LPixel Inc.

Bunkyō-ku, Japan

LPixel Inc.

Bunkyō-ku, Japan
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Higaki T.,University of Tokyo | Takigawa-Imamura H.,Kyushu University | Akita K.,University of Tokyo | Kutsuna N.,University of Tokyo | And 4 more authors.
Plant and Cell Physiology | Year: 2017

Pavement cells in cotyledons and true leaves exhibit a jigsaw puzzle-like morphology in most dicotyledonous plants. Among the molecular mechanisms mediating cell morphogenesis, two antagonistic Rho-like GTPases regulate local cell outgrowth via cytoskeletal rearrangements. Analyses of several cell wall-related mutants suggest the importance of cell wall mechanics in the formation of interdigitated patterns. However, how these factors are integrated is unknown. In this study, we observed that the application of exogenous cellulase to hydroponically grown Arabidopsis thaliana cotyledons switched the interdigitation of pavement cells to the production of smoothly elongated cells. The cellulaseinduced inhibition of cell interdigitation was not observed in a RIC1 knockout mutant. This gene encodes a Rho-like GTPase-interacting protein important for localized cell growth suppression via microtubule bundling on concave cell interfaces. Additionally, to characterize pavement cell morphologies, we developed a mathematical model that considers the balance between cell and cell wall growth, restricted global cell growth orientation, and regulation of local cell outgrowth mediated by a Rho-like GTPase-cytoskeleton system. Our computational simulations fully support our experimental observations, and suggest that interdigitated patterns form because of mechanical buckling in the absence of Rho-like GTPase-dependent regulation of local cell outgrowth. Our model clarifies the cell wall mechanics influencing pavement cell morphogenesis.

Iwayama K.,Ryukoku University | Aisaka Y.,LPixel Inc | Kutsuna N.,LPixel Inc | Kutsuna N.,University of Tokyo | And 2 more authors.
Bioinformatics | Year: 2017

Motivation: Considerable attention has been given to the quantification of environmental effects on organisms. In natural conditions, environmental factors are continuously changing in a complex manner. To reveal the effects of such environmental variations on organisms, transcriptome data in field environments have been collected and analyzed. Nagano et al. proposed a model that describes the relationship between transcriptomic variation and environmental conditions and demonstrated the capability to predict transcriptome variation in rice plants. However, the computational cost of parameter optimization has prevented its wide application. Results: We propose a new statistical model and efficient parameter optimization based on the previous study. We developed and released FIT, an R package that offers functions for parameter optimization and transcriptome prediction. The proposed method achieves comparable or better prediction performance within a shorter computational time than the previous method. The package will facilitate the study of the environmental effects on transcriptomic variation in field conditions. © The Author 2017.

Nagata K.,University of Tokyo | Hashimoto C.,University of Tokyo | Watanabe-Asaka T.,University of Tokyo | Itoh K.,University of Tokyo | And 17 more authors.
Scientific Reports | Year: 2016

Radiotherapy is widely used in cancer treatment. In addition to inducing effects in the irradiated area, irradiation may induce effects on tissues close to and distant from the irradiated area. Japanese medaka, Oryzias latipes, is a small teleost fish and a model organism for evaluating the environmental effects of radiation. In this study, we applied low-energy carbon-ion (26.7 MeV/u) irradiation to adult medaka to a depth of approximately 2.2 mm from the body surface using an irradiation system at the National Institutes for Quantum and Radiological Science and Technology. We histologically evaluated the systemic alterations induced by irradiation using serial sections of the whole body, and conducted a heart rate analysis. Tissues from the irradiated side showed signs of serious injury that corresponded with the radiation dose. A 3D reconstruction analysis of the kidney sections showed reductions in the kidney volume and blood cell mass along the irradiated area, reflecting the precise localization of the injuries caused by carbon-beam irradiation. Capillary aneurysms were observed in the gill in both ventrally and dorsally irradiated fish, suggesting systemic irradiation effects. The present study provides an in vivo model for further investigation of the effects of irradiation beyond the locally irradiated area.

Akita K.,University of Tokyo | Kobayashi M.,Tokyo University of Science | Sato M.,RIKEN | Kutsuna N.,University of Tokyo | And 7 more authors.
Protoplasma | Year: 2016

In most dicotyledonous plants, leaf epidermal pavement cells develop jigsaw puzzle-like shapes during cell expansion. The rapid growth and complicated cell shape of pavement cells is suggested to be achieved by targeted exocytosis that is coordinated with cytoskeletal rearrangement to provide plasma membrane and/or cell wall materials for lobe development during their morphogenesis. Therefore, visualization of membrane trafficking in leaf pavement cells should contribute an understanding of the mechanism of plant cell morphogenesis. To reveal membrane trafficking in pavement cells, we observed monomeric red fluorescent protein-tagged rat sialyl transferases, which are markers of trans-Golgi cisternal membranes, in the leaf epidermis of Arabidopsis thaliana. Quantitative fluorescence imaging techniques and immunoelectron microscopic observations revealed that accumulation of the red fluorescent protein occurred mostly in the curved regions of pavement cell borders and guard cell ends during leaf expansion. Transmission electron microscopy observations revealed that apoplastic vesicular membrane structures called paramural bodies were more frequent beneath the curved cell wall regions of interdigitated pavement cells and guard cell ends in young leaf epidermis. In addition, pharmacological studies showed that perturbations in membrane trafficking resulted in simple cell shapes. These results suggested possible heterogeneity of the curved regions of plasma membranes, implying a relationship with pavement cell morphogenesis. © 2016 Springer-Verlag Wien

Fujiwara M.T.,RIKEN | Fujiwara M.T.,Sophia University | Kojo K.H.,Sophia University | Kojo K.H.,University of Tokyo | And 5 more authors.
Frontiers in Plant Science | Year: 2015

Plastids in the leaf epidermal cells of plants are regarded as immature chloroplasts that, like mesophyll chloroplasts, undergo binary fission. While mesophyll chloroplasts have generally been used to study plastid division, recent studies have suggested the presence of tissue- or plastid type-dependent regulation of plastid division. Here, we report the detailed morphology of plastids and their stromules, and the intraplastidic localization of the chloroplast division-related protein AtFtsZ1-1, in the leaf epidermis of an Arabidopsis mutant that harbors a mutation in the chloroplast division site determinant gene AtMinE1. In atminE1, the size and shape of epidermal plastids varied widely, which contrasts with the plastid phenotype observed in atminE1 mesophyll cells. In particular, atminE1 epidermal plastids occasionally displayed grape-like morphology, a novel phenotype induced by a plastid division mutation. Observation of an atminE1 transgenic line harboring an AtMinE1 promoter::AtMinE1-yellow fluorescent protein fusion gene confirmed the expression and plastidic localization of AtMinE1 in the leaf epidermis. Further examination revealed that constriction of plastids and stromules mediated by the FtsZ1 ring contributed to the plastid pleomorphism in the atminE1 epidermis. These results illustrate that a single plastid division mutation can have dramatic consequences for epidermal plastid morphology, thereby implying that plastid division and morphogenesis are differentially regulated in epidermal and mesophyll plastids. © 2015 Fujiwara, Kojo, Kazama, Sasaki, Abe and Itoh.

Higaki T.,University of Tokyo | Kutsuna N.,University of Tokyo | Kutsuna N.,LPixel Inc. | Akita K.,University of Tokyo | And 3 more authors.
PLoS Computational Biology | Year: 2016

Plant leaf epidermal cells exhibit a jigsaw puzzle–like pattern that is generated by interdigitation of the cell wall during leaf development. The contribution of two ROP GTPases, ROP2 and ROP6, to the cytoskeletal dynamics that regulate epidermal cell wall interdigitation has already been examined; however, how interactions between these molecules result in pattern formation remains to be elucidated. Here, we propose a simple interface equation model that incorporates both the cell wall remodeling activity of ROP GTPases and the diffusible signaling molecules by which they are regulated. This model successfully reproduces pattern formation observed in vivo, and explains the counterintuitive experimental results of decreased cellulose production and increased thickness. Our model also reproduces the dynamics of three-way cell wall junctions. Therefore, this model provides a possible mechanism for cell wall interdigitation formation in vivo. © 2016 Higaki et al.

Nagashima T.,University of Tokyo | Oami E.,University of Tokyo | Kutsuna N.,University of Tokyo | Kutsuna N.,LPixel Inc. | And 2 more authors.
Developmental Biology | Year: 2016

The nervous system plays a critical role in the regulation of animal body sizes. In Caenorhabditis elegans, an amine neurotransmitter, dopamine, is required for the tactile perception of food and food-dependent behavioral changes, while its role in development is unknown. In this study, we show that dopamine negatively regulates body size through a D2-like dopamine receptor, DOP-3, in C. elegans. Dopamine alters body size without affecting food intake or developmental rate. We also found that dopamine promotes egg-laying, although the regulation of body size by dopamine was not solely caused by this effect. Furthermore, dopamine negatively regulates body size through the suppression of signaling by octopamine and Gq-coupled octopamine receptors, SER-3 and SER-6. Our results demonstrate that dopamine and octopamine regulate the body size of C. elegans and suggest a potential role for perception in addition to ingestion of food for growth. © 2016 Elsevier Inc.

Akita K.,University of Tokyo | Higaki T.,University of Tokyo | Kutsuna N.,University of Tokyo | Kutsuna N.,LPixel Inc. | Hasezawa S.,University of Tokyo
Plant Signaling and Behavior | Year: 2015

Leaf pavement cells are shaped like a jigsaw puzzle in most dicotyledon species. Molecular genetic studies have identified several genes required for pavement cells morphogenesis and proposed that microtubules play crucial roles in the interdigitation of pavement cells. In this study, we performed quantitative analysis of cortical microtubule orientation in leaf pavement cells in Arabidopsis thaliana. We captured confocal images of cortical microtubules in cotyledon leaf epidermis expressing GFP-tubulinβ and quantitatively evaluated the microtubule orientations relative to the pavement cell growth axis using original image processing techniques. Our results showed that microtubules kept parallel orientations to the growth axis during pavement cell growth. In addition, we showed that immersion treatment of seed cotyledons in solutions containing tubulin polymerization and depolymerization inhibitors decreased pavement cell complexity. Treatment with oryzalin and colchicine inhibited the symmetric division of guard mother cells. © 2015 Taylor & Francis Group, LLC.

Takahashi S.,University of Tokyo | Takahashi S.,University of Tsukuba | Kojo K.H.,University of Tokyo | Kojo K.H.,LPixel Inc | And 6 more authors.
Frontiers in Plant Science | Year: 2015

Ultraviolet (UV)-B irradiation leads to DNA damage, cell cycle arrest, growth inhibition, and cell death. To evaluate the UV-B stress-induced changes in plant cells, we developed a model system based on tobacco Bright Yellow-2 (BY-2) cells. Both low-dose UV-B 3 (low UV-B: 740 J m-2) and high-dose UV-B (high UV-B: 2960 J m-2) inhibited cell proliferation and induced cell death; these effects were more pronounced at high UV-B. a, Flow cytometry showed cell cycle arrest within 1 day after UV-B irradiation; neither n low- nor high-UV-B-irradiated cells entered mitosis within 12h. Cell cycle progression ,; was gradually restored in low-UV-B-irradiated cells but not in high-UV-B-irradiated cells. UV-A irradiation, which activates cyclobutane pyrimidine dimer (CPD) photolyase, reduced inhibition of cell proliferation by low but not high UV-B and suppressed high-UV-B-induced cell death. UV-B induced CPD formation in a dose-dependent manner. The amounts of CPDs decreased gradually within 3 days in low-UV-B-irradiated i, a, cells, but remained elevated after 3 days in high-UV-B-irradiated cells. Low UV-B slightly, increased the number of DNA single-strand breaks detected by the comet assay at 1 day after irradiation, and then decreased at 2 and 3 days after irradiation. High UV-B increased DNA fragmentation detected by the terminal deoxynucleotidyl transferase dUTP nick end labeling assay 1 and 3 days after irradiation. Caffeine, an inhibitor of ataxia telangiectasia mutated (ATM) and ataxia telangiectasia and Rad3-related (ATR) al checkpoint kinases, reduced the rate of cell death in high-UV-B-irradiated cells. Our data suggest that low-UV-B-induced CPDs and/or DNA strand-breaks inhibit DNA replication and proliferation of BY-2 cells, whereas larger contents of high-UV-B-induced CPDs and/or DNA strand-breaks lead to cell death. © 2015 Takahashi, Kojo, Kutsuna, Endo, Toki, Isoda and Hasezawa.

Fujiwara T.,Nagoya University | Kawachi M.,Nagoya University | Sato Y.,Nagoya University | Mori H.,Nagoya University | And 4 more authors.
FEBS Journal | Year: 2015

Zinc (Zn) is an essential micronutrient required for plant growth and development. In Arabidopsis thaliana, several families of Zn transporters engaged in Zn import, export and intracellular compartmentalization play important roles in Zn homeostasis. We describe a novel Zn transporter, A. thaliana metal tolerance protein 12 (AtMTP12), which belongs to the cation diffusion facilitator family. AtMTP12 is predicted to consist of 798 amino acids and have 14 transmembrane segments. The expression of AtMTP12 in suspension-cultured cells was not affected by Zn deficiency or excess. Heterologous expression in a mutant of budding yeast (Saccharomyces cerevisiae) that lacks Msc2p, an orthologue of AtMTP12, revealed that AtMTP12 complements the growth phenotype of the msc2 mutant when AtMTP5t1, one of the splicing variants of AtMTP5, is coexpressed. Transient expression of AtMTP12-fused green fluorescent protein in A. thaliana mesophyll protoplasts demonstrated that AtMTP12 is localized to the Golgi apparatus. Moreover, AtMTP12 and AtMTP5t1 interact in the Golgi, as determined by a bimolecular fluorescence complementation assay. These results suggest that AtMTP12 forms a functional complex with AtMTP5t1 to transport Zn into the Golgi. © 2015 FEBS.

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