Novel Omics Technologies in Food Science (Turkish with English Abstract)

Abstract

The complete sequencing of the human genome has ushered in a new era of systems biology referred to as omics technology. The term omics refers to the comprehensive analysis of biological systems. Novel omics technologies and bioinformatic tools offer enormous potential to research the complex relationship between nutrition, food and metabolism. In the recent years, a variety of omics subdisciplines have began to emerge, with their own set of instruments, techniques, reagents and software. 'Omics' tools and technologies have dramatically changed the experimental approaches by which complex biological systems can be characterized. The omics technology that has driven these new areas of research consists of DNA and protein microarrays, mass spectrometry and a number of other instruments that enable high-throughput analyses. An overview of omics technologies in food research, which focuses on recent applications of genomics, transcriptomics, proteomics and metabolomics in food science, is presented in this paper.

Keywords

• Genomics, transcriptomics, proteomics, metabolomics, system biology

Gıda Biliminde Yeni Omik Teknolojileri

Abstract

İnsan genomunun tümüyle dizisinin çıkarılması, sistem biyolojide omik teknolojileri denilen yeni bir çağ açmıştır. Omik terimi, biyolojik sistemlerin kapsamlı analizi olarak ifade edilmektedir. Yeni omik teknolojileri ve biyoinformatik araçlar, beslenme, gıda ve metabolizma arasındaki karmaşık ilişkinin araştırılması konusunda çok büyük bir potansiyel sunmaktadır. Son yıllarda çok çeşitli omik alt disiplinleri oluşmuş olup, her birinin kendine özgü bir takım araçları, teknikleri, belirteçleri ve yazılımları bulunmaktadır. Omik araçları ve teknolojileri, karmaşık biyolojik sistemlerin tanımlanabildiği deneysel yaklaşımları çarpıcı biçimde değiştirmiştir. Bu yeni araştırma alanlarını harekete geçiren omik teknolojileri, DNA ve protein mikrodizileri, kütle spektrometresi ve yüksek işlem hacimli analizlere imkân veren diğer birçok aracı kapsamaktadır. Bu sahadaki araştırmalar hücre, doku ve organizmaların genom, transkriptom, proteom ve metabolomunu inceler ve aralarındaki etkileşimi sorgular. Bu çalışmada, genomik, transkriptomik, proteomik ve metabolomikteki en son uygulamalar üzerinde yoğunlaşan, gıda araştırma alanındaki omik teknolojilerine genel bir bakış sunulmuştur.

Keywords

• Genomik, transkriptomik, proteomik, metabolomik, sistem biyoloji

References

1. Coşkun T, 2007. Nutrisyonel Genomik. Çocuk Sağlığı ve Hastalıkları Dergisi, 50; 47-66.
2. Davies H, 2010. A role for ''omics" technologies in food safety assessment. Food Control, 21(12), 1601-1610
3. Ordovas JM, Corella D. 2004. Nutritional Genomics. Annu Rev Genomics Hum Gene, 5;71-118.
4. Elaine TM, Cindy D, Milner J. 2006. Nutrigenomics, Proteomics, Metabolomics. Pract Dietetics, 106(3), 403-413.
5. Carbonaro M, 2008. Proteomics: Present and future in food quality evaluation. Trend Food Sci Tech, 15; 209-216.
6. Wishart DS. 2008. Metabolomics: applications to food science and nutrition research. Trend Food Sci Tech, 19; 482-493.
7. Baugher JL, Klaenhammer TR. 2011. Application of omics tools to understanding probiotic functionality. J Dairy Sci, 94(10): 4753-4765
8. Fukushima A, Kusano M, Redestig H, Arita M, Saito K. 2009. Integrated omics approaches in plant systems biology. Curr Opin Chem Biol, 13: 532-538

9. Langridge P, Fleury D.2011. Making the most of 'omics' for crop breeding. Trends Biotechnol, 29 (1): 33-40
10. Fernie AR, Schauer N. 2009. Metabolomics- assisted breeding: a viable option for crop improvement?. Trends Genet 25: 39-48
11. Saito K, Matsuda F. 2010. Metabolomics for functional genomics, systems biology, and biotechnology. Annu Rev Plant Biol 61: 463-489 12. Ioannidis JPA. 2010. Expectations, validity, and reality in omics. J Clin Epidemiol 63: 945-949 13. Ghosh D, Poisson LM. 2009. "Omics" data and levels of evidence for biomarker discovery. Genomics 93(1): 13-16.
12. Zhang X, Yeeleng Y, Dong W, Chen G, Chen F. 2008. Novel omics based technology in nutrition research. Biotechnol Adv 26: 169-176.
13. Wheelock CE, Kawashima S, Diez D, Kanehisa M, van Erk M, Kleemann R, Haeggstrom JZ, Goto S. 2009. Systems biology approaches and pathway tools for investigating cardiovascular disease. Mol Biosystems 5(6), 588-602.
14. Marco M, Bennik H. 2007. Impact of bacterial genomics on determining quality and safety in the dairy production chain. Int Dairy J 112: 195- 196.
15. Brul S, Schuren F, Montijn R, Keijser BJF, Spek H, Oomes SJM. 2006. The impact of functional genomics on microbioloical food quality and safety. Int J Food Safety 112: 195-199. 18. Mutch DM, Wahli W, Williamson G. 2005. Nutrigenomics and nutrigenetics; the emerging faces of nutrition. FASEB J 19: 1602-1616.
16. Spielbauer B, Stahl F. 2005. Impact of microarray technology in nutrition and food research. Mol Nutr Food Res 49 (10): 908-917.
17. Lucchini S, Thompson A, Hinton JC. 2001. Microarrays for microbiologists. Microbiol 147: 1403-1414.
18. Kato H, Kenji S, Takeshi K. 2005. A perspective on DNA microarray technology in food and nutritional science. Curr Opin Clin Nutr Metab Care 8 (5): 516-522
19. Aebersold R, Mann M. 2003. Mass spectrometry- based proteomics. Nature 422:198-207.
20. Amiour N, Merlino M, 2002. Proteomic analysis amphilic proteins of hexaploid wheat kernls. Proteomics 2: 632-641.
21. Jian-Zhong H, Yan-Bo W. 2008. Proteomics: present and future in food science and technology. Trend Food Sci Tech 19: 26-30.
22. Doherty MK, Mc Lean L, Hayter JR, Pratt JM, Robertson DH, El Shafei A. 2004. The proteom of chicken skelatal muscle; changes in soluble protein expression during growth in a layer strain. Proteomics 4: 2082-2093.
23. Tomita M. 2008. Metabolome analysis and systems biology. J Biotechnol 136: 1-20.
24. Jacobs DM, Gaudier E, van Duynhoven J. 2009. Non-Digestible Food Ingredients, Colonic Microbiota and the Impact on Gut Health and Immunity: A Role for Metabolomics. Curr Drug Metabolism 10(1): 41-54.
25. Moco S, Bino RJ, Vorst O, Verhoeven HA, Groot J, Beek TA. 2006. A liquid chromatography -mass spectrometry-based metabolome database for tomato. Plant Physiol 141: 1205-1218.
26. Hu F, Furihata K, Kato Y, Tanokura M. 2007. Nondestructive quantification of organic compounds in whole milk without pretreatment by two- dimensional NMR spectroscopy. J Agr Food Chem 55: 4307-4311.
27. Mattivi F, Guzzon R, Vrhovsek U, Stefanini M and Velasco R. 2006. Metabolite profiling of grape: flavanoids and anthocyanins. J Agr Food Chem 54, 7692-7702.
28. Almeida C, Duarte IF, Barros A, Rodrigues J, Spraul M, Gil AM. 2006. Composition of beer by 1H NMR spectroscopy: effects of brewing site and date of production. J Agr Food Chem 54: 700–706.
29. Ogrinc N, Kosir IJ, Spangenberg JE, Kidric J. 2003. The application of NMR and MS methods for detection of adulteration of wine, fruit juices and olive oil. Anal Bioanal Chem 376: 424-430.
30. Lindon JC, Holmes E, Bollard ME Stanley EG, Nicholson JK. 2004. Metabonomics technologies and their applications in physiological monitoring, drug safety assessment and disease diagnosis. Biomarkers 9: 1-31.
31. Gibney MJ, Walsh M, Brennan L, Roche HM, German B, Ommen B. 2005. Metabolomics in human nutrition: opportunities and challenges. Am J Clin Nutr 82: 497-503.
32. Zeisel SH. 2007. Nutrigenomics and metabolomics will change clinical nutriction and public health practice: insights from studies on dietary requirements for choline. Am J Clin Nutr 86: 542-548.
33. Elizabeth MS, McNiven JBG, Carolyn MS. 2011. Analytical metabolomics: nutritional opportunities for personalized health. J Nutri Biochem, 22:995-1002
34. Christopher J, Haselssen JN. 2008. Metabolic profiling as a tool for understanding mechanisms of toxicity. Toxicol Pathol 36 (1): 140-147.
35. Mashego MR, Rumbold K, Marjan De Mey, Vandamme E, Soetaert W, Heijnen J. 2007. Microbial metabolomics: past, present and future methodologies. Biotechnol Lett 29:1-16
36. Kuiper H.A., Kok E.J., Engel K.H., 2003. Exploitation of molecular profiling techniques for GM food safety assessment. Curr Opin Biotechnol 14: 238-243.
37. Ghosh D. 2009. Future Perspectives of Nutrigenomics Foods: Benefits vs. Risk. Indian J Biochem Bio 46 (1): 31-36.
38. Chassy BM. 2010. Can –omics inform a food safety assessment?. Regul Toxicol Pharm 58: 62-70 42. Lay Jr. JO, Borgmann S, Liyanage R, Wilkins CL. 2006. Problems with the''omics". Trends Anal Chem 25, 1046-1056.
39. Urano K, KuriharaY, Seki M, Shinozaki K. 2010. 'Omics' analyses of regulatory networks in plant abiotic stres. Curr Opin Plant Biol 13:132-138 44. Timothy EJ, Behrens OS. 2011. Human connectomics. Curr Opin Neurobiol 22: 1-10
40. Skudlarski P, Jagannathan K, Calhoun VD, Hampson M, Skudlarska BA, Pearlson G. 2008. Measuring brain connectivity: diffusion tensor imaging validates resting state temporal correlations. Neuroimage, 43:554-561.
41. Hye RJ, Tuulia S, Kaisa MK, Kirill T, Dimple K, Kim E. 2011. High throughput quantitative molecular lipidomics. Biochim Biophys Acta 1811: 925-934
42. Shevchenko A, Simons K. 2010. Lipidomics: coming to grips with lipid diversity. Nat Rev Mol Cell Biol 11: 593-598.
43. Ivanova PT, Milne SB, Myers DS, Brown HA. 2009. Lipidomics: a mass spectrometry based systems level analysis of cellular lipids. Curr Opin Chem Biol 13: 526-531.
44. Niemela PS, Castillo S, Sysi-Aho M, Oresi M. 2009. Bioinformatics and computational methods for lipidomics. J Chromatogr B 877: 2855-2862