Team:NYMU-Taipei/Modeling/Overview

Overview

This year, our team targets to tackle a challenging problem all over the world - CCD, colony collapse disorder by creating a special kind of E. coli. Our project can mainly be separated into four main parts – prevention, sensing and killing, suicuding, and safety.

In the first part prevention, monosidase is used, which can inhibit Nosema polarfilament development. This part is mainly done by experiment.

In the second part sensing and killing, it can further divide into three parts – entrance, sensing, and killing. In entrance part, we use beads (encapsulation) to make it easy for our bacteria getting into the bee. For sensing part, we choose ROS-induced promoters, which can be triggered due to the increase concentration of active transcription factor(OxyR or SoxR). As for killing part, microbial peptides defensin and abaecin are used to pierce Nosema cell wall and then let it be bursted.

Here we are interested in the relationship between concentration ROS, active transcription factor and ROS-induced promoters’ open strength. Furthermore, we also want to know the lag time between sensing the invasion and the production of the killing protein to see if the device can save the bees from being killed by Nosema. As a result, we use sensor model to attain this goal.

However, the spread of E.coli from bee to bee is also another important factor influencing the efficiency of killing Nosema. Consequently, epidemic model is applied to see the relationship between Nosema infection and E, coli treatment.

In the third part suiciding, ethanol is used to make bees which are fail to survive after E.coli loses to kill Nosema to suicide itself. Because this part should not be easily opened, otherwise, bees will under the threat of being killed all the time even without the presence of Nosema, we add several terminals behind promoter. Here, ethanol model is used to simulate how many terminals do we need as a threshold.

The last part is safety issue. Since it may be disastrous to the environment if E.coli escapes from bee’s body, we want E.coli to be killed once it leaves bees’ body. Light sensor is used to achieve this goal.

Model highlight 1: PoPS for promoter strength

Mostly, promoter strength is determined by single-round in vitro transcriptions (sequences containing -35motifs, spacer, -10motifs, disc, start, initial transcribed region - bits) like the model of PWMs or in vivo GFP fluorescent assays. However, there are several drawbacks for using such methods to determine promoter strength. For example, promoter strength determined by sequences may be incorrect due to interdependency of motifs [1]; GFP fluorescent assays can only determine the relative promoter strength but the absolute one.

Concerning the disadvantages above, we choose PoPS mechanism for promoter strength for it is closer to the real situation. PoPS is defined as the level of transcription as the number of RNA polymerase molecules that pass a point on DNA each second, on a per DNA copy basis (PoPS = Polymerase Per Second; PoPSdc = PoPS per DNA copy).