CiteULike: Synthetic_Biology_Literature's library http://www.citeulike.org/user/Synthetic_Biology_Literature CiteULike.org en-gb Copyright © 2004-2011 citeulike.org http://www.citeulike.org/user/Synthetic_Biology_Literature/article/2338471 <i>J Biotechnol, Vol. 130, No. 4. (15 July 2007), pp. 329-345, doi:10.1016/j.jbiotec.2007.05.014</i><br /><br />With the recent development of a wide range of inducible mammalian transgene control systems it has now become possible to create functional synthetic gene networks by linking and connecting systems into various configurations. The past 5 years has thus seen the design and construction of the first synthetic mammalian gene regulatory networks. These networks have built upon pioneering advances in prokaryotic synthetic networks and possess an impressive range of functionalities that will some day enable the engineering of sophisticated inter- and intra-cellular functions to become a reality. At a relatively simple level, the modular linking of transcriptional components has enabled the creation of genetic networks that are strongly analogous to the architectural design and functionality of electronic circuits. Thus, by combining components in different serial or parallel configurations it is possible to produce networks that follow strict logic in integrating multiple independent signals (logic gates and transcriptional cascades) or which temporally modify input signals (time-delay circuits). Progressing in terms of sophistication, synthetic transcriptional networks have also been constructed which emulate naturally occurring genetic properties, such as bistability or dynamic instability. Toggle switches which possess &#34;memory&#34; so as to remember transient administered inputs, hysteric switches which are resistant to stochastic fluctuations in inputs, and oscillatory networks which produce regularly timed expression outputs, are all examples of networks that have been constructed using such properties. Initial steps have also been made in designing the above networks to respond not only to exogenous signals, but also endogenous signals that may be associated with aberrant cellular function or physiology thereby providing a means for tightly controlled gene therapy applications. Moving beyond pure transcriptional control, synthetic networks have also been created which utilize phenomena, such as post-transcriptional silencing, translational control, or inter-cellular signaling to produce novel network-based control both within and between cells. It is envisaged in the not-too-distant future that these networks will provide the basis for highly sophisticated genetic manipulations in biopharmaceutical manufacturing, gene therapy and tissue engineering applications.<br /><i>D Greber, M Fussenegger</i> Mammalian synthetic biology: engineering of sophisticated gene networks. D Greber M Fussenegger doi:10.1016/j.jbiotec.2007.05.014 J Biotechnol, Vol. 130, No. 4. (15 July 2007), pp. 329-345, doi:10.1016/j.jbiotec.2007.05.014 2009-02-07T16:02:18-00:00 2007 J Biotechnol 0168-1656 130 4 329 345 genetic_networks mammalian review http://www.citeulike.org/user/Synthetic_Biology_Literature/article/4022024 <i>Handbook of experimental pharmacology, No. 178. (2007), pp. 73-105, doi:10.1007/978-3-540-35109-2_4</i><br /><br />Controlling gene activity in space and time represents a cornerstone technology in gene and cell therapeutic applications, bioengineering, drug discovery as well as fundamental and applied research. This chapter provides a comprehensive overview of the different approaches for regulating gene activity and product protein formation at different biosynthetic levels, from genomic rearrangements over transcription and translation control to strategies for engineering inducible secretion and protein activity with a focus on the development during the past 2 years. Recent advances in designing second-generation gene switches, based on novel inducer administration routes (gas phase) as well as on the combination of heterologous switches with endogenous signals, will be complemented by an overview of the emerging field of mammalian synthetic biology, which enables the design of complex synthetic and semisynthetic gene networks. This article will conclude with an overview of how the different gene switches have been applied in gene therapy studies, bioengineering and drug discovery.<br /><i>W Weber, M Fussenegger</i> Novel gene switches. W Weber M Fussenegger doi:10.1007/978-3-540-35109-2_4 Handbook of experimental pharmacology, No. 178. (2007), pp. 73-105, doi:10.1007/978-3-540-35109-2_4 2009-02-07T16:01:21-00:00 2007 Handbook of experimental pharmacology 0171-2004 178 73 105 control gene_expression switch http://www.citeulike.org/user/Synthetic_Biology_Literature/article/4022022 <i>Biotechnology and bioengineering, Vol. 96, No. 6. (15 April 2007), pp. 1155-1166, doi:10.1002/bit.21235</i><br /><br />We describe an efficient inducible gene expression system in HEK.EBNA cells, a well-established cell system for the rapid transient expression of research-tool proteins. The transgene control system of choice is the novel acetaldehyde-inducible regulation (AIR) technology, which has been shown to modulate transgene levels following exposure of cells to acetaldehyde. For application in HEK.EBNA cells, AlcR transactivator plasmids were constructed and co-expressed with the secreted alkaline phosphatase (SEAP) gene under the control of a chimeric mammalian promoter (P(AIR)) for acetaldehyde-regulated expression. Several highly inducible transactivator cell lines were established. Adjustable transgene induction by gaseous acetaldehyde led to high induction levels and tight repression in transient expression trials and in stably transfected HEK.EBNA cell lines. Thus, the AIR technology can be used for inducible expression of any desired recombinant protein in HEK.EBNA cells. A possible application for inducible gene expression is a controlled proliferation strategy. Clonal HEK.EBNA cell lines, expressing the fungal transactivator protein AlcR, were engineered for gas-adjustable expression of the cell-cycle regulator p27(Kip1). We show that expression of p27(Kip1) via transient or stable transfection led to a G1-phase specific growth arrest of HEK.EBNA cells. Furthermore, production pools engineered for gas-adjustable expression of p27(Kip1) and constitutive expression of SEAP showed enhanced productive capacity.<br /><i>NS Werner, W Weber, M Fussenegger, S Geisse</i> A gas-inducible expression system in HEK.EBNA cells applied to controlled proliferation studies by expression of p27(Kip1). NS Werner W Weber M Fussenegger S Geisse doi:10.1002/bit.21235 Biotechnology and bioengineering, Vol. 96, No. 6. (15 April 2007), pp. 1155-1166, doi:10.1002/bit.21235 2009-02-07T15:59:18-00:00 2007 Biotechnology and bioengineering 0006-3592 96 6 1155 1166 gas_inducible mammalian promoter http://www.citeulike.org/user/Synthetic_Biology_Literature/article/4007538 <i>Nucleic Acids Research, Vol. 37, No. 4. (01 March 2009), pp. e33-e33, doi:10.1093/nar/gkp014</i><br /><br />Electric signal processing has evolved to manage rapid information transfer in neuronal networks and muscular contraction in multicellular organisms and controls the most sophisticated man-built devices. Using a synthetic biology approach to assemble electronic parts with genetic control units engineered into mammalian cells, we designed an electric power-adjustable transcription control circuit able to integrate the intensity of a direct current over time, to translate the amplitude or frequency of an alternating current into an adjustable genetic readout or to modulate the beating frequency of primary heart cells. Successful miniaturization of the electro-genetic devices may pave the way for the design of novel hybrid electro-genetic implants assembled from electronic and genetic parts. 10.1093/nar/gkp014<br /><i>Wilfried Weber, Stefan Luzi, Maria Karlsson, Carlota Sanchez-Bustamante, Urs Frey, Andreas Hierlemann, Martin Fussenegger</i> A synthetic mammalian electro-genetic transcription circuit Wilfried Weber Stefan Luzi Maria Karlsson Carlota Sanchez-Bustamante Urs Frey Andreas Hierlemann Martin Fussenegger doi:10.1093/nar/gkp014 Nucleic Acids Research, Vol. 37, No. 4. (01 March 2009), pp. e33-e33, doi:10.1093/nar/gkp014 2009-02-07T15:56:14-00:00 2009 Nucleic Acids Research 1362-4962 37 4 e33 e33 Oxford University Press electrochemical interface mammalian promoter http://www.citeulike.org/user/Synthetic_Biology_Literature/article/3995823 <i>Nucl. Acids Res., Vol. 37, No. 5. (1 April 2009), e38, doi:10.1093/nar/gkp022</i><br /><br />Synthetic biology aims to the design or redesign of biological systems. In particular, one possible goal could be the rewiring of the transcription regulation network by exchanging the endogenous promoters. To achieve this objective, we have adapted current methods to the inference of a model based on ordinary differential equations that is able to predict the network response after a major change in its topology. Our procedure utilizes microarray data for training. We have experimentally validated our inferred global regulatory model in Escherichia coli by predicting transcriptomic profiles under new perturbations. We have also tested our methodology in silico by providing accurate predictions of the underlying networks from expression data generated with artificial genomes. In addition, we have shown the predictive power of our methodology by obtaining the gene profile in experimental redesigns of the E. coli genome, where rewiring the transcriptional network by means of knockouts of master regulators or by upregulating transcription factors controlled by different promoters. Our approach is compatible with most network inference methods, allowing to explore computationally future genome-wide redesign experiments in synthetic biology. 10.1093/nar/gkp022<br /><i>Javier Carrera, Guillermo Rodrigo, Alfonso Jaramillo</i> Model-based redesign of global transcription regulation Javier Carrera Guillermo Rodrigo Alfonso Jaramillo doi:10.1093/nar/gkp022 Nucl. Acids Res., Vol. 37, No. 5. (1 April 2009), e38, doi:10.1093/nar/gkp022 2009-02-02T13:20:35-00:00 2009 Nucl. 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Bor Chen Wei Wu Math Biosci (Nov 2007) 2009-02-02T11:06:12-00:00 2007 Math Biosci applications http://www.citeulike.org/user/Synthetic_Biology_Literature/article/3994085 <i>Science., Vol. 314 (Oct 2006), pp. 300-304, doi:10.1126/science.1130716</i><br /><i>Narasimhan Sudarsan, Ming Hammond, Kirsten Block, Rudiger Welz, Jeffrey Barrick, Adam Roth, Ronald Breaker</i> Tandem Riboswitch Architectures Exhibit Complex Gene Control Functions Narasimhan Sudarsan Ming Hammond Kirsten Block Rudiger Welz Jeffrey Barrick Adam Roth Ronald Breaker doi:10.1126/science.1130716 Science., Vol. 314 (Oct 2006), pp. 300-304, doi:10.1126/science.1130716 2009-02-02T11:06:12-00:00 2006 Science. 314 300 304 applications http://www.citeulike.org/user/Synthetic_Biology_Literature/article/3994084 <i>Nature Biotechnology, Vol. advanced online publication (May 2007), pp. 795-801</i><br /><i>Keller Rinaudo, Leonidas Bleris, Rohan Maddamsetti, Sairam Subramanian, Ron Weiss, Yaakov Benenson</i> A universal RNAi-based logic evaluator that operates in mammalian cells Keller Rinaudo Leonidas Bleris Rohan Maddamsetti Sairam Subramanian Ron Weiss Yaakov Benenson Nature Biotechnology, Vol. advanced online publication (May 2007), pp. 795-801 2009-02-02T11:06:12-00:00 2007 Nature Biotechnology advanced online publication 795 801 applications http://www.citeulike.org/user/Synthetic_Biology_Literature/article/3994083 <i>Science, Vol. 319 (Mar 2008), pp. 1539-1543, doi:10.1126/science.1151153</i><br /><i>Caleb Bashor, Noah Helman, Shude Yan, Wendell Lim</i> Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics Caleb Bashor Noah Helman Shude Yan Wendell Lim doi:10.1126/science.1151153 Science, Vol. 319 (Mar 2008), pp. 1539-1543, doi:10.1126/science.1151153 2009-02-02T11:06:11-00:00 2008 Science 319 1539 1543 protein scaffolding http://www.citeulike.org/user/Synthetic_Biology_Literature/article/3994082 <i>Nat Biotech, Vol. 23 (Nov 2005), pp. 1374-1376, doi:10.1038/nbt1105-1374</i><br /><i>Adam Margolin, Milan Stojanovic</i> Boolean calculations made easy (for ribozymes) Adam Margolin Milan Stojanovic doi:10.1038/nbt1105-1374 Nat Biotech, Vol. 23 (Nov 2005), pp. 1374-1376, doi:10.1038/nbt1105-1374 2009-02-02T11:06:11-00:00 2005 Nat Biotech 23 1374 1376 applications http://www.citeulike.org/user/Synthetic_Biology_Literature/article/3994081 <i>Nature biotechnology., Vol. 23 (Oct 2005), pp. 1424-1433, doi:10.1038/nbt1155</i><br /><i>Robert Penchovsky, Ronald Breaker</i> Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes Robert Penchovsky Ronald Breaker doi:10.1038/nbt1155 Nature biotechnology., Vol. 23 (Oct 2005), pp. 1424-1433, doi:10.1038/nbt1155 2009-02-02T11:06:11-00:00 2005 Nature biotechnology. 23 1424 1433 applications http://www.citeulike.org/user/Synthetic_Biology_Literature/article/3994080 <i>Chemical Reviews, Vol. 107 (xx 2007), doi:10.1021/cr0306743</i> Functional Aptamers and Aptazymes in Biotechnology, Diagnostics, and Therapy doi:10.1021/cr0306743 Chemical Reviews, Vol. 107 (xx 2007), doi:10.1021/cr0306743 2009-02-02T11:06:11-00:00 2007 Chemical Reviews 107 3715 applications http://www.citeulike.org/user/Synthetic_Biology_Literature/article/3994078 <i>Nature, Vol. 456 (Oct 2008), pp. 516-519, doi:10.1038/nature07389</i><br /><i>Jesse Stricker, Scott Cookson, Matthew Bennett, William Mather, Lev Tsimring, Jeff Hasty</i> A fast, robust and tunable synthetic gene oscillator Jesse Stricker Scott Cookson Matthew Bennett William Mather Lev Tsimring Jeff Hasty doi:10.1038/nature07389 Nature, Vol. 456 (Oct 2008), pp. 516-519, doi:10.1038/nature07389 2009-02-02T11:06:11-00:00 2008 Nature 456 516 519 applications http://www.citeulike.org/user/Synthetic_Biology_Literature/article/3993995 <i>Mol Syst Biol, Vol. 2 (Aug 2006)</i><br /><i>Anthony Forster, George Church</i> Towards synthesis of a minimal cell Anthony Forster George Church Mol Syst Biol, Vol. 2 (Aug 2006) 2009-02-02T10:55:49-00:00 2006 Mol Syst Biol 2 synthetic_biology http://www.citeulike.org/user/Synthetic_Biology_Literature/article/3993994 <i>Mol Syst Biol, Vol. 1 (Mar 2005), pp. 1-1</i><br /><i>George Church</i> From systems biology to synthetic biology George Church Mol Syst Biol, Vol. 1 (Mar 2005), pp. 1-1 2009-02-02T10:55:49-00:00 2005 Mol Syst Biol 1 1 1 synthetic_biology http://www.citeulike.org/user/Synthetic_Biology_Literature/article/3993993 <i>Journal of molecular biology., Vol. 359 (Jun 2006), pp. 1107-1124</i><br /><i>Yusuke Maeda, Masaki Sano</i> Regulatory dynamics of synthetic gene networks with positive feedback. 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William Blake Farren Isaacs Trends in biotechnology., Vol. 22 (Jul 2004), pp. 321-324 2009-02-02T10:55:49-00:00 2004 Trends in biotechnology. 22 321 324 synthetic_biology http://www.citeulike.org/user/Synthetic_Biology_Literature/article/3993981 <i>Engineering Bacteria for Drug Production</i><br /><i>Jay Keasling</i> Engineering Bacteria for Drug Production Jay Keasling Engineering Bacteria for Drug Production 2009-02-02T10:55:49-00:00 Engineering Bacteria for Drug Production synthetic_biology http://www.citeulike.org/user/Synthetic_Biology_Literature/article/3993980 <i>Current opinion in biotechnology., Vol. 16 (Aug 2005), pp. 476-483</i><br /><i>Ryan Mcdaniel, Ron Weiss</i> Advances in synthetic biology: on the path from prototypes to applications. Ryan Mcdaniel Ron Weiss Current opinion in biotechnology., Vol. 16 (Aug 2005), pp. 476-483 2009-02-02T10:55:49-00:00 2005 Current opinion in biotechnology. 16 476 483 synthetic_biology http://www.citeulike.org/user/Synthetic_Biology_Literature/article/3993979 <i>Chaos: An Interdisciplinary Journal of Nonlinear Science, Vol. 16 (xx 2006), pp. 026101-026101</i><br /><i>Peter Swain, Andre Longtin</i> Noise in genetic and neural networks Peter Swain Andre Longtin Chaos: An Interdisciplinary Journal of Nonlinear Science, Vol. 16 (xx 2006), pp. 026101-026101 2009-02-02T10:55:49-00:00 2006 Chaos: An Interdisciplinary Journal of Nonlinear Science 16 026101 026101 genetic network synthetic_biology http://www.citeulike.org/user/Synthetic_Biology_Literature/article/3993978 <i>BioSocieties. Cambridge University Press (Jun 2006), pp. 137-158</i><br /><i>Alain Pottage</i> Too Much Ownership: Bio-prospecting in the Age of Synthetic Biology Alain Pottage BioSocieties. 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