Modeling the adaptive immune system: predictions and simulations

Lundegaard, Claus; Lund, Ole; Kesmir, Can; Brunak, Søren; Nielsen, Morten

The adaptive immune system of vertebrates is thought to be only 400 million years old and exists in most fish, amphibians, reptiles, birds and mammals (Thompson, 1995) . Adaptive immunity is induced by lymphocytes and can be classified into two types: humoral immunity, mediated by antibodies, which are secreted by B lymphocytes and can neutralize pathogens outside the cells; and cellular immunity, mediated by T lymphocytes that eliminate infected or malfunctioning cells, and provide help to other immune responses. Diversity is the hallmark of the adaptive immune systems. Both the B and T lymphocyte-specific receptors for antigen recognition are assembled from variable (V), diversity (D), and joining (J) gene segments early in the lymphocyte development. There are multiple copies of V, D and J segments, and a huge repertoire of T and B cells is generated by the recombination of these segments, reviewed by Li et al. (2004) . Another task faced by the immune system is the tolerance to self, which is handled by continuously removing receptors that react to self-epitopes.