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Nagoya-shi, Japan

Nakamura T.,Japan Institute for Molecular Science | Makabe K.,Japan Institute for Molecular Science | Makabe K.,Graduate University for Advanced Studies | Tomoyori K.,University of Tokyo | And 8 more authors.
Journal of Molecular Biology

Is the folding pathway conserved in homologous proteins? To address this question, we compared the folding pathways of goat α-lactalbumin and canine milk lysozyme using equilibrium and kinetic circular dichroism spectroscopy. Both Ca2+-binding proteins have 41% sequence identity and essentially identical backbone structures. The Φ-value analysis, based on the effect of Ca2+ on the folding kinetics, showed that the Ca2+-binding site was well organized in the transition state in α-lactalbumin, although it was not yet organized in lysozyme. Equilibrium unfolding and hydrogen-exchange 2D NMR analysis of the molten globule intermediate also showed that different regions were stabilized in the two proteins. In α-lactalbumin, the Ca2+-binding site and the C-helix were weakly organized, whereas the A- and B-helices, both distant from the Ca2+-binding site, were well organized in lysozyme. The results thus provide an example of highly homologous proteins taking different folding pathways. To understand the molecular origin of this difference, we investigated the native three-dimensional structures of the proteins in terms of non-local contact clusters, a parameter based on the residue-residue contact map and known to be well correlated with the folding rate of non-two-state proteins. There were remarkable differences between the proteins in the distribution of the non-local contact clusters, and these differences provided a reasonable explanation of the observed difference in the folding initiation sites. In conclusion, the protein folding pathway is determined not only by the backbone topology but also by the specific side-chain interactions of contacting residues. © 2010 Elsevier Ltd. Source

Suzuki S.,Leibniz Institute of Atmospheric Physics | Suzuki S.,NagoyaUniversity | Lubken F.-J.,Leibniz Institute of Atmospheric Physics | Baumgarten G.,Leibniz Institute of Atmospheric Physics | And 5 more authors.
Journal of Atmospheric and Solar-Terrestrial Physics

To investigate the vertical propagation of gravity waves from the lower to the upper atmosphere, combined measurements with an airglow imager and lidars were carried out at the Arctic Lidar Observatory for Middle Atmosphere Research (ALOMAR) station (69.3°N, 16.0°E) in northern Norway. Airglow imaging reveals the two-dimensional structure of gravity waves in the mesopause region, while the ALOMAR Rayleigh/Mie/Raman (RMR) lidar and sodium lidar provide the vertical structures between the stratosphere and the lower thermosphere. On 26 November 2010, the imager identified a mesoscale gravity wave structure in the sodium airglow that had a horizontal wavelength of 277km, a wave period of 59min, and propagated northeastward at a phase speed of 78m s-1. Simultaneous lidar measurements also showed upward wave signatures with a similar wave period in the temperature perturbations; the vertical wavelength of the upward wave seen in the temperature data is consistent with the dispersion relation for gravity waves. Based on the combined measurements with the imager and sodium lidar, the momentum flux of this gravity wave was estimated to be 1.0m2 s-2 at the sodium airglow height. Ray-tracing analysis suggested that the observed gravity wave was generated by a distortion of the polar jet at the tropopause via a geostrophic adjustment process. © 2013 Elsevier Ltd. Source

Asakura Y.,Honda Electronics Co. | Fukutomi S.,Nagoya University | Yasuda K.,NagoyaUniversity | Koda S.,Nagoya University
Journal of Chemical Engineering of Japan

For any sonochemical process, the maximum effect depends on a range of conditions and process optimization can lead to a considerable savings in electric power. In this paper, the optimization investigation focuses on the acoustic features of the ultrasonic reactor, such as the transducer impedance and the frequency components of sound pressure with respect to the reactor configuration, namely the liquid height and the upper end configuration for a cylindrically shaped sonochemical reactor. Measurements were carried out for the liquid heights varying in the range of 142 to 163 mm with and without an aluminum reflector mounted on the upper end of the liquid column for a ultrasonic frequency of 129 kHz. Our data revealed that the impedance of the transducer and the sonochemical efficiency are strongly dependent on the liquid height and on the upper part configuration of the reactor: free or fixed end. Moreover, the maximum sonochemical efficiency was attained at liquid heights where the transducer impedance showed minimum values, the distance between two consecutive maxima being λ/ 2 (where λ=11.6 mm in this work). The frequency components of the sound pressure into the liquid were also investigated, and it was discovered that the maximum sonochemical efficiency was reached when the harmonic components were enhanced and subharmonic were reduced. An automatic control system for increasing the sonochemical efficiency by maintaining the impedance at the minimum level with the help of frequency is presented here. © 2010 The Society of Chemical Engineers, Japan. Source

Fujiwara T.,Meijo University | Nakajima M.,Nagoya University | Ichikawa A.,Meijo University | Ohara K.,Meijo University | And 4 more authors.
IEEE-NANO 2015 - 15th International Conference on Nanotechnology

Muhi-graphene cubic structure was fabricated by a nanomanipulation system. Two nanomanipulators were coordinately used with three degrees of freedoms to handle two end-effectors respectively. A cubic net was designed and fabricated using a multi graphene by a FIB (Focused Ion Beam) etching. A tungsten probe was also reformed by the FIB etching to adjust the size of cubic net design for bending manipulation. 1 he each surface of cubic net was bent to form a cubic 3D structure. In this study, the bending stress of multi graphene were also measured using a silicon cantilever to reveal the elastic or plastic deformation regions by bending manipulation. © 2015 IEEE. Source

Nakajima M.,NagoyaUniversity | Takeuchi M.,Nagoya University | Hisamoto N.,Nagoya University | Fukuda T.,Nagoya University | And 4 more authors.
Proceedings - IEEE International Conference on Robotics and Automation

This paper presents a novel In situ nanomanipulation integrated with scanning electron microscope- computed tomography (SEM-CT) imaging system for 3D nanomanipulation. In our previous works, a nanorobotic manipulation system was established inside an environmental-SEM (E-SEM) for water-contained samples, including biological organism, based on a real-time high resolution SEM observation. However, the SEM image is limited in two dimensional (2D) and surficial information from the signals of secondly electrons. For nanosurgery applications, such as nanoinjection, it is needed to evaluate the sample in 3D space with its internal information after manipulation. The SEM-CT imaging system is developed for In situ nanomanipulation based on SEM observation. The CT is an effective method to obtain the internal 3D information as a non-destructive manner. The imaging resolution of our SEM-CT system is in less than 400 nm. A Caenorhabditis elegans (C. elegans) was used as a target of biological sample. To improve the contrast of SEM-CT imaging of C. elegans, the X-ray was tested by generating using brass and copper materials. Finally, the nanoinjection was demonstrated with SEM-CT imaging system to C. elegans using the nanoinjector which was fabricated by focused ion beam (FIB) process. © 2016 IEEE. Source

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