Applied Biotechnology and Bioinformatics: Agriculture, Pharmaceutical Research and Environment

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

Table of Contents:
Preface xvii Part I: Agriculture 1 1 Next-Generation Sequencing in Vegetable Crops 3 Meenu Kumari, Tanya Barpanda, Meghana Devireddy, Ankit Kumar Sinha, R. S. Pan and A. K. Singh 1.1 Introduction 4 1.2 Next-Generation Sequencing Approach in Genomics 5 1.3 NGS Approach in Single-Nucleotide Polymorphic Markers Development 13 1.4 Next-Generation Sequencing Approach in Trait-Specific Breeding 15 1.5 Next-Generation Sequencing Approach in Metagenomics 18 1.6 Next-Generation Sequencing Approach in Transcriptomics 19 1.7 Next-Generation Sequencing Approach in Exome and Captured Sequencing 22 1.8 Applications of Exome and Captured Sequencing in Crop Research 23 1.9 Conclusion and Future Prospects 24 References 25 2 Application of Bioinformatics Tools in Rice Genomics Research 37 Dhanawantari L. Singha, Debajit Das and Jitendra Maharana 2.1 Introduction 38 2.2 Role of Genomics in Rice Research 38 2.3 Model Plant for Genomic Research: Rice 39 2.4 High-Throughput Sequencing 41 2.5 Genome-Wide Association Study (GWAS) 45 2.6 Bioinformatics Approach to Study Stress Conditions in Rice 46 2.7 Application of Bioinformatics Tools in Advanced Rice Genomics Research 51 2.8 Current Challenges of Bioinformatics Tools for Rice Genomics Research 57 2.9 Conclusion 60 Conflict of Interest 60 References 61 3 Computer-Aided Vaccine Design: Applications in Agriculture 73 Tanmaya Kumar Sahu and Atmakuri Ramakrishna Rao 3.1 Introduction 74 3.2 Agriculturally Important Animals 75 3.3 Diseases Affecting Animal Health in Agriculture 75 3.4 Vaccination in Agriculture 77 3.5 Vaccine 77 3.6 Intervention of Computer in Vaccine Designing 81 3.7 In Silico Vaccine Designing: Agricultural Applications 90 3.8 Conclusion and Future Prospects 91 References 92 4 Genomics to Phenomics: A Paradigm Shift in Crop Science Research 97 Biswajit Lenka, Manasi Dash and Lakesh Muduli 4.1 Introduction 98 4.2 Genomics in Crop Improvement 98 4.3 Advances in Genomics-Assisted Breeding 98 4.4 Phenotyping 103 4.5 Phenomics 103 4.6 Phenomics Approaches in Crop Improvement 104 4.7 Conclusion 105 References 105 Part II: Pharmaceutical Research 109 5 Molecular Modeling and Drug Development 111 Howida A. Elseedy, Caroline Kiriacos and Triveena M. Ramsis 5.1 Introduction 111 5.2 Structure-Based Drug Design 112 5.3 Docking 115 5.4 Ligand-Based Drug Design 117 5.5 Pharmacophore 118 5.6 QSAR 119 5.7 Virtual Screening 122 5.8 Pharmacophore-Based VS 124 5.9 Similarity-Based VS 125 5.10 Homology Modeling and Protein Folding 125 5.11 In Silico Pharmacokinetics 128 5.12 Conclusion 131 References 132 6 Comparative Study on Tannase Sequence and Structure of Lactiplantibacillus: An In Silico Protein Variability Analysis and Its Impact on Microbial Speciation 139 Ishita Biswas, Debanjan Mitra and Pradeep K. Das Mohapatra 6.1 Introduction 140 6.2 Materials and Methods 141 6.3 Results and Discussion 143 6.4 Conclusion 153 References 153 7 Probiotics: A Novel Natural Therapy for Oral Health 157 Preeti Pallavi, Vikas Kumar, Sangeeta Prakash and Sangeeta Raut 7.1 Introduction 158 7.2 Background 160 7.3 Mechanism in Oral Diseases Prevention by Probiotics 166 7.4 Probiotic Formulation 169 7.5 Prevention and Oral Health Management 172 7.6 Concluding Remarks 173 7.7 Future Aspects 174 References 176 8 The Preventative and Curative Functions of Probiotics: A Paradigm of Food as Drug Revolution 181 Mohammad Zaki Shamim, Jibanjyoti Panda, Gargee Mohanty, Bhaswati Gogoi, Kaustuvmani Patowary, Bishwambhar Mishra and Yugal Kishore Mohanta 8.1 Introduction 182 8.2 Criteria for Choosing Probiotics and the Bare Minimum Needed 183 8.3 Action Mechanism of Probiotics 184 8.4 Probiotics in the Clinical Practice: A Growing Trend 185 8.5 Potential Preventative Roles of Probiotics 186 8.6 Therapeutic Use of Probiotics 195 8.7 Recent Advancement in Probiotics 202 8.8 Conclusion and Recommendation 208 Acknowledgments 208 References 209 9 Probiotics in the Prevention and Treatment of Psoriasis 217 Prativa Biswasroy, Deepak Pradhan, Dilip Kumar Pradhan, Goutam Rath and Goutam Ghosh 9.1 Introduction 218 9.2 Interruption of the Microbiome: A Pathogenic Effect in Psoriasis 219 9.3 Therapeutic Effect of Probiotics for Psoriasis 223 9.4 Conclusion 229 References 230 10 A Gateway to Multi-Omics‐Based Clinical Research 235 Ashutosh Sahoo, Deepanshu Verma and Prajnadipta Panda 10.1 Introduction 236 10.2 Importance of Multi-Omics 237 10.3 Genomics and Relevant Clinical Studies Along with Its Tools and Methods 239 10.4 Proteomics and Relevant Clinical Studies Along with Its Tools and Methods 242 10.5 Sample Type and Acquisition 242 10.6 Various Data Acquisition Methods for Proteomics Data Include the Following 242 10.7 Techniques Used in Clinical Proteomics 244 10.8 Analysis Tools in Clinical Proteomics 244 10.9 Metabolomics and Relevant Clinical Studies Along with Its Tools and Methods 245 10.10 Different Types of Metabolomics 245 10.11 Techniques and Tools Used in Metabolomics 246 10.12 Metabolite Databases 248 10.13 Data Analysis Tools and Software 249 10.14 Application of Metabolomics in Clinical Studies 249 10.15 Conclusion 250 References 251 11 Inherent Observation of Mucosal Non-Specific Immune Parameters in Indian Major Carps 257 Supriya Dash and Swagat Kumar Das 11.1 Introduction 258 11.2 Materials and Methods 258 11.3 Results and Discussion 259 11.4 Conclusion 266 References 266 Part III: Environment 269 12 Eco-Friendly Approaches for Converting Organic Waste to Bioenergy for Sustainable Development 271 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 272 12.2 Organic Waste in the Bioenergy Generation 274 12.3 Categories and Characteristics of Organic Waste 275 12.4 Organic Waste Based on Origin 276 12.5 Organic Waste Based on the State of Matter 277 12.6 Organic Waste Based on the Level of Production 278 12.7 Characteristics of Organic Waste 278 12.8 Greenhouse Gases (GHGs) 279 12.9 Benefits of Organic Waste 280 12.10 Current and Prospective Use of Organic Waste 281 12.11 Sustainable Bioenergy and Biofuels from Organic Waste 282 12.12 Conversion of Organic Waste into Bioenergy and High-Valued Products 286 12.13 Biofuels from Organic Waste: Biochemical and Thermochemical Processes 286 12.14 Fermentation 286 12.15 Anaerobic Digestion 289 12.16 Combustion 290 12.17 Pyrolysis 290 12.18 Gasification 291 12.19 Biorefinery Concept Based on Organic Waste for Clean Energy Management 292 12.20 Success and Challenges of Organic Waste for Bioenergy 293 12.21 Conclusion and Recommendations 294 References 295 13 Utilization of Food Waste for Bioenergy Production 303 Srutee Rout, Rakesh Kumar Gupta, Sangeetha Karunanithi, Gnana Moorthy Eswaran U., Proshanta Guha and Prem Prakash Srivastav 13.1 Introduction 304 13.2 Potential of Food Waste for Bioenergy Production 306 13.3 Bioenergy from Food Waste 308 13.4 Conclusion 323 References 324 14 Photosynthetic Microalgal Microbial Fuel Cell (PMMFC): A Novel Strategy for Wastewater Treatment and Bioenergy Generation 331 Jagdeep Kumar Nayak, Rahul Gautam, Kundan Samal and Uttam Kumar Ghosh 14.1 Introduction 332 14.2 Microbial Fuel Cell 333 14.3 Types of PMFC 336 14.4 Role of Algae in PMFC 338 14.5 Conclusion 341 References 342 15 Self-Cleaning Aquarium: The Microbial Biofilm Approach for Ammonia Bioremediation 347 Shaon Ray Chaudhuri, Tethi Biswas and Indranil Mukherjee 15.1 Current Scenario of Fresh Water Scarcity and Impact of Aquaculture 348 15.2 Existing Technologies for Aquaculture Effluent Treatment for Environmental Sustenance 349 15.3 The Novel Rapid Biofilm Reactor-Based Ammonia Removing System 352 15.4 The Case Study of the Self-Cleaning Aquarium 358 15.5 Conclusion and Future Application 362 Acknowledgments 363 References 364 16 Metagenomics Unveiled: Deciphering Microbial Responses to Climate Change 369 Megha Kaviraj, Manojit Singh, Soumendranath Chatterjee and Upendra Kumar 16.1 Introduction 370 16.2 Climate Change and Its Impact on the Environment and Microbiome 372 16.3 Metagenomics as a Tool for Climate Change Research 374 16.4 Microbial Adaptation to Climate Change 376 16.5 Feedback Loops and Climate Change 377 16.6 Metagenomics in Climate Change Mitigation 379 16.7 Case Studies and Research Findings 380 16.8 Metagenomic Climate Model Frame 384 16.9 Challenges and Future Directions 386 16.10 Conclusion 387 Acknowledgments 387 Author Contributions 387 Conflict of Interest 388 References 388 17 Biosensor: A Tool for Assessment of Soil Pollutants 395 Saheed Garnaik and Jagamohan Nayak 17.1 Introduction 396 17.2 Working Principles 397 17.3 Types of Biosensors 398 17.4 Application of Biosensors 400 17.5 Advantages, Disadvantages, and Adoption of Biosensors 402 17.6 Ethical Considerations and Future Challenges 403 17.7 Conclusion 404 References 405 18 Transcriptome-Guided Characterization of Molecular Resources in Mussels 407 Snigdha Baliarsingh, Mariadoss Selvanayagam, Hrudayanath Thatoi, Shailesh Saurabh, Yong Seok Lee and Bharat Bhusan Patnaik 18.1 Introduction 408 18.2 Species of Mussels Sequenced at the Transcriptome Level 414 18.3 Transcriptome Pipeline for Mussel Molecular Resources 417 18.4 Mussel Transcriptome Assembly and Annotation 425 18.5 Conclusions and Future Perspectives 430 Acknowledgments 430 References 430 Index 437