1. Nitrogen Metabolism of Saccharomyce cervisiae A Matlab numerical simulation based on the research of ter Schure published in the Journal of Bacteriology and Microbiology Sarah Carratt BIOL 398/MATH 388 Loyola Marymount University February 24, 2011

2. Overview  Context and purpose for model  State variables  Parameters  Terms for Equations  How do they fit context?  Differential Equations  Simulation graphs (D=.05,.29)  Trends  Brief comparison with ter Schure studies

3. Context and Purpose The System = The Cell Model shows change over time as related to state variables. By changing the parameters, starting concentrations, ect., my model allows observation of consequent changes in cell

4. State Variables  factors to watch/model as they change over time  Ammonium → nitrogen  α-ketoglutarate  Glutamate  Glutamine

5. Parameters  V # = indirect measure of enzyme level (ke)  GDA, GS, NAD-GDH, NADPH-GDH  k # = rate constant for each enzyme  Du = source, inflow (dilution rate*feed concentration)  u = nitrogen + carbon  D = 1/time

6. Understanding the Math V4, k4 V2, k2 V3, k3V1, k1 V5, k5 Adding/subtracting these terms in differential equation can show production/consumption of product

7. Differential Equations ddxdt(keto) = V3(mate/(k3+mate))-V4(keto/(k4+keto)) ddxdt(mine) = V2(mate/(k2+mate))-V1(mine/(k1+mine)) ddxdt(mate) = V1(mine/(k1+mine))- V2(mate*NH4/(k2+mate*NH4))+V3(keto*NH4/(k3+keto*NH4))- V4(mate/(k4+mate))+V5(keto*mine/(k5+keto*mine)) ddxdt(NH4) = D*u+V1(mine/(k1+mine))+V3(mate/(k3+mate))- V2(NH4/(k2+NH4))-V4(NH4/(k4+NH4))

8. Simulation at Microbiology Dilution Rates K values= 2 V values = 5 u = 10 t = 0-10 x0 = 10 or 20 FUTURE: Expand model to provide better comparison between dilution rates and alter other variables/parameters in equations

9. Overview of Model  “Ends” of process were mostly constant (  -ketoglutarate and glutamine)  Glutamate is positive and linear  Place in metabolism/Pathways that produce glutamate in cycle  Ammonium is mostly constant  Slight loss initially followed by low growth in.29 (positive trend)  Steeper loss initially followed by low loss in.05 (negative trend)  FUTURE  Expand model to provide better comparison between dilution rates  Alter other variables/parameters in equations

10. Comparision with ter Schure Papers MicrobiologyBacteriology My Model CONSTANTS Ammonium and glucose Ammonium fluxAmmonium and feed concentration CHANGES Dilution rateAmmonium concentration Dilution rate GOALS Determine what is the regulating factor in nitrogen metabolism. Study transcription and effect of changing carbon and nitrogen fluxes and dilution rates. Produce a model to illustrate interaction of the four substrates of nitrogen metabolism Microbiology paper helped to clarify methods of Bacteriology paper My model shows interaction of substrates ter Schure measured

11. Review  Model shows how state variables/substrates change over time.  State variables:  Ammonium → nitrogen, α-ketoglutarate, Glutamate, Glutamine  Parameters:  V, k, D, u  Assigned constants to reactions and +/- in equation shows production/consumption  Simulation graphs (D=.05,.29)  Trends:  Middle vs. Ends  The goal was to examine the interaction of substrates in nitrogen metabolism proposed by ter Schure studies  accomplished?

12. References  Nitrogen-regulated transcription and enzyme activities in continuous cultures of Saccharomyces cerevisia (Microbiology, 1995, 141, pp1101-1108)  The Concentration of Ammonia Regulates Nitrogen Metabolism in Saccharomyces cerevisiae (Bacteriology, 1995, 177, no. 22, pp6672-6675)  Images from class presentations by Dr. Dahlquist and Dr. Fitzpatrick