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Compute steady states of gene expression


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#1 cascadeless

cascadeless

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Posted 13 March 2019 - 09:39 AM

Task
A bacteria that normally divides every 20 minutes express gene X. The production rate of protein X is 5nM/min. The protein is stable and does not degrade.
  1. What is the concentration of X in the steady state?
     
  2. The same bacteria enter into a stress state at t=0 for 3 hours (before t=0 the level of protein X is at the steady state you found in a). In this state of X increases to 20nM/min but the cell division time changes to 60 min. Calculate the dynamic level of protein X starting t=0. What is the steady state in this case?
     
  3. At t=3 hours the bacteria gets a signal that cases the protein X to become unstable with half-life of 10 min. Calculate now the dynamic level of protein X and the steady state. How would the maximal level of X change if the bacteria got this signal after only 1 hour?
 
Relevant infos
beta ... production rate
 
• Degradation/dilution rate in units of 1/time
alpha = alpha_dil + alpha_deg
 
• Change in concentration of Y
dY/dt = beta - alpha * Y
 
• Steady state (solving for dY/dt=0)
Y_ST = beta / alpha
 
Further information on "An Introduction to Systems Biology" by Uri Alon.
 
Attempt
 
For the first, I have to determine alpha and beta. Beta is obviously 5, and I thought alpha is 1/20, thus 0.05. I am not sure if this is true since the assignment states that the protein does not degrade. Forgive me, I am not that into biology. So the steady state should be 5/0.05 = 100.
 
I am not sure how to do that with the time shift. I tried to plot it and see how it is looking, so I let MatLab solve the differential equation stated above with initial condition 100. When t is below 180 (3 hours) I set beta to 20 and alpha to 1/60. And when t is higher than 180 then I set the parameters as before. However, that looks like the following: Attached File  Screenshot 2019-03-13 at 19.10.49.png   29.82KB   0 downloads
Unfortunately, I don't know how to calculate the dynamic level of protein X starting with t=0 by hand. 
 
For 3 I've no idea currently.

 

I appreciate any help!





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