Modeling

In our mathematical model we tried to reproduce the ideal dynamics of the system species. The model was realized by means of ordinary differential equations in which the variables correspond to the cellular species while the parameters represent actual biochemical constants. Assumptions are made in order to make the model clear and intuitive; each of them will be discussed and justified in the following sections. Since our systems literally “counts” yeast cell cycles, we decided to describe the model results following the natural progression of the cell replicative lifespan, i.e., we start by describing the cellular events in the first cell cycle and then we move on to describe the actual counting system in the following two cycles.

First cell cycle - the daughter cell resetter

Our system was designed in order to “reset” the age counter in newly born daughter cells. To accomplish this, one of the key components of the age counter, dCas9, is not produced in the very first cell cycle of daughter cells. As a consequence, the gRNA molecules that leak into the daughter cell during cell division won’t be able to induce the production of any fluorescent protein. As can be seen in fig. 1 we expect only Csy4 to be produced in the first cell cycle. To be noted, the G1-specific degradation tag inserted in both Csy4 and dCas9 is expected to trigger the respective degradation of the species at the end of the G1 phase. This feature can also be seen in fig1, in which Csy4 is rapidly depleted after the end of G1 phase.

Figure 1. Schematic representation of the logical AND gate with the input and output signals.