Abstract
Synthetic Biology is founded on the idea that complex biological systems are built most effectively when the task is divided in abstracted layers and all required components are readily available and well-described. This requires interdisciplinary collaboration at several levels and a common understanding of the functioning of each component. Standardization of the physical composition and the description of each part is required as well as a controlled vocabulary to aid design and ensure interoperability. Here, we describe standardization initiatives from several disciplines, which can contribute to Synthetic Biology. We provide examples of the concerted standardization efforts of the BioBricks Foundation comprising the request for comments (RFC) and the Registry of Standardized Biological parts as well as the international Genetically Engineered Machine (iGEM) competition.
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References
Leduc, S. (1912) La biologie synthétique, étude de biophysique (Poinat, A., Ed.). Paris.
Szybalski, W., and Skalka, A. (1978) Nobel prizes and restriction enzymes., Gene 4, 181–2.
Gaisser, S., Reiss, T., Lunkes, A., Müller, K. M., and Bernauer, H. (2009) Making the most of synthetic biology. Strategies for synthetic biology development in Europe., EMBO reports 10 Suppl 1, S5-8.
Berman, H. M. (2008) The Protein Data Bank: a historical perspective., Acta crystallographica. Section A, Foundations of crystallography. International Union of Crystallography 64, 88–95.
Strasser, B. J. (2008) Genetics. GenBank – Natural history in the 21st Century?, Science (New York, N.Y.) 322, 537–8.
Quackenbush, J. (2009) Data reporting standards: making the things we use better., Genome medicine 1, 111.
Kettner, C., Field, D., Sansone, S.-A., Taylor, C., Aerts, J., Binns, N., Blake, A., Britten, C. M., Marco, A. de, Fostel, J., Gaudet, P., González-Beltrán, A., Hardy, N., Hellemans, J., Hermjakob, H., Juty, N., Leebens-Mack, J., Maguire, E., Neumann, S., Orchard, S., Parkinson, H., Piel, W., Ranganathan, S., Rocca-Serra, P., Santarsiero, A., Shotton, D., Sterk, P., Untergasser, A., and Whetzel, P. L. (2010) Meeting Report from the Second “Minimum Information for Biological and Biomedical Investigations” (MIBBI) workshop., Standards in genomic sciences 3, 259–66.
Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., Aach, J., Ansorge, W., Ball, C. A., Causton, H. C., Gaasterland, T., Glenisson, P., Holstege, F. C., Kim, I. F., Markowitz, V., Matese, J. C., Parkinson, H., Robinson, A., Sarkans, U., Schulze-Kremer, S., Stewart, J., Taylor, R., Vilo, J., and Vingron, M. (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data., Nature genetics 29, 365–71.
Taylor, C. F., Paton, N. W., Lilley, K. S., Binz, P., Jalain, Jr, R. K. J., R, A., Zhu, W., Apweiler, R., Aebersold, R., Deutsch, E. W., Dunn, M. J., Heck, A. J. R., Leitner, A., Macht, M., Mann, M., Martens, L., Neubert, T. A., Patterson, S. D., Ping, P., Seymour, S. L., Souda, P., Tsugita, A., Vandekerckhove, J., and Vondriska, T. M. (2007) The minimum information about a proteomics experiment (MIAPE), Nature Biotechnology 25, 887–893.
Vizcaíno, J. A., Martens, L., Hermjakob, H., Julian, R. K., and Paton, N. W. (2007) The PSI formal document process and its implementation on the PSI website., Proteomics 7, 2355–7.
Gibson, F., Anderson, L., Babnigg, G., Baker, M., Berth, M., Binz, P.-A., Borthwick, A., Cash, P., Day, B. W., Friedman, D. B., Garland, D., Gutstein, H. B., Hoogland, C., Jones, N. A., Khan, A., Klose, J., Lamond, A. I., Lemkin, P. F., Lilley, K. S., Minden, J., Morris, N. J., Paton, N. W., Pisano, M. R., Prime, J. E., Rabilloud, T., Stead, D. A., Taylor, C. F., Voshol, H., Wipat, A., and Jones, A. R. (2008) Guidelines for reporting the use of gel electrophoresis in proteomics., Nature biotechnology 26, 863–4.
Orchard, S., Salwinski, L., Kerrien, S., Montecchi-Palazzi, L., Oesterheld, M., Stümpflen, V., Ceol, A., Chatr-aryamontri, A., Armstrong, J., Woollard, P., Salama, J. J., Moore, S., Wojcik, J., Bader, G. D., Vidal, M., Cusick, M. E., Gerstein, M., Gavin, A.-C., Superti-Furga, G., Greenblatt, J., Bader, J., Uetz, P., Tyers, M., Legrain, P., Fields, S., Mulder, N., Gilson, M., Niepmann, M., Burgoon, L., De Las Rivas, J., Prieto, C., Perreau, V. M., Hogue, C., Mewes, H.-W., Apweiler, R., Xenarios, I., Eisenberg, D., Cesareni, G., and Hermjakob, H. (2007) The minimum information required for reporting a molecular interaction experiment (MIMIx)., Nature biotechnology 25, 894–8.
Taylor, C. F., Binz, P.-A., Aebersold, R., Affolter, M., Barkovich, R., Deutsch, E. W., Horn, D. M., Hühmer, A., Kussmann, M., Lilley, K., Macht, M., Mann, M., Müller, D., Neubert, T. A., Nickson, J., Patterson, S. D., Raso, R., Resing, K., Seymour, S. L., Tsugita, A., Xenarios, I., Zeng, R., and Julian, R. K. (2008) Guidelines for reporting the use of mass spectrometry in proteomics., Nature biotechnology 26, 860–1.
Jones, A. R., Carroll, K., Knight, D., MacLellan, K., Domann, P. J., Legido-Quigley, C., Huang, L., Smallshaw, L., Mirzaei, H., Shofstahl, J., and Paton, N. W. (2010) Guidelines for reporting the use of column chromatography in proteomics, Nature Biotechnology. Nature Publishing Group 28, 654–654.
Hoogland, C., OʼGorman, M., Bogard, P., Gibson, F., Berth, M., Cockell, S. J., Ekefjärd, A., Forsstrom-Olsson, O., Kapferer, A., Nilsson, M., Martínez-Bartolomé, S., Albar, J. P., Echevarría-Zomeño, S., Martínez-Gomariz, M., Joets, J., Binz, P. -A., Taylor, C. F., Dowsey, A., and Jones, A. R. (2010) Guidelines for reporting the use of gel image informatics in proteomics, Nature Biotechnology. Nature Publishing Group 28, 655–656.
Domann, P. J., Akashi, S., Barbas, C., Huang, L., Lau, W., Legido-Quigley, C., McClean, S., Neusüß, C., Perrett, D., Quaglia, M., Rapp, E., Smallshaw, L., Smith, N. W., Smyth, W. F., and Taylor, C. F. (2010) Guidelines for reporting the use of capillary electrophoresis in proteomics, Nature Biotechnology 28, 654–655.
WHO. (2009) HANDBOOK GOOD LABORATORY PRACTICE (GLP) (Kioy, D., Long, D., Bhalla, S., and Seiler, J., Eds.).
Schulz, K. F., Altman, D. G., and Moher, D. (2010) CONSORT 2010 statement: updated guidelines for reporting parallel group randomised trials., BMJ (Clinical research ed.) 340, c332.
Andrianantoandro, E., Basu, S., Karig, D. K., and Weiss, R. (2006) Synthetic biology: new engineering rules for an emerging discipline, Molecular Systems Biology 1–14.
Knight, T. (2007) BBF RFC 10: Draft Standard for Biobrick Biological Parts, http://dspace.mit.edu/handle/1721.1/45138.
Knight, T. (2003) Idempotent Vector Design for Standard Assembly of Biobricks, http://dspace.mit.edu/handle/1721.1/21168 1–11.
Müller, K. M., Arndt, K. M., IGEM_Freiburg, 2007, and Grünberg, R. (2008) BBF RFC 25: Fusion Protein (Freiburg) BioBrick assembly standard, http://dspace.mit.edu/handle/1721.1/45140.
Hwang, C.-S., Shemorry, A., Auerbach, D., and Varshavsky, A. (2010) The N-end rule pathway is mediated by a complex of the RING-type Ubr1 and HECT-type Ufd4 ubiquitin ligases., Nature cell biology. Nature Publishing Group 12, 1177–85.
Hecky, J., and Müller, K. M. (2005) Structural perturbation and compensation by directed evolution at physiological temperature leads to thermostabilization of beta-lactamase., Biochemistry 44, 12640–54.
Peccoud, J., Anderson, J. C., Chandran, D., Densmore, D., Galdzicki, M., Lux, M. W., Rodriguez, C. A., Stan, G.-bart, and Sauro, H. M. (2011) Essential information for synthetic DNA sequences., Nature biotechnology. Nature Publishing Group 29, 22; discussion 22–3.
Canton, B., Labno, A., and Endy, D. (2008) Refinement and standardization of synthetic biological parts and devices., Nature Biotechnology 26, 787–93.
Arkin, A. (2008) Setting the standard in synthetic biology., Nature biotechnology 26, 771–4.
Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L. J., Eilbeck, K., Ireland, A., Mungall, C. J., Leontis, N., Rocca-Serra, P., Ruttenberg, A., Sansone, S.-A., Scheuermann, R. H., Shah, N., Whetzel, P. L., and Lewis, S. (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration., Nature biotechnology 25, 1251–5.
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., Harris, M. A., Hill, D. P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J. C., Richardson, J. E., Ringwald, M., Rubin, G. M., and Sherlock, G. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium., Nature genetics 25, 25–9.
Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., Kitano, H., Arkin, A. P., Bornstein, B. J., Bray, D., Cornish-Bowden, A., Cuellar, A. A., Dronov, S., Gilles, E. D., Ginkel, M., Gor, V., Goryanin, I. I., Hedley, W. J., Hodgman, T. C., Hofmeyr, J.-H., Hunter, P. J., Juty, N. S., Kasberger, J. L., Kremling, A., Kummer, U., Le Novère, N., Loew, L. M., Lucio, D., Mendes, P., Minch, E., Mjolsness, E. D., Nakayama, Y., Nelson, M. R., Nielsen, P. F., Sakurada, T., Schaff, J. C., Shapiro, B. E., Shimizu, T. S., Spence, H. D., Stelling, J., Takahashi, K., Tomita, M., Wagner, J., and Wang, J. (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models., Bioinformatics (Oxford, England) 19, 524–31.
Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D Eustachio, P., Schaefer, C., Luciano, J., Schacherer, F., Martinez-Flores, I., Hu, Z., Jimenez-Jacinto, V., Joshi-Tope, G., Kandasamy, K., Lopez-Fuentes, A. C., Mi, H., Pichler, E., Rodchenkov, I., Splendiani, A., Tkachev, S., Zucker, J., Gopinath, G., Rajasimha, H., Ramakrishnan, R., Shah, I., Syed, M., Anwar, N., Babur, Ö., Blinov, M., Brauner, E., Corwin, D., Donaldson, S., Gibbons, F., Goldberg, R., Hornbeck, P., Luna, A., Murray-Rust, P., Neumann, E., Reubenacker, O., Samwald, M., Iersel, M. van, Wimalaratne, S., Allen, K., Braun, B., Whirl-Carrillo, M., Cheung, K.-H., Dahlquist, K., Finney, A., Gillespie, M., Glass, E., Gong, L., Haw, R., Honig, M., Hubaut, O., Kane, D., Krupa, S., Kutmon, M., Leonard, J., Marks, D., Merberg, D., Petri, V., Pico, A., Ravenscroft, D., Ren, L., Shah, N., Sunshine, M., Tang, R., Whaley, R., Letovksy, S., Buetow, K. H., Rzhetsky, A., Schachter, V., Sobral, B. S., Dogrusoz, U., McWeeney, S., Aladjem, M., Birney, E., Collado-Vides, J., Goto, S., Hucka, M., Novère, N. L., Maltsev, N., Pandey, A., Thomas, P., Wingender, E., Karp, P. D., Sander, C., and Bader, G. D. (2010) The BioPAX community standard for pathway data sharing, Nature Biotechnology 28, 935–942.
Strömbäck, L., Hall, D., and Lambrix, P. (2007) A review of standards for data exchange within systems biology., Proteomics 7, 857–67.
Church, G. M. (2005) From systems biology to synthetic biology., Molecular systems biology 1, 2005.0032.
Macdonald, J. T., Barnes, C., Kitney, R. I., Freemont, P. S., and Stan, G.-B. V. (2011) Computational design approaches and tools for synthetic biology., Integrative biology : quantitative biosciences from nano to macro 97–108.
Matsuoka, Y., Ghosh, S., and Kitano, H. (2009) Consistent design schematics for biological systems: standardization of representation in biological engineering., Journal of the Royal Society, Interface/the Royal Society 6 Suppl 4, S393-404.
Grünberg, R. (2009) BBF RFC 30: Draft of an RDF-based framework for the exchange and integration of Synthetic Biology data Relation to other BBF RFCs, http://hdl.handle.net/1721.1/45143 1–13.
Galdzicki, M., Rodriguez, C., Chandran, D., Sauro, H. M., and Gennari, J. H. (2011) Standard Biological Parts Knowledgebase, PLoS ONE (Schönbach, C., Ed.) 6, e17005.
Rai, A., and Boyle, J. (2007) Synthetic biology: caught between property rights, the public domain, and the commons., PLoS biology 5, e58.
Endy, D., and Grewal, D. (2010) The BioBrick Public Agreement DRAFT Version 1a, http://dspace.mit.edu/handle/1721.1/50999 1–8.
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Müller, K.M., Arndt, K.M. (2012). Standardization in Synthetic Biology. In: Weber, W., Fussenegger, M. (eds) Synthetic Gene Networks. Methods in Molecular Biology, vol 813. Humana Press. https://doi.org/10.1007/978-1-61779-412-4_2
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DOI: https://doi.org/10.1007/978-1-61779-412-4_2
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