Modeling

At this step of the wiki, the careful readers has certainly understand that the goal is to rise up ethical question by creating a agar lemon covered with bacteria - E.coli in practice. But, before start more investigation and experimentation there is a real need to ensure that our project is feasable. And that's why we thought that modeling is so much important in an iGEM project.

• Firstly, we wonder if bacteria could live and develop them-solves correctly in the agar media.

Actually, ultimatly we hope create our lemon with the help of 3D-printer wich would use a mix of melted agar media and bacteria solution. A first ingredient which is desirable is oxygen. That's why we decided to model the oxygen diffusion in an agar medium.

• Now that we know if bacteria could develop in agar or not a natural issue is to predict the bacterial growth

Without spoiling, we can just say that the previous model confirm the intution we could have : while oxygen couldn't easily go into the medium, the growth on the surface area is sufficiently more important than in the medium to neglect the first one. More precisly, our bacteria is colorfull and the surface will be whole covered before intern-colony have time to develop enought to be visible. Finaly, when we could hope observe intern-bacteria the surface-one have allready done an opaque layer. So, this part aims to predict the bacterial population growth on an ellipsoidal object - a fake lemon in practice - over time.

More precisely, we have te determine the initial proportion of bacteria threshold from which we are sure that the population will never extinct, if this threshold exists...!

• An important aspect of our project is the transition from green to yellow in order to emulate the lemon maturation. To do this, we use a fusion protein. Before start the fusion of the two -blue and yellow- chromoproteins, we have to check the compatibility of the both. That's why we will then discuss the structural modeling of the it. We used here the bioinformatics tools developed by the Swiss Institute of Bioinformatics and by the Xu group of Chicago University.

We would have like modeling the salycilate inducible system to better understand this system but, unfortunatly, we do not have time anymore at last...

• Last but not least, the lemon scent !

Actually, we have modify E.coli in order to let her produce pinene, limonene and Geraniol but thus do not ensure us that we will smell the lemon fragance : the concentrations of this three fragance have to stay compatible and that's why we will study the evolution of these concentrations over time.

Note : We have tried to illustrate our work with figures which could be understood for themselves, without knowing the method to get it. Morever, we will just add one or two -for the warrior- star(s) to parts which need more mathematical background in order to don't disgust not-mathematical readers from mathematics.