National Academies Press: OpenBook
« Previous: 5 What Is Success and How to Get There: Recommendations
Suggested Citation:"References." National Research Council. 2015. Industrialization of Biology: A Roadmap to Accelerate the Advanced Manufacturing of Chemicals. Washington, DC: The National Academies Press. doi: 10.17226/19001.
×

References

  1. National Bioeconomy Blueprint; The White House: Washington, DC, 2012.
  2. (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.
  3. 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)
  4. Golden, J. S.; Handfield, R. B. Why Biobased? Opportunities in the Emerging Bioeconomy; U. S. Department of Agriculture: Washington, DC, 2014.
  5. (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.
  6. National Human Genome Research Institute. The Human Genome Project Completion: Frequently Asked Questions. http://www.genome.gov/11006943 (accessed February 2, 2015).
  7. (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).
  8. (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.
Suggested Citation:"References." National Research Council. 2015. Industrialization of Biology: A Roadmap to Accelerate the Advanced Manufacturing of Chemicals. Washington, DC: The National Academies Press. doi: 10.17226/19001.
×
  1. 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.
  2. 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.
  3. (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.
  4. OECD (Organisation for Economic Co-operation and Development). The Application of Biotechnology to Industrial Sustainability; OECD Publishing: France, 2001.
  5. National Research Council. A New Biology for the 21st Century; The National Academies Press: Washington, DC, 2009.
  6. 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).
  7. Merriam-Webster. Biotechnology in Merriam-Webster. http://www.merriam-webster.com/dictionary/biotechnology (accessed February 3, 2015).
  8. Merriam-Webster. Genetic Engineering in Merriam Webster. http://www.merriamwebster.com/dictionary/genetic%20engineering (accessed February 3, 2015).
  9. UK Synthetic Biology Roadmap Coordination Group. A Synthetic Biology Roadmap for the UK; Technology Strategy Board: Swindon, Wiltshire, 2012.
  10. 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.
  11. 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).
  12. 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).
  13. (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).
  14. OECD. The Bioeconomy to 2030: Designing a Policy Agenda; OECD Publishing, 2009.
  15. Palsson, B. Cell Factory Design. Presented at Workshop on the Industrialization of Biology, May 28, 2014.
  16. BCC Research. Synthetic Biology: Global Markets; BCC Research: Wellesley, MA, 2014.
  17. Milken Institute. Unleashing the Power of the Bio-Economy; Milken Institute: Santa Monica, CA, 2013.
  18. McKinsey Global Institute. Disruptive Technologies: Advances that Will Transform Life, Business, and the Global Economy; McKinsey & Company: Washington, DC, 2013.
  19. 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.
  20. MIT (Massachusetts Institute of Technology). The Third Revolution: The Convergence of the Life Sciences, Physical Sciences, and Engineering [online]; MIT Washington Office:
Suggested Citation:"References." National Research Council. 2015. Industrialization of Biology: A Roadmap to Accelerate the Advanced Manufacturing of Chemicals. Washington, DC: The National Academies Press. doi: 10.17226/19001.
×
  1. Washington, DC, 2011. http://dc.mit.edu/sites/dc.mit.edu/files/MIT%20White%20Paper%20on%20Convergence.pdf (accessed December 4, 2014).

  2. 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).
  3. Kopchik, K. Bucknell Forum: Designer Neri Oxman to Speak Tonight. The Bucknellian, 2010.
  4. OECD. Emerging Policy Issues in Synthetic Biology [online]; OECD Publishing, 2014. http://dx.doi.org/10.1787/9789264208421-en (accessed December 11, 2014).
  5. Serger, S. S.; Breidne, M. China’s Fifteen-Year Plan for Science and Technology: An Assessment. Asia Pol’y 2007, 4(1), 135-64.
  6. (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.
  7. (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.
  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.
  9. 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.
  10. (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.
  11. 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.
Suggested Citation:"References." National Research Council. 2015. Industrialization of Biology: A Roadmap to Accelerate the Advanced Manufacturing of Chemicals. Washington, DC: The National Academies Press. doi: 10.17226/19001.
×
  1. Brophy, J. A. N.; Voigt, C. A. Principles of Genetic Circuit Design. Nat. Methods 2014, 11(5), 508-520.
  2. 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.
  3. (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.
  4. 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.
  5. (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.
  6. (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.
  7. 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.
  8. Lu, T. K.; Khalil, A. S.; Collins, J. J. Next-generation synthetic gene networks. Nat. Biotechnol. 2009, 27(12), 1139-50.
  9. 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.
  10. 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.
  11. Bennett, J. W. The Time Line Adrenalin and cherry trees. Mod. Drug Discovery 2001, 4, 47-8.
  12. Shuler, M. L.; Kargi, F. Bioprocess Engineering: Basic Concepts. Prentice Hall: Upper Saddle River, New Jersey, 2002.
  13. 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.
  14. Bailey, J. E. Toward a Science of Metabolic Engineering. Science 1991, 252(5013), 1668-75.
  15. Stephanopoulos, G.; Vallino, J. Network rigidity and metabolic engineering in metabolite overproduction. Science 1991, 252(5013), 1675-81.
  16. 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.
  17. 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,
Suggested Citation:"References." National Research Council. 2015. Industrialization of Biology: A Roadmap to Accelerate the Advanced Manufacturing of Chemicals. Washington, DC: The National Academies Press. doi: 10.17226/19001.
×
  1. G. J. Biocatalytic Asymmetric Synthesis of Chiral Amines from Ketones Applied to Sitagliptin Manufacture. Science 2010, 329(5989), 305-9.

  2. WHO (World Health Organization). World Malaria Report 2005. UNICEF: Geneva, 2005.
  3. (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.
  4. Enserink, M. Source of New Hope Against Malaria is in Short Supply. Science 2005, 307(5706), 33.
  5. Schmid, G.; Hofheinz, W. Total Synthesis of Qinghaosu. J. Am. Chem. Soc. 1983, 105(3), 624-5.
  6. (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.
  7. 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.
  8. 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).
  9. 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).
  10. Rude, M. A.; Schirmer, A. New Microbial Fuels: A Biotech Perspective. Curr. Opin. Microbiol. 2009, 12(3), 274-81.
  11. (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.
  12. 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.
  13. 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.
  14. Festel, G.; Boles, E.; Weber, C.; Brat, D. Fermentative production of isobutanol with yeast. U.S. Patent 8,530,226 B2, September 10, 2013.
  15. Knothe, G. Biodiesel and renewable diesel: A comparison. Prog. Energy Combust. Sci. 2010, 36, 364-73.
  16. 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.
  17. Burk, M. Personal Comments. Presented at Workshop on the Industrialization of Biology, May 28, 2014.
  18. (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
Suggested Citation:"References." National Research Council. 2015. Industrialization of Biology: A Roadmap to Accelerate the Advanced Manufacturing of Chemicals. Washington, DC: The National Academies Press. doi: 10.17226/19001.
×
  1. 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.

  2. BCC Research. Global Markets for Enzymes in Industrial Applications; BCC Research: Wellesley, MA, 2014.
  3. Scheufele, D. A. Communicating science in social settings. Proc. Natl. Acad. Sci. U. S. A. 2013, 110(Supplement 3), 14040-7.
  4. NIH (National Institutes of Health). Final NIH Genomic Data Sharing Policy. Fed Regist. 2014, 79(167), 51345–54.
  5. 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.
  6. 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.
  7. (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.
  8. (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.
  9. 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.
  10. (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.
  11. (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.
  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.
  13. 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.
  14. 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.
Suggested Citation:"References." National Research Council. 2015. Industrialization of Biology: A Roadmap to Accelerate the Advanced Manufacturing of Chemicals. Washington, DC: The National Academies Press. doi: 10.17226/19001.
×
  1. 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.
  2. Tullo, A. H. Hunting for Biobased Acrylic Acid. Chem. Eng. News 2013, 91(46), 18-9.
  3. 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.
  4. Anderson, A. J.; Dawes, E. A. Occurrence, Metabolism, Metabolic Role, and Industrial Uses of Bacterial Polyhydroxyalkanoates. Microbiol. Rev. 1990, 54(4), 450-72.
  5. Zhang, S., Fabrication of Novel Biomaterials through Molecular Self-Assembly. Nat. Biotechnol. 2003, 21(10), 1171-8.
  6. (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.
  7. (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.
  8. Christensen, C. M.; Raynor, M. E. The Innovator’s Solution: Creating and Sustaining Successful Growth. Harvard Business School Press: Boston, MA, 2003.
  9. 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).
  10. 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).
  11. Kojima, M.; Johnson, T. Potential for biofuels for transport in developing countries. ESMAP Knowledge Exchange Series 2005, 4, 1-4.
  12. 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).
  13. (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.
  14. 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.
  15. He, M. Cell-free protein synthesis: applications in proteomics and biotechnology. New Biotechnol. 2008, 25(2-3), 126-32.
Suggested Citation:"References." National Research Council. 2015. Industrialization of Biology: A Roadmap to Accelerate the Advanced Manufacturing of Chemicals. Washington, DC: The National Academies Press. doi: 10.17226/19001.
×
  1. 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.
  2. Vallino, J. J.; Stephanopoulos, G. Metabolic Flux Distributions in Corynebacterium Glutamicum During Growth and Lysine Overproduction. Biotechnology and Bioengineering 2000, 67(6), 872-85.
  3. (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.
  4. Xiong, Z.; Laird, P. W. COBRA: A Sensitive and Quantitative DNA Methylation Assay. Nucleic Acids Res. 1997, 25(12), 2532-4.
  5. 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.
  6. 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.
  7. (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.
  8. 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.
  9. 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.
  10. 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.
  11. Herscovitch, M.; Perkins, E.; Baltus, A.; Fan, M. Addgene provides an open forum for plasmid sharing. Nat. Biotechnol. 2012, 30(4), 316-7.
  12. (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.
  13. Raab, A. M.; Lang, C. Oxidative versus reductive succinic acid production in the yeast Saccharomyces cerevisiae. Bioengineered Bugs 2011, 2(2), 120-3.
  14. 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.
  15. 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.
  16. De Ferrari, L.; Mitchell, J. B. From sequence to enzyme mechanism using multi-label machine learning. BMC Bioinformatics 2014, 15, 150.
  17. Esvelt, K. M.; Carlson, J. C.; Liu, D. R. A system for the continuous directed evolution of biomolecules. Nature 2011, 472(7344), 499-503.
  18. (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-
Suggested Citation:"References." National Research Council. 2015. Industrialization of Biology: A Roadmap to Accelerate the Advanced Manufacturing of Chemicals. Washington, DC: The National Academies Press. doi: 10.17226/19001.
×
  1. 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.

  2. Adrio, J.-L.; Demain, A. L. Recombinant organisms for production of industrial products. Bioengineered Bugs 2010, 1(2), 116-131.
  3. (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.
  4. 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.
  5. 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.
  6. (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.
  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.
  8. National Renewable Energy Laboratory. Biomass Research. http://www.nrel.gov/biomass/biorefinery.html (accessed January 13, 2015).
  9. (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.
  10. Galzie, Z. What is protein engineering? Biochem. Educ. 1991, 19(2), 74-75.
Suggested Citation:"References." National Research Council. 2015. Industrialization of Biology: A Roadmap to Accelerate the Advanced Manufacturing of Chemicals. Washington, DC: The National Academies Press. doi: 10.17226/19001.
×

This page intentionally left blank.

Suggested Citation:"References." National Research Council. 2015. Industrialization of Biology: A Roadmap to Accelerate the Advanced Manufacturing of Chemicals. Washington, DC: The National Academies Press. doi: 10.17226/19001.
×
Page 111
Suggested Citation:"References." National Research Council. 2015. Industrialization of Biology: A Roadmap to Accelerate the Advanced Manufacturing of Chemicals. Washington, DC: The National Academies Press. doi: 10.17226/19001.
×
Page 112
Suggested Citation:"References." National Research Council. 2015. Industrialization of Biology: A Roadmap to Accelerate the Advanced Manufacturing of Chemicals. Washington, DC: The National Academies Press. doi: 10.17226/19001.
×
Page 113
Suggested Citation:"References." National Research Council. 2015. Industrialization of Biology: A Roadmap to Accelerate the Advanced Manufacturing of Chemicals. Washington, DC: The National Academies Press. doi: 10.17226/19001.
×
Page 114
Suggested Citation:"References." National Research Council. 2015. Industrialization of Biology: A Roadmap to Accelerate the Advanced Manufacturing of Chemicals. Washington, DC: The National Academies Press. doi: 10.17226/19001.
×
Page 115
Suggested Citation:"References." National Research Council. 2015. Industrialization of Biology: A Roadmap to Accelerate the Advanced Manufacturing of Chemicals. Washington, DC: The National Academies Press. doi: 10.17226/19001.
×
Page 116
Suggested Citation:"References." National Research Council. 2015. Industrialization of Biology: A Roadmap to Accelerate the Advanced Manufacturing of Chemicals. Washington, DC: The National Academies Press. doi: 10.17226/19001.
×
Page 117
Suggested Citation:"References." National Research Council. 2015. Industrialization of Biology: A Roadmap to Accelerate the Advanced Manufacturing of Chemicals. Washington, DC: The National Academies Press. doi: 10.17226/19001.
×
Page 118
Suggested Citation:"References." National Research Council. 2015. Industrialization of Biology: A Roadmap to Accelerate the Advanced Manufacturing of Chemicals. Washington, DC: The National Academies Press. doi: 10.17226/19001.
×
Page 119
Suggested Citation:"References." National Research Council. 2015. Industrialization of Biology: A Roadmap to Accelerate the Advanced Manufacturing of Chemicals. Washington, DC: The National Academies Press. doi: 10.17226/19001.
×
Page 120
Next: Appendix A: Glossary »
Industrialization of Biology: A Roadmap to Accelerate the Advanced Manufacturing of Chemicals Get This Book
×
Buy Paperback | $60.00 Buy Ebook | $47.99
MyNAP members save 10% online.
Login or Register to save!
Download Free PDF

The tremendous progress in biology over the last half century - from Watson and Crick's elucidation of the structure of DNA to today's astonishing, rapid progress in the field of synthetic biology - has positioned us for significant innovation in chemical production. New bio-based chemicals, improved public health through improved drugs and diagnostics, and biofuels that reduce our dependency on oil are all results of research and innovation in the biological sciences. In the past decade, we have witnessed major advances made possible by biotechnology in areas such as rapid, low-cost DNA sequencing, metabolic engineering, and high-throughput screening. The manufacturing of chemicals using biological synthesis and engineering could expand even faster. A proactive strategy - implemented through the development of a technical roadmap similar to those that enabled sustained growth in the semiconductor industry and our explorations of space - is needed if we are to realize the widespread benefits of accelerating the industrialization of biology.

Industrialization of Biology presents such a roadmap to achieve key technical milestones for chemical manufacturing through biological routes. This report examines the technical, economic, and societal factors that limit the adoption of bioprocessing in the chemical industry today and which, if surmounted, would markedly accelerate the advanced manufacturing of chemicals via industrial biotechnology. Working at the interface of synthetic chemistry, metabolic engineering, molecular biology, and synthetic biology, Industrialization of Biology identifies key technical goals for next-generation chemical manufacturing, then identifies the gaps in knowledge, tools, techniques, and systems required to meet those goals, and targets and timelines for achieving them. This report also considers the skills necessary to accomplish the roadmap goals, and what training opportunities are required to produce the cadre of skilled scientists and engineers needed.

  1. ×

    Welcome to OpenBook!

    You're looking at OpenBook, NAP.edu's online reading room since 1999. Based on feedback from you, our users, we've made some improvements that make it easier than ever to read thousands of publications on our website.

    Do you want to take a quick tour of the OpenBook's features?

    No Thanks Take a Tour »
  2. ×

    Show this book's table of contents, where you can jump to any chapter by name.

    « Back Next »
  3. ×

    ...or use these buttons to go back to the previous chapter or skip to the next one.

    « Back Next »
  4. ×

    Jump up to the previous page or down to the next one. Also, you can type in a page number and press Enter to go directly to that page in the book.

    « Back Next »
  5. ×

    Switch between the Original Pages, where you can read the report as it appeared in print, and Text Pages for the web version, where you can highlight and search the text.

    « Back Next »
  6. ×

    To search the entire text of this book, type in your search term here and press Enter.

    « Back Next »
  7. ×

    Share a link to this book page on your preferred social network or via email.

    « Back Next »
  8. ×

    View our suggested citation for this chapter.

    « Back Next »
  9. ×

    Ready to take your reading offline? Click here to buy this book in print or download it as a free PDF, if available.

    « Back Next »
Stay Connected!