Osaka University

About: Osaka University is a education organization based out in Osaka, Japan. It is known for research contribution in the topics: Laser & Catalysis. The organization has 83778 authors who have published 185669 publications receiving 5158122 citations. The organization is also known as: Ōsaka daigaku.

Redox-responsive self-healing materials formed from host–guest polymers

Abstract: Stimulus-responsive hydrogels have previously been developed that display heat-, light-, pH- or redox-induced sol–gel transitions. Nakahata et al. develop a self-healing supramolecular hydrogel based on host–guest polymers in which redox potential can induce a reversible sol–gel phase transition.

Defect physics of the CuInSe 2 chalcopyrite semiconductor

Abstract: We studied the defect physics in ${\mathrm{CuInSe}}_{2},$ a prototype chalcopyrite semiconductor. We showed that (i) it takes much less energy to form a Cu vacancy in ${\mathrm{CuInSe}}_{2}$ than to form cation vacancies in II-VI compounds (ii) defect formation energies vary considerably both with the Fermi energy and with the chemical potential of the atomic species, and (iii) the defect pairs such as $({2\mathrm{V}}_{\mathrm{Cu}}^{\mathrm{\ensuremath{-}}}{+\mathrm{I}\mathrm{n}}_{\mathrm{Cu}}^{2+})$ and $({2\mathrm{C}\mathrm{u}}_{\mathrm{In}}^{2\mathrm{\ensuremath{-}}}{+\mathrm{I}\mathrm{n}}_{\mathrm{Cu}}^{2+})$ have particularly low formation energies (under certain conditions, even exothermic). Using (i)--(iii), we (a) explain the existence of unusual ordered compounds ${\mathrm{CuIn}}_{5}{\mathrm{Se}}_{8},$ ${\mathrm{CuIn}}_{3}{\mathrm{Se}}_{5},$ ${\mathrm{Cu}}_{2}{\mathrm{In}}_{4}{\mathrm{Se}}_{7},$ and ${\mathrm{Cu}}_{3}{\mathrm{In}}_{5}{\mathrm{Se}}_{9}$ as a repeat of a single unit of $({2\mathrm{V}}_{\mathrm{Cu}}^{\mathrm{\ensuremath{-}}}{+\mathrm{I}\mathrm{n}}_{\mathrm{Cu}}^{2+})$ pairs for each $n=4,$ 5, 7, and 9 units, respectively, of ${\mathrm{CuInSe}}_{2};$ (b) attribute the very efficient $p$-type self-doping ability of ${\mathrm{CuInSe}}_{2}$ to the exceptionally low formation energy of the shallow defect Cu vacancies; (c) explained in terms of an electronic passivation of the ${\mathrm{In}}_{\mathrm{Cu}}^{2+}$ by ${2\mathrm{V}}_{\mathrm{Cu}}^{\mathrm{\ensuremath{-}}}$ the electrically benign character of the large defect population in ${\mathrm{CuInSe}}_{2}.$ Our calculation leads to a set of new assignment of the observed defect transition energy levels in the band gap. The calculated level positions agree rather well with available experimental data.

Accurate secondary structure prediction and fold recognition for circular dichroism spectroscopy

Abstract: Circular dichroism (CD) spectroscopy is a widely used technique for the study of protein structure. Numerous algorithms have been developed for the estimation of the secondary structure composition from the CD spectra. These methods often fail to provide acceptable results on α/β-mixed or β-structure–rich proteins. The problem arises from the spectral diversity of β-structures, which has hitherto been considered as an intrinsic limitation of the technique. The predictions are less reliable for proteins of unusual β-structures such as membrane proteins, protein aggregates, and amyloid fibrils. Here, we show that the parallel/antiparallel orientation and the twisting of the β-sheets account for the observed spectral diversity. We have developed a method called β-structure selection (BeStSel) for the secondary structure estimation that takes into account the twist of β-structures. This method can reliably distinguish parallel and antiparallel β-sheets and accurately estimates the secondary structure for a broad range of proteins. Moreover, the secondary structure components applied by the method are characteristic to the protein fold, and thus the fold can be predicted to the level of topology in the CATH classification from a single CD spectrum. By constructing a web server, we offer a general tool for a quick and reliable structure analysis using conventional CD or synchrotron radiation CD (SRCD) spectroscopy for the protein science research community. The method is especially useful when X-ray or NMR techniques fail. Using BeStSel on data collected by SRCD spectroscopy, we investigated the structure of amyloid fibrils of various disease-related proteins and peptides.

Biodiversity of Vibrios

Abstract: Vibrios are ubiquitous and abundant in the aquatic environment. A high abundance of vibrios is also detected in tissues and/or organs of various marine algae and animals, e.g., abalones, bivalves, corals, fish, shrimp, sponges, squid, and zooplankton. Vibrios harbour a wealth of diverse genomes as revealed by different genomic techniques including amplified fragment length polymorphism, multilocus sequence typing, repetetive extragenic palindrome PCR, ribotyping, and whole-genome sequencing. The 74 species of this group are distributed among four different families, i.e., Enterovibrionaceae, Photobacteriaceae, Salinivibrionaceae, and Vibrionaceae. Two new genera, i.e., Enterovibrio norvegicus and Grimontia hollisae, and 20 novel species, i.e., Enterovibrio coralii, Photobacterium eurosenbergii, V. brasiliensis, V. chagasii, V. coralliillyticus, V. crassostreae, V. fortis, V. gallicus, V. hepatarius, V. hispanicus, V. kanaloaei, V. neonatus, V. neptunius, V. pomeroyi, V. pacinii, V. rotiferianus, V. superstes, V. tasmaniensis, V. ezurae, and V. xuii, have been described in the last few years. Comparative genome analyses have already revealed a variety of genomic events, including mutations, chromosomal rearrangements, loss of genes by decay or deletion, and gene acquisitions through duplication or horizontal transfer (e.g., in the acquisition of bacteriophages, pathogenicity islands, and super-integrons), that are probably important driving forces in the evolution and speciation of vibrios. Whole-genome sequencing and comparative genomics through the application of, e.g., microarrays will facilitate the investigation of the gene repertoire at the species level. Based on such new genomic information, the taxonomy and the species concept for vibrios will be reviewed in the next years.