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Contributors x Preface xiii Biography of Martin Kussmann xiv Section I Genes, Proteins, and Nutrition 1 1 The use of transcriptomics as a tool to identify differences in the response to diet 3 Juri C. Matualatupauw and Lydia A. Afman
1.1 New concepts in nutrition research 3
1.2 Comprehensive phenotyping 3
1.3 Phenotypic flexibility 4
1.4 Factors that influence the transcriptome response to diet 5
1.5 Using transcriptomics to explain mechanism behind differences in response to diet 10
1.6 Conclusion 10
1.7 Future perspectives 15 References 16 2 Genetic or nutritional disturbances in folate]related pathways and epigenetic interactions 19 Daniel Leclerc and Rima Rozen
2.1 Introduction 19
2.2 Nutrition and one]carbon metabolism 20
2.3 Importance of DNAmethylation at CpG dinucleotides 23
2.4 Folate]dependent disorders: Dietary impact 24
2.5 Genetic influences on phenotype and interactions with epigenetics 27
2.6 Epigenetic inheritance across generations 31
2.7 Conclusions 34 References 35 3 Early]life development and epigenetic mechanisms: Mediators of metabolic programming and obesity risk 42 Felicia M. Low, Peter D. Gluckman, and Keith M. Godfrey
3.1 Introduction 42
3.2 Origins of DOHaD and its conceptual basis 43
3.3 Epigenetic mechanisms 44
3.4 Early]life nutrition, epigenetics, and metabolic programming 48
3.5 Paternal effects 52
3.6 Transgenerational epigenetic inheritance 54
3.7 The potential value of DOHaD principles and epigenetic biology to the improvement of human health 55
3.8 Conclusion 57 Acknowledgments 57 References 58 Section II Bioactives and Phytonutrients 65 4 Bioactive interactions in food and natural extracts 67 Sofia Moco and Denis Barron
4.1 Natural compounds as all compounds produced by nature 67
4.2 Not all natural compounds are created active 70
4.3 On the road of modern technologies for bioactive discovery 71
4.4 Metabolomics strategies applied to bioactives biochemistry 77
4.5 Bioactives as multi]target network instigators 81
4.6 ''Let food be thy medicine and medicine be thy food'' - outlook 85 Acknowledgments 85 References 85 5 Anthocyanins in metabolic health and disease 92 John Overall, Mary Ann Lila, and Slavko Komarnytsky
5.1 Introduction 92
5.2 Chemical structure 93
5.3 Structural effects on stability 93
5.4 Systemic bioavailability and tissue distribution 96
5.5 Metabolism and nutrigenomic effects 102
5.6 Conclusions 114 Acknowledgments 114 References 114 6 Dietary antioxidants and bioflavonoids in atherosclerosis and angiogenesis 125 Mohsen Meydani and Angelo Azzi
6.1 Introduction 125
6.2 Dietary vitamins E and C and CVD 126
6.3 Dietary polyphenols and CVD 128
6.4 Flavonoids and angiogenesis 134
6.5 Conclusion 135 Acknowledgments 136 References 137 7 Genomics and proteomics approaches to identify resveratrol targets in cancer 143 César López]Camarillo, Rubiceli Medina]Aguilar, Carlos Palma]Flores, and Laurence A. Marchat
7.1 Introduction 143
7.2 Sources and health benefits of resveratrol 144
7.3 Resveratrol for cancer prevention and therapy 145
7.4 Functional genomics approaches to identify resveratrol targets in cancer 147
7.5 Proteomics approaches to identify resveratrol targets in cancer 148
7.6 Metabolomics approaches to identify pathways modified by resveratrol in cancer 150
7.7 Epigenomic events induced by resveratrol in cancer 152
7.8 Conclusions and perspectives 153 References 153 8 Genomic effects of food bioactives in neuroprotection 156 Ashraf Virmani, Syed Ali, Luigi Pinto, Saf Zerelli, and Zbigniew Binienda
8.1 Introduction: Nature and nurture 156
8.2 Mechanism underlying food nurture 156
8.3 Natural cellular nurture mechanisms 157
8.4 Effects of food bioactives on genomic activity 158
8.5 Epigenetic modulation 158
8.6 Modulation of the epigenome by food bioactives 159
8.7 Possible role of the genome in neuroprotection 160
8.8 Countering risk factors associated with neurodegeneration 161
8.9 Using food bioactives to restore epigenetic balance 161
8.10 Targeting inflammation, energy, and free radicals 161
8.11 Food bioactives that reduce inflammation 163
8.12 Food bioactive effects on bioenergetics and redox balance 163
8.13 Role of food bioactive acetyl]l]carnitine in neurodegeneration 163
8.14 Process of S]palmitoylation and the role of carnitine palmitoyltransferase 1c enzyme in the brain 164
8.15 Conclusion 164 References 165 9 MicroRNAs: Bioactive molecules at the nexus of nutrition and disease 170 Lisa M. Farmer and Kendal D. Hirschi
9.1 Introduction to micro RNAs as dietary bioactive compounds 170
9.2 Characteristics, biogenesis, and functions of miRNAs 171
9.3 miRNA detection methods 173
9.4 Small RNAs in the circulation 174
9.5 Endogenous miRNAs and metabolic control 176
9.6 miRNAs as biomarkers for diet and disease 178
9.7 Absorption of dietary animal miRNAs in animal consumers 184
9.8 Absorption of dietary plant miRNAs in animal consumers 185
9.9 Contradictory evidence of dietary miRNA uptake 188
9.10 Therapeutic potential of miRNAs 190
9.11 Gut pathology may influence dietary miRNA uptake 191
9.12 Conclusion 193 Acknowledgments 195 References 195 Section III Prebiotics, Probiotics, Synbiotics, and the Gut Ecosystem 201 10 Gut health and the personal microbiome 203 Carolin A. Kolmeder and Willem M. de Vos
10.1 Gut health and its concepts 203
10.2 Microbiome and gut health - from composition to function 206
10.3 The personalized microbiome - towards precision nutrition 211
10.4 Conclusions and next]generation interventions 214 Acknowledgments 215 References 215 11 Infant nutrition and the microbiome: Systems biology approaches to uncovering host-microbe interactions 220 Mei Wang, Ivan Ivanov, Laurie A. Davidson, Robert S. Chapkin, and Sharon M. Donovan
11.1 Introduction 220
11.2 Environmental factors influencing development of the infant gut microbiota 221
11.3 Infant nutrition and the development of gut microbiota 223
11.4 Host genetics and the development of gut microbiota 226
11.5 Host-microbe interactions regulating host phenotype and gene expression 230
11.6 Systems biology approaches to diet]dependent host-microbe interaction 243
11.7 Summary and conclusions 247 References 247 12 Bioactive host-microbial metabolites in human nutrition with a focus on aromatic amino acid co]metabolism 258 François]Pierre J. Martin and Martin Kussmann
12.1 Introduction: Gut microbiota metabolism in nutrition, health and disease 258
12.2 Short]chain fatty acid metabolism 259
12.3 Bile acid metabolism 260
12.4 Aromatic amino acid metabolism 261
12.5 Conclusions and perspectives 269 References 270 Section IV Nutrigenomic and Proteomic Technologies 275 13 Network analysis in systems nutrition 277 Marie]Pier Scott-Boyer and Corrado Priami
13.1 Introduction 277
13.2 Biological networks 278
13.3 Network topology 281
13.4 A general framework for network analysis of throughput data 282
13.5 Examples of network analyses 284
13.6 Conclusions and perspectives 286 References 287 14 Nutrigenomics analyses: Biostatistics and systems biology approaches 290 Damien Valour and Bernard Valour
14.1 Gene selection for nutrigenomics studies 290
14.2 Specificity of high]dimension data and preprocessing before gene selection 291
14.3 Exploratory and differential gene expression analysis 292
14.4 Biomarker discovery in nutrigenomics: Gene selection and discrimination 297
14.5 A step towards data integration: searching for correlation/covariance between two datasets 310
14.6 From gene selection to systems biology 313 References 315 Index 319