研究者業績

浦久保 秀俊

ウラクボ ヒデトシ  (Hidetoshi Urakubo)

基本情報

所属
藤田医科大学 医学部・医用データ科学講座 准教授
学位
博士(工学)(2003年3月 東京大学)

研究者番号
40512140
J-GLOBAL ID
201101036451836391
researchmap会員ID
B000004615

外部リンク

脳は、記憶により駆動されるシステムです。私たちは、過去の記憶・経験に基づいて思考し、より良い未来を目指して行動します。人工ニューラルネットワークがトレーニングに基づいて神経結合を形成して機能を決定するように、記憶(経験)がその人のありようを決定するのです。

 私は、記憶がどのように入力されるかについて、分子神経科学の実験的知見をコンピュータシミュレーションにより統合して動作を検証する研究を行ってきました。記憶は「シナプス」と呼ばれる素子を単位として生じます。ただし、シナプスへの記憶の入力方法は極めて多様で、ある時は各々独立に、時には共同して生じますし、発達・情動・精神疾患により大きく影響を受けます。

 私は、多様な記憶入力について数学的ルールを抽出し、脳がどのように記憶・学習を形づくるかについて明らかにします。物質としての脳から機能的実体が生じる初めの一歩に注目して研究を進める予定です。詳しくは「研究紹介」をご覧ください。


委員歴

 1

受賞

 1

論文

 29
  • Takashi Miyata, Daisuke Hagiwara, Ryosei Ashida, Satoshi Naito, Yohei Kawaguchi, Tomoko Handa, Tomoko Kobayashi, Mariko Sugiyama, Takeshi Onoue, Shintaro Iwama, Hidetaka Suga, Ryoichi Banno, Mami Matsumoto, Hidetoshi Urakubo, Nobuhiko Ohno, Hiroshi Arima
    Cell and Tissue Research 2025年10月4日  査読有り
    Abstract Familial neurohypophysial diabetes insipidus (FNDI) is an autosomal dominant disorder caused by mutations in the arginine vasopressin (AVP) gene. In AVP neurons in a mouse model of FNDI, aggregates of mutant AVP precursors accumulate within a specific compartment of the endoplasmic reticulum (ER). However, as FNDI mice aged, or were exposed to repeated water deprivation, the ER lumen dilated and mutant aggregates dispersed throughout the ER. Meanwhile, autophagic isolation membranes, known as phagophores, emerged to envelop ER containing these aggregates, indicating induction of ER-phagy. Previous in vitro studies showed that phagophores originate from ER membranes, but the structural relationship between phagophores and the ER membrane in vivo remains unknown. In this study, we used serial block-face scanning electron microscopy to investigate the structural relationship between phagophores, ER membranes, and protein aggregates within dilated ER of AVP neurons from FNDI mice subjected to intermittent water deprivation for 4 weeks. Three-dimensional analysis revealed that phagophores enveloped aggregates located within the dilated ER. Serial imaging further demonstrated a physical connection between these phagophores and intact ER membranes. This study provides the first in vivo evidence of the structural continuity between phagophores and the ER membrane in AVP neurons in a mouse model of FNDI.
  • Hidetoshi Urakubo
    Microscopy 74(3) 223-232 2025年6月  査読有り招待有り筆頭著者最終著者責任著者
  • Vikas Pandey, Tomohisa Hosokawa, Yasunori Hayashi, Hidetoshi Urakubo
    Cell Reports 44(4) 115504 2025年4月8日  査読有り最終著者責任著者
  • Tomonobu Ezure, Kyoichi Matsuzaki, Hidetoshi Urakubo, Nobuhiko Ohno
    Scientific reports 15(1) 4195-4195 2025年2月4日  
    This study developed a three-dimensional ultrastructural analysis application using serial block-face scanning electron microscopy (SBF-SEM) to investigate surgically acquired human skin tissues containing the arrector pili muscle. We utilized the en bloc staining, including reduced osmium, thiocarbohydrazide, and lead aspartate, as well as the embedding using a carbon-based conductive resin. Next, we obtained serial images with SBF-SEM. The results revealed dense nerve fiber networks branching from nearby nerve fiber bundles outside the muscle and running among muscle fibers. Additionally, the dense nerve network running through and along arrector pili muscle fibers rarely penetrates the connective tissues between smooth muscle fibers and epithelial cells. Furthermore, in the observation area, no individual smooth muscle fibers formed adhesion structures with the epithelial cells of the hair follicle, ending in the dermal extracellular matrix near the epithelial cells. These results indicate the usefulness of this approach for three-dimensional ultrastructural analyses of human skin tissues comprising follicular units and revealing structural changes in skin tissues, especially the arrector pili muscle and nerve fibers with hair follicular epithelium, in aging and diseased conditions.
  • Takayuki Onai, Noritaka Adachi, Hidetoshi Urakubo, Fumiaki Sugahara, Toshihiro Aramaki, Mami Matsumoto, Nobuhiko Ohno
    iScience 26(12) 108338 2023年11月  査読有り
  • Sergey Mursalimov, Mami Matsumoto, Hidetoshi Urakubo, Elena Deineko, Nobuhiko Ohno
    Annals of Botany 132(6) 1159-1174 2023年7月25日  査読有り
  • Sehyung Lee, Hideaki Kume, Hidetoshi Urakubo, Haruo Kasai, Shin Ishii
    Neural networks 152 57-69 2022年8月  査読有り
  • Hidetoshi Urakubo, Sho Yagishita, Haruo Kasai, Yoshiyuki Kubota, Shin Ishii
    PLOS Computational Biology 17(9) e1009364-e1009364 2021年9月30日  査読有り筆頭著者責任著者
  • Laxmi Kumar Parajuli, Hidetoshi Urakubo, Ai Takahashi-Nakazato, Roberto Ogelman, Hirohide Iwasaki, Masato Koike, Hyung-Bae Kwon, Shin Ishii, Won Chan Oh, Yugo Fukazawa, Shigeo Okabe
    eNeuro 2020年10月27日  査読有り
    Precise information on synapse organization in a dendrite is crucial to understanding the mechanisms underlying voltage integration and the variability in the strength of synaptic inputs across dendrites of different complex morphologies. Here, we used focused ion beam/scanning electron microscope (FIB/SEM) to image the dendritic spines of mice in the hippocampal CA1 region, CA3 region, somatosensory cortex, striatum, and cerebellum (CB). Our results show that the spine geometry and dimensions differ across neuronal cell types. Despite this difference, dendritic spines were organized in an orchestrated manner such that the postsynaptic density (PSD) area per unit length of dendrite scaled positively with the dendritic diameter in CA1 proximal stratum radiatum (PSR), cortex and CB. The ratio of the PSD area to neck length was kept relatively uniform across dendrites of different diameters in CA1 PSR. Computer simulation suggests that a similar level of synaptic strength across different dendrites in CA1 PSR enables the effective transfer of synaptic inputs from the dendrites towards soma. Excitatory postsynaptic potentials (EPSPs), evoked at single spines by glutamate uncaging and recorded at the soma, show that the neck length is more influential than head width in regulating the EPSP magnitude at the soma. Our study describes thorough morphological features and the organizational principles of dendritic spines in different brain regions.Significance statement Little is known about the characteristic anatomical features underlying the organization of spine synapses in a dendrite. This study used volume electron microscopy to make an extensive characterization of dendritic spine synapses in multiple regions of the mouse brain to uncover the principles underlying their placement along a dendritic shaft. By using a combination of approaches such as two-photon imaging, glutamate uncaging, electrophysiology, and computer simulation, we reveal the functional importance of regulated spine placement along a dendritic trunk. Our research presents a crucial step in understanding the synaptic computational principle in dendrites by highlighting the generalizable features of dendritic spine organization in a neuron.
  • Hidetoshi Urakubo, Sho Yagishita, Haruo Kasai, Shin Ishii
    PLoS computational biology 16(7) e1008078 2020年7月  査読有り筆頭著者責任著者
    Animals remember temporal links between their actions and subsequent rewards. We previously discovered a synaptic mechanism underlying such reward learning in D1 receptor (D1R)-expressing spiny projection neurons (D1 SPN) of the striatum. Dopamine (DA) bursts promote dendritic spine enlargement in a time window of only a few seconds after paired pre- and post-synaptic spiking (pre-post pairing), which is termed as reinforcement plasticity (RP). The previous study has also identified underlying signaling pathways; however, it still remains unclear how the signaling dynamics results in RP. In the present study, we first developed a computational model of signaling dynamics of D1 SPNs. The D1 RP model successfully reproduced experimentally observed protein kinase A (PKA) activity, including its critical time window. In this model, adenylate cyclase type 1 (AC1) in the spines/thin dendrites played a pivotal role as a coincidence detector against pre-post pairing and DA burst. In particular, pre-post pairing (Ca2+ signal) stimulated AC1 with a delay, and the Ca2+-stimulated AC1 was activated by the DA burst for the asymmetric time window. Moreover, the smallness of the spines/thin dendrites is crucial to the short time window for the PKA activity. We then developed a RP model for D2 SPNs, which also predicted the critical time window for RP that depended on the timing of pre-post pairing and phasic DA dip. AC1 worked for the coincidence detector in the D2 RP model as well. We further simulated the signaling pathway leading to Ca2+/calmodulin-dependent protein kinase II (CaMKII) activation and clarified the role of the downstream molecules of AC1 as the integrators that turn transient input signals into persistent spine enlargement. Finally, we discuss how such timing windows guide animals' reward learning.
  • Lee S, Negishi M, Urakubo H, Kasai H, Ishii S
    Neural networks 125 92-103 2020年5月  査読有り
  • Ishii S, Lee S, Urakubo H, Kume H, Kasai H
    Microscopy 69(2) 79-91 2020年4月  査読有り招待有り
  • Hidetoshi Urakubo, Torsten Bullmann, Yoshiyuki Kubota, Shigeyuki Oba, Shin Ishii
    Scientific reports 9(1) 19413-19413 2019年12月19日  査読有り
    Recently, there has been rapid expansion in the field of micro-connectomics, which targets the three-dimensional (3D) reconstruction of neuronal networks from stacks of two-dimensional (2D) electron microscopy (EM) images. The spatial scale of the 3D reconstruction increases rapidly owing to deep convolutional neural networks (CNNs) that enable automated image segmentation. Several research teams have developed their own software pipelines for CNN-based segmentation. However, the complexity of such pipelines makes their use difficult even for computer experts and impossible for non-experts. In this study, we developed a new software program, called UNI-EM, for 2D and 3D CNN-based segmentation. UNI-EM is a software collection for CNN-based EM image segmentation, including ground truth generation, training, inference, postprocessing, proofreading, and visualization. UNI-EM incorporates a set of 2D CNNs, i.e., U-Net, ResNet, HighwayNet, and DenseNet. We further wrapped flood-filling networks (FFNs) as a representative 3D CNN-based neuron segmentation algorithm. The 2D- and 3D-CNNs are known to demonstrate state-of-the-art level segmentation performance. We then provided two example workflows: mitochondria segmentation using a 2D CNN and neuron segmentation using FFNs. By following these example workflows, users can benefit from CNN-based segmentation without possessing knowledge of Python programming or CNN frameworks.
  • Chiaki Kobayashi, Kazuki Okamoto, Yasuhiro Mochizuki, Hidetoshi Urakubo, Kenta Funayama, Tomoe Ishikawa, Tetsuhiko Kashima, Ayako Ouchi, Agnieszka F. Szymanska, Shin Ishii, Yuji Ikegaya
    Neuroscience Research 146 22-35 2019年9月  査読有り
    See also: https://youtu.be/GWVtrtwNovw
  • Yuichiro Hayashi, Shin Ishii, Hidetoshi Urakubo
    PLOS ONE 9(12) e115464 2014年12月  査読有り
  • Ken Nakae, Yuji Ikegaya, Tomoe Ishikawa, Shigeyuki Oba, Hidetoshi Urakubo, Masanori Koyama, Shin Ishii
    PLOS COMPUTATIONAL BIOLOGY 10(11) e1003949 2014年11月  査読有り
  • Sho Yagishita, Akiko Hayashi-Takagi, Graham C. R. Ellis-Davies, Hidetoshi Urakubo, Shin Ishii, Haruo Kasai
    SCIENCE 345(6204) 1616-1620 2014年9月  査読有り
  • Takuya Koumura, Hidetoshi Urakubo, Kaoru Ohashi, Masashi Fujii, Shinya Kuroda
    PLOS ONE 9(6) e99040 2014年6月  査読有り
  • Hidetoshi Urakubo, Miharu Sato, Shin Ishii, Shinya Kuroda
    BIOPHYSICAL JOURNAL 106(6) 1414-1420 2014年3月  査読有り
  • Minoru Honda, Hidetoshi Urakubo, Takuya Koumura, Shinya Kuroda
    Neural Networks 43 114-124 2013年7月  査読有り筆頭著者
  • Minoru Honda, Hidetoshi Urakubo, Keiko Tanaka, Shinya Kuroda
    JOURNAL OF NEUROSCIENCE 31(4) 1516-1527 2011年1月  査読有り
  • Hidetoshi Urakubo, Minoru Honda, Keiko Tanaka, Shinya Kuroda
    HFSP JOURNAL 3(4) 240-254 2009年8月  査読有り
  • Hidetoshi Urakubo, Minoru Honda, Robert C. Froemke, Shinya Kuroda
    JOURNAL OF NEUROSCIENCE 28(13) 3310-3323 2008年3月  査読有り
  • Takashi Shinozaki, Hideyuki Cateau, Hidetoshi Urakubo, Masato Okada
    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 76(4) 044806 2007年4月  査読有り
  • Hidetoshi Urakubo, Masataka Watanabe, Shunsuke Kondo
    Systems and Computers in Japan 38(1) 41-50 2007年1月  査読有り
  • Akio Maeda, Yu-ichi Ozaki, Sudhir Sivakumaran, Tetsuro Akiyama, Hidetoshi Urakubo, Ayako Usami, Miharu Sato, Kozo Kaibuchi, Shinya Kuroda
    GENES TO CELLS 11(9) 1071-1083 2006年9月  査読有り
  • H Urakubo, T Aihara, S Kuroda, M Watanabe, S Kondo
    JOURNAL OF COMPUTATIONAL NEUROSCIENCE 16(3) 251-265 2004年5月  査読有り
  • H Urakubo, M Watanabe
    ICONIP'02: PROCEEDINGS OF THE 9TH INTERNATIONAL CONFERENCE ON NEURAL INFORMATION PROCESSING 25-29 2002年  査読有り
  • H Urakubo, M Watanabe
    ICONIP'02: PROCEEDINGS OF THE 9TH INTERNATIONAL CONFERENCE ON NEURAL INFORMATION PROCESSING 1490-1494 2002年  査読有り

MISC

 26

担当経験のある科目(授業)

 6

共同研究・競争的資金等の研究課題

 12