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Yoshiki Kubota

Publications and source records attributed to Yoshiki Kubota.

15 recordsLinked to original sources
PubMed2006

Two novel nuclear genes, OsSIG5 and OsSIG6, encoding potential plastid sigma factors of RNA polymerase in rice: tissue-specific and light-responsive gene expression.

Two novel nuclear genes, OsSIG5 and OsSIG6, encoding potential plastid sigma factors of RNA polymerase (RNAP) were identified in Oryza sativa. The deduced amino acid sequences contain conserved regions, regions 1.2-4.2, and a novel region A/B at the N-terminus. Tissue-specific and light-responsive transcripts of OsSIG5 and OsSIG6 were observed. The N-terminal region of OsSig5 conferred import of green fluorescent protein into the chloroplast. Specific transcripts of rice psbA were synthesized in vitro by reconstituted OsSig5-RNAP holoenzymes. These results indicated that OsSig5 is a plastid sigma factor. This is the first report of the Sig5-type sigma factor in crops.

Amino Acid Sequence↗
PubMed2006

An analytical approach to determine the pore shape and size of MCM-41 materials from X-ray diffraction data.

The pore shape and size of MCM-41 were studied analytically by comparing the observed powder X-ray diffraction intensities with that derived from the MCM-41 crystal structure models, with two different pore shapes, a hexagon and a circle. The powder diffraction patterns from the as-synthesized and the calcined MCM-41 were measured by a synchrotron radiation at SPring-8, Japan. The MCM-41 structure with circular and hexagonal pore shapes explains well for the as-synthesized and the calcined MCM-41 crystals, respectively. The pore size and boundary obtained by this approach agree with those obtained from an N2 gas adsorption measurement combined with the Fourier synthesized density map.

Journal Article↗
PubMed2006

Single structure widely distributed in a GeTe-Sb2Te3 pseudobinary system: a rock salt structure is retained by intrinsically containing an enormous number of vacancies within its crystal.

GeTe(1-x)-Sb2Te3(x) sputtered amorphous film was crystallized into a simple NaCl-type structure through instantaneous laser irradiation over a wide composition range from x = 0 to at least 2/3. When the ratio of Sb2Te3 increases, a vacancy is generated at every Na site for two Sb atoms. The fraction of vacancies, v(x), changes according to x/(1 + 2x), and the cubic root unit cell volume varies with a strong correlation to v(x). Through these created vacancies, valence electrons provided by adjacent Ge/Sb and Te atoms remain constant regardless of the composition, ensuring that these electrons occupy predominantly the bonding molecular orbitals. This results in crystal chemical stability, with the closed shell p-p bondings in the valence electrons arranging the crystal's atomic configuration into an NaCl-type structure.

Journal Article↗
PubMed2005

Formation and characterization of crystalline molecular arrays of gas molecules in a 1-dimensional ultramicropore of a porous copper coordination polymer.

Molecules and atoms confined in a nanospace may have properties distinctly different from those of the bulk fluid, owing to the formation of a specific molecular array characteristic of nanospace. In situ synchrotron powder X-ray diffraction measurements have been used to observe confined guest molecules such as N2, O2, Ar, and CH4 in the well-regulated ultramicropore of a copper coordination polymer, 1 ([Cu2(pzdc)2pyz]: pzdc = 2,3-pyrazinedicarboxylate and pyz = pyrazine). The obtained crystal structures indicate that guest molecules are confined in a linear fashion to form crystalline-like regular ordered arrays, in contrast to the situation in the gas and liquid state, even at temperatures above the boiling point, and the ordered arrays are characteristic of the kind of gas molecule and the geometrical and potential properties of the ultramicropore of 1.

Journal Article↗
PubMed2005

Extremely long period-stacking structure in the Sb-Te binary system.

The crystal structure of the delta-phase in the Sb-Te binary system has been determined by synchrotron powder diffraction. It is clearly shown that many intermetallic compounds, which have different stacking periods depending on compound composition, exist in this phase. These structures are based on the cubic ABC stacking structure, and two kinds of fundamental structural units form an intergrowth along the stacking direction at the atomic level. The chemical formulae of these compounds are expressed as Sb(2n)Te3, where n is an integer and the number of stacking layers is 2n + 3. There is a relationship of inverse proportionality between the stacking period and the Te concentration.

Antimony↗
PubMed2005

Highly controlled acetylene accommodation in a metal-organic microporous material.

Metal-organic microporous materials (MOMs) have attracted wide scientific attention owing to their unusual structure and properties, as well as commercial interest due to their potential applications in storage, separation and heterogeneous catalysis. One of the advantages of MOMs compared to other microporous materials, such as activated carbons, is their ability to exhibit a variety of pore surface properties such as hydrophilicity and chirality, as a result of the controlled incorporation of organic functional groups into the pore walls. This capability means that the pore surfaces of MOMs could be designed to adsorb specific molecules; but few design strategies for the adsorption of small molecules have been established so far. Here we report high levels of selective sorption of acetylene molecules as compared to a very similar molecule, carbon dioxide, onto the functionalized surface of a MOM. The acetylene molecules are held at a periodic distance from one another by hydrogen bonding between two non-coordinated oxygen atoms in the nanoscale pore wall of the MOM and the two hydrogen atoms of the acetylene molecule. This permits the stable storage of acetylene at a density 200 times the safe compression limit of free acetylene at room temperature.

Journal Article↗
PubMed2005

Refolding and purification of recombinant OsNifU1A domain II that was expressed by Escherichia coli.

OsNifU1A is a NifU-like rice (Oryza sativa) protein, discovered recently. Its amino acid sequence is very homologous to the sequence of cyanobacterial CnfU and to the sequences of NifU C-terminal domains. Based on its sequence, OsNifU1A is probably a modular structure consisting of two CnfU-like domains, with domain I (formed by residues Leu73 to Gly153) and domain II (formed by residues Leu154 to Ser226). Domain I have a conserved Cys-X-X-Cys motif, which may function as an iron-sulfur cluster assembly scaffold. Domain II lacks a Cys-X-X-Cys motif and therefore, cannot function analogously. Other NifU-like proteins, with sequences homologous to OsNifU1A domain II, have been identified during plant genomic projects; however, the biological roles of these domains remain unknown. We successfully constructed an Escherichia coli expression system for OsNifU1A domain II that enabled us to synthesize and purify milligram quantities of protein for use in structural and functional studies. Using the Gateway system, we built DNA sequences corresponding to two OsNifU1A domain II fusion proteins. One construct has a (His)6 sequence upstream of the OsNifU1A domain II sequence; the other has an upstream thioredoxin-(His)6 sequence. Recombinant OsNifU1A domain II fusion proteins were extracted from E. coli inclusion bodies by dissolving them in 6 M guanidine-HCl. About 36% of the total (His)6/OsNifU1A domain II fusion protein initially present remained soluble after guanidine-HCl was completely removed by step-wise dialysis; whereas, recovery of soluble Trx-(His)6 fusion protein was about 60% of the total cell lysate. About 2 mg of 15N-labeled OsNifU1A domain II was purified for NMR spectral studies. Examination of the OsNifU1A domain II 1H-15N HSQC NMR spectrum indicated that the purified protein was monomeric and correctly folded. Therefore, we established an efficient procedure for synthesis and purification of 15N-labeled OsNifU1A domain II in quantities sufficient for heteronuclear NMR solution structure studies.

Escherichia coli↗
PubMed2005

[A successful treatment of percutaneous radio frequency ablation for advanced thyroid cancer].

The patient was a 69-year-old woman. She received chemotherapy and radiation for thyroid tumor (undifferentiated cancer) following an operation in 1998. The chemotherapy was regularly repeated for relapse. The tumor increased gradually and came to cause dysphagia. She initially rejected nutritional management that depends on intravenous hyper alimentation or gastrostomy. After receiving an informed consent, we performed percutaneous radio frequency ablation (RFA) for the tumor using a Cool-tip needle on April 2, 2003. The algorithm of RFA was 9 min: 30 --> 120 W, 12 min: 50 --> 110 W, 9 min: 50 --> 100 W. After 2 days, the covered stent was implanted in the esophagus and an oral intake was started. Although the operation for undifferentiated thyroid cancer is controversial, we performed RFA and esophageal stenting for improving of QOL. This is the first case report in Japan.

Aged↗
PubMed2004

Structures of stable and metastable Ge2Sb2Te5, an intermetallic compound in GeTe-Sb2Te3 pseudobinary systems.

The most widely used memory materials for rewritable phase-change optical disks are the GeTe-Sb2Te3 pseudobinary compounds. Among these compounds, Ge2Sb2Te5 crystallizes into a cubic close-packed structure with a six-layer period (metastable phase) in the non-thermal equilibrium state, and a trigonal structure with a nine-layer period (stable phase) in the thermal equilibrium state. The structure of the stable phase has Ge/Sb layers in which Ge and Sb are randomly occupied, as does the structure of the metastable phase, while the conventionally estimated structure had separate layers of Ge and Te. The metastable and stable phases are very similar in that Te and Ge/Sb layers stack alternately to form the crystal. The major differences between these phases are: (i) the stable phase has pairs of adjacent Te layers that are not seen in the metastable phase and (ii) only the metastable phase contains vacancies of ca 20 at. % in the Ge/Sb layers.

Journal Article↗
PubMed2004

Guest shape-responsive fitting of porous coordination polymer with shrinkable framework.

In situ synchrotron X-ray powder diffraction patterns of porous coordination polymers [[Cu(2)(pzdc)(2)(bpy)].G] have been measured (pzdc = pyrazine-2,3-dicarboxylate, bpy = 4,4'-bipyridine) (where G = H(2)O for CPL-2 superset H(2)()O, G = benzene for CPL-2 superset benzene, and G = void for the apohost). The structures of apohost and CPL-2 superset benzene were determined from Rietveld analysis. Adsorption of benzene in the channels induced a remarkable contraction in the crystal (b axis; 6.8%, volume; 4.9%), although the channels were occupied by the benzene molecules. This crystal transformation provides a new pore structure that is well suited for benzene molecules, and we denote it as a "shape-responsive fitting" transformation. This type of pore gives rise to a new guideline: frameworks can be composed of flexible motifs that are linked via strong bond and/or stiff motifs that are connected via weaker bonds.

Journal Article↗
PubMed2002

Formation of a one-dimensional array of oxygen in a microporous metal-organic solid.

We report the direct observation of dioxygen molecules physisorbed in the nanochannels of a microporous copper coordination polymer by the MEM (maximum entropy method)/Rietveld method, using in situ high-resolution synchrotron x-ray powder diffraction measurements. The obtained MEM electron density revealed that van der Waals dimers of physisorbed O2 locate in the middle of nanochannels and form a one-dimensional ladder structure aligned to the host channel structure. The observed O-O stretching Raman band and magnetic susceptibilities are characteristic of the confined O2 molecules in one-dimensional nanochannels of CPL-1 (coordination polymer 1 with pillared layer structure).

Journal Article↗