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Nara, Japan

Nara Institute of Science and Technology , abbreviated as NAIST, is a Japanese national university located in Ikoma, Nara of Kansai Science City. It was founded in 1991 with a focus on research and consists solely of graduate schools in three integrated areas: Biological science, Information science, and Material science. In 2010, NAIST ranked first overall among the 86 Japanese national universities by the Japanese government in its first-ever six-year assessment of national university standards and achievements.The university has a total of about 1,000 Master's and Doctoral students in its three graduate schools , among which 10% are international students . There are about 200 faculty members and 170 staff . Wikipedia.

Morita M.T.,Nara Institute of Science and Technology
Annual Review of Plant Biology | Year: 2010

Plants can reorient their growth direction by sensing organ tilt relative to the direction of gravity. With respect to gravity sensing in gravitropism, the classic starch statolith hypothesis, i.e., that starch-accumulating amyloplast movement along the gravity vector within gravity-sensing cells (statocytes) is the probable trigger of subsequent intracellular signaling, is widely accepted. Several lines of experimental evidence have demonstrated that starch is important but not essential for gravity sensing and have suggested that it is reasonable to regard plastids (containers of starch) as statoliths. Although the word statolith means sedimented stone, actual amyloplasts are not static but instead possess dynamic movement. Recent studies combining genetic and cell biological approaches, using Arabidopsis thaliana, have demonstrated that amyloplast movement is an intricate process involving vacuolar membrane structures and the actin cytoskeleton. This review covers current knowledge regarding gravity sensing, particularly gravity susception, and the factors modulating the function of amyloplasts for sensing the directional change of gravity. Specific emphasis is made on the remarkable differences in the cytological properties, developmental origins, tissue locations, and response of statocytes between root and shoot systems. Such an approach reveals a common theme in directional gravity-sensing mechanisms in these two disparate organs. Copyright © 2010 by Annual Reviews. All rights reserved. Source

Yoshida A.,Nara Institute of Science and Technology
Blood | Year: 2013

The ubiquitin ligase constitutively photomorphogenic 1 (COP1) is involved in many biological responses in mammalian cells, but its role in tumorigenesis remains unclear. Here we show that COP1 is a ubiquitin ligase for the tumor suppressor CCAAT/enhancer-binding protein (C/EBPα) and promotes its degradation in vivo, thereby blocking myeloid differentiation of hematopoietic cells for tumorigenesis. In this process, mammalian homolog of Tribbles, Trib1, which contains a COP1-binding motif, is essential for down-regulation of C/EBPα expression. Murine bone marrow transplantation experiments showed that coexpression of COP1 accelerates development of acute myeloid leukemia induced by Trib1, which pathologically resembles that of p42C/EBPα-deficient mice. Interestingly, coexpression of ligase activity-deficient COP1 mutant abrogated Trib1-induced leukemogenesis. These results indicate that COP1 and Trib1 act as an oncoprotein complex functioning upstream of C/EBPα, and its ligase activity is crucial for leukemogenesis. Source

Shoji T.,Nara Institute of Science and Technology
International Review of Cell and Molecular Biology | Year: 2014

Plants have developed elaborate detoxification mechanisms to cope with a large number of potentially toxic compounds, which include exogenous xenobiotics and endogenous metabolites, especially secondary metabolites. After enzymatic modification or synthesis, such compounds are transported and accumulated in apoplastic cell walls or central vacuoles in plant cells. Membrane transporters actively catalyze translocation of a diverse range of these compounds across various membranes within cells. Biochemical, molecular, and genetic studies have begun to reveal functions of a handful of ATP-binding cassette and multidrug and toxic compound extrusion family transporters engaged in transport of organic xenobiotics, heavy metals, metalloids, aluminum, alkaloids, flavonoids, terpenoids, terpenoid-derived phytohormones, cuticle lipids, and monolignols in plants. This detoxification versatility and metabolic diversity may underlie the functional diversification in plants of these families of transporters, which are largely involved in multidrug resistance in microorganisms and animals. © 2014 Elsevier Inc. Source

Kawabata T.,Nara Institute of Science and Technology
Proteins: Structure, Function and Bioinformatics | Year: 2010

Detection of pockets on protein surfaces is an important step toward finding the binding sites of small molecules. In a previous study, we defined a pocket as a space into which a small spherical probe can enter, but a large probe cannot. The radius of the large probes corresponds to the shallowness of pockets. We showed that each type of binding molecule has a characteristic shallowness distribution. In this study, we introduced fundamental changes to our previous algorithm by using a 3D grid representation of proteins and probes, and the theory of mathematical morphology. We invented an efficient algorithm for calculating deep and shallow pockets (multiscale pockets) simultaneously, using several different sizes of spherical probes (multiscale probes). We implemented our algorithm as a new program, ghecom (grid-based HECOMi finder). The statistics of calculated pockets for the structural dataset showed that our program had a higher performance of detecting binding pockets, than four other popular pocketfinding programs proposed previously. The ghecom also calculates the shallowness of binding ligands, R inaccess(minimum radius of inaccessible spherical probes) that can be obtained from the multiscale molecular volume. We showed that each part of the binding molecule had a bias toward a specific range of shallowness. These findings will be useful for predicting the types of molecules that will be most likely to bind putative binding pockets, as well as the configurations of binding molecules. The program ghecom is available through the Web server ( http://biunit.naist.jp/ghecom). © 2009 Wiley-Liss, Inc. Source

Kimata Y.,Nara Institute of Science and Technology | Kohno K.,Nara Institute of Science and Technology
Current Opinion in Cell Biology | Year: 2011

Upon endoplasmic reticulum (ER) stress, ER-located transmembrane stress sensors evoke diverse protective responses. Although ER stress-dependent activation of the sensor proteins is partly explained through their negative regulation by the ER-located chaperone BiP under non-stress conditions, each of the sensors is also regulated by distinct mechanism(s). For instance, yeast Ire1 is fully activated via its direct interaction with unfolded proteins accumulated in the ER. This insight is consistent with a classical notion that unfolded proteins per se trigger ER-stress responses, while various stress stimuli also seem to activate individual sensors independently of unfolded proteins and in a stimuli-specific manner. These properties may account for the different responses observed under different conditions in mammalian cells, which carry multiple ER-stress sensors. © 2010 Elsevier Ltd. Source

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