Team:Stockholm/Modelling/model discuss
From 2010.igem.org
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==== References ==== | ==== References ==== | ||
- | # Analysis of the Lactose Metabolism in E Coli Using Sum of Squares Decomposition. | + | # Analysis of the Lactose Metabolism in E Coli Using Sum of Squares Decomposition. A. Ahmadzadeh, A. Halasz, S. Prajna, A. Jadbabaie, V. Kumar. Proceedings of the IEEE Conference on Decision and Control (CDC), Seville, Spain. 2005 |
- | A. Ahmadzadeh, A. Halasz, S. Prajna, A. Jadbabaie, V. Kumar. | + | # Feedback Regulation in the Lactose Operon: A Mathematical Modeling Study and Comparison with Experimental Data Necmettin Yildirim and Michael C. Mackey, Biophys J. 2003 May; 84(5): 2841–2851. |
- | Proceedings of the IEEE Conference on Decision and Control (CDC), Seville, Spain. 2005 | + | # All things must pass: contrasts and commonalities in eukaryotic and bacterial mRNA decay, Joel G. Belasc, Nature Reviews Molecular Cell Biology 11, 467-478 (July 2010) | doi:10.1038/nrm2917 |
+ | # Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with desired expression levels in prokaryotes, Dokyun Na, Sunjae Lee and Doheon Lee, BMC Systems Biology 2010, 4:71doi:10.1186/1752-0509-4-71 | ||
+ | # Codon usage determines translation rate in Escherichia coli, Michael A. Sørensen1, C. G. Kurland and Steen Pedersen, J Mol Biol. 1989 May 20;207(2):365-77 | ||
+ | #Cooperation Between Translating Ribosomes and RNA Polymerase in Transcription Elongation, Sergey Proshkin, A. Rachid Rahmouni, Alexander Mironov, Evgeny Nudler, Science 23 April 2010: Vol. 328. no. 5977, pp. 504 - 508 DOI: 10.1126/science.1184939 | ||
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=== Network analysis and prove of concept === | === Network analysis and prove of concept === | ||
[[Image:Net_Image_confidence_View_igem_stockholm_modelling_report.png|590px|thumb|center|Figure 1 Produced by STRING database Jensen et al. Nucleic Acids Res. 2009, 37(Database issue):D412-6]] | [[Image:Net_Image_confidence_View_igem_stockholm_modelling_report.png|590px|thumb|center|Figure 1 Produced by STRING database Jensen et al. Nucleic Acids Res. 2009, 37(Database issue):D412-6]] |
Revision as of 19:21, 26 October 2010
DiscussionReferences
Network analysis and prove of conceptCurrently Wet-lab members are working on several proteins that according to previous research have been pointed out to have a positive effect on repigmentation of vitiligo affected skin areas. The idea behind why we chose the biomolecules of interest is presented under the section planning on our wiki homepage. In this section we try to explain a simple interaction network of the specific genes coding the biomolecules. The goal is to give a clear picture of how the genes interact with other potential genes in a way that could result a restroring of the affected skin color. As a starting point, we began with the article Strömberg S et al. (2008). In this paper they identified some 859 genes as differentially regulated genes in pigment skin cells called melanocytes. These genes can be classified in several groups based on their possible cellular role (Strömberg et al. 2008). These groups are:
In fig. 1, a summarized regulatory network of some candidate genes are illustated. We intentionally chose to present interactions that have currently been investigated in order to support our study. out of those genes, it seemed that MITF is one of the most regulated and regulating genes in vitiligo disease. This was the first block of the map. . The MITF promoter is targeted by several transcription factors that are important in neural-crest development and signaling. Transcription factors implicated in the regulation of the MITF promoter include PAX3, cAMP-responsive element binding protein (CREB), SOX10, LEF1 (also known as TCF), one cut domain 2 (ONECUT-2) and MITF itself, Fig. 2 (Levy et al., 2006). It also regulates both the survival and differentiation of melanocytes, and enzymes which are necessary for melanin production. (Levy et al., 2006; T.J. Hemesath et al., 1994; N.J. Bentley et al., 1994; K. Yasumoto et al., 1994; C. Bertolotto et al., 1998). So, the regulation of multiple pigmentation and differentiation related genes by MITF (Levy et al., 2006) convinced us that MITF is a central regulator of melanogenesis.
We hypothesized that extra levels of SOD could improve the Melanocytes survivability and help re-pigmentation.
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