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Biodefense in the Age of Synthetic Biology (2018)

Chapter: REFERENCES

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REFERENCES ACAAI (American College of Allergy, Asthma, and Immunology). 2017. Allergy Symptoms. Available at: http://acaai.org/allergies/symptoms. Accessed November 3, 2017. AFHSB (Armed Forces Health Surveillance Branch). 2017. Global Emerging Infections Surveillance and Tesponse System. Available at: https://health.mil/Military-Health- Topics/Health-Readiness/Armed-Forces-Health-Surveillance-Branch/Global-Emerging- Infections-Surveillance-and-Response. Accessed November 14, 2017. Alibek, K. 1998. Behind the Mask: Biological Warfare. Perspective 9(1). Available at: http://www.bu.edu/iscip/vol9/Alibek.html. Accessed November 14, 2017. Anderson, R.M., C. Fraser, A.C. Ghani, C.A. Donnelly, S. Riley, N.M. Ferguson, G.M. Leung, T.H. Lam, and A.J. Hedley. 2004. Epidemiology, transmission dynamics and control of SARS: The 2002–2003 epidemic. Philosophical Transactions of the Royal Society London B 359(1447):1091–1105. Atkinson, N.J., J. Willeveldt, D.J. Evans, and P. Simmonds. 2014. The influence of CpG and UpA dinucleotide frequencies on RNA virus replication and characterization of the innate cellular pathways underlying virus attenuation and enhanced replication. Nucleic Acids Research 42(7):4527–4545. Aubry, F., A. Nougairède, L. de Fabritus, G. Querat, E.A. Gould, and X. de Lamballerie. 2014. Single-stranded positive-sense RNA viruses generated in days using infectious subgenomic amplicons. Journal of General Virology 95(Pt. 11):2462–2467. Awan, A.R., B.A. Blount, D.J. Bell, W.M. Shaw, J.C.H. Ho. R.M. McKiernan, and T. Ellis. 2017. Biosynthesis of the antibiotic nonribosomal peptide penicillin in baker’s yeast. Nature Communications 8:15202. Baker Lab. 2017. Rosetta. University of Washington. Available at http://boinc.bakerlab.org/rosetta. Accessed November 8, 2017. Barquist, L., C.J. Boinett, and A.K. Cain. 2013. Approaches to querying bacterial genomes with transposon-insertion sequencing. RNA Biology 10(7):1161–1169. Barton, G.M., and R. Medzhitov. 2002. Retroviral delivery of small interfering RNA into primary cells. Proceedings of the National Academy of Sciences of the United States of America 99(23):14943–14945. Becker, M.M., M.M., R.L. Graham, E.F. Donaldson, B. Rockx, A. Sims, T. Sheahan, R.J. Pickles, D. Corti, R.E. Johnston, R.S. Baric, and M.R. Denison. 2008. Synthetic recombinant bat SARS-like coronavirus is infectious in cultured cells and in mice. Proceedings of the National Academy of Sciences of the United States of America 105(50):19944–19949. Benner, S.A., and A.M. Sismour. 2005. Synthetic biology. Nature Reviews Genetics 6(7):533– 543. Bennett, R.L., and J.D. Licht. 2018. Targeting epigenetics in cancer. Annual Reviews of Pharmacology and Toxicology 58:187–207. Benson, R.A., I.B. McInnes, P. Garside, and J.M. Brewer. 2018. Model answers: Rational application of murine models in arthritis research. European Journal of Immunology 48(1):32–38. 160 PREPUBLICATION COPY: UNCORRECTED PROOFS

References 161 Berg, P., D. Baltimore, H.W. Boyer, S.N. Cohen, R.W. Davis, D.S. Hogness, D. Nathans, R. Roblin, J.D. Watson, S. Weissman, and N.D. Zinder. 1974. Potential biohazards of recombinant DNA molecules. Science 185(4148):303. Berkeley Lights. 2017. Berkeley Lights Automates Biological Processing to Reduce Drug Development Timelines and Bring Therapies to Market Faster. News: September 12, 2017. Available at https://www.berkeleylights.com/berkeley-lights-automates- biological-processing-reduce-drug-development-timelines-bring-therapies-market-faster/ Accessed January 31, 2018. Black, J.B., P. Perez-Pinera, and C.A. Gersbach. 2017. Mammalian synthetic biology: Engineering biological systems. Annual Review of Biomedical Engineering 19:249–277. Blair, J. M., M.A. Webber. A.J. Baylay, D.O. Ogbolu, and L.J. Piddock. 2015. Molecular mechanisms of antibiotic resistance. Nature Reviews Microbiology 13:41–51. Blue Ribbon Study Panel on Biodefense. 2015. A National Blueprint for Biodefense: Leadership and Major Reform Needed to Optimize Efforts-Bipartisan Report of the Blue Ribbon Study Panel on Biodefense. Hudson Institute: Washington, DC: Hudson Institute. October 2015. Available at: http://www.biodefensestudy.org/a-national-blueprint-for- biodefense. Accessed February 20, 2018. Bogers, W.M., H. Oostermeijer, P. Mooij, G. Koopman, E.J. Verschoor, D. Davis, J.B. Ulmer, L.A. Brito, Y. Cu, K. Banerjee, G.R. Otten, B. Burke, A. Dey, J.L. Heeney, X. Shen, G.D. Tomaras, C. Labranche, D.C. Montefiori, H.X. Liao, B. Haynes, A.J. Geall, and S.W. Barnett. 2015. Potent immune responses in rhesus macaques induced by nonviral delivery of a self-amplifying RNA vaccine expressing HIV Type 1 envelope with a cationic nanoemulsion. Journal of Infectious Diseases 211(6):947–955. Böhme, L. and T. Rudel. 2009. Host cell death machinery as a target for bacterial pathogens. Microbes and Infection 11(13):1063–1070. Bornscheuer, U.T., G.W. Huisman, R.J. Kazlauskas, S. Lutz, J.C. Moore, and K. Robins. 2012. Engineering the third wave of biocatalysis. Nature 485(7397):185–194. Breaker, R. 2017. Presentation at the First Meeting for Committee on Strategies for Identifying and Addressing Biodefense Vulnerabilities Posed by Synthetic Biology, January 26, 2017, Washington, DC. Brocken, D.J.W., M. Tark-Dame, and R.T. Dame. 2017. dCas9: A versatile tool for epigenome editing. Current Issues in Molecular Biology 26:15–32. Brojatsch, J., A. Casadevall, and D. Goldman. 2014. Molecular determinants for a cardiovascular collapse in anthrax. Frontiers in Bioscience 6:139–147. Brophy, J.A., and C.A. Voigt. 2014. Principles of genetic circuit design. Nature Methods 11(5):508–520. Brubaker, S.W., K.S. Bonham, I. Zanoni, and J.C. Kagan. 2015. Innate immune pattern recognition: A cell biological perspective. Annual Review of Immunology 33:257–290. Buchan, J.R., L.S. Aucott, and I. Stansfield. 2006. tRNA properties help shape codon pair preferences in open reading frames. Nucleic Acids Research 34(3):1015–1027. Burns, C.C., J. Shaw, R. Campagnoli, J. Jorba, A. Vincent, J. Quay, and O.M. Kew. 2006 Modulation of polio virus replicative fitness in HeLa cells by deoptimization of synonymous codon usage in the capsid region. Journal of Virology 80(7):3259–3272. Burstein, D., L.B. Harrington, S.C. Strutt, A.J. Probst, K. Anantharaman, B.C. Thomas, J.A. Doudna, and J.F. Banfield. 2017. New CRISPR-Cas systems from uncultivated microbes. Nature 542(7640):237–241. PREPUBLICATION COPY: UNCORRECTED PROOFS

162 Biodefense in the Age of Synthetic Biology Butler, D. 2013. When Google got flu wrong: US outbreak foxes a leading web-based method for tracking seasonal flu. Nature 494(7436):155–156. Butterfield, G.L., M.J. Lajoie, H.H. Gustafson, D.L. Sellers, U. Nattermann, D. Ellis, J.B. Bale, S. Ke, G.H. Lenz, A. Yehdego, R. Ravichandran, S.H. Pun, N.P. King, and D. Baker. 2017. Evolution of a designed protein assembly encapsulating its own RNA genome. Nature 552(7685):415–420. BWC (Biological Weapons Convention). 1972. On the Prohibition of the Development, Production, and Stockpiling of Bacteriological (Biological) and Toxin Weapons and on Their Destruction. Available at: https://www.unog.ch/80256EDD006B8954/(httpAssets)/C4048678A93B6934C1257188 004848D0/$file/BWC-text-English.pdf. Accessed January 26, 2017. Byerly, C.R. 2010. The U.S. military and the influenza pandemic of 1918–1919. Public Health Reports 125(Suppl. 3):82–91. Candela, M., E. Biagi, S. Maccaferri, S. Turroni, and P. Brigidi. 2012. Intestinal microbiota is a plastic factor responding to environmental changes. Trends in Microbiology 20(8):385– 391. Carbonell, P., A. Currin, A.J. Jervis, N.J.W. Rattray, N. Swainston, C. Yan, E. Takano, and R. Breitling. 2016. Bioinformatics for the synthetic biology of natural products: Integrating across the Design–Build–Test cycle. Natural Product Reports 33(8):925–932. Carleton, H.A., and P. Gerner-Smidt. 2016. Whole-genome sequencing is taking over foodborne disease surveillance. Microbe 11(7):311–317. Carson, R. 2005. Splice it yourself. Wired, May 1, 2005. Available at: https://www.wired.com/2005/05/splice-it-yourself/ Accessed November 14, 2017. Carter, S.R., and R.M. Friedman. 2015. DNA Synthesis and Biosecurity: Lessons Learned and Options for the Future. J. Craig Venter Institute. Available at: http://www.jcvi.org/cms/fileadmin/site/research/projects/dna-synthesis-biosecurity- report/report-complete.pdf. Accessed January 31, 2018. Carus, W.S. 2017. A Short History of Biological Warfare: From Pre-History to the 21st Century. CSWMD Occasional Paper 12. Center for the Study of Weapons of Mass Destruction, National Defense University. August 7, 2017. Available at: http://wmdcenter.ndu.edu/Publications/Publication-View/Article/1270642/a-short- history-of-biological-warfare-from-pre-history-to-the-21st-century. Accessed on November 13, 2017. Casadevall, A., and D.A. Relman. 2010. Microbial threat lists: Obstacles in the quest for biosecurity? Nature Reviews Microbiology 8(2):149–154. Cavallo, R., G. Antonelli, and H.H. Hirsch. 2013. Viruses and immunity in transplant patients. Clinical and Developmental Immunology 2013:492352. CBC. 2017. Women Accused of Poisoning North Korea’s Kim Jong-nam Arrive at Malaysia Court. CBC News, July 27, 2017. Available at http://www.cbc.ca/news/world/north- korea-kim-jong-nam-malaysia-1.4225369. Accessed on November 2, 2017. CDC (Centers for Disease Control and Prevention). 2001. The Public Health Response to Biological and Chemical Terrorism: Interim Planning Guidance for State Public Health Officials. July 2001. Available at: https://emergency.cdc.gov/documents/planning/planningguidance.pdf. Accessed May 12, 2017. PREPUBLICATION COPY: UNCORRECTED PROOFS

References 163 CDC. 2014a. Laboratory Network for Biological Terrorism. Available at: https://emergency.cdc.gov/lrn/biological.asp. Accessed November 14, 2017. CDC. 2014b. Laboratory Response Network for Chemical Threats (LRN-C). Available at: https://emergency.cdc.gov/lrn/chemical.asp. Accessed November 14, 2017. CDC. 2014c. About Quarantine and Isolation. Available at: https://www.cdc.gov/quarantine/quarantineisolation.html. Accessed November 14, 2017. CDC. 2017. Preparation and Planning for Bioterrorism Emergencies. Available at: https://emergency.cdc.gov/bioterrorism/prep.asp. Accessed on May 12, 2017. CDC. 2017a. Epi-X. Available at: https://www.cdc.gov/mmwr/epix/epix.html. Accessed November 14, 2017. CDC. 2017b. Overview of Influenza Surveillance in the United States. Available at: https://www.cdc.gov/flu/weekly/overview.htm. Accessed November 14, 2017. CDC. 2017c. PulseNet. Available at: https://www.cdc.gov/pulsenet/index.html. Accessed November 14, 2017. CDC. 2017d. Microbenet. Available at: https://www.cdc.gov/microbenet/index.html. Accessed November 14, 2017. CDC. 2017e. Strategic National Stockpile. Available at: https://www.cdc.gov/phpr/stockpile/index.htm. Accessed November 14, 2017. CDC/APHIS (Animal and Plant Health Inspection Service). 2017. Select Agents and Toxins List. Available at: https://www.selectagents.gov/selectagentsandtoxinslist.html. Accessed November 6, 2017. Cello, J., A.V. Paul, and E. Wimmer. 2002. Chemical synthesis of poliovirus cDNA: Generation of infectious virus in the absence of natural template. Science 297(5583):1016–1018. Champer, J., R. Reeves, S.Y. Oh, C. Liu, J. Liu, A.G. Clark, and P.W. Messer. 2017. Novel CRISPR/Cas9 gene drive constructs reveal insights into mechanisms of resistance allele formation and drive efficiency in genetically diverse populations. PLoS Genetics 13(7):e1006796. Chan, L.Y., S. Kosuri, and D. Endy. 2005. Refactoring bacteriophage T7. Molecular Systems Biology 1(1):2005.0018. Chan, Y.K., and M.U. Gack. 2016. Viral evasion of intracellular DNA and RNA sensing. Nature Reviews in Microbiology 14(6):360–373. Chao, R., Y. Yuan, and H. Zhao. 2015. Building biological foundries for next-generation synthetic biology. Science China Life Science 58(7):658–665. Charles-Smith, L.E., T.L. Reynolds, M.A. Cameron, M. Conway, E.H.Y. Lau, J.M. Olsen, J.A. Pavlin, M. Shigematsu, L.C. Streichert, K.J. Suda, and C.D. Corle. 2015. Using social media for actionable disease surveillance and outbreak management: A systematic literature review. PLoS ONE 10(10):e0139701. Chinnadurai, G., S. Chinnadurai, and J. Brusca. 1979. Physical mapping of a large-plaque mutation of adenovirus type 2. Journal of Virology 32(2):623–628. Chiolero, A., V. Santschi, and F. Paccaud. 2013. Public health surveillance with electronic medical records: At risk of surveillance bias and overdiagnosis. European Journal of Public Health 23(3):350–351. CIDAR Lab. 2016. Eugene. Boston University. Available at: http://cidarlab.org/eugene/. Accessed November 8, 2017. Citorik, R.J., M. Mimee, and T.K. Lu. 2014. Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases. Nature Biotechnology 32(11):1141–1145. PREPUBLICATION COPY: UNCORRECTED PROOFS

164 Biodefense in the Age of Synthetic Biology Clapper, J.E. 2016. Worldwide Threat Assessment of the U.S. Intelligence Community. Statement for the Record by James R. Clapper, Director of National Intelligence. Senate Armed Service Committee, February 16, 2016. Available at: https://www.dni.gov/files/documents/SASC_Unclassified_2016_ATA_SFR_FINAL.pdf. Accessed May 19, 2017. Clemen, R. 1991. Making Hard Decisions: An Introduction to Decision Analysis. Boston: PWS- Kent. Cobb, R.E., N. Sun, and H. Zhao. 2013. Directed evolution as a powerful synthetic biology tool. Methods 60(1):81–90. Cockrell, A.S., B.L Yount, T. Scobey, K. Jensen, M. Douglas, A. Beall, X.C. Tang, W.A. Marasco, M.T. Heise, and R.S. Baric. 2016. A mouse model for MERS coronavirus induced acute respiratory distress syndrome. Nature Microbiology 2:16226. Coen, D.M., and D.D. Richman. 2013. Antiviral agents. Pp. 338–373 in Field’s Virology, 6th Ed., D.M. Knipe, and P.M. Howley, eds. Philadelphia, PA: Lippincott Williams and Wilkins. Coleman, J.R., D. Papamichail, S. Skiena, B. Futcher, E. Wimmer, and S. Mueller. 2008. Virus attenuation by genome-scale changes in codon pair bias. Science 320(5884):1784–1787. Committee on Homeland Security. 2006. Engineering Bio-Terror Agents: Lessons from the Offensive U.S. and Russian Biological Weapons Programs. Hearing Before the Subcommittee on Prevention of Nuclear and Biological Attack of the Committee on Homeland Security, House of Representatives One Hundred Ninth Congress First Session, July 13, 2005. Washington, DC: U.S. Government Printing Office [includes testimony from Roger Brent and Mike Callahan]. Cong, L., F.A. Ran, D. Cox, S. Lin, R. Barretto, N. Habib, P.D. Hsu, X. Wu, W. Jiang, L.A. Marraffini, and F. Zhang. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science 339(6121):819–823. Cox, I.J., M.L. Miller, J.A. Bloom, J. Fridrich, and T. Kalker 2008. Digital Watermarking and Steganography, 2nd Ed. Burlington, MA: Morgan Kaufmann. Cox, M.S., and A.F. Woolf. 2002. Preventing Proliferation of Biological Weapons: U.S. Assistance to the Former Soviet States. CRC Report for Congress RL31368. Available at: https://fas.org/sgp/crs/nuke/RL31368.pdf. Accessed November 14, 2017. Cress, B.F., J.A. Englaender, W. He, D. Kasper, R.J. Linhardt, and M.A. Koffas. 2014. Masquerading microbial pathogens: Capsular polysaccharides mimic host-tissue molecules. FEMS Microbiology Reviews 38(4):660–697. Cui, J., Y. Yin, Q. Ma, G. Wang, C. Olman, Y. Zhang, W. Chou, C. S. Hong, C. Zhang, S. Cao, X. Mao, Y. Li, S. Qin, S. Zhao, J. Jiang, P. Hastings, F. Li, and Y. Xu. 2015. Comprehensive characterization of the genomic alterations in human gastric cancer. International Journal of Cancer 137(1):86–95. Cullen, B.R. 2013. MicroRNAs as mediators of viral immune evasion. Nature Immunology 14(3):205–210. Cummings, C.L., and J. Kuzma. 2017. Societal Risk Evaluation Scheme (SRES): Scenario-based multi-criteria evaluation of synthetic biology applications. PLoS ONE 12(1):e0168564. Daigle, K.A., C.M. Logan, and R.S. Kotwal. 2015. Comprehensive performance nutrition for Special Operations Forces. Journal of Special Operations Medicine 15(4):40–53. DARPA (Defense Advanced Research Projects Agency). 2017. Safe Genes. Available at: https://www.darpa.mil/program/safe-genes. Accessed November 14, 2017. PREPUBLICATION COPY: UNCORRECTED PROOFS

References 165 Datlinger, P., A.F. Rendeiro, C. Schmidl, T. Krausgruber, P. Traxler, J. Klughammer, L. C. Schuster, A. Kuchler, D. Alpar, and C. Bock. 2017. Pooled CRISPR screening with single-cell transcriptome readout. Nature Methods 14:297–301. Davey, R.T., L. Dodd, M.A. Proschan, J. Neaton, J.N. Nordwall, J.S. Koopmeiners, J. Beigel, J. Tierney, H.C. Lane, A.S. Fauci, M.B.F. Massaquoi, F. Sahr, and D. Malvy. 2016. A randomized, controlled trial of ZMapp for Ebola virus infection. The New England Journal of Medicine 375(15):1448–1456. de Fabritus, L., A. Nougairède, F. Aubry, E.A. Gould, and X. de Lamballerie. 2015. Attenuation of tick-borne encephalitis virus using large-scale random codon re-encoding. PLoS Pathogens 11(3):e1004738. de Paz, H.D., P. Brotons, and C. Muñoz-Almagro. 2014. Molecular isothermal techniques for combating infectious diseases: Towards low-cost point-of-care diagnostics. Expert Review of Molecular Diagnostics 14(7):827–843. de Vries, R.P., W. Peng, O.C. Grant, A.J. Thompson, X. Zhu, K.M. Bouwman, A.T.T. de la Pena, M.J. van Breemen, I.N.A. Wickramasinghe, C.A.M. de Haan, W. Yu, R. McBride, R.W. Sanders, R.J. Woods, M.H. Verheije, I.A. Wilson, and J.C. Paulson. 2017. Three mutations switch H7N9 influenza to human-type receptor specificity. PLoS Pathogens 13(6):e1006390. Dhar, P.K., and R. Weiss. 2007. Enabling the new biology of the 21st century. Systems and Synthetic Biology 1(1):1–2. DiEuliis, D., and J. Giordano. 2017. Why gene editors like CRISPR/Cas may be a game-changer for neuroweapons. Health Security 15(3):296–302. DiEuliis, D., S.R. Carter, and G.K. Gronvall. 2017a. Options for synthetic DNA order screening, revisited. mSphere 2(4):e00319–17. DiEuliis, D., K. Berger, and G. Gronvall. 2017b. Biosecurity implications for the synthesis of horsepox, an orthopoxvirus. Health Security 15(6):629–637. Dittrich, P.S., and A. Manz. 2006. Lab-on-a-chip: Microfluidics in drug discovery. Nature Reviews Drug Discovery 5(3):210–218. DOJ (U.S. Department of Justice). 2010. Amerithrax Investigative Summary, February 19, 2010. Available at: https://www.justice.gov/archive/amerithrax/docs/amx-investigative- summary.pdf. Accessed November 6, 2017. Donia, M.S., and M.A. Fischbach. 2015. Small molecules from the human microbiota. Science 349(6246):1254766. Dormitzer, P.R,, P. Suphaphiphat, D.G. Gibson, D.E. Wentworth, T.B. Stockwell, M.A. Algire, N. Alperovich, M. Barro, D.M. Brown, S. Craig, B.M. Dattilo, E.A. Denisova, I. De Souza, M. Eickmann, V.G. Dugan, A. Ferrari, R.C. Gomilla, L. Han, C. Judge, S. Mane, M. Matrosovich, C. Merryman, G. Palladino, G.A. Palmer, T. Spencer, T. Strecker, H. Trusheim, J. Uhlendorff, Y. Wen, A.C. Yee, J. Zaveri, B. Zhou, S. Becker, A. Donabedian, P.W. Mason, J.I. Glass, R. Rappouli, and J.C. Venter. 2013. Synthetic generation of influenza vaccine viruses for rapid response to pandemics. Science and Translational Medicine 5(185):185ra68. Doudna, J.A., and E. Charpentier. 2014. The new frontier of genome engineering with CRISPR- Cas9. Science 346(6213):1258096. Duffy, J. 1951. Smallpox and the Indians in the American colonies. Bulletin of the History of Medicine 25(4):324–341. PREPUBLICATION COPY: UNCORRECTED PROOFS

166 Biodefense in the Age of Synthetic Biology Edelstein, M.L., M.R. Abedi, and J. Wixon. 2007. Gene therapy clinical trials worldwide to 2007--an update. The Journal of Gene Medicine 9(10):833–842. Elowitz, M.B., and S. Leibler. 2000. A synthetic oscillatory network of transcriptional regulators. Nature 403(6767):335–338. Endy, D. 2005. Foundations for engineering biology. Nature 438(7067):449–453. Endy, D. 2008. Synthetic biology: Can we make biology easy to engineer? Industrial Biotechnology 4(4):340–351. Endy, D., S. Galanie, and C.D. Smolke. 2015. Complete absence of thebaine biosynthesis under home-brew fermentation conditions bioRxiv doi:10.1101/024299. Eppinger, M., M.K. Mammel, J.E. Leclerc, J. Ravel, and T.A. Cebula. 2011. Genomic anatomy of Escherichia coli O157:H7 outbreaks. Proceedings of the National Academy of Sciences of the United States of America 108(50):20142–20147. Esvelt, K.M., A.L. Smidler, F. Catteruccia, and G.M. Church. 2014. Concerning RNA-guided gene drives for the alteration of wild populations. eLife 3:e03401. Fan, R.L., S.A. Valkenburg, C.K. Wong, O.T. Li, J.M. Nicholls, R. Rabadan, J.S. Peiris, and L.L. Poon. 2015. Generation of live attenuated influenza virus by using codon usage bias. Journal of Virology 89(21):10762–10773. FDA (U.S. Food and Drug Administration). 2017a. FDA Approval Brings First Gene Therapy to the United States. FDA News: August 30, 2017. Available at: https://www.fda.gov/NewsEvents/Newsroom/PressAnnouncements/ucm574058.htm. Accessed January 30, 2017. FDA. 2017b. FDA Approves CAR-T Cell Therapy to Treat Adults with Certain Types of Large B-cell Lymphoma. FDA News: October 18, 2017. Available at: https://www.fda.gov/NewsEvents/Newsroom/PressAnnouncements/ucm581216.htm. Accessed January 31, 2017. FDA. 2017c. What are Medical Countermeasures? Available at: https://www.fda.gov/EmergencyPreparedness/Counterterrorism/MedicalCountermeasures /AboutMCMi/ucm431268.htm. Accessed November 14, 2017. FERN (Food Emergency Response Network). 2017. Uniting Federal State and Local Laboratories for Food Emergency Response. Available at: https://www.fernlab.org. Accessed November 14, 2017. Filkins, B. 2014. Health Care Cyberthreat Report: Widespread Compromises Detected, Compliance Nightmare on Horizon. SANS Institute, February 2014. Available at: https://www.sans.org/reading-room/whitepapers/analyst/health-care-cyberthreat-report- widespread-compromises-detected-compliance-nightmare-horizon-34735. Accessed November 2, 2017. Finlay, B.B., and G. McFadden. 2006. Anti-immunology: Evasion of the host immune system by bacterial and viral pathogens. Cell 124(4):767–782. Firoved, A. 2016. The Federal Perspective on the State of Our Nation’s Biodefense. Testimony of Aaron Firoved, Acting Director, OHA National Bio-surveillance Integration Center, for a Senate Committee on Homeland Security and Governmental Affairs, April 14, 2016. Available at: https://www.dhs.gov/news/2016/04/14/written-testimony-oha-senate- committee-homeland-security-and-governmental-affairs. Accessed November 14, 2017. Fischer, N.O., A. Rasley, M. Corzett, M.H. Hwang, P.D. Hoeprich, and C.D. Blanchette. 2013. Colocalized delivery of adjuvant and antigen using nanolipoprotein particles enhances the PREPUBLICATION COPY: UNCORRECTED PROOFS

References 167 immune response to recombinant antigens. Journal of the American Chemical Society 135(6):2044–2047. Fischer, N.O., D.R. Weilhammer, A. Dunkle, C. Thomas, M. Hwang, M. Corzett, C. Lychak, W. Mayer, S. Urbin, N. Collette, J.C. Chang, G.G. Loots, A. Rasley, and C.D. Blanchette. 2014. Evaluation of nanolipoprotein particles (NLPs) as an in vivo delivery platform. PLoS ONE 9(3):e93342. Fouchier, R.A. 2015. Studies on influenza virus transmission between ferrets: the public health risks revisited. mBio 6(1):e02560–14. Frerichs, R.L., R.M. Salerno, K.M. Vogel, N.B. Barnett, J. Gaudioso, L.T. Hickok, D. Estes, and D.F. Jung. 2004. Historical Precedence and Technical Requirements of Biological Weapons Use: A Threat Assessment. SAND2004-1854. Albuquerque, NM: Sandia National Laboratories. Available at http://prod.sandia.gov/techlib/access- control.cgi/2004/041854.pdf. Accessed January 31, 2018. Friedman, D.J., R.G. Parrish, and D.A. Ross. 2013. Electronic health records and U.S. public health: Current realities and future promise. American Journal of Public Health 103(9):1560–1567. Friedmann, E.I. 1994. Viable microorganisms in permafrost. Pp. 21–26 in Permafrost as Microbial Habitat, D.A. Gilichinsky, ed. Pushchino: Russian Academy of Sciences. Fung, I,C.H., Z.C.H. Tse, and K.W. Fu. 2015. The use of social media in public health surveillance. Western Pacific Surveillance and Response Journal 6(2):3–6. Fung, I.C.H., C.H. Duke, K.C. Finch, K.R. Snook, P.L. Tseng, A.C. Hernandez, M. Gambhir, K.W. Fu, and Z.T.H. Tse. 2016. Ebola virus disease and social media: A systematic review. American Journal of Infection Control 44(12):1660–1671. Galanie, S., K. Thodey, I.J. Trenchard, M.F. Interrante, and C.D. Smolke. 2015. Complete biosynthesis of opioids in yeast. Science 349(6252):1095–1100. Gao, L., and Y.A. Kwaik. 2000. The modulation of host cell apoptosis by intracellular bacterial pathogens. Trends in Microbiology 8(7):306–313. Gardner, T.S., C.R. Cantor, and J.J. Collins. 2000. Construction of a genetic toggle switch in Escherichia coli. Nature 403(6767):339–342. Garfinkel, M.S., D. Endy, G.L. Epstein, and R.M. Friedman. 2007. Synthetic Genomics | Options for Governance. J. Craig Venter Institute. Available at: http://www.jcvi.org/cms/fileadmin/site/research/projects/synthetic-genomics- report/synthetic-genomics-report.pdf. Accessed March 5, 2018. Ghaisas, S., J. Maher, and A. Kanthasamy. 2016. Gut microbiome in health and disease: Linking the microbiome-gut-brain axis and environmental factors in the pathogenesis of systemic and neurodegenerative diseases. Pharmacology and Therapeutics 158:52–62. GHR (Genome Home Reference). 2018. What are single nucleotide polymorphisms (SNPs)? Available at https://ghr.nlm.nih.gov/primer/genomicresearch/snp. Accessed January 29, 2018. Gibson, D.G., G.A. Benders, C. Andrews-Pfannkoch, E.A. Denisova, H. Baden-Tillson, J. Zaveri, T.B. Stockwell, A. Brownley, D.W. Thomas, M.A. Algire, C. Merryman, L. Young, V.N. Noskov, J.I. Glass, J.C. Venter, C.A. Hutchison III, and H.O. Smith. 2008. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319(5867):1215–1220. PREPUBLICATION COPY: UNCORRECTED PROOFS

168 Biodefense in the Age of Synthetic Biology Gibson, D.G., L. Young, R. Chuang, J.C. Venter, C.A. Hutchison, III, and H.O. Smith. 2009. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nature Methods 6(5):343–345. Gibson, D.G., J.I. Glass, C. Lartigue, V.N. Noskov, R.Y. Chuang, M.A. Algire, G.A. Benders, M.G. Montague, L. Ma, M.M. Moodie, C. Merryman, S. Vashee, R. Krishnakumar, N. Assad-Garcia, C. Andrews-Pfannkoch, E.A. Denisova, L. Young, Z.Q. Qi, T.H. Segall- Shapiro, C.H. Calvey, P.P. Parmar, C.A. Hutchison III, H.O. Smith, and J.C. Venter. 2010. Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329(5987):52–56. Gronvall, G.K. 2017. Prevention of the development or use of biological weapons. Health Security 15(1):36–37. Guenther, C.M., B.E. Kuypers, M.T. Lam., T.M. Robinson, J. Zhao, and J. Suh. 2014. Synthetic virology: Engineering viruses for gene delivery. Wiley Interdisciplinary Review of Nanomedicine and Nanobiotechnology 6(6):548–558. Guichard, A., V. Nizet, and E. Bier. 2012. New insights into the biological effects of anthrax toxins: Linking cellular to organismal responses. Microbes and Infection 14(2):97–118. Guillemin, J. 2006. Biological Weapons: From the Invention of State-Sponsored Programs to Contemporary Bioterrorism. New York: Columbia University Press. Hacein-Bey-Abina, S., F. Le Deist, F. Carlier, C. Bouneaud, C. Hue, J.P. De Villartay, A.J. Thrasher, N. Wulffraat, R. Sorensen, S. Dupuis-Girod, A. Fischer, E.G. Davies, W. Kuis, L. Leiva, and M. Cavazzana-Calvo. 2002. Sustained correction of X-linked severe combined immunodeficiency by ex vivo gene therapy. The New England Journal of Medicine 346(16):1185–1193. Hadadi, N., J. Hafner, A. Shajkofci, A. Zisaki, and V. Hatzimanikatis. 2016. ATLAS of biochemistry: A repository of all possible biochemical reactions for synthetic biology and metabolic engineering studies. ACS Synthetic Biology 5(10):1155–1166. Haddad, D. 2017. Genetically engineered vaccinia viruses as agents for cancer treatment, imaging, and transgene delivery. Frontiers in Oncology 7:96. Hall, B. 2011. Evolution: Principles and Processes. Sudbury, Massachusetts: Jones and Bartlett Publishers. Hall, R.A., and J. Macdonald. 2016. Synthetic biology provides a toehold in the fight against Zika. Cell Host and Microbe 19(6):752–754. Hammond, A., R. Galizi, K. Kyrou, A. Simoni, C. Siniscalchi, D. Katsanos, M. Gribble, D. Baker, E. Marois, S. Russell, A. Burt, N. Windbichler, A. Crisanti, and T. Nolan. 2016. A CRISPR-Cas9 gene drive system targeting female reproduction in the malaria mosquito vector Anopheles gambiae. Nature Biotechnology 34(1):78–83. Harris, A., A.R. McKerney, D. Nimmo, Z. Curtis, I. Black, S.A. Morgan, M.N. Oviedo, R. Lacroix, N. Naish, N.I. Morrison, A. Collado, J. Stevenson, S. Scaife, T. Dafa'alla, G.Fu, C. Phillips, A. Miles, N. Raduan, N. Kelly, C. Beech, C.A. Donnelly, W.D. Petrie, and L. Alphey. 2012. Successful suppression of a field mosquito population by sustained release of engineered male mosquitoes. Nature Biotechnology 30(9):828– 830. He, X.J., T. Chen, and J.K. Zhu. 2011. Regulation and function of DNA methylation in plants and animals. Cell Research 21(3):442–465. Heider, D., and A. Barnekow. 2008. DNA watermarks: A Proof of concept. BMC Molecular Biology 9:40. PREPUBLICATION COPY: UNCORRECTED PROOFS

References 169 Heise, M.T., and H.W. Virgin. 2013. Pathogenesis of viral infection. Pp. 254–285 in Field’s Virology, 6th Ed., D.M. Knipe, and P.M. Howley, eds. Philadelphia, PA: Lippincott Williams and Wilkins. Hekele, S., S. Bertholet, J. Archer, D.G. Gibson, G. Palladino, L.A. Brito, G.R. Otten, M. Brazzoli, S. Buccato, A. Bonci, D. Casini, D. Maione, Z.Q. Qi, J.E. Gill, N.C. Caiazza, J. Urano, B. Hubby, G.F. Gao, Y. Shu, E. de Gregorio, C.W. Mandl, P.W. Mason, E.C. Settembre, J.B. Ulmer, J.C. Venter, P.R. Dormitzer, R. Rappuoli, and A.J. Geall. 2013. Rapidly produced SAM® vaccine against H7N9 influenza is immunogenic in mice. Emerging Microbes and Infections 2(8):e52. Herfst, S., E.J. Schrauwen, M. Linster, S. Chatinimitkul, E. de Wit, V.J. Munster, E.M. Sorrell, T.M. Bestebroer, D.F. Burke, D.J. Smith, G.F. Rimmelzwaan, A.D. Osterhaus, and R.A. Fouchier. 2012. Airborne transmission of influenza A/H5N1 virus between ferrets. Science 336(6088):1534–1541. Herfst, S., M. Böhringer, B. Karo, P. Lawrence, N.S. Lewis, M.J. Mina, C.J. Russell, J. Steel, R.L. de Swart, and C. Menge. 2017. Drivers of airborne human-to-human pathogen transmission. Current Opinion in Virology 22:22–29. HHS (U.S. Department of Health and Human Services). 2010. Screening Framework Guidance for Providers of Synthetic Double-Stranded DNA. Available at: https://www.phe.gov/Preparedness/legal/guidance/syndna/Documents/syndna- guidance.pdf. Accessed on November 14, 2017. HHS. 2013. Framework for Guiding Funding Decisions about Research Proposals with the Potential for Generating Highly Pathogenic Avian Influenza H5N1 Viruses That Are Transmissible Among Mammals by Respiratory Droplets. February 2013. Available at: https://www.phe.gov/s3/dualuse/Documents/funding-hpai-h5n1.pdf. Accessed May 11, 2017. HHS. 2017a. Framework for Guiding Funding Decisions about Proposed Research Involving Enhanced Potential Pandemic Pathogens. Available at: https://www.phe.gov/s3/dualuse/Documents/p3co.pdf. Accessed January 25, 2018. HHS. 2017b. PHEMCE Strategy and Implementation Plan: 2017–2018. Available at: https://www.phe.gov/Preparedness/mcm/phemce/Pages/strategy.aspx. Accessed January 31, 2018. Holloway, D. T. 2013. Regulating Amateurs. The Scientist, March 2013. Available at: http://www.the-scientist.com/?articles.view/articleNo/34444/title/Regulating-Amateurs Accessed January 25, 2018. Holmes, E.C. 2003. Error thresholds and the constraints to RNA virus evolution. Trends in Microbiology 11(12):543–546. Huang, P., S.E. Boyken, and D. Baker. 2016. The coming of age of de novo protein design. Nature 537:320–327. Huang, Q., K. Gumireddy, M. Schrier, C. le Sage, R. Nagel, S. Nair, D.A. Egan, A. Li, G. Huang, A.J. Klein-Szanto, P.A. Gimotty, D. Katsaros, G. Coukos, L. Zhang, E. Puré, and R. Agami. 2008. The microRNAs miR-373 and miR-520c promote tumour invasion and metastasis. Nature Cell Biology 10(2):202–210. Hughes, J., B. Shelton, and T. Hughes. 2010. Suspected dietary supplement injuries in special operations soldiers. Journal of Special Operations Medicine 10(3):14–24. IAP (Inter Academy Partnership). 2015. The Biological and Toxin Weapons Convention: Implications of Advances in Science and Technology. Available at: PREPUBLICATION COPY: UNCORRECTED PROOFS

170 Biodefense in the Age of Synthetic Biology https://royalsociety.org/~/media/policy/projects/biological-toxin-weapons- convention/biological-weapons-technical-document.pdf. Accessed January 31, 2018. IARPA (Intelligence Advanced Research Projects Agency). 2017a. Functional Genomic and Computational Assessment of Threats (FunGCAT), Available at: https://www.iarpa.gov/index.php/research-programs/fun-gcat. Accessed November 14, 2017. IARPA. 2017b. Finding Engineering-Linked Indicators (FELIX). Available at: https://www.iarpa.gov/index.php/research-programs/felix. Accessed November 14, 2017. iGEM (International Genetically Engineered Machine). 2017. Synthetic Biology Based on Standard Parts. Available at: http://igem.org/Main_Page. Accessed on November 14, 2017. IGSC (International Gene Synthesis Consortium). 2017. Harmonized Screening Protocol© v2.0 Gene Sequence & Customer Screening to Promote Biosecurity, 19 November 2017. Available at https://genesynthesisconsortium.org/wp- content/uploads/IGSCHarmonizedProtocol11-21-17.pdf. Accessed January 25, 2018. Imai, M., T. Watanabe, M. Hatta, S.C. Das, M. Ozawa, K. Shinya, G. Zhong, A. Hanson, H. Katsura, S. Watanabe, C. Li, E. Kawakami, S. Yamada, M. Kiso, Y. Suzuki, E.A. Maher, G. Neumann, and Y. Kawaoka. 2012. Experimental adaptation of an influenza H5 HA confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets. Nature 486(7403):420–428. Independent. 2017. North Korea Says It 'Will Take Revenge' for US Saying It Is Developing Biological Weapons. News: December 20, 2017. Available at: http://www.independent.co.uk/news/world/americas/us-politics/north-korea-biological- weapons-us-revenge-trump-kim-jong-un-pyongyang-a8120376.html. Accessed January 31, 2018. IOM (Institute of Medicine). 2013. Gulf War and Health: Treatment for Chronic Multisymptom Illness. Washington, DC: The National Academies Press. IOM/NRC (Institute of Medicine and National Research Council). 2006. Globalization, Biosecurity, and the Future of the Life Sciences. Washington, DC: The National Academies Press. IPCS (International Programme on Chemical Safety). 1996. Principles and Methods for Assessing Direct Immunotoxicity Associated with Exposure to Chemicals. Environmental Health Criteria 180. Geneva: World Health Organization. Available at http://www.inchem.org/documents/ehc/ehc/ehc180.htm. Accessed November 3, 2017. ISID (International Society for Infection Diseases). 2017. ProMED –mail. Available at: http://www.isid.org/promedmail/promedmail.shtml. Accessed January 25, 2018. Iwasaki, A., and R. Medzhitov. 2013. Innate responses to viral infection. Pp. 189–213 in Field’s Virology, 6th Ed., D.M. Knipe, and P.M. Howley, eds. Philadelphia, PA: Lippincott Williams and Wilkins. Jackson, R.J., A.J. Ramsay, C.D. Christensen, S. Beaton, D.F. Hall, and I.A. Ramshaw. 2001. Expression of mouse interleukin-4 by a recombinant ectromelia virus suppresses cytotoxic lymphocyte responses and overcomes genetic resistance to mousepox. Journal of Virology 75(3):1205–1210. Jaing, C., S. Gardner, K. McLoughlin, J.B. Thissen, and T. Slezak. 2011. Detection of adventitious viruses from biologicals using a broad-spectrum microbial detection array. PDA Journal of Pharmaceutical Science and Technology 65(6):668–674. PREPUBLICATION COPY: UNCORRECTED PROOFS

References 171 Jalani, G., R. Naccache, D.H. Rosenzweig, L. Haglund, F. Vetrone, and M. Cerruti. 2016. Photocleavable hydrogel-coated upconverting nanoparticles: A multifunctional theranostic platform for NIR imaging and on-demand macromolecular delivery. Journal of the American Chemical Society 138(3):1078–1083. JCVI (J. Craig Venter Institute). 2010. First Self-Replicating Synthetic Bacterial Cell. J. Craig Venter Institute News, May 20, 2010. Available at: http://www.jcvi.org/cms/press/press-releases/full-text/article/first-self-replicating- synthetic-bacterial-cell-constructed-by-j-craig-venter-institute-researcher/. Accessed January 18, 2018. Jefferson, C., F. Lentzos, and C. Marris. 2014. Synthetic biology and biosecurity: Challenging the “myths.” Frontiers in Public Health 2:115. Jinek, M., K. Chylinski, I. Fonfara, M. Hauer, J.A. Doudna, and E. Charpentier. 2012. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337(6096):816–821. Jinek, M., A. East, A. Cheng, S. Lin, E. Ma, and J. Doudna. 2013. RNA-programmed genome editing in human cells. eLife 2:e00471. Jochem, G. 2017. Pet Store Puppies Linked to Campylobacter Outbreak in People. NPR News: September 12, 2017. Available at http://www.npr.org/sections/health- shots/2017/09/12/550423656/pet-store-puppies-linked-to-campylobacter-outbreak-in- people. Accessed November 3, 2017. Jones, P.A., and S.B. Baylin. 2007. The epigenomics of cancer. Cell 128(4):683–692. June, C.H., J.T. Warshauer, and J.A. Bluestone. 2017. Is autoimmunity the Achilles' heel of cancer immunotherapy? Nature Medicine 23:540–547. Kadlec, R.P., and A.P. Zelicoff. 2000. Implications of the biotechnology revolution for weapons development and arms control. Pp. 11–26 in Biological Warfare: Modern Offense and Defense, R. Zilinskas, ed. Boulder, CO: Lynne Rienner. Kampranis, S.C., and A.M. Makris. 2012. Developing a yeast cell factory for the production of terpenoids. Computational and Structural Biotechnology Journal 3:e201210006. Kan, S.B., X. Huang, Y. Gumulya, K. Chen, and F.H. Arnold. 2017. Genetically programmed chiral organoborane synthesis. Nature 552(7683):132–136. Kaper, G.B., J.P. Nataro, and H.L. Mobley. 2004. Pathogenic Escherichia coli. Nature Reviews Microbiology 2(2):123–140. Kaplan, G., J. Lubinski, A. Dasgupta, and V. R. Racaniello. 1985. In vitro synthesis of infectious poliovirus RNA. Proceedings of the National Academy of Sciences 82(24):8424–8428. Kau, A.L., P.P. Ahern, N.W. Griffin, A.L. Goodman, and J.I. Gordon. 2011. Human nutrition, the gut microbiome and the immune system. Nature 474(7351):327–336. Kay, M.A., J.C. Glorioso, and L. Naldini. 2001. Viral vectors for gene therapy: The art of turning infectious agents into vehicles of therapeutics. Nature Medicine 7(1):33–40. Kellogg, S. 2012. The Rise of DIY Scientists: Is it Time for Regulation? Washington Lawyer, May 2012. Available at: https://www.dcbar.org/bar-resources/publications/washington- lawyer/articles/may-2012-diy-scientist.cfm. Accessed January 25, 2018. Keeney, R. 1992. Value-focused Thinking: A Path to Creative Decisionmaking. Cambridge, MA: Harvard University Press. Keeney, R., and H. Raiffa. 1993. Decisions with Multiple Objectives: Preferences and Tradeoffs. Cambridge, UK: Cambridge University Press. PREPUBLICATION COPY: UNCORRECTED PROOFS

172 Biodefense in the Age of Synthetic Biology Khalil, R.K., C. Skinner, S. Patfield, and X. He. 2016. Phage-mediated Shiga toxin (Stx) horizontal gene transfer and expression in non-Shiga toxigenic Enterobacter and Escherichia coli strains. Pathogens and Disease 74(5):ftw037. Kim, J.Y., J.Y. Shin, M.R. Kim, S.K. Hann, and S.H. Oh. 2012. siRNA-mediated knock-down of COX-2 in melanocytes suppresses melanogenesis. Experimental Dermatology 21(6):420– 425. Kim, R.S., N. Goossens, and Y. Hoshida. 2016. Use of big data in drug development for precision medicine. Expert Review of Precision Medicine and Drug Development 1(3): 245–253. Klompas, M., J. McVetta, R. Lazarus, E. Eggleston, G. Haney, B.A. Kruskal, W.K. Yih, P. Daly, P. Oppedisano, B. Beagan, M. Lee, C. Kirby, D. Heisey-Grove, A. DeMaria, Jr., and R. Platt. 2012. Integrating clinical practice and public health surveillance using electronic medical record systems. American Journal of Public Health 102(Suppl. 3):S325–S332. Knight, T. 2003. Idempotent Vector Design for Standard Assembly of Biobricks. MIT Synthetic Biology Working Group Technical Reports. Available at: https://dspace.mit.edu/bitstream/handle/1721.1/21168/biobricks.pdf. Accessed on July 14, 2017. Koblentz, G.D. 2017. The de novo synthesis of horsepox virus: Implications for biosecurity and recommendations for preventing the reemergence of smallpox. Health Security 15(6):620–628. Kolodziejczyk, B. 2017. Do-it-yourself biology shows safety risks of an open innovation movement. Brookings, October 2017. Available at https://www.brookings.edu/blog/techtank/2017/10/09/do-it-yourself-biology-shows- safety-risks-of-an-open-innovation-movement/ Accessed November 14, 2017. Koroleva, M.Y., T.Y. Nagovitsina, D.A. Bidanov, O.S. Gorbachevski, and E.V. Yurtov. 2016. Nano- and microcapsules as drug-delivery systems. Resource-Efficient Technologies 2(4):233–239. Kosal, M.E. 2009. Nanotechnology for Chemical and Biological Defense. Springer. Kosal, M.E. 2014. A new role for public health in bioterrorism deterrence. Frontiers in Public Health 2:278. Kotula, J.W., S.J. Kerns, L.A. Shaket, L. Siraj, J.J. Collins, J.C. Way, and P.A. Silver. 2014. Programmable bacteria detect and record an environmental signal in the mammalian gut. Proceedings of the National Academy of the United States of America 111(13):4838– 4843. Kouranova, E., K. Forbes, G. Zhao, J. Warren, A. Bartels, Y. Wu, and X. Cui. 2016. CRISPRs for optimal yargeting: Delivery of CRISPR components as DNA, RNA, and protein into cultured cells and single-cell embryos. Human Gene Therapy 27(6):464–475. Kranz, L.M., M. Diken, H. Haas, S. Kreiter, C. Loquai, K.C. Reuter, M. Meng, D. Fritz, F. Vascotto, H. Hefesha, C. Grunwitz, M. Vormehr, Y. Husemann, A. Selmi, A. N. Kuhn, J. Buck, E. Derhovanessian, R. Rae, S. Attig, J. Diekmann, R.A. Jabulowsky, S. Heesch, J. Hassell, P. Langguth, S. Grabbe, C. Huber, O. Tureci, and U. Sahin. 2016. Systemic RNA delivery to dendritic cells exploits antiviral defence for cancer immunotherapy. Nature 534(7607):396–401. Krebs on Security. 2013. Wash. Hospital Hit by $1.03 Million Cyberheist. April 2013. Available at https://krebsonsecurity.com/2013/04/wash-hospital-hit-by-1-03-million-cyberheist/. Accessed November 2, 2017. PREPUBLICATION COPY: UNCORRECTED PROOFS

References 173 Kreuzer-Martin, H.W., and K.H. Jarman. 2007. Stable isotope ratios and forensic analysis of microorganisms. Applied and Environmental Microbiology 73(12):3896–3908. Krishnamurthy, M., R.T. Moore, S. Rajamani, and R.G. Panchal. 2016. Bacterial genome engineering and synthetic biology: Combating pathogens. BMC Microbiology 16:258. Kupferschmidt, K. 2017. How Canadian researchers reconstituted an extinct poxvirus for $100,000 using mail-order DNA. Science, News: July 6, 2017. Available at: http://www.sciencemag.org/news/2017/07/how-canadian-researchers-reconstituted- extinct-poxvirus-100000-using-mail-order-dna. Accessed November 6, 2017. Kuss, S.K., G.T. Best, C.A. Etheredge, A.J. Pruijssers, J.M. Frierson, L.V. Hooper, T.S. Dermody, and J.K. Pfeiffer. 2011. Intestinal microbiota promote enteric virus replication and systemic pathogenesis. Science 334(6053):249–252. Lauring, A.S., A. Acevado, S.B. Cooper, and R. Andino. 2012. Codon usage determines the mutational robustness, evolutionary capacity and virulence of an RNA virus. Cell Host and Microbe 12(5):623–632. Lehner, B.A.E., D.T. Schmieden, and A.S. Meyer. 2017. A straightforward approach for 3D bacterial printing. ACS Synthetic Biology 6(7):1124–1130. Lempinen, E.W. 2011. FBI, AAAS Collaborate on Ambitious Outreach to Biotech Researchers and DIY Biologists. American Association for the Advancement of Science News: April 1, 2011.Available at: https://www.aaas.org/news/fbi-aaas-collaborate-ambitious- outreach-biotech-researchers-and-diy-biologists. Accessed November 14, 2017. Li, W., Z. Shi, M. Yu, W. Ren, C. Smith, J.H. Epstein, H. Wang, C. Crameri, Z. Hu, H. Zhang, J. Zhang, J. McEachern, H. Field, P. Daszak, B.T. Eaton, S. Zhang, and L.F. Wang. 2005. Bats are natural reservoirs of SARS-like coronaviruses. Science 310(5748):676–679. Lim, W.A., and C.H. June. 2017. The principles of engineering immune cells to treat cancer. Cell 168:724–740. Lindler, L.E., E. Choffnes, and G.W. Korch. 2005. Definition and overview of emerging threats. Pp. 351–359 in Biological Weapons Defense: Infectious Disease and Counterbioterrorism, Part III. Emerging Threats and Future Preparation, L.E. Lindler, F.J. Lebeda, and G. Korch, eds. Totowa, NJ: Humana Press. Linster, M., S. van Boheemen, M. de Graaf, E.J.A. Schrauwen, P. Lexmond, B. Mänz, T.M. Bestebroer, J. Baumann, D. van Riel, G.F. Rimmelzwaan, A.D.M.E. Osterhaus, M. Matrosovich, R.A.M. Fouchier, and S. Herfst. 2014. Identification, characterization, and natural selection of mutations driving airborne transmission of A/H5N1 virus. Cell 157(2):329–339. Lipsitch, M. 2014. Can limited scientific value of potential pandemic pathogen experiments justify the risks? mBio 5(5):e02008-14. Liu, J., T. Gaj, Y. Yang, N. Wang, S. Shui, S. Kim, C. N. Kanchiswamy, J. Kim, and C. F. Barbas III. 2015. Efficient delivery of nuclease proteins for genome editing in human stem cells and primary cells. Nature Protocols 10:1842–1859. Lotz, M.T., and R.S. Peebles, Jr. 2012. Mechanisms of respiratory syncytial virus modulation of airway immune responses. Current Allergy and Asthma Reports 12(5):380–387. Low, N., A. Bavdekar, L. Jeyaseelan, S. Hirve, K. Ramanathan, N.J. Andrews, N. Shaikh, R.S. Jadi, A. Rajagopal, K.E. Brown, D. Brown, J.B. Fink, O. John, P. Scott, X. Riveros- Balta, M. Greco, R. Dhere, P.S. Kulkarni, and A.M.H. Restrepo. 2015. A randomized, controlled trial of an aerosolized vaccine against measles. The New England Journal of Medicine 372(16):1519–1529. PREPUBLICATION COPY: UNCORRECTED PROOFS

174 Biodefense in the Age of Synthetic Biology Lu, T.K., A.S. Khalil, and J.J. Collins. 2009. Next-generation synthetic gene networks. Nature Biotechnology 27(12):1139–1150. Lu, T.K., J. Bowers, and M.S. Koeris. 2013. Advancing bacteriophage-based microbial diagnostics with synthetic biology. Trends in Biotechnology 31(6):325–327. Luo, M. L., A. S. Mullis, R. T. Leenay, and C. L. Beisel. 2015. Repurposing endogenous type I CRISPR-Cas systems for programmable gene repression. Nucleic Acids Research 43(1): 674–681. Macho, A.P., and C. Zipfel. 2015. Targeting of plant pattern recognition receptor-triggered immunity by bacteria type-III secretion system effectors. Current Opinions in Microbiology 23:14–22. Madoff, L.C. 2004. ProMED-mail: An early warning system for emerging diseases. Clinical Infectious Diseases 39(2):227–232. Mali, P., L.H. Yang, K.M. Esvelt, J. Aach, M. Guell, J.E. DiCarlo, J.E. Norville, and G.M. Church. 2013. RNA-guided human genome engineering via Cas9. Science 339(6121):823–826. Martinez, M.A., A. Jordan-Paiz, S. Franco, and M. Nevot. 2016. Synonymous virus genome recoding as a tool to impact viral fitness. Trends in Microbiology 24(2):134–147. Matheson, R. 2016. Reprogramming gut bacteria as “living therapeutics” MIT News, April 6, 2016. Available at: http://news.mit.edu/2016/startup-synlogic-reprogramming-gut- bacteria-living-therapeutics-0405. Accessed November 9, 2017. Mendoza, B.J., and C.T. Trinh. 2018. Enhanced guide–RNA design and targeting analysis for precise CRISPR genome editing of single and consortia of industrially relevant and non- model organisms. Bioinformatics 34(1):16–23. Meng, J., S. Lee, A.L. Hotard, and M.L. Moore. 2014. Refining the balance of attenuation and immunogenicity of respiratory syncytial virus by targeted codon deoptimization of virulence genes. mBio 5(5):e01704–14. Mercy, G., J. Mozziconacci, V.F. Scolari, K. Yang, G. Zhao, A. Thierry, Y. Luo, L.A. Mitchell, M. Shen, Y. Shen, R. Walker, W. Zhang, Y. Wu, Z.X. Xie, Z. Luo, Y. Cai, J. Dai, H. Yang, Y.J. Yuan, J.D. Boeke, J.S. Bader, H. Muller, and R. Koszul. 2017. 3D organization of synthetic and scrambled chromosomes. Science 355(6329):eaaf4597. Miele, E., G.P. Spinelli, E. Miele, E. Di Fabrizio, E. Ferretti, S. Tomao, and A. Gulino. 2012. Nanoparticle-based delivery of small interfering RNA: Challenges for cancer therapy. International Journal of Nanomedicine 7:3637–3657. Milinovich, G.J., G.M. Williams, A.C. Clements, and W. Hu. 2014. Internet-based surveillance systems for monitoring emerging infectious diseases. Lancet Infectious Diseases 14(2):160–168. Miller, S. D., W. J. Karpus, and T. S. Davidson. 2007. Experimental autoimmune encephalomyelitis in the mouse. Current Protocols in Immunology 15–1. Mimee, M., A.C. Tucker, C.A. Voigt, and T.K. Lu. 2015. Programming a human commensal bacterium, Bacteroides thetaiotaomicron, to sense and respond to stimuli in the murine gut microbiota. Cell Systems 1(1):62–71. Mingozzi, F., and K.A. High. 2013. Immune responses to AAV vectors: Overcoming barriers to successful gene therapy. Blood 122(1):23–36. MIT Media Lab. 2017. Global Community bio Summit, September 22–24, 2017. Community Biotechnology Initiative, Massachusetts Institute of Technology. Available at: https://www.biosummit.org. Accessed November 14, 2017. PREPUBLICATION COPY: UNCORRECTED PROOFS

References 175 Mitchell, L.A., A. Wang, G. Stracquadanio, Z. Kuang, X. Wang, K. Yang, S. Richardson, J.A. Martin, Y. Zhao, R. Walker, Y. Luo, H. Dai, K. Dong, Z. Tang, Y. Yang, Y. Cai, A. Heguy, B. Ueberheide, D. Fenyö, J. Dai, J.S. Bader, and J.D. Boeke. 2017. Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond. Science 355(6329):eaaf4831. Moon, T.S., C. Lou, A. Tamsir, B.C. Stanton, and C.A. Voigt. 2012. Genetic programs constructed from layered logic gates in single cells. Nature 491(7423):249–253. Morgan, M.G., and M. Henrion. 1990. Uncertainty: A Guide to Dealing with Uncertainty in Quantitative Risk and Policy Analysis. Cambridge, UK: Cambridge University Press. Morgan, K.M., M.L. DeKay, P.S. Fischbeck, M.G. Morgan, B. Fischhoff, and H.K. Florig. 2001. A deliberative method for ranking risks (II): Evaluation of validity and agreement among risk managers. Risk Analysis 21(5):923–937. Moss, J.A. 2014. Gene therapy review. Radiologic Technology 86(2):155–180. Mou, H., Z. Kennedy, D.G. Anderson, H. Yin, and W. Xue. 2015. Precision cancer mouse models through genome editing with CRISPR-Cas9. Genome Medicine 7:53. Műllbacher, A., and M. Lobigs. 2001. Creation of killer poxvirus could have been predicted. Journal of Virology 75(18):8353–8355. Muehlbauer, S.M., T.H. Evering, G. Bonuccelli, R.C. Squires, A.W. Ashton, S.A. Porcelli, M.P. Lisanti, and J. Brojatsch. 2007. Anthrax lethal toxin kills macrophages in a strain-specific manner by apoptosis or caspase-1-mediated necrosis. Cell Cycle 6:758–766. Mueller, S., J.R. Coleman, D. Papamichail, C.B. Ward, A. Nimnual, B. Futcher, S. Skiena, and E. Wimmer. 2010. Live attenuated influenza virus vaccines by computer-aided rational design. Nature Biotechnology 28(7):723–726. Nafissi, N., and R. Slavcev. 2012. Construction and characterization of an in-vivo linear covalently closed DNA vector production system. Microbial Cell Factories 11:154. Naldini, L., U. Blömer, P. Gallay, D. Ory, R. Mulligan, F.H. Gage, I.M. Verma, and D. Trono. 1996. In vivo gene delivery and stable transduction of nondividing cells by a lentiviral vector. Science 272(5259):263–267. National Academies of Sciences, Engineering and Medicine. 2016. Gene Drives on the Horizon: Advancing Science, Navigating Uncertainty, and Aligning Research with Public Values. Washington, DC: The National Academies Press. National Academies of Sciences, Engineering and Medicine. 2017. A Proposed Framework for Identifying Potential Biodefense Vulnerabilities Posed by Synthetic Biology: Interim Report. Washington, DC: The National Academies Press. National Academies of Sciences, Engineering and Medicine. 2017a. Dual Use Research of Concern in the Life Sciences: Current Issues and Controversies. Washington, DC: The National Academies Press. National Academies of Sciences, Engineering and Medicine. 2017b. Fostering Integrity in Research. Washington, DC: The National Academies Press. National Academies of Sciences, Engineering and Medicine. 2017c. Microbiomes of the Built Environment: From Research to Application. Washington, DC: The National Academies Press. Nature Biotechnology. 2009. What’s in a name? Nature Biotechnology 27(12):1071–1073. NCBI (National Center for Biotechnology Information). 2017. GenBank. Available at: https://www.ncbi.nlm.nih.gov/genbank. Accessed November 25, 2017. PREPUBLICATION COPY: UNCORRECTED PROOFS

176 Biodefense in the Age of Synthetic Biology Neumann, G., T. Watanabe, H. Ito, S. Watanabe, H. Goto, P. Gao, M. Hughes, D. R. Perez, R. Donis, E. Hoffmann, G. Hobom, and Y. Kawaoka. 1999. Generation of influenza A viruses entirely from cloned cDNAs. Proceedings of the National Academy of Sciences 96(16):9345–9350. Nicklin, S.A., and A.H. Baker. 2002. Tropism-modified adenoviral and adeno-associated viral vectors for gene therapy. Current Gene Therapy 2(3):273–293. Nielsen, A.A., B.S. Der, J. Shin, P. Vaidyanathan, V. Paralanov, E.A. Strychalski, D. Ross, D. Densmore, and C.A. Voigt. 2016. Genetic circuit design automation. Science 352(6281): aac7341. Niu, Y.Y., B. Shen, Y.Q. Cui, Y.C. Chen, J.Y. Wang, L. Wang, Y. Kang, X.Y. Zhao, W. Si, W. Li, A.P. Xiang, J.K. Zhou, X.J. Guo, Y. Bi, C.Y. Si, B. Hu, G.Y. Dong, H. Wang, Z.M. Zhou, T.Q. Li, T. Tan, X.Q. Pu, F. Wang, S.H. Ji, Q. Zhou, X.X. Huang, W.Z. Ji, and J.H. Sha. 2014. Generation of gene-modified cynomolgus monkey via Cas9/RNA- mediated gene targeting in one-cell embryos. Cell 156(4):836–843. NNDSS. 2017. National Notifiable Diseases Surveillance System. Available at: https://wwwn.cdc.gov/nndss. Accessed May 11, 2017. Nougairede, A., L. De Fabritus, F. Aubry, E.A. Gould, E.C. Holmes, and X. de Lamballerie. 2013. Random codon re-encoding induces stable reduction of replicative fitness of Chikungunya virus in primate and mosquito cells. PLoS Pathogens 9(2):e1003172. Noyce, R.S., S. Lederman, and D.H. Evans. 2018. Construction of an infectious horsepox virus vaccine from chemically synthesized DNA fragments. PLoS ONE 13(1):e0188453. NRC (National Research Council). 1992. The capacity of toxic agents to compromise the immune system (Biologic markers of immunosuppression). Pp. 63–82 in Biological Markers in Immunotoxicology. Washington, DC: National Academy Press. NRC. 2004. Biotechnology Research in an Age of Terrorism. Washington, DC: The National Academies Press. NRC. 2014. Convergence: Facilitating Transdisciplinary Integration of Life Sciences, Physical Sciences, Engineering, and Beyond. Washington, DC: The National Academies Press. NRC. 2015. Industrialization of Biology: A Roadmap to Accelerate the Advanced Manufacturing of Chemicals. Washington, DC: The National Academies Press. O’Bryan, S., S. Dong, J.M. Mathis, and S.K. Alahari. 2017. The roles of oncogenic miRNAs and their therapeutic importance in breast cancer. European Journal of Cancer 72:1–11. Ostrov, N., M. Landon, M. Guell, G. Kuznetsov, J. Teramoto, N. Cervantes, M. Zhou, K. Singh, M.G. Napolitano, M. Moosburner, E. Shrock, B.W. Pruitt, N. Conway, D.B. Goodman, C.L. Gardner, G. Tyree, A. Gonzales, B.L. Wanner, J.L. Norville, M.J. Lajoie, and G.M. Church. 2016. Design, synthesis, and testing toward a 57-codon genome. Science 353(6301):819–822. Palmer, M.J., F. Fukuyama, and D.A. Relman. 2015. A more systematic approach to biological risk. Science 350(6267):1471–1473. Palsson Lab. 2017. COBRA Tools. University of California. Available at: http://systemsbiology.ucsd.edu/COBRATools. Accessed November 8, 2017. Palumbo, R.N., and C. Wang. 2006. Bacterial invasin: Structure, function, and implication for targeted oral gene delivery. Current Drug Delivery 3(1):47–53. Pan, X., Y. Yang, and J. Zhang. 2014. Molecular basis of host specificity in human pathogenic bacteria. Emerging Microbes & Infections 3(3):e23. PREPUBLICATION COPY: UNCORRECTED PROOFS

References 177 Pardee, K., A.A. Green, T. Ferrante, D.E. Cameron, A.D. Keyser, P. Yin, and J.J. Collins. 2014. Paper-based synthetic gene networks. Cell 159(4):940–954. Pardi, N., M.J. Hogan, R.S. Pelc, H. Muramatsu, H. Andersen, C.R. DeMaso, K.A. Dowd, L.L. Sutherland, R.M Scearce, R. Parks, W. Wagner, A. Granados, J. Greenhouse, M. Walker, E. Willis, J. Yu, C.E. McGee, G.D. Sempowski, B.L. Mui, Y.K. Tam, Y. Huang, D. Vanlandingham, V.M. Holmes, H. Balachandran, S. Sahu, M. Lifton, S. Higgs, S.E. Hensley, T.D. Madden, M.J. Hope, K. Kariko, S. Santra, B.S. Graham, M.G. Lewis, T.C. Pierson, B.F. Haynes. and D. Weissman. 2017. Zika virus protection by a single low-dose nucleoside-modified mRNA vaccination. Nature 543(7644):248–251. parts.igem.org. 2017. Registry of Standard Biological Parts. Available at: http://parts.igem.org/Main_Page. Accessed on May 19, 2017. PCAST (President’s Council of Advisors on Science and Technology). 2016. Action Needed to Protect Against Biological Attack. November 2016. Available at: https://obamawhitehouse.archives.gov/sites/default/files/microsites/ostp/PCAST/pcast_bi odefense_letter_report_final.pdf. Accessed on May 11, 2017. Peng, Y., S. Allen, R.J. Millwood, and C.N. Stewart Jr. 2014. “Fukusensor”: A genetically engineered plant for reporting DNA damage in response to gamma radiation. Plant Biotechnology Journal 12(9):1329–1332. Perakslis, E.D. 2014. Cybersecurity in health care. The New England Journal of Medicine 371(5):395–397. Petsch, B., M. Schnee, A.B. Vogel, E. Lange, B. Hoffman, D. Voss, T. Schlake, A, Thess, K.J. Kallen, L. Stitz, and T. Kramps. 2012. Protective efficacy of in vitro synthesized, specific mRNA vaccines against influenza A virus infection. Nature Biotechnology 30(12):1210– 1218. Pettitt, J., L. Zeitlin, D.H. Kim, C. Working, J.C. Johnson, O. Bohorov, B. Bratcher, E. Hiatt, S.D. Hume, A.K. Johnson, J. Morton, M.H. Pauly, K.J. Whaley, M.F. Ingram, A. Zovanyi, M. Heinrich, A. Piper, J. Zelko, and G.G. Olinger. 2013. Therapeutic intervention of Ebola virus infection in rhesus macaques with the MB-003 monoclonal antibody cocktail. Science Translational Medicine 5(199):199ra113. Petzold, C.J., L.J.G. Chan, M. Nhan, and P.D. Adams. 2015. Analytics for metabolic engineering. Frontiers in Bioengineering and Biotechnology 3:135. Plesa, C., A.M. Sidore, N.B. Lubock, D. Zhang, and S. Kosuri. 2018. Multiplexed gene synthesis in emulsions for exploring protein functional landscapes. Science 359(6373):343–347. Plowright, R.K., C.R. Parish, H. McCallum, P.J. Hudson, A.I. Ko, A.L. Graham, and J.O. Lloyd- Smith. 2017. Pathways to zoonotic spillover. Nature Reviews Microbiology 15(8):502– 510. Polozov, I.V., L. Bezrukov, K. Gawrisch, and J. Zimmerberg. 2008. Progressive ordering with decreasing temperature of the phospholipids of influenza virus. Nature Chemistry and Biology 4(4):248–255. Ponemon Institute. 2013. Cost of Data Breach Study: Global Analysis. May 2013. Available at: https://www.ponemon.org/blog/2013-cost-of-data-breach-global-analysis. Accessed November 2, 2017. Poptsova, M.S., and J.P. Gogarten. 2010. Using comparative genome analysis to identify problems in annotated microbial genomes. Microbiology 156(Pt. 7):1909–1917. PR Newswire. 2018. International Gene Synthesis Consortium Updates Screening Protocols for Synthetic DNA Products and Services. News: January 3, 2018. Available at: PREPUBLICATION COPY: UNCORRECTED PROOFS

178 Biodefense in the Age of Synthetic Biology https://www.prnewswire.com/news-releases/international-gene-synthesis-consortium- updates-screening-protocols-for-synthetic-dna-products-and-services-300576867.html. Accessed January 31, 2018. Ptashne, M. 1986. A Genetic Switch: Gene Control and Phage Lambda. Oxford: Cell Press & Blackwell Scientific. Qin, Z., B.G. Compton, J.A. Lewis, and M.J. Buehler. 2015. Structural optimization of 3D- printed synthetic spider webs for high strength. Nature Communications 6:Art.7038. Quenee, L.E., T.M. Hermanas, N. Ciletti, H. Louvel, N.C. Miller, D. Elli, B. Blaylock, A. Mitchell, J. Schroeder, T. Krausz, J. Kanabrocki, and O. Schneewind. 2012. Heriditary hemochromatosis restores the virulence of plague vaccine strains. Journal of Infectious Diseases 206(7):1050–1058. Quick, J., N.J. Loman, S. Duraffour, J.T. Simpson, E. Severi, L. Cowley, J.A. Bore, R. Koundouno, G. Dudas, A. Mikhail, N. Ouédraogo, B. Afrough, A. Bah, J.H. Baum, B. Becker-Ziaja, J.P. Boettcher, M. Cabeza-Cabrerizo, A. Camino-Sánchez, L.L. Carter, J. Doerrbecker, T. Enkirch, I. Carcia-Dorival, N. Hetzelt, J. Hinzmann, T. Holm, L.E. Kafetzopoulou, M. Koropogui, A. Kosgey, E. Kuisma, C.H. Logue, A. Mazzarelli, S. Meisel, M. Mertens, J. Michel, D. Ngabo, K. Nitzsche, E. Pallash, L.V. Patrono, J. Portmann, J.G. Repits, N.Y. Rickett, A. Sachse, K. Singethan, I. Vitoriano, R.L. Yemanaberhan, E.G. Zekeng, R. Trina, A. Bello, A.A. Sall, O. Faye, N. Magassouba, C.V. Williams, V. Amburgey, L. Winona, E. Davis, J. Gerlach, F. Washington, V. Monteil, M. Jourdain, M. Bererd, A. Camara, H. Somlare, M. Gerard, G. Bado, B. Baillet, D. Delaune,K.Y. Nebie, A. Diarra, Y. Savane, R.B. Pallawo, G.J. Gutierrez, N. Milhano, I. Roger, C.J. Williams, F. Yattara, K. Lewandowski, J. Taylor, P. Rachwal, D. Turner, G. Pollakis, J.A. Hiscox, D.A. Matthews, M.K. O’Shea, A.M. Johnson, D. Wilson, E. Hutley, E. Smit, A. Di Caro, R. Woelfel, K. Stoecker, E. Fleischmann, M. Gabriel, S.A. Weller, L. Koivogui, B. Diallo, S. Keita, A. Rambaut, P. Formenty, S. Gunther, and M.W. Carroll. 2016. Real-time portable genome sequencing for Ebola surveillance. Nature 530(7589):228–232. Racaniello, V.R. 2012. Science should be in the public domain. mBio 3(1):e0004-12. Ran, F.A., L. Cong, W.X. Yan, D.A. Scott, J.S. Gootenberg, A.J. Kriz, B. Zetsche, O. Shalem, X. Wu, K.S. Makarova, E. Koonin, P.A. Sharp, and F. Zhang. 2015. In vivo genome editing using Staphylococcus aureus Cas9. Nature 520(7546):186–191. Repin, V.E., V.G. Pugachev, O.S. Taranov, and E.V. Brenner. 2007. Potential hazard of microorganisms which came from the past [in Russian]. Pp. 183–190 in Yukagir Mammoth, G.G. Boeskorov, A.N. Tichonov, and N. Suzuki, eds. Moscow: Saint- Petersburg State University. Revich, B.A., and M.A. Podolnaya. 2011. Thawing of permafrost may disturb historic cattle burial grounds in East Siberia. Global Health Action 4(1):8482. Revill, J., and C. Jefferson. 2014. Tacit knowledge and the biological weapons regime. Science and Public Policy 41(5):597–610. Ribet, D., and P. Cossart. 2015. How bacterial pathogens colonize their hosts and invade deeper tissues. Microbes and Infection 15(3):173–183. Richards, D.J., Y. Tan, J. Jia, H. Yao, and Y. Mei. 2013. 3D printing for tissue engineering. Israel Journal of Chemistry 53(9-10):805–814. PREPUBLICATION COPY: UNCORRECTED PROOFS

References 179 Richardson, S.M., L.A. Mitchell, G. Stracquadanio, K. Yang, J.S. Dymond, J.E. DiCarlo, D. Lee, C.L. Huang, S. Chandrasegaran, Y. Cai, J.D. Boeke, and J.S. Bader. 2017. Design of a synthetic yeast genome. Science 355(6329):1040–1044. Richner, J.M., S. Himansu, K.A. Dowd, S.L. Butler, V. Salazar, J.M. Fox, J.G. Julander, W.W. Tang, S. Shresta, T.C. Pierson, G. Ciaramella, and M.S. Diamond. 2017. Modified mRNA vaccines protect against Zika infection. Cell 168(6):1114–1125. Robbins, J.B., V. Gorgen, P. Min, B.R. Shepherd, and S.C. Presnell. 2013. A novel in vitro three-dimensional bioprinted liver tissue system for drug development. Abstract 7979. Poster presented at Experimental Biology, April 20–24, 2013, Boston, MA. Available at: http://organovo.com/wp-content/uploads/2015/07/04-18-13_EB_Poster_v2.pdf. Accessed November 2, 2017. Roberts, D.M., A. Nanda, M.J. Havenga, P. Abbink, D.M. Lynch, B.A. Ewald, J. Liu, A.R. Thorner, P.E. Swanson, D.A. Gorgone, M.A. Lifton, A.A. Lemckert, L. Holterman, B. Chen, A. Dilraj, A. Carville, K.G. Mansfield, J. Goudsmit, and D.H. Barouch. 2006. Hexon-chimaeric adenovirus serotype 5 vectors circumvent pre-existing anti-vector immunity. Nature 441(7090):239–243. Robinson, K.M., and J.C. Dunning Hotopp. 2014. Mobile elements and viral integrations prompt considerations for bacteria DNA integration as a novel carcinogen. Cancer Letters 352(2):137–144. Roco, M.C. 2008. Possibilities for global governance of converging technologies. Journal of Nanoparticle Research 10(1):11–29. Rodriguez, P.L., T, Harada, D.A. Christian, D.A. Pantano, R.K. Tsai, and D.E. Discher. 2013. Minimal “self” peptides that inhibit phagocytic clearance and enhance delivery of nanoparticles. Science 339(6122):971–975. Rosen, A., and L. Casciola-Rosen. 2016. Autoantigens as partners in initiation and propagation of autoimmune rheumatic diseases. Annual Review of Immunology 34:395–420. Runguphan, W., X. Qu, and S.E. O’Connor. 2010. Integrating carbon-halogen bond formation into medicinal plant metabolism. Nature 468(7322):461–464. Sabin, A.B. 1985. Oral poliovirus vaccine: History of its development and use and current challenge to eliminate poliomyelitis from the world. The Journal of Infectious Diseases 151(3):420–436. Salis Lab. 2017. RBS Calculator. Penn State University. Available at https://salislab.net/software. Accessed November 8, 2017. Saraiva, C., C. Praca, R. Ferreira, T. Santos, L. Ferreira, and L. Bernardino. 2016. Nanoparticle- mediated brain drug delivery: Overcoming blood-brain barrier to treat neurodegenerative diseases. Journal of Controlled Release 235:34–47. Sastalla, I., D.M. Monack, and K.F. Kubatzky. 2016. Bacterial exotoxins: How bacteria fight the immune system [editorial]. Frontiers in Immunology 7:Art.300. Savile, C., J.M. Janey, E.C. Mundorff, J.C. Moore, S. Tam, W.R. Jarvis, J.C. Colbeck, A. Krebber, F.J. Fleitz, J. Brands, P.N. Devine, G.W. Huisman, and G.J. Hughes. 2010. Biocatalytic asymmetric synthesis of chiral amines from ketones applied to sitagliptin manufacture. Science 329(5989):305–309. sbolstandard. org. 2017. SBOL: The Synthetic Biology Open Language. Newcastle University Center for Synthetic Biology. Available at: http://sbolstandard.org. Accessed November 9, 2017. PREPUBLICATION COPY: UNCORRECTED PROOFS

180 Biodefense in the Age of Synthetic Biology Schmidt, F., and R.J. Platt. 2017. Applications of CRISPR-Cas for synthetic biology and genetic recording. Current Opinion in Systems Biology 5:9–15. Schwarz, M.C., M. Sourisseau, M.M. Espino, E.S. Gray, M.T. Chambers, D. Tortorella, and M.J. Evans. 2016. Rescue of the 1947 Zika virus prototype strain with a cytomegalovirus promoter-driven cDNA clone. mSphere 1(5):e00246-16. Selle, K., and R. Barrangou. 2015. Harnessing CRISPR-Cas systems for bacterial genome editing. Trends in Microbiology 23(4):225–232. Shen, S.H., C.B. Stauft, O. Gorbatsevych, Y. Song, C.B. Ward, A. Yurovsky, S. Mueller, B. Futcher, and E. Wimmer. 2015. Large scale re-coding of an arbovirus genome to rebalance its insect versus mammalian preference. Proceedings of the National Academy of Science of the United States of America 112(15):4749–4754. Shen, Y., Y. Wang, T. Chen, F. Gao, J. Gong, D. Abramczyk, R. Walker, H. Zhao, S. Chen, W. Liu, Y. Luo, C.A. Müller, A. Paul-Dubois-Taine, B. Alver, G. Stracquadanio, L.A. Mitchell, Z. Luo, Y. Fan, B. Zhou, B. Wen, F. Tan, Y. Wang, J. Zi, Z. Xie, B. Li, K. Yang, S.M. Richardson, H. Jiang, C.E. French, C.A. Nieduszynski, R. Koszul, A.L. Marston, Y. Yuan, J. Wang, J.S. Bader, J. Dai, J.D. Boeke, X. Xu, Y. Cai, and H. Yang. 2017. Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome. Science 355(6329):eaaf4791. Shirakawa, K., L. Chavez, S. Hakre, V. Calvanese, and E. Verdin. 2013. Reactivation of latent HIV by histone deacetylase inhibitors. Trends in Microbiology 21(6):277–285. Sieber, K.B., P. Gajer, and J.C. Dunning Hotopp. 2016. Modeling the integration of bacterial rRNA fragments into the human cancer genome. BMC Bioinformatics 17:134. Siegel, J.B. A. Zanghellini, H.M. Lovick, G. Kiss, A.R. Lambert, J.L. St Clair, J.L. Gallaher, D. Hilvert, M.H. Gelb, B.L. Stoddard, K.N. Houk, F.E. Michael, and D. Baker. 2010. Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science 329(5989):309–313. Sleator, R. D. 2010. The story of Mycoplasma mycoides JCVI-syn1.0. Bioengineered Bugs 1(4): 229–230. Slomovic, S., K. Pardee, and J.J. Collins. 2015. Synthetic biology devices for in vitro and in vivo diagnostics. Proceedings of the National Academy of the United States of America 112(47):14429–14435. Smanski, M.J., S. Bhatia, D. Zhao, Y.J. Park, L.B.A. Woodruff, G. Giannoukos, D. Ciulla, M. Busby, J. Calderon, R. Nicol, D.B. Gordon, D. Densmore, and C.A. Voigt. 2014. Functional optimization of gene clusters by combinatorial design and assembly. Nature Biotechnology 32:1241–1249. Smanski, M.J., H. Zhou, J. Claesen, B. Shen, M.A. Fischbach, and C.A. Voigt. 2016. Synthetic biology to access and expand nature’s chemical diversity. Nature Reviews Microbiology 14(3):135–149. Spark Therapeutics. 2017. FDA Approves Spark Therapeutics’ LUXTURNA™ (voretigene neparvovec-rzyl), a One-time Gene Therapy for Patients with Confirmed Biallelic RPE65 Mutation-associated Retinal Dystrophy. Press Release: December 19, 2017. Available at: http://ir.sparktx.com/news-releases/news-release-details/fda-approves-spark-therapeutics- luxturnatm-voretigene-neparvovec. Accessed January 31, 2017. Steinle, H., A. Behring, C. Schlensak, H.P. Wendel, and M. Avci-Adali. 2017. Concise review: Application of in vitro transcribed messenger RNA for cellular engineering and reprogramming: progress and challenges. Stem Cells 35(1):68–79. PREPUBLICATION COPY: UNCORRECTED PROOFS

References 181 Steinmetz, M., and R. Richter. 1994. Plasmids designed to alter the antibiotic resistance expressed by insertion mutations in Bacilus subtilis, through in vivo recombination. Gene 142:79–83. Strauch, E., J.A. Hammer, A. Konietzny, S. Schneiker-Bekel, W. Arnold, A. Goesmann, A. Pühler, and L. Beutin. 2008. Bacteriophage 2851 is a prototype phage for dissemination of the Shiga toxin variant gene 2c in Escherichia coli O157:H7. Infection and Immunity 76(12):5466–5477. Suntharalingam, G., M. R. Perry, S. Ward, S. J. Brett, A. Castello-Cortes, M. D. Brunner, and N. Panoskaltsis. 2006. Cytokine storm in a phase 1 trial of the anti-CD28 monoclonal antibody TGN1412. The New England Journal of Medicine 355(10):1018–1028. Swenson, K. 2015. Drugs, Viruses, and Robots: Weapons on the Rise for a Better Fight Against Cancer. Autodesk News: March 24, 2015. Available at https://www.autodesk.com/redshift/drugs-viruses-and-robots-weapons-on-the-rise-for-a- better-fight-against-cancer. Accessed January 31, 2018. Synlogic. 2017. IND-Enabling Studies. Available at: https://www.synlogictx.com/pipeline/pipeline/ Accessed November 9, 2017. Szybalski, W. 1974. In vivo and in vitro initiation of transcription. Pp. 23–24 in Control of Gene Expression, A. Kohn, and A. Shatkay, eds. New York: Plenum Press. Tanaka, A., P.S. Leung, and M.E. Gershwin. 2018. Environmental basis of primary biliary cholangitis. Experimental Biology and Medicine 243(2):184–189. Tanaka, T., W. Zhang, Y. Sun, Z. Shuai, A.S. Chida, T.P. Kenny, G.X. Yang, I. Sanz, A. Ansari, C.L. Bowlus, G.C. Ippolito, R.L. Coppel, K. Okazaki, X.S. He, P.S.C. Leung, and M.E. Gershwin. 2017. Autoreactive monoclonal antibodies from patients with primary biliary cholangitis recognize environmental xenobiotics. Hepatology 66(3):885–895. Taneja, V., and C. S. David. 2001. Lessons from animal models for human autoimmune diseases. Nature Immunology 2(9): 781–784. Tate, M.D., E.R. Job, Y. Deng, V. Gunalan, S. Maurer-Stroh, and P.C. Reading. 2014. Playing hide and seek: How glycosylation of the influenza virus hemagglutinin can modulate the immune response to infection. Viruses 6(3):1294–1316. The Australia Group. 2007. Fighting the Spread of Chemical and Biological Weapons: Strengthening Global Security. Available at: http://www.australiagroup.net/en/agb_july2007.pdf. Accessed November 29, 2017. The Royal Society. 2015. The Chemical Weapons Convention and Convergent Trends in Science and Technology. Available at: https://royalsociety.org/~/media/policy/projects/brain- waves/2013-08-04-chemical-weapons-convention-and-convergent-trends.pdf. Accessed May 11, 2017. Thissen, J.B., K. McLoughlin, S. Gardner, S. Gu, S. Mabery, T. Slezak, and C. Jaing. 2014. Analysis of sensitivity and rapid hybridization of a multiplexed Microbial Detection Array. Journal of Virological Methods 201:73–78. Tizei, P. A.G., E. Csibra, L. Torres, V.B. Pinheiro. 2016. Selection platforms for directed evolution in synthetic biology. Biochemical Society Transactions 44(4):1165–1175. Toman, Z., C. Dambly-Chaudière, L. Tenenbaum, and M. Radman. 1985. A system for detection of genetic and epigenetic alterations in Escherichia coli induced by DNA-damaging agents. Journal of Molecular Biology 186(1):97–105. Tucker, J.B. 2012. Innovation, Dual Use, and Security: Managing the Risks of Emerging Biological and Chemical Technologies. Cambridge: The MIT Press. PREPUBLICATION COPY: UNCORRECTED PROOFS

182 Biodefense in the Age of Synthetic Biology Tulman, E.R., G. Delhon, C.L. Alfonso, Z. Lu, L. Zsak, N.T. Sandybaev, U.Z. Kerembekova, V.L. Zaitsev, G.F. Kutish, and D.L. Rock. 2006. Genome of horsepox virus. Journal of Virology 80(18):9244–9258. UN (The United Nations). 2017. The Biological Weapons Convention. UN Office at Geneva. Available at: https://www.unog.ch/80256EE600585943/(httpPages)/04FBBDD6315AC720C12571800 04B1B2F?OpenDocument. Accessed November 13, 2017. UN Security Council. 2004. Resolution 1540 (2004). S/RES/1540 (2004). Available at: http://www.un.org/en/ga/search/view_doc.asp?symbol=S/RES/1540%20(2004). Accessed November 15, 2017. U.S. Government. 2012. United States Government Policy for Oversight of Life Sciences Dual Use Research of Concern. March 29, 2012. Available at: https://www.phe.gov/s3/dualuse/Documents/us-policy-durc-032812.pdf. Accessed on May 11, 2017. U.S. Government. 2014. United States Government Policy for Institutional Oversight of Life Sciences Dual-use Research of Concern. September 24, 2014. Available at: https://www.phe.gov/s3/dualuse/Documents/durc-policy.pdf. Accessed on May 11, 2017. Vabret, N., M. Bailly-Bechet, A. Lepelly, V. Najburg, O. Schwartz, B. Verrier, and F. Tangy. 2014. Large-scale nucleotide optimization of simian immunodeficiency virus reduces its capacity to stimulate type I interferon in vitro. Journal of Virology 88(8):4161–4172. van Courtland Moon, J.E. 2006. The US biological weapons program. Pp. 9–46 in Deadly Cultures: Biological Weapons since 1945, M.L. Wheelis, L. Rózsa, and M.R. Dando, eds. Cambridge, MA: Harvard University Press. van den Broek, M., M.F. Bachmann, G. Köhler, M. Barner, R. Escher, R. Zinkernagel, and M. Kopf. 2000. IL-4 and IL-10 antagonize IL-12-mediated protection against acute vaccina virus infection with a limited role of IFN-γ and nitric oxide synthetase 2. The Journal of Immunology 164(1):371–378. Velasco, E., T. Agheneza, K. Denecke, G. Kirchner, and T. Eckmanns. 2014. Social media and internet-based data in global systems for public health surveillance: A systematic review. Milbank Quarterly 92(1):7–33. Verma, I.M., and N. Somia. 1997. Gene therapy – promises, problems, and prospects. Nature 389:239–242. Vidic, J., M. Manzano, C.M. Chang, and N. Jaffrezic-Renault. 2017. Advanced biosensors for detection of pathogens related to livestock and poultry. Veterinary Research 48(1):11. Vogel, K.M. 2012. Phantom Menace or Looming Danger? A New Framework for Assessing Bioweapons Threats. Baltimore, MD: Johns Hopkins University Press. Vogel, K.M. 2013. The need for greater multidisciplinary, sociotechnical analysis: The bioweapons case. Studies in Intelligence 57(3):1–10. Voigt, C.A. 2012. Synthetic biology [editorial]. ACS Synthetic Biology 1:1–2. Wain-Hobson, S. 2014. An avian H7N1 gain-of-function experiment of great concern. mBio 5(5):e01882-14. Wang, B., C. Yang, G. Tekes, S. Mueller, A. Paul, S.P. Whelan, and E. Wimmer. 2015. Recoding of the vesicular stomatitis virus L gene by computer-aided design provides a live attenuated vaccine candidate. mBio 6(2):e00237-15. PREPUBLICATION COPY: UNCORRECTED PROOFS

References 183 Wang, H.H., F.J. Isaacs, P.A. Carr. Z.Z. Sun, G. Xu, C.R. Forest, and G.M. Church. 2009. Programming cells by multiplex genome engineering and accelerated evolution. Nature 460(7257):894–898. Wang, J., Z. Lu, M.G. Wientjes, and J.L.S. Au. 2010. Delivery of siRNA therapeutics: Barriers and carriers. The AAPS Journal 12(4):492–503. Wang, Y., Z. Zhang, S. Seo, P. Lynn, T. Lu, Y. Jin, and H. P. Blaschek. 2016. Bacterial genome editing with CRISPR-Cas9: Deletion, integration, single nucleotide modification, and desirable “clean” mutant selection in Clostridium beijerinckii as an example. American Chemical Society Synthetic Biology 5(7):721–732. Weber, W., and M. Fussenegger. 2012. Engineering biomedical applications of synthetic biology. Nature Reviews 13:21–35. Weiss, R., S. Basu, S. Hooshangi, A. Kalmbach, D. Karig, R. Mehreja, and I. Netravali. 2003. Genetic circuit building blocks for cellular computation, communication, and signal processing. Natural Computing 2:47–84. Westfall, P.J., D.J. Pitera, J.R. Lenihan, D. Eng, F.X. Woolard, R. Regentin, T. Horning, H. Tsuruta, D.J. Melis, A. Owens, S. Fickes, D. Diola, K.R. Benjamin, J.D. Keasling, M.D. Leavell, D.J. McPhee, N.S. Renninger, J.D. Newman, and C.J. Paddon. 2012. Production of amorphadiene in yeast, and its conversion to dihydroartemisinic acid, precursor to the antimalarial agent artemisinin. Proceedings of the National Academy of Sciences of the United States of America 109(3):E111–E118. Wheelis, M. 2002. Biological warfare at the 1346 siege of Caffa. Emerging Infectious Diseases 8(9):971–975. White House. 2012. National Bioeconomy Blueprint. Available at: https://obamawhitehouse.archives.gov/sites/default/files/microsites/ostp/national_bioecon omy_blueprint_april_2012.pdf. Accessed on June 22, 2017. Willis, H.H., M.L. DeKay, M.G. Morgan, H.K. Florig, and P.S. Fischbeck. 2004. Ecological risk ranking: Development and evaluation of a method for improving public participation in environmental decision making. Risk Analysis 24(2):363–378. Willis, H.H., J.M. Gibson, R.A. Shih, S. Geschwind, S. Olmstead, J. Hu, A.E. Curtright, G. Cecchine, and M. Moore. 2010. Prioritizing environmental health risks in the UAE. Risk Analysis 30(12):1842–1856. Wimmer, E. 2006. The test-tube synthesis of a chemical called poliovirus: The simple synthesis of a virus has far-reaching societal implications EMBO Reports 7(Spec.):S3–S9. Wimmer, E, and A.V. Paul. 2011. Synthetic poliovirus and other designer viruses: What have we learned from them? Annual Review of Microbiology 65:583–609. Wimmer, E., S. Mueller, T.M. Tumpy, and J.K. Taubenberger. 2009. Synthetic viruses: A new opportunity to understand and prevent viral disease. Nature Biotechnology 27(12):1163– 1172. Wolinsky, H. 2016. The FBI and biohackers: an unusual relationship. EMBO Reports 17(6): 793–796. WRAIR (Walter Reed Army Institute of Research). 2017. Multidrug-resistant Organism Repository and Surveillance Network (MRSN). Available at: http://www.wrair.army.mil/OtherServices_MRSN.aspx. Accessed November 14, 2017. Wu, Y., B.Z. Li, M. Zhao, L.A. Mitchell, Z.X. Xie, Q.H. Lin, X. Wang, W.H. Xiao, Y. Wang, X. Zhou, H. Liu, X. Li, M.Z. Ding, D. Liu, L. Zhang, B.L. Liu, X.L. Wu, F.F. Li, X.T. Dong, B. Jia, W.Z. Zhang, G.Z. Jiang, Y. Liu, X. Bai, T.Q. Song, Y. Chen, S.J. Zhou, PREPUBLICATION COPY: UNCORRECTED PROOFS

184 Biodefense in the Age of Synthetic Biology R.Y. Zhu, F. Gao, Z. Kuang, X. Wang, M. Shen, K. Yang, G. Stracquadanio, S.M. Richardson, Y. Lin, L. Wang, R. Walker, Y. Luo, P.S. Ma, H. Yang, Y. Cai, J. Dai, J.S. Bader, J.D. Boeke, and Y.J. Yuan. 2017. Bug mapping and fitness testing of chemically synthesized chromosome X. Science 355(6329): eaaf4706. Xie, Z.X., B.Z. Li, L.A. Mitchell, Y. Wu, X. Qi, Z. Jin, B. Jia, X. Wang, B.X. Zeng, H.M. Liu, X.L. Wu, Q. Feng, W.Z. Zhang, W. Liu, M.Z. Ding, X. Li, G.R. Zhao, J.J. Qiao, J.S. Cheng, M. Zhao, Z. Kuang, X. Wang, J.A. Martin, G. Stracquadanio, K. Yang, X. Bai, J. Zhao, M.L. Hu, Q.H. Lin, W.Q. Zhang, M.H. Shen, S. Chen, W. Su, E.X. Wang, R. Guo, F. Zhai, X.J. Guo, H.X. Du, J.Q. Zhu, T.Q. Song, J.J. Dai, F.F. Li, G.Z. Jiang, S.L. Han, S.Y. Liu, Z.C. Yu, X.N. Yang, K. Chen, C. Hu, D.S. Li, N. Jia, Y. Liu, L.T. Wang, S. Wang, X.T. Wei, M.Q. Fu, L.M. Qu, S.Y. Xin, T. Liu, K.R. Tian, X.N. Li, J.H. Zhang, L.X. Song, J.G. Liu, J.F. Lv, H. Xu, R. Tao, Y. Wang, T.T. Zhang, Y.X. Deng, Y.R. Wang, T. Li, G.X. Ye, X.R. Xu, Z.B. Xia, W. Zhang, S.L. Yang, Y.L. Liu, W.Q. Ding, Z.N. Liu, J.Q. Zhu, N.Z. Liu, R. Walker, Y. Luo, Y. Wang, Y. Shen, H. Yang, Y. Cai, P.S. Ma, C.T. Zhang, J.S. Bader, J.D. Boeke, and Y.J. Yuan. 2017. Perfect" designer chromosome V and behavior of a ring derivative. Science 355(6329):eaaf4704. Xiu-Hua, J., L. Shao-Chun, H. Bing, Z. Xiang, Z. Jing, L. Wei-Hua, L. Qian, L. Ting, X. Xiao- Ping, and C. Xi-Gu. 2010. Tyrosinase small interfering RNA effectively suppresses tyrosinase gene expression in vitro and in vivo. Molecular Biology International 2010:240472. Yang, C., S. Skiena, B. Futcher, S. Mueller, and E. Wimmer. 2013. Deliberate reduction of hemagglutinin and neuraminidase expression of influenza virus leads to an ultraprotective live vaccine in mice. Proceedings of the National Academy of Science of the United States of America 110(23):9481-9486. Yang, J., K. D. Hirschi, and L.M. Farmer. 2015. Dietary RNAs: New stories regarding oral delivery. Nutrients 7(5):3184-3199. Yao, L., J. Ou, C.Y. Cheng, H. Steiner, W. Wang, G. Wang, and H. Ishii. 2015. bioLogic: Natto cells as nanoactuators for shape changing interfaces. Pp. 1-10 in CHI’15: Proceedings of the 33rd Annual ACM Conference on Human Factors in Computing Systems, April 18-23, 2015, Seoul, Republic of Korea. New York: ACM. Yim, H., R. Haselbeck, W. Niu, C. Pujol-Baxley, A. Burgard, J. Boldt, J. Khandurina, J.D. Trawick, R.E. Osterhout, R. Stephen, J. Estadilla, S. Teisan, H.B. Schreyer, S. Andrae, T.H. Yang, S.Y. Lee, M.J. Burk, and S.V. Dien. 2011. Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. Nature Chemical Biology 7:445- 452. Young, S.D. 2015. A “big data” approach to HIV. Epidemiology and Prevention. Preventive Medicine 70:17-18. Zarogoulidis, P., K. Darwiche, W. Hohenforst-Schmidt, H. Huang, Q. Li, L. Freitag, and K. Zarogoulidis. 2013. Inhaled gene therapy in lung cancer: Proof-of-concept for nano- oncology and nanobiotechnology in the management of lung cancer. Future Oncology 9(8):1171-1194. Zetsche, B., J.S. Gootenberg, O.O. Abudayyeh, I.M. Slaymaker, K.S. Makarova, P. Essletzbichler, S.E. Volz, J. Joung, J. van der Oost, A. Regev, E.V. Koonin, and F. Zhang. 2015. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163(3):759-771. Zhang, B., X. Pan, G.P. Cobb, and T.A. Anderson. 2007. microRNAs as oncogenes and tumor suppressors. Developmental Biology 302(1):1-12. PREPUBLICATION COPY: UNCORRECTED PROOFS

References 185 Zhang, H., Q. Cheng, A. Liu, G. Zhao, and J. Wang. 2017. A novel and efficient method for bacteria genome editing employing both CRISPR/Cas9 and an antibiotic resistance cassette. Frontiers in Microbiology 8:812. Zhang, L., D. Hou, Z. Chen, D. Li, L. Zhu, Y. Zhang, J. Li, Z. Bian, X. Liang, X. Cai, Y. Yin, C. Wang, T. Zhang, D. Zhu, D. Zhang, J. Xu, Q. Chen, Y. Ba, J. Liu, Q. Wang, J. Chen, J. Wang, M. Wang, Q. Zhang, J. Zhang, K. Zen and C. Zhang. 2012. Exogenous plant MIR168a specifically targets mammalian LDLRAP1: Evidence of cross-kingdom regulation by microRNA. Cell Research 22(1):107-126. Zhang, W., G. Zhao, Z. Luo, Y. Lin, L. Wang, Y. Guo, A. Wang, S. Jiang, Q. Jiang, J. Gong, Y. Wang, S. Hou, J. Huang, T. Li, Y. Qin, J. Dong, Q. Qin, J. Zhang, X. Zou, X. He, L. Zhao, Y. Xiao, M. Xu, E. Cheng, N. Huang, T. Zhou, Y. Shen, R. Walker, Y. Luo, Z. Kuang, L.A. Mitchell, K. Yang, S.M. Richardson, Y. Wu, B.Z. Li, Y.J. Yuan, H. Yang, J. Lin, G.Q. Chen, Q. Wu, J.S. Bader, Y. Cai, J.D. Boeke, and J. Dai. 2017. Engineering the ribosomal DNA in a megabase synthetic chromosome. Science 355(6329):eaaf3981. Zhang, Y., B. M. Lamb, A. W. Feldman, A. X. Zhou, T. Lavergne, L. Li, and F. E. Romesberg. 2016. A semisynthetic organism engineered for the stable expansion of the genetic alphabet. Proceedings of the National Academy of Sciences 114(6):1317-1322. Zhang, Y., J.L. Ptacin, E.C. Fischer, H.R. Aerni, C.E. Caffaro, K. San Jose, A.W. Feldman, C.R. Turner, and F.E. Romesberg. 2017. A semi-synthetic organism that stores and retrieves increased genetic information. Nature 551(7682):644-647. Zivot, J.B., and W.D. Hoffman. 1995. Pathogenic effects of endotoxin. New Horizons 3(2):267- 275. Zolnik, B.S., A. Gonzalez-Fernandez, N. Sadrieh, and M.A. Dobrovolskaia. 2010. Nanoparticles and the immune system. Endocrinology 151(2):458-465. PREPUBLICATION COPY: UNCORRECTED PROOFS

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Scientific advances over the past several decades have accelerated the ability to engineer existing organisms and to potentially create novel ones not found in nature. Synthetic biology, which collectively refers to concepts, approaches, and tools that enable the modification or creation of biological organisms, is being pursued overwhelmingly for beneficial purposes ranging from reducing the burden of disease to improving agricultural yields to remediating pollution. Although the contributions synthetic biology can make in these and other areas hold great promise, it is also possible to imagine malicious uses that could threaten U.S. citizens and military personnel. Making informed decisions about how to address such concerns requires a realistic assessment of the capabilities that could be misused.

Biodefense in the Age of Synthetic Biology explores and envisions potential misuses of synthetic biology. This report develops a framework to guide an assessment of the security concerns related to advances in synthetic biology, assesses the levels of concern warranted for such advances, and identifies options that could help mitigate those concerns.

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