Team:Heidelberg/Project References


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Introduction

 * "Synthetic Biology. Applying Engineering to Biology". Report of a NEST High-Level Expert Group. European Commission, Directorate-General for Research. Available online at http://www.synbiosafe.eu/uploads///pdf/EU-highlevel-syntheticbiology.pdf


 * Endy, D. Foundations for engineering biology. Nature 438: 449-453 (2005).


 * Endy, D. & Deese I. Adventures in synthetic biology (comic). Nature 438: 449-453 (2005) Available online at nature.com


 * http://www.partsregistry.org/Assembly:Standard_assembly (Website, accessed 10/15/2009)


 * Kelly J. R., Rubin A. J., Davis J. H., Ajo-Franklin C. M., Cumbers J., Czar M. J., de Mora K., Glieberman A. L., Monie D. D. & Endy D. Measuring the activity of BioBrick promoters using an in vivo reference standard. Journal of Biological Engineering 3:4 (2009).


 * Voigt, C. Genetic parts to program bacteria. Current Opinion in Biotechnology 17 (5): 548–557 (2006).


 * Andrianantoandro E., Basu S., Karig D. K. & Weiss R. Synthetic biology: new engineering rules for an emerging discipline. Molecular Systems Biology 2: article number 0028 (2006).


 * http://2009.igem.org/About (Website, accessed 10/15/2009)


 * Goodman, C. Engineering ingenuity at iGEM. Nat Chem Biology 4:13 (2008).


 * Basu, S. A synthetic multicellular system for programmed pattern formation. Nature 434: 1130-1133 (2005).


 * Ellis T., Wang X. & Collins J.J. Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nature Biotechnology 27: 465-471 (2009).


 * Canton, B., Anna Labno A. & Endy D. Refinement and standardization of synthetic biological parts and devices. Nature Biotechnology 26: 787-793 (2009).


 * Weber, W. & Fussenegger, M. Engineering of Synthetic Mammalian Gene Networks. Chemistry and Biology 16: 287-297 (2009).


 * http://openwetware.org/wiki/The_BioBricks_Foundation:Standards/Technical/Formats (Website, accessed 10/19/2009)


 * Ducrest A-L., Amacker M., Lingner J. & Nabholz M. Detection of promoter activity by flow cytometric analysis of GFP reporter expression. Nucleic Acids Res. 30: e65 (2002).


 * Venter M. Synthetic promoters: genetic control through cis engineering. Trends in Plant Science 12: 118-124 (2007). (and the references cited therein)


 * Ogawa R. Construction of strong mammalian promoters by random cis-acting element elongation. Biotechniques 42: 628-632 (2007).


 * Tornoe J. Generation of a synthetic mammalian promoter library by modification of sequences spacing transcription factor binding sites. Gene 297: 21-32 (2002).


 * Dorer D. E. & Nettelbeck D. Targeting cancer by transcriptional control in cancer gene therapy and viral oncolysis. Advanced Drug Delivery Reviews 61: 554-557 (2009).


 * Weber W. & Fussenegger M. The impact of synthetic biology on drug discovery. Drug Discovery Today 14: 956-963 (2009).

Natural Promoters

 * Alberts B., Johnson A., Walter P. & Lewis J. Molecular Biology of the Cell. 4th edition, 2008. Garland Science, Chapter 6, p. 357-359.


 * Clarke N., Arenzana N., Hai T., Minden A. & Prywes R. Epidermal Growth Factor Induction of the c-jun Promoter by a Rac Pathway. Mol Cell Biol 18: 1065–1073 (1998).


 * Hoffman L. M., Garcha K., Karamboulas K., Cowan M. F., Drysdale L. M., Horton W. A. & Underhill T. M. BMP action in skeletogenesis involves attenuation of retinoid signaling. J Cell Biol 174: 101–113 (2006).


 * Castoreno A. B., Wang Y., Stockinger W., Jarzylo L. A., Du H., Pagnon J. C., Shieh E. C. & Nohturfft A. Transcriptional regulation of phagocytosis-induced membrane biogenesis by sterol regulatory element binding proteins. Proc Natl Acad Sci U S A 102: 13129–13134 (2005).


 * Schmidt M., Heimberger T., Gruensfelder P., Schler G. & Hoppe F. Inducible promoters for gene therapy of head and neck cancer: an in vitro study. Eur Arch Otorhinolaryngol 261: 208–215 (2004).


 * Jorgensen E. C. B. & Autrup H. Autoregulation of human CYP1A1 gene promoter activity in HepG2 and MCF-7 cells. Carcinogenesis 17: 435-441 (1996).


 * Schreiber T. D., Köhle C., Buckler F., Schmohl S., Braeuning A., Schmiechen A., Schwarz M. & Münzel P.A. Regulation of CYP1A1 expression by the antioxidant Tert butylhydroquinone. Drug Metabolism And Disposition 43: 1096–1101 (2006).

Synthetic Promoters

 * Alberts B., Johnson A., Walter P. & Lewis J. Molecular Biology of the Cell. 4th edition, 2008. Garland Science, p. 432-453


 * Fussenegger M. & Weber, W. Engineering of Synthetic Mammalian Gene Networks. Chemistry and Biology 16: 287-297 (2009).


 * Gossen M. & Bujard, L. Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. PNAS 89: 5547-5551 (1992).


 * Dorer D. E. & Nettelbeck, D. Targeting cancer by transcriptional control in cancer gene therapy and viral oncolysis. Advanced Drug Delivery Reviews 61: 554-557 (2009).


 * Venter M. Synthetic promoters: genetic control through cis engineering. Trends in Plant Science 12: 118-124 (2007). (and the references cited therein)


 * Rushton P. J., Reinstädler A., Lipka V., Lippok B. & Somssich I. E. Synthetic plant promoters containing defined regulatory elements provide novel insights into pathogen- and wound-induced signalling. Plant Cell 14: 749–762 (2002).


 * Ogawa R. Construction of strong mammalian promoters by random cis-acting element elongation. Biotechniques 42: 628-632 (2007).


 * Edelman G. M., Meech R., Owens G. C. & Jones F. S. Synthetic promoter elements obtained by nucleotide sequence variation and selection for activity. PNAS 97: 3038-43 (2000).


 * Ellis T., Wang X. & Collins J. J. Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nature Biotechnology 27: 465-471 (2009).


 * Tornoe J. Generation of a synthetic mammalian promoter library by modification of sequences spacing transcription factor binding sites. Gene 297: 21-32 (2002).


 * Heintzman N. D. & Ren B. The gateway to transcription: identifying, characterizing and understanding promoters in the eukaryotic genome. Cellular and Molecular Life Science 64: 386-400 (2007).


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 * Rattner A. NF-&kappa;B activates the HIV promoter in neurons. EMBO 12: 4261–4267 (1993).


 * Yokoyama D. K., Ohler U. & Wray G. A. Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships. Nuc Acids Res: 1-21 (2009).


 * del Val C., Pelz O., Glatting K-H, Barta E. & Hotz-Wagenblatt A. PromoterSweep: a tool for identification of transcription factor binding site. Theor Chem Acc (in press)


 * Ghosh S., May M. J. & Kopp E. B. Rel/NF-&kappa;B and IKB proteins: an overview. Seminars in Cancer Biology 8: 63-73 (1997).


 * Moyano P. & Rotwein P. Mini-review: estrogen action in the uterus and insulin-like growth factor-I. Growth Hormone & IGF Research 14: 431-435 (2009).

Stable cell line

 * Zhou H. Development of site-specific integration system to high-level expression recombinant proteins in CHO cells. Chinese journal of biotechnology 23: 756-62 (2007).


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 * Schmidt M., Schwarzwaelder K., Bartholomae C., Zaoui K., Ball B., Pilz I., Braun S., Glimm H., von Kalle C., High-resolution insertion-site analysis by linear amplification–mediated PCR (LAM-PCR). Nature Methods 4 (12): 1051-1057 (2005).

Outlook and Summary

 * Venter M. Synthetic promoters: genetic control through cis engineering. Trends in Plant Science 12: 118-24 (2007).
 * Carey M., Smale S. T. & Hughes H., Transcriptional Regulation in Eukaryotes: Concepts, Strategies and Techniques. New York: CSHL: p. 18-25 (2000).

Measurement

 * Kelly J. R., Rubin A. J., Davis J. H., Ajo-Franklin C. M., Cumbers J., Czar M. J., de Mora K., Glieberman A. L., Monie D. D. & Endy D. Measuring the activity of BioBrick promoters using an in vivo reference standard. Journal of Biological Engineering 3 (2009).


 * Endy, D. & Deese I. Adventures in synthetic biology (comic) Nature 438: 449-453 (2005). Available online at nature.com


 * Alberts B., Johnson A., Walter P. & Lewis J. Molecular Biology of the Cell. 5th edition, 2008. Garland Science, Chapter 6


 * http://www.promega.com/tbs/tm058/tm058.html


 * Zhou H. Development of site-specific integration system to high-level expression recombinant proteins in CHO cells. Chinese journal of biotechnology 23: 756-62 (2007).


 * Alberts B., Johnson A., Walter P. & Lewis J. Molecular Biology of the Cell. 5th edition, 2008. Garland Science, Chapter 7, p. 467-476


 * Zhu X. D. & Sadowski P. D. Cleavage-dependent Ligation by the FLP Recombinase. J Biol Chem 270: 23044-23054 (1995).


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 * Alberts B., Johnson A., Walter P. & Lewis J. Molecular Biology of the Cell. 5th edition, 2008. Garland Science) Chapter 7, p. 905-908


 * Tornoe, J. Generation of a synthetic mammalian promoter library by modification of sequences spacing transcription factor binding sites. Gene 297: 21-32 (2002).


 * Alberts B., Johnson A., Walter P. & Lewis J. Molecular Biology of the Cell. 5th edition, 2008. Garland Science, Chapter 7, p. 492


 * Ducrest, A. L., Amacker M., Lingner J. & Nabholz M. Detection of promoter activity by flow cytometric analysis of GFP reporter expression. Nucleic Acids Res. 30: e65 (2002).


 * Rushton P. J., Reinstädler A., Lipka V., Lippok B. & Somssich I. E. Synthetic plant promoters containing defined regulatory elements provide novel insights into pathogen- and wound-induced signalling. Plant Cell 14: 749-762 (2002).


 * Degenhardt T., Rybakova K. N., Tomaszewska A., Moné M. J., Westerhoff H. V., Bruggeman F. J. & Carlberg C. Population-Level Transcription Cycles Derive from Stochastic Timing of Single-Cell Transcription. Cell 138: 489-501 (2009).


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 * http://www1.qiagen.com/Products/RnaStabilizationPurification/RNeasySystem/RNeasyPlantMini.aspx


 * http://www1.qiagen.com/products/automation/qiacube.aspx


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 * https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=604109&tab=DetailInfo


 * Ormerod M.G.: Flow cytometry: a practical approach (Book. 3rd edition, 2000. Oxford University Press) Chapter 1, p. 7-21.

Material and Methods

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Eukaryopedia

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