.2 Amoxicillin
3.3.2 Cephalosporins
3.3.2.1 Mechanism of Action
3.3.2.2 Clinical Indications. 3.3.2.2.1 Cephalexin (Keflex)
3.3.3 Macrolides
3.3.3.1 Mechanism of Action
3.3.3.2 Clinical Indications
3.3.3.2.1 Erythromycin (E‐Mycin)
3.3.3.2.2 Clarithromycin (Biaxin)
3.3.3.2.3 Azithromycin (Zithromax)
3.3.4 Fluoroquinolones
3.3.4.1 Mechanism of Action
3.3.4.2 Clinical Indication. 3.3.4.2.1 Ciprofloxacin
3.3.4.2.2 Levofloxacin
3.3.4.2.3 Ofloxacin
3.3.5 Sulfonamides
3.3.5.1 Mechanism of Action
3.3.5.2 Clinical Indication. 3.3.5.2.1 Sulfamethoxazole‐Trimethoprim
3.3.6 Tetracyclines
3.3.6.1 Mechanism of Action
3.3.6.2 Clinical Indication. 3.3.6.2.1 Tetracyclines
3.3.6.2.2 Doxycycline
3.3.7 Aminoglycosides
3.3.7.1 Mechanism of Action
3.3.7.2 Clinical Indication. 3.3.7.2.1 Gentamicin
3.3.7.2.2 Tobramycin
3.4 Antifungal Agents
3.4.1 Polyenes
3.4.1.1 Mechanism of Action
3.4.1.2 Clinical Indication
3.4.2 Azoles
3.4.2.1 Mechanism of Action
3.4.2.2 Clinical Indication. 3.4.2.2.1 Fluconazole
3.4.2.2.2 Itraconazole
3.4.2.2.3 Voriconazole
3.4.2.2.4 Posaconazole
3.4.2.2.5 Isavuconazole
3.4.3 Echinocandins
3.4.3.1 Mechanism of Action
3.4.3.2 Clinical Indication. 3.4.3.2.1 Caspofungin
3.4.3.2.2 Micafungin
3.4.3.2.3 Anidulafungin
3.4.4 Flucytosine
3.4.4.1 Mechanism of Action
3.4.4.2 Clinical Implication
3.5 Antiviral agents
3.6 Antiparasitic Agents
3.6.1 Antiprotozoan Agents
3.6.2 Antihelminthic Agents
3.6.3 Ectoparasiticides
3.7 Antimicrobial Resistance
3.7.1 Genetic Basis of AMR
3.7.2 Mechanistic Basis of Antimicrobial Resistance
3.8 Conclusion
Acknowledgment
References
4 Trends in Antimicrobial Therapy : Current Approaches and Future Prospects
4.1 Introduction
4.2 Antibiotics: A Brief History
4.2.1 Classification of Antibiotics
4.2.2 Evolution of Antibiotics
4.2.3 Mechanism of Action of Antibiotics
4.3 AMR: A Global Burden
4.3.1 Global Scenario
4.3.2 Origin of SUPERBUGS and the “END of Antibiotics”
4.4 Antimicrobial Resistance and Virulence
4.4.1 Molecular Insights and Mechanism of AMR
4.4.2 Antibiotic Resistance in Bacteria. 4.4.2.1 Horizontal Gene Transfer
4.4.2.2 Increased Mutation Rate
4.4.2.3 Antibiotic Inactivation
4.4.2.4 Alteration of the Antibiotic Targets
4.4.2.5 Changes in Cell Permeability and Efflux
4.4.2.6 The Major Facilitator Superfamily
4.4.2.7 The ATP‐Binding Cassette Superfamily
4.4.2.8 The Multidrug and Toxic Compound Extrusion Family
4.4.2.9 The Resistance–Nodulation–Division (RND) Superfamily
4.4.2.10 The Small Multidrug‐Resistance Family
4.4.3 Development of Antibiotic Resistance
4.4.4 Prioritization of Antibiotic Resistant Bacteria
4.4.5 Understanding Biofilm Resistance
4.5 Alternatives to Antibiotics. 4.5.1 Peptide Antibiotics
4.5.1.1 Cationic Antimicrobial Peptides (CAMPs)
4.5.1.2 Marine Antimicrobial Peptides
4.5.2 Nano Drugs
4.5.3 Probiotics
4.5.4 Bacteriocins
4.5.5 Bdellovibrio
4.5.6 Bdellovibrio as Live Antimicrobial Agent
4.6 Antibiotics: Global Action Plan on Antimicrobial Resistance
4.7 Conclusion
Acknowledgment
References
5 Fermentation Strategies in the Food and Beverage Industry
5.1 Introduction
5.2 Current Trends in Food Fermentation
5.2.1 Fermentation Types
5.2.1.1 Spontaneous Fermentation
5.2.1.2 Back‐Slopping Fermentation
5.2.1.3 Starter‐Culture Fermentation
5.2.2 Microbial Cultures
5.2.2.1 Starter Cultures
5.2.2.1.1 Yeasts
5.2.2.1.2 Lactic Acid Bacteria (LAB)
5.2.2.1.3 Other Starter Organisms
5.2.2.2 Adjunct Cultures
5.2.2.3 Bio‐protective Cultures
5.2.2.4 Probiotic Cultures
5.3 Future Directions
5.3.1 Use of Defined Mixed Cultures
5.3.2 Nanotechnology
5.3.2.1 Nanosensors
5.3.2.2 Nanoparticles
5.3.2.3 Nanocomposites
5.3.3 Meat Analogues
5.4 Conclusions
5.5 Questions for Thought
References
6 Bioactive Oligosaccharides : Production, Characterization, and Applications
6.1 Introduction
6.2 Sources, Types, Structure of Oligosaccharides
6.2.1 Plant Source
6.2.2 Animal Source
6.2.3 Insect Source
6.2.4 Marine Source
6.2.5 Microbial Source
6.2.6 Synthetic Oligosaccharides
6.2.7 Pseudo‐oligosaccharides
6.3 Production Methods of Oligosaccharides
6.3.1 Chemical Methods
6.3.2 Physical Methods
6.3.3 Enzymatic Hydrolysis
6.3.4 Microbial Production of Oligosaccharides
6.4 Extraction, Separation, and Purification of Oligosaccharides
6.5 Characterization of Oligosaccharides
6.6 Functional Properties of Oligosaccharides
6.7 Applications of Oligosaccharides
6.7.1 Functional Foods, Nutraceuticals, and Prebiotics
6.7.2 Pharmaceutical and Medical Applications. 6.7.2.1 Effects on Intestinal Microflora
6.7.2.2 Effects on Urogenital Infections
6.7.2.3 Type II Diabetes and Obesity
6.7.2.4 Immunomodulatory and Antitumor Activities
6.7.2.5 Effect on Cardiovascular Risk
6.7.2.6 Lowering of Cholesterol
6.7.2.7 Role in Osteoporosis
6.7.2.8 Antihypertensive Effects
6.7.2.9 Hepatic Protection
6.7.2.10 Antioxidant and Neuroprotective Agent
6.7.2.11 Antimicrobial Activity
6.7.2.12 Antibiotics
6.7.2.13 Oligosaccharides as Vaccine Components
6.7.3 Environmental Fortification
6.7.4 Cosmetics
6.7.5 Elicitors and Agriculture
6.7.6 Novel Biomaterials
6.8 Market Potential of Oligosaccharides
6.9 Future Prospects
References
7 Biopolymers : A Retrospective Analysis in the Facet of Biomedical Engineering
7.1 Introduction
7.2 Natures’ Advanced Materials: A Glance at Its Structure and Properties. 7.2.1 Polypeptides
7.2.1.1 Collagen
7.2.1.2 Elastin
7.2.1.3 Silk Fibroin
7.2.1.4 Gelatin
7.2.1.5 Albumin
7.2.1.6 Casein
7.2.2 Polysaccharides. 7.2.2.1 Cellulose
7.2.2.2 Starch
7.2.2.3 Cyclodextrin
7.2.2.4 Hyaluronic Acid
7.2.2.5 Chitosan
7.2.2.6 K‐carrageenan
7.2.2.7 Agarose
7.2.2.8 Alginate
7.2.3 Polynucleotides‐based Biopolymers
7.3 Smart Biopolymers
7.3.1 Chemical‐Responsive Biopolymers. 7.3.1.1 pH‐Sensitive Smart Biopolymers
7.3.1.2 Glucose‐Responsive Biopolymers
7.3.2 Physically Responsive Biopolymers. 7.3.2.1 Temperature‐Sensitive Smart Biopolymers
7.3.2.2 Light‐Responsive Smart Polymers
7.3.2.3 Electric‐Responsive Smart Polymers
7.3.2.4 Magnetic‐Responsive Smart Polymers
7.3.2.5 Redox‐Responsive Biopolymer
7.3.3 Biochemical Stimuli‐Responsive Biopolymers. 7.3.3.1 Enzyme‐Responsive Biopolymer
7.4 Fundamental Applications of Biopolymers in Biomedical Engineering. 7.4.1 Biopolymers in Cancer Theranostics
7.4.1.1 Drug Delivery
7.4.1.2 Cancer Diagnosis and Molecular Imaging
7.4.2 Biopolymeric‐based Biosensor
7.4.3 Wound Healing
7.4.4 Tissue Engineering and Regenerative Medicine
7.4.4.1 Biopolymers as Bioink for 3D Scaffolds
7.4.4.2 Corneal Regeneration
7.4.4.3 Neural Tissue Engineering
7.4.4.4 Bone Tissue Engineering
7.4.4.5 Cartilage Tissue Regeneration
7.4.5 Biopolymers for Biological Implants
7.4.6 Biopolymers in Other Applications
7.5 Processing Techniques for the Contrivance of Biopolymers. 7.5.1 3D Bioprinting
7.5.2 4D Bioprinting
7.5.3 Electrospinning
7.6 Conclusion
Acknowledgments
References
8 Metabolic Engineering Strategies to Enhance Microbial Production of Biopolymers
8.1 Introduction
8.2 Microbes as Cell Factories for the Production of Speciality Biochemicals
8.2.1 Bacteria as Cell Factories for the Production of Biopolymers
8.2.1.1 Polysaccharides
8.2.1.2 Polyesters
8.2.1.3 Polyamides
8.2.2 Fungus as Cell Factories for the Production of Biopolymers
8.2.2.1 Polysaccharides
8.2.2.2 Polyester
8.2.2.3 Polyamides
8.2.3 Microalgae as Cell Factories for the Production of Biopolymers
8.2.3.1 Polysaccharides from Microalgae
8.2.3.2 Polyester
8.2.3.3 Polyamides
8.3 Microbial Production Pathways for Various Types of Biopolymers. 8.3.1 Polysaccharide Production Pathways in Bacteria
8.3.2 Mechanism of Fungal Polysaccharides Synthesis
8.3.3 Mechanism of Synthesis of Polyester in Bacteria
8.3.4 Mechanism of Synthesis of Polyamide in Bacteria
8.4 Tools and Technologies Available for Metabolic Engineering
8.4.1 Metabolic Pathway Reconstruction
8.4.2 Metabolic Flux Analysis
8.4.3 Metabolic Control Analysis
8.4.4 Omics Analysis
8.5 Dynamic Metabolic Flux Analysis and its Role in Metabolic Engineering
8.6 Production of Biopolymers from Metabolically Engineered Microbes
8.6.1 Metabolic Modification of Pathway for Synthesis of Polysaccharides
8.6.2 Levan
8.6.3 Metabolic Modification of Pathway for Synthesis of Polyester
8.6.4 Metabolic Modification of Pathway for Synthesis of Polyamides
8.6.5 Culture of Metabolically Engineered Microbes in Fermentation or Bioreactor for Production of Biopolymer
8.7 Recovery and Purification of Biopolymers from Fermentation Broth
8.7.1 Separation and Purification of Xanthan
8.7.2 Separation of Poly‐L‐lysine
8.8 Conclusion and Future Challenges
Acknowledgments
References
Web References
9 Bioplastics Production : What Have We Achieved?
9.1 Introduction
9.2 Current Trends
9.3 Different Types of Bioplastics
9.3.1 Bio‐based Polyethylene (Bio‐PE)
9.3.2 Bio‐based PET
9.3.3 Polylactic Acid
9.3.4 Starch Blends
9.3.5 Polyhydroxyalkanoate
9.3.6 Polybutylene Succinate
9.3.7 Polybutylene Adipate Terephthalate
9.3.8 Polycaprolactone
9.3.9 Epoxies
9.3.10 Cellulose Acetate
9.4 Challenges Facing the Bioplastics Industry
9.5 Misconceptions and Negative Impacts
9.6 Take Home Message and Future Directions
9.7 Questions for Thought
Acknowledgments
Conflict of Interest
References
10 Conversion of Lignocellulosic Biomass to Ethanol: Recent Advances
10.1 Introduction
10.2 LCB: Structure, Composition, and Recalcitrance
10.3 LCB to Ethanol: Bioprocess Strategies
10.4 Pretreatment of LCB
10.4.1 Physical Pretreatment
10.4.2 Physicochemical Pretreatment
10.4.2.1 Steam Explosion
10.4.2.2 Liquid Hot Water
10.4.2.3 Ammonia Fiber Explosion
10.4.3 Chemical Pretreatment
10.4.3.1 Dilute Acid Pretreatment (DAP)
10.4.3.2 Alkali Pretreatment
10.4.3.3 Organosolv
10.4.3.4 Ionic Liquid (IL) and Deep Eutectic Solvent (DES)
10.4.3.5 Supercritical Fluid Pretreatment
10.4.4 Biological Pretreatment. 10.4.4.1 Bacterial Pretreatment
10.4.4.2 Fungal Pretreatment
10.4.4.3 Enzymatic Pretreatment
10.4.5 Optimization of Pretreatment Process
10.5 Enzymatic Hydrolysis
10.5.1 Cellulose Hydrolysis
10.5.2 Xylan Hydrolysis
10.5.3 Accessory Enzymes
10.5.4 Auxiliary Activity and Non‐Hydrolytic Enzymes
10.5.5 Enzyme Cocktail for Biomass Hydrolysis
10.5.5.1 Cocktail Development
10.6 High Solids Loading Enzymatic Hydrolysis (HSLEH)
10.6.1 Enzyme Inhibitors and Detoxification
10.6.2 Cellulase Feedback Inhibition
10.6.3 Rheology
10.6.4 Reactors and Impellers
10.7 Fermentation
10.8 Genetic Engineering in LCB Bioconversion
10.9 Conclusions
Acknowledgments
References
11 Advancement in Biogas Technology for Sustainable Energy Production
11.1 Introduction
11.2 Biogas Developments Worldwide
11.3 Biogas Development in India
11.4 Recent Issues in Biogas Production
11.5 Current Trends in Biogas Production
11.6 Advanced Anaerobic Digestion Methodologies
11.6.1 Anaerobic Membrane Reactor (AnMBRs)
11.6.2 Dry Anaerobic Digestion Technology (DADT)
11.6.3 Anaerobic Co‐digestion Technology (AcoD)
11.7 Role of Biotechnology in Enhancing Biogas Production
11.8 Application of Nanotechnology in Biogas and Methane Production
11.9 Biogas Upgrading Technologies
11.10 Conclusion
References
12 Biofertilizers : A Sustainable Approach Towards Enhancing the Agricultural Productivity
12.1 Introduction
12.2 Types of Biofertilizers
12.2.1 Nitrogen‐Fixing Biofertilizer
12.2.1.1 Free‐Living Nitrogen‐Fixing Microorganisms
12.2.1.2 Photosynthetic Nitrogen‐Fixing Microorganisms
12.2.2 Phosphorus Biofertilizer
12.2.2.1 Phosphate‐solubilizing Bacteria (PSB)
12.2.2.2 Phosphate‐mobilizing Microorganisms
12.2.3 Plant‐Growth‐promoting Biofertilizers
12.3 Effect on Bioremediation of Environmental Pollutants
12.4 Bioformulations and Its Types
12.5 Preparation of Biofertilizers
12.6 Various Modes of Biofertilizer Application
12.7 Challenges to Commercialization of Biofertilizers
12.8 Future Perspective
References
13 Biofertilizers from Food and Agricultural By‐Products and Wastes
13.1 Introduction
13.2 Biofertilizer
13.2.1 N2‐fixing Biofertilizer
13.2.1.1 Free‐living N2‐fixing Biofertilizer
13.2.1.1.1 Azotobacteria
13.2.1.1.2 Cyanobacteria
13.2.1.2 Symbiotic N2‐Fixing Biofertilizer. 13.2.1.2.1 Rhizobium Biofertilizers
13.2.1.2.2 Azolla Biofertilizers
13.2.1.2.3 Azospirillum Biofertilizers
13.2.2 Phosphate‐solubilizing Biofertilizers
13.2.3 Phosphate‐mobilizing Biofertilizer
13.2.4 Plant‐Growth‐ promoting Biofertilizers
13.3 Agricultural Waste
13.3.1 Agro‐industrial Wastes
13.4 Food Waste
13.5 Biofertilizer Production Using Fermentation Technology
13.5.1 Solid‐State Fermentation (SSF)
13.5.2 Submerged Fermentation (SmF)
13.5.3 Production of N2‐fixing Biofertilizer
13.5.3.1 Production of Rhizobium Biofertilizer
13.5.3.2 Production of Azotobacter Biofertilizer
13.5.3.3 Production of Azospirillum Biofertilizer
13.5.4 Production of Phosphate‐solubilizing Biofertilizer
13.5.5 Production of Phosphate‐mobilizing Biofertilizer
13.6 Biofertilizer for Organic Farming
13.7 Conclusion
Conflict of Interest
References
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