Previous Projects

Previous Projects (2005–2022)

Regulation of stem cell fate: molecular control of pluripotent stem cells

Animals capable of whole-body regeneration possess a large pool of somatic pluripotent stem cells. During regeneration, these stem cells can self-renew, proliferate, and differentiate into any cell type. However, the molecular mechanisms controlling these stem cells are not well understood. To develop a new model system for molecular studies, we first sequenced the genome of a highly regenerative acoel worm. We then investigated stem cell regulation in this acoel using single-cell and epigenetic approaches.

Evolution of animal genomes: comparative genomics and transcriptomics of lophotrochozoans

Brachiopods (lamp shells), phoronids (horseshoe worms), and nemerteans (ribbon worms) are closely related to lophotrochozoans, yet they remain poorly studied despite their significance in ecology, evolution, and paleontology. We decoded the genomes of the brachiopod Lingula anatina, the phoronid Phoronis australis, and the nemertean Notospermus geniculatus to gain insights into animal genome evolution. Our findings revealed that Lingula lacks genes involved in bone formation, suggesting an independent origin of its phosphate biominerals. We also found that lophotrochozoans share many gene families with deuterostomes, indicating that lophotrochozoans have retained a core bilaterian gene repertoire. Additionally, transcriptomic analyses suggest a possible common origin of bilaterian head patterning. Overall, our study highlights the dual nature of lophotrochozoans, where bilaterian-conserved and lineage-specific features shape the evolution of their genomes.

Evolution of gene regulatory networks in deuterostomes: axial patterning in sea urchins

Using immunolocalization with a phospho-Smad1/5 antibody, we discovered that BMP signaling is asymmetrically activated on the left side of the sea urchin larva, specifically in the first asymmetrical structure, the hydroporic canal. By perturbing BMP signals with pharmaceutical treatments and morpholinos, we demonstrated that BMP signaling activates the expression of several transcription factors necessary for the formation of the hydroporic canal. Our findings suggest a deep evolutionary origin for the opposing roles of BMP and Nodal signaling in patterning the left–right axis in deuterostomes.

Specification of germlines and sensory neurons in chordates: cell fate specification in amphioxus

Amphioxus, a fish-like basal chordate, is critical in understanding vertebrate evolution and development. To study the roles of localized RNAs during germline specification, we quantified the aggregation of a structure known as the pole plasm, which contains Piwi-interacting RNAs, including vasa and nanos mRNAs, in fertilized eggs. By separating blastomeres at the two-cell stage, we discovered that the absence of pole plasm inheritance in one of the twin embryos leads to defects in larval tail development. This observation suggests that Vasa-positive cells derived from the pole plasm are essential for germline specification and the differentiation and growth of somatic structures. Additionally, we reconstructed a three-dimensional neural structure of the larva and identified an increase in clustered GABA-positive peripheral neurons after perturbing Notch signaling. Our results also indicate that BMP signaling functions upstream of Notch signaling to induce a ventral neurogenic domain. We hypothesize that BMP signaling has a conserved role in promoting peripheral neuron formation across bilaterians.

Coral–dinoflagellate endosymbiosis: dynamics of the lipid content between corals and algae

Coral–dinoflagellate endosymbiosis is a phenomenon where algal symbionts reside inside the animal host cells, specifically within the inner tissue layer known as the gastrodermis. To study these symbiotic cells, we developed a method to isolate tissue layers in corals. Using this technique, we discovered that lipid bodies, which are lipid storage organelles, undergo dynamic changes in lipid content within coral cells under continuous light or dark conditions. Through ratiometric imaging with the fluorescent probe Nile red, we analyzed the polar and neutral lipid content in these lipid bodies. After inducing coral bleaching, we observed a depletion of neutral lipids in the lipid bodies. This finding suggests that the morphological and compositional changes in lipid bodies indicate the symbiotic status.