Allorecognition, the ability to distinguish self from non-self tissue, is the foundation in both arms of mammalian immunity: adaptive and innate. In mammalian systems, recognition of self from non-self is dependent upon the major histocompatibility complex (MHC) and has been extensively studied. Interestingly, components of the MHC-based immunity have not been identified below the jawed vertebrates based on sequence homology. This pose the questions of how the MHC evolved and how immune cells are educated against self-MHC; neither are fully understood.

Here we utilized Botryllus schlosseri as a model organism to investigate the evolution of MHC and the mechanism of immune education. B. schlosseri is a colonial ascidian (sea squirt) belonging to the subphylum Tunicata, the most primitive chordates. They sit at a key evolutionary position since tunicates are considered the closest living relatives of the vertebrates. With a well-document natural transplantation ability to fuse with another individual outside of their bodies, B. schlosseri can offer new insights and understanding to these enigmatic, important questions.

The B. schlosseri allorecognition system parallels that of the vertebrate Natural Killer (NK) cell's "missing-self" recognition. When two individuals come into contact at the peripheries of their extra-corporeal vasculature system, they can either anastomose to form a hematopoietic and vascular chimera or undergo a blood based inflammatory "rejection" response and form a melanin scar at the site of interaction. The allorecognition response is dependent on a single highly polymorphic locus called the fusion / histocompatibility locus (fuhc ). If two individuals share at least one fuhc allele, then a fusion will occur; otherwise they will reject. This simplified allorecognition system makes B. schlosseri an attractive experimental model to further our understanding of how MHC evolved and the mechanisms underlying immune cell education.

As an emerging model organism, B. schlosseri is able to provide new insights to the evolution and mechanisms of allorecognition. However, there are not many established protocols to thoroughly investigate the allorecognition system in B. schlosseri. Here we report the generation of new in culture, in vitro, and in silico tools to establish a stronger molecular foundation for future work in B. schlosseri (Chapter II). From this toolkit, we discovered genotypes in the population that express specific levels of uncle fester that exhibit preferential POR localization (Chapter III). Finally, we characterized in vitro an allorecognition candidate, Botryllus histocompatibility factor , and reported a new isoform along with their subcellular localization when expressed in mammalian cells (Chapter IV).