- National Bioeconomy Blueprint; The White House: Washington, DC, 2012.
- (a) Carlson, R. Synthesis. The U.S. Bioeconomy in 2012 Reached $350 Billion in Revenues, or About 2.5% of GDP. http://www.synthesis.cc/2014/01/the-us-bioeconomy-in-2012.html (accessed July 18, 2014); (b) Solomon, D. Industrial Views on Synthetic Biology. Presented at Tooling the U.S. Bioeconomy: Synthetic Biology Conference, Washington, DC, November 5, 2013. ACS Science & the Congress Project, 2013.
- Cha, A. E. Companies Rush to Build ‘Biofactories’ for Medicines, Flavorings and Fuels. The Washington Post, October 24, 2013. http://www.washingtonpost.com/national/health-science/companies-rush-to-build-biofactories-for-medicines-flavorings-andfuels/2013/10/24/f439dc3a-3032-11e3-8906-3daa2bcde110_story.html (accessed December 2, 2014)
- Golden, J. S.; Handfield, R. B. Why Biobased? Opportunities in the Emerging Bioeconomy; U. S. Department of Agriculture: Washington, DC, 2014.
- (a) Kosuri, S.; Church, G. M. Large-scale de novo DNA synthesis: technologies and applications. Nat. Methods 2014, 11(5), 499-507; (b) Carlson, R. The Pace and Proliferation of Biological Technologies. Biosecurity and Bioterrorism 2003, 1(3), 203-14.
- National Human Genome Research Institute. The Human Genome Project Completion: Frequently Asked Questions. http://www.genome.gov/11006943 (accessed February 2, 2015).
- (a) 1000 Genomes Project Consortium. An Integrated Map of Genetic Variation from 1,092 Human Genomes. Nature 2012, 491(7422), 56-65; (b) Clark, L. Illumina Announces Landmark $1,000 Human Genome Sequencing. http://www.wired.co.uk/news/archive/2014-01/15/1000-dollar-genome (accessed December 30, 2014).
- (a) Benson, D. A.; Karsch-Mizrachi, I.; Lipman, D. J.; Ostell, J.; Wheeler, D. L. GenBank. Nucleic Acids Res. 2008, 36(Database Issue), D25-30; (b) Benson, D. A.; Karsch-Mizrachi, I.; Lipman, D. J.; Ostell, J.; Sayers, E. W. GenBank. Nucleic Acids Res. 2009, 37(Database Issue), D26-31.
- Wang, H. H.; Isaacs, F. J.; Carr, P. A.; Sun, Z. Z.; Xu, G.; Forest, C. R.; Church, G. M. Programming cells by multiplex genome engineering and accelerated evolution. Nature 2009, 460(7257), 894-8.
- Haurwitz, R. E.; Jinek, M.; Wiedenheft, B.; Zhou, K.; Doudna, J. A. Sequence-and Structure-Specific RNA Processing by a CRISPR Endonuclease. Science 2010, 329(5997), 1355-8.
- (a) Ladisch, M. The Role of Bioprocess Engineering in Biotechnology. The Bridge 2004, 34(3), 26-32; (b) Mosier, N. S.; Ladisch, M. R. Biotechnology. In Modern Biotechnology: Connecting Innovations in Microbiology and Biochemistry to Engineering Fundamentals; John Wiley & Sons: Hoboken, NJ, 2011; pp 1-25.
- OECD (Organisation for Economic Co-operation and Development). The Application of Biotechnology to Industrial Sustainability; OECD Publishing: France, 2001.
- National Research Council. A New Biology for the 21st Century; The National Academies Press: Washington, DC, 2009.
- Obama, B. Remarks by the President on the Economy in Osawatomie, Kansas. http://www.whitehouse.gov/the-press-office/2011/12/06/remarks-president-economyosawatomie-kansas (accessed December 20, 2014).
- Merriam-Webster. Biotechnology in Merriam-Webster. http://www.merriam-webster.com/dictionary/biotechnology (accessed February 3, 2015).
- Merriam-Webster. Genetic Engineering in Merriam Webster. http://www.merriamwebster.com/dictionary/genetic%20engineering (accessed February 3, 2015).
- UK Synthetic Biology Roadmap Coordination Group. A Synthetic Biology Roadmap for the UK; Technology Strategy Board: Swindon, Wiltshire, 2012.
- Mutalik, V. K.; Guimaraes, J. C.; Cambray, G.; Lam, C.; Christoffersen, M. J.; Mai, Q. A.; Tran, A. B.; Paull, M.; Keasling, J. D.; Arkin, A. P.; Endy, D. Precise and Reliable Gene Expression via Standard Transcription and Translation Initiation Elements. Nat. Methods 2013, 10(4), 354-60.
- The European Commission. The European Bioeconomy in 2030: Delivering Sustainable Growth by Addressing the Grand Societal Challenges, 2012. http://www.epsoweb.org/file/560 (accessed January 12, 2015).
- de Jong, E.; Higson, A.; Walsh, P.; Wellisch, M. Bio-based Chemicals Value Added Products from Biorefineries [online]; IEA Bioenergy: Wageningen, The Netherlands, 2012. http://www.ieabioenergy.com/wp-content/uploads/2013/10/Task-42-Biobased-Chemicalsvalue-added-products-from-biorefineries.pdf (accessed December 12, 2014).
- (a) OECD. Industrial Biotechnology and Climate Change: Opportunities and Challenges [online]; OECD Publishing: 2011. http://www.oecd.org/sti/biotech/49024032.pdf (accessed December 11, 2014); (b) OECD. Emerging Policy Issues in Synthetic Biology [online]; OECD Publishing, 2014. http://dx.doi.org/10.1787/9789264208421-en (accessed December 11, 2014).
- OECD. The Bioeconomy to 2030: Designing a Policy Agenda; OECD Publishing, 2009.
- Palsson, B. Cell Factory Design. Presented at Workshop on the Industrialization of Biology, May 28, 2014.
- BCC Research. Synthetic Biology: Global Markets; BCC Research: Wellesley, MA, 2014.
- Milken Institute. Unleashing the Power of the Bio-Economy; Milken Institute: Santa Monica, CA, 2013.
- McKinsey Global Institute. Disruptive Technologies: Advances that Will Transform Life, Business, and the Global Economy; McKinsey & Company: Washington, DC, 2013.
- Kelley, N. J.; Whelan, D. J.; Kerr, E.; Apel, A.; Beliveau, R.; Scanlon, R. Engineering Biology to Address Global Problems: Synthetic Biology Markets, Needs, and Applications. Ind. Biotechnol. 2014, 10(3), 140-9.
- MIT (Massachusetts Institute of Technology). The Third Revolution: The Convergence of the Life Sciences, Physical Sciences, and Engineering [online]; MIT Washington Office:
-
Washington, DC, 2011. http://dc.mit.edu/sites/dc.mit.edu/files/MIT%20White%20Paper%20on%20Convergence.pdf (accessed December 4, 2014).
- AAAS (American Academy of Arts and Sciences). ARISE II: Unleashing America’s Research & Innovation Enterprise [online]; AAAS: Washington, DC, 2013. https://www.amacad.org/multimedia/pdfs/publications/researchpapersmonographs/arise2.pdf (accessed October 10, 2014).
- Kopchik, K. Bucknell Forum: Designer Neri Oxman to Speak Tonight. The Bucknellian, 2010.
- OECD. Emerging Policy Issues in Synthetic Biology [online]; OECD Publishing, 2014. http://dx.doi.org/10.1787/9789264208421-en (accessed December 11, 2014).
- Serger, S. S.; Breidne, M. China’s Fifteen-Year Plan for Science and Technology: An Assessment. Asia Pol’y 2007, 4(1), 135-64.
- (a) Kodumal, S. J.; Patel, K. G.; Reid, R.; Menzella, H. G.; Welch, M.; Santi, D. V. Total synthesis of long DNA sequences: Synthesis of a contiguous 32-kb polyketide synthase gene cluster. Proc. Natl. Acad. Sci. U. S. A. 2004, 101(44), 15573-8; (b) Bayer, T. S.; Widmaier, D. M.; Temme, K.; Mirsky, E. A.; Santi, D. V.; Voigt, C. A. Synthesis of Methyl Halides from Biomass Using Engineered Microbes. J. Am. Chem. Soc. 2009, 131(18), 6508-15.
- (a) Gibson, D. G.; Glass, J. I.; Lartigue, C.; Noskov, V. N.; Chuang, R.-Y.; Algire, M. A.; Benders, G. A.; Montague, M. G.; Ma, L.; Moodie, M. M.; Merryman, C.; Vashee, S.; Krishnakumar, R.; Assad-Garcia, N.; Andrews-Pfannkoch, C.; Denisova, E. A.; Young, L.; Qi, Z.-Q.; Segall-Shapiro, T. H.; Calvey, C. H.; Parmar, P. P.; Hutchison, C. A.; Smith, H. O.; Venter, J. C. Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. Science 2010, 329(5987), 52-56; (b) Annaluru, N.; Muller, H.; Mitchell, L. A.; Ramalingam, S.; Stracquadanio, G.; Richardson, S. M.; Dymond, J. S.; Kuang, Z.; Scheifele, L. Z.; Cooper, E. M.; Cai, Y.; Zeller, K.; Agmon, N.; Han, J. S.; Hadjithomas, M.; Tullman, J.; Caravelli, K.; Cirelli, K.; Guo, Z.; London, V.; Yeluru, A.; Murugan, S.; Kandavelou, K.; Agier, N.; Fischer, G.; Yang, K.; Martin, J. A.; Bilgel, M.; Bohutski, P.; Boulier, K. M.; Capaldo, B. J.; Chang, J.; Charoen, K.; Choi, W. J.; Deng, P.; DiCarlo, J. E.; Doong, J.; Dunn, J.; Feinberg, J. I.; Fernandez, C.; Floria, C. E.; Gladowski, D.; Hadidi, P.; Ishizuka, I.; Jabbari, J.; Lau, C. Y.; Lee, P. A.; Li, S.; Lin, D.; Linder, M. E.; Ling, J.; Liu, J.; Liu, J.; London, M.; Ma, H.; Mao, J.; McDade, J. E.; McMillan, A.; Moore, A. M.; Oh, W. C.; Ouyang, Y.; Patel, R.; Paul, M.; Paulsen, L. C.; Qiu, J.; Rhee, A.; Rubashkin, M. G.; Soh, I. Y.; Sotuyo, N. E.; Srinivas, V.; Suarez, A.; Wong, A.; Wong, R.; Xie, W. R.; Xu, Y.; Yu, A. T.; Koszul, R.; Bader, J. S.; Boeke, J. D.; Chandrasegaran, S. Total Synthesis of a Functional Designer Eukaryotic Chromosome. Science 2014, 344(6179), 55-8.
- Nielsen, A. A. K.; Segall-Shapiro, T. H.; Voigt, C. A. Advances in Genetic Circuit Design: Novel Biochemistries, Deep Part Mining, and Precision Gene Expression. Curr. Opin. Chem. Biol. 2013, 17(6), 878-92.
- Hsu, P. D.; Scott, D. A.; Weinstein, J. A.; Ran, F. A.; Konermann, S.; Agarwala, V.; Li, Y.; Fine, E. J.; Wu, X.; Shalem, O.; Cradick, T. J.; Marraffini, L. A.; Bao, G.; Zhang, F. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat. Biotechnol. 2013, 31(9), 827-32.
- (a) Becker, S. A.; Feist, A. M.; Mo, M. L.; Hannum, G.; Palsson, B. O.; Herrgard, M. J., Quantitative Prediction of Cellular Metabolism with Constraint-Based Models: the COBRA Toolbox. Nat. Protoc. 2007, 2(3), 727-738; (b) Burgard, A. P.; Pharkya, P.; Maranas, C. D. Optknock: A Bilevel Programming Framework for Identifying Gene Knockout Strategies for Microbial Strain Optimization. Biotechnology & Bioengineering 2003, 84(6), 647-57.
- Smanski, M. J.; Bhatia, S.; Zhao, D.; Park, Y.; B A Woodruff, L.; Giannoukos, G.; Ciulla, D.; Busby, M.; Calderon, J.; Nicol, R.; Gordon, D. B.; Densmore, D.; Voigt, C. A. Functional Optimization of Gene Clusters by Combinatorial Design and Assembly. Nat. Biotechnol. 2014, 32(12), 1241-9.
- Brophy, J. A. N.; Voigt, C. A. Principles of Genetic Circuit Design. Nat. Methods 2014, 11(5), 508-520.
- Cardinale, S.; Arkin, A. P., Contextualizing Context for Synthetic Biology – Identifying Causes of Failure of Synthetic Biological Systems. Biotechnol. J. 2012, 7(7), 856-66.
- (a) Mutalik, V. K.; Guimaraes, J. C.; Cambray, G.; Lam, C.; Christoffersen, M. J.; Mai, Q. A.; Tran, A. B.; Paull, M.; Keasling, J. D.; Arkin, A. P.; Endy, D. Precise and reliable gene expression via standard transcription and translation initiation elements. Nat. Methods 2013, 10(4), 354-60; (b) Baker, D.; Church, G.; Collins, J.; Endy, D.; Jacobson, J.; Keasling, J.; Modrich, P.; Smolke, C.; Weiss, R. Engineering Life: Building a FAB for Biology. Sci. Am. 2006, 294(6), 44-51.
- Galdzicki, M.; Clancy, K. P.; Oberortner, E.; Pocock, M.; Quinn, J. Y.; Rodriguez, C. A.; Roehner, N.; Wilson, M. L.; Adam, L.; Anderson, J. C.; Bartley, B. A.; Beal, J.; Chandran, D.; Chen, J.; Densmore, D.; Endy, D.; Grunberg, R.; Hallinan, J.; Hillson, N. J.; Johnson, J. D.; Kuchinsky, A.; Lux, M.; Misirli, G.; Peccoud, J.; Plahar, H. A.; Sirin, E.; Stan, G.-B.; Villalobos, A.; Wipat, A.; Gennari, J. H.; Myers, C. J.; Sauro, H. M. The Synthetic Biology Open Language (SBOL) Provides a Community Standard for Communicating Designs in Synthetic Biology. Nat. Biotechnol. 2014, 32(6), 545-50.
- (a) Donia, M. S.; Cimermancic, P.; Schulze, C. J.; Wieland Brown, L. C.; Martin, J.; Mitreva, M.; Clardy, J.; Linington, R. G.; Fischbach, M. A. A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics. Cell 2014, 158(6), 1402-14; (b) Scharschmidt, T. C.; Fischbach, M. A. What Lives On Our Skin: Ecology, Genomics and Therapeutic Opportunities Of the Skin Microbiome. Drug Discovery Today: Dis. Mech. 2013, 10(3-4), e83–9.
- (a) Hatzimanikatis, V.; Li, C.; Ionita, J. A.; Henry, C. S.; Jankowski, M. D.; Broadbelt, L. J. Exploring the Diversity of Complex Metabolic Networks. Bioinformatics 2005, 21(8), 1603-1609; (b) Li, C.; Henry, C. S.; Jankowski, M. D.; Ionita, J. A.; Hatzimanikatis, V.; Broadbelt, L. J. Computational Discovery of Biochemical Routes to Specialty Chemicals. Chem. Eng. Sci. 2004, 59(22-23), 5051-60.
- Srivastava, S.; Kotker, J.; Hamilton, S.; Ruan, P.; Tsui, J.; Anderson, J. C.; Bodik, R.; Seshia, S. A. In Pathway Synthesis Using the Act Ontology in Proceedings of the 4th International Workshop on Bio-Design Automation (IWBDA): San Francisco, CA, 2012.
- Lu, T. K.; Khalil, A. S.; Collins, J. J. Next-generation synthetic gene networks. Nat. Biotechnol. 2009, 27(12), 1139-50.
- Zhang, F.; Carothers, J. M.; Keasling, J. D. Design of a Dynamic Sensor-Regulator System for Production of Chemicals and Fuels Derived from Fatty Acids. Nat. Biotechnol. 2012, 30(4), 354-9.
- Chen, A. Y.; Deng, Z.; Billings, A. N.; Seker, U. O. S.; Lu, Michelle Y.; Citorik, R. J.; Zakeri, B.; Lu, T. K. Synthesis and patterning of tunable multiscale materials with engineered cells. Nat. Mater. 2014, 13(5), 515-23.
- Bennett, J. W. The Time Line Adrenalin and cherry trees. Mod. Drug Discovery 2001, 4, 47-8.
- Shuler, M. L.; Kargi, F. Bioprocess Engineering: Basic Concepts. Prentice Hall: Upper Saddle River, New Jersey, 2002.
- Cohen, S. N.; Chang, A. C.; Boyer, H. W.; Helling, R. B. Construction of biologically functional bacterial plasmids in vitro. Proc. Natl. Acad. Sci. U. S. A. 1973, 70(11), 3240-4.
- Bailey, J. E. Toward a Science of Metabolic Engineering. Science 1991, 252(5013), 1668-75.
- Stephanopoulos, G.; Vallino, J. Network rigidity and metabolic engineering in metabolite overproduction. Science 1991, 252(5013), 1675-81.
- Bornscheuer, U. T.; Huisman, G. W.; Kazlauskas, R. J.; Lutz, S.; Moore, J. C.; Robins, K. Engineering the third wave of biocatalysis. Nature 2012, 485(7397), 185-94.
- Savile, C. K.; Janey, J. M.; Mundorff, E. C.; Moore, J. C.; Tam, S.; Jarvis, W. R.; Colbeck, J. C.; Krebber, A.; Fleitz, F. J.; Brands, J.; Devine, P. N.; Huisman, G. W.; Hughes,
-
G. J. Biocatalytic Asymmetric Synthesis of Chiral Amines from Ketones Applied to Sitagliptin Manufacture. Science 2010, 329(5989), 305-9.
- WHO (World Health Organization). World Malaria Report 2005. UNICEF: Geneva, 2005.
- (a) Korenromp, E. L.; Williams, B. G.; Gouws, E.; Dye, C.; Snow, R. W. Measurement of trends in childhood malaria mortality in Africa: an assessment of progress toward targets based on verbal autopsy. Lancet Infect. Dis. 2003, 3(6), 349-358; (b) Marsh, K. Malaria disaster in Africa. The Lancet 1998, 352(9132), 924.
- Enserink, M. Source of New Hope Against Malaria is in Short Supply. Science 2005, 307(5706), 33.
- Schmid, G.; Hofheinz, W. Total Synthesis of Qinghaosu. J. Am. Chem. Soc. 1983, 105(3), 624-5.
- (a) Haynes, R. K.; Vonwiller, S. C. Cyclic peroxyacetal lactone, lactol and ether compounds. U.S. Patent 5,420,299, May 30, 1995; (b) Roth, R. J.; Acton, N., A simple conversion of artemisinic acid into artemisinin. J. Nat. Prod. 1989, 52(5), 1183-5.
- Paddon, C. J.; Westfall, P. J.; Pitera, D. J.; Benjamin, K.; Fisher, K.; McPhee, D.; Leavell, M. D.; Tai, A.; Main, A.; Eng, D.; Polichuk, D. R.; Teoh, K. H.; Reed, D. W.; Treynor, T.; Lenihan, J.; Fleck, M.; Bajad, S.; Dang, G.; Dengrove, D.; Diola, D.; Dorin, G.; Ellens, K. W.; Fickes, S.; Galazzo, J.; Gaucher, S. P.; Geistlinger, T.; Henry, R.; Hepp, M.; Horning, T.; Iqbal, T.; Jiang, H.; Kizer, L.; Lieu, B.; Melis, D.; Moss, N.; Regentin, R.; Secrest, S.; Tsuruta, H.; Vazquez, R.; Westblade, L. F.; Xu, L.; Yu, M.; Zhang, Y.; Zhao, L.; Lievense, J.; Covello, P. S.; Keasling, J. D.; Reiling, K. K.; Renninger, N. S.; Newman, J. D. High-level semi-synthetic production of the potent antimalarial artemisinin. Nature 2013, 496(7446), 528-32.
- WHO Prequalificaion of Medicines Programme. Acceptance Of Non-Plant-Derived-Artemisinin Offers Potential To Increase Access To Malaria Treatment [online]. 2013. http://apps.who.int/prequal/info_press/documents/PQ_non-plant_derived_artemisinin_1. pdf (accessed December 12, 2014).
- Marris, C. SciDeveNet. Synthetic biology’s malaria promises could backfire [Online], 2013. http://www.scidev.net/global/biotechnology/opinion/synthetic-biology-smalaria-promises-could-backfire.html (accessed January 5, 2015).
- Rude, M. A.; Schirmer, A. New Microbial Fuels: A Biotech Perspective. Curr. Opin. Microbiol. 2009, 12(3), 274-81.
- (a) Buelter, T.; Meinhold, P.; Feldman, R.; Hawkins, A.; Bastian, S.; Arnold, F. H.; Urano, J. Engineered microorganisms capable of producing target compounds under anaerobic conditions. U.S. Pat. Appl. 0058532 A1, 2012; (b) Donaldson, G. K.; Eliot, A.; Flint, D.; Maggio-Hall, A.; Nagarajan, V. Fermentative production of four carbon alcohols. U.S. Pat. Appl. 0313206 A1, 2007.
- Hong, K. K.; Nielsen, J. Metabolic engineering of Saccharomyces cerevisiae: a key cell factory platform for future biorefineries. Cell. Mol. Life Sci. 2012, 69(16), 2671-90.
- Donaldson, G. K.; Eliot, A.; Flint, D.; Maggio-Hall, A.; Nagarajan, V. Fermentative production of four carbon alcohols. U.S. U.S. Pat. Appl. 0092957 A1, 2007.
- Festel, G.; Boles, E.; Weber, C.; Brat, D. Fermentative production of isobutanol with yeast. U.S. Patent 8,530,226 B2, September 10, 2013.
- Knothe, G. Biodiesel and renewable diesel: A comparison. Prog. Energy Combust. Sci. 2010, 36, 364-73.
- Trimbur, D.; Im, C.-S.; Dillon, H.; Day, A.; Franklin, S.; Coragliotti, A. Production of oil in microorganisms. U.S. Patent 8,889,401, November 18, 2014.
- Burk, M. Personal Comments. Presented at Workshop on the Industrialization of Biology, May 28, 2014.
- (a) Yim, H.; Haselbeck, R.; Niu, W.; Pujol-Baxley, C.; Burgard, A.; Boldt, J.; Khandurina, J.; Trawick, J. D.; Osterhout, R. E.; Stephen, R.; Estadilla, J.; Teisan, S.; Schreyer, H. B.; Andrae, S.; Yang, T. H.; Lee, S. Y.; Burk, M. J.; Van Dien, S. Metabolic engineering of
-
Escherichia coli for direct production of 1,4-butanediol. Nat. Chem. Biol. 2011, 7(7), 445-52; (b) Burk, M. J. Sustainable production of industrial chemicals from sugars. Int. Sugar J. 2010, 112(1333), 30.
- BCC Research. Global Markets for Enzymes in Industrial Applications; BCC Research: Wellesley, MA, 2014.
- Scheufele, D. A. Communicating science in social settings. Proc. Natl. Acad. Sci. U. S. A. 2013, 110(Supplement 3), 14040-7.
- NIH (National Institutes of Health). Final NIH Genomic Data Sharing Policy. Fed Regist. 2014, 79(167), 51345–54.
- Werpy, T.; Petersen, G. Top Value Added Chemicals from Biomass: Volume I—Results of Screening for Potential Candidates from Sugars and Synthesis Gas; U.S. Department of Energy: Oak Ridge, TN, 2004.
- Newman, D. J.; Cragg, G. M.; Snader, K. M. Natural products as sources of new drugs over the period 1981-2002. J. Nat. Prod. 2003, 66(7), 1022-37.
- (a) Draths, K. M.; Knop, D. R.; Frost, J. W. Shikimic acid and quinic acid: Replacing isolation from plant aources with recombinant microbial biocatalysis. J. Am. Chem. Soc. 1999, 121(7), 1603-4; (b) Krämer, M.; Bongaerts, J.; Bovenberg, R.; Kremer, S.; Müller, U.; Orf, S.; Wubbolts, M.; Raeven, L. Metabolic engineering for microbial production of shikimic acid. Metab. Eng. 2003, 5(4), 277-83.
- (a) Pollard, D. J.; Woodley, J. M. Biocatalysis for pharmaceutical intermediates: the future is now. Trends in Biotechnol. 2007, 25(2), 66-73; (b) Clouthier, C. M.; Pelletier, J. N. Expanding the organic toolbox: A guide to integrating biocatalysis in synthesis. Chem. Soc. Rev. 2012, 41(4), 1585-605.
- Savile, C. K.; Janey, J. M.; Mundorff, E. C.; Moore, J. C.; Tam, S.; Jarvis, W. R.; Colbeck, J. C.; Krebber, A.; Fleitz, F. J.; Brands, J.; Devine, P. N.; Huisman, G. W.; Hughes, G. J. Biocatalytic asymmetric synthesis of chiral amines from ketones applied to sitagliptin manufacture. Science 2010, 329(5989), 305-9.
- (a) Müller, K.; Faeh, C.; Diederich, F. Fluorine in pharmaceuticals: Looking beyond intuition. Science 2007, 317(5846), 1881-6; (b) Purser, S.; Moore, P. R.; Swallow, S.; Gouverneur, V. Fluorine in medicinal chemistry. Chem. Soc. Rev. 2008, 37(2), 320-30; (c) Eustaquio, A. S.; O’Hagan, D.; Moore, B. S. Engineering fluorometabolite production: Fluorinase expression in Salinispora tropica yields fluorosalinosporamide. J. Nat. Prod. 2010, 73(3), 378-82; (d) Runguphan, W.; Qu, X.; O’Connor, S. E. Integrating carbon-halogen bond formation into medicinal plant metabolism. Nature 2010, 468(7322), 461-4; (e) Walker, M. C.; Thuronyi, B. W.; Charkoudian, L. K.; Lowry, B.; Khosla, C.; Chang, M. C., Expanding the Fluorine Chemistry of Living Systems Using Engineered Polyketide Synthase Pathways. Science 2013, 341(6150), 1089-94.
- (a) Coelho, P. S.; Brustad, E. M.; Kannan, A.; Arnold, F. H. Olefin cyclopropanation via carbene transfer catalyzed by engineered cytochrome P450 enzymes. Science 2013, 339(6117), 307-10; (b) McIntosh, J. A.; Coelho, P. S.; Farwell, C. C.; Wang, Z. J.; Lewis, J. C.; Brown, T. R.; Arnold, F. H. Enantioselective intramolecular C-H amination catalyzed by engineered cytochrome P450 enzymes in vitro and in vivo. Angew. Chem., Int. Ed. 2013, 52(35), 9309-12.
- Treimer, J. F.; Zenk, M. H. Purification and Properties of Strictosidine Synthase, the Key Enzyme in Indole Alkaloid Formation. Eur. J. Biochem. 1979, 101(1), 225-33.
- Kim, H. J.; Ruszczycky, M. W.; Choi, S. H.; Liu, Y. N.; Liu, H. W. Enzyme-catalysed [4+2] cycloaddition is a key step in the biosynthesis of spinosyn A. Nature 2011, 473(7345), 109-12.
- IREA (International Renewable Energy Agency). Production of bio-ethylene (Technology Brief I13); International Renewable Energy Agency and Energy Technology Systems Analysis Programme; IREA: Abu Dhabi, UAE, 2013.
- Yim, H.; Haselbeck, R.; Niu, W.; Pujol-Baxley, C.; Burgard, A.; Boldt, J.; Khandurina, J.; Trawick, J. D.; Osterhout, R. E.; Stephen, R.; Estadilla, J.; Teisan, S.; Schreyer, H. B.; Andrae, S.; Yang, T. H.; Lee, S. Y.; Burk, M. J.; Van Dien, S. Metabolic Engineering of Escherichia coli for Direct Production of 1,4-Butanediol. Nat. Chem. Biol. 2011, 7(7), 445-52.
- Tullo, A. H. Hunting for Biobased Acrylic Acid. Chem. Eng. News 2013, 91(46), 18-9.
- Madhavan Nampoothiri, K.; Nair, N. R.; John, R. P. An overview of the recent developments in polylactide (PLA) research. Bioresour. Technol. 2010, 101(22), 8493-501.
- Anderson, A. J.; Dawes, E. A. Occurrence, Metabolism, Metabolic Role, and Industrial Uses of Bacterial Polyhydroxyalkanoates. Microbiol. Rev. 1990, 54(4), 450-72.
- Zhang, S., Fabrication of Novel Biomaterials through Molecular Self-Assembly. Nat. Biotechnol. 2003, 21(10), 1171-8.
- (a) Fahnestock, S.; Rich, A. Ribosome-catalyzed polyester formation. Science 1971, 173(3994), 340-3; (b) Mao, C.; Solis, D. J.; Reiss, B. D.; Kottmann, S. T.; Sweeney, R. Y.; Hayhurst, A.; Georgiou, G.; Iverson, B.; Belcher, A. M. Virus-based toolkit for the directed synthesis of magnetic and semiconducting nanowires. Science 2004, 303(5655), 213-7; (c) Ohta, A.; Murakami, H.; Higashimura, E.; Suga, H. Synthesis of polyester by means of genetic code reprogramming. Chemistry & Biology 2007, 14(12), 1315-22.
- (a) Addadi, L.; Weiner, S. Interactions between acidic proteins and crystals: Stereo-chemical requirements in biomineralization. Proc. Natl. Acad. Sci. U. S. A. 1985, 82(12), 4110-4; (b) Mann, S.; Archibald, D. D.; Didymus, J. M.; Douglas, T.; Heywood, B. R.; Meldrum, F. C.; Reeves, N. J. Crystallization at Inorganic-organic Interfaces: Biominerals and Biomimetic Synthesis. Science 1993, 261(5126), 1286-92; (c) Belcher, A. M.; Wu, X. H.; Christensen, R. J.; Hansma, P. K.; Stucky, G. D.; Morse, D. E. Control of crystal phase switching and orientation by soluble mollusc-shell proteins. Nature 1996, 381(6577), 56-8; (d) Banfield, J. F.; Welch, S. A.; Zhang, H.; Ebert, T. T.; Penn, R. L. Aggregation-Based Crystal Growth and Microstructure Development in Natural Iron Oxyhydroxide Biomineralization Products. Science 2000, 289(5480), 751-4; (e) Sundar, V. C.; Yablon, A. D.; Grazul, J. L.; Ilan, M.; Aizenberg, J. Fibre-optical features of a glass sponge. Nature 2003, 424(6951), 899-900.
- Christensen, C. M.; Raynor, M. E. The Innovator’s Solution: Creating and Sustaining Successful Growth. Harvard Business School Press: Boston, MA, 2003.
- U.S. Energy Information Administration. U.S. Number of Operable Refineries as of January 1. http://www.eia.gov/dnav/pet/hist/LeafHandler.ashx?n=PET&s=8_NA_8O0_NUS_C&f=A (accessed July 25, 2014).
- Carlson, R.; Wehbring, R. Microbrewing the Bioeconomy: Innovation and Changing Scale in Industrial Production. http://www.biodesic.com/library/Microbrewing_the_Bioeconomy.pdf (accessed January 5, 2015).
- Kojima, M.; Johnson, T. Potential for biofuels for transport in developing countries. ESMAP Knowledge Exchange Series 2005, 4, 1-4.
- Agricultural Marketing Resource Center. A National Information Resource for Value-Added Agriculture: Corn. http://www.agmrc.org/commodities__products/grains__oilseeds/corn_grain/ (accessed December 30, 2015).
- (a) Fang, Z. Converting Lignocellulosic Biomass to Low Cost Fermentable Sugars. In Pretreatment Techniques for Biofuels and Biorefineries; Springer: Berlin, 2013; pp 133-150; (b) Beckman, E. J. Supercritical and near-critical CO 2 in green chemical synthesis and processing. J. Supercrit. Fluids 2004, 28(2), 121-91.
- Singh, R. K.; Tiwari, M. K.; Singh, R.; Lee, J.-K. From Protein Engineering to Immobilization: Promising Strategies for the Upgrade of Industrial Enzymes. Int. J. Mol. Sci. 2013, 14(1), 1232-77.
- He, M. Cell-free protein synthesis: applications in proteomics and biotechnology. New Biotechnol. 2008, 25(2-3), 126-32.
- Rollin, J. A.; Tam, T. K.; Zhang, Y. H. P. New biotechnology paradigm: cell-free bio-systems for biomanufacturing. Green Chem. 2013, 15(7), 1708-19.
- Vallino, J. J.; Stephanopoulos, G. Metabolic Flux Distributions in Corynebacterium Glutamicum During Growth and Lysine Overproduction. Biotechnology and Bioengineering 2000, 67(6), 872-85.
- (a) Bairoch, A. PROSITE: A Dictionary of Sites and Patterns in Proteins. Nucleic Acids Res. 1991, 19(Supplemental), 2241-5; (b) Hulo, N.; Bairoch, A.; Bulliard, V.; Cerutti, L.; De Castro, E.; Langendijk-Genevaux, P. S.; Pagni, M.; Sigrist, C. J. A. The PROSITE database. Nucleic Acids Res. 2006, 34(Supplemental), D227-30.
- Xiong, Z.; Laird, P. W. COBRA: A Sensitive and Quantitative DNA Methylation Assay. Nucleic Acids Res. 1997, 25(12), 2532-4.
- Hillson, N. DNA Assembly Method Standardization for Synthetic Biomolecular Circuits and Systems. In Design and Analysis of Biomolecular Circuits, Koeppl, H.; Setti, G.; di Bernardo, M.; Densmore, D., Eds. Springer: New York, 2011; pp 295-314.
- Onken, M.; Eichelberg, M.; Riesmeier, J.; Jensch, P. Digital Imaging and Communications in Medicine. In Biomedical Image Processing, Deserno, T. M., Ed. Springer: Berlin, 2011; pp 427-54.
- (a) Canton, B.; Labno, A.; Endy, D. Refinement and standardization of synthetic biological parts and devices. Nat. Biotechnol. 2008, 26(7), 787-93; (b) Brown, J. The iGEM competition: building with biology. Synthetic Biology, IET 2007, 1(1.2), 3-6.
- Ham, T. S.; Dmytriv, Z.; Plahar, H.; Chen, J.; Hillson, N. J.; Keasling, J. D. Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools. Nucleic Acids Res. 2012, 40(18), e141.
- Cooling, M. T.; Rouilly, V.; Misirli, G.; Lawson, J.; Yu, T.; Hallinan, J.; Wipat, A. Standard virtual biological parts: a repository of modular modeling components for synthetic biology. Bioinformatics 2010, 26(7), 925-31.
- Seiler, C. Y.; Park, J. G.; Sharma, A.; Hunter, P.; Surapaneni, P.; Sedillo, C.; Field, J.; Algar, R.; Price, A.; Steel, J.; Throop, A.; Fiacco, M.; LaBaer, J. DNASU plasmid and PSI:Biology-Materials repositories: resources to accelerate biological research. Nucleic Acids Res. 2013, 42(Database Issue), D1253-60.
- Herscovitch, M.; Perkins, E.; Baltus, A.; Fan, M. Addgene provides an open forum for plasmid sharing. Nat. Biotechnol. 2012, 30(4), 316-7.
- (a) Eisenreich, W.; Bacher, A.; Arigoni, D.; Rohdich, F., Biosynthesis of isoprenoids via the non-mevalonate pathway. Cell. Mol. Life Sci. 2004, 61(12), 1401-26; (b) Rohmer, M. The discovery of a mevalonate-independent pathway for isoprenoid biosynthesis in bacteria, algae and higher plants. Natural Products Reports 1999, 16(5), 565-74.
- Raab, A. M.; Lang, C. Oxidative versus reductive succinic acid production in the yeast Saccharomyces cerevisiae. Bioengineered Bugs 2011, 2(2), 120-3.
- Rahman, S. A.; Cuesta, S. M.; Furnham, N.; Holliday, G. L.; Thornton, J. M. EC-BLAST: a tool to automatically search and compare enzyme reactions. Nat. Methods 2014, 11(2), 171-4.
- Altschul, S. F.; Madden, T. L.; Schäffer, A. A.; Zhang, J.; Zhang, Z.; Miller, W.; Lipman, D. J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25(17), 3389-402.
- De Ferrari, L.; Mitchell, J. B. From sequence to enzyme mechanism using multi-label machine learning. BMC Bioinformatics 2014, 15, 150.
- Esvelt, K. M.; Carlson, J. C.; Liu, D. R. A system for the continuous directed evolution of biomolecules. Nature 2011, 472(7344), 499-503.
- (a) Fox, R. J.; Davis, S. C.; Mundorff, E. C.; Newman, L. M.; Gavrilovic, V.; Ma, S. K.; Chung, L. M.; Ching, C.; Tam, S.; Muley, S.; Grate, J.; Gruber, J.; Whitman, J. C.; Sheldon, R. A.; Huisman, G. W. Improving catalytic function by ProSAR-driven enzyme evolu-
-
tion. Nature Biotechnol. 2007, 25(3), 338-44; (b) Luetz, S.; Giver, L.; Lalonde, J. Engineered enzymes for chemical production. Biotechnology and Bioengineering 2008, 101(4), 647-53.
- Adrio, J.-L.; Demain, A. L. Recombinant organisms for production of industrial products. Bioengineered Bugs 2010, 1(2), 116-131.
- (a) Niewoehner, O.; Jinek, M.; Doudna, J. A., Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases. Nucleic Acids Res. 2014, 42(2), 1341-53; (b) Gao, X.; Tsang, J. C. H.; Gaba, F.; Wu, D.; Lu, L.; Liu, P. Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers. Nucleic Acids Res. 2014, 42(20), e155.
- Heap, J. T.; Pennington, O. J.; Cartman, S. T.; Carter, G. P.; Minton, N. P. The ClosTron: a universal gene knock-out system for the genus Clostridium. J. Microbiol. Methods 2007, 70(3), 452-64.
- Joung, J. K.; Sander, J. D. TALENs: a widely applicable technology for targeted genome editing. Nat. Rev. Mol. Cell Biol. 2013, 14(1), 49-55.
- (a) Carroll, D. Genome Engineering With Zinc-Finger Nucleases. Genetics 2011, 188(4), 773-782; (b) Guo, J.; Gaj, T.; Barbas, C. F. Directed evolution of an enhanced and highly efficient FokI cleavage domain for Zinc Finger Nucleases. J. Mol. Biol. 2010, 400(1), 96-107; (c) Cathomen, T.; Keith Joung, J. Zinc-finger Nucleases: The Next Generation Emerges. Mol. Ther. 2008, 16(7), 1200-7.
- Wang, H. H.; Isaacs, F. J.; Carr, P. A.; Sun, Z. Z.; Xu, G.; Forest, C. R.; Church, G. M. Programming Cells by Multiplex Genome Engineering and Accelerated Evolution. Nature 2009, 460(7257), 894-8.
- National Renewable Energy Laboratory. Biomass Research. http://www.nrel.gov/biomass/biorefinery.html (accessed January 13, 2015).
- (a) Schellenberger, J.; Que, R.; Fleming, R. M. T.; Thiele, I.; Orth, J. D.; Feist, A. M.; Zielinski, D. C.; Bordbar, A.; Lewis, N. E.; Rahmanian, S.; Kang, J.; Hyduke, D. R.; Palsson, B. O. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat. Protoc. 2011, 6(9), 1290-307; (b) Ebrahim, A.; Lerman, J. A.; Palsson, B. O.; Hyduke, D. R. COBRApy: constraints-based reconstruction and analysis for python. BMC Systems Biology 2013, 7(1), 74.
- Galzie, Z. What is protein engineering? Biochem. Educ. 1991, 19(2), 74-75.