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Table 1 State transitions obtained through Boolean model simulation using 'GINsim’

From: Understanding the sequential activation of Type III and Type VI Secretion Systems in Salmonella typhimurium using Boolean modeling

(A)  
  Nodes
State Transition Glucose Iron Magnesium Calcium Osmolarity Stationary phase Mlc HilE HilD HilC RtsA HilA Ihf SirA-BarA CsrBC CsrA Fur H-NS PhoP SlyA SsrAB Fis EnvZ OmpR YfhA MviA RcsB PmrA SciS VrgS SciG SPI -1 SPI -2 T6SS
1 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2 0 1 1 1 1 1 1* 1* 0 0 0 0 1* 1* 0 1* 1* 1* 0 0 0 1* 1* 1* 1* 0 0 0 0 0 0 0 0 0
3 0 1 1 1 1 1 1 0* 0 0 0 0 1 1 1* 1 1 1 0 0 0 1 1 0* 0* 1* 1* 0 0 0 0 0 0 0
4 0 1 1 1 1 1 1 0 0 0 0 0 1 1 1 0* 1 1 0 0 0 1 1 0 0 1 0* 0 0 0 0 0 0 0
5 0 1 1 1 1 1 1 0 1* 0 0 0 1 1 1 0 1 1 0 0 0 1 1 0 0 1 0 0 0 0 0 0 0 0
6 0 1 1 1 1 1 1 0 1 1* 1* 0 1 1 1 0 1 1 0 0 0 1 1 0 0 1 0 0 0 0 0 0 0 0
7 0 1 1 1 1 1 1 0 1 1 1 1* 1 1 1 0 1 1 0 0 0 1 1 0 0 1 0 0 0 0 0 0 0 0
8 0 1 1 1 1 1 1 0 1 1 1 1 1 1 1 0 1 1 0 0 0 1 1 0 0 1 0 0 0 0 0 1* 0 0
(B)  
  Nodes
State Transition Glucose Iron Magnesium Calcium Osmolarity Stationary phase Mlc HilE HilD HilC RtsA HilA Ihf SirA-BarA CsrBC CsrA Fur H-NS PhoP SlyA SsrAB Fis EnvZ OmpR YfhA MviA RcsB PmrA SciS VrgS SciG SPI -1 SPI -2 T6SS
1 1 1 0 0 0 1 0 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
2 1 1 0 0 0 1 0 1* 1 1 1 1 0 0 0 1* 1* 1* 1* 1* 0 1* 0 1* 1* 0 0 0 0 0 0 1 0 0
3 1 1 0 0 0 1 0 1 0* 1 1 0* 0 0 0 1 1 1 1 1 1* 1 0 1 1 0 1* 1* 0 0 0 1 0 0
4 1 1 0 0 0 1 0 1 0 1 1 0 0 0 0 1 1 1 1 1 0* 1 0 1 1 0 1 1 0 1* 1* 0* 1* 0
5 1 1 0 0 0 1 0 1 0 1 1 0 0 0 0 1 1 1 1 1 0 1 0 1 1 0 1 1 1* 1 1 0 0* 0
6 1 1 0 0 0 1 0 1 0 1 1 0 0 0 0 1 1 1 1 1 0 1 0 1 1 0 1 1 1 1 1 0 0 1*
  1. The rows represent the dynamic behavior of the network (constituting 34 nodes) under study. ′0′ represents inactive state and ′1′ represents active state. Row 1 represents the values specified as the initial states for simulation. A node’s transit from an inactive state to an active state (0 → 1) or vice-versa (1 → 0) has been marked with asterisks (*). (A) Simulation considering the distal intestinal lumen environment, which is the site of infection by S. typhimurium. The 8th row corresponds to the steady state attained by the network (representing an activated SPI-1) (B) Simulation considering the intra-macrophageal environment faced by S. typhimurium after it has been engulfed by the macrophage. The 6th row corresponds to the steady state attained by the network (representing an activated T6SS).
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