Team:Heidelberg/Project References

References

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 [http://www.nature.com/nature/comics/syntheticbiologycomic/index.html 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 (2009)

• Voigt, C. Genetic parts to program bacteria. Current Opinion in Biotechnology 17: 548–557

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

• https://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

• 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. and 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, 5th 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).

• Stemmer W. P., Crameri A., Ha K. D., Brennan T. M., Heyneker H. L. Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Gene 164, 49-53 (1995).

• Rattner A. NF-κ 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-κB 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)

• Andrews, B. J., Proteau, G. A., Beatty, L. G. & Sadowski, P. D. The FLP Recombinase of the 2μ Circle DNA of Yeast: Interaction with Its Target Sequences. Cell 40: 795-803 (1985)

• Senecoff, J. F., Bruckner, R. C. & COX, M. M. The FLP recombinase of the yeast 2-μ plasmid: Characterization of its recombination site. Proc. Nati. Acad. Sci. USA 82: 7270-7274 (1985)

• Holmberg A., Blomstergren A., Nord O., Lukacs M., Lundeberg J., Uhlén M. The biotin-streptavidin interaction can be eversibly broken using water at elevated temperatures. Electrophoresis 26(3):501-10. (2005)

• 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, 12:118-12
• Carey M., Smale S. T., Hughes H., Transcriptional Regulation in Eukaryotes: Concepts, Strategies and Techniques. New York:CSHL, p. 18-25 (2000)

Modeling

HEARTBEAT Fuzzy Modeling

• Harbison C. T., Gordon D. B., Lee T. I., Rinaldi N. J., Macisaac K. D., Danford T. W., Hannett N. M., Tagne J. B., Reynolds D. B., Yoo J., Jennings E. G., Zeitlinger J., Pokholok D. K., Kellis M., Rolfe P. A., Takusagawa K. T., Lander E. S., Gifford D. K., Fraenkel E., Young R. A. Transcriptional regulatory code of a eukaryotic genome. Nature 431, 99-104 (2004).
  

• Hu, Z., Killion, P. J. & Iyer, V. R. Genetic reconstruction of a functional transcriptional regulatory network. Nature Genet. 39, 683-687 (2007).
  

• Gertz, J., Siggia E. D. & Cohen, B. A. Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature 457. 215-218 (2009)
  

• Roider H. G., Kanhere A., Manke T., Vingron M. Predicting transcription factor affinities to DNA from a biophysical model. Bioinformatics 23, 134-141 (2006)
  

• ref to come
  

• Andrianantoandro E., Basu S., Karig D. K., Weiss R. Synthetic biology: new engineering rules for an emerging discipline. Mol Sys Biol (2006)
  

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

• Vardhanabhuti, S., Wang, J. & Hannenhalli, S. Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation. Nucl Acid Res 35, 3203-3213 (2007).
  

• Yokoyama, K. D., 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. Nucl Acid Res, 1-21 (2009)
  

• Nelles, O. Nonlinear System Identification. Springer, 2000.
  

• Bosl, W. J. BMC systems biology 1, 13 (2007).
  

• Mathematical modeling of the lambda switch:a fuzzy logic approach.
  

• B. B. Aldridge, J. Saez-Rodriguez, J. L. Muhlich et al., PLoS computational biology 5 (4), e1000340 (2009).

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 [http://www.nature.com/nature/comics/syntheticbiologycomic/index.html 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).
  

• York J. D., Odom A. R., Murphy R., Ives E. B., Wente S. R. A phospholipase C-dependent inositol polyphosphate kinase pathway required for efficient messenger RNA export. Science 285, 96-100 (1999).
  

• 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 et al. 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).
  

• Lottspeich, F. and Engels, J. W.: "Bioanalytik" (Book. 2nd edition, 2006. Spektrum Akademischer Verlag) Chapter 5, p. 95-96.

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

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

• http://www1.qiagen.com/literature/render.aspx?id=398

• 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

• Brady N. Bioquant Heidelberg, Eils group; Personal communication.
  
• Schilde J. Institute for human genetics at the University of Heidelberg; Personal communication.
  
• Panigrahy D., Singer, S., Shen L. Q., Butterfield C. E., Freedman D. A., Chen E. J., Moses M. A., Kilroy S., Duensing S., Fletcher C., Fletcher J. A., Hlatky L., Hahnfeldt P., Folkman J., Kaipainen A. PPARγ ligands inhibit primary tumor growth and metastasis by inhibiting angiogenesis. Journal of clinical cancer 110: 923-932 (2002)
  
• Lucarelli E., Sangiorgi L., Maini V., Lattanzi G., Marmiroli S., Reggian, M., Mordenti M., Gobbi G. A., Scrimieri F., Bertoja A. Z. & Picci P. Troglitazione affects survival of human osteosarcoma cells. International Journal of Cancer 98 (3): 344-351 (2002)
  
• Komarov,P. G., Komarova E. A., Kondratov R. V., Christov-Tselkov K., Coon J. S., Chernov M. V., Gudkov A. V. A chemical inhibitor of p53 that protects mice from the side effects of cancer therapy. Science 285(5434):1733-7 (1999)
  
• Wang S. H., Liang C. T., Liu Y. W., Huang M. C., Huang S. C., Hong W. F., Su J. G. Crosstalk between activated forms of the aryl hydrocarbon receptor and glucocorticoid receptor. Toxicology. 262(2):87-97 (2009)
  
• Diesing D., Cordes T., Fischer D., Diedrich K., Friedrich M. Vitamin D--metabolism in the human breast cancer cell line MCF-7. Anticancer Res. 26(4A): 2755-9 (2006)
  
• Bartz F., Kern L., Erz D., Zhu M., Gilbert D., Meinhof T., Wirkner U., Erfle H., Muckenthaler M., Pepperkok R., Runz H. Identification of Cholesterol-Regulating Genes by Targeted RNAi Screening. Cell Metabolism 10: 63-75 (2009)
  

Eukaryopedia

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