Core Research for Evolutional Science and Technology

Tsukuba, Japan

Core Research for Evolutional Science and Technology

Tsukuba, Japan
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Bunsupa S.,Chiba University | Katayama K.,Chiba University | Ikeura E.,Chiba University | Oikawa A.,RIKEN | And 5 more authors.
Plant Cell | Year: 2012

Lysine decarboxylase (LDC) catalyzes the first-step in the biosynthetic pathway of quinolizidine alkaloids (QAs), which form a distinct, large family of plant alkaloids. A cDNA of lysine/ornithine decarboxylase (L/ODC) was isolated by differential transcript screening in QA-producing and nonproducing cultivars of Lupinus angustifolius. We also obtained L/ODC cDNAs from four other QA-producing plants, Sophora flavescens, Echinosophora koreensis, Thermopsis chinensis, and Baptisia australis. These L/ODCs form a phylogenetically distinct subclade in the family of plant ornithine decarboxylases. Recombinant L/ODCs from QA-producing plants preferentially or equally catalyzed the decarboxylation of L-lysine and L-ornithine. L. angustifolius L/ODC (La-L/ODC) was found to be localized in chloroplasts, as suggested by the transient expression of a fusion protein of La-L/ODC fused to the N terminus of green fluorescent protein in Arabidopsis thaliana. Transgenic tobacco (Nicotiana tabacum) suspension cells and hairy roots produced enhanced levels of cadaverine-derived alkaloids, and transgenic Arabidopsis plants expressing (La-L/ODC) produced enhanced levels of cadaverine, indicating the involvement of this enzyme in lysine decarboxylation to form cadaverine. Site-directed mutagenesis and protein modeling studies revealed a structural basis for preferential LDC activity, suggesting an evolutionary implication of L/ODC in the QAproducing plants. © 2012 American Society of Plant Biologists. All rights reserved.

News Article | November 30, 2015

"A global shortage of fresh water is a long-term challenge that mankind faces in this century," said the director of the ROBUST membrane project, Professor Toshinori Tsuru. Professor Tsuru and his team have designed a new kind of ultra-thin layered membrane that acts as a sieve and separates salt from seawater to produce fresh water, a technique known as reverse osmosis. The membrane is partly made from silicon and overcomes several challenges of existing designs by tolerating the harsh conditions inside desalination plant equipment. The research has been published in the Journal of Membrane Science. One practical problem of separation membranes is "biofouling", where biofilms form on the membrane surface. This slows the amount of water that can pass through the membrane. Sodium hypochlorite is commonly used to remove these biofilms; however, the chlorine can also damage the membrane. Professor Tsuru, who is supported by CREST (Core Research for Evolutional Science and Technology) and is a member of the Center for Research on Environmentally Friendly Smart Materials at Hiroshima University's Institute of Engineering, said that the new membranes are more robust, which makes them resistant to chlorine. They are also heat resistant, meaning they can be used in desalination at a temperature of 80°C. "We are developing ROBUST membranes using three materials: silicon-based, hydrocarbon, and chemical vapor deposition. First we have developed silicon-based ROBUST membranes," Professor Tsuru said. "We expect Japan to continue to be one of the leading countries in membrane technologies and membrane-treatment systems," he said. Explore further: New membranes deliver clean water more efficiently

Jung J.-H.,Seoul National University | Jung J.-H.,University of Cambridge | Park J.-H.,Seoul National University | Lee S.,Seoul National University | And 6 more authors.
Plant Cell | Year: 2013

Exposure to short-term cold stress delays flowering by activating the floral repressor FLOWERING LOCUS C (FLC) in Arabidopsis thaliana. The cold signaling attenuator HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE1 (HOS1) negatively regulates cold responses. Notably, HOS1-deficient mutants exhibit early flowering, and FLC expression is suppressed in the mutants. However, it remains unknown how HOS1 regulates FLC expression. Here, we show that HOS1 induces FLC expression by antagonizing the actions of FVE and its interacting partner histone deacetylase 6 (HDA6) under short-term cold stress. HOS1 binds to FLC chromatin in an FVE-dependentmanner, and FVE is essential for the HOS1-mediated activation of FLC transcription. HOS1 also interacts with HDA6 and inhibits the binding of HDA6 to FLC chromatin. Intermittent cold treatments induce FLC expression by activating HOS1, which attenuates the activity of HDA6 in silencing FLC chromatin, and the effects of intermittent cold are diminished in hos1 and fve mutants. These observations indicate that HOS1 acts as a chromatin remodeling factor for FLC regulation under short-term cold stress. © 2013 American Society of Plant Biologists. All rights reserved.

Nakanishi H.,University of Tokyo | Nakanishi H.,Core Research for Evolutional Science and Technology | Iida Y.,University of Tokyo | Iida Y.,Core Research for Evolutional Science and Technology | And 3 more authors.
Journal of Biochemistry | Year: 2010

Endogenous phosphatidylcholine in biological membranes exists as isomers with acyl moieties at the sn-1 or sn-2 positions of the glycerol backbone. However, detailed biochemical information on these positional isomers is not generally available. This study is the first report on the separation and identification of positional isomers of endogenous phosphatidylcholine using reversed-phase LC-ESIMS/MS. The separation of positional isomers in PC was achieved by using ultra performance LC, which uses a high-resolution HPLC system. To identify positional isomers in individual PC species, their lyso-PC-related fragments and fatty acids, which were obtained by MS/MS analysis in the negative ion mode, were used. From the application results of biological samples, the lipid extracts of mouse brain were found to be abundant in PC containing 22:6 at the sn-1 position of the glycerol backbone. However, the lipid extracts from mouse heart and liver were not abundant in positional isomers. This achievement demonstrates that the relative amounts of positional isomers in various tissues or molecular species differ. These results will be useful for the clarification of the biological mechanisms of remodelling enzymes such as phospholipase and acyltransferase. Thus, our report provides a novel and critical milestone in understanding how molecular composition of phospholipids is established and their biological roles.

Murashima T.,Kyoto University | Murashima T.,Core Research for Evolutional Science and Technology | Taniguchi T.,Kyoto University | Taniguchi T.,Core Research for Evolutional Science and Technology
Journal of the Physical Society of Japan | Year: 2012

Polymer melts exhibit flow-history-dependent behavior. To clearly show this behavior, we have investigated the flow behavior of an entangled polymer melt around two cylinders placed in tandem along the flow direction in a two-dimensional periodic system. In this system, polymer states around a cylinder on the downstream side differ from those around a cylinder on the upstream side because the former have a memory of the strain they experienced when passing around the cylinder on the upstream side but the latter have no such memory. Therefore, the shear stress distributions around two cylinders are found to differ. Moreover, we have found that the mean flow velocity decreases accordingly with increasing distance between the two cylinders, whereas the applied external force is constant. Although this behavior is consistent with that of the Newtonian fluid, the flow-history-dependent behavior is found to enhance the reduction in the flow resistance. We have also discussed the microscopic states during the flow, observing the mean length of polymer chains, the mean number of entanglements, and the degree of orientation of polymer chains, which represented the flow-history-dependent behavior that reflects each relaxation process. © 2012 The Physical Society of Japan.

Sato Y.,Eisai Co. | Sato Y.,Core Research for Evolutional Science and Technology | Nakamura T.,Eisai Co. | Nakamura T.,Core Research for Evolutional Science and Technology | And 4 more authors.
Analytical Chemistry | Year: 2010

Normal-phase or reverse-phase liquid chromatography has been used in phospholipidomics for lipid separation prior to mass spectrometry analysis. However, separation using a single separation mode is often inadequate, as high-abundance phospholipids can mask large numbers of low-abundance lipids of interest. In order to detect and quantify low-abundance phospholipids, we present a novel two-dimensional (2D) approach for sensitive and quantitative global analysis of phospholipids. The methodology monitors individual glycerolipids and phospholipids through the use of a new quantitative normal-phase, solid-phase extraction procedure, followed by molecular characterization and relative quantification using an ion-trap Orbitrap equipped with a reverse-phase liquid chromatograph, with data processing by MS++ software. The CV (%) of the peak area of each lipid standard was less than 15% with this extraction method. When the method was applied to a liver sample, we could detect more phosphatidylserine (PS) compared to the previous method. Finally, our developed method was applied to Alzheimer's disease (AD) plasma samples. Several hundred peaks were detected from a 60 μL plasma sample. A partial-least-squares discriminant analysis (PLS-DA) plot using peak area ratio gave a unique group of PLS scores which could distinguish plasma samples of Alzheimer's disease (AD) patients from those of age-matched healthy controls. © 2010 American Chemical Society.

Kitao A.,Japan Science and Technology Agency | Kitao A.,Core Research for Evolutional Science and Technology
Journal of Chemical Physics | Year: 2011

Transform and relax sampling (TRS) is proposed as a conformational sampling method to enhance soft fluctuation in highly anisotropic systems using molecular dynamics simulation. This method consists of three stages; transform, relax, and sampling. In the transform stage, molecular dynamics simulation is performed with randomly assigned force bias to enhance the fluctuations along relatively soft collective movements, as expected from the linear response theory. After relaxing the heated system to equilibrium without force bias in the relax stage, Monte Carlo-type determination is made as to whether the generated state is accepted or not. The sampling stage is then conducted for conformational sampling by conventional molecular dynamics simulation. TRS is first applied for the idealized multidimensional double-well Cα model to mimic protein open-close transition. Subsequently, it is applied to three different all-atom protein systems in an explicit solvent model; T4 lysozyme, glutamine binding protein, and a mini-protein chignolin. Investigation of structural variations in the hinge angle of T4 lysozyme in crystals is demonstrated by TRS. The liganded close structure of the glutamine binding protein is sampled starting from the unliganded open form. Chignolin is shown to fold into a native structure multiple times starting from highly extended structures within 100 ns. It is concluded that TRS sampled a reasonable conformational space within a relatively short simulation time in these cases. Possible future extensions of TRS are also discussed. © 2011 American Institute of Physics.

Suzuki C.,Kyoto University | Miyamoto C.,Kyoto University | Furuyashiki T.,Kyoto University | Furuyashiki T.,Core Research for Evolutional Science and Technology | And 3 more authors.
FEBS Letters | Year: 2011

We found that centrally administered prostaglandin (PG) E2 exhibited anxiolytic-like activity in the elevated plus-maze and open field test in mice. Agonists selective for EP1 and EP4 receptors, among four receptor subtypes for PGE2, mimicked the anxiolytic-like activity of PGE2. The anxiolytic-like activity of PGE2 was blocked by an EP1 or EP4 antagonist, as well as in EP4 but not EP1 knockout mice. Central activation of either EP1 or EP4 receptors resulted in anxiolytic-like activity. The PGE2-induced anxiolytic-like activity was inhibited by antagonists for serotonin 5-HT1A, dopamine D1 and GABAA receptors. Taken together, PGE2 exhibits anxiolytic-like activity via EP1 and EP4 receptors, with downstream involvement of 5-HT1A, D1 and GABAA receptor systems. © 2011 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Sano T.,Kyoto University | Nagata S.,Kyoto University | Nagata S.,Core Research for Evolutional Science and Technology
FEBS Letters | Year: 2011

Eyes absent (EYA) has tyrosine- and threonine-phosphatase activities in their C-terminal and N-terminal regions, respectively. Using various mutants of mouse EYA3, we showed that the 68-amino acid domain between positions 53 and 120 was necessary and sufficient for its threonine-phosphatase activity. Point mutations were then introduced, and residues Cys-56, Tyr-77, His-79, and Tyr-90 were essential for the EYA3s threonine-phosphatase. The 68-amino acid domain is not well conserved among the four mouse EYA members, but is evolutionally highly conserved in the orthologous EYA members of different species, suggesting that the threonine-phosphatase of EYA3 has a function distinct from that of the other EYAs. © 2011 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

News Article | February 15, 2017

Tabletops can be shared spaces for collaborative work and are useful for a variety of tasks. For instance, documents, materials, mock-ups, and other objects can be exchanged between multiple people seated around a table. Taking inspiration from such real-life scenarios, it is a current aim to achieve a virtual-reality system that can be used for collaborative tabletop communications. To achieve such tabletop communications that are as natural as possible, a number of requirements must be satisfied. First, it should be possible to view 3D images over a full 360° range. Second, ordinary tabletop activities should not be inhibited. Third, the number of viewers should not be limited, and last, no special 3D glasses or wearable tracking system should be required. Although recently developed virtual-reality systems (i.e., head-mounted displays) can be used for collaborative work, they only satisfy the first tabletop requirement. Moreover, the user experience with these systems is that of a totally immersive virtual world where people depart from real-life communications. In addition, volumetric (volume-swept) displays1 can also be used to generate glasses-free 3D images with 360° viewing angles and thereby satisfy the first, third, and fourth requirements. However, they also include the use of showcase-like mechanical components on the table and thus do not satisfy the second of the requirements. Furthermore, several glasses-free tabletop 3D displays that satisfy all four conditions have previously been proposed.2, 3 These methods, however, generally involve the use of a horizontal high-speed rotation disk on the table (or a few high-refresh-rate projectors). Such high-speed components therefore mean that tradeoffs—between color-depth range, refresh rate, and the number of directions that can be displayed per second—are required. These systems thus generally entail substantial shortcomings when they are used to display full-color animations and interactive content. In addition, the moving component is usually bulky and gives rise to difficult momentum control when the display is enlarged. In our work,4 we have therefore developed a novel glasses-free tabletop 3D imaging technology—known as fVisiOn—with which we aim to display virtual 3D media alongside real media (in a natural manner). We can use this device to display full-color, 10cm-wide, 5cm-tall real-time 3D animations. We install the complete mechanism underneath the table to satisfy the second of the initial requirements. The system thus forms a 360° annular viewing area around the table, and provides horizontal parallax without the need for 3D glasses or head tracking in the horizontal plane (i.e., so that the third and fourth conditions are satisfied). Any number of viewers seated around the table (as in the first requirement), or standing at a distance of 1–2m, can therefore observe the 3D images from the ‘sweet direction’ of the fVisiOn system (i.e., at an elevation angle of 35° from the center of the table). An example of fVisiOn in use, is shown in Figure 1, where a real mirror and a toy duck are placed on the table around the displayed 3D computer-generated objects. From this photograph it is obvious that the virtual and real objects are both reflected by the mirror in a natural manner (because of the horizontal parallax that exists around the table). One of the distinctive features of our method is the ability to ‘float’ 3D images on an empty, flat tabletop by using only static components (see Figure 2), and the hardware components within our latest prototype are shown in Figure 3. The exterior of this prototype looks like an ordinary round table, with a diameter of 90cm and a height of 70cm. In this case, the conical rear-projection screen is installed beneath the table and its curved surface causes anisotropic diffusion of the incoming rays (i.e., it diffuses the light in the direction of the shape's edge so that it passes in the direction of the circumference). To demonstrate the operation of our prototype, we arranged 288 tiny projectors in a circle to generate light rays with many directions. Each pixel cast by these projectors corresponds to a particular ray. On a vertical plane, each ray enters the screen and exits at an angle. Part of this fan-like diffused light from the ray is then caught by the viewer's eyes (see Figure 2, left). In contrast, on a horizontal plane, the orientation of the rays that are produced from a series of projection centers is preserved after they pass through the screen (see Figure 2, right). At any position around the annular viewing area, the eye observes the slit-like parts in each projector's rays. The retina therefore collects fractional slit-like images from different projectors and forms an appropriate image for the perspective of each viewing point. Additional benefits that arise from our methodology include the blank space that surrounds the 3D images, and the fact that the tabletop is merely covered by a semi-transparent acrylic plate. Some sensors (e.g., cameras and magnetic devices) can thus be set underneath the table. Some examples of applications of our interactive 3D display are illustrated in Figure 4. For example, ‘imaginary 3D games’ from manga (graphic novels) and science fiction movies are enabled. By placing cards in a certain area of a table, the creatures on the cards are ‘summoned’ to the table as glasses-free 3D images. Multiple players can watch the creatures fight from any direction (i.e., over the full 360° range) around the table. fVisiOn is also suitable for ordinary collaborative activities around tabletops, e.g., it can be used during group discussions and teleconferences to share digital documents and virtual mock-ups. In summary, we have developed the so-called fVisiOn system as a novel glasses-free 3D imaging technology that can be used for various collaborative and gaming applications. We have also successfully demonstrated the use of a prototype, i.e., multiple viewers can view the 3D computer-generated objects around a 360° viewing range, at distance of about 0.5–2m, and with the correct perspective (i.e., an elevation angle of 35°). In our current work we have confirmed and realized our methodology with only the use of a ‘homemade’ prototype. Our displayed 3D images are thus somewhat blurry and unfocused (because of the limited precision of our equipment). In the next stages, we therefore aim to improve the 3D image quality we obtain with our system. For example, we need to shorten the angular pitch of the projectors so that we can generate sharper results. By employing fabrication techniques that are used in industry, we hope to create an improved system. Part of this research was supported by the Japan Science and Technology Agency's Core Research for Evolutional Science and Technology program.

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