1. Nan Hao, Erin K O’Shea

2. + How is an environmental stimuli transmitted into a cell? + How a cell respond to a specific signal? – Here the signal can be any change in the environment.

3. Signal & Response

4. http://howardhughes.trinity.duke.edu/blogs/2011/06/24/zinc-fingers- plasmids-and-my-battle-with-e-coli

5. http://www.michaeleisen.org/blog/wp-content/uploads/2008/10/fps.png

6. + Binding of transcription factor to gene promoter

7. + Saccharomyces cerevisiae (yeast) + Msn2 is TF that binds to DNA stress response element. + Stress stimuli: dephosphorylated, enter the nucleus, activate genes.

8. + Observe how Msn2 respond to different stress – Glucose limitation – Osmotic stress – Oxidative stress

9. Top row: average of single –cell time traces of Msn2-YFP translocation Bottom row: representative single cell time traces of Msn2-YFP nuclear translocation

10. + Sporadic, heterogeneous translocation burst after the initially relatively uniform nuclea burst.

12. + Similarly uniform initial nuclear burst, fewer subsequence sporadic burst

14. + Prolonged nuclear enrichment of Msn2

16. + Observe how Msn2 respond to different stress + What is the gene expression corresponding to Msn2? – Hill equation – Curve fitting

19. + Observe how Msn2 respond to different stress + What is the gene expression corresponding to Msn2? + How dynamical modulation would affect gene expression – Experiment – Computational model

20. + Is it only the Msn2 nuclear localization level and time that matter, or is it influenced by the dynamic profile of Msn2 activation?

21. + Area under curve of nuclear trace—max expression Single pu;se (black blue red) Oscillatory input (orange)

22. + Max expression to Amplitude(change duration), Duration(change amplitude), Frequency

23. + Observe how Msn2 respond to different stress + What is the gene expression corresponding to Msn2? + How dynamical modulation would affect gene expression + Hypothetical model simulation – Change parameters in computation model

24. + Different TF binding parameter Kd, n, same promoter kinetic + AM is sensitive

25. + Same binding parameter, different promoter kinetics k1,k2 + DM and FM are sensitive.

26. + All different + Combines the results

27. + Observe how Msn2 respond to different stress + What is the gene expression corresponding to Msn2? + How dynamical modulation would affect gene expression + Hypothetical model simulation + Analysis of a simplified model

28. + Time scale of promoter transition