DNA microarray technology in nutraceutical and food safety.

The quality and quantity of diet is a key determinant of health and disease. Molecular diagnostics may play a key role in food safety related to genetically modified foods, food-borne pathogens and novel nutraceuticals. Functional outcomes in biology are determined, for the most part, by net balance between sets of genes related to the specific outcome in question. The DNA microarray technology offers a new dimension of strength in molecular diagnostics by permitting the simultaneous analysis of large sets of genes. Automation of assay and novel bioinformatics tools make DNA microarrays a robust technology for diagnostics. Since its development a few years ago, this technology has been used for the applications of toxicogenomics, pharmacogenomics, cell biology, and clinical investigations addressing the prevention and intervention of diseases. Optimization of this technology to specifically address food safety is a vast resource that remains to be mined. Efforts to develop diagnostic custom arrays and simplified bioinformatics tools for field use are warranted.

[1]  L. Ferguson,et al.  Dietary and medicinal antimutagens and anticarcinogens: molecular mechanisms and chemopreventive potential--highlights of a symposium. , 2003, Mutation research.

[2]  L. Poirier,et al.  Breaks in genomic DNA and within the p53 gene are associated with hypomethylation in livers of folate/methyl-deficient rats. , 1995, Cancer research.

[3]  Sang-Woon Choi,et al.  Gene-nutrient interactions and DNA methylation. , 2002, The Journal of nutrition.

[4]  Mouse Genome Sequencing Consortium.  Initial sequencing and comparative analysis of the mouse genome , 2002, Nature.

[5]  S. Krane,et al.  Differential effects of 1,25-dihydroxyvitamin D3 on human lymphocytes and monocyte/macrophages: inhibition of interleukin-2 and augmentation of interleukin-1 production. , 1986, Cellular immunology.

[6]  P. Reade,et al.  The role of ascorbic acid in oral cancer and carcinogenesis. , 2008, Oral diseases.

[7]  R. Atkinson,et al.  Overexpression of Polygalacturonase in Transgenic Apple Trees Leads to a Range of Novel Phenotypes Involving Changes in Cell Adhesion1 , 2002, Plant Physiology.

[8]  G. P. Studzinski,et al.  Inhibition of DNA synthesis by an inducer of differentiation of leukemic cells, 1 alpha, 25 dihydroxy vitamin D3, precedes down regulation of the c‐myc gene , 1986, Journal of cellular physiology.

[9]  P. Desmarchelier,et al.  A PCR Specific for Escherichia coli O157 Based on the rfb Locus Encoding O157 Lipopolysaccharide , 1998, Journal of Clinical Microbiology.

[10]  Jun-yan Hong,et al.  Dietary effects on cytochromes P450, xenobiotic metabolism, and toxicity , 1992, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[11]  R. Stierum,et al.  Niacin, poly(ADP-ribose) polymerase-1 and genomic stability. , 2001, Mutation research.

[12]  A. Wolffe,et al.  DNA methylation in health and disease , 2000, Nature Reviews Genetics.

[13]  C. Sen,et al.  Vitamin E sensitive genes in the developing rat fetal brain: a high‐density oligonucleotide microarray analysis , 2002, FEBS letters.

[14]  Esther J Kok,et al.  Substantial equivalence--an appropriate paradigm for the safety assessment of genetically modified foods? , 2002, Toxicology.

[15]  J. Palmgren,et al.  Alpha-Tocopherol and beta-carotene supplements and lung cancer incidence in the alpha-tocopherol, beta-carotene cancer prevention study: effects of base-line characteristics and study compliance. , 1996, Journal of the National Cancer Institute.

[16]  R. Tauxe.  Emerging foodborne pathogens. , 2002, International journal of food microbiology.

[17]  C. Ulrich,et al.  Lack of association between the C677T MTHFR polymorphism and colorectal hyperplastic polyps. , 2000, Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology.

[18]  Y. Yun,et al.  Chemoprevention of colon cancer by Korean food plant components. , 2003, Mutation research.

[19]  I. Nagano,et al.  Detection of Verotoxin‐Producing Escherichia coli O157:H7 by Multiplex Polymerase Chain Reaction , 1998, Microbiology and immunology.

[20]  L. Fox,et al.  Sensitivity of bacteriologic culture for detection of Escherichia coli O157:H7 in bovine feces , 1995, Journal of clinical microbiology.

[21]  C. Yamashiro,et al.  PCR-Based DNA Amplification and Presumptive Detection of Escherichia coli O157:H7 with an Internal Fluorogenic Probe and the 5′ Nuclease (TaqMan) Assay , 1998, Applied and Environmental Microbiology.

[22]  M. Chatterjee,et al.  Vitamin D and genomic stability. , 2001, Mutation research.

[23]  M. Jäättelä,et al.  Apoptosis induced by vitamin D compounds in breast cancer cells is inhibited by Bcl-2 but does not involve known caspases or p53. , 1999, Cancer research.

[24]  M. J. Coon,et al.  Cytochrome P450: progress and predictions , 1992, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[25]  J F Gregory,et al.  Polymorphisms of methylenetetrahydrofolate reductase and other enzymes: metabolic significance, risks and impact on folate requirement. , 1999, The Journal of nutrition.

[26]  S. Kersten,et al.  Nutrigenomics: goals and strategies , 2003, Nature Reviews Genetics.

[27]  R. Woutersen,et al.  Modulation of pancreatic carcinogenesis by antioxidants. , 1999, Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association.

[28]  H. Strobel,et al.  Cytochrome P-450-mediated redox cycling of estrogens. , 1986, The Journal of biological chemistry.

[29]  B Rowe,et al.  International increase in Salmonella enteritidis: A new pandemic? , 1990, Epidemiology and Infection.

[30]  Li Jj,et al.  Estrogen carcinogenesis in Syrian hamster tissues: role of metabolism. , 1987 .

[31]  H. Norppa,et al.  Chromosomal aberrations in lymphocytes predict human cancer independently of exposure to carcinogens. European Study Group on Cytogenetic Biomarkers and Health. , 2000, Cancer research.

[32]  B T Butman,et al.  Detection of Escherichia coli O157:H7 in meat by an enzyme-linked immunosorbent assay, EHEC-Tek , 1995, Applied and environmental microbiology.

[33]  Wei Pan,et al.  A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments , 2002, Bioinform..

[34]  J. A. Duerre,et al.  Effect of zinc deficiency on methionine metabolism, methylation reactions and protein synthesis in isolated perfused rat liver. , 1985, The Journal of nutrition.

[35]  S. Vollset,et al.  The controversy over homocysteine and cardiovascular risk. , 2000, The American journal of clinical nutrition.

[36]  H. Kuiper,et al.  Assessment of the food safety issues related to genetically modified foods. , 2001, The Plant journal : for cell and molecular biology.

[37]  L. Machlin.  Handbook of Vitamins , 1991 .

[38]  Ji Huang,et al.  [Serial analysis of gene expression]. , 2002, Yi chuan = Hereditas.

[39]  A. Fruth,et al.  Subtyping of pathogenic Escherichia coli strains using flagellar (H)-antigens: serotyping versus fliC polymorphisms. , 2003, International journal of medical microbiology : IJMM.

[40]  H. Griffiths,et al.  Vitamin C exhibits pro-oxidant properties , 1998, Nature.

[41]  S. Meydani,et al.  Vitamin E and genome stability. , 2001, Mutation research.

[42]  D. Kemp,et al.  Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl-paper and hybridization with DNA probes. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[43]  D. Llewellyn,et al.  Expression of the Talaromyces flavus glucose oxidase gene in cotton and tobacco reduces fungal infection, but is also phytotoxic , 2004, Molecular Breeding.

[44]  I. Rosenberg,et al.  Relation between folate status, a common mutation in methylenetetrahydrofolate reductase, and plasma homocysteine concentrations. , 1996, Circulation.

[45]  R. Tauxe.  Salmonella Enteritidis and Salmonella Typhimurium DT104: Successful Subtypes in the Modern World , 1999 .

[46]  E. Castanas,et al.  Potent inhibitory action of red wine polyphenols on human breast cancer cells , 2000, Journal of cellular biochemistry.

[47]  P. Brown,et al.  A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. , 1996, Genome research.

[48]  A. Rasooly,et al.  Microarray Analysis of Microbial Virulence Factors , 2001, Applied and Environmental Microbiology.

[49]  F. Brockman,et al.  Detecting and genotyping Escherichia coli O157:H7 using multiplexed PCR and nucleic acid microarrays. , 2001, International journal of food microbiology.

[50]  P Scott.  Firepower in the Lab: Automation in the Fight Against Infectious Diseases and Bioterrorism , 2001 .

[51]  L. Bianchi,et al.  Chemoprevention of Indirect and Direct Chemical Carcinogenesis by Carotenoids as Oxygen Radical Quenchers a , 1988, Annals of the New York Academy of Sciences.

[52]  F. Speleman,et al.  Modulation of the peroxisomal gene expression pattern by dehydroepiandrosterone and vitamin D: therapeutic implications. , 2002, The Journal of endocrinology.

[53]  Colin N. Dewey,et al.  Initial sequencing and comparative analysis of the mouse genome. , 2002 .

[54]  A. Marchetti,et al.  Human telomerase reverse transcriptase mRNA expression assessed by real-time reverse transcription polymerase chain reaction predicts chemosensitivity in patients with ovarian carcinoma. , 2003, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[55]  F. Guengerich,et al.  Pharmacogenomics of cytochrome P450 and other enzymes involved in biotransformation of xenobiotics , 2000 .

[56]  A. Conney,et al.  Nutrient regulation of chemical metabolism in humans. , 1985, Federation proceedings.

[57]  Ronald W. Davis,et al.  Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray , 1995, Science.

[58]  M R Cullen,et al.  Risk factors for lung cancer and for intervention effects in CARET, the Beta-Carotene and Retinol Efficacy Trial. , 1996, Journal of the National Cancer Institute.

[59]  D. Birt,et al.  Effects of dietary protein level on hepatic microsomal mixed-function oxidase systems during aging in two generations of Syrian hamsters. , 1983, Toxicology and applied pharmacology.

[60]  S. Gygi,et al.  Correlation between Protein and mRNA Abundance in Yeast , 1999, Molecular and Cellular Biology.

[61]  H. Karch,et al.  Prevalence and clinical manifestations of shiga toxin-producingEscherichia coli infections in Austrian children , 1996, European Journal of Clinical Microbiology and Infectious Diseases.

[62]  V. Dixit,et al.  Death receptors: signaling and modulation. , 1998, Science.

[63]  A. Bennett,et al.  Analysis of tomato polygalacturonase expression in transgenic tobacco. , 1990, The Plant cell.

[64]  M. Fenech.  The role of folic acid and Vitamin B12 in genomic stability of human cells. , 2001, Mutation research.

[65]  B. Halliwell.  Vitamin C and genomic stability. , 2001, Mutation research.

[66]  P. Beyer,et al.  Engineering the provitamin A (beta-carotene) biosynthetic pathway into (carotenoid-free) rice endosperm. , 2000, Science.

[67]  T. Shimada,et al.  Cytochrome P450 1B1: a target for inhibition in anticarcinogenesis strategies. , 2003, Mutation research.

[68]  A. Riggs,et al.  DNA methylation and gene function. , 1980, Science.

[69]  J. Heritage,et al.  The fate of antibiotic resistance marker genes in transgenic plant feed material fed to chickens. , 2002, The Journal of antimicrobial chemotherapy.

[70]  M. B. Jensen,et al.  Induction of cytochrome P450IA1 in rat colon and liver by indole-3-carbinol and 5,6-benzoflavone. , 1990, Carcinogenesis.

[71]  M. Rothstein,et al.  Accelerating effect of ascorbic acid on N-nitrosamine formation and nitrosation by oxyhyponitrite. , 1979, Cancer research.

[72]  Ying Xu,et al.  Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees , 2002, Bioinform..

[73]  S. Altekruse,et al.  Emerging foodborne diseases. , 1997, Emerging infectious diseases.

[74]  E. Kilbourne,et al.  Tryptophan produced by Showa Denko and epidemic eosinophilia-myalgia syndrome. , 1996, The Journal of rheumatology. Supplement.

[75]  Timothy B. Stockwell,et al.  The Sequence of the Human Genome , 2001, Science.

[76]  G. Zardo,et al.  The Unmethylated State of CpG Islands in Mouse Fibroblasts Depends on the Poly(ADP-ribosyl)ation Process* , 1998, The Journal of Biological Chemistry.

[77]  Ke,et al.  Seed-specific overexpression of phytoene synthase: increase in carotenoids and other metabolic effects , 1999, The Plant journal : for cell and molecular biology.

[78]  S. Dudoit,et al.  Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. , 2002, Nucleic acids research.

[79]  N. Walker,et al.  17 beta-estradiol hydroxylation catalyzed by human cytochrome P450 1B1. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[80]  S. Ratnam,et al.  Sorbitol-MacConkey medium for detection of Escherichia coli O157:H7 associated with hemorrhagic colitis , 1986, Journal of clinical microbiology.

[81]  A. Pardee,et al.  Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. , 1992, Science.

[82]  R. Einspanier,et al.  The fate of forage plant DNA in farm animals: a collaborative case-study investigating cattle and chicken fed recombinant plant material , 2001 .

[83]  J. Wells,et al.  A multistate outbreak of Escherichia coli O157:H7-associated bloody diarrhea and hemolytic uremic syndrome from hamburgers. The Washington experience. , 1994, JAMA.

[84]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[85]  B. Ames,et al.  Ascorbic acid protects against endogenous oxidative DNA damage in human sperm. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[86]  J. Michael Cherry,et al.  Microarray data quality analysis: lessons from the AFGC project , 2004, Plant Molecular Biology.

[87]  C. Sen,et al.  Functional genomics: high-density oligonucleotide arrays. , 2002, Methods in enzymology.

[88]  L. McCaig,et al.  Food-related illness and death in the United States. , 1999, Emerging infectious diseases.

[89]  H. Wiseman.  Vitamin D is a membrane antioxidant Ability to inhibit iron‐dependent lipid peroxidation in liposomes compared to cholesterol, ergosterol and tamoxifen and relevance to anticancer action , 1993, FEBS letters.

[90]  Y. Sasaki,et al.  The influence of antioxidants on cigarette smoke-induced DNA single-strand breaks in mouse organs: a preliminary study with the alkaline single cell gel electrophoresis assay. , 2000, Toxicological sciences : an official journal of the Society of Toxicology.

[91]  R. Edenharder,et al.  Development and application of test methods for the detection of dietary constituents which protect against heterocyclic aromatic amines. , 2003, Mutation research.

[92]  D. Heimburger,et al.  The accumulation of ascorbic acid by squamous cell carcinomas of the lung and larynx is associated with global methylation of DNA , 2000, Cancer.

[93]  BIOTECHNOLOGIES AND FOOD: ASSURING THE SAFETY OF FOODS PRODUCED BY GENETIC MODIFICATION , 1990 .

[94]  C. Sen,et al.  Antioxidant regulation of gene expression: analysis of differentially expressed mRNAs. , 1999, Methods in enzymology.

[95]  R. Raag,et al.  Cytochrome P450cam: crystallography, oxygen activation, and electron transfer1 , 1992, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[96]  James L. Winkler,et al.  Accessing Genetic Information with High-Density DNA Arrays , 1996, Science.

[97]  A. Norman,et al.  1,25(OH)2‐Vitamin D3 receptors: gene regulation and genetic circuitry , 1988, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[98]  J. Olson.  Vitamin A and carotenoids as antioxidants in a physiological context. , 1993, Journal of nutritional science and vitaminology.

[99]  W. Willett,et al.  Methylenetetrahydrofolate reductase polymorphism, dietary interactions, and risk of colorectal cancer. , 1997, Cancer research.

[100]  S. P. Fodor,et al.  Light-directed, spatially addressable parallel chemical synthesis. , 1991, Science.

[101]  S. Mayne,et al.  Beta-Carotene and lung cancer promotion in heavy smokers--a plausible relationship? , 1996, Journal of the National Cancer Institute.

[102]  V. McKelvey-Martin,et al.  Effect of antioxidant vitamin supplementation on DNA damage and repair in human lymphoblastoid cells. , 1997, Nutrition and cancer.

[103]  J. Yu,et al.  Cloning and characterization of the eae gene of enterohaemorrhagic Escherichia coli O157:H7 , 1992, Molecular microbiology.