Information - Glossary

Nutrigenomics is Interdisciplinary Science

One of the exciting aspects of nutritional genomics is its interdisciplinary nature - we must interact and collaborate with experts in many fields of research.  However, this is also a challenge since different fields have different terminology.  Specific meanings may not be clear to the nonexpert.  We provide an inexhaustive glossary of terms used in nutrigenomics research from many of these disciplines.  The glossary was developed for the edited book:  Nutritional Genomics: Discovering the Path to Personalized Nutrition (Kaput and Rodriguez, eds) Wiley and Sons (2006). 

 

The Glossary

Adipogenesis - The formation of adipose tissue (fat cells). May also refer to the production of fat, either fatty degeneration or fatty infiltration.

Adipose tissue - Specialized tissue that stores fat.

Agonist  -  Induced Activation - For nuclear receptors, a small molecule -binds to an inactive nuclear receptor causing conformational changes that result in protein-DNA interaction, recruitment of cofactors, transcription factors ultimately leading to gene transcription. After dissociation of the agonist, the nuclear receptor may return to its inactive state.

Alleles - One of two forms of a gene.  One of the alleles is inherited from the mother, the other from the father.  Two copies of the same allele for a given gene are called the homozygous condition while two different alleles for the same gene is called the heterozygous condition.

Alpha-linolenic acid (ALA) - An essential fatty acid consisting of a chain of 18-carbons with 3 double-bonds near the methyl or "omega" end of the carbon chain. ALA is an omega-3 (or n-3) fatty acid and is the precursor of eicosapentaenoic acid (EPA) and docasahexaenoic acid (DHA). EPA can be converted to the eicosanoids, prostaglandins, leukotrienes and thromboxanes via cyclo-oxygenases 1 and 2 (COX1-2) and lypoxygenase (see essential fatty acids and eicosanoids).

American Society for Testing and Materials (ASTM) - A section of the American National Standards Institute (ANSI) that has a subcommittee (E31) for general healthcare informatics. This E31 Subcommittee on Healthcare Informatics develops standards related to the architecture, content, storage, security, confidentiality, functionality, and communication of information used within healthcare and healthcare decision making, including patient-specific information and knowledge.

Aneuploidy - An abnormal number of chromosomes.  In the case of humans, any chromosome number more or less than 46, is referred to as aneuploid condition. 

Antioxidant - Chemical that inhibits oxidation and reacts with free radicals to form a harmless product.  An antioxidant will have one or more unpaired electrons.

Apolipoprotein - The protein component that combines with a lipid to form a lipoprotein.

Apoptosis - Programmed cell death.  A normal cellular sequence of reactions that destroys the cell without releasing harmful substances into the surrounding area.

Array Analysis - A solid support on which a collection of gene  - specific nucleic acids are placed at defined locations, either by spotting or direct chemical synthesis. In array analysis, a nucleic acid sample is labeled and then hybridized with the gene  - specific targets on the array. Based on the amount of probe hybridized to each target spot, information is gained about the specific identify and quantity of the nucleic acid in the sample. The advantage of arrays is that they allow target sequences to be interrogated by the thousands instead of individually.

Asthma is the most common chronic disease of children. It is characterized by inflammation of the airways leading to airway obstruction and restricted breathing. Airway obstruction either resolves spontaneously or with the use of medications like albuterol, the most common of these medications.  In the U.S., Puerto Ricans have the highest asthma prevalence while Puerto Ricans and African Americans have the highest asthma severity and mortality.

Atherosclerosis - The progressive narrowing and hardening of the arteries over time and is often used to describe a condition where lipids (fats) collect under the inner lining of damaged artery walls.

Bifidobacteria - Lactic acid producing microorganisms that inhabit the gastrointestinal track.

Bilirubin - A chemical found in bile that is the normal degradation products of hemoglobin and other heme-containing proteins.

Bioactivation - The conversion of an inactive compound into an active one within a living organism.

Bioactive - A chemical (often found in various foods) that interacts with the molecular components of a living organism.

Biobank - A collection of biological specimens.  Often used to describe a collection of DNA samples.

Biocomputation - Analyses of biological data usually with algorithms or programs for reducing complexity of the data.

Bioinformatics - The collection, storage, manipulation, management, and retrieval of biological data.

Biological system  - An organism and its design properties, which specify phenotypic outputs given perturbation inputs.

Biomarker - A substance sometimes found in the blood, other body fluids, or tissues that can be used to measure the presence or progress of disease or the effects of treatment.

Bowman Birk inhibitor - A protease inhibitor of trypsin and chymotrypsin found in soybeans.

BMI = Body Mass Index - BMI is calculated by dividing a person's weight (in kilograms) by height in meters squared.  (BMI = kilogram/meter2).

Buffering - The process by which a robust system absorbs changing inputs from the environment, while maintaining stable outputs .  Based on the concept of a chemical buffer, which is a solution (usually) consisting of a weak acid and its salt or a weak base and its salt that maintain changes in pH.

Buffering capacity - The amount of stability/robustness that a gene or genetic module imparts on the system in response to a particular perturbation input; reflects the strength of genetic interaction .

Buffering specificity  - The combined selectivity and capacity of genetic interactions across a series of different perturbations .

Calorie - The amount of heat (i.e., energy) needed to raise the temperature of a one gram of water from 15 to 16 Celsius or 4.184 absolute joules.  One food calorie is equivalent to 1000 calories or 1 kilocalorie. Calories are used to describe the energy content of various foods.  For nutrition, a food calorie can be defined practically as the amount of energy consumed by a 150 lb. individual during one minute of sleep.

Carcinogen - A substance or chemical agent that perturbs normal cellular processes leading to unscheduled cell division and cancer, or the increased risk of cancer.

Carcinogenesis - The molecular processes that result in cancer.

Catechins - A natural plant compound belonging to the class of polyphenol present in high concentrations in green tea. Catechins like ECGC are potent antioxidants and have been shown to block signaling pathways that lead to cell proliferation in human and animal cells.

Cellular context - The perturbation state of the cell, which changes as a function of genetic and environmental alterations. Genetic interaction, and thus genetic buffering, is always measured with respect to cellular context .

Chemopreventive Agent - A chemical constituent, drug or food supplement that prevents disease by interrupting deleterious biological reactions or processes.

Chimera - An organism, organ, or part consisting of two or more tissues of different genetic composition, produced as a result of organ transplant, grafting, or genetic engineering.

Chromatin - A complex of proteins (primarily histones) and DNA that make up the chromosome. Chromatin exists as transcriptionally active "euchromatin" and transcriptionally silent "heterochromatin."  With a few exceptions, chromatin can transition between euchromatin and heterochromatin depending on how the DNA and histones are epigenetically modified.

Chronic disease - A disease that persists for a long time. A chronic disease is one lasting 3 months or more, by the definition of the U.S. National Center for Health Statistics. Chronic diseases generally cannot be prevented by vaccines or cured by medication, nor do they just disappear. Eighty-eight percent of Americans over 65 years of age have at least one chronic health condition (as of 1998). Health damaging behaviors - particularly tobacco use, lack of physical activity, and poor eating habits - are major contributors to the leading chronic diseases.  From MedicineNet.com.

Common genetic variant - Genetic differences between individuals involving a single nucleotide pair or small insertions or deletions of a few nucleotides.  "Common" refers to the fact that these differences occur in more than 1% of the population and therefore, are not considered mutations.

Current Procedural Terminology (CPT) - A uniform set of codes that identify each service, procedure, or supply for diagnosis, symptom, condition, or problem.  CPT(R)Current Procedural Terminology was developed by the American Medical Association in 1966.  See also International Classification of Diseases.

Cytochrome P450s - A family of liver enzymes involved in metabolism of exogenous and endogenous chemicals.

Data Model - A conceptual framework for the development of a new or enhanced software application.  The purpose of data modeling is to develop an accurate model, which may be shown in a graphical representation such as UML, of the information needs and business processes addressed by a particular application or connected set of operations

Dauer - Metabolically dormant larva stage.

Detoxification - Any process that removes a toxin.  In biological systems, a process that usually requires enzymes for modifying reactive chemicals. For example, the liver enzyme, NAT2, can detoxify aromatic amines in tobacco smoke.

Diallelic - A condition in which a gene at a given locus is represented by two alleles as opposed to monoallelism, a condition where one allele is missing or silenced.

Diet - The sum total of all the nourishing materials (food, drink and supplements) consumed by an organism.  In humans (and most animals), a proper diet requires certain essential vitamins, minerals, proteins and fats. The balance between starvation and obesity depends on the amount of nourishing materials consumed as fuel and the amount of energy expended.

Dietary phytosterols - Plant derived chemicals with a typical ring structure similar to sterols found in animals.

Dietary Reference Intake (DRI) - Estimates of daily minimal dietary intake of established nutrients provided by the Food and Nutrition Board of the National Research Council. Optimal levels have not been formally established. Also known as Recommended Daily Intake (RDI).

Digital Imaging and Communications in Medicine (DICOM) -The Digital Imaging and Communications in Medicine (DICOM) Standard was developed for the transmission of images and is used internationally for Picture Archiving and Communication Systems (PACS). This standard was developed by the joint committee of the ACR (the American College of Radiology) and NEMA (the National Electrical Manufacturers Association) to meet the needs of manufacturers and users of medical imaging equipment for interconnection of devices on standard networks.

Dosage compensation - Any system that equalizes the amount of product produced by genes present in different numbers.  In mammals, it describes the X - inactivation mechanism that ensures equal amounts of X - specific gene activity in XY male and XX female cells.

Dyslipidemia - Abnormal lipid profiles usually characterized by high triglyceride concentrations, low HDL cholesterol, and increased concentrations of small, dense LDL; associated with metabolic disorder such as insulin resistance, obesity and Type 2 diabetes.

Ectopic gene expression - Expression of a gene in a cell where it is typically not expressed.

Eicosanoids - Extremely potent hormone-like molecules made from long-chain, unsaturated fatty acids like arachidonic acid and eicosapentaenoic acid (EPA).  Unlike hormones, eicosanoids, like prostaglandins, thromboxanes and leukotrienes, act in and near the tissue where they are synthesized. Series 1 and 3 prostaglandins generally prevent blood clotting, reduce pain and inflammation, reduce blood sodium, reduce water retention, relax blood vessels and lowers blood pressure.  Series 2 prostaglandins produce the opposite affects. Leukotrienes are involved in muscle contraction in the lungs and overproduction can cause asthmatic attacks (see essential fatty acids, LA and ALA).

Endothelial cells - Cells that line the interior surface of heart, blood vessels, and serous cavities of the body.

Enhancers - A set of short sequence elements which stimulate transcription of a gene and whose function is not critically dependent on their precise position or orientation.

Epidemiology - Classically, the study of the occurrence of a disease in a population, especially the factors that influence incidence, severity, and distribution.

Epistasis - In its strictest classical genetic definition, is the interaction of one gene (or locus) with another.

Epigenetics - The study of those reversible and heritable changes in gene function that do not involve changes in the DNA sequence.  Epigenetics (meaning above or on top of genetics) can serve as a powerful modifier and potentiator of genetic influences and it can be highly responsive to environmental factors like nutrition.

Epigenetic modifications- The chemical "marking" of chromatin (DNA and associated histone proteins) that is passed from cell to cell and generation  to generation by mitosis or meiosis.  Modifications include DNA methylation at cytosine nucleotides to produce 5-methylcytosine (5mC) as well as the methylation and acetylation of histone proteins H3 and H4, respectively.  Methylation of DNA and histone H3 tends to silence genes while acetylation of histone H4 (particularly lysine 16) tends to activate gene expression.

Essential Fatty Acids - There are two fatty acids that must be obtained from dietary sources because they cannot be synthesized by the body: linoleic acid (18:2) and alpha-linolenic acid (18:3).  Sunflower, safflower and walnut oils are good sources of linoleic acid while perilla and flaxseed oils are good sources of alpha-linolenic acids. While ocean fish like halibut, herring and salmon are relatively low in alpha-linolenic acids, they are good sources of the omega-3 fatty acid, DHA (see alpha-linolenic acid, linoleic acid and eicosanoids).

Epigenome - The sum total of all epigenetic modifications of an individual's genome. An individual's phenotype is ultimately a combination of the genotype (all genes and their alleles in the genome) and epigenome (all the chemical modifications of the chromatin).

Etiology - The causes or origins of disease.

Exon - DNA sequences which occur in mRNAs which contain ribosomal binding sites, protein coding sequences, and information for mRNA stability and perhaps cellular location.

Expression - A term used to describe the synthesis of mRNA from a gene by the process of transcription.  Transcription is achieved with a complex consisting of RNA polymerase II, and several transcription factors all acting on a region of the gene called the promoter. Expression is synonymous with gene activation while lack of expression is equivalent to gene silencing.

Folic Acid - A yellowish-orange compound, C19H19N7O6, of the vitamin B complex group, occurring in green plants, fresh fruit, liver, and yeast. Also called folacin, folate, vitamin Bc.

Gene activity  - Transcription, translation, stability, physical association or enzymatic function of molecules ultimately attributable to the same segment of DNA.

Genetic association studies  - Statistical analyses that link chromosomal regions with disease subphenotypes or incidence.

Genetic buffering - A property of biological systems whereby stability (robustness) of phenotypic outputs is conferred by gene activities that interact to absorb system perturbations .

Genetic interaction - The non-additive effect that variation (gene deletion) at one genetic locus has on the phenotypic response of a biological system to a defined perturbation. Interactions can be synergistic (enhancing effect of perturbation) or antagonistic (suppressing effect of perturbation).

Genetic interaction network - An experimentally determined set of genetic interactions derived by quantitative phenotypic analysis of single gene knockout strains in comparison with an isogenic reference (i.e., no deletion) strain. Genetic interaction networks are dynamic, depending upon the panel of knockout strains used and the genetic and/or environmental cellular contexts tested .

Genetic system - The genetic underpinnings of a biological system, i.e. the attributes of gene activities and the organization of their interactions that confers properties upon biological systems.

Genetic buffering capacity - The strength of interaction between a gene, or genetic module, and a particular perturbation. Strong interactions indicate genes with high buffering capacity, meaning that the gene activity is required for phenotypic stability in response to even weak intensity of perturbation .

Genetic buffering selectivity - The qualitative pattern of interactions for a gene or genetic module, where gene interaction is measured in the context of different perturbation types .

Genetic buffering specificity - The combined buffering capacity and selectivity of a gene or genetic module. Genetic interaction modules are defined on the basis of shared genetic buffering specificity between individual genes. Hierarchical clustering of quantitative interaction data is presented as one strategy for depicting genetic buffering specificity and identifying genetic interaction modules.

Genetic buffering protocol  - The organization of genetic buffering modules and their molecular activities that confer cellular robustness in response to a perturbation. Connectivity between genetic interaction modules together with molecular genetic knowledge of the functions of genes in each module facilitates hypotheses about genetic buffering protocols.

Genetic epidemiology - The study of genetic components in complex biological system.

Genetic interaction module  - A set of genes sharing the same genetic buffering specificity. Gene interaction modules are experimentally defined using knockout strains in a co-isogenic genetic background, are dynamic with respect to the perturbations and gene deletions tested, and are also dependent upon the method used for classifying genes according to their shared buffering specificity (e.g., hierarchical clustering) .

Genetic polymorphism - The difference in DNA sequence from a reference sequence.

Genistein - A chemical of the isoflavone class found in plants that has a structure similar to estrogen.  Hence, it is a phytoestrogen.

Genomics  - The high throughput, highly parallel study of all the genes (and gene products - RNA and proteins) as a dynamic system, over time, determining how they interact and influence biological pathways, networks, and physiology, in a global sense.

Genotype - An individual's genetic identity based on the specific set of alleles from maternal and paternal chromosomes.  The genotype is not outwardly visible.

Gut microflora - All of the microbes in the gastrointestinal tract.

Haplotype - A contraction of the phrase "haploid genotype".  A specific collection of linked polymorphism (e.g., SNPs, simple tandem repeats, or insertions and deltions) within a cluster of related genes or region of a chromosome.

Haplo - sufficient - When one functional allele suffices as well as two to produce the normal phenotype.

Health disparity - Referring to gap in the quality of health or health care between ethnic/racial groups and the general population. These population-specific differences are frequently observed as increased frequency, earlier onset, greater severity, higher morbidity and/or unresponsiveness to treatment for a particular disease.

Health Information Standards Board (HISB) - A subgroup of the American National Standards Institute (ANSI). The American National Standards Institute's Healthcare Informatics Standards Board (ANSI HISB) provides an open, public forum for the voluntary coordination of healthcare informatics standards among all United States' standard developing organizations.

Health Insurance Portability and Accountability Act (HIPAA) -The Administrative Simplification provisions of the Health Insurance Portability and Accountability Act of 1996 are intended to reduce the costs and administrative burdens of health care by making possible the standardized, electronic transmission of many administrative and financial transactions that are currently carried out manually on paper. HIPAA also has some significant implications for the solicitation of participants to become research subjects in research settings.

Health Level 7 (HL7) - A standards development organization formed in 1987 to produce a standard for hospital information systems. HL7 received ANSI accreditation as an Accredited Standards Development Organization in 1994. The HL7 standard is an American National Standard for electronic data exchange in health care that enables disparate computer applications to exchange key sets of clinical and administrative information. HL7 is primarily concerned with movement within institutions of orders; clinical observations and data, including test results, admission, transfer and discharge records, and charge and billing information (coordinating here with X12). HL7 is the selected standard for the interfacing of clinical data for most health care institutions.

Hepatocarciogenesis - The formation of cancer in the liver.

Hepatocyte - A cell of the liver.

Heritability - The degree to which the variance in the distribution of a phenotype is attributable to genetics. For example, high and weight in humans are from 40% to 70% heritable or due to genetics.

Heterocyclic amines - A class of chemicals with a ring structure and amine groups.  Can be formed by cooking food.

Heterologous genes - Usually refers to introduction of a foreign gene in another organism. 

HL7 Reference Information Model  - A conceptual model that defines all the information from which the data content of HL7 messages is drawn. The HL7 version 3 RIM has many features necessary for representing and modeling nearly any process in a healthcare setting.

Homologous genes - Two or more genes whose sequences are significantly related because of a close evolutionary relationship, either between species or within a species.

Hyperforin - A chemical found St John's wort (and other plants) that is bioactive.  It can bind and activate expression of genes involved in drug metabolism.

Hypertension - Arterial disease in which chronic high blood pressure is the primary symptom.

Imprinting - The silencing of genes on maternal and paternal chromosomes by methylation of DNA (and acetylation of certain lysine residues in histone H3).  Imprints are erased in primordial germline cells and reapplied to the maternal and paternal chromosomes during oogenesis and spermatogenesis.  Methylating enzymes are needed to maintain chromosome imprints during each and every cell division. Loss of imprinting (LOI) can have serious health consequences.

Insulin resistance - Reduced sensitivity to insulin by the body's insulin-dependent processes (as glucose uptake, lipolysis, and inhibition of glucose production by the liver) that results in lowered activity of these processes or an increase in insulin production or both.  Insulin resistance is typical of type 2 diabetes but often occurs in the absence of diabetes.

International Classification of Diseases (ICD-9-CM) -The International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) was developed in the United States to provide a way to classify morbidity data for indexing of medical records, medical case reviews, and ambulatory and other medical care programs, as well as for basic health statistics. It is based on the World Health Organization (WHO) international ICD-9. A version based on ICD-10 (ICD-10-CM) is in preparation.  See also CPT.

Isoflavones - A class of plant metabolites similar in structure to estrogen.  The isoflavones, diadzin and genistein are found in soybeans and other plants and believed to provide health benefits.

Isoelectric point - The pH at which an amphoteric molecule has a net charge equal to zero.

IRB protocol - Institutional review board (IRB) is a committee of physicians, statisticians, researchers, community advocates and others that ensures that a clinical trial is ethical and the rights of study participants are protected.  Procedures for studies must be approved by the IRB before being carried out.  IRB approval is required for clinical trials and any research involving humans.

Knock - out (KO) - The targeted inactivation of a gene typically in a cell culture, plant, or experimental animal.

Ligand - A molecule that binds to a specific site on a protein such a nuclear hormone receptor, membrane receptor, enzyme or antibody.  A ligand can be an activator or inhibitor.

Linkage disequilibrium (LD) - LD describes a condition where alleles occur together more frequently than can be accounted for by chance. When alleles (or genetic marker) are in strong LD, this indicates that the two alleles are physically close to each on the chromosome. Genetic markers in strong LD with an inherited disease can be used to map and characterize candidate genes involved in that disease.

Linoleic acid (LA) - An essential fatty acid consisting of a chain of 18-carbons with 2 double-bonds near the methyl or "omega" end of the carbon chain.  Therefore, LA is called an omega-6 (or n-6) fatty acid and it is a precursor of arachidonic acid (20:4).  Arachidonic acid is used by cyclo-oxygenases 1 and 2 (COX1-2) to produce eicosanoids like prostaglandins, leukotrienes and thromboxanes (see essential fatty acids and eicosanoids).

Lipogenesis - The synthesis of lipids from nonlipid precursors.

Logical Observations - Identifiers, Names, Codes (LOINC).  Coding system for the electronic exchange of laboratory test results and other observations. LOINC development involved a public-private partnership comprised of several federal agencies, academia, and the vendor community. This model can be applied to other standards setting domains.  www.loinc.org

Long terminal repeats (LTRs) - Long repeating sequences of DNA usually at either end of DNA sequence.  They encode sites of recombinase binding and action or transcriptional activity.

Lumen - The central cavity of a cell.

Mass spectroscopy (MS) - A technique for separating ions based on their mass to charge ratios.

Metabolomics  - The measurement of many metabolites simultaneously. 

Maternal effect - The contribution that the mother makes to embryo survival.

Metabolic fingerprinting or profiling - Classifying a sample by the types and amounts of metabolites relative to a reference sample(s). 

Metabolite - Any substance produced by metabolism or by a metabolic process.

Metabolome - The sum total of all metabolites in a cell, tissue, organ or organism.

Metabolomics - Defined as the global analysis of metabolites - - small molecules generated in the process of metabolism - -that represent the sum total of all the metabolic pathways in an organism, with a focus on the identification of each pathway and its role in an organism's function.

Micronutrients - A substance, such as a vitamin or mineral, that is essential in minute amounts for the proper growth and metabolism of a living organism.

Molecular buffering - The biochemical basis for genetic buffering. Genetic buffering is defined experimentally by genetic interaction networks, however hypotheses about the molecular basis for connectivity between genetic interaction modules can be generated based on information about the molecular functions of individual genes and their positions on the interaction network .

Molecular epidemiology - A science that focuses on the contribution of potential genetic and environmental risk factors, identified at the molecular level, to the etiology, distribution and prevention of disease within families and across populations.

Molecular markers - Any DNA, protein, RNA, metabolite that is used as a surrogate for a phenotype or more complex biological process.

Monoallelic - See diallelic.

NAD - Nicotinamide adenine dinucleotide (oxidized form). Coenzymes that act as electron and hydrogen carriers in some oxidation-reduction reactions.

NADH - Nicotinamide adenine dinucleotide (reduced form).

National Council for Prescription Drug Programs (NCPDP) - Founded in 1978, the NCPDC focuses on prescription drug messages and works to create and promote data interchange and processing standards for the pharmacy services sector of the health care industry. This is the standard for billing retail drug sales. The NCPDP is currently working on a standard for physicians to submit prescriptions electronically. 

Natural selection - The process in nature by which only the organisms best adapted to their environment tend to survive and transmit their genetic information in increasing numbers to succeeding generations while those less adapted tend to be eliminated.

Nicotinamide - A form of B complex vitamin niacin.  A component of NAD which is involved in a wide range of biological processes such as energy production and production of fatty acids, steroids and cholesterol.

Nuclear Magnetic ResonAnce Spectroscopy (NMR) - A form of spectroscopy that depends on the absorption by and emission of energy from changes in spin states of the nucleus of an atom.  Absorption and emission are affected by local chemical environment.

Nuclear receptor - Nuclear receptors are ligand-inducible transcription factors. Their natural ligands are in various chemical classes such as steroid hormones, dietary lipids and their derivatives, oxysterols, bile acids, eicosanoids, and lipid soluble vitamins.

Nucleosome - The basic unit of chromatin consisting of a core of eight histone proteins (two, H2A, two H2B, two H3 and two H4) around which is wrapped two turns of DNA, or about 146 nucleotides.  Nucleosomes aggregate into higher order structures to make up the chromosome.

Nucleotide excision repair pathway - A sequence of enzymatic reactions involved in the repair of DNA.

Nutrigenetics - A sub-discipline of nutritional genomics usually referring to the association of a gene variant (see SNP - single nucleotide polymorphism) with an intermediate risk factor (e.g., cholesterol level, or glucose response) that is influenced by a particular nutrients (e.g., saturated fat). Because of genes-genes interactions (see epistasis), nutrigenetics is most informative when viewed in the context of the entire genome.

Nutrigenomics - The use of genomics to investigate diet and gene interactions involved in health or disease, often used interchangeably with nutritional genomics.  This term implies that other portions of the genome play a role in the genetic response to a nutrient (even if researchers cannot assess the total genome).

Nutrition -  A three-step process by which nourishing materials (food, drink and supplements) are ingested, broken down, and utilized in metabolism, to achieve health by sustaining normal cellular activity.  As a discipline, nutrition is the study of these processes in the context of health and disease.

Nutritional Epigenomics - The identification and study of those reversible, heritable epigenetic modifications on chromosomes that alter gene expression leading to phenotypic variation in health outcomes.  These modifications can vary by lifestage, by tissue/organ system and can be influenced by diet and/or drugs.

Nutritional genomics - or nutrigenomics - The study of how foods affect the expression of genetic information in an individual and how an individual's genetic makeup metabolizes and responds to nutrients and bioactives. 

Oligonucleotides - Short single stranded DNA sequences.

Oligosacharides - Compounds containing 2 - ~10 monosaccharides linked in a linear or branched chain.

Omega-3 fatty acid - Any of various polyunsaturated fatty acids that are found primarily in fish, fish oils, vegetable oils, and leafy green vegetables.  See alpha-linolenic acid.

Omics technologies - High throughput technologies to analyze various kinds of macromolecules, simultaneously.  For example, transcriptomics measures many transcripts, proteomics measures many proteins and metabolomics measures many metabolites.

Oncogene - A gene that can cause cancer or the transformation of normal cells into cancer cells.  Normally, an oncogene is an altered version of a normal gene.

Ontology - A controlled vocabulary that describes objects and the relations between them in a formal way.  Ontologies have a grammar for using the vocabulary terms to express something meaningful within a specified domain of interest.

Osteoporosis - A condition characterized by a decrease in bone mass and density.

Oxidative damage - Damage to cells caused by oxidants.

Pathophysiology - The physiology of abnormal states; specifically: the functional changes that accompany a particular syndrome or disease

Penetrance - The frequency (%) that a genotype will be expressed in the phenotypeAlleles not fully expressed in an individual are said to have reduced or low phenotype. Alleles not fully expressed in an individual are said to have reduced or low penetrance (<100%).")';>penetrance (<100%).

Perturbation - A changed input into a biological system - typically an environmental or genetic alteration in the cell .

Pharmacogenetics and pharmacogenomics - The convergence of pharmacology and genetics dealing with genetically determined responses to drugs.

Phenotype - An individual's observable characteristics or traits (e.g., height, weight, hair color or disease) directed by the genotype. The phenotypic can also be affected by epigenetics.

Phytochemicals - A nonnutritive bioactive plant substance, such as a flavonoid or carotenoid, considered to be beneficial to human health.

Phytonutrients - Nonessential bioactive dietary chemicals derived originally from the plant kingdom.

Pluripotent cells - Cells capable of differentiating into numerous cell types.

Polymorphisms - Differences between otherwise identical macromolecules.  Usually refers to changes in DNA.  See single nucleotide polymorphisms.

Polyphenol - A group of chemicals usually from plants characterized by the presence of more than one phenolic group.

Positional isomers - Chemicals having the same atomic composition but differing in one position.

Post - prandial state - The physiological and metabolic state following food intake.

Power - Statistical power is the capability of a test to detect a significant effect.  The components of a power calculation are sample size, effect size (magnitude of trend), alpha level (odds of concluding the presence of an effect due to chance only), and power (odds of finding the presence of an effect when there is one.

Prebiotics - A dietary constituent or food supplement that nourishes and promotes the growth of beneficial bacteria already in the digestive system.

Probiotics - Live, active cultures of necessary bacteria that are actually ingested and promote health. Live culture yogurt is an example of a probiotics.

Promoter - A region in DNA, (usually) 5' to the coding sequence of the gene, that encodes regulatory sequences needed for gene transcription.

Proteome - The total collection of proteins in a cell or cellular substructure.

Proteomics - The study of all proteins in a cell or organism.

Proteosome - A collection of proteins in a defined structure involved in degradation of proteins.

Pseudogenes - A nonfunctional gene derived from an ancestral active gene.

Recommended Daily Allowance (RDA) -  The amount of essential nutrients that the Food and Drug Administration considers adequate to meet the nutrient requirement of nearly all healthy individuals in a particular life stage and gender group.

Recommended Daily Intake (RDI) - Estimates of daily minimal dietary intake of established nutrients provided by the Food and Nutrition Board of the National Research Council. Optimal levels have not been formally established. Also known as Dietary Reference Intake (DRI).

Repository (biobank) - The physical storage of biological samples.

Response Elements - Response elements are sequence specific recognition sites of transcription factors. Most response elements are located within 1 kb from the transcriptional start site. 

Retinol - A 20 carbon primary alcohol.  A fat-soluble vitamin or a mixture of vitamins, especially vitamin A1 or a mixture of vitamins A1 and A2, occurring principally in fish-liver oils, milk, and some yellow and dark green vegetables, and functioning in normal cell growth and development. Also called vitamin A.

Retrotransposon - A transposable DNA element that transposes by means of an RNA intermediate.  Retrotransposons encode a reverse transcriptase that acts on the RNA transcript to make a cDNA copy, which then integrates into chromosomal DNA at a different location.

Robustness - Constancy, or resilience to change. Cellular robustness is the maintenance of stable phenotypic outputs in response to perturbation, which is presumed to result from natural selection for buffering interactions between genes, other genes, and the environment .

RT-PCR - Real time polymerase chain reaction.  A method for monitoring the amplification of RNA molecules from a particular sample into many copies of DNA molecules.

Signal transduction - A network of cellular enzymatic reactions stimulated by an extracellular signal interacting at the cell surface.  The reactions alter signaling molecules that cause changes in the level of other proteins, enzymes, or metabolites and ultimately effects a change in the cell's function.

Single nucleotide polymorphism (SNP) - Common genetic variant consisting of a single nucleotide pair difference between the DNA of the subject or patient and a reference individual.  There are about 7 million SNPs in the human genome - some in genes (coding SNPs) and some between genes (noncoding SNPs).

Sir2 - An NAD-dependent histone deacetylase and member of the sirtuin gene family.

Systematized Nomenclature of Medicine (SNOMED) - SNOMED-CT (Clinical Terminology) has been created from the combination of SNOMED-RT (Reference Terminology) and Read codes. NLM and others are working to bring coding systems such as this SNOMED-CT (clinical terms) into the public domain.

Systems biology - An approach for studying biological systems that analyzes multiple macromolecular species (DNA polymorphisms, RNA, protein, metabolites, etc) in one experiment.  A holistic approach to studying biological systems. 

Transactivation - Activation of gene transcription, which is induced by binding of a transcription factor or nuclear receptor to a DNA regulatory sequence.

Transcription Coactivator - Transcriptional coactivators can potentiate transcriptional properties, mediated by nuclear receptors. Many coactivators are associated in large multi protein complexes.

Transcription Corepressor - Certain nuclear receptors, when bound in absence of their ligand to their target genes can inhibit gene transcription.

Transrepression - Processes through which nuclear receptors can antagonize the transcriptional activity of other transcription factors without DNA-binding or altering the DNA-activity.

Transcription factor - Generally a protein that functions to initiate, enhance, or inhibit the transcription of a gene. Transcription factors bind to DNA-regulatory sequences of target genes to modify the rate of transcription initiation.

Trans fatty acid - A fatty acid that has been produced by hydrogenating an unsaturated fatty acid (and so changing its shape); found in processed foods such as margarine and fried foods and puddings and commercially baked goods and partially hydrogenated vegetable oils.

Transfection - Introduction of (usually) foreign DNA into a eukaryotic cell.

Transgenerational epigenetic inheritance - Inheritance of somatic DNA methylation patterns from parents to offspring.

Ubiqutin pathway - A series of enzymatic reactions that ultimately degrades proteins.  Ubiquitin is added to proteins targeting them for degradation.

Unified Modeling Language (UML) - A graphical language for visualizing, specifying, constructing, and documenting the artifacts of a software system.

Unified Modeling Language System (UMLS) - Developed by the National Library of Medicine as a standard health vocabulary that enables cross-referencing to other terminology and classification systems. Includes a meta-thesaurus, a semantic network, and an information sources map. The purpose of UMLS is to help health professionals and researchers retrieve and integrate electronic biomedical information from a variety of sources, irrespective of the variations in the way similar concepts are expressed in different sources and classifications systems. Has incorporated many source vocabularies including SnoMED, ICD-9 and CPT.

Xenobiotic chemicals - A chemical which is not a natural component of the organism or its diet.

X12N - Dominant standard for electronic commerce. The American National Standards Institute Accredited Standards Committee X12 (ASC X12) selected X12N as the standard for electronic data interchange (EDI) used in administrative and financial health care transactions (excluding retail pharmacy transactions) in compliance with the Health Insurance Portability and Accountability Act of 1996. Used for external financial transactions, financial coverage verification and insurance transactions and claims. 

Zoonutrients -  Nonessential bioactive dietary chemicals derived solely from animal tissue.