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Applied Biotechnology and Bioinformatics

Agriculture, Pharmaceutical Research and Environment

Edited by Hrudayanath Thatoi, Sonali Mohapatra, Swagat Kumar Das and Sukanta Kumar Pradhan
Copyright: 2024   |   Expected Pub Date:2024/10/30
ISBN: 9781119896401  |  Hardcover  |  
460 pages

One Line Description
This comprehensive reference book discusses the convergent and next-generation technologies for product-derived applications relevant to agriculture, pharmaceuticals, nutraceuticals, and the environment.

Audience
The book will interest biotechnology researchers and bioinformatics professionals working in the areas of applied biotechnology, bioengineering, biomedical sciences, microbiology, agriculture and environmental sciences.

Description
The field of modern biotechnology is a multidisciplinary and groundbreaking area of biology that includes several cutting-edge methods due to developments in forensics and molecular modeling. Bioinformatics is a full-fledged multidisciplinary field that combines advances in computer and information technology. Numerous applications of bioinformatics—primarily in the areas of gene and protein identification, structural and functional prediction, drug development and design, folding of genes and proteins and their complexity, vaccine design, and organism identification—have contributed to the advancement of biotechnology. Biotechnology is also essential to crop improvement in agriculture because it allows genes to transfer across plants to increase traits such as disease resistance and yield. It also plays a broad role in healthcare, including genetic testing, gene therapy, pharmacogenomics, and drug development. Bioremediation and biodegradation, using microbial technologies to clean up environmental contamination, waste management technologies, and the conversion of organic waste to biofuels. Bioinformatics plays a critical role in analyzing different types of data created by high-throughput research methods—such as genomic, transcriptomic, and proteomic datasets—that are useful in addressing various problems related to disease management, clean environment, alternative energy sources, agricultural productivity, and more.

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Author / Editor Details
Hrudayanath Thatoi, PhD, is the Research Director at the Center for Industrial Biotechnology, Siksha ‘O’ Anusandhan (SOA) University, Odisha, India. He obtained his doctorate in botany from Utkal University, Odisha, India. His research interests include sustainable production of renewable energy, mushroom diversity and bioactivity, bioremediation, etc. He has published 25 books and more than 300 research papers in national and international journals. He is the recipient of the Samanta Chandrasekhar Award by DST, Govt. of Odisha.

Sonali Mohapatra, PhD, is a post-doc research associate in the Department of Biological Systems Engineering, University of Wisconsin, Madison, USA after obtaining her doctorate in biotechnology engineering. Her research focuses on bioprocessing technologies. Apart from her publications and edited books, she has also been part of successful scale-up projects in the synthesis of prebiotics from dairy waste streams.

Swagat Kumar Das, PhD, is an assistant professor in the Department of Biotechnology, Odisha University of Technology and Research, Bhubaneswar, Odisha, India. He obtained his doctorate from Ravenshaw University, Odisha, India. He is a fellow recipient of the Eurasian Academy of Environmental Sciences (FEAES) and the Society of Innovative Educationalists, Scientific Research Professionals (FSIESRP). He has published more than 30 publications in various national and international journals and 12 book chapters.

Sukanta Kumar Pradhan, PhD, serves as HOD in the Department of Bioinformatics, Odisha University of Agriculture and Technology, Odisha, India. He obtained his doctorate in biotechnology from Ravenshaw University, Odisha, India. His research interests include genomics, metagenomics, transcriptomics, and bioinformatics. He has published more than 60 research papers in reputed national and international journals and 8 book chapters.

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Table of Contents
Preface
Part I: Agriculture
1. Next-Generation Sequencing in Vegetable Crops
Meenu Kumari, Tanya Barpanda, Meghana Devireddy, Ankit Kumar Sinha, R. S. Pan and A. K. Singh
1.1 Introduction
1.2 Next-Generation Sequencing Approach in Genomics
1.2.1 Solanaceous
1.2.2 Malvaceae
1.2.3 Brassicaceae
1.2.4 Cucurbitaceae
1.2.5 Apiaceae
1.2.6 Moringaceae
1.3 NGS Approach in Single-Nucleotide Polymorphic Markers Development
1.4 Next-Generation Sequencing Approach in Trait-Specific Breeding
1.5 Next-Generation Sequencing Approach in Metagenomics
1.6 Next-Generation Sequencing Approach in Transcriptomics
1.7 Next-Generation Sequencing Approach in Exome and Captured Sequencing
1.8 Applications of Exome and Captured Sequencing in Crop Research
1.9 Conclusion and Future Prospects
References
2. Application of Bioinformatics Tools in Rice Genomics Research
Dhanawantari L. Singha, Debajit Das and Jitendra Maharana
2.1 Introduction
2.2 Role of Genomics in Rice Research
2.3 Model Plant for Genomic Research: Rice
2.4 High-Throughput Sequencing
2.5 Genome-Wide Association Study (GWAS)
2.6 Bioinformatics Approach to Study Stress Conditions in Rice
2.6.1 Rice Stress Responsive Transcription Factor Database (RiceSRTFDB)
2.6.2 RiceMetaSys
2.6.3 Rice Oligonucleotide Array Database (ROAD 2.0)
2.6.4 Plant Stress Protein Database (PSPDB)
2.6.5 Plant Stress Gene Database (PSGD)
2.6.6 Drought Stress Gene Database (Drought DB)
2.7 Application of Bioinformatics Tools in Advanced Rice Genomics Research
2.7.1 CRISPR/Cas-Based Study in Rice
2.7.2 The Application of Derivatives of CRISPR/Cas Tools in Rice
2.7.3 Base Editing and Prime Editing in Rice
2.7.4 Computational Tools for CRISPR/Cas Based Study in Rice
2.7.5 Advanced Machine Learning Approaches for CRISPR/Cas
2.7.6 Bioinformatics Approach for CRISPR/Cas Off Target Detection
2.7.7 Detection of Direct Off Target Mutation Detection Through NGS Analysis
2.8 Current Challenges of Bioinformatics Tools for Rice Genomics Research
2.8.1 Estimation of Heterosis
2.8.2 De Novo Domestication of Rice
2.8.3 Using Genome Editing to Revolutionize Rice Breeding
2.8.4 Uncovering the Wide Range of Diversity in Rice Varieties
2.9 Conclusion
Conflict of Interest
References
3. Computer-Aided Vaccine Design: Applications in Agriculture
Tanmaya Kumar Sahu and Atmakuri Ramakrishna Rao
3.1 Introduction
3.2 Agriculturally Important Animals
3.3 Diseases Affecting Animal Health in Agriculture
3.4 Vaccination in Agriculture
3.5 Vaccine
3.5.1 Types of Vaccines
3.5.2 Steps of Vaccine Designing
3.5.2.1 Identification of the Pathogen
3.5.2.2 Identification of Key Antigens
3.5.2.3 Vaccine Platform Selection
3.5.2.4 Vaccine Formulation
3.5.2.5 Preclinical and Clinical Testing
3.5.2.6 Regulatory Approval
3.5.2.7 Manufacturing and Distribution
3.6 Intervention of Computer in Vaccine Designing
3.6.1 Computer-Aided Vaccine Design
3.6.2 Artificial Intelligence for Vaccine Design
3.6.3 Epitope Prediction in Vaccine Designing
3.6.3.1 Epitopes: The Antigenic Determinants
3.6.3.2 Sequence-Based Epitope Prediction
3.6.3.3 Structure-Based Epitope Prediction Methods
3.7 In Silico Vaccine Designing: Agricultural Applications
3.8 Conclusion and Future Prospects
References
4. Genomics to Phenomics: A Paradigm Shift in Crop Science Research
Biswajit Lenka, Manasi Dash and Lakesh Muduli
4.1 Introduction
4.2 Genomics in Crop Improvement
4.3 Advances in Genomics-Assisted Breeding
4.4 Phenotyping
4.5 Phenomics
4.6 Phenomics Approaches in Crop Improvement
4.7 Conclusion
References
Part II: Pharmaceutical Research
5. Molecular Modeling and Drug Development
Howida A. Elseedy, Caroline Kiriacos and Triveena M. Ramsis
5.1 Introduction
5.2 Structure-Based Drug Design
5.3 Docking
5.4 Ligand-Based Drug Design
5.5 Pharmacophore
5.6 QSAR
5.6.1 Advantages of the QSAR Method
5.6.2 Limitations of the QSAR Method
5.6.3 Examples of Applications of QSAR in Drug Discovery
5.7 Virtual Screening
5.7.1 Structure-Based Virtual Screening
5.7.2 Ligand-Based Virtual Screening
5.8 Pharmacophore-Based VS
5.9 Similarity-Based VS
5.10 Homology Modeling and Protein Folding
5.10.1 Template Selection
5.10.2 Alignment Correction
5.10.3 Backbone Model Building
5.10.3.1 Loop Modeling
5.10.3.2 Adding Amino Acid Side Chains
5.10.3.3 Model Optimization
5.10.3.4 Model Evaluation and Validation
5.11 In Silico Pharmacokinetics
5.11.1 Absorption
5.11.2 Bioavailability
5.11.3 Metabolism
5.11.4 Toxicity
5.12 Conclusion
References
6. Comparative Study on Tannase Sequence and Structure of Lactiplantibacillus: An In Silico Protein Variability Analysis and Its Impact on Microbial Speciation
Ishita Biswas, Debanjan Mitra and Pradeep K. Das Mohapatra
6.1 Introduction
6.2 Materials and Methods
6.2.1 Dataset
6.2.2 Analysis of Protein Sequences
6.2.3 Homology Modeling
6.2.4 Analysis of Crystal Structure
6.2.5 Molecular Dynamics Simulations
6.3 Results and Discussion
6.3.1 Physicochemical Properties of Tannase
6.3.2 Validation of Modeled Protein Structures
6.3.3 Secondary Structure Assessment
6.3.4 Intra-Protein Interactions
6.3.5 Stability in Simulation Studies
6.3.6 Hydrogen Bonds
6.4 Conclusion
References
7. Probiotics: A Novel Natural Therapy for Oral Health
Preeti Pallavi, Vikas Kumar, Sangeeta Prakash and Sangeeta Raut
7.1 Introduction
7.2 Background
7.2.1 Methods for Treatment of Oral Diseases
7.2.2 Probiotics in Prevention of Caries
7.2.3 Probiotics Against Periodontal Disease
7.2.4 Probiotics Against Halitosis
7.3 Mechanism in Oral Diseases Prevention by Probiotics
7.3.1 Caries Prevention by Probiotics
7.3.2 Periodontics Prevention by Probiotics
7.3.3 Halitosis Prevention by Probiotics
7.4 Probiotic Formulation
7.5 Prevention and Oral Health Management
7.6 Concluding Remarks
7.7 Future Aspects
References
8. The Preventative and Curative Functions of Probiotics: A Paradigm of Food as Drug Revolution
Mohammad Zaki Shamim, Jibanjyoti Panda, Gargee Mohanty, Bhaswati Gogoi, Kaustuvmani Patowary, Bishwambhar Mishra and Yugal Kishore Mohanta
8.1 Introduction
8.2 Criteria for Choosing Probiotics and the Bare Minimum Needed
8.3 Action Mechanism of Probiotics
8.4 Probiotics in the Clinical Practice: A Growing Trend
8.5 Potential Preventative Roles of Probiotics
8.5.1 Inhibiting Carcinogenesis with Probiotics as a Preventative Measure
8.5.2 Enteral Nutrition and Probiotics in the Treatment of Acute Pancreatitis
8.5.3 Infection with Clostridium difficile in Individuals with Colitis
8.5.4 Probiotics Prevent Postoperative Infections
8.5.5 Newborns with Extremely Low Birth Weights, Late-Onset Sepsis, and Necrotizing Enterocolitis
8.5.6 Probiotics in Ventilator-Associated Pneumonia (VAP)
8.6 Therapeutic Use of Probiotics
8.6.1 Role of Probiotics in Hypertension Treatment
8.6.2 Role of Probiotics Against Intervention for Inflammatory and Autoimmune Diseases
8.6.3 Curative Role of Probiotics Against Helicobacter pylori
8.6.4 Role of Probiotics Against Inflammatory Bowel Disease
8.6.5 Role of Probiotics in the Treatment of Oral Candidiasis Colonization (OCC) in Denture Wearers
8.6.6 Role of Probiotics in the Treatment of Migraines
8.6.7 Role of Probiotics for the Treatment Diabetes
8.6.8 Role of Probiotic in the Treatment of Autism Spectrum Condition
8.7 Recent Advancement in Probiotics
8.7.1 Recent Progress in Treatment of Acute Pancreatitis
8.7.2 Autophagy: A Novel Mechanism for the Anti‑Inflammatory Effects of Probiotics
8.7.3 Synthetic Engineering of Probiotics for Therapeutic and Preventative Purposes
8.7.4 Probiotics in Anti-Oxidation Process
8.7.5 Preventing Protozoal Infections and Harmful Element Levels in Hair
8.8 Conclusion and Recommendation
Acknowledgments
References
9. Probiotics in the Prevention and Treatment of Psoriasis
Prativa Biswasroy, Deepak Pradhan, Dilip Kumar Pradhan, Goutam Rath and Goutam Ghosh
9.1 Introduction
9.2 Interruption of the Microbiome: A Pathogenic Effect in Psoriasis
9.2.1 Skin Dysbiosis in a Psoriasis Patient
9.2.2 Gut Dysbiosis in a Psoriasis Patient
9.3 Therapeutic Effect of Probiotics for Psoriasis
9.4 Conclusion
References
10. A Gateway to Multi-Omics‑Based Clinical Research
Ashutosh Sahoo, Deepanshu Verma and Prajnadipta Panda
10.1 Introduction
10.2 Importance of Multi-Omics
10.3 Genomics and Relevant Clinical Studies Along with Its Tools and Methods
10.3.1 Structural Genomics
10.3.2 Functional Genomics
10.3.3 Comparative Genomics
10.3.4 Mutational Genomics
10.4 Proteomics and Relevant Clinical Studies Along with Its Tools and Methods
10.5 Sample Type and Acquisition
10.6 Various Data Acquisition Methods for Proteomics Data Include the Following
10.7 Techniques Used in Clinical Proteomics
10.8 Analysis Tools in Clinical Proteomics
10.9 Metabolomics and Relevant Clinical Studies Along with Its Tools and Methods
10.10 Different Types of Metabolomics
10.11 Techniques and Tools Used in Metabolomics
10.12 Metabolite Databases
10.13 Data Analysis Tools and Software
10.14 Application of Metabolomics in Clinical Studies
10.15 Conclusion
References
11. Inherent Observation of Mucosal Non-Specific Immune Parameters in Indian Major Carps
Supriya Dash and Swagat Kumar Das
11.1 Introduction
11.2 Materials and Methods
11.2.1 Collection and Preparation of Mucus Extracts
11.2.2 Protein Precipitation
11.2.3 Partial Protein Purification by Dialysis
11.2.4 Protein Estimation
11.2.5 Enzyme Activity
11.2.6 Mucus Protein Profiling by SDS-PAGE
11.3 Results and Discussion
11.3.1 Protein Estimation
11.3.2 Enzyme Activities
11.3.2.1 Lysozyme Activity
11.3.2.2 Alkaline Phosphatase Activity
11.3.2.3 Protease Activity
11.3.3 SDS-PAGE
11.4 Conclusion
References
Part III: Environment
12. Eco-Friendly Approaches for Converting Organic Waste to Bioenergy for Sustainable Development
Krishna Kumar Jaiswal, Chandrama Roy Chowdhury, Deepti Yadav, Swapnamoy Dutta, Ishita Banerjee, Km Smriti Jaiswal, Arun Prasath Ramaswamy, Mrinal, Sangmesh B., Amit K. Jaiswal, Vinod Kumar and Krishnan Kanny
12.1 Introduction
12.2 Organic Waste in the Bioenergy Generation
12.3 Categories and Characteristics of Organic Waste
12.4 Organic Waste Based on Origin
12.4.1 Plant-Based (Vegetal) Origin
12.4.2 Animal-Based Origin
12.5 Organic Waste Based on the State of Matter
12.5.1 Solid Wastes
12.5.2 Liquid Wastes
12.5.3 Gaseous Waste
12.6 Organic Waste Based on the Level of Production
12.6.1 Agricultural Level
12.6.2 Household Level
12.6.3 Commercial Level
12.6.4 Industrial Level
12.7 Characteristics of Organic Waste
12.7.1 Biodegradability
12.8 Greenhouse Gases (GHGs)
12.9 Benefits of Organic Waste
12.10 Current and Prospective Use of Organic Waste
12.11 Sustainable Bioenergy and Biofuels from Organic Waste
12.12 Conversion of Organic Waste into Bioenergy and High-Valued Products
12.13 Biofuels from Organic Waste: Biochemical and Thermochemical Processes
12.14 Fermentation
12.15 Anaerobic Digestion
12.16 Combustion
12.17 Pyrolysis
12.18 Gasification
12.19 Biorefinery Concept Based on Organic Waste for Clean Energy Management
12.20 Success and Challenges of Organic Waste for Bioenergy
12.21 Conclusion and Recommendations
References
13. Utilization of Food Waste for Bioenergy Production
Srutee Rout, Rakesh Kumar Gupta, Sangeetha Karunanithi, Gnana Moorthy Eswaran U., Proshanta Guha and Prem Prakash Srivastav
13.1 Introduction
13.2 Potential of Food Waste for Bioenergy Production
13.3 Bioenergy from Food Waste
13.3.1 Bioelectricity
13.3.2 Biofuel
13.3.3 Biogas
13.3.4 Biohydrogen from Food Waste
13.3.5 Biohythane from Food Waste
13.3.6 Bio-Butanol
13.4 Conclusion
References
14. Photosynthetic Microalgal Microbial Fuel Cell (PMMFC): A Novel Strategy for Wastewater Treatment and Bioenergy Generation
Jagdeep Kumar Nayak, Rahul Gautam, Kundan Samal and Uttam Kumar Ghosh
14.1 Introduction
14.2 Microbial Fuel Cell
14.2.1 Photosynthetic Microalgal Microbial Fuel Cell (PMMFC)
14.3 Types of PMFC
14.3.1 Single-Chambered PMFC
14.3.2 Dual-Chambered PMFC
14.3.3 Tubular PMFC
14.4 Role of Algae in PMFC
14.4.1 Algae at Anode
14.4.2 Algae at Cathode
14.4.3 Advantages
14.4.4 Disadvantages
14.4.5 Challenges
14.5 Conclusion
References
15. Self-Cleaning Aquarium: The Microbial Biofilm Approach for Ammonia Bioremediation
Shaon Ray Chaudhuri, Tethi Biswas and Indranil Mukherjee
15.1 Current Scenario of Fresh Water Scarcity and Impact of Aquaculture
15.2 Existing Technologies for Aquaculture Effluent Treatment for Environmental Sustenance
15.3 The Novel Rapid Biofilm Reactor-Based Ammonia Removing System
15.4 The Case Study of the Self-Cleaning Aquarium
15.5 Conclusion and Future Application
Acknowledgments
References
16. Metagenomics Unveiled: Deciphering Microbial Responses to Climate Change
Megha Kaviraj, Manojit Singh, Soumendranath Chatterjee and Upendra Kumar
16.1 Introduction
16.2 Climate Change and Its Impact on the Environment and Microbiome
16.3 Metagenomics as a Tool for Climate Change Research
16.4 Microbial Adaptation to Climate Change
16.5 Feedback Loops and Climate Change
16.6 Metagenomics in Climate Change Mitigation
16.7 Case Studies and Research Findings
16.7.1 Arctic Soil Microbial Communities
16.7.2 Amazon Rainforest Microbial Biodiversity
16.7.3 Methane-Emitting Wetlands
16.7.4 Coral Microbiomes and Climate Resilience
16.7.5 Permafrost Microbial Responses
16.7.6 Industrial Waste Contaminated Microbe Response
16.8 Metagenomic Climate Model Frame
16.9 Challenges and Future Directions
16.10 Conclusion
Acknowledgments
Author Contributions
Conflict of Interest
References
17. Biosensor: A Tool for Assessment of Soil Pollutants
Saheed Garnaik and Jagamohan Nayak
17.1 Introduction
17.2 Working Principles
17.3 Types of Biosensors
17.3.1 Nanomaterial-Based Biosensors
17.3.2 Microbial Biosensors
17.3.3 Enzymatic Biosensors
17.3.4 Immunoassay-Based Biosensors
17.3.5 DNA-Based Biosensors
17.3.6 Optical Biosensors
17.3.7 Piezoelectric Biosensors
17.4 Application of Biosensors
17.4.1 Heavy Metal Detection
17.4.2 Organic Pollutant Monitoring
17.4.3 Emerging Pollutants
17.5 Advantages, Disadvantages, and Adoption of Biosensors
17.5.1 Advantages and Disadvantages of Biosensors
17.5.2 Strategies Explored to Overcome These Limitations and Improve the Overall Performance of Biosensors
17.5.3 Integration and Adoption
17.6 Ethical Considerations and Future Challenges
17.7 Conclusion
References
18. Transcriptome-Guided Characterization of Molecular Resources in Mussels
Snigdha Baliarsingh, Mariadoss Selvanayagam, Hrudayanath Thatoi, Shailesh Saurabh, Yong Seok Lee and Bharat Bhusan Patnaik
18.1 Introduction
18.2 Species of Mussels Sequenced at the Transcriptome Level
18.3 Transcriptome Pipeline for Mussel Molecular Resources
18.4 Mussel Transcriptome Assembly and Annotation
18.5 Conclusions and Future Perspectives
Acknowledgments
References
Index

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