Hiroshi Matsuno

Petri Net Based Descriptions for Systematic Understanding of Biological Pathways

Petri nets have recently become widely accepted as a description method for biological pathways by researchers in computer science as well as those in biology. This paper gives an overview of Petri net formalisms to describe biological pathways and discusses their use in modelings and simulations for the systematic understandings of biological pathways. After reviewing the use of various types of Petri nets for the biological pathway modelings, we showed the examples that analyze fundamental properties of biological pathways using T-invariant, P-invariant, siphon, and trap. Applications of hybrid Petri nets for producing new biological hypotheses through simulations are also illustrated.

A Case Study of HFPN Simulation: Finding Essential Roles of Ror Gene in the Interaction of Feedback Loops in Mammalian Circadian Clock

Mammalian circadian clock is composed of two feedback loops, a Per-Cry and Clock-Bmal loops. The role of Rev-Erb gene, which interconnects these two feedback loops by the inhibition of Bmal from PER/CRY complex, has been investigated through biological experiments as well as computational simulations. However, for the role of Ror gene, which exerts contrary effect on the same target gene Bmal as the Rev-Erb, enough consideration has not been paid so far. This paper first improves the previous hybrid functional Petri net (HFPN) model of the circadian clock so that both of the Per-Cry and Clock-Bmal loops can participate in the maintenance of the circadian oscillations. This improvement is incomplete, however, because a fixed level of PER/CRY eliminates all the circadian oscillations. Although this problem can be resolved by the introduction of Ror into the HFPN model, another inconsistency remains, Bmal oscillation is not abolished by the knock-out of the Cry. Then we further incorporate a hypothetical path into the HFPN model, succeeding in eliminating this inconsistency while keeping complementary actions of two feedback loop.