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1.  Nutrigenomics and Nutrigenetics 
The nutrients are able to interact with molecular mechanisms and modulate the physiological functions in the body. The Nutritional Genomics focuses on the interaction between bioactive food components and the genome, which includes Nutrigenetics and Nutrigenomics. The influence of nutrients on f genes expression is called Nutrigenomics, while the heterogeneous response of gene variants to nutrients, dietary components and developing nutraceticals is called Nutrigenetics. Genetic variation is known to affect food tolerances among human subpopulations and may also influence dietary requirements and raising the possibility of individualizing nutritional intake for optimal health and disease prevention on the basis of an individual’s genome. Nutrigenomics provides a genetic understanding for how common dietary components affect the balance between health and disease by altering the expression and/or structure of an individual’s genetic makeup. Nutrigenetics describes that the genetic profile have impact on the response of body to bioactive food components by influencing their absorption, metabolism, and site of action.
In this way, considering different aspects of gene–nutrient interaction and designing appropriate diet for every specific genotype that optimize individual health, diagnosis and nutritional treatment of genome instability, we could prevent and control conversion of healthy phenotype to diseases.
PMCID: PMC3481686  PMID: 23113033
Nutritional genomics; Nutrigenomics; Nutrigenetics; Genetic variation
2.  Choline: Clinical Nutrigenetic/Nutrigenomic Approaches for Identification of Functions and Dietary Requirements 
Nutrigenetics/nutrigenomics (the study of the bidirectional interactions between genes and diet) is a rapidly developing field that is changing research and practice in human nutrition. Though eventually nutrition clinicians may be able to provide personalized nutrition recommendations, in the immediate future they are most likely to use this knowledge to improve dietary recommendations for populations. Currently, estimated average requirements are used to set dietary reference intakes because scientists cannot adequately identify subsets of the population that differ in requirement for a nutrient. Recommended intake levels must exceed the actual required intake for most of the population in order to assure that individuals with the highest requirement ingest adequate amounts of the nutrient. As a result, dietary reference intake levels often are set so high that diet guidelines suggest almost unattainable intakes of some foods. Once it is possible to identify common subgroups that differ in nutrient requirements using nutrigenetic/nutrigenomic profiling, targeted interventions and recommendations can be refined. In addition, when a large variance exists in response to a nutrient, statistical analyses often argue for a null effect. If responders could be differentiated from nonre-sponders based on nutrigenetic/nutrigenomic profiling, this statistical noise could be eliminated and the sensitivity of nutrition research greatly increased.
doi:10.1159/000314512
PMCID: PMC3601485  PMID: 20436254
3.  Nutrigenetics, Nutrigenomics, and Selenium 
Selenium (Se) is an important micronutrient that, as a component of selenoproteins, influences oxidative and inflammatory processes. Its’ levels vary considerably, with different ethnic and geographic population groups showing varied conditions, ranging from frank Se deficiencies to toxic effects. An optimum Se level is essential for the maintenance of homeostasis, and this optimum may vary according to life stage, general state of health, and genotype. Nutrigenetic studies of different Se levels, in the presence of genetic variants in selenoproteins, suggest that an effective dietary Se intake for one individual may be very different from that for others. However, we are just starting to learn the significance of various genes in selenoprotein pathways, functional variants in these, and how to combine such data from genes into pathways, alongside dietary intake or serum levels of Se. Advances in systems biology, genetics, and genomics technologies, including genetic/genomic, epigenetic/epigenomic, transcriptomic, proteomic, and metabolomic information, start to make it feasible to assess a comprehensive spectrum of the biological activity of Se. Such nutrigenomic approaches may prove very sensitive biomarkers of optimal Se status at the individual or population level. The premature cessation of a major human Se intervention trial has led to considerable controversy as to the value of Se supplementation at the population level. New websites provide convenient links to current information on methodologies available for nutrigenetics and nutrigenomics. These new technologies will increasingly become an essential tool in optimizing the level of Se and other micronutrients for optimal health, in individuals and in population groups. However, definitive proof of such effects will require very large collaborative studies, international agreement on study design, and innovative approaches to data analysis.
doi:10.3389/fgene.2011.00015
PMCID: PMC3268570  PMID: 22303312
selenium; selenoprotein; nutrigenetics; nutrigenomics
4.  Nutrigenetics and Metabolic Disease: Current Status and Implications for Personalised Nutrition 
Nutrients  2013;5(1):32-57.
Obesity, particularly central adiposity, is the primary causal factor in the development of insulin resistance, the hallmark of the metabolic syndrome (MetS), a common condition characterized by dyslipidaemia and hypertension, which is associated with increased risk of cardiovascular disease (CVD) and type 2 diabetes (T2DM). Interactions between genetic and environmental factors such as diet and lifestyle, particularly over-nutrition and sedentary behavior, promote the progression and pathogenesis of these polygenic diet-related diseases. Their current prevalence is increasing dramatically to epidemic proportions. Nutrition is probably the most important environmental factor that modulates expression of genes involved in metabolic pathways and the variety of phenotypes associated with obesity, the MetS and T2DM. Furthermore, the health effects of nutrients may be modulated by genetic variants. Nutrigenomics and nutrigenetics require an understanding of nutrition, genetics, biochemistry and a range of “omic” technologies to investigate the complex interaction between genetic and environmental factors relevant to metabolic health and disease. These rapidly developing fields of nutritional science hold much promise in improving nutrition for optimal personal and public health. This review presents the current state of the art in nutrigenetic research illustrating the significance of gene-nutrient interactions in the context of metabolic disease.
doi:10.3390/nu5010032
PMCID: PMC3571637  PMID: 23306188
nutrigenetics; metabolic health; dietary fat; obesity; insulin resistance; metabolic syndrome; diabetes; metabotype; gene-nutrient interaction
5.  Negotiating the boundary between medicine and consumer culture: Online marketing of nutrigenetic tests☆ 
Social Science & Medicine (1982)  2010;70(5):744-753.
Genomics researchers and policy makers have accused nutrigenetic testing companies—which provide DNA-based nutritional advice online—of misleading the public. The UK and USA regulation of the tests has hinged on whether they are classed as “medical” devices, and alternative regulatory categories for “lifestyle” and less-serious genetic tests have been proposed. This article presents the findings of a qualitative thematic analysis of the webpages of nine nutrigenetic testing companies. We argue that the companies, mirroring and negotiating the regulatory debates, were creating a new social space for products between medicine and consumer culture. This space was articulated through three themes: (i) how “genes” and tests were framed, (ii) how the individual was imagined vis a vis health information, and (iii) the advice and treatments offered. The themes mapped onto four frames or models for genetic testing: (i) clinical genetics, (ii) medicine, (iii) intermediate, and (iv) lifestyle. We suggest that the genomics researchers and policy makers appeared to perform what Gieryn (Gieryn, T.F. (1983). Boundary-work and the demarcation of science from non-science: strains and interests in professional ideologies of scientists. American Sociological Review, 48, 781–795.) has termed “boundary work”, i.e., to delegitimize the tests as outside proper medicine and science. Yet, they legitimated them, though in a different way, by defining them as lifestyle, and we contend that the transformation of the boundaries of science into a creation of such hybrid or compromise categories is symptomatic of current historical times. Social scientists studying medicine have referred to the emergence of “lifestyle” products. This article contributes to this literature by examining the historical, regulatory and marketing processes through which certain goods and services become defined this way.
doi:10.1016/j.socscimed.2009.10.066
PMCID: PMC2824846  PMID: 20022680
Genetics; Science and technology studies; Boundary work; UK; USA; Nutrigenetics; Direct-to-consumer genetic testing
6.  Nutrigenomics and metabolomics will change clinical nutrition and public health practice: insights from studies on dietary requirements for choline2 
Science is beginning to understand how genetic variation and epigenetic events alter requirements for, and responses to, nutrients (nutrigenomics). At the same time, methods for profiling almost all of the products of metabolism in a single sample of blood or urine are being developed (metabolomics). Relations between diet and nutrigenomic and metabolomic profiles and between those profiles and health have become important components of research that could change clinical practice in nutrition. Most nutrition studies assume that all persons have average dietary requirements, and the studies often do not plan for a large subset of subjects who differ in requirements for a nutrient. Large variances in responses that occur when such a population exists can result in statistical analyses that argue for a null effect. If nutrition studies could better identify responders and differentiate them from nonresponders on the basis of nutrigenomic or metabolomic profiles, the sensitivity to detect differences between groups could be greatly increased, and the resulting dietary recommendations could be appropriately targeted. It is not certain that nutrition will be the clinical specialty primarily responsible for nutrigenomics or metabolomics, because other disciplines currently dominate the development of portions of these fields. However, nutrition scientists' depth of understanding of human metabolism can be used to establish a role in the research and clinical programs that will arise from nutrigenomic and metabolomic profiling. Investments made today in training programs and in research methods could ensure a new foundation for clinical nutrition in the future.
PMCID: PMC2430757  PMID: 17823415
Nutrigenomics; epigenetics; metabolomics; single-nucleotide polymorphism; clinical nutrition
7.  Answering biological questions: querying a systems biology database for nutrigenomics 
Genes & Nutrition  2010;6(1):81-87.
The requirement of systems biology for connecting different levels of biological research leads directly to a need for integrating vast amounts of diverse information in general and of omics data in particular. The nutritional phenotype database addresses this challenge for nutrigenomics. A particularly urgent objective in coping with the data avalanche is making biologically meaningful information accessible to the researcher. This contribution describes how we intend to meet this objective with the nutritional phenotype database. We outline relevant parts of the system architecture, describe the kinds of data managed by it, and show how the system can support retrieval of biologically meaningful information by means of ontologies, full-text queries, and structured queries. Our contribution points out critical points, describes several technical hurdles. It demonstrates how pathway analysis can improve queries and comparisons for nutrition studies. Finally, three directions for future research are given.
doi:10.1007/s12263-010-0190-x
PMCID: PMC3040802  PMID: 21437033
Querying; Bioinformatics; Nutrigenomics; Systems biology; Biological databases
8.  Answering biological questions: querying a systems biology database for nutrigenomics 
Genes & Nutrition  2010;6(1):81-87.
The requirement of systems biology for connecting different levels of biological research leads directly to a need for integrating vast amounts of diverse information in general and of omics data in particular. The nutritional phenotype database addresses this challenge for nutrigenomics. A particularly urgent objective in coping with the data avalanche is making biologically meaningful information accessible to the researcher. This contribution describes how we intend to meet this objective with the nutritional phenotype database. We outline relevant parts of the system architecture, describe the kinds of data managed by it, and show how the system can support retrieval of biologically meaningful information by means of ontologies, full-text queries, and structured queries. Our contribution points out critical points, describes several technical hurdles. It demonstrates how pathway analysis can improve queries and comparisons for nutrition studies. Finally, three directions for future research are given.
doi:10.1007/s12263-010-0190-x
PMCID: PMC3040802  PMID: 21437033
Querying; Bioinformatics; Nutrigenomics; Systems biology; Biological databases
9.  Complexity of Type 2 Diabetes Mellitus Data Sets Emerging from Nutrigenomic Research: A Case for Dimensionality Reduction? 
Mutation research  2007;622(1-2):19-32.
Nutrigenomics promises personalized nutrition and an improvement in preventing, delaying, and reducing the symptoms of chronic diseases such as diabetes. Nutritional genomics is the study of how foods affect the expression of genetic information in an individual and how an individual's genetic makeup affects the metabolism and response to nutrients and other bioactive components in food. The path to those promises has significant challenges, from experimental designs that include analysis of genetic heterogeneity to the complexities of food and environmental factors. One of the more significant complications in developing the knowledge base and potential applications is how to analyze high-dimensional datasets of genetic, nutrient, metabolomic (clinical), and other variables influencing health and disease processes. Type 2 diabetes mellitus (T2DM) is used as an illustration of the challenges in studying complex phenotypes with nutrigenomics concepts and approaches.
doi:10.1016/j.mrfmmm.2007.02.033
PMCID: PMC1994901  PMID: 17559889
10.  Diet and disease: exploring the link through nutrigenomics. 
he success of the Human Genome Project and the powerful tools of molecular biology have ushered in a new era of medicine and nutrition. An emerging discipline, known as nutrigenomics, which allows the relationship between diet, genetics and disease to be delineated, looks set to transform clinical pet nutrition. In this article, Professor John Innes, from the University of Liverpool, evaluates the implications of nutrigenomics on pet health and takes a closer look at how this exciting technology is already being used to alleviate some of the symptoms of canine osteoarthritis (OA).
PMCID: PMC2828390  PMID: 16536232
11.  The challenges for molecular nutrition research 3: comparative nutrigenomics research as a basis for entering the systems level 
Genes & Nutrition  2008;3(3-4):101-106.
Human nutrition and metabolism may serve as the paradigm for the complex interplay of the genome with its environment. The concept of nutrigenomics now enables science with new tools and comprehensive analytical techniques to investigate this interaction at all levels of the complexity of the organism. Moreover, nutrigenomics seeks to better define the homeostatic control mechanisms, identify the de-regulation in the early phases of diet-related diseases, and attempts to assess to what extent an individual‘s sensitizing genotype contributes to the overall health or disease state. In a comparative approach nutrigenomics uses biological systems of increasing complexity from yeast to mammalian models to define the general rules of metabolic and genetic mechanisms in adaptations to the nutritional environment. Powerful information technology, bioinformatics and knowledge management tools as well as new mathematical and computational approaches now make it possible to study these molecular mechanisms at the cellular, organ and whole organism level and take it on to modeling the processes in a “systems biology” approach. This review summarizes some of the concepts of a comparative approach to nutrigenomics research, identifies current lacks and proposes a concerted scientific effort to create the basis for nutritional systems biology.
doi:10.1007/s12263-008-0089-y
PMCID: PMC2593016  PMID: 18830658
Functional genomics; Comparative genetics; Systems approaches
12.  Connecting the Human Variome Project to nutrigenomics 
Genes & Nutrition  2010;5(4):275-283.
Nutrigenomics is the science of analyzing and understanding gene–nutrient interactions, which because of the genetic heterogeneity, varying degrees of interaction among gene products, and the environmental diversity is a complex science. Although much knowledge of human diversity has been accumulated, estimates suggest that ~90% of genetic variation has not yet been characterized. Identification of the DNA sequence variants that contribute to nutrition-related disease risk is essential for developing a better understanding of the complex causes of disease in humans, including nutrition-related disease. The Human Variome Project (HVP; http://www.humanvariomeproject.org/) is an international effort to systematically identify genes, their mutations, and their variants associated with phenotypic variability and indications of human disease or phenotype. Since nutrigenomic research uses genetic information in the design and analysis of experiments, the HVP is an essential collaborator for ongoing studies of gene–nutrient interactions. With the advent of next generation sequencing methodologies and the understanding of the undiscovered variation in human genomes, the nutrigenomic community will be generating novel sequence data and results. The guidelines and practices of the HVP can guide and harmonize these efforts.
doi:10.1007/s12263-010-0186-6
PMCID: PMC2989367
Nutrigenomics; Human Variome Project; Harmonization
13.  The Extended Nutrigenomics – Understanding the Interplay between the Genomes of Food, Gut Microbes, and Human Host 
Comprehensive investigation of nutritional health effects at the molecular level requires the understanding of the interplay between three genomes, the food, the gut microbial, and the human host genome. Food genomes are researched for discovery and exploitation of macro- and micronutrients as well as specific bioactives, with those genes coding for bioactive proteins and peptides being of central interest. The human gut microbiota encompasses a complex ecosystem in the intestine with profound impact on host metabolism. It is being studied at genomic and, more recently, also at proteomic and metabonomic level. Humans are being characterized at the level of genetic pre-disposition and inter-individual variability in terms of (i) response to nutritional interventions and direction of health trajectories; (ii) epigenetic, metabolic programming at certain life stages with health consequences later in life and even for subsequent generations; and (iii) acute genomic expression as a holistic response to diet, monitored at gene transcript, protein and metabolite level. Modern nutrition science explores health-related aspects of bioactive food components, thereby promoting health, preventing, or delaying the onset of disease, optimizing performance and assessing benefits and risks in individuals and subpopulations. Personalized nutrition means adapting food to individual needs, depending on the human host’s life stage, -style, and -situation. Traditionally, nutrigenomics and nutri(epi)genetics are seen as the key sciences to understand human variability in preferences and requirements for diet as well as responses to nutrition. This article puts the three nutrition and health-relevant genomes into perspective, namely the food, the gut microbial and the human host’s genome, and calls for an “extended nutrigenomics” approach in order to build the future tools for personalized nutrition, health maintenance, and disease prevention. We discuss examples of these genomes, proteomes, transcriptomes, and metabolomes under the definition of genomics as the overarching term covering essentially all Omics rather than the sole study of DNA and RNA.
doi:10.3389/fgene.2011.00021
PMCID: PMC3268576  PMID: 22303317
nutrigenomics; nutrigenetics; epigenetics; personalized nutrition; biomarker; bioactive; gut microbiota
14.  Harnessing Nutrigenomics: Development of web-based communication, databases, resources, and tools 
Genes & Nutrition  2006;1(1):5-11.
Nutrient — gene interactions are responsible for maintaining health and preventing or delaying disease. Unbalanced diets for a given genotype lead to chronic diseases such as obesity, diabetes, cardiovascular, and are likely to contribute to increased severity and/or early-onset of many age-related diseases. Many nutrition and many genetic studies still fail to properly include both variables in the design, execution, and analyses of human, laboratory animal, or cell culture experiments. The complexity ofnutrient-gene interactions has led to the realization that strategic international alliances are needed to improve the completeness of nutrigenomic studies — a task beyond the capabilities of a single laboratory team. Eighty-eight researchers from 22 countries recently outlined the issues and challenges for harnessing the nutritional genomics for public and personal health. The next step in the process of forming productive international alliances is the development of a virtual center for organizing collaborations and communications that foster resources sharing, best practices improvements, and creation of databases. We describe here plans and initial efforts of creating the Nutrigenomics Information Portal, a web-based resource for the international nutrigenomics society. This portal aims at becoming the prime source ofinformation and interaction for nutrigenomics scientists through a collaborative effort.
doi:10.1007/BF02829931
PMCID: PMC3454813  PMID: 18850216
Best practices; Information portal; International alliances; Nutrigenomics
15.  Nutrigenomics: a case for the common soil between cardiovascular disease and cancer 
Genes & Nutrition  2008;3(1):19-24.
The border between health and disease is often set by a complex equilibrium between two elements, genetics on one hand, lifestyle on the other, To know it better, means to give new weapons, often crucial, in the hands of the doctors and their patients. It also means to adjust therapies, to find out which drug is good for a patient and which prevention strategy will work better for him/her. Nutrigenomics is an approach to individualize or personalize food and nutrition, and ultimately health, by tailoring the food to the individual genotype. In this review, we present the interaction between certain genetic polymorphisms and diet and increased cardiovascular or cancer risk. It is, indeed, now clear that a large number of bioactive food components may provide risk or protection at several stages of both atherosclerosis and cancer formation processes. We are giving here few examples of gene-food interactions relevant for both the risk of cardiovascular disease and cancer, since a common soil could exist in the genesis of cardiovascular disease and of some types of cancer (mainly gastrointestinal tract and hormone-dependent).
doi:10.1007/s12263-008-0079-0
PMCID: PMC2311494  PMID: 18850195
Nutrigenomics; Cardiovascular disease; Cancer; Polyunsaturated fatty acids
16.  Evolutionary conservation of metabolism explains howDrosophila nutrigenomics can help us understand human nutrigenomics 
Genes & Nutrition  2006;1(2):75-83.
While large populations in the third world are enduring famine, much of the developed world is undergoing an obesity epidemic. In addition to reflecting an unbalanced distribution of food, the “epidemic of overabundance” is ironically leading to a decrease in the health and longevity of the obese and improperly nourished in the first world. International consortia, such as the European Nutrigenomics Organization (NuGO), are increasing our knowledge of nutrientgene interactions and the effects of diet and obesity on human health. In this review, we summarize both previous and ongoing nutrigenomics studies in Drosophila and we explain how these studies can be used to provide insights into molecular mechanisms underlying nutrigenomics in humans. We will discuss how quantitative trait locus (QTL) experiments have identified genes that affect triglyceride levels in Drosophila, and how microarray analyses show that hundreds of genes have altered gene expression under different dietary conditions. Finally, we will discuss ongoing combined microarray-QTL studies, termed “genetical genomics,” that promise to identify “master modulatory loci” that regulate global responses of potentially hundreds of genes under different dietary conditions. When “master modulatory loci” are identified in Drosophila, then experiments in mammalian models can be used to determine the relevance of these genes to human nutrition and health.
doi:10.1007/BF02829949
PMCID: PMC3454681  PMID: 18850201
Drosophila; Genetical Genomics; Metabolism; Nutrigenomics
17.  Owner controlled data exchange in nutrigenomic collaborations: the NuGO information network 
Genes & Nutrition  2009;4(2):113-122.
New ‘omics’ technologies are changing nutritional sciences research. They enable to tackle increasingly complex questions but also increase the need for collaboration between research groups. An important challenge for successful collaboration is the management and structured exchange of information that accompanies data-intense technologies. NuGO, the European Nutrigenomics Organization, the major collaborating network in molecular nutritional sciences, is supporting the application of modern information technologies in this area. We have developed and implemented a concept for data management and computing infrastructure that supports collaboration between nutrigenomics researchers. The system fills the gap between “private” storing with occasional file sharing by email and the use of centralized databases. It provides flexible tools to share data, also during experiments, while preserving ownership. The NuGO Information Network is a decentral, distributed system for data exchange based on standard web technology. Secure access to data, maintained by the individual researcher, is enabled by web services based on the the BioMoby framework. A central directory provides information about available web services. The flexibility of the infrastructure allows a wide variety of services for data processing and integration by combining several web services, including public services. Therefore, this integrated information system is suited for other research collaborations.
doi:10.1007/s12263-009-0123-8
PMCID: PMC2690731  PMID: 19408032
Nutrigenomics; Data management; Data integration; Distributed information system; Web services
18.  Celiac Disease, Inflammation and Oxidative Damage: A Nutrigenetic Approach 
Nutrients  2012;4(4):243-257.
Celiac disease (CD), a common heritable chronic inflammatory condition of the small intestine caused by permanent intolerance to gluten/gliadin (prolamin), is characterized by a complex interplay between genetic and environmental factors. Developments in proteomics have provided an important contribution to the understanding of the biochemical and immunological aspects of the disease and the mechanisms involved in toxicity of prolamins. It has been demonstrated that some gliadin peptides resistant to complete proteolytic digestion may directly affect intestinal cell structure and functions by modulating gene expression and oxidative stress. In recent years, the creation of the two research fields Nutrigenomics and Nutrigenetics, has enabled the elucidation of some interactions between diet, nutrients and genes. Various dietary components including long chain ω-3 fatty acids, plant flavonoids, and carotenoids have been demonstrated to modulate oxidative stress, gene expression and production of inflammatory mediators. Therefore their adoption could preserve intestinal barrier integrity, play a protective role against toxicity of gliadin peptides and have a role in nutritional therapy of celiac disease.
doi:10.3390/nu4040243
PMCID: PMC3347005  PMID: 22606367
celiac disease; gliadin peptides; nutrigenetic; nutrigenomic; proteomic; fitonutrients; oxidative stress; inflammation
19.  Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis 
BMC Genomics  2009;10:596.
Background
The application of high-throughput genomic tools in nutrition research is a widespread practice. However, it is becoming increasingly clear that the outcome of individual expression studies is insufficient for the comprehensive understanding of such a complex field. Currently, the availability of the large amounts of expression data in public repositories has opened up new challenges on microarray data analyses. We have focused on PPARα, a ligand-activated transcription factor functioning as fatty acid sensor controlling the gene expression regulation of a large set of genes in various metabolic organs such as liver, small intestine or heart. The function of PPARα is strictly connected to the function of its target genes and, although many of these have already been identified, major elements of its physiological function remain to be uncovered. To further investigate the function of PPARα, we have applied a cross-species meta-analysis approach to integrate sixteen microarray datasets studying high fat diet and PPARα signal perturbations in different organisms.
Results
We identified 164 genes (MDEGs) that were differentially expressed in a constant way in response to a high fat diet or to perturbations in PPARs signalling. In particular, we found five genes in yeast which were highly conserved and homologous of PPARα targets in mammals, potential candidates to be used as models for the equivalent mammalian genes. Moreover, a screening of the MDEGs for all known transcription factor binding sites and the comparison with a human genome-wide screening of Peroxisome Proliferating Response Elements (PPRE), enabled us to identify, 20 new potential candidate genes that show, both binding site, both change in expression in the condition studied. Lastly, we found a non random localization of the differentially expressed genes in the genome.
Conclusion
The results presented are potentially of great interest to resume the currently available expression data, exploiting the power of in silico analysis filtered by evolutionary conservation. The analysis enabled us to indicate potential gene candidates that could fill in the gaps with regards to the signalling of PPARα and, moreover, the non-random localization of the differentially expressed genes in the genome, suggest that epigenetic mechanisms are of importance in the regulation of the transcription operated by PPARα.
doi:10.1186/1471-2164-10-596
PMCID: PMC2801700  PMID: 20003344
20.  Nutrigenomics and Cancer 
Cancer incidence is projected to increase in the future and an effectual preventive strategy is required to face this challenge. Alteration of dietary habits is potentially an effective approach for reducing cancer risk. Assessment of biological effects of a specific food or bioactive component that is linked to cancer and prediction of individual susceptibility as a function of nutrient-nutrient interactions and genetics is an essential element to evaluate the beneficiaries of dietary interventions. In general, the use of biomarkers to evaluate individuals susceptibilities to cancer must be easily accessible and reliable. However, the response of individuals to bioactive food components depends not only on the effective concentration of the bioactive food components, but also on the target tissues. This fact makes the response of individuals to food components vary from one individual to another. Nutrigenomics focuses on the understanding of interactions between genes and diet in an individual and how the response to bioactive food components is influenced by an individual's genes. Nutrients have shown to affect gene expression and to induce changes in DNA and protein molecules. Nutrigenomic approaches provide an opportunity to study how gene expression is regulated by nutrients and how nutrition affects gene variations and epigenetic events. Finding the components involved in interactions between genes and diet in an individual can potentially help identify target molecules important in preventing and/or reducing the symptoms of cancer.
PMCID: PMC3558114  PMID: 23407612
Bioactive food components; Biomarker; Cancer prevention; Nutrigenetics; Nutrigenomics
22.  Nutrigenomic Analysis of Diet-Gene Interactions on Functional Supplements for Weight Management 
Current Genomics  2008;9(4):239-251.
Recent advances in molecular biology combined with the wealth of information generated by the Human Genome Project have fostered the emergence of nutrigenomics, a new discipline in the field of nutritional research. Nutrigenomics may provide the strategies for the development of safe and effective dietary interventions against the obesity epidemic. According to the World Health Organization, more than 60% of the global disease burden will be attributed to chronic disorders associated with obesity by 2020. Meanwhile in the US, the prevalence of obesity has doubled in adults and tripled in children during the past three decades. In this regard, a number of natural dietary supplements and micronutrients have been studied for their potential in weight management. Among these supplements, (–)-hydroxycitric acid (HCA), a natural extract isolated from the dried fruit rind of Garcinia cambogia, and the micronutrient niacin-bound chromium(III) (NBC) have been shown to be safe and efficacious for weight loss. Utilizing cDNA microarrays, we demonstrated for the first time that HCA-supplementation altered the expression of genes involved in lipolytic and adipogenic pathways in adipocytes from obese women and up-regulated the expression of serotonin receptor gene in the abdominal fat of rats. Similarly, we showed that NBC-supplementation up-regulated the expression of myogenic genes while suppressed the expression of genes that are highly expressed in brown adipose tissue in diabetic obese mice. The potential biological mechanisms underlying the observed beneficial effects of these supplements as elucidated by the state-of-the-art nutrigenomic technologies will be systematically discussed in this review.
doi:10.2174/138920208784533638
PMCID: PMC2682937  PMID: 19452041
Insulin resistance; glucose tolerance factor; supplemental chromium; Garcinia cambogia; (-)-hydroxycitric acid; overweight; obesity; diabetes; cardiovascular disease; nutritional interventions; microarrays; nutrigenomics.
23.  Translational Regulation in Nutrigenomics12 
Advances in Nutrition  2011;2(6):511-519.
The emergence of genome-wide analysis to interrogate cellular DNA, RNA, and protein content has revolutionized the study of the control network that mediates cellular homeostasis. Nutrigenomics addresses the effect of nutrients on gene expression, which provides a basis for understanding the biological activity of dietary components. Translation of mRNAs represents the last step of genetic flow and primarily defines the proteome. Translational regulation is thus critical for gene expression, in particular, under nutrient excess or deficiency. Until recently, it was unclear how the global effects of translational control are influenced by nutrient signaling. An emerging concept of translational reprogramming addresses how to maintain the expression of specific proteins during pathophysiological conditions by translation of selective mRNAs. Here we describe recent advances in our understanding of translational control, nutrient signaling, and their dysregulation in aging and cancer. The mechanistic understanding of translational regulation in response to different nutrient conditions may help identify potential dietary and therapeutic targets to improve human health.
doi:10.3945/an.111.001057
PMCID: PMC3226388  PMID: 22332093
24.  A multifactorial analysis of obesity as CVD risk factor: Use of neural network based methods in a nutrigenetics context 
BMC Bioinformatics  2010;11:453.
Background
Obesity is a multifactorial trait, which comprises an independent risk factor for cardiovascular disease (CVD). The aim of the current work is to study the complex etiology beneath obesity and identify genetic variations and/or factors related to nutrition that contribute to its variability. To this end, a set of more than 2300 white subjects who participated in a nutrigenetics study was used. For each subject a total of 63 factors describing genetic variants related to CVD (24 in total), gender, and nutrition (38 in total), e.g. average daily intake in calories and cholesterol, were measured. Each subject was categorized according to body mass index (BMI) as normal (BMI ≤ 25) or overweight (BMI > 25). Two artificial neural network (ANN) based methods were designed and used towards the analysis of the available data. These corresponded to i) a multi-layer feed-forward ANN combined with a parameter decreasing method (PDM-ANN), and ii) a multi-layer feed-forward ANN trained by a hybrid method (GA-ANN) which combines genetic algorithms and the popular back-propagation training algorithm.
Results
PDM-ANN and GA-ANN were comparatively assessed in terms of their ability to identify the most important factors among the initial 63 variables describing genetic variations, nutrition and gender, able to classify a subject into one of the BMI related classes: normal and overweight. The methods were designed and evaluated using appropriate training and testing sets provided by 3-fold Cross Validation (3-CV) resampling. Classification accuracy, sensitivity, specificity and area under receiver operating characteristics curve were utilized to evaluate the resulted predictive ANN models. The most parsimonious set of factors was obtained by the GA-ANN method and included gender, six genetic variations and 18 nutrition-related variables. The corresponding predictive model was characterized by a mean accuracy equal of 61.46% in the 3-CV testing sets.
Conclusions
The ANN based methods revealed factors that interactively contribute to obesity trait and provided predictive models with a promising generalization ability. In general, results showed that ANNs and their hybrids can provide useful tools for the study of complex traits in the context of nutrigenetics.
doi:10.1186/1471-2105-11-453
PMCID: PMC2941694  PMID: 20825661
25.  Neurogenetic Impairments of Brain Reward Circuitry Links to Reward Deficiency Syndrome (RDS): Potential Nutrigenomic Induced Dopaminergic Activation 
Work from our laboratory in both in-patient and outpatient facilities utilizing the Comprehensive Analysis of Reported Drugs (CARD)™ found a significant lack of compliance to prescribed treatment medications and a lack of abstinence from drugs of abuse during active recovery. This unpublished, ongoing research provides an impetus to develop accurate genetic diagnosis and holistic approaches that will safely activate brain reward circuitry in the mesolimbic dopamine system. This editorial focuses on the neurogenetics of brain reward systems with particular reference to genes related to dopaminergic function. The terminology “Reward Deficiency Syndrome” (RDS), used to describe behaviors found to have an association with gene-based hypodopaminergic function, is a useful concept to help expand our understanding of Substance Use Disorder (SUD), process addictions, and other obsessive, compulsive and impulsive behaviors. This editorial covers the neurological basis of pleasure and the role of natural and unnatural reward in motivating and reinforcing behaviors. Additionally, it briefly describes the concept of natural dopamine D2 receptor agonist therapy coupled with genetic testing of a panel of reward genes, the Genetic Addiction Risk Score (GARS). It serves as a spring-board for this combination of novel approaches to the prevention and treatment of RDS that was developed from fundamental genomic research. We encourage further required studies.
doi:10.4172/2157-7412.1000e115
PMCID: PMC3525955  PMID: 23264886

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