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E-raamat: Nutrigenomics and Proteomics in Health and Disease: Towards a Systems-level Understanding of Gene-diet Interactions

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"This volume brings together leading experts in the areas of nutrition, nutrigenomics, metabolic programming, food-based bioactive dietary components and the gut microbiome, as well as those expert in the application of innovative tools and methods for statistical and biological network analysis, which are now at the forefront of nutritional and biomedical sciences. The articles provide a roadmap for the integration of normative science methods and approaches with more comprehensive systems biology-basedinvestigations that deploy a multitude of omic platforms. This integration is essential to escape the bottleneck in knowledge generation by applying decades of knowledge of nutrients and their function to comprehensive omics and clinical data acquisition, processing, visualization, and interpretation. Achieving a systems-level understanding of nutrient function in health and disease will usher in an age of precision nutrition in support of maximizing human health and potential"--

Now in a revised second edition, Nutrigenomics and Proteomics in Health and Disease brings together the very latest science based upon nutrigenomics and proteomics in food and health. Coverage includes many important nutraceuticals and their impact on gene interaction and health. Authored by an international team of multidisciplinary researchers, this book acquaints food and nutrition professionals with these new fields of nutrition research and conveys the state of the science to date.

Thoroughly updated to reflect the most current developments in the field, the second edition includes six new chapters covering gut health and the personal microbiome; gut microbe-derived bioactive metabolites; proteomics and peptidomics in nutrition; gene selection for nutrigenomic studies; gene-nutrient network analysis, and nutrigenomics to nutritional systems biology. An additional five chapters have also been significantly remodelled. The new text includes a rethinking of in vitro and in vivo models with regard to their translatability into human phenotypes, and normative science methods and approaches have been complemented by more comprehensive systems biology-based investigations, deploying a multitude of omic platforms in an integrated fashion. Innovative tools and methods for statistical treatment and biological network analysis are also now included.

Contributors x
Preface xiii
Biography of Martin Kussmann xiv
Section I Genes, Proteins, and Nutrition
1(64)
1 The use of transcriptomics as a tool to identify differences in the response to diet
3(16)
Juri C. Matualatupauw
Lydia A. Afman
1.1 New concepts in nutrition research
3(1)
1.2 Comprehensive phenotyping
3(1)
1.3 Phenotypic flexibility
4(1)
1.4 Factors that influence the transcriptome response to diet
5(5)
1.5 Using transcriptomics to explain mechanism behind differences in response to diet
10(1)
1.6 Conclusion
10(5)
1.7 Future perspectives
15(4)
References
16(3)
2 Genetic or nutritional disturbances in folate-related pathways and epigenetic interactions
19(23)
Daniel Leclerc
Rima Rozen
2.1 Introduction
19(1)
2.2 Nutrition and one-carbon metabolism
20(3)
2.3 Importance of DNA methylation at CpG dinucleotides
23(1)
2.4 Folate-dependent disorders: Dietary impact
24(3)
2.5 Genetic influences on phenotype and interactions with epigenetics
27(4)
2.6 Epigenetic inheritance across generations
31(3)
2.7 Conclusions
34(8)
References
35(7)
3 Early-life development and epigenetic mechanisms: Mediators of metabolic programming and obesity risk
42(23)
Felicia M. Low
Peter D. Gluckman
Keith M. Godfrey
3.1 Introduction
42(1)
3.2 Origins of DOHaD and its conceptual basis
43(1)
3.3 Epigenetic mechanisms
44(4)
3.4 Early-life nutrition, epigenetics, and metabolic programming
48(4)
3.5 Paternal effects
52(2)
3.6 Transgenerational epigenetic inheritance
54(1)
3.7 The potential value of DOHaD principles and epigenetic biology to the improvement of human health
55(2)
3.8 Conclusion
57(8)
Acknowledgments
57(1)
References
58(7)
Section II Bioactives and Phytonutrients
65(136)
4 Bioactive interactions in food and natural extracts
67(25)
Sofia Moco
Denis Barron
4.1 Natural compounds as all compounds produced by nature
67(3)
4.2 Not all natural compounds are created active
70(1)
4.3 On the road of modern technologies for bioactive discovery
71(6)
4.4 Metabolomics strategies applied to bioactives biochemistry
77(4)
4.5 Bioactives as multi-target network instigators
81(4)
4.6 `Let food be thy medicine and medicine be thy food' --- outlook
85(7)
Acknowledgments
85(1)
References
85(7)
5 Anthocyanins in metabolic health and disease
92(33)
John Overall
Mary Ann Lila
Slavko Komarnytsky
5.1 Introduction
92(1)
5.2 Chemical structure
93(1)
5.3 Structural effects on stability
93(3)
5.4 Systemic bioavailability and tissue distribution
96(6)
5.5 Metabolism and nutrigenomic effects
102(12)
5.6 Conclusions
114(11)
Acknowledgments
114(1)
References
114(11)
6 Dietary antioxidants and bioflavonoids in atherosclerosis and angiogenesis
125(18)
Mohsen Meydani
Angelo Azzi
6.1 Introduction
125(1)
6.2 Dietary vitamins E and C and CVD
126(2)
6.3 Dietary polyphenols and CVD
128(6)
6.4 Flavonoids and angiogenesis
134(1)
6.5 Conclusion
135(8)
Acknowledgments
136(1)
References
137(6)
7 Genomics and proteomics approaches to identify resveratrol targets in cancer
143(13)
Cesar Lopez-Camarillo
Rubiceli Medina-Aguilar
Carlos Palma-Flores
Laurence A. Marchat
7.1 Introduction
143(1)
7.2 Sources and health benefits of resveratrol
144(1)
7.3 Resveratrol for cancer prevention and therapy
145(2)
7.4 Functional genomics approaches to identify resveratrol targets in cancer
147(1)
7.5 Proteomics approaches to identify resveratrol targets in cancer
148(2)
7.6 Metabolomics approaches to identify pathways modified by resveratrol in cancer
150(2)
7.7 Epigenomic events induced by resveratrol in cancer
152(1)
7.8 Conclusions and perspectives
153(3)
References
153(3)
8 Genomic effects of food bioactives in neuroprotection
156(14)
Ashraf Virmani
Syed Ali
Luigi Pinto
Saf Zerelli
Zbigniew Binienda
8.1 Introduction: Nature and nurture
156(1)
8.2 Mechanism underlying food nurture
156(1)
8.3 Natural cellular nurture mechanisms
157(1)
8.4 Effects of food bioactives on genomic activity
158(1)
8.5 Epigenetic modulation
158(1)
8.6 Modulation of the epigenome by food bioactives
159(1)
8.7 Possible role of the genome in neuroprotection
160(1)
8.8 Countering risk factors associated with neurodegeneration
161(1)
8.9 Using food bioactives to restore epigenetic balance
161(1)
8.10 Targeting inflammation, energy, and free radicals
161(2)
8.11 Food bioactives that reduce inflammation
163(1)
8.12 Food bioactive effects on bioenergetics and redox balance
163(1)
8.13 Role of food bioactive acetyl-L-carnitine in neurodegeneration
163(1)
8.14 Process of S-palmitoylation and the role of carnitine palmitoyltransferase 1c enzyme in the brain
164(1)
8.15 Conclusion
164(6)
References
165(5)
9 MicroRNAs: Bioactive molecules at the nexus of nutrition and disease
170(31)
Lisa M. Farmer
Kendal D. Hirschi
9.1 Introduction to micro RNAs as dietary bioactive compounds
170(1)
9.2 Characteristics, biogenesis, and functions of miRNAs
171(2)
9.3 miRNA detection methods
173(1)
9.4 Small RNAs in the circulation
174(2)
9.5 Endogenous miRNAs and metabolic control
176(2)
9.6 miRNAs as biomarkers for diet and disease
178(6)
9.7 Absorption of dietary animal miRNAs in animal consumers
184(1)
9.8 Absorption of dietary plant miRNAs in animal consumers
185(3)
9.9 Contradictory evidence of dietary miRNA uptake
188(2)
9.10 Therapeutic potential of miRNAs
190(1)
9.11 Gut pathology may influence dietary miRNA uptake
191(2)
9.12 Conclusion
193(8)
Acknowledgments
195(1)
References
195(6)
Section III Prebiotics, Probiotics, Synbiotics, and the Gut Ecosystem
201(74)
10 Gut health and the personal microbiome
203(17)
Carolin A. Kolmeder
Willem M. de Vos
10.1 Gut health and its concepts
203(3)
10.2 Microbiome and gut health --- from composition to function
206(5)
10.3 The personalized microbiome --- towards precision nutrition
211(3)
10.4 Conclusions and next-generation interventions
214(6)
Acknowledgments
215(1)
References
215(5)
11 Infant nutrition and the microbiome: Systems biology approaches to uncovering host--microbe interactions
220(38)
Mei Wang
Ivan Ivanov
Laurie A. Davidson
Robert S. Chapkin
Sharon M. Donovan
11.1 Introduction
220(1)
11.2 Environmental factors influencing development of the infant gut microbiota
221(2)
11.3 Infant nutrition and the development of gut microbiota
223(3)
11.4 Host genetics and the development of gut microbiota
226(4)
11.5 Host--microbe interactions regulating host phenotype and gene expression
230(13)
11.6 Systems biology approaches to diet-dependent host--microbe interaction
243(4)
11.7 Summary and conclusions
247(11)
References
247(11)
12 Bioactive host--microbial metabolites in human nutrition with a focus on aromatic amino acid co-metabolism
258(17)
Francois-Pierre J. Martin
Martin Kussmann
12.1 Introduction: Gut microbiota metabolism in nutrition, health and disease
258(1)
12.2 Short-chain fatty acid metabolism
259(1)
12.3 Bile acid metabolism
260(1)
12.4 Aromatic amino acid metabolism
261(8)
12.5 Conclusions and perspectives
269(6)
References
270(5)
Section IV Nutrigenomic and Proteomic Technologies
275(44)
13 Network analysis in systems nutrition
277(13)
Marie-Pier Scott-Boyer
Corrado Priami
13.1 Introduction
277(1)
13.2 Biological networks
278(3)
13.3 Network topology
281(1)
13.4 A General Framework for Network Analysis of Throughput data
282(2)
13.5 Examples of network analyses
284(2)
13.6 Conclusions and perspectives
286(4)
References
287(3)
14 Nutrigenomics analyses: Biostatistics and systems biology approaches
290(29)
Damien Valour
Bernard Valour
14.1 Gene selection for nutrigenomics studies
290(1)
14.2 Specificity of high-dimension data and preprocessing before gene selection
291(1)
14.3 Exploratory and differential gene expression analysis
292(5)
14.4 Biomarker discovery in nutrigenomics: Gene selection and discrimination
297(13)
14.5 A Step Towards Data Integration: Searching for Correlation/Covariance Between Two Datasets
310(3)
14.6 From gene selection to systems biology
313(6)
References
315(4)
Index 319
About the Editors

Martin Kussmann is Professor of "Systems Biology in Nutrition and Health" at the Liggins Institute, University of Auckland, New Zealand. He is also Chief Scientist of New Zealand's National Science Challenge "High-Value Nutrition". In 2011, Martin joined the Nestlè Institute of Health Sciences (NIHS) on the campus of the Ecole Polytechnique Fèdèrale Lausanne (EPFL), Switzerland, as Head of the "Molecular Biomarkers Core". From 2012 to 2016, he has been Lecturer at the Faculty of Life Sciences, EPFL. Since June 2009, Martin is Honorary Professor for Nutritional Science at the Faculty of Science, Aarhus University, Denmark. He holds a MSc and PhD in Chemistry from the University of Konstanz, Germany.

Patrick J. Stover is Professor and Director of the Division of Nutritional Sciences at Cornell University. He graduated from Saint Joseph's University with a BS degree in Chemistry, and received a PhD degree in Biochemistry and Molecular Biophysics from the Medical College of Virginia, and performed his postdoctoral studies in Nutritional Sciences at the University of California at Berkeley.