Genomics, Proteomics and Metabolomics in Nutraceuticals and Functional Foods

Debasis Bagchi, Ph.D., MACN, CNS, MAIChEUniversity of Houston College of Pharmacy, Houston, TX, USAAnand Swaroop, Ph.D.Cepham Inc., Piscataway, NJ, USAManashi Bagchi, Ph.D., FACNCepham Inc., Piscataway, NJ, USA

• Contributors xxivPreface xxxiPart I Introduction 11 Novel Omics Technologies in Food Nutrition 3Xuewu Zhang, Lijun You, Wei Wang, and Kaijun Xiao1.1 Introduction 31.2 Transcriptomics in Nutritional Research 41.3 Proteomics in Nutritional Research 51.4 Metabolomics in Nutritional Research 71.5 Systems Biology in Nutritional Research 91.6 Conclusions 92 Seafood Authentication using Foodomics: Proteomics, Metabolomics, and Genomics 14Karola Böhme, Jorge Barros-Velázquez, Pilar Calo-Mata, José M. Gallardo, and Ignacio Ortea2.1 Introduction 142.2 Proteomic Approaches 152.3 Metabolomic Approaches 192.4 Genomic Approaches 202.5 Conclusions 253 A Foodomics Approach Reveals Hypocholesterolemic Activity of Red Microalgae 31Irit Dvir, Aliza H. Stark, and Shoshana (Malis) Arad3.1 Introduction 313.2 Marine Functional Foods and Supplements 323.3 Microalgae 333.4 Summary 37Part II Genomics 414 Gene]Diet Interaction and Weight Management 43Lu Qi4.1 Introduction 434.2 Diet and Lifestyle Modifications in Weight Management 444.3 The Role of Genetic Factors in Determining Body Weight and Weight Loss 444.4 Gene-Diet Interactions on Body Weight and Risk of Obesity 464.5 Gene-Diet Interactions on Weight Loss in Randomized Clinical Trials 474.6 Gene]Diet Interactions on Weight Maintenance 484.7 Personalized Weight Management through Diet and Lifestyle Modifications 494.8 Summary and Concluding Remarks 505 NutrimiRomics: The Promise of a New Discipline in Nutrigenomics 53Amitava Das and Chandan K. Sen5.1 Introduction 535.2 miRomics: A New Cornerstone 565.3 Nutrigenomics and miR 576 Genomics as a Tool to Characterize Anti]inflammatory Nutraceuticals 61Amitava Das, Scott Chaffee, and Sashwati Roy6.1 Chronic Inflammation in Disease 616.2 Nutraceuticals in the Management of Chronic Inflammation 646.3 GeneChipTM as a Tool to Characterize the Anti]Inflammatory Properties of Nutraceuticals 657 Nutrigenomics, Inflammaging, and Osteoarthritis: A Review 71Ali Mobasheri, Richard Barrett-Jolley, Caroline A. Staunton, Chris Ford, and Yves Henrotin7.1 Introduction 717.2 Osteoarthritis (OA) 727.3 Antioxidants and the Inflammatory Microenvironment 737.4 Inflammaging 757.5 Nutrigenomics 767.6 Muscle Inflammation in OA 777.7 Conclusions 808 Genetic Basis of Anti-Inflammatory Properties of Boswellia Extracts 85Golakoti Trimurtulu, Chandan K. Sen, Alluri V. Krishnaraju, Kiran Bhupathiraju, and Krishanu Sengupta8.1 Introduction 858.2 Boswellia serrata 868.3 Mechanism of Action 878.4 Development of 5-LOXIN (BE-30) 878.5 Gene Chip Probe Array Analysis 888.6 Proteomics 898.7 Molecular Basis of Anti-Inflammatory Properties of 5-LOXIN 958.8 In vivo Studies 968.9 Safety of 5-LOXIN 968.10 Clinical Efficacy of 5-LOXIN in the Management of Osteoarthritis 978.11 An Advanced 5-LOXIN: Aflapin 998.12 Conclusion 1009 Cancer Chemopreventive Phytochemicals Targeting NF-κB and Nrf2 Signaling Pathways 102Hye-Kyung Na and Young-Joon Surh9.1 Introduction 1029.2 Molecular-Based Cancer Chemoprevention 1049.3 Nuclear Factor-Kappa B (NF-κB) 1059.4 Nrf2 1089.5 Interplay/Crosstalk between Nrf2 and NF]κB Signaling Pathways 1149.6 Conclusion 11510 The Beneficial Health Effects of Fucoxanthin 122Kazuo Miyashita and Masashi Hosokawa10.1 Introduction 12210.2 The Beneficial Health Effects of Carotenoids as Antioxidants 12410.3 Anticancer Activity of Fucoxanthin 12410.4 Anti-Obesity Effects of Fucoxanthin 12610.5 Anti-Diabetic Effects of Fucoxanthin 12710.6 Conclusion 13011 Nutrition, Genomics, and Human Health: A Complex Mechanism for Wellness 135Okezie I. Aruoma11.1 Introduction 13511.2 Nutrition Sciences and Clinical Applications in Nutritional Genomics 13612 Application of Genomics and Bioinformatics Analysis in Exploratory Study of Functional Foods 140Kohsuke Hayamizu and Aiko Manji12.1 Introduction 14012.2 Analysis Tools 14112.3 Interpretation Tools 14212.4 Application Example of Kale (Brassica oleracea L. Var Acephala DC) 14312.5 Conclusion 14813 Omics Analysis and Databases for Plant Science 150Masaaki Kobayashi, Hajime Ohyanagi, and Kentaro Yano13.1 Introduction 15013.2 NGS Technologies and Data Processing 15113.3 De novo Plant Genome Assembly by NGS 15113.4 Plant Genome Resequencing by NGS 15313.5 Plant Transcriptome Analysis by NGS 15413.6 Plant Genome and Annotation Databases 15413.7 Plant Omics Databases 15513.8 Conclusion 15614 Synergistic Plant Genomics and Molecular Breeding Approaches for Ensuring Food Security 160Shouvik Das and Swarup K. Parida14.1 Introduction 16014.2 Plant Genomics, Transcriptomics, Proteomics, and Metabolomics Resources 16114.3 Molecular Markers in Plant Genome Analysis 16314.4 Identification of Functionally Relevant Molecular Tags Governing Agronomic Traits 16714.5 Genomics]Assisted Crop Improvement 17015 Combinatorial Approaches Utilizing Nutraceuticals in Cancer Chemoprevention and Therapy: A Complementary Shift with Promising Acuity 185Madhulika Singh and Yogeshwer Shukla15.1 Introduction 18515.2 Nutraceuticals 18715.3 Nutraceuticals and Key Events in Cancer Development 18915.4 Nutraceuticals in Combinatorial Therapy of Human Cancer: A Pledge of the Future 19115.5 Curcumin: Potential for Combination Therapy 19515.6 Resveratrol: Potential for Combination Therapy 19915.7 Lycopene (a Carotenoid): Potential for Combinations Therapy 20215.8 Soy Nutraceuticals: Potential for Combination Therapy 20315.9 Tea Polyphenols Potential for Combinatorial Therapy 20415.10 D-Limonene: Potential for Combination Therapy 20715.12 Conclusion 20816 Nutrigenomic Approaches to Understanding the Transcriptional and Metabolic Responses of Phytochemicals to Diet-Induced Obesity and its Complications 218Myung-Sook Choi and Eun-Young Kwon16.1 Introduction 21816.2 Nutrigenomics 21916.3 Obesity and Cardiometabolic Syndrome 22216.4 Anti-Obesity Action of Luteolin 22516.5 Conclusion 22617 Going Beyond the Current Native Nutritional Food Through the Integration of the Omic Data in the Post]Genomic Era: A Study in (Resistant) Starch Systems Biology 230Treenut Saithong and Saowalak Kalapanulak17.1 Introduction 23017.2 Starch and its Yield Improvement in Plants 23117.3 An Extension of the (Resistant) Starch Yield Improvement Research on the Systems Biology Regime: Integration of the Omic Data from the Post-Genomic Technology 233Part III Proteomics 24318 Proteomics and Nutrition Research: An Overview 245Arun K. Tewari, Sudhasri Mohanty, and Sashwati Roy18.1 Introduction 24518.2 Proteomics 24518.3 Nutrition and Proteins 24618.4 Nutritional Biomarkers 24818.5 Nutritional Bioactives 24818.6 Diet-Based Proteomics Application to Animal Products (Livestock Applications) 24918.7 Proteomics and Food Safety 24918.8 Conclusion 24918.9 Significance 25019 Proteomics Analysis for the Functionality of Toona sinensis 253Sue-Joan Chang and Chun-Yung Huang19.1 Introduction 25319.2 Toona sinensis 25319.3 TSLs Regulate Functions of Testes/Spermatozoa 25419.4 TSLs Regulate Liver Metabolism 25719.5 TSL as a Novel Antioxidant 26119.6 Possible Active Compounds in TSL Extracts 26119.7 Conclusion 26120 Proteomic Approaches to Identify Novel Therapeutics and Nutraceuticals from Filamentous Fungi: Prospects and Challenges 265Samudra Prosad Banik, Suman Khowala, Chiranjib Pal, and Soumya Mukherjee20.1 Introduction 26520.2 Mushroom Derived Immunomodulators and their Target Cells in the Immune System 26620.3 Mushroom Derived Metabolites in Treating Cancer 27120.4 Mushroom Derived Metabolites in Infectious Diseases 27120.5 Fungal Enzymes as Therapeutics and Dietary Supplements 27420.6 Identification and Characterization of Mushroom Derived Bioactive Therapeutics 27520.7 Challenges in Intracellular Proteome Preparation 27920.8 Challenges in Extracellular Proteome Preparation 27920.9 New Generation MS Technologies to Track the Dynamic Proteome 28020.10 Glycoproteomics: A New Arsenal in the Proteomic Toolbox 28020.11 Glycoproteomics of Filamentous Fungi 28120.12 High]Throughput Approaches to Decipher Fungal Glycan Structures 28220.13 Challenges in MS Studies of Glycans/Glycopeptides 28420.14 Optimized MS Instrumentation for Glycan Analysis 28420.15 Tandem Mass Spectrometry 28520.16 Bioinformatics for Glycoproteomics: Hitting Databases with MS Peaks 28520.17 Predicting Glycan Structures with Computational Tools 28620.18 Concluding Remarks: The Road Ahead 28721 Proteomics and Metaproteomics for Studying Probiotic Activity 296Rosa Anna Siciliano and Maria Fiorella Mazzeo21.1 Introduction 29621.2 Molecular Mechanisms of Probiotic Action as Studied by Proteomics 29721.3 Probiotics and Prebiotics 29921.4 Investigation on Human Microbiota Dynamics by Proteomics 30021.5 Concluding Remarks and Future Directions 30122 Proteomics Approach to Assess the Potency of Dietary Grape Seed Proanthocyanidins and Dimeric Procyanidin B2 304Hai-qing Gao, Bao-ying Li, Mei Cheng, Xiao-li Li, Fei Yu, and Zhen Zhang22.1 Chemoprotective Properties of GSPs 30522.2 Proteomic Platform 30922.3 Proteomics Analysis of the Actions of GSPs 31122.4 Functional Confirmation of Proteins 31722.5 Future Perspectives 31723 Genomic and Proteomic Approaches to Lung Transplantation: Identifying Relevant Biomarkers to Improve Surgical Outcome 321John Noel, Ronald Carnemola, and Shampa Chatterjee23.1 Introduction 32123.2 Lung Transplantation 32223.3 Challenges of Lung Transplantation 32323.4 Inflammatory Biomarkers with Lung Rejection: Markers of Inflammation Signaling such as CAMs, Chemokines, and Cytokines and their Status with Transplants 32423.5 Microarray Technology to Identify Transplant Rejection Biomarkers 32423.6 Challenges and Future Directions 32524 Proteomics in Understanding the Molecular Basis of Phytochemicals for Health 328Jung Yeon Kwon, Sanguine Byun, and Ki Won Lee24.1 Introduction 32824.2 Proteomics in Phytochemical Research in Cancer Prevention 32924.3 Perspectives 33124.4 Proteomics in Phytochemical Research for Metabolic Diseases 33324.5 Proteomics for Neuroprotective Phytochemicals 33324.6 Proteomics for Phytochemicals with Other Functions for Health Benefits 33424.7 Conclusions 33425 Genomics/Proteomics of NEXT-II, a Novel Water]Soluble, Undenatured Type II Collagen in Joint Health Care 338Orie Yoshinari, Hiroyoshi Moriyama, Manashi Bagchi, and Debasis Bagchi25.1 Introduction 33825.2 Mechanism of RA 33925.3 About NEXT-II 34025.4 Hypothesized Mechanism of NEXT-II 34225.5 Future Perspectives 34325.6 Conclusion 343Part IV Metabolomics 34726 Harnessing Metabolic Diversity for Nutraceutical Plant Breeding 349Ashish Saxena and Vicki L. Schlegel26.1 What is Metabolomics? 34926.2 Nutraceuticals 35026.3 Importance of Secondary Metabolites 35026.4 Complementing Plant Breeding with "Omics" 35126.5 Nutraceutical Breeding 35226.6 Crop Quality 35326.7 Metabolomics and Plant Stresses 35326.8 Food Safety 35426.9 Future 35427 Metabolomics and Fetal-Neonatal Nutrition: An Overview 357Angelica Dessì, Flaminia Cesare Marincola, and Vassilios Fanos27.1 Introduction 35727.2 IUGR and LGA: Fetal Programming 35827.3 Metabolomics in Nutritional Research 35827.4 Nutrimetabolomics in Animal Models 36027.5 Nutrimetabolomics in Human Models 36127.6 Conclusions 36228 Metabolomics, Bioactives, and Cancer 365Shannon R. Sweeney, John DiGiovanni, and Stefano Tiziani28.1 Introduction 36528.2 Nuclear Magnetic Resonance Spectroscopy 36628.3 Mass Spectrometry 36728.4 Application of Scientific Computing and Data Analysis 36828.5 Metabolomics, Bioactive Food Components, and Cancer 36928.6 Future Perspectives 37329 NMR]Based Metabolomics of Foods 379Takuya Miyakawa, Tingfu Liang, and Masaru Tanokura29.1 Introduction 37929.2 Principal Aspects of NMR in Food Analyses 38029.3 NMR Techniques Applied to Food Metabolomics 38029.4 Monitoring of Metabolic Changes in Food Processing Using Quantitative NMR 38129.5 NMR Profiling Based on Multivariate Analyses 38229.6 Conclusion 38630 Cancer Chemopreventive Effect of Curcumin through Suppressing Metabolic Crosstalk between Components in the Tumor Microenvironment 388Dong Hoon Suh and Yong-Sang Song30.1 Introduction 38830.2 Cancer Metabolism 38930.3 Metabolic Onco-Targets of Curcumin in the Tumor Microenvironment 39130.4 Clinical Trials of Curcumin as Metabolic Modulators in Cancer 39330.5 Conclusions and Future Perspectives 39331 Metabolomics of Green Tea 397Yoshinori Fujimura and Hirofumi Tachibana31.1 Introduction 39731.2 Metabolic Profiling 39831.3 Tea Chemical Composition 40131.4 Metabolic Responses to Tea Consumption 40231.5 Biotransformation of Dietary Tea Components 40331.6 Conclusion 404Part V Epigenetics 40732 The Potential Epigenetic Modulation of Diabetes Influenced by Nutritional Exposures In Utero 409Jie Yan and Huixia Yang32.1 Introduction 40932.2 Insulin Resistance 40932.3 Skeletal Muscle 41032.4 Type 2 Diabetes 41032.5 Influence of High]Fat Diet 41032.6 Obesity 41032.7 Intrauterine Growth Restriction (IUGR) 41132.8 Environmental Factors and Epigenetic Modifications 41132.9 Mitochondria and Energy Homeostasis 41332.10 Diabetes Progression 41332.11 Conclusion 41433 The Time has Come (and the Tools are Available) for Nutriepigenomics Studies 418Pearlly S. Yan33.1 Introduction: Great Strides in Deciphering Methylomes 41833.2 Recent Findings in Methylome Research and their Implications for Future Nutriepigenomic Research 41933.3 Strategies for Identifying and Optimizing a Small Number of Promising Methylation Markers 41933.4 Validation of Methylation Markers Performance in Large Cohorts using Highly Targeted Assays 42133.5 Summaries 42234 Natural Phytochemicals as Epigenetic Modulators 424Gauri Deb and Sanjay Gupta34.1 Introduction 42434.2 Epigenetic Mechanisms in Mammals 42534.3 Natural Phytochemicals and Epigenetic Mechanisms 42734.4 Conclusion and Future Perspectives 433Part VI Peptidomics 44135 Detection and Identification of Food-Derived Peptides in Human Blood: Food-Derived Short Chain Peptidomes in Human Blood 443Kenji Sato and Daisuke Urado35.1 Introduction 44335.2 Detection of Apparent Bioactive Peptides in Human Blood 44435.3 Identification of Food]Derived Peptides in Human Blood 44435.4 Future Prospects 448Part VII Nutrigenomics and Human Health 45336 Use of Omics Approaches for Developing Immune-Modulatory and Anti-Inflammatory Phytomedicines 455Shu-Yi Yin, Pradeep M. S., and Ning-Sun Yang36.1 Introduction 45536.2 Transcriptomics Study in Medicinal Plant Research 45836.3 Proteomics Studies on Research into Medicinal Plants 46236.4 Metabolomics Study on the Research of Medicinal Plants 46336.5 Lipidomics Study on the Research of Medicinal Plants 46636.6 Comparative and Bioinformatics Tools for Omics Studies 46636.7 Challenges and Perspectives 46937 The Application of Algae for Cosmeceuticals in the Omics Age 476Nyuk Ling Ma, Su Shiung Lam, and Rahman Zaidah37.1 Introduction 47637.2 Metabolomics 47737.3 Genomics 47737.4 Proteomics 48137.5 Conclusion 48338 Gut Microbiome and Functional Foods: Health Benefits and Safety Challenges 489Abhai Kumar, Smita Singh, and Anil Kumar Chauhan38.1 Introduction 48938.2 Microbiome Symbiosis 49038.3 Functional Food Intervention of Gut Microbiota 49238.4 Types of Functional Foods and Their Effects 49338.5 Regulations and Safety of Functional Food 49738.6 Safety Challenges of Functional Food 49938.7 Functional Foods and Nutrigenomics 49938.8 Conclusions 50039 An Overview on Germinated Brown Rice and its Nutrigenomic Implications 504Mustapha Umar Imam and Maznah Ismail39.1 Diet and Health: The Role of Staple Foods and Nutrigenomic Implications 50439.2 Health Implications of White Rice and Brown Rice Consumption 50639.3 Germinated Brown Rice: Bioactives, Functional Effects, and Mechanistic Insights 50639.4 Conclusions 51339.5 Future Considerations 51340 Novel Chromium (III) Supplements and Nutrigenomics Exploration: A Review 518Sreejayan Nair, Anand Swaroop, and Debasis Bagchi40.1 Introduction 51840.2 Trivalent Chromium, Insulin Regulation, and Signaling 51940.3 Regulatory Pathways 51940.4 MicroRNAs 52240.5 Summary and Conclusions 522Part VIII Transcriptomics 52541 Transcriptomics of Plants Interacting with Pathogens and Beneficial Microbes 527Hooman Mirzaee, Louise Shuey, and Peer M. Schenk41.1 Introduction 52741.2 Plant Defense Responses against Pathogens 52841.3 Transcriptomics during Plant]Pathogen Interactions 52941.4 Plant Responses during Interactions with Beneficial Microbes 53041.5 Transcriptomics during Beneficial Plant]Microbe Interactions 53141.6 Knowledge on Modulation of Host Immunity by Pathogens and Beneficial Microbes May Lead to New Resistance Strategies 53242 Transcriptomic and Metabolomic Profiling of Chicken Adipose Tissue: An Overview 537Brynn H. Voy, Stephen Dearth, and Shawn R. Campagna42.1 Introduction 53742.2 Chicken as a Model Organism 53742.3 Chicken Genome and Genetic Diversity 53842.4 Chicken as a Model for Studies of Adipose Biology and Obesity 53842.5 Natural and Selected Models of Differential Fatness 53842.6 Transcriptomics and Metabolomics as Tools for the Studies of Adipose Biology in Chicken 53942.7 Insight into Control of Adipose Tissue Growth and Metabolism in Chickens from Transcriptomics and Metabolomics 54142.8 Conclusions and Future Directions 54343 Nutritional Transcriptomics: An Overview 545M. R. Noori]Daloii and A. Nejatizadeh43.1 Introduction 54543.2 Molecular Nutrition 54643.3 From Nutrients to Genes Expression Profiling 54743.4 Biological Actions of Nutrients 54843.5 Nutritional Transcriptomics 54843.6 Transcriptomic Technologies 54943.7 Transcriptomics and Development of New Nutritional Biomarkers 55243.8 The Micronutrient Genomics Project 55343.9 Transcriptomics in Nutrition Research 55343.10 Perspectives 55444 Dissecting Transcriptomes of Cyanobacteria for Novel Metabolite Production 557Sucheta Tripathy, Deeksha Singh, Mathumalar C., and Abhishek Das44.1 Introduction 55744.2 Phylogenetic Relationships in Cyanobacteria 55844.3 Genomic Studies of Cyanobacteria 56044.4 Plasmids in Cyanobacteria 56244.5 Dissecting Transcriptomes of Cyanobacteria 56344.6 Conclusion 57145 Inflammation, Nutrition, and Transcriptomics 573Gareth Marlow and Lynnette R. Ferguson45.1 Introduction 57345.2 Inflammation 57345.3 Nutrition 57545.4 Nutrigenomics 57545.5 Dietary Factors and Inflammation 57645.6 Transcriptomics 57745.7 Conclusions 57846 Transcriptomics and Nutrition in Mammalians 581Carmen Arnal, Jose M. Lou-Bonafonte, María V. Martínez]Gracia, María J. Rodríguez-Yoldi, and Jesús Osada46.1 Introduction 58146.2 Adipocyte Transcriptome 58446.3 Intestinal Transcriptome 58746.4 Hepatic Transcriptome 59046.5 Muscular Transcriptome 59946.6 Conclusion 601Part IX Nutriethics 60947 Nutritional Sciences at the Intersection of Omics Disciplines and Ethics: A Focus on Nutritional Doping 611Nicola Luigi Bragazzi47.1 Introduction 61147.2 Nutrigenomics and Nutriproteomics 61247.3 Sports Nutriproteogenomics 61447.4 Nutritional and Sports Ethics 61547.5 Conclusions 617Part X Nanotechnology 62348 Current Relevant Nanotechnologies for the Food Industry 625Kelvii Wei Guo48.1 Introduction 62548.2 Nanotechnology in Food Industry 62648.3 Natural Biopolymers 63048.4 Nanotechnology for Food Packaging 63048.5 Outstanding State-of-the-Art Issues 63348.6 Conclusion 633References 634Index 637