A

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A References Ayub, M., and H. Bayley. 2012. Individual RNA base recognition in immobi- lized oligonucleotides using a protein nanopore. Nano Letters 12(11):5637– 5643. Center for Research Information. 2004. Health effects of project SHAD biologi- cal agent: Bacillus globigii. Prepared for the National Academies, Wash- ington, DC. http://www.iom.edu/~/media/files/report%20files/2007/long- term-health-effects-of-participation-in-project-shad-shipboard-hazard-and-defense/ bacillusglobigii.pdf (accessed June 29, 2013). Cieslak, T. J., and E. M. Eitzen. 1999. Clinical and epidemiologic principles of anthrax. Emerging Infectious Diseases 5(4):552–555. Clarke, J., H.-C. Wu, L. Jayasinghe, A. Patel, S. Reid, and H. Bayley. 2009. Continuous base identification for single-molecule nanopore DNA sequenc- ing. Nature Nanotechnology 4(4):265–270. Eid, J., A. Fehr, J. Gray, K. Luong, J. Lyle, G. Otto, P. Peluso, D. Rank, P. Baybayan, B. Bettman, A. Bibillo, K. Bjornson, B. Chaudhuri, F. Christians, R. Cicero, S. Clark, R. Dalal, A. deWinter, J. Dixon, M. Foquet, A. Gaertner, P. Hardenbol, C. Heiner, K. Hester, D. Holden, G. Kearns, X. Kong, R. Kuse, Y. Lacroix, S. Lin, P. Lundquist, C. Ma, P. Marks, M. Maxham, D. Murphy, I. Park, T. Pham, M. Phillips, J. Roy, R. Sebra, G. Shen, J. Sorenson, A. Tomaney, K. Travers, M. Trulson, J. Vieceli, J. Wegener, D. Wu, A. Yang, D. Zaccarin, P. Zhao, F. Zhong, J. Korlach, and S. Turner. 2009. Real-time DNA sequencing from single polymerase mole- cules. Science 323(5910):133–138. Flusberg, B. A., D. R. Webster, J. H. Lee, K. J. Travers, E. C. Olivares, T. A. Clark, J. Korlach, and S. W. Turner. 2010. Direct detection of DNA meth- ylation during single-molecule, real-time sequencing. Nature Methods 7(6):461–465. 95

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APPENDIX A 97 Murphy, K. M., K. D. Berg, and J. R. Eshleman. 2005. Sequencing of genomic DNA by combined amplification and cycle sequencing reaction. Clinical Chemistry 51(1):35–39. Regan, D. F., A. J. Makarewicz, B. J. Hindson, T. R. Metz, D. M. Gutierrez, T. H. Corzett, D. R. Hadley, R. C. Mahnke, B. D. Henderer, J. W. Breneman IV, T. H. Weisgraber, and J. M. Dzentis. 2008. Environmental monitoring for biological threat agents using the autonomous pathogen detection system with multiplexed polymerase chain reaction. Analytical Chemistry 80(19): 7422–7429. Rider, T. H., M. S. Petrovick, F. E. Nargi, J. D. Harper, E. D. Schwoebel, R. H. Mathews, D. J. Blanchard, L. T. Bortolin, A. M. Young, J. Chen, and M. A. Hollis. 2003. A B cell-based sensor for rapid identification of pathogens. Science 301(5630):213–215. Rissin, D. M., C. W. Kan, T. G. Campbell, S. C. Howes, D. R. Fournier, L. Song, T. Piech, P. P. Patel, L. Chang, A. J. Rivnak, E. P. Ferrell, J. D. Randall, G. K. Provuncher, D. R. Walt, and D. C. Duffy. 2010. Single- molecule enzyme-linked immunosorbent assay detects serum proteins at subfemtomolar concentrations. Nature Biotechnology 28(6):595–599. Sanchez, M., L. Probst, E. Blazevic, B. Nakao, and M. A. Northrup. 2011. The microfluidic bioagent autonomous networked detector (M-BAND): An up- date. Fully integrated, automated, and networked field identification of air- borne pathogens. Proceedings of SPIE 8189, Optics and Photonics for Counterterrorism and Crime Fighting VII; Optical Materials in Defense Systems Technology VIII; and Quantum-Physics-Based Information Secu- rity. 818907. Shea, D. A., and S. A. Lister. 2003. The BioWatch program: Detection of bio- terrorism. CRS Report No. RL32152. Washington, DC: Congressional Research Service. http://www.fas.org/sgp/crs/terror/RL32152.html#_1_2 (accessed June 29, 2013). Shiroguchi, K., T. Z. Jia, P. A. Sims, and X. S. Xie. 2012. Digital RNA sequenc- ing minimizes sequence-dependent bias and amplification noise with opti- mized single-molecule barcodes. Proceedings of the National Academy of Sciences of the United States of America 109(4):1347–1352. Song, Y., N. Talaty, K. Datseko, B. L. Wanner, and R. G. Cooks. 2009. In vivo recognition of Bacillus subtilis by desorption electrospray ionization mass spectrometry (DESI-MS). Analyst 134(5):838–841. Soskine, M., A. Biesemans, B. Moeyaert, S. Cheley, H. Bayley, and G. Maglia. 2012. An engineered ClyA nanopore detects folded target proteins by selec- tive external association and pore entry. Nano Letters 12(9):4895–4900. Steele, P. T., G. R. Farquar, A. N. Martin, K. R. Coffee, V. J. Riot, S. I. Martin, D. P. Fergenson, E. E. Gard, and M. Frank. 2008. Autonomous, broad- spectrum detection of hazardous aerosols in seconds. Analytical Chemistry 80(12):4583–4589.

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98 TECHNOLOGIES TO ENABLE AUTONOMOUS DETECTION FOR BIOWATCH Stoddart, D., A. J. Heron, E. Mikhailova, G. Maglia, and H. Bayley. 2009. Sin- gle-nucleotide discrimination in immobilized DNA oligonucleotides with a biological nanopore. Proceedings of the National Academy of Sciences of the United States of America 106(19):7702–7707. Towler, W. I., J. D. Church, J. R. Eshleman, M. G. Fowler, L. A. Guay, J. B. Jackson, and S. H. Eshleman. 2008. Analysis of nevirapine resistance muta- tions in cloned HIV type 1 variants from HIV-infected Ugandan infants us- ing a single-step amplification-sequencing method (AmpliSeq). AIDS Research and Human Retroviruses 24(9):1209–1213. Vilfan, I. D., Y.-C. Tsai, T. A. Clark, J. Wegener, Q. Dai, C. Yi, T. Pan, S. W. Turner, and J. Korlach. 2013. Analysis of RNA base modification and struc- tural rearrangement by single-molecule real-time detection of reverse transcrip- tion. Journal of Nanobiotechnology 11(1):8–11. Vogelstein, B., and K. W. Kinzler. 1999. Digital PCR. Proceedings of the Na- tional Academy of Sciences of the United States of America 96(16):9236– 9241. Whale, A. S., S. Cowen, C. A. Foy, and J. F. Huggett. 2013. Methods for apply- ing accurate digital PCR analysis on low copy DNA samples. PLoS ONE 8(3):e58177. White House. 2004. Biodefense for the 21st century. No. HSPD-10. Washington, DC: Office of Homeland Security, Executive Office of the President. http://www.fas.org/irp/offdocs/nspd/hspd-10.html (accessed July 3, 2013). Woyke, T., D. Tighe, K. Mavromatis, A. Clum, A. Copeland, W. Schackwitz, A. Lapidus, D. Wu, J. P. McCutcheon, B. R. McDonald, N. A. Moran, J. Bristow, and J.-F. Cheng. 2010. One bacterial cell, one complete genome. PLoS ONE 5(4):e10314. Yang, Q., H. Wang, J. D. Maas, W. J. Chappell, N. E. Manicke, R. G. Cooks, and Z. Ouyang. 2012. Paper spray ionization devices for direct, biomedical analysis using mass spectrometry. International Journal of Mass Spectrom- etry 312:201–207.