References

General References on Biofuels

1. Anne Ruffing (2013) “Metabolic Engineering of Hydrocarbon Biosynthesis for Biofuel Production”. InTech. 263-298.
2. C. Dellomonaco, F. Fava, and R. Gonzalez (2010) “The path to next generation biofuels: successes and challenges in the era of synthetic biology” Microbial Cell Factories. 9(3) .
3. C. Martin, D.. Nielsen, K.Solomon and K. Jones Prather (2009) “Synthetic Metabolism: Engineering Biology at the Protein and Pathway Scales” Chemistry & Biology. 16(3) , 277-286.
4. D. Savage, J. Way, and P. Silver (2008) “Defossiling Fuel: How Synthetic Biology Can Transform Biofuel Production” ACS Chemical Biology. 3(1) , 13-16.
5. Jay Keasling on Biofuels - a collection of links [https://static.igem.org/mediawiki/2013hs/2/24/Jay_Keasling_etc....pdf]
6. L. Jarboe, X. Zhang, X. Wang, J.. Moore, K. Shanmugam, and L. Ingram (2010) “Metabolic Engineering for Production of Biorenewable Fuels and Chemicals: Contributions of Synthetic Biology” Journal of Biomedicine and Biotechnology.
7. Michael Brenner et. al. (2006) “Engineering Microorganisms for Energy Production” Office of Biological and Environmental Research of the Department of Energy.
8. Pamela Peralta-Yahya1 and Jay Keasling (2010) “Advanced biofuel production in microbes” . Biotechnology Journal. 5(2) , 147-162.
9. R. Radakovits, R. Jinkerson, A. Darzins, and M.. Posewitz (2010) “Genetic Engineering of Algae for Enhanced Biofuel Production” American Society for Microbiology. 9(4) , 486-501.
10. S. Lee, H. Chou, T. Ham, T. Lee and J. Keasling (2008) “Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels” Science Direct. 19, 556-563.

Cyanobacteria and Pyruvate Kinase References

1. A. Schramm, B. Siebers, B. Tjaden, H. Brinkmann, and R. Hensel (2000) “Pyruvate Kinase of the Hyperthermophilic Crenarchaeote Thermoproteus tenax: Physiological Role and Phylogenetic Aspects” Journal of Bacteriology. 182(7) , 2001–2009.
2. Ana Ramos et al. (2004) “Effect of pyruvate kinase overproduction on glucose metabolism of Lactococcus lactis” Microbiology. 150, 1103–1111.
3. Aron Fenton and Aileen Alontaga (2009) “The Impact of Ions on Allosteric Functions in Human Liver Pyruvate Kinase”. Methods in Enzymology. 466, 83-107.
4. D. Gong, Z. Gong, Y. Guo, and J. Zhu (2002) “Expression, Activation, and Biochemical Properties of a Novel Arabidopsis Protein Kinase” Plant Physiology. 129, 225–234.
5. H. Huang, D. Camsund, P. Lindblad and T. Heidorn (2010) “Design and characterization of molecular tools for a Synthetic Biology approach towards developing cyanobacterial biotechnology” Nucleic Acids Research. 38(8) , 2577–2593.
6. H. Knoop, Y. Zilliges, W. Lockau, and R. Steuer (2010) “The Metabolic Network of Synechocystis sp. PCC 6803: Systemic Properties of Autotrophic Growth” Plant Physiology. 154, 410–422.
7. Hsin-Ho Huang and Peter Lindblad (2013) “Wide-dynamic-range promoters engineered for cyanobacteria” Journal of Biological Engineering. 7(10) .
8. Jiro Hattori et al. (1995) “Pyruvate kinase isozymes: Ancient diversity retained in modern plant cells” Biochemical Systematics and Ecology. 23(7–8) , 773–777, 779–780.
9. M. Malcovati and G. Valentini (1982) “AMP- and Fructose 1,6,-Biphosphate-activated pyruvate kinases from Escherichia coli”. Methods in Enzymology. 90, 170-179.
10. Open Wetware Synthetic Biology Course Website with information on Algal Biofuels http://openwetware.org/wiki/CH391L/S13/Algal_Biofuels
11. S. Nagarajan, D. Sherman, I. Shaw, and L. Shermana(2012) “Functions of the Duplicated hik31 Operons in Central Metabolism and Responses to Light, Dark, and Carbon Sources in Synechocystis sp. Strain PCC 6803” J. Bacteriol. 194(2) , 448.
12. T. Dandekar, S. Schuster, B. Snel, M. Huynen and P. Bork (1999) “Pathway alignment: application to the comparative analysis of glycolytic enzymes” Biochem. J. 343, 115-124.
13. Takakazu Kaneko et al. (1996) “Sequence Analysis of the Genome of the Unicellular Cyanobacterium Synechocystis sp. Strain PCC6803. II. Sequence Determination of the Entire Genome and Assignment of Potential Protein-coding Regions” DNA Research. 3, 109-136.
14. Thomas P. Howard et al. (2013) “Synthesis of customized petroleum-replica fuel molecules by targeted modification of free fatty acid pools in Escherichia coli” PNAS. 110 (19), 7636–7641.
15. V. Knowles, C.Smith, C. Smith, and W. Plaxton (2001) “Structural and Regulatory Properties of Pyruvate Kinase from the Cyanobacterium Synechococcus PCC 6301” J. Biol. Chem. 276, 20966-20972.
16. Vicki L. Knowles and William C. Plaxton (2003) “From Genome to Enzyme: Analysis of Key Glycolytic and Oxidative Pentose Phosphate Pathway Enzymes in the Cyanobacterium Synechocystis sp. PCC 6803” Plant Cell Physiol. 44(7) , 758–763.
17. Wolfgang H. Nitschmann and Gunter A. Peschek (1986) “Oxidative Phosphorylation and Energy Buffering in Cyanobacteria” J. Bacteriol. 168(3), 1205.
18. X. Liu, S. Fallon, J. Sheng, and R. Curtiss III ( 2011) “CO2-limitation-inducible Green Recovery of fatty acids from cyanobacterial biomass” PNAS. 108(17) , 6905–6908.
19. Y. Guo et al. (2012) “Beta-Cell Injury in Ncb5or-null Mice is Exacerbated by Consumption of a High-Fat Diet”. Eur J Lipid Sci Technol. 114(3), 233-243.

Synthetic Biology

1. Caltech Synthetic Biology Journal Club http://openwetware.org/wiki/Caltech_Synthetic_Biology_Journal_Club
2. R.Shetty, D. Endy and T. Knight Jr (2008) “Engineering BioBrick vectors from BioBrick parts” Journal of Biological Engineering. 2(5).
3. Tom Knight (1996) “Idempotent Vector Design for Standard Assembly of Biobricks” PNAS. 93(20), 10891-6.

Diagrams

1. Pathway Diagram01 https://static.igem.org/mediawiki/2013hs/8/8c/Pathway_Diagram.PDF
2. Pathway Diagram02
3. Jansson, Christer. "Figure 1." Earth Science Division. Lawrence Berkeley National Laboratory. Web. 22 May 2013. http://esd.lbl.gov/about/staff/christerjansson/cyanofuels.html.
4. Ruffing, Anne M. "Figure 3." Intech. InTech, 20 Mar. 2013. Web. 22 May 2013. http://www.intechopen.com/books/liquid-gaseous-and-solid-biofuels-conversion-techniques/metabolic-engineering-of-hydrocarbon-biosynthesis-for-biofuel-production.