title: Stochastic Petri Net Modeling of Hypoxia Pathway Predicts a Novel Incoherent Feed-Forward Loop Controlling SDF-1 Expression in Acute Kidney Injury.
abstract: Homing of stem cells to the sites of injury is crucial for tissue regeneration. Stromal derived factor 1 (SDF-1) is among the most important chemokines recruiting these cells. Unexpectedly, our previous experimental data on mouse models of acute kidney injury showed that SDF-1 has a declining trend following ischemic kidney insult. To describe this unforeseen observation, a stochastic Petri net model of SDF-1 regulation in the hypoxia pathway was constructed based on main related components extracted from literature. Using this strategy, predictions regarding the underlying mechanisms of SDF-1 kinetics are generated and a novel incoherent feed forward loop regulating SDF-1 expression is proposed. The computational approach suggested here can be exploited to propose novel therapies for debilitating disorders such as kidney injury.
authors.forename: Zarifeh
authors.initials: Z
authors.lastname: Heidary
authors.forename: Jafar
authors.initials: J
authors.lastname: Ghaisari
authors.forename: Shiva
authors.initials: S
authors.lastname: Moein
authors.forename: Mahmood
authors.initials: M
authors.lastname: Naderi
authors.forename: Yousof
authors.initials: Y
authors.lastname: Gheisari
mesh_terms: D058186:Acute Kidney Injury / Q000378:metabolism*; D000818:Animals; D054377:Chemokine CXCL12 / Q000378:metabolism*; D003198:Computer Simulation; D025461:Feedback, Physiological; D000860:Hypoxia / Q000378:metabolism*; D008297:Male; D051379:Mice; D008807:Mice, Inbred BALB C; D013234:Stem Cells; D049490:Systems Biology
chemical_list: D054377:Chemokine CXCL12; C515256:Cxcl12 protein, mouse