Difference between revisions of "Team:UCopenhagen/Model"
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Revision as of 03:27, 2 November 2017
Introduction
The modelling part of IGEM Copenhagen 2017 simulates the behavior of the Number Control and Interdependency subprojects of our synthetic endosymbiosis. The modelling parameters are as far as possible based on experimental results and estimates.
The modelling was meant to serve 3 main tasks:
- 1)As an in silico representation of the combined host-endosymbiont system which we couldn’t physically create in the wet lab given the available amount of time and resources at our disposal.
- 2)As a way to predict parameter dependencies and feasibility of the real system and thus give inspiration to the design of wet lab experiments and future usages.
- 3)As a very simple software toolbox to be used in practical implementations of future synthetic endosymbiosis setups.
A total of 4 different models have been made and are described separately below. All parameters and sources can be found in Table 1.
References
Summeren-Wesenhagen, P. V., & Marienhagen, J. (2014). Metabolic Engineering of Escherichia coli for the Synthesis of the Plant Polyphenol Pinosylvin. Applied and Environmental Microbiology, 81(3), 840-849. doi:10.1128/aem.02966-14
Gu, P., Yang, F., Kang, J., Wang, Q., & Qi, Q. (2012). One-step of tryptophan attenuator inactivation and promoter swapping to improve the production of L-tryptophan in Escherichia coli. Microbial Cell Factories, 11(1), 30. doi:10.1186/1475-2859-11-30
Wang, J., Cheng, L., Wang, J., Liu, Q., Shen, T., & Chen, N. (2013). Genetic engineering of Escherichia coli to enhance production of l-tryptophan. Applied Microbiology and Biotechnology, 97(17), 7587-7596. doi:10.1007/s00253-013-5026-3
Sigma-Aldrich. (2017). Yeast Synthetic Drop-out Medium Supplements Y1501. (n.d.). Retrieved October 31, 2017, from http://www.sigmaaldrich.com/catalog/product/sigma/y1501?lang=en®ion=DK
Bianciotto, V., Lumini, E., Lanfranco, L., Minerdi, D., Bonfante, P., & Perotto, S. (2000). Detection and Identification of Bacterial Endosymbionts in Arbuscular Mycorrhizal Fungi Belonging to the Family Gigasporaceae. Applied and Environmental Microbiology, 66(10), 4503-4509. doi:10.1128/aem.66.10.4503-4509.2000
Reference for USER cloning:
Nour-Eldin, H. H., Hansen, B. G., Nørholm, M. H., Jensen, J. K., & Halkier, B. A. (2006). Advancing uracil-excision based cloning towards an ideal technique for cloning PCR fragments. Nucleic Acids Research, 34(18). doi:10.1093/nar/gkl635
Reference for USER fusion:
Geu-Flores, F., Nour-Eldin, H. H., Nielsen, M. T., & Halkier, B. A. (2007). USER fusion: a rapid and efficient method for simultaneous fusion and cloning of multiple PCR products. Nucleic Acids Research, 35(7). doi:10.1093/nar/gkm106
