References

[1] Ayyadurai, V.A. and Dewey, C.F. (2011) CytoSolve: A Scalable Computational Method for Dynamic Integration of Multiple Molecular Pathway Models. Cellular and Molecular Bioengineering, 4, 28-45.

http://dx.doi.org/10.1007/s12195-010-0143-x

[2] Kodama, T., et al. (2011) Qualitative PCR Method for Roundup Ready Soybean: Interlaboratory Study. Journal of AOAC International, 94, 224-231.

[3] Deonikar, P., et al. (2015) Discovery of Key Molecular Pathways of C1 Metabolism and Formaldehyde Detoxification in Maize through a Systematic Bioinformatics Literature Review. Agricultural Sciences, 6, 571-585.

http://dx.doi.org/10.4236/as.2015.65056

[4] Kothandaram, S., Deonikar, P., Mohan, M., Venugopal, V. and Ayyadurai, V.A.S. (2015) In Silico Modeling of C1 Metabolism. American Journal of Plant Sciences, 6, 1444-1465.

http://dx.doi.org/10.4236/ajps.2015.69144

[5] Mohan, M., Kothandaram, S., Deonikar, P., Venugopal, V. and Ayyadurai, V.A.S. (2015) Integrative Modeling of Oxidative Stress and C1 Metabolism Reveals Upregulation of Formaldehyde and Down Regulation of Glutathione. American Journal of Plant Sciences, 6, 1527-1542.

http://dx.doi.org/10.4236/ajps.2015.69152

[6] Arruda, S.C., Barbosa, H.S., Azevedo, R.A. and Arruda, M.A. (2013) Comparative Studies Focusing on Transgenic through cp4EPSPS Gene and Non-Transgenic Soybean Plants: An Analysis of Protein Species and Enzymes. Journal of Proteomics, 93, 107-116.

http://dx.doi.org/10.1016/j.jprot.2013.05.039

[7] Barbosa, H.S., Arruda, S.C., Azevedo, R.A. and Arruda, M.A. (2012) New Insights on Proteomics of Transgenic Soybean Seeds: Evaluation of Differential Expressions of Enzymes and Proteins. Analytical and Bioanalytical Chemistry, 402, 299-314.

http://dx.doi.org/10.1007/s00216-011-5409-1

[8] Mataveli, L.R., Pohl, P., Mounicou, S., Arruda, M.A. and Szpunar, J. (2010) A Comparative Study of Element Concentrations and Binding in Transgenic and Non-Transgenic Soybean Seeds. Metallomics, 2, 800-805.

http://dx.doi.org/10.1039/c0mt00040j

[9] Sammons, R.D. and Gaines, T.A. (2014) Glyphosate Resistance: State of Knowledge. Pest Management Science, 70, 1367-1377.

http://dx.doi.org/10.1002/ps.3743

[10] Funke, T., Han, H., Healy-Fried, M.L., Fischer, M. and Schonbrunn, E. (2006) Molecular Basis for the Herbicide Resistance of Roundup Ready Crops. Proceedings of the National Academy of Sciences of the United States of America, 103, 13010-13015.

http://dx.doi.org/10.1073/pnas.0603638103

[11] Roberts, A.F. (2010) A Review of the Environmental Safety of the CP4 EPSPS Protein. Center for Environmental Risk Assessment, ILSI Research Foundation, Washington DC.

[12] Fernandez-Cornejo, J. (2014) Recent Trends in GE Adoption.

http://www.ers.usda.gov/data-products/adoption-of-genetically-engineered-crops-in-the-us/recent-trends-in-ge-adoption.aspx.

[13] de Vendomois, J.S., et al. (2010) Debate on GMOs Health Risks after Statistical Findings in Regulatory Tests. International Journal of Biological Sciences, 6, 590-598.

http://dx.doi.org/10.7150/ijbs.6.590

[14] Devos, Y., Sanvido, O., Tait, J. and Raybould, A. (2014) Towards a More Open Debate about Values in Decision-Making on Agricultural Biotechnology. Transgenic Research, 23, 933-943.

http://dx.doi.org/10.1007/s11248-013-9754-z

[15] McHughen, A. (2013) GM Crops and Foods: What Do Consumers Want to Know? GM Crops & Food, 4, 172-182.

http://dx.doi.org/10.4161/gmcr.26532

[16] Ricroch, A.E. and Hénard-Damave, M.-C. (2015) Next Biotech Plants: New Traits, Crops, Developers and Technologies for Addressing Global Challenges. Critical Reviews in Biotechnology, 1-16.

http://dx.doi.org/10.3109/07388551.2015.1004521

[17] Rottman, D. (2013) Why We Will Need Genetically Modified Foods.

[18] Aldemita, R.R., Reaño, I.M.E., Solis, R.O. and Hautea, R.A. (2015) Trends in Global Approvals of Biotech Crops (1992-2014). GM Crops & Food.

http://dx.doi.org/10.1080/21645698.2015.1056972

[19] Domingo, J.L. and Gine Bordonaba, J. (2011) A Literature Review on the Safety Assessment of Genetically Modified Plants. Environment International, 37, 734-742.

http://dx.doi.org/10.1016/j.envint.2011.01.003

[20] Paoletti, C., Flamm, E., Yan, W.; Meek, S., Renckens, S., Fellous, M. and Kuiper, H. (2008) GMO Risk Assessment around the World: Some Examples. Trends in Food Science & Technology, 19, S70-S78.

http://dx.doi.org/10.1016/j.tifs.2008.07.007

[21] Goldberger, B.A. (2001) The Evolution of Substantial Equivalence in FDA’s Premarket Review of Medical Devices. Food and Drug Law Journal, 56, 317-337.

[22] Administration, F.A.D. (2001) Draft Guidance for Industry: Voluntary Labeling Indicating Whether Foods Have or Have Not Been Developed Using Bioengineering: Notice of Availability. Federal Register.

[23] Marris, C. (2001) Public Views on GMOs: Deconstructing the Myths. Stakeholders in the GMO Debate Often Describe Public Opinion as Irrational. But Do They Really Understand the Public? EMBO Reports, 2, 545-548.

http://dx.doi.org/10.1093/embo-reports/kve142

[24] Phillips, T. (2008) Genetically Modified Organisms (GMOs): Transgenic Crops and Recombinant DNA Technology. Nature Education, 1, 213.

[25] Holdren, J.P., Shelanski, H., Vetter, D. and Glodfuss, C. (2015) Improving Transparency and Ensuring Continued Safety in Biotechnology.

https://www.whitehouse.gov/blog/2015/07/02/improving-transparency-and-ensuring-continued-safety-biotechnology

[26] Borghini, A. (2014) Substantial Equivalence. In: Thompson, P.B. and Kaplan, D.M., Eds., Encyclopedia of Food and Agricultural Ethics, Springer Science + Business Media, Dordrecht, 1-6.

[27] Schauzu, M. (2000) The Concept of Substantial Equivalence in Safety Assessment of Foods Derived from Genetically Modified Organisms. Ag. Biotech. Net, 2, 1-4.

[28] Lennox, K. (2014) Substantially Unequivalent: Reforming FDA Regulation of Medical Devices. University of Illinois Law Review, 1363-1400.

[29] Patwardhan, B., Warude, D., Pushpangadan, P. and Bhatt, N. (2005) Ayurveda and Traditional Chinese Medicine: A Comparative Overview. Evidence-Based Complementary and Alternative Medicine, 2, 465-473.

http://dx.doi.org/10.1093/ecam/neh140

[30] Ayyadurai, V.A.S. (2014) The Control Systems Engineering Foundation of Traditional Indian Medicine: The Rosetta Stone for Siddha and Ayurveda. International Journal of System of Systems Engineering, 5.

http://dx.doi.org/10.1504/IJSSE.2014.064836

[32] Tepfer, M., Jacquemond, M. and Garcia-Arenal, F. (2015) A Critical Evaluation of Whether Recombination in Virus-Resistant Transgenic Plants Will Lead to the Emergence of Novel Viral Diseases. New Phytologist, 207, 536-541.

http://dx.doi.org/10.1111/nph.13358

[33] Harrigan, G.G., et al. (2010) Natural Variation in Crop Composition and the Impact of Transgenesis. Nature Biotechnology, 28, 402-404.

http://dx.doi.org/10.1038/nbt0510-402

[34] Millstone, E., Brunner, E. and Mayer, S. (1999) Beyond “Substantial Equivalence”. Nature, 401, 525-526.

http://dx.doi.org/10.1038/44006

[35] Miller, H.I. (1999) Substantial Equivalence: Its Uses and Abuses. Nature Biotechnology, 17, 1042-1043.

http://dx.doi.org/10.1038/14987

[36] Halford, N.G., et al. (2014) Safety Assessment of Genetically Modified Plants with Deliberately Altered Composition. Plant Biotechnology Journal, 12, 651-654.

http://dx.doi.org/10.1111/pbi.12194

[37] Simo, C., Ibanez, C., Valdes, A., Cifuentes, A. and Garcia-Canas, V. (2014) Metabolomics of Genetically Modified Crops. International Journal of Molecular Sciences, 15, 18941-18966.

http://dx.doi.org/10.3390/ijms151018941

[38] Vahl, C.I. and Kang, Q. (2015) Equivalence Criteria for the Safety Evaluation of a Genetically Modified Crop: A Statistical Perspective. The Journal of Agricultural Science, 24 p.

http://dx.doi.org/10.1017/S0021859615000271

[39] Miller, J.G. (1978) Living Systems. McGraw-Hill, New York.

[40] Klir, G.J. (1972) Trends in General Systems Theory. Wiley-Interscience, New York.

[41] Boulding, K.E. (1953) The Organization Revolution: A Study in The Ethics of Economic Organization. Harper, New York.

[42] von Bertalanffy, L. (1968) General System Theory. George Braziller, Inc., New York.

[43] Ideker, T., et al. (2001) Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network. Science, 292, 929-934.

http://dx.doi.org/10.1126/science.292.5518.929

[44] Schuler, G.D., et al. (1996) A Gene Map of the Human Genome. Science, 274, 540-546.

http://dx.doi.org/10.1126/science.274.5287.540

[45] Pennisi, E. (2003) Human Genome. A Low Number Wins the GeneSweep Pool. Science, 300, 1484.

http://dx.doi.org/10.1126/science.300.5625.1484b

[46] Hodgkin, J. (2001) What Does a Worm Want with 20,000 Genes? Genome Biology, 2. COMMENT2008.

[47] Putnam, N.H., et al. (2007) Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization. Science, 317, 86-94.

http://dx.doi.org/10.1126/science.1139158

[48] Watson, J.D. and Crick, F.H. (1953) Molecular Structure of Nucleic Acids; a Structure for Deoxyribose Nucleic Acid. Nature, 171, 737-738.

http://dx.doi.org/10.1038/171737a0

[49] Schaffner, K.F. (1969) The Watson-Crick Model and Reductionism. British Journal for the Philosophy of Science, 20, 325-348.

http://dx.doi.org/10.1093/bjps/20.4.325

[50] Hood, L., Heath, J.R., Phelps, M.E. and Lin, B. (2004) Systems Biology and New Technologies Enable Predictive and Preventative Medicine. Science, 306, 640-643.

http://dx.doi.org/10.1126/science.1104635

[51] Subbarayappa, B.V. (1997) Siddha Medicine: An Overview. The Lancet, 350, 1841-1844.

http://dx.doi.org/10.1016/S0140-6736(97)04223-2

[52] Cannon, W.B. (1933) The Wisdom of the Body. Norton, New York.

[53] Wiener, N. (1948) Cybernetics or Control and Communication in the Animal Machine. The MIT Press, Cambridge.

[54] Kitano, H. (2001) Foundations of Systems Biology. The MIT Press, Cambridge.

[55] Keller, E.F. (2007) A Clash of Two Cultures. Nature, 445, 603.

http://dx.doi.org/10.1038/445603a

[56] Noble, D. (2006) Systems Biology and the Heart. Biosystems, 83, 75-80.

http://dx.doi.org/10.1016/j.biosystems.2005.05.013

[57] Duarte, N.C., et al. (2007) Global Reconstruction of the Human Metabolic Network Based on Genomic and Bibliomic Data. Proceedings of the National Academy of Sciences of the United States of America, 104, 1777-1782.

http://dx.doi.org/10.1073/pnas.0610772104

[58] Bhalla, U.S. (2003) Understanding Complex Signaling Networks through Models and Metaphors. Progress in Biophysics and Molecular Biology, 81, 45-65.

http://dx.doi.org/10.1016/S0079-6107(02)00046-9

[59] Ayyadurai, V.A.S. (2011) Services-Based Systems Architecture for Modeling the Whole Cell: A Distributed Collaborative Engineering Systems Approach. Communications in Medical and Care Compunetics, 1, 115-168.

http://dx.doi.org/10.1007/8754_2010_1

[60] Hornberg, J.J., Bruggeman, F.J., Westerhoff, H.V. and Lankelma, J. (2006) Cancer: A Systems Biology Disease. BioSystems, 83, 81-90.

http://dx.doi.org/10.1016/j.biosystems.2005.05.014

[61] Snoep, J.L., Bruggeman, F., Olivier, B.G. and Westerhoff, H.V. (2006) Towards Building the Silicon Cell: A Modular Approach. Biosystems, 83, 207-216.

http://dx.doi.org/10.1016/j.biosystems.2005.07.006

[62] Klipp, E. and Liebermeister, W. (2006) Mathematical Modeling of Intracellular Signaling Pathways. BMC Neuroscience, 7, S10.

http://dx.doi.org/10.1186/1471-2202-7-s1-s10

[63] Asthagiri, A.R. and Lauffenburger, D.A. (2000) Bioengineering Models of Cell Signaling. Annual Review of Biomedical Engineering, 2, 31-53.

http://dx.doi.org/10.1146/annurev.bioeng.2.1.31

[64] Ma’ayan, A., et al. (2005) Formation of Regulatory Patterns during Signal Propagation in a Mammalian Cellular Network. Science, 309, 1078-1083.

http://dx.doi.org/10.1126/science.1108876

[65] Lauffenburger, D.A. (2000) Cell Signaling Pathways as Control Modules: Complexity for Simplicity? Proceedings of the National Academy of Sciences of the United States of America, 97, 5031-5033.

http://dx.doi.org/10.1073/pnas.97.10.5031

[66] Ayyadurai, V.A.S. (2007) Scalable Computational Architecture for Integrating Biological Pathway Models. Massachusetts Institute of Technology, Biological Engineering Division. p. 2 v. (xvii, 303 leaves).

[67] Hanson, A.D. and Roje, S. (2001) One-Carbon Metabolism in Higher Plants. Annual Review of Plant Physiology and Plant Molecular Biology, 52, 119-137.

http://dx.doi.org/10.1146/annurev.arplant.52.1.119

[68] Hanson, A.D., Gage, D.A. and Shachar-Hill, Y. (2000) Plant One-Carbon Metabolism and Its Engineering. Trends in Plant Science, 5, 206-213.

http://dx.doi.org/10.1016/S1360-1385(00)01599-5

[69] Vanyushin, B.F. (2006) DNA Methylation in Plants. Current Topics in Microbiology and Immunology, 301, 67-122.

http://dx.doi.org/10.1007/3-540-31390-7_4

[70] Havir, E.A. and McHale, N.A. (1989) Enhanced-Peroxidatic Activity in Specific Catalase Isozymes of Tobacco, Barley, and Maize. Plant Physiology, 91, 812-815.

http://dx.doi.org/10.1104/pp.91.3.812

[71] Jozefczak, M., Remans, T., Vangronsveld, J. and Cuypers, A. (2012) Glutathione Is a Key Player in Metal-Induced Oxidative Stress Defenses. International Journal of Molecular Sciences, 13, 3145-3175.

http://dx.doi.org/10.3390/ijms13033145

[72] Achkor, H., et al. (2003) Enhanced Formaldehyde Detoxification by Overexpression of Glutathione-Dependent Formaldehyde Dehydrogenase from Arabidopsis. Plant Physiology, 132, 2248-2255.

http://dx.doi.org/10.1104/pp.103.022277

[73] Wippermann, U., et al. (1999) Maize Glutathione-Dependent Formaldehyde Dehydrogenase: Protein Sequence and Catalytic Properties. Planta, 208, 12-18.

http://dx.doi.org/10.1007/s004250050529

[74] Chew, O., Whelan, J. and Millar, A.H. (2003) Molecular Definition of the Ascorbate-Glutathione Cycle in Arabidopsis Mitochondria Reveals Dual Targeting of Antioxidant Defenses in Plants. The Journal of Biological Chemistry, 278, 46869-46877.

http://dx.doi.org/10.1074/jbc.m307525200

[75] Martinez, M.C., et al. (1996) Arabidopsis Formaldehyde Dehydrogenase. Molecular Properties of Plant Class III Alcohol Dehydrogenase Provide Further Insights into the Origins, Structure and Function of Plant Class p and Liver Class I Alcohol Dehydrogenases. European Journal of Biochemistry, 241, 849-857.

http://dx.doi.org/10.1111/j.1432-1033.1996.00849.x

[76] Nijhout, H.F., Reed, M.C., Budu, P. and Ulrich, C.M. (2004) A Mathematical Model of the Folate Cycle: New Insights into Folate Homeostasis. The Journal of Biological Chemistry, 279, 55008-55016.

http://dx.doi.org/10.1074/jbc.m410818200

[77] Yokota, A., Kitaoka, S., Miura, K. and Wadano, A. (1985) Reactivity of Glyoxylate with Hydrogen Perioxide and Simulation of the Glycolate Pathway of C3 Plants and Euglena. Planta, 165, 59-67.

http://dx.doi.org/10.1007/BF00392212

[78] Goyer, A., et al. (2004) Characterization and Metabolic Function of a Peroxisomal Sarcosine and Pipecolate Oxidase from Arabidopsis. The Journal of Biological Chemistry, 279, 16947-16953.

http://dx.doi.org/10.1074/jbc.m400071200