Table 1.
ABM Agent Types, Model Variables and Manifestation in ABM Rules
| Agents and Variables | 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 |
This table presents a list of the agent classes representing cellular, bacterial and environmental types, variables of those types corresponding to identified mediators and compounds, and the rule-sets for behavior involving those compounds as instantiated in the ABM. It should be noted that the list of rules reflects the programming code semantics for the biological mechanisms of the simulated compounds. For a more detailed biological description of selected compounds (noted by an asterisk "*") readers are directed to Table 2.