Nutrition and food science go genomic

A novel FCTF evaluation and prediction model for food efficacy based on association rule mining

Introduction

Food-components-target-function (FCTF) is an evaluation and prediction model based on association rule mining (ARM) and network interaction analysis, which is an innovative exploration of interdisciplinary integration in the food field.

Methods

Using the components as the basis, the targets and functions are comprehensively explored in various databases and platforms under the guidance of the ARM concept. The focused active components, key targets and preferred efficacy are then analyzed by different interaction calculations. The FCTF model is particularly suitable for preliminary studies of medicinal plants in remote and poor areas.

Results

The FCTF model of the local medicinal food Laoxianghuang focuses on the efficacy of digestive system cancers and neurological diseases, with key targets ACE, PTGS2, CYP2C19 and corresponding active components citronellal, trans-nerolidol, linalool, geraniol, α-terpineol, cadinene and α-pinene.

Discussion

Centuries of traditional experience point to the efficacy of Laoxianghuang in alleviating digestive disorders, and our established FCTF model of Laoxianghuang not only demonstrates this but also extends to its possible adjunctive efficacy in neurological diseases, which deserves later exploration. The FCTF model is based on the main line of components to target and efficacy and optimizes the research level from different dimensions and aspects of interaction analysis, hoping to make some contribution to the future development of the food discipline.

Nutrigenomics in Regulating the Expression of Genes Related to Type 2 Diabetes Mellitus

Nutrigenomics is the study of the gene-nutrient interaction and it indicates that some nutrients, called bioactive compounds, can mold the genetic expression or change the nucleotide chain. Polyphenols are secondary metabolites found in plants that are regularly consumed in functional foods and help prevent or delay the onset of type 2 diabetes mellitus (T2DM) and its complications. This article objected to review studies about the interaction of diet with polyphenols and Mediterranean diet in the expression of human genes related to T2DM. Resveratrol acts as an antioxidant, anti-inflammatory, and increases mitochondrial function. Regular consumption of quercetin resulted in improvement of hypertension and suppression of diabetes-induced vasoconstriction. Genistein also showed positive results in T2DM, such as increased cell mass and improved glucose tolerance and insulin levels. Catechins showed efficiency in inducing genes in triacylglycerol biosynthesis, inhibition of fatty acids and cholesterol, and resulting in their participation in mitigating complications of diabetes. Lastly, curcumin was demonstrated to be a protector of the pancreatic islets against streptozotocin-induced oxidative stress. Growing evidence suggest that bioactive compounds such as polyphenols have an important role in T2DM and the prevention and treatment of its complication, as they cause activation or inhibition of related genes.

Metabolomics for Evaluating Flavor-Associated Metabolites in Plant-Based Products

Plant-based diets (PBDs) are associated with environmental benefits, human health promotion and animal welfare. There is a worldwide shift towards PBDs, evident from the increased global demand for fresh plant-based products (PBPs). Such shifts in dietary preferences accompanied by evolving food palates, create opportunities to leverage technological advancements and strict quality controls in developing PBPs that can drive consumer acceptance. Flavor, color and texture are important sensory attributes of a food product and, have the largest influence on consumer appeal and acceptance. Among these, flavor is considered the most dominating quality attribute that significantly affects overall eating experience. Current state-of-art technologies rely on physicochemical estimations and sensory-based tests to assess flavor-related attributes in fresh PBPs. However, these methodologies often do not provide any indication about the metabolic features associated with unique flavor profiles and, consequently, can be used in a limited way to define the quality attributes of PBPs. To this end, a systematic understanding of metabolites that contribute to the flavor profiles of PBPs is warranted to complement the existing methodologies. This review will discuss the use of metabolomics for evaluating flavor-associated metabolites in fresh PBPs at post-harvest stage, alongside its applications for quality assessment and grading. We will summarize the current research in this area, discuss technical challenges and considerations pertaining to sampling and analytical techniques, as well as s provide future perspectives and directions for government organizations, industries and other stakeholders associated with the quality assessment of fresh PBPs.

Quantifying diet for nutrigenomic studies

The field of nutrigenomics shows tremendous promise for improved understanding of the effects of dietary intake on health. The knowledge that metabolic pathways may be altered in individuals with genetic variants in the presence of certain dietary exposures offers great potential for personalized nutrition advice. However, although considerable resources have gone into improving technology for measurement of the genome and biological systems, dietary intake assessment remains inadequate. Each of the methods currently used has limitations that may be exaggerated in the context of gene × nutrient interaction in large multiethnic studies. Because of the specificity of most gene × nutrient interactions, valid data are needed for nutrient intakes at the individual level. Most statistical adjustment efforts are designed to improve estimates of nutrient intake distributions in populations and are unlikely to solve this problem. An improved method of direct measurement of individual usual dietary intake that is unbiased across populations is urgently needed.

Healthy and adverse effects of plant-derived functional metabolites: the need of revealing their content and bioactivity in a complex food matrix

In recent years, both food quality and its effect on human health have become a fundamental issue all over the world. As a consequence of this new and increased awareness, American, European, and Asian policymakers have strongly encouraged the research programs on food quality and safety thematic. Attempts to improve human health and to satisfy people's desire for healthcare without intake of pharmaceuticals, has led the food industry to focus attention on functional or nutraceutical food. For a long time, compounds with nutraceutical activity have been produced chemically, but the new demands for a sustainable life have gradually led the food industry to move towards natural compounds, mainly those derived from plants. Many phytochemicals are known to promote good health, but, sometimes, undesirable effects are also reported. Furthermore, several products present on the market show few benefits and sometimes even the reverse - unhealthy effects; the evidence of efficacy is often unconvincing and epidemiological studies are necessary to prove the truth of their claims. Therefore, there is a need for reliable analytical control systems to measure the bioactivity, content, and quality of these additives in the complex food matrix. This review describes the most widespread nutraceutics and an analytical control of the same using recently developed biosensors which are promising candidates for routine control of functional foods.

Foodomics: MS-based strategies in modern food science and nutrition

Modern research in food science and nutrition is moving from classical methodologies to advanced analytical strategies in which MS-based techniques play a crucial role. In this context, Foodomics has been recently defined as a new discipline that studies food and nutrition domains through the application of advanced omics technologies in which MS techniques are considered indispensable. Applications of Foodomics include the genomic, transcriptomic, proteomic, and/or metabolomic study of foods for compound profiling, authenticity, and/or biomarker-detection related to food quality or safety; the development of new transgenic foods, food contaminants, and whole toxicity studies; new investigations on food bioactivity, food effects on human health, etc. This review work does not intend to provide an exhaustive revision of the many works published so far on food analysis using MS techniques. The aim of the present work is to provide an overview of the different MS-based strategies that have been (or can be) applied in the new field of Foodomics, discussing their advantages and drawbacks. Besides, some ideas about the foreseen development and applications of MS-techniques in this new discipline are also provided.

Nutritional systems biology: definitions and approaches

Nutrigenetics and nutrigenomics are nascent areas that are evolving quickly and riding on the wave of "personalized medicine" that is providing opportunities in the discovery and development of nutraceutical compounds. The human genome sequence and sequences of model organisms provide the equivalent of comprehensive blueprints and parts lists that describe dynamic networks and the bases for understanding their responses to external and internal perturbations. Unfolding the interrelationships among genes, gene products, and dietary habits is fundamental for identifying individuals who will benefit most from, or be placed at risk by, intervention strategies. More accurate assessment of the inputs to human health and the consequences of those inputs measured as accurate transcriptomic, proteomic, and metabolomic analyses would bring personalized health/diet to practice far faster than would waiting for a predictive knowledge of genetic variation. It is widely recognized that systems and network biology has the potential to increase our understanding of how nutrition influences metabolic pathways and homeostasis, how this regulation is disturbed in a diet-related disease, and to what extent individual genotypes contribute to such diseases.

Nutrição no pós-genoma: fundamentos e aplicações de ferramentas ômicas

Após seqüenciamento do genoma humano, os estudos genômicos têm se voltado à elucidação das funções de todos os genes, bem como à caracterização de suas interações com fatores ambientais. A nutrigenômica surgiu no contexto do pós-genoma humano e é considerada área-chave para a nutrição nesta década. Seu foco de estudo baseia-se na interação gene-nutriente. Esta ciência recente tem como objetivo principal o estabelecimento de dietas personalizadas, com base no genótipo, para a promoção da saúde e a redução do risco de doenças crônicas não transmissíveis como as cardiovasculares, o câncer, o diabetes, entre outras. Nesse contexto, é fundamental a aplicação na área de nutrição das ferramentas de genômica funcional para análise do transcritoma (transcritômica), do proteoma (proteômica) e do metaboloma (metabolômica). As aplicabilidades dessas metodologias em estudos nutricionais parecem ilimitadas, pois podem ser conduzidas em cultura de células, modelos de experimentação em animais, estudos pré-clinicos e clínicos. Tais técnicas apresentam potencial para identificar biomarcadores que respondem especificamente a um determinado nutriente ou composto bioativo dos alimentos e para estabelecer as melhores recomendações dietéticas individuais para redução do risco das doenças crônicas não transmissíveis e promoção da saúde.

Genotype-phenotype associations: modulation by diet and obesity

Changes in diet are likely to reduce chronic disorders, but after decades of active research and heated discussion, the question still remains: what is the optimal diet to achieve this elusive goal? Is it a low-fat diet, as traditionally recommended by multiple medical societies? Or a high monounsaturated fat (MUFA) diet as predicated by the Mediterranean diet? Perhaps a high polyunsaturated fat (PUFA) diet based on the cholesterol-lowering effects? The right answer may be all of the above but not for everybody. A well-known phenomenon in nutrition research and practice is the dramatic variability in interindividual response to any type of dietary intervention. There are many other factors influencing response, and they include, among many others, age, sex, physical activity, alcohol, and smoking as well as genetic factors that will help to identify vulnerable populations/individuals that will benefit from a variety of more personalized and mechanistic-based dietary recommendations. This potential could and needs to be developed within the context of nutritional genomics that in conjunction with systems biology may provide the tools to achieve the holy grail of dietary prevention and therapy of chronic diseases and cancer. This approach will break with the traditional public health approach of "one size fits all." The current evidence based on nutrigenetics has begun to identify subgroups of individuals who benefit more from a low-fat diet, whereas others appear to benefit more from high MUFA or PUFA diets. The continuous progress in nutrigenomics will allow some time in the future to provide targeted gene-based dietary advice.

Integrating anticipated nutrigenomics bioscience applications with ethical aspects

Nutrigenomics is a subspecialty of nutrition science which aims to understand how gene-diet interactions influence individuals' response to food, disease susceptibility, and population health. Yet ethical enquiry into this field is being outpaced by nutrigenomics bioscience. The ethical issues surrounding nutrigenomics face the challenges of a rapidly evolving field which bring forward the additional dimension of crossdisciplinary integrative research between social and biomedical sciences. This article outlines the emerging nutrigenomics definitions and concepts and analyzes the existing ethics literature concerning personalized nutrition and presents "points to consider" over ethical issues regarding future nutrigenomics applications. The interest in nutrigenomics coincides with a shift in emphasis in medicine and biosciences toward prevention of future disease susceptibilities rather than treatment of already established disease. Hence, unique ethical issues emerge concerning the extent to which nutrigenomics can alter our relation to food, boundaries between health and disease, and the folklore of medical practice. Nutrigenomics can result in new social values, norms, and responsibilities for both individuals and societies. Nutrigenomics is not only another new application of "-omics" technologies in the context of gene-diet interactions. Nutrigenomics may fundamentally change the way we perceive human illness while shifting the focus and broadening the scope of health interventions from patients to healthy individuals. In resource- and time-limited healthcare settings, this creates unique ethical dilemmas and distributive justice issues. Ethical aspects of nutrigenomics applications should be addressed proactively, as this new science develops and increasingly coalesces with other applications of genomics in medicine and public health.

High throughput ‘omics’ approaches to assess the effects of phytochemicals in human health studies

Human health is affected by many factors. Diet and inherited genes play an important role. Food constituents, including secondary metabolites of fruits and vegetables, may interact directly with DNA via methylation and changes in expression profiles (mRNA, proteins) which results in metabolite content changes. Many studies have shown that food constituents may affect human health and the exact knowledge of genotypes and food constituent interactions with both genes and proteins may delay or prevent the onset of diseases. Many high throughput methods have been employed to get some insight into the whole process and several examples of successful research, namely in the field of genomics and transcriptomics, exist. Studies on epigenetics and RNome significance have been launched. Proteomics and metabolomics need to encompass large numbers of experiments and linked data. Due to the nature of the proteins, as well as due to the properties of various metabolites, experimental approaches require the use of comprehensive high throughput methods and a sufficiency of analysed tissue or body fluids. In this contribution, we describe the basic tools currently used in nutrigenomics studies and indicate the general requirements for future technology methodological routings.

Plant metabolomics and its potential application for human nutrition

With the growing interest in the use of metabolomic technologies for a wide range of biological targets, food applications related to nutrition and quality are rapidly emerging. Metabolomics offers us the opportunity to gain deeper insights into, and have better control of, the fundamental biochemical basis of the things we eat. So doing will help us to design modified breeding programmes aimed at better quality produce; optimised food processing strategies and ultimately, improved (micro)nutrient bioavailability and bioefficacy. A better understanding of the pathways responsible for the biosynthesis of nutritionally relevant metabolites is key to gaining more effective control of the absence/level of presence of such components in our food. Applications of metabolomic technologies in both applied and fundamental science strategies are therefore growing rapidly in popularity. Currently, the world has two highly contrasting nutrition-related problems--over-consumption and under-nourishment. Dramatic increases in the occurrence of overweight individuals and obesity in developed countries are in staggering contrast to the still-familiar images of extreme malnutrition in many parts of the developing world. Both problems require a modified food supply, achieved through highly contrasting routes. For each, metabolomics has a future role to play and this review shall deal with this key dichotomy and illustrate where metabolomics may have a future part to play. In this short overview, attention is given to how the various technologies have already been exploited in a plant-based food context related to key issues such as biofortification, bioprotectants and the general link between food composition and human health. Research on key crops such as rice and tomato are used as illustration of potentially broader application across crop species. Although the focus is clearly on food supply, some attention is given to the complementary field of research, nutrigenomics, where similar technologies are being applied to understand nutrition better from the human side.

The Potential of Metabolomics Tools in Bioremediation Studies

As a post-genomics tool, metabolomics is a young and vibrant field of science in its exponential growth phase. Metabolome analysis has become very popular recently, and novel techniques for acquiring and analyzing metabolomics data continue to emerge that are useful for a variety of biological studies. The bioremediation field has a lot to gain from the advances in this emerging area. Thus, this review article focuses on the potential of various experimental and conceptual approaches developed for metabolomics to be applied in bioremediation research, such as strategies for elucidation of biodegradation pathways using isotope distribution analysis and molecular connectivity analysis, the assessment of mineralization process using metabolic footprinting analysis, and the improvement of the biodegradation process via metabolic engineering. We demonstrate how the use of metabolomics tools can significantly extend and enhance the power of existing bioremediation approaches by providing a better overview of the biodegradation process.

Characterization of major enzymes and genes involved in flavonoid and proanthocyanidin biosynthesis during fruit development in strawberry (Fragaria ×ananassa)

The biosynthesis of flavonoids and proanthocyanidins was studied in cultivated strawberry (Fragaria xananassa) by combining biochemical and molecular approaches. Chemical analyses showed that ripe strawberries accumulate high amounts of pelargonidin-derived anthocyanins, and a larger pool of 3',4'-hydroxylated proanthocyanidins. Activities and properties of major recombinant enzymes were demonstrated by means of in vitro assays, with special emphasis on specificity for the biologically relevant 4'- and 3',4'-hydroxylated compounds. Only leucoanthocyanidin reductase showed a strict specificity for the 3',4'-hydroxylated leucocyanidin, while other enzymes accepted either hydroxylated substrate with different relative activity rates. The structure of late flavonoid pathway genes, leading to the synthesis of major compounds in ripe fruits, was elucidated. Complex developmental and spatial expression patterns were shown for phenylpropanoid and flavonoid genes in fruits throughout ripening as well as in leaves, petals and roots. Presented results elucidate key steps in the biosynthesis of strawberry flavonoid end products.

Using genetic variation to optimize nutritional preemption

One of the promises of nutritional genomics is a set of dietary recommendations that leverage our understanding of nutrient-gene interaction in the preemptive dietary management of complex chronic diseases. Whether nutritional genomics can deliver on this promise is a matter of debate and controversy. Although nutritional genomics is often viewed as an extension of pharmacogenomics, the pharmacogenomics paradigm is a disease-centric reductionistic model that overshadows both the complexities and opportunities to be leveraged in preemptive nutritional pharmacology. Moreover, the pharmacogenomics model tends to set clinical expectations that nutritional genomics may not be able to achieve. The biological boundaries of nutritional pharmacology are being tested in many areas of preventive medicine such as cardiovascular disease and cancer. In this regard, the lessons learned in one disease may be germane to the other. Recent results from the Vitamin Intervention for Stroke Prevention (VISP), the Norwegian Vitamin (NORVIT), and the Heart Outcomes Prevention Evaluation (HOPE) 2 trials underscore the incertitude of translating epidemiologic data into preemptive nutritional guidance. Moving ahead, the genetic determinism of the nutrigenomic model needs to take on a more holistic and phenotypic focus. To the extent this can be done, preemptive nutrition may one day become a safe and practical reality.

Monitoring the health to disease continuum with global metabolic profiling and systems biology

Global metabolic profiling, which includes both metabolomics and metabonomics studies, is the latest ‘omics’ research platform that is being applied to understand the health and disease continuum. Metabolic profiling analyses have been demonstrated for the investigation of inborn errors of metabolism, organ transplant rejection, drug toxicity, disease diagnosis and prognosis, drug efficacy and nutritional status. Combining information generated from a metabolic profiling platform with that obtained based on genetics, transcriptomics and proteomics research paradigms will pave the way for a better understanding of the mechanisms of disease and toxicity. Metabolomics and nutrition will lay the groundwork for the application of personalized medicine in the 21st century.