Unsupervised principal component analysis of NMR metabolic profiles for the assessment of substantial equivalence of transgenic grapes (vitis vinifera)

Journal of Agricultural and Food Chemistry

Volumn 59, Issue 17, 2011, Pages 9271-9279

  Picone, Gianfranco ^a   Mezzetti, Bruno ^b   Babini, Elena ^a,c   Capocasa, Franco ^b   Placucci, Giuseppe ^a   Capozzi, Francesco ^a,c  

^a UNIVERSITY OF BOLOGNA   (Italy)

^b UNIVERSITÀ POLITECNICA DELLE MARCHE   (Italy)

^c UNIVERSITY OF FLORENCE   (Italy)

Author keywords

1H NMR profile; auxin; metabolites; metabonomics; PCA; transgenic grapes

Indexed keywords

1H NMR PROFILE; AUXIN; METABONOMICS; PCA; TRANSGENICS;

DATA REDUCTION; FRUITS; GENETIC ENGINEERING; METABOLITES; MULTIVARIANT ANALYSIS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PLANTS (BOTANY); PRINCIPAL COMPONENT ANALYSIS;

METABOLISM;

INDOLEACETIC ACID DERIVATIVE;

ARTICLE; CHEMISTRY; COMPARATIVE STUDY; FRUIT; GENETICALLY MODIFIED FOOD; METABOLISM; METABOLOME; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; TRANSGENIC PLANT; VITIS;

FOOD, GENETICALLY MODIFIED; FRUIT; INDOLEACETIC ACIDS; MAGNETIC RESONANCE SPECTROSCOPY; METABOLOME; PLANTS, GENETICALLY MODIFIED; VITIS;

VITACEAE; VITIS VINIFERA;

EID: 80052603272     PISSN: 00218561     EISSN: 15205118     Source Type: Journal    
DOI: 10.1021/jf2020717     Document Type: Article

References (60)

1. Levidow, L.; Murphy, J.; Carr, S. Recasting "substantial equivalence": trans-Atlantic governance of GM food Sci. Technol. Hum. Val. 2007, 32, 26-64
2. Millstone, E.; Brunner, E.; Mayer, S. Beyond "substantial equivalence" Nature 1999, 401, 525-526
3. Kuiper, H. A.; Kleter, G. A.; Noteborn, H. P. J. M.; Kok, E. J. Assessment of the food safety issues related to genetically modified foods Plant J. 2001, 27, 503-528 (Pubitemid 32961463)
4. Kuiper, H. A.; Kok, E. J.; Engel, K.-H. Exploitation of molecular profiling techniques for GM food safety assessment Curr. Opin. Biotechnol. 2003, 14, 238-243 (Pubitemid 36561239)
5. Batista, R.; Saibo, N.; Lourenço, T.; Oliveira, M. M. Microarray analyses reveal that plant mutagenesis may induce more transcriptomic changes than transgene insertion Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 3640-3645 (Pubitemid 351723605)
6. Ruebelt, M. C.; Leimgruber, N. K.; Lipp, M.; Reynolds, T. L.; Nemeth, M. A.; Astwood, J. D.; Engel, K.-H.; Jany, K.-D. Application of two-dimensional gel electrophoresis to interrogate alterations in the proteome of genetically modified crops. 1. Assessing analytical validation J. Agric. Food Chem. 2006, 54, 2154-2161
7. Nicholson, J. K.; Lindon, J. C.; Holmes, E. 'Metabonomics': understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data Xenobiotica 1999, 29, 1181-1189
8. Abdel-Farid, I. B.; Kim, H. K.; Choi, Y. H.; Verpoorte, R. Metabolic characterization of Brassica rapa leaves by NMR spectroscopy J. Agric. Food Chem. 2007, 55, 7936-7943 (Pubitemid 47522210)
9. Zhang, X.; Wu, H.; Liao, P.; Li, X.; Ni, J.; Pei, F. NMR-based metabonomic study on the subacute toxicity of aristolochic acid in rats Food Chem. Toxicol. 2006, 44, 1006-1014 (Pubitemid 43850068)
10. Keun, H. C. Metabonomic modeling of drug toxicity Pharmacol. Ther. 2006, 109, 92-106 (Pubitemid 41740817)
11. Gavaghan, C. L.; Wilson, I. D.; Nicholson, J. K. Physiological variation in metabolic phenotyping and functional genomic studies: use of orthogonal signal correction and PLS-DA FEBS Lett. 2002, 530, 191-196 (Pubitemid 35248210)
12. 1H NMR-based metabonomic techniques in nutrition research - metabolic effects of dietary isoflavones in humans J. Nutr. Biochem. 2005, 16, 236-244 (Pubitemid 40460985)
13. Betoret, E.; Betoret, N.; Vidal, D.; Fito, P. Functional foods development: trends and technologies Trends Food Sci. Technol. 2011, (doi:10.1016/j.tifs.2011.05.004)
14. Bertram, H. C.; Knudsen, K. E. B.; Serena, A.; Malmendal, A.; Nielsen, N. C.; Fretté, X. C.; Andersen, H. J. NMR-based metabonomic studies reveal changes in the biochemical profile of plasma and urine from pigs fed high-fibre rye bread Br. J. Nutr. 2006, 95, 955-962 (Pubitemid 43805383)
15. Young, J.; Larsen, L.; Malmendal, A.; Nielsen, N.; Straadt, I.; Oksbjerg, N.; Bertram, H. Creatine-induced activation of antioxidative defence in myotube cultures revealed by explorative NMR-based metabonomics and proteomics J. Int. Soc. Sports Nutr. 2010, 7, 9
16. Bertram, H. C.; Duus, J. ø.; Petersen, B. O.; Hoppe, C.; Larnkjær, A.; Schack-Nielsen, L.; Mølgaard, C.; Michaelsen, K. F. Nuclear magnetic resonance-based metabonomics reveals strong sex effect on plasma metabolism in 17-year-old Scandinavians and correlation to retrospective infant plasma parameters Metabolism 2009, 58, 1039-1045
17. Kemsley, E. K.; Le Gall, G. N. L.; Dainty, J. R.; Watson, A. D.; Harvey, L. J.; Tapp, H. S.; Colquhoun, I. J. Multivariate techniques and their application in nutrition: a metabolomics case study Br. J. Nutr. 2007, 98, 1-14 (Pubitemid 47272140)
18. Primrose, S.; Draper, J.; Elsom, R.; Kirkpatrick, V.; Mathers, J. C.; Seal, C.; Beckmann, M.; Haldar, S.; Beattie, J. H.; Lodge, J. K.; Jenab, M.; Keun, H.; Scalbert, A. Metabolomics and human nutrition Br. J. Nutr. 2011, 105, 1277-1283
19. Castro, C.; Manetti, C. A multiway approach to analyze metabonomic data: a study of maize seeds development Anal. Biochem. 2007, 371, 194-200 (Pubitemid 350015974)
20. Bertram, H. C.; Weisbjerg, M. R.; Jensen, C. S.; Pedersen, M. G.; Didion, T.; Petersen, B. O.; Duus, J. ø.; Larsen, M. K.; Nielsen, J. H. Seasonal changes in the metabolic fingerprint of 21 grass and legume cultivars studied by nuclear magnetic resonance-based metabolomics J. Agric. Food Chem. 2010, 58, 4336-4341
21. de Vos, R. C. H.; Hall, R. D.; Moing, A. Metabolomics of a model fruit: tomato. Annu. Plant Rev. 2011, 43, 109-155.
22. Bekiroglu, S. An emerging powerful technique: NMR applications on quality assessments of fish and related products. In Handbook of Seafood Quality, Safety and Health Applications; Wiley-Blackwell: Oxford, U.K., 2011; pp 181-193.
23. Rodrigues, J. A.; Barros, A. S.; Carvalho, B.; Brandão, T.; Gil, A. M. Probing beer aging chemistry by nuclear magnetic resonance and multivariate analysis Anal. Chim. Acta 2011, 702, 178-187
24. Manetti, C.; Bianchetti, C.; Bizzarri, M.; Casciani, L.; Castro, C.; D'Ascenzo, G.; Delfini, M.; Di Cocco, M. E.; Laganà, A.; Miccheli, A.; Motto, M.; Conti, F. NMR-based metabonomic study of transgenic maize Phytochemistry 2004, 65, 3187-3198 (Pubitemid 39550386)
25. Krishnan, P.; Kruger, N. J.; Ratcliffe, R. G. Metabolite fingerprinting and profiling in plants using NMR J. Exp. Bot. 2005, 56, 255-265 (Pubitemid 40191443)
26. Kyong Kim, H.; Choi, Y. H.; Verpoorte, R. NMR-based metabolomic analysis of plants Nat. Protoc. 2010, 5, 536-549
27. Colquhoun, I. J. Use of NMR for metabolic profiling in plant systems J. Pestic. Sci. 2007, 32, 200-212 (Pubitemid 47347646)
28. 1H NMR metabonomics Food Chem. 2010, 120, 907-914
29. Nørgaard, L.; Bro, R.; Westad, F.; Engelsen, S. B. A modification of canonical variates analysis to handle highly collinear multivariate data J. Chemom. 2006, 20, 425-435
30. Alonso-Salces, R. M.; Héberger, K.; Holland, M. V.; Moreno-Rojas, J. M.; Mariani, C.; Bellan, G.; Reniero, F.; Guillou, C. Multivariate analysis of NMR fingerprint of the unsaponifiable fraction of virgin olive oils for authentication purposes Food Chem. 2010, 118, 956-965
31. Faber, N. M.; Rajkó, R. How to avoid over-fitting in multivariate calibration - the conventional validation approach and an alternative Anal. Chim. Acta 2007, 595, 98-106 (Pubitemid 46990314)
32. Llabjani, V.; Trevisan, J. L.; Jones, K. C.; Shore, R. F.; Martin, F. L. Binary mixture effects by PBDE congeners (47, 153, 183, or 209) and PCB congeners (126 or 153) in MCF-7 cells: biochemical alterations assessed by IR spectroscopy and multivariate analysis Environ. Sci. Technol. 2010, 44, 3992-3998
33. Rotino, G. L.; Perri, E.; Zottini, M.; Sommer, H.; Spena, A. Genetic engineering of parthenocarpic plants Nat. Biotechnol. 1997, 15, 1398-1401 (Pubitemid 28022736)
34. Ficcadenti, N.; Sestili, S.; Pandolfini, T.; Cirillo, C.; Rotino, G. L.; Spena, A. Genetic engineering of parthenocarpic fruit development in tomato Mol. Breed. 1999, 5, 463-470 (Pubitemid 29429135)
35. Acciarri, N.; Restaino, F.; Vitelli, G.; Perrone, D.; Zottini, M.; Pandolfini, T.; Spena, A.; Rotino, G. Genetically modified parthenocarpic eggplants: improved fruit productivity under both greenhouse and open field cultivation BMC Biotechnol. 2002, 2, 4
36. Pandolfini, T.; Rotino, G.; Camerini, S.; Defez, R.; Spena, A. Optimisation of transgene action at the post-transcriptional level: high quality parthenocarpic fruits in industrial tomatoes BMC Biotechnol. 2002, 2, 1
37. Carmi, N.; Salts, Y.; Dedicova, B.; Shabtai, S.; Barg, R. Induction of parthenocarpy in tomato via specific expression of the rolB gene in the ovary Planta 2003, 217, 726-735 (Pubitemid 37181463)
38. Mezzetti, B.; Landi, L.; Pandolfini, T.; Spena, A. The defH9-iaaM auxin-synthesizing gene increases plant fecundity and fruit production in strawberry and raspberry BMC Biotechnol. 2004, 4, 4
39. Wang, H.; Jones, B.; Li, Z.; Frasse, P.; Delalande, C.; Regad, F.; Chaabouni, S.; Latche, A.; Pech, J.-C.; Bouzayen, M. The tomato Aux/IAA transcription factor IAA9 is involved in fruit development and leaf morphogenesis Plant Cell 2005, 17, 2676-2692
40. Yin, Z.; Malinowski, R.; Ziólkowska, A.; Sommer, H.; Plcader, W.; Malepszy, S. The DefH9-iaaM-containing construct efficiently induces parthenocarpy in cucumber Cell. Mol. Biol. Lett. 2006, 11, 279-290 (Pubitemid 44492484)
41. Mezzetti, B.; Pandolfini, T.; Navacchi, O.; Landi, L. Genetic transformation of Vitis vinifera via organogenesis BMC Biotechnol. 2002, 2, 18
42. Costantini, E.; Landi, L.; Silvestroni, O.; Pandolfini, T.; Spena, A.; Mezzetti, B. Auxin synthesis-encoding transgene enhances grape fecundity Plant Physiol. 2007, 143, 1689-1694 (Pubitemid 46849479)
43. Mezzetti, B.; Landi, L.; Scortichini, L.; Rebori, A.; Spena, A.; Pandolfini, T. Genetic engineering of parthenocarpic fruit development in strawberry Acta Hortic. 2002, 567, 101-104
44. Craig, A.; Cloarec, O.; Holmes, E.; Nicholson, J. K.; Lindon, J. C. Scaling and normalization effects in NMR spectroscopic metabonomic data sets Anal. Chem. 2006, 78, 2262-2267
45. Kozak, M.; Scaman, C. H. Unsupervised classification methods in food sciences: discussion and outlook J. Sci. Food Agric. 2008, 88, 1115-1127 (Pubitemid 351655866)
46. Cevallos-Cevallos, J. M.; Reyes-De-Corcuera, J. I.; Etxeberria, E.; Danyluk, M. D.; Rodrick, G. E. Metabolomic analysis in food science: a review Trends Food Sci. Technol. 2009, 20, 557-566
47. Wishart, D. S. Metabolomics: applications to food science and nutrition research Trends Food Sci. Technol. 2008, 19, 482-493 (Pubitemid 352004154)
48. Jolliffe, I. Principal component analysis. In Encyclopedia of Statistics in Behavioral Science; Wiley: New York, 2005.
49. 1H NMR and chemometrics to characterize mature grape berries in four wine-growing areas in Bordeaux, France J. Agric. Food Chem. 2005, 53, 6382-6389 (Pubitemid 41169389)
50. Cañas, R. A.; Amiour, N.; Quilleré, I.; Hirel, B. An integrated statistical analysis of the genetic variability of nitrogen metabolism in the ear of three maize inbred lines (Zea mays L.) J. Exp. Bot. 2011, 62, 2309-2318
51. Sobolev, A.; Capitani, D.; Giannino, D.; Nicolodi, C.; Testone, G.; Santoro, F.; Frugis, G.; Iannelli, M.; Mattoo, A.; Brosio, E.; Gianferri, R.; D'Amico, I.; Mannina, L. NMR-Metabolic methodology in the study of GM foods Nutrients 2010, 2, 1-15
52. Piccioni, F.; Capitani, D.; Zolla, L.; Mannina, L. NMR metabolic profiling of transgenic maize with the Cry1A(b) gene J. Agric. Food Chem. 2009, 57, 6041-6049
53. Schervish, M. J. P values: what they are and what they are not Am. Stat. 1996, 50, 203-206
54. van der Krol, A. R.; Mur, L. A.; Beld, M.; Mol, J. N. M.; Stuitje, A. R. Flavonoid Genes in petunia: addition of a limited number of gene copies may lead to a suppression of gene expression Plant Cell Online 1990, 2, 291-299 (Pubitemid 120029589)
55. Gelvin, S. B. Agrobacterium -mediated plant transformation: the biology behind the "gene-jockeying" tool Microbiol. Mol. Biol. Rev. 2003, 67, 16-37 (Pubitemid 36314782)
56. Acciarri, N.; Restaino, F.; Vitelli, G.; Perrone, D.; Zottini, M.; Pandolfini, T.; Spena, A.; Rotino, G. L. Improved fruit productivity under both greenhouse and open field cultivation BMC Biotechnol. 2002, 2, 4
57. François, O.; Currat, M.; Ray, N.; Han, E.; Excoffier, L.; Novembre, J. Principal component analysis under population genetic models of range expansion and admixture Mol. Biol. Evol. 2010, 27, 1257-1268
58. Woodward, A. W.; Bartel, B. Auxin: regulation, action, and interaction Ann. Bot. (London) 2005, 95, 707-735 (Pubitemid 41238659)
59. Molesini, B.; Pandolfini, T.; Rotino, G. L.; Dani, V.; Spena, A. Aucsia gene silencing causes parthenocarpic fruit development in tomato Plant Physiol. 2009, 149, 534-548
60. Picone, G.; Balling Engelsen, S.; Savorani, F.; Testi, S.; Badiani, A.; Capozzi, F. Metabolomics as a powerful tool for molecular quality assessment of the fish Sparus aurata Nutrients 2011, 3, 212-227