Research topics
ようこそ。ここは吉田真明の研究内容を紹介する個人ページです。
隠岐臨海実験所の利用申請や共同研究に関してはHPか、以下のリーフレットを参考にしてください。
「利用の手引き」印刷用ファイルはこちら（pdf 8,623KB)
さらに、研究内容は以下のweb記事もご参照ください。
取材対応 佐藤喬 週プレNEWS 「まるでエイリアン！？ イカがセントラルドグマを逸脱していた」週間プレイボーイ (29) 2021年7月9日
AMED国際戦略推進部 HFSP獲得セミナー～HFSP Research Grantsプロポーザル作成のコツ～
実験所の共同利用について
以下の研究内容について、また実験所周辺で採れる生き物について (ヒメイカ、コウイカ、アオイガイ、マダコ、ヌタウナギ、タコノマクラ、ベニクラゲムシ、カブトクラゲなど)、共同研究・情報共有・採集依頼などがあれば下記のメールアドレスまでご連絡ください。
また、下記の施設は、共同研究を目的とする場合、隠岐臨海実験所の共同利用施設としてご利用いただけます。
ナリシゲマイクロインジェクションシステムMN-153+１軸油圧マニピュレータ＋電動インジェクター、ナリシゲプラー、冷却器付きオーバーフロー水槽３基、屋外円形水槽(200L)、集合水槽、ＯＬＹＭＰＵＳ蛍光顕微鏡BX-41、簡易クライオスタット(リラトームREM-710)、PCR, 冷凍庫など
e-mail: okimbs"at"life.shimane-u.ac.jp ("at" を@に変更してください)
研究室紹介2020卒研配属S.pdfCurrent research interests
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 stages. Based 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.
Hidden/deep homology found in re-appearance phenomena of Argonauta shells
Argonaute octopuses, also known as the paper nautiluses, form own outer shells and harvest the eggs in the shells. It is clear that the argonautes acquired the shell again since the ancestral octopods have lost the outer shell. This is contrary to Dollo's law, proposed by paleontologist Louis Dollo, that is "an organism never returns exactly to a former state”. The mechanism that the argonautes were able to form the shell, especially the genetic background, has not yet been elucidated. Regarding the responsible genes of shell formation, the argonautes possibly 1) lost the shell-forming genes, but developed novel type of shell-forming genes or 2) recruited the shell-forming genes through the shell-less octopuses keep the gene sets in the genome.
Argonauta argo and A. hians are often found around the Oki Islands, Shimane, Japan. We clarified the shell-forming genes by using bioinformatics and transcriptome analysis of the two species. The transcripts were reconstructed from the RNA-Seqs from the first arm, the second arm, and mantle, and compared the gene expression among those tissues. Homology searches found 45 shell-forming genes, showing homology to that of bivalves, snails, and Nautilus, in the two argonautes in common. It was also revealed that the shell-forming genes are present not only in the first arm, which was believed to secrete the shell but in the other sites. Phylogenetic analysis revealed that the homologs of shell-forming genes were also kept genome of California-two-spot octopus (Octopus bimaculoides) as well. From these results, our data support hypothesis 2), the shell-forming genes are preserved even after the octopus has lost the outer shell and are not used in the shell formation process in common octopus.
We've won HFSP program grant 2017 on this topic!
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.
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.
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.
知夫島のタヌキの糞便解析と生物多様性
島根県隠岐諸島の知夫里島に人為的に移入され国内外来生物として定着したタヌキ（Nyctereutes procyonoides）の遺伝的多様性とその由来を明らかにすることを目的として、知夫タヌキのDNA分析を行った。人獣共通感染症の危険のあるタヌキを扱うこと、知夫里島の多地点からサンプルを集める必要性から、本研究では糞便DNA解析を用いた。まず、母方系統に注目し、ミトコンドリアDNAの２種類の領域のDNA断片を増幅させ、シーケンスした。シーケンス結果の比較から、シーケンス13個のサンプルのDNA型は全て一致し、知夫タヌキの母方系統は１系統のみである可能性が非常に高いという結果になった。
Training course of Bioinformatics in Japanese Marine stations
We set up a research group called "Rinkai Hack" with a few volunteers to promote research education and human resources exchanges beyond the boundaries of animal/ plant research and informatics, with marine stations as the primary places of activity. Rinkai Hack is a name that means, loosely, "hack at the seaside." (There is not a perfect translation for "hack"; it means to disassemble something and create something new). The word "hackathon" (hack + marathon) is starting to become known as a label for events at which information technologists get together somewhere to focus on programming and share data. Caching on to this word, we hack marine stations to explore the way of research that exploits the potential ability of there.
Currently we only accept one event "RinkaiHackathon 2019" registration as a public offering. (deadline for submission 2019. May. 20)
https://sites.google.com/view/rinkaihack/home/events/moredetailsrinkaihackathon2019?authuser=0
