Nutrigenomics/pharmacogenomics Lactose intolerance: C/T(-13910) lactase persistence/non functions in vitro as a cis element 14kbp upstream enhancing the lactase promoter http://www.genecards.org/cgi-bin/carddisp.pl?gene=LCT

Nutrigenomics/pharmacogenomics Thiopurine methyltransferase (TPMT) metabolizes 6-mercaptopurine and azathiopurine, two drugs used in a range of indications, from childhood leukemia to autoimmune diseases CYP450 superfamily: CYP2D6 has over 75 known allelic variations, 30% of people in parts of East Africa have multiple copies of the gene, not be adequately treated with standard doses of drugs, e.g. codeine (activated by CYP2D6).

Further optimization readings Duarte et al. reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci U S A. 2007 Feb 6;104(6):1777-82. Joyce AR, Palsson BO. Toward whole cell modeling and simulation: comprehensive functional genomics through the constraint-based approach. Prog Drug Res. 2007;64:265, 267-309. Review. Herring, et al. Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat Genet. 2006 38:1406-12. Desai RP, Nielsen LK, Papoutsakis ET. Stoichiometric modeling of Clostridium acetobutylicum fermentations with non-linear constraints. J Biotechnol. 1999 71:191-205.

Human metabolic Network (Recon 1) Duarte et al. reconstruction of the human metabolic network based on genomic and bibliomic data. PNAS 2007 104:1777-82. E.coli: 1200 ORFs http://gcrg.ucsd.edu/organisms

Flux Data

C009-limited WT (LP) Dpyk (LP) Dpyk (QP) r=0.91 p=8e-8 r=0.56 r=-0.06 200 WT (LP) 180 7 160 8 140 9 120 10 Predicted Fluxes 100 14 13 11 r=0.91 p=8e-8 1 3 12 80 60 40 20 16 2 15 4 6 5 17 18 50 100 150 200 Experimental Fluxes 250 Dpyk (LP) 250 Dpyk (QP) 200 18 200 7 r=0.56 P=7e-3 150 r=-0.06 p=6e-1 150 8 7 2 8 Predicted Fluxes Predicted Fluxes 10 100 9 100 9 13 11 10 14 3 1 12 14 13 11 50 3 12 50 4 5 6 16 16 2 15 15 17 6 5 4 18 17 1 -50 -50 -50 50 100 150 200 250 -50 50 100 150 200 250 Experimental Fluxes Experimental Fluxes

Competitive growth data: reproducibility Correlation between two selection experiments Badarinarayana, et al. Nature Biotech.19: 1060

Competitive growth data On minimal media negative small selection effect C 2 p-values 4x10-3 1x10-5 LP QP Novel redundancies Position effects Hypothesis: next optima are achieved by regulation of activities.

Intelligent Design & Metabolic Evolution Fong SS, Burgard AP, Herring CD, Knight EM, Blattner FR, Maranas CD, Palsson BO. In silico design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol Bioeng. 2005 91(5):643-8. Rozen DE, Schneider D, Lenski RE Long-term experimental evolution in Escherichia coli. XIII. Phylogenetic history of a balanced polymorphism. J Mol Evol. 2005 61(2):171-80 Andries K, et al. (J&J) A diarylquinoline drug active on the ATP synthase of Mycobacterium tuberculosis. Science. 2005 307:223-7. Shendure et al. Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome Science 2005 309:1728 (Select for secretion & ‘altruism’).