Applied Biotechnology and Bioinformatics

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.

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