Researcher Database

Tomomichi Fujita
Faculty of Science Biological Sciences Cell Structure and Function

Researcher Profile and Settings


  • Faculty of Science Biological Sciences Cell Structure and Function

Job Title

  • Professor


J-Global ID

Research Interests

  • 宇宙環境生物   進化発生   植物分子細胞生物   植物発生   植物生理   細胞間コミュニケーション   極限環境耐性   不等分裂(非対称分裂)   細胞極性   成長と環境応答   

Research Areas

  • Life sciences / Applied molecular and cellular biology
  • Life sciences / Molecular biology
  • Life sciences / Plants: molecular biology and physiology

Academic & Professional Experience

  • 2016/04 - Today Hokkaido University Faculty of Science, Department of Science Biological Sciences
  • 2005/07 - 2016/03 Hokkaido University Faculty of Science, Department of Science Biological Sciences
  • 1999/10 - 2005/06 National Institutes of Natural Sciences
  • 1998/05 - 1999/09 Kyoto University Graduate School of Science
  • 1994/10 - 1998/04 Purdue University, Dept. of Biological Sciences ポストドクトラルフェロー
  • 1993/04 - 1994/09 国立予防衛生研究所(現、国立感染症研究所) ウイ ルス1部 ポストドクトラルフェロー


  • 1990/04 - 1993/03  The University of Tokyo
  •        - 1993  The University of Tokyo  Graduate School, Division of Science
  • 1988/04 - 1990/03  The University of Tokyo
  • 1984/04 - 1988/03  Waseda University  School of Education

Association Memberships

  • international molecular moss science society (iMOSS)   地衣類研究会   THE JAPANESE SOCIETY FOR BIOLOGICAL SCIENCES IN SPACE   THE BRYOLOGICAL SOCIETY OF JAPAN   日本分子生物学会   日本進化学会   日本植物生理学会   日本植物学会   

Research Activities

Published Papers

  • Furukawa, R, Aso M, Fujita, T, Akimoto, S, Tanaka, R, Tanaka, A, Yokono, M, Takabayashi, A
    Journal of Plant Research 132 (6) 867 - 880 2019/11 [Refereed][Not invited]
  • Yokono, M, Takabayashi, A, Kishimoto, J, Fujita, T, Iwai, M, Murakami, A, Akimoto, S, Tanaka, A
    Plant and Cell Physiology 60 (5) 1098 - 1108 2019/05 [Refereed][Not invited]
  • Munenori Kitagawa, Takumi Tomoi, Tomoki Fukushima, Yoichi Sakata, Mayuko Sato, Kiminori Toyooka, Tomomichi Fujita, Hitoshi Sakakibara
    Plant & cell physiology 60 (4) 738 - 751 2019/04/01 [Refereed][Not invited]
    In multi-cellular organisms, cell-to-cell communication is crucial for adapting to changes in the surrounding environment. In plants, plasmodesmata (PD) provide a unique pathway for cell-to-cell communication. PD interconnect most cells and generate a cytoplasmic continuum, allowing the trafficking of various micro- and macromolecules between cells. This molecular trafficking through PD is dynamically regulated by altering PD permeability dependent on environmental changes, thereby leading to an appropriate response to various stresses; however, how PD permeability is dynamically regulated is still largely unknown. Moreover, studies on the regulation of PD permeability have been conducted primarily in a limited number of angiosperms. Here, we studied the regulation of PD permeability in the moss Physcomitrella patens and report that molecular trafficking through PD is rapidly and reversibly restricted by abscisic acid (ABA). Since ABA plays a key role in various stress responses in the moss, PD permeability can be controlled by ABA to adapt to surrounding environmental changes. This ABA-dependent restriction of PD trafficking correlates with a reduction in PD pore size. Furthermore, we also found that the rate of macromolecular trafficking is higher in an ABA-synthesis defective mutant, suggesting that the endogenous level of ABA is also important for PD-mediated macromolecular trafficking. Thus, our study provides compelling evidence that P. patens exploits ABA as one of the key regulators of PD function.
  • Takemura K, Kamachi H, Kume A, Fujita T, Karahara I, Hanba YT
    Journal of plant research 131 (5) 887  0918-9440 2018/09 [Refereed][Not invited]
  • Pierre-François Perroud, Fabian B. Haas, Manuel Hiss, Kristian K. Ullrich, Alessandro Alboresi, Mojgan Amirebrahimi, Kerrie Barry, Roberto Bassi, Sandrine Bonhomme, Haodong Chen, Juliet C. Coates, Tomomichi Fujita, Anouchka Guyon-Debast, Daniel Lang, Junyan Lin, Anna Lipzen, Fabien Nogué, Melvin J. Oliver, Inés Ponce de León, Ralph S. Quatrano, Catherine Rameau, Bernd Reiss, Ralf Reski, Mariana Ricca, Younousse Saidi, Ning Sun, Péter Szövényi, Avinash Sreedasyam, Jane Grimwood, Gary Stacey, Jeremy Schmutz, Stefan A. Rensing
    Plant Journal 95 (1) 168 - 182 1365-313X 2018/07/01 [Refereed][Not invited]
    High-throughput RNA sequencing (RNA-seq) has recently become the method of choice to define and analyze transcriptomes. For the model moss Physcomitrella patens, although this method has been used to help analyze specific perturbations, no overall reference dataset has yet been established. In the framework of the Gene Atlas project, the Joint Genome Institute selected P. patens as a flagship genome, opening the way to generate the first comprehensive transcriptome dataset for this moss. The first round of sequencing described here is composed of 99 independent libraries spanning 34 different developmental stages and conditions. Upon dataset quality control and processing through read mapping, 28 509 of the 34 361 v3.3 gene models (83%) were detected to be expressed across the samples. Differentially expressed genes (DEGs) were calculated across the dataset to permit perturbation comparisons between conditions. The analysis of the three most distinct and abundant P. patens growth stages – protonema, gametophore and sporophyte – allowed us to define both general transcriptional patterns and stage-specific transcripts. As an example of variation of physico-chemical growth conditions, we detail here the impact of ammonium supplementation under standard growth conditions on the protonemal transcriptome. Finally, the cooperative nature of this project allowed us to analyze inter-laboratory variation, as 13 different laboratories around the world provided samples. We compare differences in the replication of experiments in a single laboratory and between different laboratories.
  • 緑色植物のPSI-PSII複合体
    横野 牧生, 高林 厚史, 岸本 純子, 藤田 知道, 岩井 優和, MURAKAMI AKIO, AKIMOTO SEIJI, 田中 歩
    光合成研究 28 (1) 15 - 19 2018/04 [Refereed][Not invited]
  • Kaori Takemura, Rina Watanabe, Ryuji Kameishi, Naoya Sakaguchi, Hiroyuki Kamachi, Atsushi Kume, Ichirou Karahara, Yuko T. Hanba, Tomomichi Fujita
    MICROGRAVITY SCIENCE AND TECHNOLOGY 29 (6) 467 - 473 0938-0108 2017/12 [Refereed][Not invited]
    The photosynthetic and anatomical responses of bryophytes to changes in gravity will provide crucial information for estimating how these plant traits evolved to adapt to changes in gravity in land plant history. We performed long-term hypergravity experiments at 10g for 4 and 8 weeks using the moss Physcomitrella patens with two centrifuges equipped with lighting systems that enable long-term plant growth under hypergravity with irradiance. The aims of this study are (1) to quantify changes in the anatomy and morphology of P. patens, and (2) to analyze the post-effects of hypergravity on photosynthesis by P. patens in relation to these changes. We measured photosynthesis by P. patens for a population of gametophores (e.g., canopy) in Petri dishes and plant culture boxes. Gametophore numbers increased by 9% for a canopy of P. patens, with 24-27% increases in chloroplast sizes (diameter and thickness) in leaf cells. In a canopy of P. patens, the area-based photosynthesis rate (A (canopy)) was increased by 57% at 10g. The increase observed in A (canopy) was associated with greater plant numbers and chloroplast sizes, both of which involved enhanced CO2 diffusion from the atmosphere to chloroplasts in the canopies of P. patens. These results suggest that changes in gravity are important environmental stimuli to induce changes in plant growth and photosynthesis by P. patens, in which an alteration in chloroplast size is one of the key traits. We are now planning an ISS experiment to investigate the responses of P. patens to microgravity.
  • Takao Yokota, Toshiyuki Ohnishi, Kyomi Shibata, Masashi Asahina, Takahito Nomura, Tomomichi Fujita, Kimitsune Ishizaki, Takayuki Kohchi
    PHYTOCHEMISTRY 136 46 - 55 0031-9422 2017/04 [Refereed][Not invited]
    Endogenous brassinosteroids (BRs) in non-flowering land plants were analyzed. BRs were found in a liverwort (Marchantia polymorpha), a moss (Physcomitrella patens), lycophytes (Selaginella moellendorffii and S. uncinata) and 13 fern species. A biologically active BR, castasterone (CS), was identified in most of these non-flowering plants but another biologically active BR, brassinolide, was not. It may be distinctive that levels of CS in non-flowering plants were orders of magnitude lower than those in flowering plants. 22-Hydroxycampesterol and its metabolites were identified in most of the non-flowering plants suggesting that the biosynthesis of BRs via 22-hydroxylation of campesterol occurs as in flowering plants. Phylogenetic analyses indicated that M. polymorpha, P. patens and S. moellendorffii have cytochrome P450s in the CYP85 clans which harbors BR biosynthesis enzymes, although the P450 profiles are simpler as compared with Arabidopsis and rice. Furthermore, these basal land plants were found to have multiple P450s in the CYP72 clan which harbors enzymes to catabolize BRs. These findings indicate that green plants were able to synthesize and inactivate BRs from the land-transition stage. (C) 2016 Elsevier Ltd. All rights reserved.
  • Kenji Fukushima, Xiaodong Fang, David Alvarez-Ponce, Huimin Cai, Lorenzo Carretero-Paulet, Cui Chen, Tien-Hao Chang, Kimberly M. Farr, Tomomichi Fujita, Yuji Hiwatashi, Yoshikazu Hoshi, Takamasa Imai, Masahiro Kasahara, Pablo Librado, Likai Mao, Hitoshi Mori, Tomoaki Nishiyama, Masafumi Nozawa, Gergo Palfalvi, Stephen T. Pollard, Julio Rozas, Alejandro Sanchez-Gracia, David Sankoff, Tomoko F. Shibata, Shuji Shigenobu, Naomi Sumikawa, Taketoshi Uzawa, Meiying Xie, Chunfang Zheng, David D. Pollock, Victor A. Albert, Shuaicheng Li, Mitsuyasu Hasebe
    NATURE ECOLOGY & EVOLUTION 1 (3) 0059  2397-334X 2017/03 [Refereed][Not invited]
    Carnivorous plants exploit animals as a nutritional source and have inspired long-standing questions about the origin and evolution of carnivory-related traits. To investigate the molecular bases of carnivory, we sequenced the genome of the heterophyllous pitcher plant Cephalotus follicularis, in which we succeeded in regulating the developmental switch between carnivorous and non-carnivorous leaves. Transcriptome comparison of the two leaf types and gene repertoire analysis identified genetic changes associated with prey attraction, capture, digestion and nutrient absorption. Analysis of digestive fluid proteins from C. follicularis and three other carnivorous plants with independent carnivorous origins revealed repeated co-options of stress-responsive protein lineages coupled with convergent amino acid substitutions to acquire digestive physiology. These results imply constraints on the available routes to evolve plant carnivory.
  • Kaori Takemura, Hiroyuki Kamachi, Atsushi Kume, Tomomichi Fujita, Ichirou Karahara, Yuko T. Hanba
    JOURNAL OF PLANT RESEARCH 130 (1) 181 - 192 0918-9440 2017/01 [Refereed][Not invited]
    The physiological and anatomical responses of bryophytes to altered gravity conditions will provide crucial information for estimating how plant physiological traits have evolved to adapt to significant increases in the effects of gravity in land plant history. We quantified changes in plant growth and photosynthesis in the model plant of mosses, Physcomitrella patens, grown under a hypergravity environment for 25 days or 8 weeks using a custom-built centrifuge equipped with a lighting system. This is the first study to examine the response of bryophytes to hypergravity conditions. Canopy-based plant growth was significantly increased at 10xg, and was strongly affected by increases in plant numbers. Rhizoid lengths for individual gametophores were significantly increased at 10xg. Chloroplast diameters (major axis) and thicknesses (minor axis) in the leaves of P. patens were also increased at 10xg. The area-based photosynthesis rate of P. patens was also enhanced at 10xg. Increases in shoot numbers and chloroplast sizes may elevate the area-based photosynthesis rate under hypergravity conditions. We observed a decrease in leaf cell wall thickness under hypergravity conditions, which is in contrast to previous findings obtained using angiosperms. Since mosses including P. patens live in dense populations, an increase in canopy-based plant numbers may be effective to enhance the toughness of the population, and, thus, represents an effective adaptation strategy to a hypergravity environment for P. patens.
  • Atsushi Takabayashi, Saeka Takabayashi, Kaori Takahashi, Mai Watanabe, Hiroko Uchida, Akio Murakami, Tomomichi Fujita, Masahiko Ikeuchi, Ayumi Tanaka
    PLANT AND CELL PHYSIOLOGY 58 (1) 0032-0781 2017/01 [Refereed][Not invited]
    The identification of protein complexes is important for the understanding of protein structure and function and the regulation of cellular processes. We used blue-native PAGE and tandemmass spectrometry to identify protein complexes systematically, and built a web database, the protein co-migration database (PCoM-DB,, to provide prediction tools for protein complexes. PCoM-DB provides migration profiles for any given protein of interest, and allows users to compare them with migration profiles of other proteins, showing the oligomeric states of proteins and thus identifying potential interaction partners. The initial version of PCoM-DB (launched in January 2013) included protein complex data for Synechocystis whole cells and Arabidopsis thaliana thylakoid membranes. Here we report PCoM-DB version 2.0, which includes new data sets and analytical tools. Additional data are included from whole cells of the pelagic marine picocya-nobacterium Prochlorococcus marinus, the thermophilic cyanobacterium Thermosynechococcus elongatus, the unicellular green alga Chlamydomonas reinhardtii and the bryophyte Physcomitrella patens. The Arabidopsis protein data now include data for intact mitochondria, intact chloroplasts, chloroplast stroma and chloroplast envelopes. The new tools comprise a multiple-protein search form and a heat map viewer for protein migration profiles. Users can compare migration profiles of a protein of interest among different organelles or compare migration profiles among different proteins within the same sample. For Arabidopsis proteins, users can compare migration profiles of a protein of interest with putative homologous proteins from non-Arabidopsis organisms. The updated PCoM-DB will help researchers find novel protein complexes and estimate their evolutionary changes in the green lineage.
  • Mori, A, Kamachi, H, Karahara, I, Kume, A, Hanba, Y.-T, Takemura, K, Fujita, T
    Biological Sciences in Space 31 9 - 13 2017 [Refereed][Not invited]
  • Liang Bao, Kotaro T. Yamamoto, Tomomichi Fujita
    Plant Signaling and Behavior 10 (3) 1559-2324 2015/04/07 [Refereed][Not invited]
    Shoot phototropism enables plants to position their photosynthetic organs in favorable light conditions and thus benefits growth and metabolism in land plants. To understand the evolution of this response, we established an experimental system to study phototropism in gametophores of the moss Physcomitrella patens. The phototropic response of gametophores occurs slowly a clear response takes place more than 24 hours after the onset of unilateral light irradiation, likely due to the slow growth rate of gametophores. We also found that red and far-red light can induce phototropism, with blue light being less effective. These results suggest that plants used a broad range of light wavelengths as phototropic signals during the early evolution of land plants.
  • Munenori Kitagawa, Tomomichi Fujita
    JOURNAL OF PLANT RESEARCH 128 (1) 63 - 72 0918-9440 2015/01 [Refereed][Not invited]
    Plant growth, development, and environmental responses require the proper regulation of intercellular movement of signals and nutrients. For this, plants have specialized cytoplasmic channels, the plasmodesmata (PD), which allow the symplasmic movement of micro- and macromolecules between neighboring cells. Internal and external signals spatio-temporally regulate the movement of molecules through the PD to control plant development and environmental responses. Although some aspects of targeted movement of molecules have been revealed, the mechanisms of non-targeted, diffusible flow of molecules through PD, and its regulation and function, remain poorly understood, particularly at the cellular level. Previously, we developed a system to quantitatively analyze non-targeted movement of a photoconvertible fluorescent protein, Dendra2, at the single-cell level in the filamentous protonemata tissue of the moss Physcomitrella patens. In protonemata, one-dimensional intercellular communication can be easily observed and quantitatively analyzed at the cellular level. In this review, we describe how protonemata and leaves of P. patens can be used to study symplasmic movement through PD, and discuss how this system can help improve our understanding of PD regulation and function in development and environmental responses in plants.
  • Tomomichi Fujita
    JOURNAL OF PLANT RESEARCH 128 (1) 3 - 5 0918-9440 2015/01 [Refereed][Not invited]
  • 藤田拓矢, 高林厚史, 田中歩, 藤田知道
    せん苔類研究 11 (3) 92  1343-0254 2014/12 [Not refereed][Not invited]
  • Kanako Ito, Junling Ren, Tomomichi Fujita
    GENE 544 (2) 241 - 247 0378-1119 2014/07 [Refereed][Not invited]
    Cell polarity is fundamentally important to growth and development in higher plants, from pollen tubes to root hairs. Basal land plants (mosses and ferns) also have cell polarity, developing protonemal apical cells that show polar tip growth. Flowering plants have a distinct group of Rho GTPases that regulate polarity in polarized cell growth. Rop/RAC signaling module components have been identified in non-flowering plants, but their roles remain unclear. To understand the importance and evolution of Rop/RAC signaling in polarity regulation in land plants, we examined the functions of PpRop and PpRopGEF in protonemal apical cells of the moss Physcomitrella patens. Inducible overexpression of PpRop2 or PpRopGEF3 caused depolarized growth of tip-growing apical cells. PpRop2 overexpression also caused aberrant cross wall formation. Fluorescent protein-tagged PpRop2 localized to the plasma membrane, including the cross wall membrane, and fluorescent-tagged PpRopGEF3 showed polarized localization to the tip region in apical cells. Thus, our results suggest common functions of PpRop and PpRopGEF in the tip-growing apical cells and the importance of a conserved Rop/RAC signaling module in the control of cell polarity in land plants. (C) 2014 Elsevier B.V. All rights reserved.
  • Munenori Kitagawa, Tomomichi Fujita
    JOURNAL OF PLANT RESEARCH 126 (4) 577 - 585 0918-9440 2013/07 [Refereed][Not invited]
    Cell-to-cell transport of molecules in plants must be properly regulated for plant growth and development. One specialized mechanism that plants have evolved involves transport through plasmodesmata (PD), but when and how transport of molecules via PD is regulated among individual cells remains largely unknown, particularly at the single-cell level. Here, we developed a tool for quantitatively analyzing cell-to-cell transport via PD at a single-cell level using protonemata of Physcomitrella patens and a photoconvertible fluorescent protein, Dendra2. In the filamentous protonemal tissues, one-dimensional intercellular communication can be observed easily. Using this system, we found that Dendra2 was directionally transported toward the apex of the growing protonemata. However, this directional transport could be eliminated by incubation in the dark or treatment with a metabolic inhibitor. Thus, we propose that directional transport of macromolecules can occur via PD in moss protonemata, and may be affected by the photosynthetic and metabolic activity of cells.
  • Jo Ann Banks, Tomoaki Nishiyama, Mitsuyasu Hasebe, John L. Bowman, Michael Gribskov, Claude dePamphilis, Victor A. Albert, Naoki Aono, Tsuyoshi Aoyama, Barbara A. Ambrose, Neil W. Ashton, Michael J. Axtell, Elizabeth Barker, Michael S. Barker, Jeffrey L. Bennetzen, Nicholas D. Bonawitz, Clint Chapple, Chaoyang Cheng, Luiz Gustavo Guedes Correa, Michael Dacre, Jeremy DeBarry, Ingo Dreyer, Marek Elias, Eric M. Engstrom, Mark Estelle, Liang Feng, Cedric Finet, Sandra K. Floyd, Wolf B. Frommer, Tomomichi Fujita, Lydia Gramzow, Michael Gutensohn, Jesper Harholt, Mitsuru Hattori, Alexander Heyl, Tadayoshi Hirai, Yuji Hiwatashi, Masaki Ishikawa, Mineko Iwata, Kenneth G. Karol, Barbara Koehler, Uener Kolukisaoglu, Minoru Kubo, Tetsuya Kurata, Sylvie Lalonde, Kejie Li, Ying Li, Amy Litt, Eric Lyons, Gerard Manning, Takeshi Maruyama, Todd P. Michael, Koji Mikami, Saori Miyazaki, Shin-ichi Morinaga, Takashi Murata, Bernd Mueller-Roeber, David R. Nelson, Mari Obara, Yasuko Oguri, Richard G. Olmstead, Naoko Onodera, Bent Larsen Petersen, Birgit Pils, Michael Prigge, Stefan A. Rensing, Diego Mauricio Riano-Pachon, Alison W. Roberts, Yoshikatsu Sato, Henrik Vibe Scheller, Burkhard Schulz, Christian Schulz, Eugene V. Shakirov, Nakako Shibagaki, Naoki Shinohara, Dorothy E. Shippen, Iben Sorensen, Ryo Sotooka, Nagisa Sugimoto, Mamoru Sugita, Naomi Sumikawa, Milos Tanurdzic, Guenter Theissen, Peter Ulvskov, Sachiko Wakazuki, Jing-Ke Weng, William W. G. T. Willats, Daniel Wipf, Paul G. Wolf, Lixing Yang, Andreas D. Zimmer, Qihui Zhu, Therese Mitros, Uffe Hellsten, Dominique Loque, Robert Otillar, Asaf Salamov, Jeremy Schmutz, Harris Shapiro, Erika Lindquist, Susan Lucas, Daniel Rokhsar, Igor V. Grigoriev
    SCIENCE 332 (6032) 960 - 963 0036-8075 2011/05 [Refereed][Not invited]
    Vascular plants appeared similar to 410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.
  • Yoshihisa Oda, Aiko Hirata, Toshio Sano, Tomomichi Fujita, Yuji Hiwatashi, Yoshikatsu Sato, Akeo Kadota, Mitsuyasu Hasebe, Seiichiro Hasezawa
    PLANT AND CELL PHYSIOLOGY 50 (4) 855 - 868 0032-0781 2009/04 [Refereed][Not invited]
    Eukaryotic cells have developed several essential membrane components. In flowering plants, appropriate structures and distributions of the major membrane components are predominantly regulated by actin microfilaments. In this study, we have focused on the regulatory mechanism of vacuolar structures in the moss, Physcomitrella patens. The high ability of P. patens to undergo homologous recombination enabled us stably to express green fluorescent protein (GFP) or red fluorescent protein (RFP) fusion proteins, and the simple body structure of P. patens enabled us to perform detailed visualization of the intracellular vacuolar and cytoskeletal structures. Three-dimensional analysis and high-speed time-lapse observations revealed surprisingly complex structures and dynamics of the vacuole, with inner sheets and tubular protrusions, and frequent rearrangements by separation and fusion of the membranes. Depolymerization of microtubules dramatically affected these structures and movements. Dual observation of microtubules and vacuolar membranes revealed that microtubules induced tubular protrusions and cytoplasmic strands of the vacuoles, indicative of interactions between microtubules and vacuolar membranes. These results demonstrate a novel function of microtubules in maintaining the distribution of the vacuole and suggest a functional divergence of cytoskeletal functions in land plant evolution.
  • Convergences and divergences in polar auxin transport and shoot development in land plant evolution
    Fujita, T, Hasebe, M
    Plant Signaling & Behavior 4 313 - 315 2009 [Refereed][Not invited]
  • Yuji Hiwatashi, Mari Obara, Yoshikatsu Sato, Tomomichi Fujita, Takashi Murata, Mitsuyasu Hasebe
    PLANT CELL 20 (11) 3094 - 3106 1040-4651 2008/11 [Refereed][Not invited]
    Microtubules form arrays with parallel and antiparallel bundles and function in various cellular processes, including subcellular transport and cell division. The antiparallel bundles in phragmoplasts, plant-unique microtubule arrays, are mostly unexplored and potentially offer new cellular insights. Here, we report that the Physcomitrella patens kinesins KINID1a and KINID1b (for kinesin for interdigitated microtubules 1a and 1b), which are specific to land plants and orthologous to Arabidopsis thaliana PAKRP2, are novel factors indispensable for the generation of interdigitated antiparallel microtubules in the phragmoplasts of the moss P. patens. KINID1a and KINID1b are predominantly localized to the putative interdigitated parts of antiparallel microtubules. This interdigitation disappeared in double-deletion mutants of both genes, indicating that both KINID1a and 1b are indispensable for interdigitation of the antiparallel microtubule array. Furthermore, cell plates formed by these phragmoplasts did not reach the plasma membrane in; 20% of the mutant cells examined. We observed that in the double-deletion mutant lines, chloroplasts remained between the plasma membrane and the expanding margins of the cell plate, while chloroplasts were absent from the margins of the cell plates in the wild type. This suggests that the kinesins, the antiparallel microtubule bundles with interdigitation, or both are necessary for proper progression of cell wall expansion.
  • Takayuki Inouye, Masaki Odahara, Tomomichi Fujita, Mitsuyasu Hasebe, Yasuhiko Sekine
    BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY 72 (5) 1340 - 1347 0916-8451 2008/05 [Refereed][Not invited]
    RecA protein is widespread in bacteria, and it plays a crucial role in homologous recombination. We have identified two bacterial-type recA gene homologs (PprecA1, PprecA2) in the cDNA library of the moss Physcomitrella patens. N-terminal fusion of the putative organellar targeting sequence of PpRecA2 to the green fluorescent protein (GFP) caused a targeting of PpRecA2 to the chloroplasts. Mutational analysis showed that the first AUG codon acts as initiation codon. Fusion of the full-length PpRecA2 to GFP caused the formation of foci that were colocalized with chloroplast nucleoids. The amounts of PprecA2 mRNA and protein in the cells were increased by treatment, with DNA damaging agents. PprecA2 partially complemented the recA mutation in Escherichia coli. These results suggest the involvement of PpRecA2 in the repair of chloroplast DNA.
  • Tomomichi Fujita, Hisako Sakaguchi, Yuji Hiwatashi, Steven J. Wagstaff, Motomi Ito, Hironori Deguchi, Toshiyuki Sato, Mitsuyasu Hasebe
    EVOLUTION & DEVELOPMENT 10 (2) 176 - 186 1520-541X 2008/03 [Refereed][Not invited]
    The shoot is a repeated structure made up of stems and leaves and is the basic body plan in land plants. Vascular plants form a shoot in the diploid generation, whereas nonvascular plants such as mosses form a shoot in the haploid generation. It is not clear whether all land plants use similar molecular mechanisms in shoot development or how the genetic networks for shoot development evolved. The control of auxin distribution, especially by polar auxin transport, is essential for shoot development in flowering plants. We did not detect polar auxin transport in the gametophytic shoots of several mosses, but did detect it in the sporophytes of mosses without shoot structure. Treatment with auxin transport inhibitors resulted in abnormal embryo development, as in flowering plants, but did not cause any morphological changes in the haploid shoots. We fused the soybean auxin-inducible promoter GH3 with a GUS reporter gene and used it to indirectly detect auxin distribution in the moss Physcomitrella patens. An auxin transport inhibitor NPA did not cause any changes in the putative distribution of auxin in the haploid shoot. These results indicate that polar auxin transport is not involved in haploid shoot development in mosses and that shoots in vascular plants and mosses are most likely regulated differently during development.
  • Stefan A. Rensing, Daniel Lang, Andreas D. Zimmer, Astrid Terry, Asaf Salamov, Harris Shapiro, Tomoaki Nishiyama, Pierre-Francois Perroud, Erika A. Lindquist, Yasuko Kamisugi, Takako Tanahashi, Keiko Sakakibara, Tomomichi Fujita, Kazuko Oishi, Tadasu Shin-I, Yoko Kuroki, Atsushi Toyoda, Yutaka Suzuki, Shin-ichi Hashimoto, Kazuo Yamaguchi, Sumio Sugano, Yuji Kohara, Asao Fujiyama, Aldwin Anterola, Setsuyuki Aoki, Neil Ashton, W. Brad Barbazuk, Elizabeth Barker, Jeffrey L. Bennetzen, Robert Blankenship, Sung Hyun Cho, Susan K. Dutcher, Mark Estelle, Jeffrey A. Fawcett, Heidrun Gundlach, Kousuke Hanada, Alexander Heyl, Karen A. Hicks, Jon Hughes, Martin Lohr, Klaus Mayer, Alexander Melkozernov, Takashi Murata, David R. Nelson, Birgit Pils, Michael Prigge, Bernd Reiss, Tanya Renner, Stephane Rombauts, Paul J. Rushton, Anton Sanderfoot, Gabriele Schween, Shin-Han Shiu, Kurt Stueber, Frederica L. Theodoulou, Hank Tu, Yves Van de Peer, Paul J. Verrier, Elizabeth Waters, Andrew Wood, Lixing Yang, David Cove, Andrew C. Cuming, Mitsuyasu Hasebe, Susan Lucas, Brent D. Mishler, Ralf Reski, Igor V. Grigoriev, Ralph S. Quatrano, Jeffrey L. Boore
    SCIENCE 319 (5859) 64 - 69 0036-8075 2008/01 [Refereed][Not invited]
    We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments ( e. g., flagellar arms); acquisition of genes for tolerating terrestrial stresses ( e. g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.
  • Masaki Odahara, Takayuki Inouye, Tomomichi Fujita, Mitsuyasu Hasebe, Yasuhiko Sekine
    GENES & GENETIC SYSTEMS 82 (1) 43 - 51 1341-7568 2007/02 [Refereed][Not invited]
    Homologous recombination is a universal process that contributes to genetic diversity and genomic integrity. Bacterial-type RecA generally exists in all bacteria and plays a crucial role in homologous recombination. Although RecA homologues also exist in plant mitochondria, there have been few reports about the in vivo functions of these homologues. We identified a recA gene orthologue (named PprecA1) in a cDNA library of the moss, Physcomitrella patens. N-terminal fusion of the putative organellar targeting sequence of PpRecA1 to GFP caused a targeting of PpRecA1 to mitochondria. PprecA1 partially complemented the effects of a DNA damaging agent in an Escherichia coli recA deficient strain. Additionally, the expression of PprecA1 was induced by treating the plants with DNA damaging agents. Disruption of PprecA1 by targeted replacement resulted lower rate of the recovery of the mitochondrial DNA from methyl methan sulfonate damage. This is the first report about the characteristics of a null mutant of bacterial-type recA gene in plant. The data suggest that PprecA1 participates in the repair of mitochondrial DNA in P. patens.
  • Yoshihisa Oda, Toshio Sano, Tomomichi Fujita, Yuji Hiwatashi, Yoshikatsu Sato, Natsumaro Kutsuna, Aiko Hirata, Mitsuyasu Hasebe, Seiichiro Hasezawa
    PLANT AND CELL PHYSIOLOGY 48 S24 - S24 0032-0781 2007 [Refereed][Not invited]
  • Tomomichi Fujita, Kaoru Hashimoto, Yuji Hiwatashi, Yoshikatsu Sato, Takashi Murata, Mitsuyasu Hasebe
    PLANT AND CELL PHYSIOLOGY 48 S50 - S50 0032-0781 2007 [Refereed][Not invited]
  • Yuji Hiwatashi, Tomomichi Fujita, Takashi Murata, Mitsuyasu Hasebe
    PLANT AND CELL PHYSIOLOGY 48 S88 - S88 0032-0781 2007 [Refereed][Not invited]
  • Genome-wide comparison of developmental genes in land plants
    Mitsuyasu Hasebe, Tomoaki Nishiyama, Takako Tanahashi, Naoki Aono, Tsuyoshi Aoyama, Chaoyang Cheng, Tomomichi Fujita, Kaoru Hashimoto, Tadayoshi Hirai, Yuji Hiwatashi, Masaki Ishikawa, Mineko Iwata, Minoru Kubo, Tetsuya Kurata, Koij Mikami, Saori Miyazaki, Shin-Ichi Morinaga, Takashi Murata, Mari Obara, Yasuko Oguri, Naoko Onodera, Yoshikatsu Sato, Naomi Sumikawa, Naoki Shinohara, Sachiko Wakaduki, Nagisa Sugimoto
    PLANT AND CELL PHYSIOLOGY 48 S50 - S50 0032-0781 2007 [Refereed][Not invited]
  • A Hayashida, K Takechi, M Sugiyama, M Kubo, RD Itoh, S Takio, T Fujita, Y Hiwatashi, M Hasebe, H Takano
    PLANT BIOLOGY 7 (3) 300 - 306 1435-8603 2005/05 [Refereed][Not invited]
    Eleven mutant lines exhibiting decreased numbers of chloroplasts per cell were isolated from 8800 tagged mutant lines of Physcomitrella patens by microscopic observations. Chloronema subapical cells in wild-type plants had a mean of 48 chloroplasts, whereas chloroplast numbers in subapical cells in mutant lines 215 and 222 decreased to 75% of that in the wild type. Seven mutant lines - 473, 122, 221, 129, 492, 207, and 138 had about half as many chloroplasts as the wild type. Mutant line 11 had a few remarkably enlarged chloroplasts, and mutant line 347 had chloroplasts of various sizes. Whereas the cell volume was the same as in the wild type in mutant lines 222, 473, 221, 129, 492, and 207, the cell volume of the other mutants increased. The chloroplast number of leaf cells was the same as that of chloronema cells in each mutant line when gametophores could be formed. Treatment with ampicillin decreased the number of chloroplasts in all mutant lines. Southern hybridization using DNA in tags as probes showed that only one insertion occurred in mutant lines 473 and 221. To determine whether the tagged DNA inserted into the known genes for plastid division, we isolated the PpMinD1, PpMinD2, and PPMinE1 genes. Genomic polymerase chain reaction analysis showed that the PpFtsZ and PpMinD/E genes were not disrupted by the insertion of the tags in mutant lines 11 and 347, respectively.
  • Gene tagging, gene- and enhancer-trap systems, and full-length cDNA overexpression in Physcomitrella patens. In New Frontiers in Bryology:Physiology, Molecular Biology & Functional Genomics (eds. by Wood, AJ., Oliver, MJ. and Cove, DJ.), Kluwer Academ・・・
    2004 [Not refereed][Not invited]
    Gene tagging, gene- and enhancer-trap systems, and full-length cDNA overexpression in Physcomitrella patens. In New Frontiers in Bryology:Physiology, Molecular Biology & Functional Genomics (eds. by Wood, AJ., Oliver, MJ. and Cove, DJ.), Kluwer Academic Publishers, Netherlands, pp. 111-132.
  • T Nishiyama, T Fujita, T Shin-I, M Seki, H Nishide, Uchiyama, I, A Kamiya, P Carninci, Y Hayashizaki, K Shinozaki, Y Kohara, M Hasebe
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 100 (13) 8007 - 8012 0027-8424 2003/06 [Refereed][Not invited]
    The mosses and flowering plants diverged >400 million years ago. The mosses have haploid-dominant life cycles, whereas the flowering plants are diploid-dominant. The common ancestors of land plants have been inferred to be haploid-dominant, suggesting that genes used in the diploid body of flowering plants were recruited from the genes used in the haploid body of the ancestors during the evolution of land plants. To assess this evolutionary hypothesis, we constructed an EST library of the moss Physcomitrella patens, and compared the moss transcriptome to the genome of Arabidopsis thaliana. We constructed full-length enriched cDNA libraries from auxin-treated, cytokinin-treated, and untreated gametophytes of P. patens, and sequenced both ends of >40,000 clones. These data, together with the mRNA sequences in the public databases, were assembled into 15,883 putative transcripts. Sequence comparisons of A. thaliana and P. patens showed that at least 66% of the A. thaliana genes had homologues in A patens. Comparison of the A patens putative transcripts with all known proteins, revealed 9,907 putative transcripts with high levels of similarity to vascular plant genes, and 850 putative transcripts with high levels of similarity to other organisms. The haploid transcriptome of A patens appears to be quite similar to the A. thaliana genome, supporting the evolutionary hypothesis. Our study also revealed that a number of genes are moss specific and were lost in the flowering plant lineage.
  • Y Hiwatashi, T Nishiyama, T Fujita, M Hasebe
    PLANT JOURNAL 28 (1) 105 - 116 0960-7412 2001/10 [Refereed][Not invited]
    Because of its simple body plan and ease of gene knockout and allele replacement, the moss Physcomitrella patens is often used as a model system for studies in plant physiology and developmental biology. Gene-trap and enhancer-trap systems are useful techniques for cloning genes and enhancers that function in specific tissues or cells. Additionally, these systems are convenient for obtaining molecular markers specific for certain developmental processes. Elements for gene-trap and enhancer-trap systems were constructed using the uidA reporter gene with either a splice acceptor or a minimal promoter. Through a high rate of transformation conferred by a method utilizing homologous recombination, 235 gene-trap and 1073 enhancer-trap lines were obtained from 5637 and 3726 transgenic lines, respectively. The expression patterns of these trap lines in the moss gametophyte varied. The candidate gene trapped in a gene-trap line YH209, which shows rhizoid-specific expression, was obtained by 5' and 3' RACE. This gene was named PpGLU, and forms a clade with plant acidic alpha -glucosidase genes. Thus, these gene-trap and enhancer-trap systems should prove useful to identify tissue- and cell-specific genes in Physcomitrella.

Books etc

  • An experimental system for examining phototropic response of gametophytic shoots in the moss Physcomitrella patens
    Bao L, Yamamoto K.T, Fujita T (Joint workMethods in Molecular Biology, 1924, 45-51. doi: 10.1007/978-1-4939-9015-3_5)
    Humana Press, New York, NY 2019 (ISBN: 9781493990153)
  • 緑色植物の PSI-PSII 超複合体
    横野牧生, 高林厚史, 岸本純子, 藤田知道, 岩井優和, 村上明男, 秋本誠志, 田中歩 (Others)
    光合成研究 2018
  • 植物栽培における重力環境制御の基礎
    唐原一郎, 玉置大介, 久米篤, 蒲池浩之, 半場祐子, 藤田知道 
    アグリバイオ 2017/10
  • 植物生理学概論 改訂版
    櫻井英博, 柴岡弘郎, 高橋陽介, 小関良宏, 藤田知道 (Contributor)
    培風館 2017/09
  • 植物ゲノム科学辞典
    藤田知道, 駒嶺穆, 町田泰則, 藤村達人, 田畑哲之, 三位正洋, 斉藤和季 (Others)
    朝倉書店 2009
  • 植物の百科事典「細胞極性、不等分裂」
    藤田知道, 石井龍一, 岩槻邦男, 長谷部光泰, 矢澤進, 矢原徹一, 和田正三 (Others)
    朝倉書店 2009
  • 植物細胞工学シリーズ23、植物の進化 「発生遺伝子の進化」
    長谷部光泰, 藤田知道, 倉田哲也, 佐藤良勝, 久保稔, 村田隆, 青山剛士, 三上浩司, 石川雅樹, 日渡祐二, 青野直樹, 篠原直貴, 西山智明, 棚橋貴子 (Joint work)
    秀潤社 2007
  • 植物ホルモンの分子細胞生物学「セン類、タイ類の植物ホルモン」
    藤田知道, 小柴共一, 神谷勇治, 勝見允行 
    講談社サイエンティフィク 2006
  • ヒメツリガネゴケを用いた植物幹細胞の不等分裂過程の解析−細胞極性形成から娘細胞の運命決定まで−
    植物化学調節学会 2006
  • Gene tagging, gene- and enhancer-trap systems, and full-length cDNA overexpression in Physcomitrella patens
    Fujita, T, Nishiyama, T, Hiwatashi, Y, Hasebe, M (Joint work)
    Kluwer Academic Publishers 2004
  • 植物細胞工学シリーズ20、新版植物ホルモンのシグナル伝達 「植物ホルモンの起源を探る—シダ植物,コケ植物,緑色藻類における植物ホルモンの役割から—」
    藤田 知道 
    秀潤社 2004
  • 学術月報「3度のポスドク体験から」
    藤田 知道 
    日本学術振興会 2000
  • タバコ遺伝的腫瘍の腫瘍形成に関わる遺伝子の検索
    藤田 知道 
    植物組織培養 1994
  • DNA複製機構の解明に向けてーDNA腫瘍ウイルスの手助け
    藤田 知道 
    生物工学会誌 1994
  • Habituation as a tumorous state that is interchangeable with a normal state in plant cells
    Syono, K, Fujita, T (Joint work)
    International Review of Cytology (eds. by Jeon, K. W. and Jarvik J.), 152, pp.265-299, Academic Press, 1994


  • 日本細胞生物学会大会における研究発表
  • Imaging analysis of intercellular communication of macromolecules through plasmodesmata in plants
  • アブシジン酸による細胞分裂様式変更に関わる新奇因子の単離と解析


  • Practical application of proximal remote sensing for plant growth monitoring in space
    久米 篤, 松田 修, 藤田 知道  Proceedings of The Thirty-second Space Utilization Symposium  32-  2019  [Not refereed][Not invited]
  • Tomomichi Fujita  F1000Prime  2018/06  [Not refereed][Not invited]
  • 唐原一郎, 玉置大介, 久米篤, 蒲池浩之, 半場祐子, 藤田知道  アグリバイオ  1-  (11)  1176‐1179  2017/10/20  [Not refereed][Not invited]
  • Hypergravity environment of 10 G changes plant growth, anatomy, chloroplast sizes and photosynthesis of the moss Physcomitrella patens
    Takemura, K, Watanabe, R, Kameishi, R, Sakaguchi, N, Kamachi, H, Kume, A, Fujita, T, Karahara, I, Hanba, Y.-T  Proceedings of 11th Asian Microgravity Symposium (International Journal of Microgravity Science and Application (IJMSA)  2017  [Not refereed][Not invited]
  • Fujita T, Kitagawa M  F1000Prime  2016/10  [Not refereed][Not invited]
  • 井上夏実, BAO Liang, 石川雅樹, 石川雅樹, 比嘉毅, 日渡祐二, 関根政実, 綿引雅昭, 長谷部光泰, 長谷部光泰, 和田正三, 藤田知道  日本植物学会大会研究発表記録  80th-  164  2016/09/01  [Not refereed][Not invited]
  • Fujita T, Kitagawa M  F1000Prime  2016/05  [Not refereed][Not invited]
  • Toward microgravity experiments in moss: The emerging model land plant, Physcomitrella patens on International Space Station and more
    Fujita, Tomomichi, Kamachi, Hiroyuki, Karahara, Ichiro, Kume, Atsushi, Sakata, Yoichi, Takabayashi, Atsushi, Tanaka, Ayumi, Nagashima, Hisae, Nishiyama, Tomoaki, Hashimoto, Hirofumi, Hasebe, Mitsuyasu, Hanba, Yuko, Hiwatashi, Yuji, Matsuda, Osamu, Motomura, Taizo, Yano, Sachiko  Proceedings of The Twenty-ninth Space Utilization Sysmposium  29-  19  -20  2014  [Not refereed][Not invited]
  • Toward microgravity experiments in moss: the response of hyper gravity environment of Physcomitrella patens
    Kume, Atsushi, Kamachi, Hiroyuki, Hanba, Yuko T, Takemura, Kaori, Karahara, Ichirou, Nagashima, Hisae, Yano, Sachiko, Fujita, Tomomichi  Proceedings of The Twenty-ninth Space Utilization Sysmposium  29-  21  -22  2014  [Not refereed][Not invited]
  • 長谷部光泰, 西山智明, 棚橋貴子, 青野直樹, 青山剛士, 程朝陽, 藤田知道, 橋本薫, 平井正良, 日渡祐二, 石川雅樹, 岩田美根子, 久保稔, 倉田哲也, 三上浩司, 宮崎さおり, 森長真一, 村田隆, 小原真理, 小栗康子, 小野寺直子, 佐藤良勝, 住川直美, 篠原直貴, 若月幸子, 杉本渚  日本植物生理学会年会要旨集  48th-  124  2007/03/15  [Not refereed][Not invited]
  • 植物細胞工学シリーズ20、新版植物ホルモンのシグナル伝達 「植物ホルモンの起源を探る-シダ植物,コケ植物,緑色藻類における植物ホルモンの役割から-」
    秀潤社  2004  [Not refereed][Not invited]

Awards & Honors

  • 2018 日本植物学会 Journal of Plant Research Best paper論文賞
    受賞者: 藤田 知道
  • 2014 北海道大学 北海道大学教育総長賞
    受賞者: 藤田 知道
  • 2014 日本植物学会 Journal of Plant Research Best paper論文賞
    受賞者: 藤田 知道
  • 2014 日本学術振興会 特別研究員等審査会専門委員及び国際事業委員会書面審査委員表彰者
    受賞者: 藤田 知道

Research Grants & Projects

  • ヒメツリガネゴケを用いた植物細胞極性、不等分裂、分化全能性の仕組みの解明
  • Molecular characterization of cell polarity, asymmetric cell division and totipotency in plants

Educational Activities

Teaching Experience

  • 形態機能学Ⅰ
    開講年度 : 2018
    課程区分 : 学士課程
    開講学部 : 理学部
  • Inter-Graduate School Classes(General Subject):Natural and Applied Sciences
    開講年度 : 2018
    課程区分 : 修士課程
    開講学部 : 大学院共通科目
    キーワード : 細胞増殖, 細胞極性, 細胞分化, 形態形成, 遺伝子発現, 光合成, 植物免疫, 神経回路, 動物行動学, 脳科学, 生殖機構, 発生, 内分泌,ホルモン, オムニバス, 現代生命科学, 知的財産
  • Biosystems Science
    開講年度 : 2018
    課程区分 : 修士課程
    開講学部 : 生命科学院
    キーワード : 細胞増殖、細胞極性、細胞分化、形態形成、遺伝子発現、光合成、植物免疫、神経回路、動物行動学、能科学、生殖機構、発生、内分泌、ホルモン、オムニバス、現代生命科学、知的財産
  • Higher Order Cellular Functions
    開講年度 : 2018
    課程区分 : 修士課程
    開講学部 : 生命科学院
    キーワード : コケ植物、ヒメツリガネゴケ、細胞極性、不等分裂、発生、ストレス耐性
  • Biology I
    開講年度 : 2018
    課程区分 : 学士課程
    開講学部 : 全学教育
    キーワード : 生体高分子,細胞の構造と機能,エネルギー代謝,細胞の成長と分裂,遺伝現象と遺伝子発現制御
  • Functional BioLogy III
    開講年度 : 2018
    課程区分 : 学士課程
    開講学部 : 理学部
    キーワード : 植物生理学,水と溶質の輸送,光合成,物質代謝,植物ホルモン,成長,分化,環境応答,バイオテクノロジー,食料生産,地球環境保全
  • Advanced Studies in Biology
    開講年度 : 2018
    課程区分 : 学士課程
    開講学部 : 理学部
    キーワード : 生物科学、研究実習、研究計画、成果のとりまとめ、発表
  • Literature Survey in Biology
    開講年度 : 2018
    課程区分 : 学士課程
    開講学部 : 理学部
    キーワード : 生物科学、文献講読、論文、発表
  • Freshman Seminar
    開講年度 : 2018
    課程区分 : 学士課程
    開講学部 : 全学教育
    キーワード : 分子生物学,細胞生物学,個体としての生物,生物集団,生物進化,プレゼンテーション
  • Laboratory Course in Cell Structure and Function
    開講年度 : 2018
    課程区分 : 学士課程
    開講学部 : 理学部
    キーワード : 遺伝子解析,大腸菌,DNA抽出,制限酵素地図,PCR,遺伝子クローニング,遺伝子発現,タンパク質発現・解析,突然変異体,分子遺伝学的解析,ライブセルイメージング, 画像解析,タンパク質-タンパク質相互作用

Social Contribution

Social Contribution

Social Contribution

  • 北海道大学オープンキャンパス(高校生限定プログラム)
    Role : Lecturer

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