1. The Frequency Dependence of Osmo-Adaptation in Saccharomyces cerevisae
Phillip Samayoa
– Paper Presentation
October 9, 2008
The Frequency Dependence of Osmo-Adaptation in Saccharomyces cerevisae
Jerome T. Mettetal, Dale Muzzey, Carlos Gómez-Uribe, Alexander van Oudenaarden

2. Introduction Objective Approach Significance
Determine the dominant processes of yeast’s response to osmotic shock
Approach
Systems-engineering methods
Back out a predictive model of signaling dynamics
Significance
Improved understanding of MAPK’s role in osmotic regulation
New approach to developing cellular models
Know feedback loops are involved, but their role in signaling dynamics is poorly understood
Don’t have to incorporate all reaction of a system to find the dominant ones. Suffers from missing parameters/interactions

3. High Osmolarity Response
Less glycerol export (FPS protein)
HOG1 MAPK is transported to the nucleus
indication of osmotic stress
transcription
Measurement of Osmotic Stress
HOG1 tagged with YFP
Nuclear Protein tagged with RFP
(<YFP>nuclear/<YFP>cell)population

4. Input Stimulus & Measure Output
Looking at the cell’s level of stress allows us to see how an input is processed by a cell . Need to figure out the black box that transforms the signal

5. Fourier Analysis Extracts a Predictive Model\
Example (RC circuit):
Input = Vo*sin(wt)
Vout = sin(wt)*Vo(1 + iwRC)-1
Transformed data into frequency space after allowing it to reach steady state (shake black box with multiple freqs -> amplitudes)
Looking at the data, fit a second order linear time invariant function to model A(w). Found the (complex) parameters that described the model

6. The Backed out Model can Predict the Cell’s Step Response
Shows a good fit to the phase difference as well

7. The LTI Model can be Converted into a Molecularly defined Model
Using linear algebra to pull out a two state differential equation model. Two feedback loops.
Now mutant strain with reduced Pbs2 expression to determine relative strength of feedbacks.

8. Mutant Strain Showed Delayed Short-Term Response Dynamics
But known biological details indicate that Hog-1 dependent response by synthesizing glycerol producing proteins is over much longer time scales (~30 min.) -> lack of understanding of MAPK role in osmotic regulation is incomplete (short term component)

9. Gene Expression Mediates Response Over Longer Time Scales
Cells can synthesize proteins
Cells can’t synethsize proteins
Each subsequent pulse recovered from faster without cyclohexamide. More intense shocks slower also.
In the short run, as predicted before, the transcription response isn’t a big factor and cells can respond still.

10. Summary Engineering principles to predict response of a system
Moving Forward
Measure state-space variables
Cellular networks
In more complex systems to better understand structure of network: Such as x, or glycerol concentration