Nan Hao, Erin K O’Shea

+ 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.

Signal & Response

plasmids-and-my-battle-with-e-coli

+ Binding of transcription factor to gene promoter

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

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

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

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

+ Similarly uniform initial nuclear burst, fewer subsequence sporadic burst

+ Prolonged nuclear enrichment of Msn2

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

+ 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

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

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

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

+ 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

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

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

+ All different + Combines the results

+ 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

+ Time scale of promoter transition