Nutrigenomics: From Molecular Nutrition to Prevention of Disease

Buckwheat OMICS: present status and future prospects

Buckwheat (Fagopyrum spp.) is an underutilized resilient crop of North Western Himalayas belonging to the family Polygonaceae and is a source of essential nutrients and therapeutics. Common Buckwheat and Tatary Buckwheat are the two main cultivated species used as food. It is the only grain crop possessing rutin, an important metabolite with high nutraceutical potential. Due to its inherent tolerance to various biotic and abiotic stresses and a short life cycle, Buckwheat has been proposed as a model crop plant. Nutritional security is one of the major concerns, breeding for a nutrient-dense crop such as Buckwheat will provide a sustainable solution. Efforts toward improving Buckwheat for nutrition and yield are limited due to the lack of available: genetic resources, genomics, transcriptomics and metabolomics. In order to harness the agricultural importance of Buckwheat, an integrated breeding and OMICS platforms needs to be established that can pave the way for a better understanding of crop biology and developing commercial varieties. This, coupled with the availability of the genome sequences of both Buckwheat species in the public domain, should facilitate the identification of alleles/QTLs and candidate genes. There is a need to further our understanding of the molecular basis of the genetic regulation that controls various economically important traits. The present review focuses on: the food and nutritional importance of Buckwheat, its various omics resources, utilization of omics approaches in understanding Buckwheat biology and, finally, how an integrated platform of breeding and omics will help in developing commercially high yielding nutrient rich cultivars in Buckwheat.

Integrating (Nutri-)Metabolomics into the One Health Tendency-The Key for Personalized Medicine Advancement

Metabolomics is an advanced technology, still under development, with multiple research applications, especially in the field of health. Individual metabolic profiles, the functionality of the body, as well as its interaction with the environment, can be established using this technology. The body's response to various external factors, including the food consumed and the nutrients it contains, has increased researchers' interest in nutrimetabolomics. Establishing correlations between diet and the occurrence of various diseases, or even the development of personalized nutrition plans, could contribute to advances in precision medicine. The interdependence between humans, animals, and the environment is of particular importance today, with the dramatic emergence and spread of zoonotic diseases, food, water and soil contamination, and the degradation of resources and habitats. All these events have led to an increase in risk factors for functional diseases, burdening global health. Thus, this study aimed to highlight the importance of metabolomics, and, in particular, nutrimetabolomics, as a technical solution for a holistic, collaborative, and precise approach for the advancement of the One Health strategy.

The Advent of Nutrigenomics: A Narrative Review with an Emphasis on Psychological Disorders

A new research field is emerging that combines nutrition and genetics at the molecular level, namely nutrigenomics. Several aspects of nutrigenomics are examined in this review, with a particular focus on psychological disorders. The origin of this field in the 20th century and its modern developments have been investigated. Various studies have reported the impact of genetic factors and diet on various chronic disorders, elucidating how the deficiency of several macronutrients results in significant ailments, including diabetes, cancer, cardiovascular disorders, and others. Furthermore, the application of nutrigenomics to diet and its impact on the global disease rate and quality of life have been discussed. The relationship between diet and gene expression can facilitate the classification of diet-gene interactions and the diagnosis of polymorphisms and anomalies. Numerous databases and research tools for the study of nutrigenomics are essential to the medical application of this field. The nutrition-gene interrelationships can be utilized to study brain development, impairment, and diseases, which could be a significant medical breakthrough. It has also been observed that psychological conditions are exacerbated by the interaction between gut microbes and the prevalence of malnutrition. This article focuses on the impact of nutrition on genes involved in various psychological disorders and the potential application of nutrigenomics as a revolutionary treatment method.

Utilizing the underutilized plant resources for development of life style foods: Putting nutrigenomics to use

Sufficient amount of minerals, vitamins, and proteins in human diet play indispensable role in maintaining the active metabolism for better human health. All the essential nutrients that are requisite for an individual's survival are acquired from plants as well as animals. Micronutrients and macronutrients directly influence the metabolic pathways and their deficiencies play a substantial role in development of manifold disorders. In addition to environmental factors, quality and quantity of foods are key factors in maintaining the human health. Transition from healthy to diseased state is concurrent with the pattern of gene expression that is largely influenced by nutrition and environment. A combined approach to study the influence of nutrition on expression of numerous genes can be well explored through nutrigenomic studies. Nutrigenomics includes studies wherein applied genomics is used to investigate nutritional science to understand the compartmentalization of genes that influence the cause of diet-related complications. This review describes the role of underutilized crops as frontline foods to circumvent the health complications through the nutrigenomic studies. Further dynamics of nutrigenomic tools to study the impact of nutrition on the changing pattern of genome stability and gene expression for developing precise safety measures against wide range of health ailments linked to metabolic networks. Additionally, this review provides detailed information on nutrigenomic studies undertaken to unravel the potential of underutilized crops to augment the human health and to carry the agronomic/genomic approaches to enhance nutritional profile of underutilized crops to overcome diet-related disorders.

Replacing Saturated Fat with Polyunsaturated Fat Modulates Peripheral Blood Mononuclear Cell Gene Expression and Pathways Related to Cardiovascular Disease Risk Using a Whole Transcriptome Approach

SCOPE

The aim of this study is to explore the molecular mechanisms underlying the effect of replacing dietary saturated fat (SFA) with polyunsaturated fat (PUFA) on cardiovascular disease (CVD) risk using a whole transcriptome approach.

METHODS AND RESULTS

Healthy subjects with moderate hypercholesterolemia (n = 115) are randomly assigned to a control diet (C-diet) group or an experimental diet (Ex-diet) group receiving comparable food items with different fatty acid composition for 8 weeks. RNA isolated from peripheral blood mononuclear cells (PBMCs) at baseline and after 8 weeks of intervention is analyzed by microarray technology (n = 95). By use of a linear regression model (n = 92), 14 gene transcripts are differentially altered in the Ex-diet group compared to the C-diet group. These include transcripts related to vascular smooth muscle cell proliferation, low-density lipoprotein receptor folding, and regulation of blood pressure. Furthermore, pathways mainly related to immune response and inflammation, signal transduction, development, and cytoskeleton remodeling, gene expression and protein function, are differentially enriched between the groups.

CONCLUSION

Replacing dietary SFA with PUFA for 8 weeks modulates PBMC gene expression and pathways related to CVD risk in healthy subjects with moderate hypercholesterolemia.

Influence of the Bioactive Diet Components on the Gene Expression Regulation

Diet bioactive components, in the concept of nutrigenetics and nutrigenomics, consist of food constituents, which can transfer information from the external environment and influence gene expression in the cell and thus the function of the whole organism. It is crucial to regard food not only as the source of energy and basic nutriments, crucial for living and organism development, but also as the factor influencing health/disease, biochemical mechanisms, and activation of biochemical pathways. Bioactive components of the diet regulate gene expression through changes in the chromatin structure (including DNA methylation and histone modification), non-coding RNA, activation of transcription factors by signalling cascades, or direct ligand binding to the nuclear receptors. Analysis of interactions between diet components and human genome structure and gene activity is a modern approach that will help to better understand these relations and will allow designing dietary guidances, which can help maintain good health.

Immunometabolism, Micronutrients, and Bariatric Surgery: The Use of Transcriptomics and Microbiota-Targeted Therapies

BACKGROUND

Obesity is associated with the gut microbiota and decreased micronutrient status. Bariatric surgery is a recommended therapy for obesity. It can positively affect the composition of the gut bacteria but also disrupt absorption of nutrients. Low levels of micronutrients can affect metabolic processes, like glycolysis, TCA cycle, and oxidative phosphorylation, that are associated with the immune system also known as immunometabolism.

METHODS

MEDLINE, PUBMED, and Google Scholar were searched. Articles involving gut microbiome, micronutrient deficiency, gut-targeted therapies, transcriptome analysis, micronutrient supplementation, and bariatric surgery were included.

RESULTS

Studies show that micronutrients play a pivotal role in the intestinal immune system and regulating immunometabolism. Research demonstrates that gut-targeting therapies may improve the microbiome health for bariatric surgery populations. There is limited research that examines the role of micronutrients in modulating the gut microbiota among the bariatric surgery population.

CONCLUSIONS

Investigations are needed to understand the influence that micronutrient deficiencies have on the gut, particularly immunometabolism. Nutritional transcriptomics shows great potential in providing this type of analysis to develop gut-modulating therapies as well as more personalized nutrition recommendations for bariatric surgery patients.

Expression Changes in Epigenetic Gene Pathways Associated With One-Carbon Nutritional Metabolites in Maternal Blood From Pregnancies Resulting in Autism and Non-Typical Neurodevelopment

The prenatal period is a critical window for the development of autism spectrum disorder (ASD). The relationship between prenatal nutrients and gestational gene expression in mothers of children later diagnosed with ASD or non-typical development (Non-TD) is poorly understood. Maternal blood collected prospectively during pregnancy provides insights into the effects of nutrition, particularly one-carbon metabolites, on gene pathways and neurodevelopment. Genome-wide transcriptomes were measured with microarrays in 300 maternal blood samples in Markers of Autism Risk in Babies-Learning Early Signs. Sixteen different one-carbon metabolites, including folic acid, betaine, 5'-methyltretrahydrofolate (5-MeTHF), and dimethylglycine (DMG) were measured. Differential expression analysis and weighted gene correlation network analysis (WGCNA) were used to compare gene expression between children later diagnosed as typical development (TD), Non-TD and ASD, and to one-carbon metabolites. Using differential gene expression analysis, six transcripts (TGR-AS1, SQSTM1, HLA-C, and RFESD) were associated with child outcomes (ASD, Non-TD, and TD) with genome-wide significance. Genes nominally differentially expressed between ASD and TD significantly overlapped with seven high confidence ASD genes. WGCNA identified co-expressed gene modules significantly correlated with 5-MeTHF, folic acid, DMG, and betaine. A module enriched in DNA methylation functions showed a suggestive protective association with folic acid/5-MeTHF concentrations and ASD risk. Maternal plasma betaine and DMG concentrations were associated with a block of co-expressed genes enriched for adaptive immune, histone modification, and RNA processing functions. These results suggest that the prenatal maternal blood transcriptome is a sensitive indicator of gestational one-carbon metabolite status and changes relevant to children's later neurodevelopmental outcomes. LAY SUMMARY: Pregnancy is a time when maternal nutrition could interact with genetic risk for autism spectrum disorder. Blood samples collected during pregnancy from mothers who had a prior child with autism were examined for gene expression and nutrient metabolites, then compared to the diagnosis of the child at age three. Expression differences in gene pathways related to the immune system and gene regulation were observed for pregnancies of children with autism and non-typical neurodevelopment and were associated with maternal nutrients.

Impacts and Echoes: The Lasting Influence of the White House Conference on Food, Nutrition, and Health

The 1969 White House Conference on Food, Nutrition, and Health had a significant influence on the direction of food and nutrition policy in the United States. The conference produced recommendations leading to federal legislation and programs to alleviate hunger and malnutrition, improve consumers' nutrition knowledge through education and labeling, and monitor the nutritional status of the population. Fifty years later, its legacy was revisited at a conference convened by Harvard University and Tufts University. This article reviews the literature contributing to the first author's keynote speech at the conference, its influencers, and its influences. We focus on the highlights of five domains that set the stage for the conference: the social environment, the food environment, nutrition science, public health data, and policy events. We briefly describe the conference, its proposed directions, and its lasting legacy in these five domains.

Increased protein intake affects pro-opiomelanocortin (POMC) processing, immune function and IGF signaling in peripheral blood mononuclear cells of home-dwelling old subjects using a genome-wide gene expression approach

Background

Adequate protein intake among older adults is associated with better health outcomes such as immune function and metabolic regulation of skeletal muscle, but conflicting results make it difficult to define the optimal intake. To further understand the impact of protein intake on metabolic processes, the aim of the study was to explore genome-wide gene expression changes in peripheral blood mononuclear cells (PBMCs) in home-dwelling old subjects after increased protein intake for 12 weeks.

Method

In a parallel double-blind randomized controlled intervention study, subjects (≥ 70 years) received a protein-enriched milk (2 × 20 g protein/day, n = 14, mean (±SD) age 76.9 ± 4.9 years) or an isocaloric carbohydrate drink (n = 17, mean (±SD) age 77.7 ± 4.8 years) for breakfast and evening meal for 12 weeks. PBMCs were isolated before and after the intervention. Microarray analysis was performed using Illumina technology. Serum levels of gut peptides and insulin growth factor (IGF)-1 were also measured.

Results

In total 758 gene transcripts were regulated after increased protein intake, and 649 gene transcripts were regulated after intake of carbohydrates (p < 0.05). Forty-two of these genes were overlapping. After adjusting for multiple testing, 27 of the 758 gene transcripts were regulated (FDR, q-value < 0.25) after protein intake. Of these 25 were upregulated and two downregulated. In particular, genes and signaling pathways involved in pro-opiomelanocortin (POMC) processing, immune function, and IGF signaling were significantly altered.

Conclusions

PBMCs can be used to study gene expression changes after long-term protein intake, as many signaling pathways were regulated after increased protein intake. The functional significance of these findings needs to be further investigated.

Trial registration

ClinicalTrials.gov, ID no. NCT02218333. The study was registered on August 18, 2014.

Healthy Nordic Diet Modulates the Expression of Genes Related to Mitochondrial Function and Immune Response in Peripheral Blood Mononuclear Cells from Subjects with Metabolic Syndrome-A SYSDIET Sub-Study

SCOPE

To explore the effect of a healthy Nordic diet on the global transcriptome profile in peripheral blood mononuclear cells (PBMCs) of subjects with metabolic syndrome.

METHODS AND RESULTS

Subjects with metabolic syndrome undergo a 18/24 week randomized intervention study comparing an isocaloric healthy Nordic diet with an average habitual Nordic diet served as control (SYSDIET study). Altogether, 68 participants are included. PBMCs are obtained before and after intervention and total RNA is subjected to global transcriptome analysis. 1302 probe sets are differentially expressed between the diet groups (p-value < 0.05). Twenty-five of these are significantly regulated (FDR q-value < 0.25) and are mainly involved in mitochondrial function, cell growth, and cell adhesion. The list of 1302 regulated probe sets is subjected to functional analyses. Pathways and processes involved in the mitochondrial electron transport chain, immune response, and cell cycle are downregulated in the healthy Nordic diet group. In addition, gene transcripts with common motifs for 42 transcription factors, including NFR1, NFR2, and NF-κB, are downregulated in the healthy Nordic diet group.

CONCLUSION

These results suggest that benefits of a healthy diet may be mediated by improved mitochondrial function and reduced inflammation.

Vitamin D supplementation alters the expression of genes associated with hypertension and did not induce DNA damage in rats

Vitamin D3 deficiency has been correlated with altered expression of genes associated with increased blood pressure (BP); however, the role of vitamin D3 supplementation in the genetic mechanisms underlying hypertension remains unclear. Thus, the aim of this study was investigate the consequences of vitamin D3 supplemented (10,000 IU/kg) or deficient (0 IU/kg) diets on regulation of expression of genes related to hypertension pathways in heart cells of spontaneously hypertensive rats (SHR) and normotensive Wistar Kyoto (WKY) controls. An additional aim was to assess the impact of vitamin D3 on DNA damage and oxidative stress markers. The gene expression profiles were determined by PCR array, DNA damage was assessed by an alkaline comet assay, and oxidative stress markers by measurement of thiobarbituric acid reactive substances (TBARS) and glutathione (GSH) levels. In SHR rats data showed that the groups of genes most differentially affected by supplemented and deficient diets were involved in BP regulation and renin-angiotensin system. In normotensive WKY controls, the profile of gene expression was similar between the two diets. SHR rats were more sensitive to changes in gene expression induced by dietary vitamin D3 than normotensive WKY animals. In addition to gene expression profile, vitamin D3 supplemented diet did not markedly affect DNA or levels of TBARS and GSH levels in both experimental groups. Vitamin D3 deficient diet produced lipid peroxidation in SHR rats. The results of this study contribute to a better understanding of the role of vitamin D3 in the genetic mechanisms underlying hypertension. Abbreviations: AIN, American Institute of Nutrition; EDTA, disodium ethylenediaminetetraacetic acid; GSH, glutathione; PBS, phosphate buffer solution; SHR, spontaneously hypertensive rats; TBARS, thiobarbituric acid reactive substances; WKY, Wistar Kyoto.

Employing proteomics to understand the effects of nutritional intervention in cancer treatment

Lifestyle optimizations are implementable changes that can have an impact on health and disease. Nutrition is a lifestyle optimization that has been shown to be of great importance in cancer initiation, progression, and metastasis. Dozens of clinical trials are currently in progress that focus on the nutritional modifications that cancer patients can make prior to and during medical care that increase the efficacy of treatment. In this review, we discuss various nutritional inventions for cancer patients and the analytical approaches to characterize the downstream molecular effects. We first begin by briefly explaining the many different forms of nutritional intervention currently being used in cancer treatment as well as their motivating biology. The forms of nutrient modulation described in this review include calorie restriction, the different practices of fasting, and carbohydrate restriction. The review then shifts to explain how proteomics is used to determine biomarkers of cancer and how it can be utilized in the future to determine the metabolic phenotype of a tumor, and inform physicians if nutritional intervention should be recommended for a cancer patient. Nutrigenomics aims to understand the relationship of nutrients and gene expression and can be used to understand the downstream molecular effects of nutrition restriction, partially through proteomic analysis. Proteomics is just beginning to be used as cancer diagnostic and predictive tools. However, these approaches have not been used to their full potential to understand nutritional intervention in cancer. Graphical abstract ᅟ.

Next-Gen Therapeutics for Skin Cancer: Nutraceuticals

Growing modernization and lifestyle changes with limited physical activity have impacted diet and health, leading to an increased cancer mortality rate worldwide. As a result, there is a greater need than before to develop safe and novel anticancer drugs. Current treatment options such as chemotherapy, radiotherapy and surgery, induce unintended side effects, compromising patient's quality of life, and physical well-being. Therefore, there has been an increased global interest in the use of dietary supplements and traditional herbal medicines for treatment of cancer. Recently, nutraceuticals or "natural" substances isolated from food have attracted considerable attention in the cancer field. Emerging research suggests that nutraceuticals may indeed prevent and protect against cancer. The intent of this article is to review some of the current spice-derived nutraceuticals in the treatment of melanoma and skin cancer.

Weighted Gene Co-Expression Network Analysis Identifies Gender Specific Modules and Hub Genes Related to Metabolism and Inflammation in Response to an Acute Lipid Challenge

SCOPE

Inflammation is characteristic of diet-related diseases including obesity and type 2 diabetes (T2D). However, biomarkers of inflammation that reflect the early stage metabolic derangements are not optimally sensitive. Lipid challenges elicit postprandial inflammatory and metabolic responses. Gender-specific transcriptomic networks of the peripheral blood mononuclear cell (PBMC) were constructed in response to a lipid challenge.

METHODS AND RESULTS

Eighty-six adult males and females of comparable age, anthropometric, and biochemical profiles completed an oral lipid tolerance test (OLTT). PBMC transcriptome was profiled following OLTT. Weighted gene coexpression networks were constructed separately for males and females. Functional ontology analysis of network modules was performed and hub genes identified. Two modules of interest were identified in females-an "inflammatory" module and an "energy metabolism" module. NLRP3, which plays a central role in inflammation and STARD3 that is involved in cholesterol metabolism, were identified as hub genes for the respective modules.

CONCLUSION

The OLTT induced some gender-specific correlations of gene coexpression network modules. In females, biological processes relating to energy metabolism and inflammation pathways were evident. This suggests a gender specific link between inflammation and energy metabolism in response to lipids. In contrast, G-protein coupled receptor protein signaling pathway was common to both genders.

Transcriptomic signature of high dietary organic selenium supplementation in sheep: A nutrigenomic insight using a custom microarray platform and gene set enrichment analysis

The objective of this study was to investigate the effect of a high dietary Se supplementation on the whole transcriptome of sheep. A custom sheep whole-transcriptome microarray, with more than 23,000 unique transcripts, was designed and then used to profile the global gene expression of sheep after feeding a high dietary supplementation of organic Se. Lactating crossbred ewes ( = 10; 3 to 4 yr of age and 55 to 65 kg BW) at late lactation (100 ± 8 d in milk) were acclimated to indoor individual pen feeding of a basal control diet (0.40 mg Se/d, sodium selenite) for 4 wk. Sheep were then kept on a diet with an extra (high) supplementation of organic Se (1.45 mg Se/d as Sel-Plex; Alltech Biotechnology Pty Ltd, Dandenong, Victoria, Australia) for 40 d. Whole blood was collected at 2 time points (last day of the acclimatization period [T0] and after 40 d of the organic Se supplementation [T40]), and then total RNA was isolated and labeled for the subsequent microarray analysis. Significance Analysis of Microarrays, using the -statistic, of the microarray data (T40 versus T0) evidenced the up- and downregulation of 942 and 244 transcripts (false discovery rate < 0.05), respectively. Seven genes showed the same trend of expression (up- or downregulation) when tested by quantitative real-time PCR (qPCR) in a cross-validation step. The microarray showed significant upregulation of the following selenoproteins at T40: selenium binding protein 1 (SELENBP1), selenoprotein W1 (SEPW1), glutathione peroxidase 3 (GPX3), and septin 8 (SEPT8). And the expression trends for SEPW1 and SEPT8 were validated using qPCR. Functional annotation of the differentially expressed genes showed the enrichment of several immune system-related biological processes (lymphocyte activation, cytokine binding, leukocyte activation, T cell differentiation, and B cell activation) and pathways (cytokine and interleukin signaling). Moreover, Gene Set Enrichment Analysis evidenced the enrichment of B and T cell receptors signaling pathways, with an enrichment score of 0.63 and 0.59, respectively. Overall, from a global gene expression (whole-transcriptome) point of view, short-term supplementation of a high dietary organic Se to Se-nondeficient sheep results in a transcriptomic signature that mainly reflects an induced immune system and a modulation of transcription effect. Also, the present study provides a custom whole-transcriptome microarray platform that can be used in further global gene expression studies in the ovine species.

The scientific production of Nutrition published by the Scientific Electronic Library under the gaze of the evaluation of the Coordination for the Development of Higher Education Personnel

ABSTRACT Objective: Perform analysis of the scientific production of Nutrition published by the Scientific Electronic Library under the gaze of the evaluation of Coordenação de Aperfeiçoamento de Pessoal de Nível Superior. Methods: Systematic search was performed in the 286 current title journals, using the "article search" path, the "subject index" window and the "Nutrition" indexer. The articles and periodicals selected were analyzed in order to answer the following questions: Which journals from Scientific Electronic Library publish articles on Nutrition? Do these journals have an impact factor as measured by the Journal Citation Reports? Which are? What is the classification of these journals by the areas of evaluation of Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, specifically by the area of Nutrition? Results: We analyzed 779 articles published in 85 journals. The majority of articles (n=698; 89.6%) were related to the area of Health Sciences. The five journals with higher volumes of articles were: Brazilian Journal of Nutrition, Reports in Public Health, Public Health Journal, Science & Public Health and Journal of Pediatrics. Most (62.4%) does not have Journal Citation Reports. The Nutrition area not rated any journal in strata A1 and A2, classifying them from B1 to B4. For eight areas analyzed their specific journals were induced to the upper strata of Qualis (A1, A2 and B1). Conclusion: The analyzed journals are the main vehicles of circulation of scientific paradigms of national scientific communities. Considering the correlation of forces between the vehicles of circulation of scientific knowledge in the international context, stimuli for valorization and qualification of these journals are essential.

Role of Macronutrients and Micronutrients in DNA Damage: Results From a Food Frequency Questionnaire

The links between diet and genomic instability have been under investigation for several decades, and evidence suggests a significant causal or preventive role for various dietary factors. This study investigates the influence of macronutrients (calories, protein, and glucides) and micronutrients, such as vitamins and minerals, as assessed by a food frequency questionnaire, on genotoxicity biomarkers measured by cytokinesis-blocked micronucleus assay and comet assay. The results found significant positive and negative correlations. Micronucleus frequency tends to increase with higher intake of caffeine, calcium, magnesium, zinc, and protein (P < .05, Spearman correlation). Calorie and omega-6 intakes are negatively correlated with DNA damage measured by the comet assay. These results are somewhat controversial because some of the correlations found are contrary to dominant views in the literature; however, we suggest that unraveling the association between diet and genetic instability requires a much better understanding of the modulating role of macronutrients and micronutrients.

Resource allocation and compensation during development in holometabolous insects

We provide an extensive review on current knowledge and future research paths on the topic of resource allocation and compensation during development in holometabolous insects, emphasizing the role of resource management during development, and how compensatory mechanisms may be acting to remediate nutritional deficiencies carried over from earlier stages of development. We first review resource allocation in "open" and "closed" developmental stages and then move on to the topic of modelling resource allocation and its trade-offs. In doing so, we review novel methodological developments such as response-surface methods and mixture experiments as well as nutritional geometry. We also dwell on the fascinating topic of compensatory physiology and behavior. We finish by discussing future research paths, among them the emerging field of nutrigenomics and gut microbiome, which will shed light into the yet poorly understood role of the symbiotic microbiota in nutrient compensation or assimilation.

Evaluation of Adherence to Nutritional Intervention Through Trajectory Analysis

Classical pre-post intervention studies are often analyzed using traditional statistics. Nevertheless, the nutritional interventions have small effects on the metabolism and traditional statistics are not enough to detect these subtle nutrient effects. Generally, this kind of studies assumes that the participants are adhered to the assigned dietary intervention and directly analyzes its effects over the target parameters. Thus, the evaluation of adherence is generally omitted. Although, sometimes, participants do not effectively adhere to the assigned dietary guidelines. For this reason, the trajectory map is proposed as a visual tool where dietary patterns of individuals can be followed during the intervention and can also be related with nutritional prescriptions. The trajectory analysis is also proposed allowing both analysis: 1) adherence to the intervention and 2) intervention effects. The analysis is made by projecting the differences of the target parameters over the resulting trajectories between states of different time-stamps which might be considered either individually or by groups. The proposal has been applied over a real nutritional study showing that some individuals adhere better than others and some individuals of the control group modify their habits during the intervention. In addition, the intervention effects are different depending on the type of individuals, even some subgroups have opposite response to the same intervention.

Why Are Omics Technologies Important to Understanding the Role of Nutrition in Inflammatory Bowel Diseases?

For many years, there has been confusion about the role that nutrition plays in inflammatory bowel diseases (IBD). It is apparent that good dietary advice for one individual may prove inappropriate for another. As with many diseases, genome-wide association studies across large collaborative groups have been important in revealing the role of genetics in IBD, with more than 200 genes associated with susceptibility to the disease. These associations provide clues to explain the differences in nutrient requirements among individuals. In addition to genes directly involved in the control of inflammation, a number of the associated genes play roles in modulating the gut microbiota. Cell line models enable the generation of hypotheses as to how various bioactive dietary components might be especially beneficial for certain genetic groups. Animal models are necessary to mimic aspects of the complex aetiology of IBD, and provide an important link between tissue culture studies and human trials. Once we are sufficiently confident of our hypotheses, we can then take modified diets to an IBD population that is stratified according to genotype. Studies in IBD patients fed a Mediterranean-style diet have been important in validating our hypotheses and as a proof-of-principle for the application of these sensitive omics technologies to aiding in the control of IBD symptoms.

The Association between Dystemperament and Prevention of Diseases: A Systematic Review

INTRODUCTION

Temperament or mizaj is referred to four different humors differentiating individuals and as a result, proposing different preventive measures for their diseases.

AIM

In this study, a systematic and purposeful review with emphasis on the research question was done to retrieve, evaluate and consolidate the required information.

MATERIALS AND METHODS

Computerized search of published original articles with fulltext was performed using PubMed and Web of Science, Medline data Science direct, ProQuest, SID and Cochrane Library bases as well as local references from March 1990 to March 2016. The key terms used were "temperament", "Dystemperament", "prevention", "health promotion", "sue mizaj", "treatments" and "preventive measures","preventive medicine". Original and translated books were also used. Out of 25 articles, 9 were selected.

RESULTS

The findings of this study indicated that there are six essential factors (asbab-e-sitlah Zarooriya), in preventing diseases which includes air, water, food, rest and improvement of body, soul and mind, sleeping and awakening, retention and discharge of fluids, solids, gases and energy from the body and based on the aforementioned causes, some Tadbeer were introduced as Tadabir-i-Nafas (air), Tadbeer-bil-food, Tadbeer-bil-drinks, Tadbeer bil-exercise and physical relaxation, Tadbeer-bil-sleep and wakefulness, Tadbeer bil-retention and discharge.

CONCLUSION

There are two differences between these two kinds of medicine; firstly, although some preventive factors are overlapped in traditional and mainstream medicines (including nutrition (both food and drink), physical activity and sleep), some of the traditional preventive factors become undelined (retention, air) and some new preventive factors get highlighted in mainstream medicine (e.g., not smoking, not having stress, …); secondly, rules of preventive medicine in Unani system were mentioned in detail and were different for different people with different types of temperament, while the mainstream medicine states its rules, generally for different types of people.

Nutrigenomics, the Microbiome, and Gene-Environment Interactions: New Directions in Cardiovascular Disease Research, Prevention, and Treatment: A Scientific Statement From the American Heart Association

Cardiometabolic diseases are the leading cause of death worldwide and are strongly linked to both genetic and nutritional factors. The field of nutrigenomics encompasses multiple approaches aimed at understanding the effects of diet on health or disease development, including nutrigenetic studies investigating the relationship between genetic variants and diet in modulating cardiometabolic risk, as well as the effects of dietary components on multiple "omic" measures, including transcriptomics, metabolomics, proteomics, lipidomics, epigenetic modifications, and the microbiome. Here, we describe the current state of the field of nutrigenomics with respect to cardiometabolic disease research and outline a direction for the integration of multiple omics techniques in future nutrigenomic studies aimed at understanding mechanisms and developing new therapeutic options for cardiometabolic disease treatment and prevention.

Biosynthesis of milk fat, protein, and lactose: roles of transcriptional and posttranscriptional regulation

The demand for high-quality milk is increasing worldwide. The efficiency of milk synthesis can be improved by taking advantage of the accumulated knowledge of the transcriptional and posttranscriptional regulation of genes coding for proteins involved in the synthesis of fat, protein, and lactose in the mammary gland. Research in this area is relatively new, but data accumulated in the last 10 years provide a relatively clear picture. Milk fat synthesis appears to be regulated, at least in bovines, by an interactive network between SREBP1, PPARγ, and LXRα, with a potential role for other transcription factors, such as Spot14, ChREBP, and Sp1. Milk protein synthesis is highly regulated by insulin, amino acids, and amino acid transporters via transcriptional and posttranscriptional routes, with the insulin-mTOR pathway playing a central role. The transcriptional regulation of lactose synthesis is still poorly understood, but it is clear that glucose transporters play an important role. They can also cooperatively interact with amino acid transporters and the mTOR pathway. Recent data indicate the possibility of nutrigenomic interventions to increase milk fat synthesis by feeding long-chain fatty acids and milk protein synthesis by feeding amino acids. We propose a transcriptional network model to account for all available findings. This model encompasses a complex network of proteins that control milk synthesis with a cross talk between milk fat, protein, and lactose regulation, with mTOR functioning as a central hub.

Innovations in Canine and Feline Nutrition: Technologies for Food and Nutrition Assessment

Pet owners have increasing concerns about the nutrition of their pets, and they desire foods and treats that are safe, traceable, and of high nutritive value. To meet these high expectations, detailed chemical composition characterization of ingredients well beyond that provided by proximate analysis will be required, as will information about host physiology and metabolism. Use of faster and more precise analytical methodology and novel technologies that have the potential to improve pet food safety and quality will be implemented. In vitro and in vivo assays will continue to be used as screening tools to evaluate nutrient quality and adequacy in novel ingredients prior to their use in animal diets. The use of molecular and high-throughput technologies allows implementation of noninvasive studies in dogs and cats to investigate the impact of dietary interventions by using systems biology approaches. These approaches may further improve the health and longevity of pets.

Comparison of the effects of five dietary fibers on mucosal transcriptional profiles, and luminal microbiota composition and SCFA concentrations in murine colon

SCOPE

The aim of our study was to investigate and compare the effects of five fibers on the mucosal transcriptome, together with alterations in the luminal microbiota composition and SCFA concentrations in the colon.

METHODS AND RESULTS

Mice were fed fibers that differed in carbohydrate composition or a control diet for 10 days. Colonic gene expression profiles and luminal microbiota composition were determined by microarray techniques, and integrated using multivariate statistics. Our data showed a distinct reaction of the host and microbiota to resistant starch, a fiber that was not completely fermented in the colon, whereas the other fibers induced similar responses on gene expression and microbiota. Consistent associations were revealed between fiber-induced enrichment of Clostridium cluster IV and XIVa representatives, and changes in mucosal expression of genes related to energy metabolism. The nuclear receptor PPAR-γ was predicted to be an important regulator of the mucosal responses.

CONCLUSION

Results of this exploratory study suggest that despite different sources and composition, fermentable fibers induce a highly similar mucosal response that may at least be partially governed by PPAR-γ.

Urolithin A causes p21 up-regulation in prostate cancer cells

PURPOSE

Walnuts contain several bioactive compounds, including pedunculagin, a polyphenol metabolized by microbiota to form urolithins, namely urolithin A (UA). The aim of this study was to determine gene expression changes in prostate cancer cells after incubation with UA.

METHODS

We performed a genomic analysis to study the effect of UA on LNCaP prostate cells. Cells were incubated with 40 µM UA for 24 h, and RNA was extracted and hybridized to Affymetrix Human Genome U219 array. Microarray results were analyzed using GeneSpring v13 software. Differentially expressed genes (p < 0.05, fold change > 2) were used to perform biological association networks. Cell cycle was analyzed by flow cytometry and apoptosis measured by the rhodamine method and by caspases 3 and 7 activation. Cell viability was determined by MTT assay.

RESULTS

We identified two nodes, FN-1 and CDKN1A, among the differentially expressed genes upon UA treatment. CDKN1A was validated, its mRNA and protein levels were significantly up-regulated, and the promoter activation measured by luciferase. Cell cycle analysis showed an increase in G1-phase, and we also observed an induction of apoptosis and caspases 3 and 7 activation upon UA treatment.

CONCLUSION

Our results indicate a potential role of UA as a chemopreventive agent for prostate cancer.

Ayurnutrigenomics: Ayurveda-inspired personalized nutrition from inception to evidence

Ayurveda proclaims food and drugs are intersecting concepts that are vital for human survival and for the prevention and mitigation of diseases. Food interferes with the molecular mechanisms of an organism's “physiome”. It is consumed in large amounts compared to any drug. Hence, research on its effect and interaction with genome is highly relevant toward understanding diseases and their therapies. Ayurgenomics presents a personalized approach in the predictive, preventive, and curative aspects of stratified medicine with molecular variability, which embodies the study of interindividual variability due to genetic variability in humans for assessing susceptibility, and establishing diagnosis and prognosis, mainly on the basis of the constitution type of a person's Prakriti. Ayurnutrigenomics is an emerging field of interest pervading Ayurveda systems biology, where the selection of a suitable dietary, therapeutic, and lifestyle regime is made on the basis of clinical assessment of an individual maintaining one's Prakriti. This Ayurveda-inspired concept of personalized nutrition is a novel concept of nutrigenomic research for developing personalized functional foods and nutraceuticals suitable for one's genetic makeup with the help of Ayurveda. Here, we propose and present this novel concept of Ayurnutrigenomics and its emerging areas of research, which may unfold future possibilities toward smart yet safe therapeutics.

Nutrigenomics: A controversy

Nutrigenomics is an emerging science which investigates a certain area of nutrition that uses molecular tools to search access and understand the several responses obtained through a certain diet applied between individual and population groups. The increased need for the use of personalised nutrition in patients is increasing and research is being made on its possible effects. However, research on nutrigenomics and in particular, obesity is still ongoing. Following a current metanalysis on thirty-eight nutrigenomics genes, it seems that a definite association between the genes usually examined in nutrigenomics testing and several diet-related diseases is lacking, even though there is a limited number of studies associating them. In 2014, literature search results in a great number of studies on several polymorphisms. This heterogeneity could only show the way towards new research aims. Nutrigenomics was born due to the need to move from Epidemiology and Physiology to Molecular Biology and Genetics. Currently, there are steps that need to be considered in order for nutrigenomics to be applied: the genes, the gene/protein network, and the strategy towards the determination of the nutrients' influence on gene/protein expression. It is certainly an interesting evolving science with many areas to be investigated further and from different perspectives, as it involves ethics, medicine, genetics and nutrition.

Changes in gene expression in PBMCs profiles of PPARα target genes in obese and non-obese individuals during fasting

BACKGROUND

The prevalence of obesity has risen dramatically and the World Health Organization estimates that 700 million people will be obese worldwide by 2015. Approximately, 50% of the Brazilian population above 20 years of age is overweight, and 16% is obese.

AIM

This study aimed to evaluate the differences in the expression of PPARα target genes in human peripheral blood mononuclear cells (PBMCs) and free fatty acids (FFA) in obese and non-obese individuals after 24 h of fasting. We first presented evidence that Brazilian people exhibit expression changes in PPARα target genes in PBMCs under fasting conditions.

METHODS

Q-PCR was utilized to assess the mRNA expression levels of target genes.

RESULTS

In both groups, the FFA concentrations increased significantly after 24 h of fasting. The basal FFA mean concentration was two-fold higher in the obese group compared with the non-obese group. After fasting, all genes evaluated in this study showed increased expression levels compared with basal expression in both groups.

CONCLUSION

However, our results reveal no differences in gene expression between the obese and non-obese, more studies are necessary to precisely delineate the associated mechanisms, particularly those that include groups with different degrees of obesity and patients with diabetes mellitus type 2 because the expression of the main genes that are involved in β-oxidation and glucose level maintenance are affected by these factors.

Antioxidative Effects of Germinated Brown Rice-Derived Extracts on H2O2-Induced Oxidative Stress in HepG2 Cells

The antioxidant properties of germinated brown rice (GBR) are likely mediated by multiple bioactives. To test this hypothesis, HepG2 cells pretreated with GBR extracts, rich in acylated steryl glycoside (ASG), gamma amino butyric acid GABA), phenolics or oryzanol, were incubated with hydrogen peroxide (H₂O₂) and their hydroxyl radical (OH^•) scavenging capacities and thiobarbituric acid-reactive substances (TBARS) generation were evaluated. Results showed that GBR-extracts increased OH^• scavenging activities in both cell-free medium and posttreatment culture media, suggesting that the extracts were both direct- and indirect-acting against OH^•. The levels of TBARS in the culture medium after treatment were also reduced by all the extracts. In addition, H₂O₂ produced transcriptional changes in p53, JNK, p38 MAPK, AKT, BAX, and CDK4 that were inclined towards apoptosis, while GBR-extracts showed some transcriptional changes (upregulation of BAX and p53) that suggested an inclination for apoptosis although other changes (upregulation of antioxidant genes, AKT, JNK, and p38 MAPK) suggested that GBR-extracts favored survival of the HepG2 cells. Our findings show that GBR bioactive-rich extracts reduce oxidative stress through improvement in antioxidant capacity, partly mediated through transcriptional regulation of antioxidant and prosurvival genes.

Fish oil supplementation induces expression of genes related to cell cycle, endoplasmic reticulum stress and apoptosis in peripheral blood mononuclear cells: a transcriptomic approach

BACKGROUND

Fish oil supplementation has been shown to alter gene expression of mononuclear cells both in vitro and in vivo. However, little is known about the total transcriptome profile in healthy subjects after intake of fish oil. We therefore investigated the gene expression profile in peripheral blood mononuclear cells (PBMCs) after intake of fish oil for 7 weeks using transcriptome analyses.

DESIGN

In a 7-week, double-blinded, randomized, controlled, parallel-group study, healthy subjects received 8 g day(-1) fish oil (1.6 g day(-1) eicosapentaenoic acid + docosahexaenoic acid) (n = 17) or 8 g day(-1) high oleic sunflower oil (n = 19). Microarray analyses of RNA isolated from PBMCs were performed at baseline and after 7 weeks of intervention.

RESULTS

Cell cycle, DNA packaging and chromosome organization are biological processes found to be upregulated after intake of fish oil compared to high oleic sunflower oil using a moderated t-test. In addition, gene set enrichment analysis identified several enriched gene sets after intake of fish oil. The genes contributing to the significantly different gene sets in the subjects given fish oil compared with the control group are involved in cell cycle, endoplasmic reticulum (ER) stress and apoptosis. Gene transcripts with common motifs for 35 known transcription factors including E2F, TP53 and ATF4 were upregulated after intake of fish oil.

CONCLUSION

We have shown that intake of fish oil for 7 weeks modulates gene expression in PBMCs of healthy subjects. The increased expression of genes related to cell cycle, ER stress and apoptosis suggests that intake of fish oil may modulate basic cellular processes involved in normal cellular function.

Utilization of rye as energy source affects bacterial translocation, intestinal viscosity, microbiota composition, and bone mineralization in broiler chickens

Two independent trials were conducted to evaluate the utilization of rye as energy source on bacterial translocation (BT), intestinal viscosity, gut integrity, gut microbiota composition, and bone mineralization, when compared with a traditional cereal (corn) in broiler chickens. In each experiment, day-of-hatch, broiler chickens were randomly assigned to either a corn or a rye diet (n = 20 chickens/group). At 10 d of age, in both experiments, 12 chickens/group were randomly selected, and given an oral gavage dose of fluorescein isothiocyanate dextran (FITC-d). After 2.5 h of oral gavage, blood samples were collected to determine the passage of FITC-d. The liver was collected from each bird to evaluate BT. Duodenum, ileum, and cecum gut sections were collected to evaluate intestinal viscosity and to enumerate gut microbiota. Tibias were collected for observation of bone parameters. Broilers fed with rye showed increased (p < 0.05) intestinal viscosity, BT, and serum FITC-d. Bacterial enumeration revealed that chickens fed with rye had increased the number of total lactic acid bacteria in all three sections of the gastrointestinal tract evaluated when compared to chickens fed with corn. Chickens fed with rye also had significantly higher coliforms in duodenum and ileum, whereas the total number of anaerobes increased only in duodenum. A significant reduction in bone strength and bone mineralization was observed in chickens fed with rye when compared with corn fed chickens. In conclusion, rye evoked mucosal damage in chickens that alter the intestinal viscosity, increased leakage through the intestinal tract, and altered the microbiota composition as well as bone mineralization. Studies to evaluate dietary inclusion of selected DFM candidates that produce exogenous enzymes in rye fed chickens are currently being evaluated.

Life Course Perspective: evidence for the role of nutrition

The "Life Course Perspective" proposes that environmental exposures, including biological, physical, social, and behavioral factors, as well as life experiences, throughout the entire life span, influence health outcomes in current and future generations. Nutrition, from preconception to adulthood, encompasses all of these factors and has the potential to positively or negatively shape the individual or population health trajectories and their intergenerational differences. This paper applies the T2E2 model (timing, timeline, equity and environment), developed by Fine and Kotelchuck, as an overlay to examine advances in nutritional science, as well as the complex associations between life stages, nutrients, nutrigenomics, and access to healthy foods, that support the life course perspective. Examples of the application of nutrition to each of the four constructs are provided, as well as a strong recommendation for inclusion of nutrition as a key focal point for all health professionals as they address solutions to optimize health outcomes, both domestically and internationally. The science of nutrition provides strong evidence to support the concepts of the life course perspective. These findings lend urgency to the need to improve population health across the life span and over generations by ensuring ready access to micronutrient-dense foods, opportunities to balance energy intake with adequate physical activity and the need for biological, social, physical, and macro-level environments that support critical phases of human development. Recommendations for the application of the life course perspective, with a focus on the emerging knowledge of nutritional science, are offered in an effort to improve current maternal and child health programs, policies, and service delivery.

Obesity and chronic stress are able to desynchronize the temporal pattern of serum levels of leptin and triglycerides

Disruption of the circadian system can lead to metabolic dysfunction as a response to environmental alterations. This study assessed the effects of the association between obesity and chronic stress on the temporal pattern of serum levels of adipogenic markers and corticosterone in rats. We evaluated weekly weight, delta weight, Lee index, and weight fractions of adipose tissue (mesenteric, MAT; subcutaneous, SAT; and pericardial, PAT) to control for hypercaloric diet-induced obesity model efficacy. Wistar rats were divided into four groups: standard chow (C), hypercaloric diet (HD), stress plus standard chow (S), and stress plus hypercaloric diet (SHD), and analyzed at three time points: ZT0, ZT12, and ZT18. Stressed animals were subjected to chronic stress for 1h per day, 5 days per week, during 80 days. The chronic exposure to a hypercaloric diet was an effective model for the induction of obesity and metabolic syndrome, increasing delta weight, Lee index, weight fractions of adipose tissue, and triglycerides and leptin levels. We confirmed the presence of a temporal pattern in the release of triglycerides, corticosterone, leptin, and adiponectin in naïve animals. Chronic stress reduced delta weight, MAT weight, and levels of triglycerides, total cholesterol, and leptin. There were interactions between chronic stress and obesity and serum total cholesterol levels, between time points and obesity and adiponectin and corticosterone levels, and between time points and chronic stress and serum leptin levels. In conclusion, both parameters were able to desynchronize the temporal pattern of leptin and triglyceride release, which could contribute to the development of metabolic diseases such as obesity and metabolic syndrome.

Resistant starch induces catabolic but suppresses immune and cell division pathways and changes the microbiome in the proximal colon of male pigs

Consumption of resistant starch (RS) has been associated with various intestinal health benefits, but knowledge of its effects on global gene expression in the colon is limited. The main objective of the current study was to identify genes affected by RS in the proximal colon to infer which biologic pathways were modulated. Ten 17-wk-old male pigs, fitted with a cannula in the proximal colon for repeated collection of tissue biopsy samples and luminal content, were fed a digestible starch (DS) diet or a diet high in RS (34%) for 2 consecutive periods of 14 d in a crossover design. Analysis of the colonic transcriptome profiles revealed that, upon RS feeding, oxidative metabolic pathways, such as the tricarboxylic acid cycle and β-oxidation, were induced, whereas many immune response pathways, including adaptive and innate immune system, as well as cell division were suppressed. The nuclear receptor peroxisome proliferator-activated receptor γ was identified as a potential key upstream regulator. RS significantly (P < 0.05) increased the relative abundance of several butyrate-producing microbial groups, including the butyrate producers Faecalibacterium prausnitzii and Megasphaera elsdenii, and reduced the abundance of potentially pathogenic members of the genus Leptospira and the phylum Proteobacteria. Concentrations in carotid plasma of the 3 main short-chain fatty acids acetate, propionate, and butyrate were significantly higher with RS consumption compared with DS consumption. Overall, this study provides novel insights on effects of RS in proximal colon and contributes to our understanding of a healthy diet.

Risks of nutrigenomics and nutrigenetics? What the scientists say

Nutrigenomics and nutrigenetics (hereafter NGx) have stimulated expectations for beneficial applications in public health and individuals. Yet, the potential achievability of such promise is not without socioethical considerations that challenge NGx implementation. This paper focuses on the opinions of NGx researchers about potential risks raised by NGx. The results of an online survey show that these researchers (n = 126) are fairly confident about the potential benefits of NGx, and that most downplay its potential risks. Researchers in this field do not believe that NGx will reconfigure foods as medication or transform the conception of eating into a health hazard. The majority think that NGx will produce no added burden on individuals to get tested or to remain compliant with NGx recommendations, nor that NGx will threaten individual autonomy in daily food choice. The majority of researchers do not think that NGx will lead to discrimination against and/or stigmatization of people who do not comply with NGx dietary recommendations. Despite this optimism among NGx researchers, we suggest that key risk factors raised by the socioethical context in which NGx applications will be implemented need to be considered.