Table 1.
Summary of the agents, signals and behaviors in the Basic Immune Simulator.
| AGENT TYPES AND ZONES | IMMUNE CELLS REPRESENTED AND FUNCTIONAL DESCRIPTION | SIGNALS | CYTOKINES, CHEMOKINES [28] AND MOLECULES REPRESENTED BY EACH SIGNAL |
| Parenchymal Cell Agent (PC) Zone 1 | Functional tissue cells | (Parenchymal-kine 1) PK1 | Stress factors such as Heat Shock Proteins [66], Uric Acid [67], and Chemerin [68], chemokines such as CX3CL1, CCL3, CCL5, CCL6 |
| Virus | Virus particles | ||
| Apoptotic bodies | Apoptotic bodies or dead cells associated with programmed cell death | ||
| Necrosis factors | Cell fragments associated with death by necrosis | ||
| Dendritic Cell Agent (DC1, DC2) Zones 1, 2 | Tissue surveillance, antigen presentation, INNATE immunity | (Mono-kine 1) MK1 | IL-12, IL-8 (CXCL8) [69], CCL3, CCL4, CCL5, CXCL9, CXCL10, CXCL11 |
| (Mono-kine 2) MK2 | IL-10, CCL1, CCL17, CCL22, CCL11, CCL24, CCL26 | ||
| Macrophage Agent (MΦ1, MΦ2)Zone 1 | Scavenging of dead cell debris, antigen presentation, INNATE immunity | MK1 | IL-12, IL-8 (CXCL8), CCL3, CCL4, CCL5, CXCL9, CXCL10, CXCL11 |
| MK2 | IL-10, CCL1, CCL17, CCL22, CCL11, CCL24, CCL26 | ||
| T Cell Agent (T, T1, T2) Zones 2,3,1 | T HELPER lymphocytes, cell-mediated, ADAPTIVE immunity | (Cytokine 1) CK1 | IFN-γ, IL-2, TNF-β |
| (Cytokine 2) CK2 | TGF-β, IL-4, IL-5, IL-6, IL-10, IL-13 | ||
| Cytotoxic T Lymphocyte Agent (CTL) Zones 2,3,1 | T CYTOTOXIC lymphocytes, cell-mediated, ADAPTIVE immunity | CK1 | IFN-γ |
| Natural Killer Cell Agent (NK) Zone 1 | Natural Killer Cells, cell-mediated immunity, kills stressed cells, INNATE immunity | CK1 | IFN-γ |
| B Cell Agent (B, B1, B2) Zones 2,3,1 | B Lymphocytes, ADAPTIVE, humoral immunity, makes antibodies | (Antibody 1) Ab1 | Cytotoxic and neutralizing antibody |
| (Antibody 2) Ab2 | Targeting and neutralizing antibody | ||
| Complement | Bound antibody catalyzes complement product formation, C3a, C5a [70] | ||
| Granulocyte Agent (Gran) Zones 3,1 | Neutrophils, Eosinophils and Basophils, INNATE immunity, releases enzymes and toxins by degranulation and produces reactive oxygen species | (Degranulation product 1) G1 | Degranulation products, reactive oxygen products |
| Portal Agent Zones 1,2,3 | Blood vessels, lymphatic ducts. The only agent representing a structure rather than a cell type. |
All of the programmed entities that exist in the simulation are listed in the "AGENT TYPES AND ZONES" and "SIGNALS" columns. The words "cell" or "lymphocyte" are meant to refer to the actual living structure. The word "agent" refers to the representation or programmed object that exists in the simulation.