Team:Shenzhen BGIC ATCG/modeling

Blueprint

Our project based a lot on cell cycle, especially the cyclin-promoters and cyclin-degradation tags. Through modelling Cell cycle is one of the most complex network in biology world. Better understanding of cell cycle and it’s regulation, to some extent, faciliate the fermentation industry because we can easily accelarate or decelarate a cell cycle or even one phase in the cycle which are important for metabolism product synthesis. In order to simulation and predict the experimets of the effeciency of Sic1, alternative splicing and degradation tags in the whole cell cycle, we build tree ordinary differential equation system models.

Cell Cycle

Cell Synchronization

Previously study reported the introduction of sic1p could prevent the cell to enter S phase. Based on the sic1 system in yeast, we developed an artificial sic1 system (SIC1_Art). By adding galactose or modifying the phosphorylated sites, we can regulate the synthesis (Ka) and degradation (Kd) rates of the sic1_Art. We are trying to utilize this artificial system to precisely regulate the phase in yeast cell cycle, and our goal is to understand the synchronization behavior in yeast.

SIC1_Art on G1 stage

G1 length:

Alternative Splicing by CRISPRi

Degradation Rate

Degradation tags were also obtained from cyclins because cyclins should degrade fast enough to avoid binding to cdc28 and delaying its own phase. From our simulation we can find out that transformed proteins can also be degraded at a convenient speed.

Parameter Table

As Degradation tags could not fully help tell apart each phase by the light of XFP, we built targeting peptide into model to make a more distinguishable visual result. As shown here, we present a 3D simulation result by adding another axis to specify different organelles.