Team:Stockholm/Modelling/model discuss

Discussion

References

1. 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

1. 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.

1. 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

1. Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with desired expression levels in prokaryotes Dokyun Na1,2, Sunjae Lee1 and Doheon Lee*1

Codon usage determines translation rate in Escherichia coli*1 Michael A. Sørensen1, C. G. Kurland2 and Steen Pedersen1 Varying Rate of RNA Chain Elongation during rrn Transcription in Escherichia coli P. P. Dennis,1* M. Ehrenberg,2 D. Fange,2 and H. Bremer3 Cooperation Between Translating Ribosomes and RNA Polymerase in Transcription Elongation Sergey Proshkin,1,2 A. Rachid Rahmouni,3 Alexander Mironov,2 Evgeny Nudler1,

Network analysis and prove of concept

Figure 1 Produced by STRING database Jensen et al. Nucleic Acids Res. 2009, 37(Database issue):D412-6

Currently 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 [http://www.ncbi.nlm.nih.gov/pubmed/18426409 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:

1. Developing melanocytes
2. Melanin synthesis (melanogenesis) and transport of melanosomes to keratinocytes
3. Cell adhesion
4. Antigen presenting

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.

Figure 2 Regulators and transcription-factor binding sites on the MITF promoter. Levy et al., 2006

out of those genes, it seemed that [http://www.ncbi.nlm.nih.gov/gene/4286 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.

There are evidences for the accumulation of H2O2 in vitiliginous skin (K. U. Schallreuter et al., 1999, 2001, 2006) and low levels of SOD and CAT (A. Jalel et. al., 2008; Koca R et. al., 2004; K. U. Schallreuter et al. 1991; Maresca V et. al. , 1997; ). It was also shown that calcium uptake is defective in vitiliginous skin in keratocytes (K. U. Schallreuter et al. 1988) as well as Melanocytes(K.U. Schallreuter et al., 1996), later the effect of accumulation of H2O2 in the epidermis of patients with vitiligo which leads to disruption calcium homeostasis in the skin was observed (K. U. Schallreuter et al. ,2007). This suggests that an oxidative stress is a pathogenic event in the degeneration of melanocytes (Strömberg S et al. ,2008).

We hypothesized that extra levels of SOD could improve the Melanocytes survivability and help re-pigmentation.

When thinking about re-pigmentation in vitiliginous skin, the first thing comes to mind is lack of melanin. There are evidences that melanocytes are still available in depigmented epidermis of patients with vitiligo even after 25 years (Tobin DJ et. al., 2000). So if melanocytes can't deliver melanin to keratinocytes or they are producing very low amount, it is possible to produce melanin using synthetic biology and deliver it to help re-pigmentation.

[http://www.nature.com/jid/journal/v125/n2/full/5603495a.html ]