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