process model for jak-stat signal transduction pathway using stochastic pi machine (spim) and...
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Process Model for JAK-‐STAT signal transduc8on pathway using Stochas8c Pi Machine(SPiM) and COmplex PAthway SImulator (COPASI)
Students: Vishakha Sharma(CS), Yifei Bao(CS) Advisors: Prof. Adriana Compagnoni(CS)
IntroducAon The JAK(Janus kinase)-STAT(Signal transducer and activator of transcription) signal transduction pathway is a cascade of downstream cellular events initiated from outside the cell through cell surface to the DNA in the nucleus, causing transcription.
Since dysregulation in the functionality of JAK-STAT pathway results in immune deficiency syndrome and cancers, like lymphomas, leukemia and breast cancer, we believe that models like this have the potential to contribute to cancer research.
Results • Time course of mRNA in cytoplasm
a. COPASI b. SPiM • Time course of SOCS1
a. COPASI b. SPiM
• Time course of STAT1n*-‐STAT1n*
a. COPASI b. SPiM
• Overview of different species in JAK-‐STAT signal transducAon pathway
Experiment SPiM – StochasAc Pi Machine
• The Stochastic Pi Machine, SPiM is an implementation of stochastic pi calculus and it is used to build computational models for biological processes.
COPASI – Complex Pathway Simulator
• COmplex Pathway SImulator produces determinisA simulaAon results. COPASI automaAcally converts the reacAon equaAons to ODEs using ODEPACK .
SPiM Model for JAK-‐STAT pathway • The computaAonal model consists of
46 reacAons Conclusion • In our model we scale the iniAal concentraAons
to formulate the fact that solving ordinary differenAal equaAons is faster than execuAng a concurrent model.
• The behavioral expressivity of the stochasAc pi-‐calculus out stands the analyAcal behavior of the ODEs systems.
• The simulaAon results of JAK/STAT pathway can be tested in the wet labs and contribute in the area of biological research as how specific drugs affect a parAcular reacAon in the biological system.
Graduate Student Research Conference
2011
Time, s
nM/L
JAK-STAT Signal trabsduction pathway