Table 1 ABM Agent Types, Model Variables and Manifestation in ABM Rules

Epithelial cell agents

One agent per patch, fixed (Blue Squares)

   i-Interferon-γ

Intracellular production of interferon-ϒ released during inflammation

   i-Dynorphin*

Intracellular production of dynorphin, released during ischemia/reperfusion, dynorphin expression enhanced by factor of 3 when Pseudomonas agent present

   i-Adenosine

Intracellular production of adenosine, released during ischemia

   HIF-α

Intracellular signal for adenosine production during ischemia

   TJ-level

Intracellular production of tight junction proteins, turnover 90 minutes

Pseudomonas agents

Random distribution, heading, and movement (Red Pentagons)

   i-Dynorphin*

Uptake of extracellular dynorphin and activator of mvfr

   oprF*

Membrane-bound receptor, activation proportional to [interferon-ϒ]

   RhlRI*

Conserved quorum-sensing molecule, regulated by oprF

   Luxbox*

Response element upstream of lecA

   i-adenosine

Uptake of extracellular adenosine

   Adenosine-deaminase*

Converts adenosine to inosine

   Inosine*

Activates lecA

   PstS*

Membrane-associated protein, activation proportional to [Pi]

   PhoR*

Intermediate phosphate signaling molecule

   PhoB*

Intermediate phosphate signaling molecule, binds to phobox

   pho box*

Response element upstream of mvfr

    lecA*

Gene for PA-I lectin expression, activated by inosine, PQS, luxbox

   i-PA-I-lectin

Intracellular production of PA-I lectin, causes binding to epithelial cells

   Mvfr*

Multiple virulence factor, upstream promoter for quorum sensing virulence

    TNA*

Downstream to mvfr (See mvfr box in Table 2).

    pqsABCDE*

Downstream to TNA

   i-HQNO*

Intracellular QS intermediate molecule, toxic to Lactobacillus spp.

   i-PQS*

Intracellular QS intermediate molecule, activates lecA, form epithelial toxin

   Grow-colony

Proxy for growth signal when resources (mucous layer) > endogenous flora

   Quorum-sense

Recognizes quorum based on concentration of quorum-signal

Patch Variables

   Mucous

Initial value between 90 and 100 per patch (normal distribution), remains constant and determined carrying-capacity for gut environment (proxy for food, space, shear clearance)

   Phosphate

Initial concentration random value in normal distribution between 0 and 99 (arbitrary units), where the upper value is controlled through the user interface as an experimental condition

   Endogenous flora

Initial population at maximum carrying capacity, growth impaired by HQNO

   HQNO*

Produced by Pseduomonas agents, a toxin that impairs growth of endogenous flora, decreases competition allows for population growth

   PA-I lectin*

Produced by Pseudomonas agents, a toxin that causes epithelial barrier dysfunction

   Quorum-signal

Produced by Pseudomonas agents, an intercellular communication molecule by which Pseudomonas agents sense Pseudomonas density