Aim: To understand cell control mechanism of a model genetic terminator system and to develop potential termination strategies through computational modelling .
Motivation:
The aim of IGEM- IISER Pune team is to develop a rapid, cost effective, sensitive and portable device for detection of tuberculosis. We adopt a three component tuberculosis diagnosing device consisting of
1 Hijacking Module which would take over cell cycle control inducing rapid replication
2 Detection module which forces targeted cells to produce a visual reporter in form of a pigment.
3 A termination module to self destruct cells or cease further replication to prevent uncontrolled growth.
Objective: To use computational modelling to gain insights …show more content…
The equations descibing the model are given as:
N
Cell density at given point of time
Nm
Carrying capacity k Growth rate constant
E
Concentration of toxin
A
Concentration of AHL kE Production rate of toxin dE Degradation rate of toxin kA Production rate of AHL dA Degradation rate of AHL d*E Death rate of cells
Here the first equation is a modified logistic curve with an added death rate term(dEN).
The second equation describes the productin of toxin(E) as linearly proportinal to the AHL concentration and the third assumes that AHL(A) formed is proportional to the no of cells.
Both AHL and killer protein are assumed to degrade by first order kinetics with given rate constants.
Assuming the constitutive promoter of same strength as the IPTG inducible one there would be no change in KA .
We thus solve the ODEs for the initial condition (t=0) [N=1250 , A=0 ,E=0] .
The following values of parameters were used:
Parameter
Value
Unit
d
4.0E-03
nM-1h-1 dE 2 h-1 kA
4.8E-07
nM ml h-1 kE 5 h-1 Table 1: Parameters for termination model1
Two sets of values of k , NM ,dA were used in different simulations.
Value for pH 6.2
Value for pH 6.6
Unit …show more content…
The results shown (in Results section) for Approach 1 are for the values of k , NM , dA given in pH 6.6 column
Approach 2: Delayed termination
Based on the results of Approch 1 a delay term was introduced to allow the population to reach significant numbers initially . This was incorporated as “T” the time at which the terminator module is switched on.
T is an arbitarily time after population close to Nm is reached.
It was expected that by switching it onn at a later time T(when the population is saturated) we would get better population growth initially(tT) :Terminator circuit is switched on . This is same as the the original problem with xinit=Nm
Merging the solutions leads to the full solution
The same values of parameters in Table 1 used in Aprroach 1 are used for this simulation.
The results shown are for the values of k , NM , dA given in pH 6.2 column in Table 2.
Approach 3: Pigment initiated termination.
Looking at the results of Approach 2 where the delayed termination was seen to be more effective , we decided to couple it with the detection module such that the killer gene is activated when a certain concentration of pigment is
Motivation:
The aim of IGEM- IISER Pune team is to develop a rapid, cost effective, sensitive and portable device for detection of tuberculosis. We adopt a three component tuberculosis diagnosing device consisting of
1 Hijacking Module which would take over cell cycle control inducing rapid replication
2 Detection module which forces targeted cells to produce a visual reporter in form of a pigment.
3 A termination module to self destruct cells or cease further replication to prevent uncontrolled growth.
Objective: To use computational modelling to gain insights …show more content…
The equations descibing the model are given as:
N
Cell density at given point of time
Nm
Carrying capacity k Growth rate constant
E
Concentration of toxin
A
Concentration of AHL kE Production rate of toxin dE Degradation rate of toxin kA Production rate of AHL dA Degradation rate of AHL d*E Death rate of cells
Here the first equation is a modified logistic curve with an added death rate term(dEN).
The second equation describes the productin of toxin(E) as linearly proportinal to the AHL concentration and the third assumes that AHL(A) formed is proportional to the no of cells.
Both AHL and killer protein are assumed to degrade by first order kinetics with given rate constants.
Assuming the constitutive promoter of same strength as the IPTG inducible one there would be no change in KA .
We thus solve the ODEs for the initial condition (t=0) [N=1250 , A=0 ,E=0] .
The following values of parameters were used:
Parameter
Value
Unit
d
4.0E-03
nM-1h-1 dE 2 h-1 kA
4.8E-07
nM ml h-1 kE 5 h-1 Table 1: Parameters for termination model1
Two sets of values of k , NM ,dA were used in different simulations.
Value for pH 6.2
Value for pH 6.6
Unit …show more content…
The results shown (in Results section) for Approach 1 are for the values of k , NM , dA given in pH 6.6 column
Approach 2: Delayed termination
Based on the results of Approch 1 a delay term was introduced to allow the population to reach significant numbers initially . This was incorporated as “T” the time at which the terminator module is switched on.
T is an arbitarily time after population close to Nm is reached.
It was expected that by switching it onn at a later time T(when the population is saturated) we would get better population growth initially(tT) :Terminator circuit is switched on . This is same as the the original problem with xinit=Nm
Merging the solutions leads to the full solution
The same values of parameters in Table 1 used in Aprroach 1 are used for this simulation.
The results shown are for the values of k , NM , dA given in pH 6.2 column in Table 2.
Approach 3: Pigment initiated termination.
Looking at the results of Approach 2 where the delayed termination was seen to be more effective , we decided to couple it with the detection module such that the killer gene is activated when a certain concentration of pigment is