The second wave of synthetic biology: from modules to systems (original) (raw)

• Cases, I. & de Lorenzo, V. Genetically modified organisms for the environment: stories of success and failure and what we have learned from them. Int. Microbiol. 8, 213–222 (2005).
  CAS PubMed Google Scholar
• Antunes, M. S. et al. A synthetic de-greening gene circuit provides a reporting system that is remotely detectable and has a re-set capacity. Plant Biotechnol. J. 4, 605–622 (2006).
  Article CAS PubMed Google Scholar
• Bowen, T. A., Zdunek, J. K. & Medford, J. I. Cultivating plant synthetic biology from systems biology. New Phytol. 179, 583–587 (2008).
  Article PubMed Google Scholar
• Savage, D. F., Way, J. & Silver, P. A. Defossiling fuel: how synthetic biology can transform biofuel production. ACS Chem. Biol. 3, 13–16 (2008).
  Article CAS PubMed Google Scholar
• Anderson, J. C., Clarke, E. J., Arkin, A. P. & Voigt, C. A. Environmentally controlled invasion of cancer cells by engineered bacteria. J. Mol. Biol. 355, 619–627 (2006). Introduces the novel idea of engineering bacteria that integrate information from multiple sources to determine whether mammalian cells are cancerous and, if so, invade and destroy these cells.
  Article CAS PubMed Google Scholar
• Gardner, T. S., Cantor, C. R. & Collins, J. J. Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339–342 (2000). A seminal paper that helped to establish the field of synthetic biology, demonstrating how a bistable synthetic gene network can be constructed by connecting two mutually inhibitory transcriptional repressors.
  Article CAS PubMed Google Scholar
• Kramer, B. P. et al. An engineered epigenetic transgene switch in mammalian cells. Nature Biotech. 22, 867–870 (2004).
  Article CAS Google Scholar
• Atkinson, M. R., Savageau, M. A., Myers, J. T. & Ninfa, A. J. Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 113, 597–607 (2003).
  Article CAS PubMed Google Scholar
• Ham, T. S., Lee, S. K., Keasling, J. D. & Arkin, A. P. Design and construction of a double inversion recombination switch for heritable sequential genetic memory. PLoS ONE 3, e2815 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Hooshangi, S., Thiberge, S. & Weiss, R. Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. Proc. Natl Acad. Sci. USA 102, 3581–3586 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Basu, S., Mehreja, R., Thiberge, S., Chen, M. T. & Weiss, R. Spatiotemporal control of gene expression with pulse-generating networks. Proc. Natl Acad. Sci. USA 101, 6355–6360 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Weber, W. et al. A synthetic time-delay circuit in mammalian cells and mice. Proc. Natl Acad. Sci. USA 104, 2643–2648 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Weber, W., Kramer, B. P. & Fussenegger, M. A genetic time-delay circuitry in mammalian cells. Biotechnol. Bioeng. 98, 894–902 (2007).
  Article CAS PubMed Google Scholar
• Bashor, C. J., Helman, N. C., Yan, S. & Lim, W. A. Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics. Science 319, 1539–1543 (2008). Fused a Leu-zipper domain to the Ste5 scaffold protein and connected positive- and negative-feedback elements to this pathway. This shows how synthetic signalling pathways can be engineered using new phosphorylation interactions.
  Article CAS PubMed Google Scholar
• Goh, K. I., Kahng, B. & Cho, K. H. Sustained oscillations in extended genetic oscillatory systems. Biophys. J. 94, 4270–4276 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Stricker, J. et al. A fast, robust and tunable synthetic gene oscillator. Nature 456, 516–519 (2008). A recent publication demonstrating how a relaxation oscillator can be built by connecting a transcriptional activator with a transcriptional repressor. Fine-tuning of oscillatory dynamics was achieved with external application of inducers.
  Article CAS PubMed PubMed Central Google Scholar
• Swinburne, I. A., Miguez, D. G., Landgraf, D. & Silver, P. A. Intron length increases oscillatory periods of gene expression in animal cells. Genes Dev. 22, 2342–2346 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Tigges, M., Marquez-Lago, T. T., Stelling, J. & Fussenegger, M. A tunable synthetic mammalian oscillator. Nature 457, 309–312 (2009).
  Article CAS PubMed Google Scholar
• Basu, S., Gerchman, Y., Collins, C. H., Arnold, F. H. & Weiss, R. A synthetic multicellular system for programmed pattern formation. Nature 434, 1130–1134 (2005). An engineered cell–cell communication using AHL was coupled with several variants of a synthetic signal processing network to produce a multicellular system that is capable of forming a range of spatial patterns.
  Article CAS PubMed Google Scholar
• Win, M. N. & Smolke, C. D. Higher-order cellular information processing with synthetic RNA devices. Science 322, 456–460 (2008). Novel RNA structures were constructed by fusing various sensor regions (aptamers) to catalytic regions (ribozymes). These RNA devices implement several important two-input logic functions that regulate protein expression at the translational level based on small molecule inputs.
  Article CAS PubMed PubMed Central Google Scholar
• Rinaudo, K. et al. A universal RNAi-based logic evaluator that operates in mammalian cells. Nature Biotech. 25, 795–801 (2007). Implements RNA interference-based logic circuits that regulate protein expression based on up to five simultaneous endogenous molecular inputs. Any logic formula or statement can be represented with the scheme presented in this paper.
  Article CAS Google Scholar
• Haseltine, E. L. & Arnold, F. H. Synthetic gene circuits: design with directed evolution. Annu. Rev. Biophys. Biomol. Struct. 36, 1–19 (2007).
  Article CAS PubMed Google Scholar
• Nomura, Y. & Yokobayashi, Y. Dual selection of a genetic switch by a single selection marker. Biosystems 90, 115–120 (2007).
  Article CAS PubMed Google Scholar
• Yokobayashi, Y., Weiss, R. & Arnold, F. H. Directed evolution of a genetic circuit. Proc. Natl Acad. Sci. USA 99, 16587–16591 (2002). Shows the use of directed evolution to optimize the behaviour of an engineered transcriptional cascade to meet desired input–output specifications.
  Article CAS PubMed PubMed Central Google Scholar
• Basu, S. & Weiss, R. in First Workshop on Non-Silicon Computation (NSC-1) 54–61 (Cambridge, 2002).
  Google Scholar
• Shetty, R. P., Endy, D. & Knight, T. F. Jr. Engineering BioBrick vectors from BioBrick parts. J. Biol. Eng. 2, 5 (2008).
  Article CAS Google Scholar
• Canton, B., Labno, A. & Endy, D. Refinement and standardization of synthetic biological parts and devices. Nature Biotech. 26, 787–793 (2008). Careful and thorough characterization of cell–cell communication BioBricks from the Registry of Standard Biological Parts, showing the type of information that is useful for describing the behaviour of parts.
  Article CAS Google Scholar
• Murphy, K. F., Balazsi, G. & Collins, J. J. Combinatorial promoter design for engineering noisy gene expression. Proc. Natl Acad. Sci. USA 104, 12726–12731 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Bronson, J. E., Mazur, W. W. & Cornish, V. W. Transcription factor logic using chemical complementation. Mol. Biosyst. 4, 56–58 (2008).
  Article CAS PubMed Google Scholar
• Ham, T. S., Lee, S. K., Keasling, J. D. & Arkin, A. P. A tightly regulated inducible expression system utilizing the fim inversion recombination switch. Biotechnol. Bioeng. 94, 1–4 (2006).
  Article CAS PubMed Google Scholar
• Win, M. N. & Smolke, C. D. A modular and extensible RNA-based gene-regulatory platform for engineering cellular function. Proc. Natl Acad. Sci. USA 104, 14283–14288 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Blount, K. F. & Breaker, R. R. Riboswitches as antibacterial drug targets. Nature Biotech. 24, 1558–1564 (2006).
  Article CAS Google Scholar
• Yoshida, W. & Yokobayashi, Y. Photonic Boolean logic gates based on DNA aptamers. Chem. Commun. (Camb.), 2, 195–197 (2007).
  Article Google Scholar
• Nomura, Y. & Yokobayashi, Y. Reengineering a natural riboswitch by dual genetic selection. J. Am. Chem. Soc. 129, 13814–13815 (2007).
  Article CAS PubMed Google Scholar
• Isaacs, F. J. et al. Engineered riboregulators enable post-transcriptional control of gene expression. Nature Biotech. 22, 841–847 (2004).
  Article CAS Google Scholar
• Deans, T. L., Cantor, C. R. & Collins, J. J. A tunable genetic switch based on RNAi and repressor proteins for regulating gene expression in mammalian cells. Cell 130, 363–372 (2007).
  Article CAS PubMed Google Scholar
• Rackham, O. & Chin, J. W. Cellular logic with orthogonal ribosomes. J. Am. Chem. Soc. 127, 17584–17585 (2005).
  Article CAS PubMed Google Scholar
• Rajendran, M. & Ellington, A. D. Selection of fluorescent aptamer beacons that light up in the presence of zinc. Anal. Bioanal. Chem. 390, 1067–1075 (2008).
  Article CAS Google Scholar
• Wollacott, A. M., Zanghellini, A., Murphy, P. & Baker, D. Prediction of structures of multidomain proteins from structures of the individual domains. Protein Sci. 16, 165–175 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Andre, I., Bradley, P., Wang, C. & Baker, D. Prediction of the structure of symmetrical protein assemblies. Proc. Natl Acad. Sci. USA 104, 17656–17661 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Yarov-Yarovoy, V., Schonbrun, J. & Baker, D. Multipass membrane protein structure prediction using Rosetta. Proteins 62, 1010–1025 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Dantas, G. et al. Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution. J. Mol. Biol. 362, 1004–1024 (2006).
  Article CAS PubMed Google Scholar
• Joachimiak, L. A., Kortemme, T., Stoddard, B. L. & Baker, D. Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein–protein interface. J. Mol. Biol. 361, 195–208 (2006).
  Article CAS PubMed Google Scholar
• Meiler, J. & Baker, D. ROSETTALIGAND: protein–small molecule docking with full side-chain flexibility. Proteins 65, 538–548 (2006).
  Article CAS PubMed Google Scholar
• Sood, V. D. & Baker, D. Recapitulation and design of protein binding peptide structures and sequences. J. Mol. Biol. 357, 917–927 (2006).
  Article CAS PubMed Google Scholar
• Filipovska, A. & Rackham, O. Building a parallel metabolism within the cell. ACS Chem. Biol. 3, 51–63 (2008).
  Article CAS PubMed Google Scholar
• Weiss, R. & Knight, T. F. Jr. in DNA6: Sixth International Meeting on DNA Based Computers (eds Condon, A. & Rozenberg, G.) 1–16 (LNCS 2054, Springer, Berlin, 2001).
  Google Scholar
• Bulter, T. et al. Design of artificial cell–cell communication using gene and metabolic networks. Proc. Natl Acad. Sci. USA 101, 2299–2304 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Chen, M. T. & Weiss, R. Artificial cell–cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana. Nature Biotech. 23, 1551–1555 (2005).
  Article CAS Google Scholar
• Wang, W. D., Chen, Z. T., Kang, B. G. & Li, R. Construction of an artificial intercellular communication network using the nitric oxide signaling elements in mammalian cells. Exp. Cell Res. 314, 699–706 (2008).
  Article CAS PubMed Google Scholar
• You, L., Cox, R. S. 3rd, Weiss, R. & Arnold, F. H. Programmed population control by cell–cell communication and regulated killing. Nature 428, 868–871 (2004).
  Article CAS PubMed Google Scholar
• Shou, W., Ram, S. & Vilar, J. M. Synthetic cooperation in engineered yeast populations. Proc. Natl Acad. Sci. USA 104, 1877–1882 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Brenner, K., Karig, D. K., Weiss, R. & Arnold, F. H. Engineered bidirectional communication mediates a consensus in a microbial biofilm consortium. Proc. Natl Acad. Sci. USA 104, 17300–17304 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• May, R. M. Stability and Complexity in Model Ecosystems (Princeton University Press, Princeton, 1974).
  Google Scholar
• Murray, J. D. & ebrary Inc. An Introduction. 3rd edn (Springer, New York; London, 2002).
  Google Scholar
• Renshaw, E. Modelling Biological Populations in Space and Time (Cambridge Univ. Press, Cambridge, 1993).
  Google Scholar
• Balagadde, F. K. et al. A synthetic Escherichia coli predator–prey ecosystem. Mol. Syst. Biol. 4, 187 (2008).
  Article PubMed PubMed Central Google Scholar
• Weber, W., Daoud- El Baba, M. & Fussenegger, M. Synthetic ecosystems based on airborne inter- and intrakingdom communication. Proc. Natl Acad. Sci. USA 104, 10435–10440 (2007). Implements cell–cell communication between mammalian cells and between cells of different organisms, and uses this to construct a range of multicellular systems with different 'rules' for cell survival and proliferation.
  Google Scholar
• Anderson, J. C., Voigt, C. A. & Arkin, A. P. Environmental signal integration by a modular AND gate. Mol. Syst. Biol. 3, 133 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Ajikumar, P. K. et al. Terpenoids: opportunities for biosynthesis of natural product drugs using engineered microorganisms. Mol. Pharm. 5, 167–190 (2008).
  Article CAS PubMed Google Scholar
• Martin, V. J., Pitera, D. J., Withers, S. T., Newman, J. D. & Keasling, J. D. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nature Biotech. 21, 796–802 (2003).
  Article CAS Google Scholar
• Hale, V., Keasling, J. D., Renninger, N. & Diagana, T. T. Microbially derived artemisinin: a biotechnology solution to the global problem of access to affordable antimalarial drugs. Am. J. Trop. Med. Hyg. 77, 198–202 (2007).
  Article PubMed Google Scholar
• Ro, D. K. et al. Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 440, 940–943 (2006). Shows that yeast can be engineered with a plant metabolic pathway to efficiently produce a drug precursor that is difficult and expensive to obtain using traditional methods.
  Article CAS PubMed Google Scholar
• Murtas, G. Question 7: construction of a semi-synthetic minimal cell: a model for early living cells. Orig. Life Evol. Biosph. 37, 419–422 (2007).
  Article CAS PubMed Google Scholar
• Bagh, S. et al. Plasmid-borne prokaryotic gene expression: sources of variability and quantitative system characterization. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 77, 021919 (2008).
  Article CAS PubMed Google Scholar
• Rosenfeld, N., Young, J. W., Alon, U., Swain, P. S. & Elowitz, M. B. Gene regulation at the single-cell level. Science 307, 1962–1965 (2005). Introduces the notion of intrinsic and extrinsic noise as important constituents of protein expression and genetic regulation.
  Article CAS PubMed Google Scholar
• Blake, W. J., Kærn, M. Cantor, C. R. & Collins, J. J. Noise in eukaryotic gene expression. Nature 422, 633–637 (2003).
  Article CAS PubMed Google Scholar
• Ozbudak, E. M., Thattai, M., Lim, H. N., Shraiman, B. I. & Van Oudenaarden, A. Multistability in the lactose utilization network of Escherichia coli. Nature 427, 737–740 (2004).
  Article CAS PubMed Google Scholar
• Becskei, A., Seraphin, B. & Serrano, L. Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion. EMBO J. 20, 2528–2535 (2001).
  Article CAS PubMed PubMed Central Google Scholar
• Dublanche, Y., Michalodimitrakis, K., Kümmerer, N., Foglierini, M. & Serrano, L. Noise in transcription negative feedback loops: simulation and experimental analysis. Mol. Syst. Biol. 2, 41 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Geva-Zatorsky, N. et al. Oscillations and variability in the p53 system. Mol. Syst. Biol. 2, 2006.0033 (2006).
• Nelson, D. E. et al. Oscillations in NF-κB signaling control the dynamics of gene expression. Science 306, 704–708 (2004).
  Article CAS PubMed Google Scholar
• Nelson, D. E., See, V., Nelson, G. & White, M. R. Oscillations in transcription factor dynamics: a new way to control gene expression. Biochem. Soc. Trans. 32, 1090–1092 (2004).
  Article CAS PubMed Google Scholar
• Weinberger, L. S., Burnett, J. C., Toettcher, J. E., Arkin, A. P. & Schaffer, D. V. Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity. Cell 122, 169–182 (2005).
  Article CAS PubMed Google Scholar
• Vilar, J. M., Kueh, H. Y., Barkai, N. & Leibler, S. Mechanisms of noise-resistance in genetic oscillators. Proc. Natl Acad. Sci. USA 99, 5988–5992 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Kininis, M. & Kraus, W. L. A global view of transcriptional regulation by nuclear receptors: gene expression, factor localization, and DNA sequence analysis. Nucl. Recept. Signal. 6, e005 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Costa, F. F. Non-coding RNAs, epigenetics and complexity. Gene 410, 9–17 (2008).
  Article CAS PubMed Google Scholar
• Tang, W. Y. & Ho, S. M. Epigenetic reprogramming and imprinting in origins of disease. Rev. Endocr. Metab. Disord. 8, 173–182 (2007).
  Article PubMed PubMed Central Google Scholar
• Zheng, Y. G., Wu, J., Chen, Z. & Goodman, M. Chemical regulation of epigenetic modifications: opportunities for new cancer therapy. Med. Res. Rev. 28, 645–687 (2008).
  Article CAS PubMed Google Scholar
• Tuttle, L. M., Salis, H., Tomshine, J. & Kaznessis, Y. N. Model-driven designs of an oscillating gene network. Biophys. J. 89, 3873–3883 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Francois, P. & Hakim, V. Design of genetic networks with specified functions by evolution in silico. Proc. Natl Acad. Sci. USA 101, 580–585 (2004). One of the first papers to use a computational algorithm for designing genetic circuitry to achieve desired cellular behaviours.
  Article CAS PubMed PubMed Central Google Scholar
• Salis, H. & Kaznessis, Y. N. Computer-aided design of modular protein devices: Boolean AND gene activation. Phys. Biol. 3, 295–310 (2006).
  Article CAS PubMed Google Scholar
• Sotiropoulos, V. & Kaznessis, Y. N. Synthetic tetracycline-inducible regulatory networks: computer-aided design of dynamic phenotypes. BMC Syst. Biol. 1, 7 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Tomshine, J. & Kaznessis, Y. N. Optimization of a stochastically simulated gene network model via simulated annealing. Biophys. J. 91, 3196–3205 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Dasika, M. S. & Maranas, C. D. OptCircuit: an optimization based method for computational design of genetic circuits. BMC Syst. Biol. 2, 24 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Feng, X. J. et al. Optimizing genetic circuits by global sensitivity analysis. Biophys. J. 87, 2195–2202 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Batt, G., Yordanov, B., Weiss, R. & Belta, C. Robustness analysis and tuning of synthetic gene networks. Bioinformatics 23, 2415–2422 (2007).
  Article CAS PubMed Google Scholar
• Beal, J. & Bachrach, J. in Spatial Computing Workshop, at 2nd IEEE International Conference on Self-Adaptive and Self-Organizing Systems (Venice, Italy, 2008).
  Google Scholar
• Pedersen, M. & Phillips, A. Towards programming languages for genetic engineering of living cells. J. R. Soc. Interface 15 Apr 2009 (doi: 10.1098/rsif.2008.0516.focus).
• Abelson, H. et al. Amorphous computing. Comm. ACM 43, 74–82 (2001).
  Article Google Scholar
• Nagpal, R., Kondacs, A. & Chang, C. in AAAI Spring Symposium on Computational Synthesis: From Basic Building Blocks to High Level Functionality (AAAI, Stanford, 2003).
  Google Scholar
• Rubanyi, G. M. The future of human gene therapy. Mol. Aspects Med. 22, 113–142 (2001).
  Article CAS PubMed Google Scholar
• J. Lohmueller, N. N. et al. Progress toward construction and modelling of a tri-stable toggle switch in E. Coli. IET Synth. Biol. 1, 25–28 (2007).
  Article Google Scholar
• Haynes, K. A. et al. Engineering bacteria to solve the burnt pancake problem. J. Biol. Eng. 2, 8 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Aleksic, J. et al. Development of a novel biosesnsor for the detection of arsenic in drinking water. IET Synth. Biol. 1, 87–90 (2007).
  Article Google Scholar
• Flynn, B. P. et al. Hydrogen detector testing and design using synthetic biology and fluorescence photo analysis. IET Synth. Biol. 1, 83–86 (2007).
  Article Google Scholar
• Hung, A. et al. The 'Cell-See-Us' cellular thermometer. IET Synth. Biol. 1, 79–82 (2007).
  Article Google Scholar
• Quintero, A. et al. A microbial biosensor device for iron detection under UV irradiation. IET Synth. Biol. 1, 71–73 (2007).
  Article Google Scholar
• Glass, J. I. et al. Essential genes of a minimal bacterium. Proc. Natl Acad. Sci. USA 103, 425–430 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Forster, A. C. & Church, G. M. Towards synthesis of a minimal cell. Mol. Syst. Biol. 2, 45 (2006). A thorough perspective on the requirements for creating chemical systems that can replicate and evolve. Describes accomplishments to date and suggests future goals and challenges.
  Article PubMed PubMed Central Google Scholar
• Gibson, D. G. et al. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319, 1215–1220 (2008).
  Article CAS PubMed Google Scholar
• Murtas, G., Kuruma, Y., Bianchini, P., Diaspro, A. & Luisi, P. L. Protein synthesis in liposomes with a minimal set of enzymes. Biochem. Biophys. Res. Commun. 363, 12–17 (2007).
  Article CAS PubMed Google Scholar
• Rasmussen, S. et al. Evolution: transitions from nonliving to living matter. Science 303, 963–965 (2004).
  Article CAS PubMed Google Scholar
• Noireaux, V. & Libchaber, A. A vesicle bioreactor as a step toward an artificial cell assembly. Proc. Natl Acad. Sci. USA 101, 17669–17674 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Noireaux, V., Bar-Ziv, R., Godefroy, J., Salman, H. & Libchaber, A. Toward an artificial cell based on gene expression in vesicles. Phys. Biol. 2, P1–P8 (2005).
  Article CAS PubMed Google Scholar
• Mansy, S. S. et al. Template-directed synthesis of a genetic polymer in a model protocell. Nature 454, 122–125 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Fiordemondo, D. & Stano, P. Lecithin-based water-in-oil compartments as dividing bioreactors. ChemBioChem 8, 1965–1973 (2007).
  Article CAS PubMed Google Scholar
• Kuruma, Y. Question 7: biosynthesis of phosphatidic acid in liposome compartments — toward the self-reproduction of minimal cells. Orig. Life Evol. Biosph. 37, 409–413 (2007).
  Article CAS PubMed Google Scholar
• Luisi, P. L. Chemical aspects of synthetic biology. Chem. Biodivers. 4, 603–621 (2007).
  Article CAS PubMed Google Scholar
• Stano, P. Question 7: new aspects of interactions among vesicles. Orig. Life Evol. Biosph. 37, 439–444 (2007).
  Article PubMed Google Scholar
• Stano, P. & Luisi, P. L. Basic questions about the origins of life: proceedings of the Erice international school of complexity (fourth course). Orig. Life Evol. Biosph. 37, 303–307 (2007).
  Article PubMed Google Scholar
• Ogawa, A. & Maeda, M. An artificial aptazyme-based riboswitch and its cascading system in E. coli. ChemBioChem 9, 206–209 (2008).
  Article CAS PubMed Google Scholar
• Elowitz, M. B. & Leibler, S. A synthetic oscillatory network of transcriptional regulators. Nature 403, 335–338 (2000). Another seminal paper for synthetic biology, experimentally demonstrating the construction of a synthetic genetic oscillator. This paper also fuelled interest in improving our understanding of gene expression noise.
  Article CAS PubMed Google Scholar
• Khlebnikov, A., Skaug, T. & Keasling, J. D. Modulation of gene expression from the arabinose-inducible araBAD promoter. J. Ind. Microbiol. Biotechnol. 29, 34–37 (2002).
  Article CAS PubMed Google Scholar
• Yang, W. & Paschen, W. Conditional gene silencing in mammalian cells mediated by a stress-inducible promoter. Biochem. Biophys. Res. Commun. 365, 521–527 (2008).
  Article CAS PubMed Google Scholar
• Bayer, T. S. & Smolke, C. D. Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nature Biotech. 23, 337–343 (2005).
  Article CAS Google Scholar
• Win, M. N., Klein, J. S. & Smolke, C. D. Codeine-binding RNA aptamers and rapid determination of their binding constants using a direct coupling surface plasmon resonance assay. Nucleic Acids Res. 34, 5670–5682 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Win, M. N. & Smolke, C. D. RNA as a versatile and powerful platform for engineering genetic regulatory tools. Biotechnol. Genet. Eng. Rev. 24, 311–346 (2007).
  Article CAS PubMed Google Scholar
• Saito, H. & Inoue, T. RNA and RNP as new molecular parts in synthetic biology. J. Biotechnol. 132, 1–7 (2007).
  Article CAS PubMed Google Scholar
• Wickiser, J. K., Cheah, M. T., Breaker, R. R. & Crothers, D. M. The kinetics of ligand binding by an adenine-sensing riboswitch. Biochemistry 44, 13404–13414 (2005).
  Article CAS PubMed Google Scholar
• Voigt, C. A. Community collection. Registry of Standard Biological Parts [online] (2008).
  Google Scholar
• Tikole, S. & Sankararamakrishnan, R. Prediction of translation initiation sites in human mRNA sequences with AUG start codon in weak Kozak context: A neural network approach. Biochem. Biophys. Res. Commun. 369, 1166–1168 (2008).
  Article CAS PubMed Google Scholar
• Dai, C. et al. Improved fusion protein expression of EGFP via the mutation of both Kozak and the initial ATG codon. Cell. Mol. Biol. Lett. 12, 362–369 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Rechsteiner, M. & Rogers, S. W. PEST sequences and regulation by proteolysis. Trends Biochem. Sci. 21, 267–271 (1996).
  Article CAS PubMed Google Scholar
• Elowitz, M. B., Levine, A. J., Siggia, E. D. & Swain, P. S. Stochastic gene expression in a single cell. Science 297, 1183–1186 (2002).
  Article CAS PubMed Google Scholar
• Pedraza, J. M. & van Oudenaarden, A. Noise propagation in gene networks. Science 307, 1965–1969 (2005).
  Article CAS PubMed Google Scholar