Omics Technologies and Bio-engineering: Volume 2: Towards Improving Quality of Life

Dedication
Dedication
List of contributors
List of Contributors
About the editors
About the Editors
Contents 1-5
Contents 5-10
Contents 11-15
Contents 16-20
Chapter 01
1 Microbial Omics: Applications in Biotechnology
1.1 Introduction
1.2 Structural Genomics
1.2.1 Comparative and Pan-Genomics
1.2.2 Immunogenomics
1.2.3 Post-Genomics
1.3 Functional Genomics
1.3.1 Transcriptomics
1.3.2 Proteomics (Interactomics)
1.3.3 Metabolomics
1.4 Conclusions and Perspectives
References
Chapter 02
2 Omics Approaches in Viral Biotechnology: Toward Understanding the Viral Diseases, Prevention, Therapy, and Other Applicat...
2.1 Introduction
2.2 The History of Identification of Viruses at a Molecular Level and Metagenomics
2.3 Advancements in Techniques to Study Virus–Host Interactions
2.3.1 Hybridization
2.3.1.1 Microarray Techniques
2.3.1.2 Subtractive Hybridization
2.3.2 Methods Based on PCR
2.3.2.1 Degenerate PCR
2.3.2.2 Random PCR
2.3.3 Metatranscriptomics Analysis
2.3.3.1 Metagenomics Joined With Metatranscriptomic Analyses
2.3.4 Viral Screening for Development of Therapeutics
2.3.5 Therapy
2.3.5.1 Omics Approach for Elucidating Host and Virus Interaction
2.4 Applications
2.4.1 Cell-Based Screenings
2.4.2 Gain-of-Function Method
2.4.3 Loss-of-Function Method
2.4.4 Comparative Genome Profiling
References
Further Reading
Chapter 03
3 Algal Biotechnology: An Update From Industrial and Medical Point of View
3.1 Microalgae—An Introduction
3.1.1 Biological Importance of Microalgae
3.1.1.1 Foods
3.1.1.2 Feed
3.1.1.3 Fatty Acids
3.1.1.4 Cosmetics
3.1.1.5 Biofertilizers
3.1.1.6 Anticancer Activity
3.1.1.7 Antiviral
3.1.1.8 Antibacterial
3.1.1.9 Antifungal
3.1.1.10 Biofuel
3.1.1.11 CO2 Sequestration
3.1.1.12 Wastewater Treatment
3.1.1.13 Bioremediation/Phycoremediation
3.2 Seaweeds (Macroalgae)—An Introduction
3.2.1 Seaweed Phycocolloids
3.2.2 Phycocolloids of Red Seaweeds
3.2.2.1 Agar and Its Structure
3.2.2.1.1 Carrageenan
3.2.2.2 Polysaccharides of Brown Seaweeds
3.2.2.2.1 Alginate
3.2.2.2.2 Laminarin
3.2.2.2.3 Fucoidan
3.2.2.3 Polysaccharides of Green Seaweeds
3.2.2.3.1 Ulvan
3.2.2.3.2 Food
3.2.2.4 Prebiotic Potential of Polysaccharides Present in Seaweeds
3.2.2.5 Mechanism of Action of Prebiotics
3.2.2.6 Nutraceuticals
3.2.2.7 Cosmetics and Cosmeceuticals
3.2.2.8 Pharmaceuticals
3.2.2.9 Seaweeds as Biological Control Against Animal and Plant Pathogens
3.2.2.10 Bioremediation
3.2.2.11 Pigment Extraction and Production
3.2.2.12 Seaweeds Tissue Culture
3.2.2.13 Drug Delivery
3.2.2.14 Bioenergy
3.2.2.15 Biofuel
3.2.2.16 Biomineralization
3.2.2.17 Bionanocrystallization
3.3 Conclusion
References
Further Reading
Chapter 04
4 Omics Approaches in Fungal Biotechnology: Industrial and Medical Point of View
4.1 Introduction
4.2 Insights Into Fungal Genomics
4.3 Insights Into Fungal Transcriptomics
4.4 Insights Into Fungal Proteomics
4.5 Insights Into Fungal Metabolomics
4.6 Bioinformatics
4.7 Sample Preparation Challenges
4.8 Fungal Omics—A Medical Perspective
4.8.1 Role of Fungi on Immunocompromised Patients
4.8.2 Fungi and the Gut Microflora
4.9 Fungal Omics—An Industrial Perspective
4.10 Conclusion
References
Further Reading
Chapter 05
5 Genetic Engineering for Plant Transgenesis: Focus to Pharmaceuticals
5.1 Introduction
5.2 Plants as Bioreactors
5.2.1 Recombinant Protein Production From Plants
5.2.1.1 Plants for Open-Field and Greenhouse Production of Pharmaceuticals
5.2.1.2 Plant-Based Expression Systems
5.2.1.3 Bioreactor-Based Plant Systems
5.2.1.4 Increasing Heterologous Protein Accumulation in Plants
5.2.1.5 Purification of Recombinant Proteins From Plants
5.3 Plant-Made Pharmaceuticals
5.3.1 Plantibodies
5.3.2 Edible Vaccines
5.3.3 PMPs: Commercial Status
5.4 Chloroplast Genome Engineering for Pharmaceuticals
5.5 Future Directions
References
Chapter 06
6 Agricultural Biotechnology: Engineering Plants for Improved Productivity and Quality
6.1 Introduction of Agricultural Biotechnology
6.1.1 Origin and Definition of Agricultural Biotechnology
6.1.2 Plant Breeding Program
6.1.2.1 Conventional Plant Breeding
6.1.2.2 Modern Plant Breeding
6.1.3 Application of Modern Agriculture
6.1.3.1 Yield Increase
6.1.3.2 Enhancement of Compositional Traits
6.1.3.3 Crop Adaptation
6.2 Genetic Engineering Strategies for Crop Improvement
6.2.1 Introduction of Plant Genetic Modification
6.2.2 Plant Transformation Techniques
6.2.2.1 Physicochemical Methods
6.2.2.2 Biological Methods
6.2.2.2.1 Agrobacterium-Mediated Plant Transformation
6.2.2.2.2 Virus-Mediated Plant Transformation
6.2.2.2.3 In Planta Transformation
6.3 Applications of Genetically Modified Crops
6.3.1 Resistance to Biotic Stress
6.3.1.1 Insect Resistance
6.3.1.1.1 Resistance Gene From Microorganisms
6.3.1.1.2 Resistance Genes From Higher Plants and Animals
6.3.1.2 Disease Resistance
6.3.1.3 Virus Resistance
6.3.2 Resistance to Abiotic Stresses
6.3.2.1 Herbicide Resistance
6.3.2.2 Tolerance to Water-Deficit Stresses
6.4 Genetic Manipulation for Crop Quality
6.4.1 Transgenic for Improved Fruit Storage
6.4.2 Golden Rice
6.4.3 Eco-Social Impact of Genetically Modified Crops
6.4.4 Current Status of GM Plants
6.4.5 Goals of Genetic Engineering in Crop Improvement
6.4.6 Concerns About Transgenic Plants
6.5 Genetic Assisted Plant Breeding
6.5.1 Introduction to Molecular Markers
6.5.1.1 Prerequisites and General Activities of MAB
6.5.2 Variety Identification and Seed Purity Analysis
6.5.2.1 Genetic Distance Analysis
6.5.3 MABC Breeding
6.5.3.1 Nearly Isogenic Strategies
6.5.4 Molecular Markers for Hybrid Vigor
6.6 Future Prospects
References
Chapter 07
7 Functional Food Biotechnology: The Use of Native and Genetically Engineered Lactic Acid Bacteria
7.1 Introduction
7.2 Definitions
7.3 Lactic Acid Bacteria
7.4 Nutraceutical Production by LAB
7.4.1 Vitamins
7.4.2 Bioactive Peptides
7.4.3 Exopolysaccharides
7.4.4 Antioxidant Enzymes
7.4.5 Other Beneficial Enzymes
7.5 Probiotic Effects of LAB
7.5.1 Probiotics in Intestinal Inflammation
7.5.1.1 Probiotics and Their Effects on Host’s Immunity and the Prevention of Infections
7.5.1.2 Probiotics for Obese Hosts
7.5.1.3 Probiotics and Reduction of Cardiovascular Risk
7.5.1.4 Probiotics in Cancer Prevention
7.5.1.5 Probiotics in Healthy Host
7.6 Concluding Remarks
References
Chapter 08
8 Omics and Edible Vaccines
8.1 Introduction: An Overview of Edible Vaccines
8.1.1 Production of Edible Vaccines Using Genomics
8.1.2 Production of Edible Vaccines Using Transcriptomics
8.1.3 Production of Edible Vaccines Using Proteomics
8.1.4 Production of Edible Vaccines Using Metabolomics
8.2 Edible Vaccines
8.2.1 Plasmid/Vector Mediated
8.2.2 Gene Gun or Biolistic Method
8.2.3 Electroporation/Electrotransfection
8.2.4 Lipofection
8.3 Mode of Action of Edible Vaccines
8.4 Conventional Vaccines Versus Edible Vaccines
8.5 Disadvantages of Edible Vaccines
8.6 Applications of Edible Vaccines
8.6.1 Autoimmune Diseases
8.6.2 Gastrointestinal Disorders
8.6.3 Malaria
8.6.4 Measles
8.6.5 Hepatitis B
8.7 Clinical Trials and Research Studies
8.8 Second-Generation Edible Vaccines
8.9 Current Developments
8.9.1 Banana, Tomato, and Potato
8.10 Patents on Edible Vaccines
8.11 Future Prospects
References
Further Reading
Chapter 09
9 Plant Metabolic Engineering
9.1 Introduction
9.1.1 Metabolites
9.1.1.1 Types of Metabolites
9.1.1.2 Importance of Secondary Metabolites
9.2 Metabolic Engineering—A Tool for Creating Desired Diversity
9.3 Approaches and Strategies
9.3.1 Systems for Metabolic Engineering
9.3.1.1 Plant Systems
9.3.1.2 In vitro Cultures
9.3.1.3 Microbial Cells
9.3.2 Management and Modulation of Metabolic Flux
9.3.2.1 Identification of Key Genes
9.3.2.2 Redirecting Flux by Overexpression and Silencing of Genes
9.3.2.3 Diverting Whole Pathway Flux by Regulation of Transcription Factors
9.3.2.4 Diverting Whole Pathway Flux by Using Cis-regulatory Elements
9.3.3 Systems Biology in Plant Metabolic Engineering
9.3.3.1 Strategies of Systems Biology
9.3.3.2 Integration of High-Throughput Omics Experiments
9.3.3.2.1 Genome Based Analysis
9.3.3.2.2 Transcriptome Based Analysis
9.3.3.2.3 Proteome Based Analysis
9.3.3.2.4 Metabolome Based Analysis
9.3.3.3 In silico Modeling and Simulation of Plant Metabolism
9.3.3.3.1 Kinetic Model-Based Analysis
9.3.3.3.2 Flux Model-Based Analysis
9.3.3.3.3 Genome-Scale Model-Based Analysis
9.3.3.4 Tools and Databases for In silico Modeling and Simulation
9.3.3.4.1 Integrated Metabolic Database System
9.3.3.4.2 Integrated Metabolic Networks
9.4 Applications of Metabolic Engineering
9.4.1 In Industry
9.4.2 In Food and Neutraceuticals
9.4.3 In Pharmacy and Medicine
9.4.4 In Agriculture
9.5 Current Status and Limitations
9.6 Future Aspects of Metabolic Engineering
9.7 Conclusions
References
Chapter 10
10 Biocontrol Technology: Eco-Friendly Approaches for Sustainable Agriculture
10.1 Biopesticides Versus Chemical Pesticide: Face to Face
10.2 Biocontrol: Therapy in Organic Farming
10.3 Mechanisms Employed by Biocontrol Agents for Plant Disease Management
10.3.1 Antibiosis
10.3.2 Mycoparasitism
10.3.3 Competition
10.3.4 Induced Resistance in Host Plants
10.4 Strain Improvement of Biocontrol Agents
10.4.1 Mutagenesis
10.4.2 Protoplast Fusion
10.4.3 Transformation
10.5 Omics in Biocontrol Technology
10.5.1 Genomics
10.5.2 Proteomics
10.5.3 Metabolomics
10.5.4 Secretomics
10.6 Conclusion and Future Prospects
10.7 Summary
References
Further Reading
Chapter 11
11 Bioengineering Towards Fighting Against Superbugs
11.1 Introduction
11.1.1 Global Perspective of Microbial Drug Resistance
11.1.2 Human Actions Contributing Towards MDR Development
11.2 Molecular Basis of Resistance
11.2.1 Acquired Resistance
11.2.1.1 Biochemical Inactivation of Drugs
11.3 Industrially Important Drug-Resistant Pathogens
11.3.1 MDR in Tuberculosis
11.3.1.1 Group 1
11.3.1.2 Group 2 (Streptomycin/Capreomycin)
11.3.1.3 Group 3 (FQ)
11.3.1.4 Group 4 (Ethionamide/Prothionamide, and Thiomides)
11.3.1.5 Group 5 (Linezolid and Clofazimine)
11.4 MDR in Pseudomonas aeruginosa
11.5 Drug Resistance in Candida albicans
11.6 MDR in Malaria
11.7 MDR in Herpes Simplex Virus (HSV)
11.8 Strategies to Control AMR
11.8.1 Infection Prevention and Control at Personal and Community Level
11.8.2 Policy, Cost, and Surveillance of MDR Pathogens: Political Commitment
11.8.3 Fostering Innovations
11.9 Biotechnological Interventions to Counter MDR
11.9.1 Nano-Silver: Antimicrobial Agents
11.9.2 Zinc Oxide Nanoparticles as Synergic Antimicrobials
11.10 The Antibacterial Mechanism of Nanoparticles
11.11 Conclusion and Future Perspectives
References
Chapter 12
12 Nanotechnology in Bioengineering: Transmogrifying Plant Biotechnology
12.1 Introduction
12.1.1 What is Plant/Crop Bioengineering?
12.2 Where Nanotechnology Can Help in PB?
12.2.1 Nanocides: NMs as Explant Sterilants in Plant Tissue Culture
12.2.2 Nanovehicles: NMs as Gene/Protein Delivery Vehicles
12.2.2.1 Plant Gene Transformation: What Are the Techniques?
12.2.2.2 Nano-enabled Plant Gene Transformation
12.2.2.3 Nano-enabled Vectorless or Direct Physical Methods
12.2.2.3.1 NM-enabled Transformation
12.2.2.3.2 Nanobiolistics or Nanoprojectile-based Gene Gun Technique
12.2.2.4 Other Nano-enabled Direct Techniques
12.2.2.5 Nano-enabled Chemical Techniques
12.2.2.6 Nano-enabled Vector-mediated or Indirect Gene Transformation Techniques
12.2.3 Nanosequencing: Nanopore-based Gene or Protein Sequencing Tools/Techniques
12.2.4 Nanobioimaging: NMs for High-Resolution Real-Time Imaging
12.2.5 Nanotheranostics: Nano-based Therapy and Diagnostic Products for Plant Pests and Pathogens
12.2.6 Nanobarcoding: Naming and Sorting the GM Crops
12.2.7 Nanogrowth Enhancers: NMs to Enhance Seed Germination and Plant Growth
12.2.8 Bioinspired/Nano-enabled Plants
12.3 Conclusions
References
Further Reading
Chapter 13
13 Techniques in Biotechnology: Essential for Industry
13.1 Brief History of Biotechnology
13.2 Fermentation
13.2.1 Fermentation Method
13.2.2 Inoculum (Microorganisms)
13.2.3 Substrate
13.2.4 Fermentors
13.2.5 Culture Conditions
13.2.6 Product
13.3 Biocatalysts/Enzymes
13.4 Industrial Production of Biocatalysts/Enzymes
13.4.1 Enzyme Definition
13.4.2 Enzyme Production Methods
13.4.3 Purification of Enzyme
13.4.4 Advances in Enzyme Industry
13.4.5 Application of Enzyme
13.5 Paper and Pulp Industry
13.6 Biofuels
13.7 Environmental Biotechnology
13.7.1 Application
13.8 Food Process Technology
13.8.1 Advances and Applications
13.9 Biorefinery
13.9.1 Applications
13.10 Bioreactors
13.11 Future Techniques
13.11.1 CRISPR/Cas9
13.11.2 Microbiome and Personalized Medicine
13.11.3 Sequencing
13.11.4 Mass Spectrometry
References
Further Reading
Chapter 14
14 Omics Approaches in Industrial Biotechnology and Bioprocess Engineering
14.1 Introduction
14.2 The Omics Revolution: Implications for Industrial Biotechnology
14.3 Omics Tools in Industrial Biotechnology and Bioprocess Engineering
14.3.1 Next-Generation Sequencing
14.3.2 Mutagenesis
14.3.3 Reverse Genetics
14.3.4 Cell Line Development
14.3.5 Synthetic Biology
14.3.6 Data Depository and Bioinformatics Tools
14.4 Combined Omics Approaches
14.5 Challenges in Omics-for-Industry
14.6 Conclusion and Future Perspectives
References
Chapter 15
15 Omics Approaches and Applications in Dairy and Food Processing Technology
15.1 Introduction
15.1.1 Historical Perspective
15.1.2 Biotechnological Developments in Dairy and Food Processing
15.1.2.1 Cheese
15.1.2.1.1 Microbial Rennet and Recombinant Chymosin
15.1.3 Bio Yogurt
15.2 Omics: From Farm to Fork
15.3 Proteomics: General Strategies and Analytical Methods
15.3.1 Protein Extraction
15.3.2 Protein Separation
15.3.2.1 Gel-Based Proteomic Approach
15.3.2.2 Gel-Free Proteomic Approach
15.3.3 Protein Identification
15.3.3.1 Mass Spectrometry
15.3.3.1.1 Ionization Techniques
15.3.3.2 Mass Analyzers
15.3.4 Comprehensive Data Analysis
15.4 Proteomics of Milk and Milk Products
15.4.1 Proteomics of Milk Proteins
15.5 Proteomics of Food Technology
15.5.1 Postharvest Processing
15.5.2 Cereal and Other Crops
15.6 Proteomics in Assessing
15.6.1 Quality of Foods
15.7 Transcriptomics in Food Safety
15.8 Future Prospects
15.8.1 Transcriptomics, Proteomics, and Metabolomics
15.8.2 Integrating Omics
15.9 Challenges and Opportunities in Food Omics
15.10 Conclusion
References
Chapter 16
16 Omics Approaches in Enzyme Discovery and Engineering
16.1 Introduction
16.2 Novel Enzymes Discovery for Industrial Applications
16.3 Molecular Engineering of Available Industrial Enzymes
16.4 Industrial Applications of Enzymes and Examples of Bioengineered Enzymes Currently in Common Use
16.4.1 Enzymes in the Food Industry
16.4.2 Enzymes in the Animal Feed Industry
16.4.3 Corn and Cellulose Processing
16.4.4 Enzymes in Surfactants and Detergents
16.4.5 Enzymes in Organic Bio-Synthesis
16.4.6 Other Promising Applications for Enzymes Within the Textile and Carbon Capture Industries
16.5 Conclusion and Future Perspectives
References
Chapter 17
17 Biomedical Engineering: The Recent Trends
17.1 Introduction
17.2 Areas of BME
17.2.1 Bioinstrumentation
17.2.2 Biomechanics
17.2.2.1 Sports Biomechanics
17.2.2.2 Continuum Mechanics
17.2.3 Biotribology
17.2.4 Computational Biomechanics
17.2.5 Biofluid Mechanics
17.2.6 Biomaterials
17.2.7 Tissue Engineering
17.2.8 Biorobotic
17.2.9 Biosensors
17.2.10 Neuroengineering
17.3 Future Directions
References
Further Reading
Chapter 18
18 Omics Approaches in Biofuel Technologies: Toward Cost Effective, Eco-Friendly, and Renewable Energy
18.1 Introduction
18.2 Brief Overview of the First-Generation Biofuel Technologies
18.3 Second-Generation Biofuel Technologies
18.4 Third-Generation Biofuel Technologies
18.4.1 Microalgae Cultivation
18.4.2 Microalgae Biomass Harvesting
18.4.3 Lipid Extraction and Biodiesel Production
18.5 Practical Challenges Ahead in Biofuel Technologies
18.6 Omics Advancement and Approaches for Cost-Effective Production of Renewable Energy
18.7 Conclusion and Future Perspectives
References
Further Reading
Chapter 19
19 Omics-Based Bioengineering in Environmental Biotechnology
19.1 Introduction
19.2 Application of Omics in Soil Microbial Ecology
19.2.1 Metagenomics and Soil Function
19.2.2 Metatranscriptomics and Soil Function
19.2.3 Extracting Value From Metatranscriptomics
19.2.4 Niche Specialization and Differentiation
19.3 Application of Omics in Controlling Pollution
19.4 Application of Omics-Based Bioengineering for Chemical Toxicity Screening
19.5 Omics Applications in Environmental Stress-Related Gene and Protein Modifications
19.6 Conclusion and Future Perspective
References
Further Reading
Chapter 20
20 Biochar for Carbon Sequestration: Bioengineering for Sustainable Environment
20.1 Introduction
20.1.1 What Is Environmental Sustainability?
20.1.2 Why There Are Increasing Concerns?
20.1.3 How to Address ES-Related Issues?
20.2 What Is Biochar?
20.2.1 What Are Its Types?
20.2.2 How Biochar Can be Produced?
20.2.3 Why Biochar Can be a Possible Solution for ES?
20.3 Biochar-Based Bioengineering Technologies
20.3.1 Biochar and Various Use Efficiency Strategies
20.3.1.1 Biochar as Nutrient Delivery Vehicle
20.3.1.2 Biochar Amendments Affecting Soil Nutrient Status and Enhancing Nutrient Use Efficiency
20.3.1.3 Biochar for Enhancing Water Use Efficiency
20.3.2 Biochar and Climate Change Abatement: Curbing Greenhouse Gas Emissions
20.3.3 Biochar-Based Bioengineering of Ecological Niches
20.3.3.1 Heavy Metal Removal
20.3.3.2 Organic Pollutant Removal
20.3.3.3 Sorption of Excess N or P From Wastewater
20.3.4 Biochar–Soil Microbial Community Interactions: Possible Implications
20.4 Agronomic Effects of Biochar Amendments in Vegetables
20.4.1 Biochar-Plant Growth Effects and Yield Impacts
20.5 Conclusion
References
Further Reading
Index
Index