Research topics



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Current research topics

  • Comparative evolutionary studies on cephalopod brain and heart

Coleoid cephalopods (octopuses, cuttlefishes and squids) have been called as “primates of the sea” because the big-brained invertebrates display many cognitive, behavioral, and affective traits. These evidences show that cephalopods are exclusively encephalized among marine invertebrates and an another trait of intelligent animal outside of the vertebrates. The cephalopod represent a promising group among invertebrates for studies concerning the organizing principles that underlie the architecture and ontogeny of complex brains. Although gross morphologies of the brains of the cephalopod and vertebrate are different, there are similar features such as functional localization in the brain. I am especially interested in the similarity and parallelism in the evolution. We now are applying a comparative genomic approach to the molluscan species to uncover genomic differences based on the brain evolution.

To study the brain evolution of the cephalopods, we utilize the Japanese pygmy squid, Idiosepius paradoxus, that has advantages to maintain in a laboratory and the smallest genome (2.2G bases) in the cephalopods. We also study Nautilus pompilius, that is one of the oldest cephalopods and has a simpler brain (with 13 discernible lobes) than in squids or octopuses (33-37 lobes). However, the nervous system is vastly more complex than that of any non-cephalopod molluscs. We started from determining complete gene sets of the squid and nautilus by gene model estimation utilizing the genome sequence as well as RNA-Seq from the adult tissues and developmental stagesBased on the transcriptomic analysis of the two species, we employed comparative genomic analysis among molluscs together with public genome sequences of the owl limpet and giant oyster. Our preliminary analysis already identified some gene families that the number is correlated with the complexities of the brains (Owl Limpet or oyster < Nautilus < Squid). Some gene families like vasopressin/neurophysin have already duplicated, suggesting the genes emerged before the divergence between nautiloid and coleoid cephalopods.

The cephalopods also show remarkable evolutionary convergence to vertebrates, high-pressure, closed blood vascular system supporting such complexity of the central nervous system. They develop two additional hearts and branchial hearts (BHs) to drive blood to the gills in addition to a ‘true’ central heart. In the embryonic development the BHs start pulsating before the true heart become active. The BHs expected to start from myogenic control and become integrated to make up coordinated pulsating system with neurogenic and venous pacemakers. We hypothesize that such complex cardiovascular system consists of at least 30 cell types including pacemakers, secretory, muscular cells and defense components. I have unique access to several pygmy squids (a unique transparent animals, analog of the zebrafish) and the embryos during all seasons, and provide animal resources to all members. Continuing my current work on the pygmy squid genome project, I will combine single cellular transcriptomic profilling and post-sequencing bioinformatic analysis for statistical geometry of cell type identification. I will also develop culturing of isolated heart and the pacemaker cells for functional (pharmacological and optogenetics) electrophysiology (traditional and non-invasive) with world-wide and interdiciprinal collaboration.

We've won HFSP program grant 2017 on this topic!

In the research project, four researchers from Japan (Dr. Masa-aki Yoshida, Evolutionary Biology), the United States (Dr. Eric Edsinger-Gonzales, Developmental Biology; Professor Leonid L. Moroz, Neurobiology) and France (Dr. Georges Debrégeas, Neuroimaging) constitute an international collaborative team and tackle the long-lasting unsolved question;“How the auxiliary heart (gill heart) of squids and octopuses gained autonomous pulsatility”. The team will integrate new methodologies linked to real-time dynamic imaging of physiological processes, and introduce mathematical approaches for real-time cellular and systemic analyses. Importantly, the international collaboration will establish pygmy squid as a novel experimental paradigm for the entire field of comparative and integrative biology.

The HFSP is an international project established in 1987 by then Prime Minister Yasuhiro Nakasone of Japan. For the purpose of “jointly promoting basic research centered on elucidation of complicated mechanisms of living organisms internationally and making the results widely available to the benefit of all human beings”, the HFSP gives funding for frontier research in the life sciences. It is implemented by the International Human Frontier Science Program Organization (HFSPO) with its office in Strasbourg, France.

  • Inter- and intra-species variations of Aplysia Identified neurons and the Evolutionary Cell Biology

The marine opisthobranch mollusk, Aplysia, is a powerful experimental system in cellular, molecular, and behavioral neuroscience as well as cell and evolutionary biology because of the distinctive organization of its nervous system, which makes it advantageous for cellular and comparative analysis of a variety of behaviors and learning and memory. We are sequencing the genome of Aplysia both to gain access to genomic mechanisms of basic neuronal and other functions and to study these mechanisms in real physiological time with single-neuron resolution. I focused on cell adhesion molecules (CAMs) in the Aplysia genome, since neurobiology has provided strong evidences for the participation of CAMs in memory consolidation and cellular identity. I have found a molluscan-specific CAM molecules changed the expression dramatically (>10,000 times) with responds to the memory consolidation. The new memory-related gene, NCAML1, encodes a GPI-linked adhesion molecule but not found in human and fly. Phylogenetic analysis revealed that the NCAML1 originated from Neuroglian in Spiralian lineage and was specifically found in gastropod and cephalopod species. The finding of non-conserved molecule may shed a light on not only synaptic proteome variation across bilaterian animals but also diversification of the neuronal mechanism in the learning and memory.

  • Single axon transcriptome and RNA transport in a squid giant axon

In animal nervous systems many mRNAs became widely known to be transported into axons or synapse and locally translated into proteins. The RNAs came from not only the soma but also surrounding glial cells. It is said that the local translation mechanism can modulate local function of the neurons whose axons at distances up to meters away from the nucleus and allow them to respond locally to the environment. However, a lot remains to be established about the origin of the mRNAs because it is difficult to separate the soma, axon and glial sheath from a single neuron. Axoplasm extrusion from a giant nerve system of the squids have been already established and widely used in physiological studies. The squid giant axon provides us to analyze RNA fractions of cell bodies, glial sheath and the axoplasm, independently.

I have already collected fractions of soma (a giant fiber lobe), surrounding glial cells and extruded axoplasm (approximately 10μl per axon including 1ng total RNA) from Loligo edulis and completed whole transcript amplification from the axoplasmic RNA. Our giant axon RNA-Seq analysis will offer four distinct points: (i) the RNA-Seq allow to figure out mRNA populations across a giant nerve system; (ii) the comparison across the fractions allow to trace the cellular origin of the mRNA fractions; (iii) it can be tested whether functional significant genes such as neuropeptides, receptors and channels are localized in the axoplasm; (iv) the comparative RNA-Seq may provide informations about localization of mechanisms of mRNA modification such as RNA-editing.

  • Hidden/deep homology found in re-appearance phenomena of Argonauta shells 

  • Convergence and parallelism in domestic animal evolution


  • Environmental DNA analysis in wild animal populations