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Genomics: a review on nutrition
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S. Clemente-Hernández, E. O. Oviedo-Rondon1 and Federico Salvador Torres.
Stephen F. Austin State University, Nacogdoches, Texas, 75962.
Facultad de Zootecnia de la Universidad Autónoma de Chihuahua
ABSTRACT: A variety of technologies to improve the animal nutrition is available,
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including the Genomics technologies, these technology have changed the strategy of nutrition
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research. In recent years, scientists have began to apply genomics to the field of nutrition.
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Nutritional genomics or Nutrigenomics is the study of nutrient-gene interactions, enhancing
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our understanding of metabolism and optimizing companion animal nutritional and health
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status. These will be performed with the use of microarray technology, which can monitor
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the expression of thousands of genes simultaneously. The study of nutrigenomics will be
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important in nutrients requirements determination of animals, disease prevention and
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treatment, and regulation of optimizing companion animal nutrition and health status. The
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objective of this review is to provide information about of the importance the genomics on
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the nutrition and the importance in development for animal science research.
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Key Words: Nutrigenomics, Nutrition, Microarray, Health, Genes
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Introduction
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Nutritional science is historically based on chemical characterization of feeds, definition of
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metabolic pathways, and on identification of interactions between feeds and metabolism.
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Recently research has focused on the roles of macronutrients (i.e., protein, carbohydrates, fat)
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and micronutrients (i.e., vitamins, minerals) in cellular process, enzymolgy, and the
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development of disease. A greater understanding of gene regulation and the interaction
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among their encoded proteins will enable the further extension of knowledge concerning
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nutrition. It is generally accepted that these differences in dietary effects within the
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population are a function of genetics. The same genes are present in all cells in the body,
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however differential expression of a subset of genes determines a cell’s function. Multiple
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genes are responsible for most physiological process, including nutritional process such as
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digestion and absorption. Interactions among gene products are complicated and highly
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orchestrated. Nutritional genomics, or nutrigenomics, is such an integrative science. The
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Telephone (936) 468 4433; E-mail: eoviedo@sfasu.edu
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working definition of nutrigenomics is that it seeks to provide a genetic and molecular
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understanding for how common dietary chemicals (i.e., nutrients) affect the balance between
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health and disease by altering the expression and/or structure of an individual's genetic
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makeup. The future of nutrition is tied to a clearer and to harness the power of emerging
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genomic technologies. The objective of this review is to provide information about of the
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importance the genomics on the nutrition and the importance in development for animal
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science research.
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Genomics
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These rapidly growing areas are labeled by the names of the object or field studied, suffixed
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by “omics”, such as genomics, trasncriptomics, proteomics and metabolomics (Figure 1)
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(Anderle et al., 2004; Kato and Kimura, 2003). Functional genomics may be defined as “the
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development and application of global experimental approaches to assess gene function by
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making use of the information and reagents provided by genome sequencing and mapping
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(Swanson et al., 2003). The techniques and knowledge emerging from these genome projects
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have revolutionized the process of localizing and identifying genes involved in disease
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(Kaput and Rodriguez, 2004). Genomics technologies have changed the strategy of nutrition
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research. It is now possible to measure simultaneously thousands of biological events in
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molecular detail. Scientists are now extending the analysis of gene expression and its global
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perspective to examine the other layers of biological organization, i.e., proteins and
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metabolites (Anderle et al., 2004; Hirschi et al., 2001; Waterland and Jirtle, 2004). Although
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genomics will be the essential foundation of knowledge, it is the expression of the genome
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both as the proteome (the study of entire proteins complements of cells tissues or fluids
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compartments), and more directly as the metabolome (the study of entire metabolite
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complements in cell, tissues or fluids) that will serve as the information base for modern
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nutrition (German et al., 2002; Kim et al., 2004). Lamers et al., (2003) mentioned Genomics
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will contribute to clarifying the etiology of most common genetic disease and provide
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approaches for therapeutics intervention. For other hand, functional proteomics is considered
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one of the leading technologies, not only in drug discovery, but also in the intensive hunt for
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bacterial virulence proteins (Al-Khaldi and Mossoba, 2004). The basic idea in metabolomics
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is to characterize and understand the behavior of all metabolites in an organism, and to this
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end, a number of approaches are being pursued (Noguchi et al., 2003; Lamers et al., 2003).
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The transcript reflects changes in the status of metabolites, and where the transcriptome
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analysis can be used as a global marker of the status and response of cells, organs and bodies,
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which result from changes of proteomics, metabolomics and other omics (Kato and Kimura,
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2003).
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Figure 1. Both good (beneficial, health promoting) and bad (adverse, toxic) effects of any
dietary components affect all steps of biological phenomena from gene to metabolite (arrows
left side), that is to say, all levels of the omic world. The analysis of the omics provide many
useful biomarkers of the effect of dietary factors. Thus the changes in the omics present
abundant information for the wiser choice of food and the proper intake level of each
component (arrow right side). Adapted from Kato and Kimura (2003).
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Kaput and Rodriguez, (2004) mentioned that the conceptual basis for this new branch of
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genomic research can best be summarized with the following five tenets.
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1) Common dietary chemicals act on the genome, either directly or indirectly, to alter gene
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expression or structure.
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2) Under certain circumstances and in some individuals, diet can be a serious risk factor for a
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number of diseases.
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3) Some diet-regulated genes (and their normal, common variants) are likely to play a role in
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the onset, incidence, progression, and/or severity of chronic diseases.
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4) The degree to which diet influences the balance between healthy and disease states may
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depend on an individual’s genetic makeup.
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5) Dietary intervention based on knowledge of nutritional requirement, nutritional status, and
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genotype (i.e., "individualized nutrition") can be used to prevent, mitigate or cure chronic
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disease.
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Continuing and accelerating discoveries in genomics present possibilities for an ever more
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dynamic era of scientific investigation based on understanding the effects of nutrients in
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molecular level processes in the body as well as the variable effects nutrients and non-
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nutritive dietary phytochemicals have on each of us as individuals. We call this the new era
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in nutritional science the genetic era, or nutrigenomics. On one hand, it represents a logical
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extension of biotechnology, molecular medicine and pharmacogenomics, while on the other;
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it is a revolution in how nutrition and diet are viewed (German et al., 2002).
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Nutrigenomics
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The term nutritional genomics or nutrigenomics, appears to have its origins in the context of
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plant biology wherein it referred to work at the interface of plant biochemistry (specifically,
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secondary metabolism), genomics and human nutrition. More recently, the term is used in the
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context of human biology in reference to the integration of functional genomics, nutrition,
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and health. Nutrigenomics is the study of nutrient-gene interactions. This includes how diet
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affects the way genes are expressed, and the effect of genes on the how the body (Garfinkel
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and Ruden, 2004; German et al., 2002; Kaput and Rodriguez, 2004). Nutrigenomics
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describes changes in gene expression related to a specific nutritional intervention, deviations
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in genes will have an impact on these transcriptome changes and ultimately on the
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physiologic function (Ommen, 2004; Kim et al., 2004; Labadorios and Meguid, 2004).
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Nutrigenomics seeks to provide a molecular genetic understanding for how common dietary
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chemicals (i.e., nutrition) affect health by altering the expression and/or structure of an
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individual’s genetic makeup. The fundamental concepts of the field are that the progression
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from a healthy phenotype to a chronic disease phenotype must occur by changes in gene
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expression or by differences in activities of proteins and enzymes and that dietary chemicals
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directly or indirectly regulate the expression of genomic information (Figure 2) (Kaput and
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Rodriguez, 2004). The nutritional environment is a critical determinant of cell behavior. The
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types and quantities of available nutrients directly affect genomic expression (Liu and
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Sturley, 2004).
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Figure 2. Fate and activities of nutrients in the cell. Nutrients may act directly as ligands for
transcription factor receptors (pathway A); may be metabolized by primary or secondary
metabolic pathways, thereby altering concentrations of substrates or intermediates (pathway
B) involved in gene regulation or cell signaling; or alter signal transduction pathways and
signaling (pathway C). (Adapted from Kaput and Rodriguez, 2004).
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Regulation of metabolism is achieved by coordinated actions between tissue and cells. These
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mechanisms involved the conditional regulation of specific genes in the presence or absence
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of appropriate nutrients. In multicellular organism, the control of genes expression involves
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complex interactions of appropriate nutrients, and hormonal, neuronal and nutritional factors
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(Averous et al., 2003). Our diet consists of complex mixtures of many possibly bioactive
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chemical compounds, chronically administered in different compositions, and with a
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multitude of biological effects. The vast majority of these biological responses are mediated
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through effectors genes, effects on enzyme concentration or activity, and changes in
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metabolite concentration (Ommen, 2004).
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Sensing of the nutrient is a critical step because the nutrients in food cannot be detected or
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responded to unless they interact specifically and with high sensitivity (i.e., high affinity).
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Thus nutrients provide important roles to the organism: metabolic, e.g., provision of energy,
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and informational. Three steps are critical to this process: 1) a mechanism to sense the
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nutrient, 2) the means to transducer this signal to the cell such that altered gene expression is
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the response, and 3) the ability of a gene to respond. Nutrient sensing is the function of
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sensors or receptors, which often detect individual nutrients and classes of nutrients or
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hormones that are secreted in response to nutrients (Liu and Sturley, 2004).
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In recent years, scientists have begun applying genomics to the field of nutrition. Changes in
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genes expression have been used to study a broad range of topics, including energy
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restriction (Swanson et al., 2003). In pigs, nutrients excretion was shown to vary depending
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on breed, suggesting differences in metabolism due to genotype (Crocker and Robinson,
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2002). Determination of nutrient requirements of dogs participating in different physical
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activities (e.g., dog sled racing, sprint racing or hunting/herding) also would be a worthy
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research venture. Genomics technologies can be used to further our understanding of basic
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metabolism and nutrient regulation of gene expression in developmental and pathological
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conditions (Hirschi et al., 2001). Gene-nutrition relationship, most studies including ours
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described above measure gene expression levels on a tissue-by-tissue basis. However, none
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of the tissues in the body are merely an agglutination of a homogenous population of cells.
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Organs are made up of various cell types, and even the cells of the same type have different
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functions according to their location (Kato and Kimura, 2003; Waterland and Jirtle, 2004).
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Many gene-association and genetic laboratory animal studies support an important variable
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in the expression of genetic information and a major contributor to disease development,
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namely the influence of diet on the expression of genetic information. Although many
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chemicals in foods are nutrients, i.e., are metabolized to energy or involved in key metabolic
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reactions (e.g., vitamins), some naturally occurring chemicals in foods are ligands for
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transcription factors and directly alter gene expression, whereas other dietary chemicals alter
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signal transduction pathways and chromatin structure to indirectly affect gene expression
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(Kaput, 2004).
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The current excitement of the potential use and outcomes of nutrigenomics is, indeed,
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phenomenal. The latter is perhaps not surprising, because the new technology made possible
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by the decoding of the genome has to be evaluated for its potential in providing answers to
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the complex and multifactorial nature of the role of nutrition on optimal health, disease
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prevention, and treatment (Labadorios and Meguid, 2004). Evaluation of gene expression is
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an effective way to identify genes important in the regulation of traits of economic
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importance in livestock production. The application of these research methods in animal
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science will contribute to a greater understanding of the genetic regulation of traits important
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to livestock production (Moody, 2001).
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Association nutrition-health
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The role of nutrition in health is a profoundly important example of interactions between
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genotype and environment. The current "-omic" era (genomic, proteomics, transcriptomics,
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etc.) of biomedical research has already provided an overwhelming plethora of data
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regarding the sequence blueprint that defines many organisms (e.g., humans, mice, plants,
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insects, worms, yeast, and bacteria) (Liu and Sturley, 2004; Kaput, 2004). The genome and
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its application through functional genomics are building knowledge most rapidly to identify
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the causes and complications of diseases and resolve them trough therapeutic intervention.
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Nutritionist now arrives at the genomics era with the goal go to go beyond curing disease and
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improving health of entire populations (German et al., 2002).
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Figure. 3. Health effects of food compounds are related mostly to specific interactions on a
molecular level. SNP, single nucleotide polymorphism. (Adapt from Ommen, 2004).
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The science of nutritional genomics should increase our understanding of nutrient-gene
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interactions and the effects of these interactions on health (Swanson et al., 2003). There are a
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number of potential benefits from nutritional genomics for individuals, groups and society.
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Many diseases and disorders are related to suboptimal nutrition in terms of deficits of
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essential nutrients, imbalance of macronutrients, or even toxic concentrations of certain food
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compounds. We realize more and more that the nutrition and health relationship is solidly
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anchored in interactions on the levels of DNA, RNA, protein, and metabolites (Figure 3)
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(Ommen, 2004).
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Data from quantitative trait loci (QTL) mapping illustrates one of the reasons that candidate
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gene–disease association studies are not replicated: most cases of chronic diseases are not
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caused by mutations in single genes but rather are due to complex interactions among
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variants of several to many genes (Figure 4A). QTL mapping can be done in humans, but the
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process is best explained with laboratory animals. Briefly, two parental inbred mouse strains,
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selected for differences in some observable or measurable phenotype, are bred to produce an
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F1 generation. F1 mice are backcrossed to each of the parental strains, thereby producing an
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F2 generation differing in disease susceptibility because chromosomal rearrangements occur
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during meiosis. The incidence of disease or severity of subphenotypes of the disease are
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measured in F2 mice and statistically associated with chromosomal regions from each of the
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original parental strains. A given pair of inbred mice may have 10 to 15 regions that
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contribute to the complex phenotype in those strains, and different pairs of strains may reveal
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new QTLs (Kaput, 2004).
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Figure 4. Genotype × environment interactions. Example of gene expression in healthy (A)
and unbalanced nutritional (B) states. (A) Gene 1 is a global transcription factor regulating
2 (and other transcription) factors. In turn, 2 regulate 3 and 4 expressions. Another
transcriptional regulator, 1, affects 2 expressions. Genes encoding 1, 1, 1, and 2 are
not regulated by transcription factors influenced by dietary chemicals. (B) Unbalanced
nutrition alters the expression (----) of 1, ultimately decreasing the amount of 3 (but
increasing the expression of 4 ( ). Gene 1 is expressed in response to changes in
metabolism or the altered concentration of a dietary ligand ( ). Some transcription factors or
expression of individual genes may not be affected directly or indirectly by dietary chemicals
(e.g., 1, 1 and 1, 2), whereas others ( 1 through 4 and 1) may be affected. The effects
on transcription may result from increased concentrations of ligand derived from the diet
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acting on a reference or variant (single nucleotide polymorphism) gene sequence. Changing
the concentration of effectors proteins ( 3, 4, 1) will alter metabolic flux and
concentrations of metabolites, inducing further changes in cell physiology (Adapt from
Kaput, 2004).
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The nutrition-health relationship depends on the adaptive capacity of genes and their
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functioning with the diet consumed (Chavez and Muñoz, 2003). The idea that adverse
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diet/genome interaction can cause disease is not new. The first example was the discovery of
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galactosemia by F. Gppart in 1917. Galactosemia is a rare recessive defect in galactose in the
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blood, causing a number of heath problems including mental retardation. This disease can be
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managed with diets low in lactose (Kaput and Rodriguez, 2004). Many chronic diseases are
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polygenic in nature and result from interactions of a subset of genes with environmental
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factors. The associations between specific food intake and chronic disease was first recorded
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in 1908 and was based upon observations of Ignatovski that rabbits fed meat, milk, and eggs
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developed arterial lesions resembling atherosclerosis in humans. Increase metabolism of
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protein also will increase the production of urea, with the corresponding increase in
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membrane permeable ammonia (NH3) and its ionized form NH+4. Ammonia released in the
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alimentary tract of animals by microbial enzymes can disrupt metabolic pathways, alter the
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gastrointestinal mucosa, inhibit rates of growth in animals, alter brain functions, and promote
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cancer (Kaput and Rodriguez, 2004). Effects of age, sex, environment, genetic differences,
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etc., need to be taken into account, in addition to nutritional variation and development of
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(pre-) disease stages (Ommen, 2004).
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Some diet-regulated genes
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Mammalian phenotype can be persistently altered via nutritional influences on the
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establishment and/or maintenance of epigenetic gene regulatory mechanisms. Epigenetics is
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the study of heritable changes in gene expression that are not mediated by DNA sequence
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alterations (Waterland and Jirtle, 2004; Kaput and Rodriguez, 2004). Accordingly, nutritional
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perturbation of epigenetic gene regulation is a likely link between early nutrition and later
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metabolism and chronic disease susceptibility. Since dietary chemical are regularly ingested
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and participate indirectly and directly in regulating gene expression, it follows that a subset
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of genes regulated by diet must be involved in disease initiation, progression, and severity. A
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separate confounding influence on analyses of diet-induced changes in genes expression
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patterns is the health of the subject (laboratory animal or human). (Kaput and Rodriguez,
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2004). Extensive human epidemiologic data have indicated that prenatal and early postnatal
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nutrition influence adult susceptibility to diet-related chronic diseases including
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cardiovascular disease, type 2 diabetes, obesity, and cancer (Waterland and Jirtle, 2004, Hu
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and Kong, 2004). The presence of a disease may also influence expression of genetic
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information differently depending on genetic background or the presence of a disease
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phenotype (Kaput, 2004).
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The hurt for a single macronutrient or micronutrient that will prevent chronic diseases is
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destined to fail. It is more likely that dietary imbalances from micronutrient deficiencies to
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overconsumption of macronutrients or dietary supplement are the modifiers of metabolism
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and potentiators of chronic disease. Although the complexity of food and genotypic appears
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daunting, molecular and genetic technologies may provide the means for identifying
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causative genes (or their variants) and the nutrients that regulated them (Kaput and
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Rodriguez, 2004). Concept of the nutrition and health link is fully appreciated only if
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uncoupled from a biomedical "therapy-like" approach and linked to the awareness that
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multiple minor changes in metabolism and its biochemical regulation contribute to the onset
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of chronic nutrition-related disorders such as obesity, type 2 diabetes, cardiovascular
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disorders, osteoporosis, and chronic inflammatory syndromes. In other words, in this area,
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maintaining optimal metabolism is of key importance for improving health and preventing
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diseases (Ommen, 2004).
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Individualized nutrition-the future of pet foods
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Dietary intervention based on knowledge of nutritional requirement, nutritional status, and
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genotype (i.e., “individualized nutrition”) can be used to prevent, migrate, or cure chronic
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disease (Kaput and Rodriguez, 2004; Ommen, 2004). It is now accepted that nutrients (i.e,
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macronutrients, micronutrients and antinutrients) alter molecular process such as DNA
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structure, gene expression, and metabolism, and these in turn may alter disease initiation,
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development, or progression. Individual genetic variation can influence how nutrients are
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assimilated, metabolized, stored, and excreted by the body. In the near future, quick, low-
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cost, point of care tests will be available to assist patients and physicians to achieve, manage,
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and prolong health through dietary invention. The desired outcome of nutrigenomics is the
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use of personalized diets to delay the onset of disease and optimize and maintain human and
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animals health (Kaput and Rodriguez, 2004).
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Genomic technologies are powerful tools will be applied to the pet food industry in the future
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to optimize nutritional and health status. This will be accomplished by determining minimal
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nutrient requirements and mechanisms by which “functional” ingredients act to prevent and
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treat diseases. Genotype-nutrients interactions will have to be ascertained and considered
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when formulating diets for a given genotype. Several polymorphism relating directly to
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nutritional and immunological status already have been identified in humans, dogs and cats,
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This list will continue to grow as the field of genomics mature (Swanson et al., 2003) (Figure
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Figure 5. Nutritional efficacy is subject to external and internal variabilities. The human
genome affects the relation between nutrition and health in two ways: 1) genetic variation,
resulting in interindividual differences in response, with implications toward susceptible
subgroups in the population (nutrigenetics), and 2) the effect of the many bioactive
compounds in our nutrition on gene expression and the resulting changes in physiology
(nutrigenomics)(Adapt from Ommen, 2004).
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The nutritional systems biology concept described above (functional genomics applied to
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integrated analysis of biological systems) can be used for assessment of safety and efficacy in
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the relevant physiologic human context, including interindividual variation. The
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multiparameter biomarkers will be sufficiently sensitive to be used at physiologic conditions
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and will be able to identify subtle changes from the homeostasis. Thus, in developing the
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area of nutrigenomics, new methods of safety evaluation for food compounds may be
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implemented (Ommen, 2004). Like personalized drug therapy, genomics will allow diets to
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be formulated according to genotype, which will be much more precise than some of the
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current dog diets marketed for large size or geriatric animals (Swanson et al., 2003).
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Methodology used to study functional genomics
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The evaluation of genes expression is an effective way to identity genes important in the
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regulation of traits of economics importance in livestock production. Several techniques have
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been developed for this purpose, and important resource are currently in developed that will
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facilitate continued research and discovery in this area. The application of these research
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methods in animal science will contribute to a greater understanding of the genetic regulation
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of traits important to live stock production (Moody, 2001).
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In the last two decades, techniques for the evaluation of genes expression have progressed
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from methods developed for the analysis of single, specific genes (e.g., Northern, slot, and
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dot blotting; semiquantitative and quantitative reverse transcription and PCR, and nuclease
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protection assays) to techniques focused on identifying all genes that differ in expression
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between or among experimental samples (e.g., subtractive hybridization, differential display,
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sequencing of expressed sequence tags, serial analysis of gene expression, and hybridization
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to microarray) (Moody, 2001; Swanson et al., 2003). Now the gene expression profiling may
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be performed with the use of microarray technology, which can monitor the expression of
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thousands of genes simultaneously. Microarrays are powerful alternatives to conventional,
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classic techniques that have limited past experiments to measuring only a few genes at time
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(Swanson et al., 2003; Kim et al., 2004; Anderle et al., 2004).
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Microarray technology
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Development in Pat Brow’s lab at Stanford, for analyzing the expression of all 6,200 genes
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present in yeast simultaneously, microarray have become the foundation for most recent
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functional studies of genes (DeRisi, et al., 1997: Cited by Ashwell, 2002). Microarrays are
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small glass slides that contain probes for tens of thousands of genes on a small glass surface.
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They allow researchers to simultaneously analyze the expression of all of the genes that have
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been synthesized or printed on the arrays. High-density microarray experiments, when
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properly performed, analyzed, and interpreted, have unparalleled power to perform the task
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of transcriptional profiling (Middleton et al., 2004; Ross et al., 2004). Technologies are being
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developed that allow the simultaneous determination of the expression of many thousands of
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genes at the mRNA (transcriptomics) and protein (proteomics) levels (Kato and Kimura,
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2003; Al-Khaldi and Mossoba, 2004; Hirschi et al., 2001). Multiple arrays can be normalized
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so that expression of a given transcript can be compared under different experimental
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conditions, such as numerous time points within a model of cellular differentiation (Burton
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and McGehee, 2004 ).
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Use of DNA microarray technology in food and nutrition science
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Ultimately, the field of nutrition will be fundamentally changed by molecular genetics, the
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availability of massive amounts of DNA sequence information and the development of
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technologies to exploit its use, such as microarray analysis (Hirschi et al., 2001; Burton and
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McGehee, 2004). Microarrays that include genes with currently unknown function or
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expressed sequences tags (ESTs) offer the exciting possibility of new gene discovery and
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will likely play a key role in the translation of genomics into functional genomics (Middleton
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et al., 2004; Cogburn et al., 2003; Albelda and Sheppard, 2000). The advent DNA microarray
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technologies is now permitting systematic approaches that will enable the characterization of
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nutrient metabolism and function between population groups and perhaps among individuals
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within a group. This technology will have a profound effect on basic nutritional research,
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disease diagnosis, drug development and engineering of therapeutics to alleviate nutritional
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disorders (Hirschi et al., 2001).
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Microarray analysis of genome-wide mRNA expression profiles offer a power tool to
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intercept, at an early and obligatory step, the flow of molecular information from the genome
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to the proteome. Recent studies using microarray tools to define the actions of antioxidant
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micronutrients have identified modulations of multiple gene networks in response to chronic
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changes in the micronutrient status (Gohil and Chakraborty, 2004). Our studies indicated that
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DNA microarray analysis is a highly effective way to understand the function of dietary
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proteins and the global response of the body to protein nutritional status. In addition, DNA
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microarray analysis is a promising tool for the safety evaluation of dietary components,
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including the determination of the adverse effects of an excess of an amino acid, because it
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offers an extremely wide range of biomarkers for this purpose. Safety evaluations using
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microarray analyses will probably greatly reduce the period of animal testing needed, because
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changes of gene expression usually occur faster than phenotypic changes (Kato and Kimura,
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2003). The mechanisms of action that are involved in the effects of lipids on cell regulation
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are very complex. Thus, the use of microarrays, which allows the measurement of mRNA
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levels of thousands of different genes simultaneously, is a useful tool to elucidate such
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complex systems (Anderle et al., 2004).
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Another potential use of microarray technology in the field of nutrition science is analogous
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to that of pharmacological or toxicological studies in which nutritive components of foods are
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viewed as drugs. By studying the cellular and molecular reaction to specific nutrients, in
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specific doses, between population groups and among individuals within those groups, one
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can begin to define the optimal cellular doses to produce the desired molecular responses in a
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given subpopulation (Hirschi et al., 2001). Microarrays provide the opportunity to discover
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abnormalities in the expression or sequence of genes that were never thought to be involved
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in a disease. In addition, it is possible to analyze entire groups of genes that perform similar
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functions in a cell, to determine the most affected gene groups in a disease, or to analyze
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entire groups of genes present in close proximity (at the same cytogenetic locus) to rapidly
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determine the most affected functional or genetic regions (Middleton et al., 2004).
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The strongest feature of DNA microarray analysis, which is its ability to generate huge
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amounts of data, can also be a source of troubles, especially when tissue samples in vivo are
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used. First, contamination of the very small amount of a different tissue such as, for example,
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fat and pancreas in intestine samples could result in misleading results. More care thus needs
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to be taken in planning, performing and interpreting in vivo experiments using DNA
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microarray technology (Kato and Kimura, 2003). Cogburn et al., (2003) DNA microarray
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analysis has been a fruitful strategy for the identification of functional genes in several model
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organisms (i.e., human, rodents, fruits fly, etc.). They have constructed and normalized five
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tissue-specific or multiple-tissue chicken cDNA libraries [liver, fat, breast, and leg
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muscle/epiphyseal grow plate, pituitary/hypothalamus /pineal, and reproductive tract
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(oviduct/ovary/testes)] for high-throughput DNA sequencing of expressed sequences tags
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(EST). The analysis of the changes in the gene expression profile for each tissue has
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significance when the response as a whole is the matter of interest (e.g., the response of the
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liver to a gluten diet). In contrast, if a more precise mechanism of response needs to be
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considered, the heterogeneity of the cell types within a tissue should be taken into account.
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This issue must be carefully addressed in the application of microarray technology when it is
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applied to the study of toxic effects (Kato and Kimura, 2003).
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Application of Chicken’s Microarrays
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Expressed gene (EST) sequencing projects for chicken exist at the U. of Delaware, U. of
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Hamburg (Germany), the Institute of Animal Health (England), and the Rosling Institute
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(Scotland). Conservatively, there are 30,000 + EST sequences from a variety of tissue (e.g.,
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spleen, fat, liver). A normalized cDNA library was constructed from chicken small intestine
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in an effort to generate additional EST data for Chicken related to nutrition, growth, and
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development. Approximately 11,891 unique and novel genes have been identified thus far as
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being expressed in the chicken small intestine. For these genes any number many play a role
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in either cell regulation or direct absorption of specific nutrients and thus impact growth and
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development. Functional studies of this large number of genes not easily or efficiently
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performed and will be limited to assigning specific role to genes as defined by experiments
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manipulation specific nutrients. These results indicate that it is extremely feasible to utilize
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microarrays constructed in this manner to detect changes in gene expression resulting from
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nutritional manipulation (Ashwell, 2002). The current bonanza of chicken gene sequences
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and chicken DNA microarrays for global gene expression profiling, provide a powerful
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molecular tools to advance in the new era of functional genomics in chickens (Cogburn et al.,
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2003; Burgess, 2004).
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Implications
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Genomics technologies are powerful tools that will be applied to the animal nutrition.
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Nutrigenomic will be important in the determination of nutrient requirements of animals at
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different life stages, disease prevention and treatment, and regulation in optimizing of animal
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nutrition and health status. Nutrigenomics will definitely play a vital role in the future for
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animal science research.
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