The Amemiya Laboratory uses interdisciplinary approaches in order to better understand the developmental and evolutionary aspects of vertebrate innovations, including the adaptive immune system. The lab is actively utilizing comparative genomics and molecular genetics approaches to make biological inferences. In a nutshell, they seek to unify modern genomics approaches, evolutionary biology, population genetics theory and developmental biology into a coherent line of investigation. The laboratory uses "deep branches" in vertebrate phylogeny (primarily very ancestral lineages of fishes and protochordates) in their research. These deep branches serve two purposes: first, they allow the team to study the genomic and genetic origins of characters germane to higher vertebrates, including humans; and second, they provide very good vantage points for making comparisons with other organisms and to understand the origins of biological innovations, such as limbs and adaptive immune systems.
The laboratory is currently addressing three major lines of investigation. (1) What are the primordial mechanisms used to generate an immune response? How is the genome involved in creating and diversifying such a response? And how did the adaptive and innate arms of the immune system co-evolve and become functionally interdigitated? Finally, how can genomic approaches be incorporated to address major problems with regard to the immunological arms race? (2) How have changes in genomic architecture and organization contributed to differences in body plans that we see amongst all metazoan species? What are the parallels between such evolutionary changes and disease manifestation? And (3) What is the origin and biological ramifications of vertebrate programmed genome rearrangement? Research in the laboratory has recently discovered that the sea lamprey, a basal vertebrate, undergoes unprecedented genome rearrangements during early embryogenesis and the 20% of its genome is lost. The rearrangements are programmed and result in the loss of large amounts of coding sequences as well as repetitive DNA. We seek to understand the mechanism/logic underlying these genome rearrangements and to make inferences regarding this phenomenon and the origin of the rearrangements in the immune receptor loci as well as the factors that influence genome stability in “higher vertebrates,” notably humans.