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1. A colorimetric assay of protein kinase activity based on peptide-induced coagulation of gold nanorods B Biointerfaces

Author:
Katayama, Yoshiki,   et al.   ; Kitazaki, Hirotaro; Mori, Takeshi; Kang, Jeong-Hun; Niidome, Takuro; Murata, Masaharu; Hashizume, Makoto;     Show all 7 Authors
Source:
Colloids and surfaces 2012 v.99 pp. 7-11
ISSN:
0927-7765
Subject:
absorption; cetyltrimethylammonium bromide; coagulation; colloids; color; colorimetry; gold; inhibitory concentration 50; nanorods; peptides; phosphorylation
Abstract:
... We succeeded in applying gold nanorods (NRs) for the detection of protein kinase (PK) activity based on a substrate-induced coagulation mechanism. Because NRs have cationic surface charges due to surface-adsorbed cetyltrimethylammonium bromide, phosphorylated substrate peptides, which gain augmented anionic charges by phosphorylation, induce coagulation of the NRs, resulting in a red-to-blue color ...
DOI:
10.1016/j.colsurfb.2011.08.028

2. Addition of UVA-absorber butyl methoxy dibenzoylmethane to topical ketoprofen formulation reduces ketoprofen-photoallergic reaction

Author:
Tokura, Yoshiki,   et al.   ; Atarashi, Kenji; Takano, Masashi; Kato, Shunsuke; Kuma, Hidekazu; Nakanishi, Masaru;     Show all 6 Authors
Source:
Journal of photochemistry and photobiology 2012 v.113 pp. 56-62
ISSN:
1011-1344
Subject:
benzophenones; cross reaction; local lymph node assay; anti-inflammatory activity; topical application; ears; ketoprofen; models; photochemistry; mice; gels; photosensitivity; irradiation; dermatitis; guinea pigs; adverse effects; photobiology
Abstract:
... Topical application of ketoprofen (KP) clinically evokes the allergic type of photocontact dermatitis. To avoid this adverse reaction, we investigated the beneficial effect of each ultraviolet (UV) filter that was included in topical ketoprofen formulation. We first tested the inhibitory effects of four UVA filters by a modified local lymph node assay following KP application on the mouse skin and ...
DOI:
10.1016/j.jphotobiol.2012.05.002

3. An easily traceable scenario for 80% CO₂ emission reduction in Japan through the final consumption-based CO₂ emission approach: A case study of Kyoto-city

Author:
Yamagata, Yoshiki,   et al.   ; Shigeto, Sawako; Ii, Ryota; Hidaka, Masato; Horio, Masayuki;     Show all 5 Authors
Source:
Applied energy 2012 v.90 no.1 pp. 201-205
ISSN:
0306-2619
Subject:
carbon dioxide; case studies; energy efficiency; energy recovery; greenhouse gas emissions; infrastructure; models; people; socioeconomics; transportation; wastes; wood utilization; Japan
Abstract:
... To develop a scenario, easily traceable even for ordinary citizens, toward the national challenge target of 80% CO₂ reduction by 2050, we have proposed a new model that calculates the total CO₂ emission based on the final consumption. Using the model, we have tested appropriate (locally available) technology based sub-scenarios: (1) energy saving through electrification of all transportation; (2) ...
DOI:
10.1016/j.apenergy.2011.03.049

4. A new method for quantitative analysis of the T cell receptor V region repertoires in healthy common marmosets by microplate hybridization assay

Author:
Fujii, Yoshiki,   et al.   ; Kitaura, Kazutaka; Matsutani, Takaji; Shirai, Kenji; Suzuki, Satsuki; Takasaki, Tomohiko; Shimada, Shin; Kametani, Yoshie; Shiina, Takashi; Takabayashi, Shuji; Katoh, Hideki; Ogasawara, Kouetsu; Kurane, Ichiro; Suzuki, Ryuji;     Show all 14 Authors
Source:
Journal of immunological methods 2012 v.384 no.1-2 pp. 81-91
ISSN:
0022-1759
Subject:
CD4-positive T-lymphocytes; CD8-positive T-lymphocytes; Callithrix jacchus; animal models; cDNA libraries; complementary DNA; flow cytometry; hybridization; immunity; lymph nodes; mice; monoclonal antibodies; polymerase chain reaction; quantitative analysis; spleen; superantigens; tissues
Abstract:
... The common marmoset, Callithrix jacchus, is one of the smallest primates and is increasingly used for an experimental nonhuman primate model in many research fields. Analysis of T cell receptor (TCR) repertoires is a powerful tool to investigate T cell immunity in terms of antigen specificity and variability of TCR expression. However, monoclonal antibodies specific for many TCR Vα or Vβ chains ha ...
DOI:
10.1016/j.jim.2012.07.012

5. A novel double-coating carrier produced by solid-in-oil and solid-in-water nanodispersion technology for delivery of genes and proteins into cells

Author:
Katayama, Yoshiki,   et al.   ; Tahara, Yoshiro; Kaneko, Takeshi; Toita, Riki; Yoshiyama, Chiharu; Kitaoka, Takuya; Niidome, Takuro; Kamiya, Noriho; Goto, Masahiro;     Show all 9 Authors
Source:
Journal of controlled release 2012 v.161 no.3 pp. 713-721
ISSN:
0168-3659
Subject:
cytochrome c; drug delivery systems; drugs; electrostatic interactions; encapsulation; gene expression; genes; ovalbumin; peroxidase; plasmids
Abstract:
... A novel intracellular delivery method both for genes and proteins is one of the most coveted systems in the drug delivery field. In the present study, we developed a double-coating carrier loaded with gene and protein produced by solid-in-oil and solid-in-water nanodispersion technology. The double-coating carriers did not require electrostatic interactions during the preparation so were able to e ...
DOI:
10.1016/j.jconrel.2012.05.001

6. Catch performance of coastal squid jigging boats using LED panels in combination with metal halide lamps

Author:
Matsushita, Yoshiki,   et al.   ; Yamashita, Yukiko; Azuno, Toru;     Show all 3 Authors
Source:
Fisheries research 2012 v.113 no.1 pp. 182-189
ISSN:
0165-7836
Subject:
Todarodes pacificus; boats; lamps; linear models; squid; Japan; Sea of Japan
Abstract:
... Squid attracting light systems consisting of low power light emitting diode panels (LEDs) and conventional metal halide lamps (MHs) were tested to describe the influence of combinations of LEDs and MHs on squid catch. Fishing trials using LEDs (9kW) and different numbers of MHs were carried out in August and September 2009 targeting two squid species: (1) Japanese common squid Todarodes pacificus ...
DOI:
10.1016/j.fishres.2011.10.011

7. Characteristics of enzyme hydrolysis of cellulose under static condition

Author:
Ueno, Yoshiki,   et al.   ; Taneda, Daisuke; Ikeo, Makoto; Okino, Shohei;     Show all 4 Authors
Source:
Bioresource technology 2012 v.121 pp. 154-160
ISSN:
0960-8524
Subject:
cellulose; enzymatic hydrolysis; enzymes; hydrolysis; pulp; static load; sugars; synergism
Abstract:
... The effect of enzyme loading under static and agitated conditions was investigated. Enzymatic hydrolysis of 10w/v% de-lignified cellulose slurry such as filter paper, avicel and pulp was conducted under agitated (120rpm) and static condition, and the enzyme loading ranging from 1.2 to 120mg-protein/g-dry substrate. Under the agitated condition, the final sugar concentration decreased with the decr ...
DOI:
10.1016/j.biortech.2012.06.104
PubMed:
22858480

8. Chemometric Analysis with Near-Infrared Spectroscopy for Chemically Pretreated Erianthus toward Efficient Bioethanol Production

Author:
Horikawa, Yoshiki,   et al.   ; Imai, Tomoya; Takada, Rie; Watanabe, Takashi; Takabe, Keiji; Kobayashi, Yoshinori; Sugiyama, Junji;     Show all 7 Authors
Source:
Applied biochemistry and biotechnology 2012 v.166 no.3 pp. 711-721
ISSN:
0273-2289
Subject:
correlation; vibration; Saccharum; chemical analysis; data collection; models; cellulose; near-infrared spectroscopy; ethanol production; regression analysis; chemometrics; saccharification
Abstract:
... In this paper, we report the combination of a near-infrared (NIR) spectroscopic method with multivariate analysis in order to develop a calibration model of the saccharification ratio of chemically pretreated Erianthus. The regression models clearly depend on the NIR spectral regions, and the information of CH and aromatic framework vibrations contributed most effectively to the alkaline dataset. ...
DOI:
10.1007/s12010-011-9460-3
PubMed:
22127809

9. Completely β-Selective Glycosylation Using 3,6-O-(o-Xylylene)-Bridged Axial-Rich Glucosyl Fluoride

Author:
Ashikaga, Yoshiki,   et al.   ; Okada, Yasunori; Asakura, Noriaki; Bando, Masafumi; Yamada, Hidetoshi;     Show all 5 Authors
Source:
Journal of the American Chemical Society 2012 v.134 no.16 pp. 6940-6943
ISSN:
1520-5126
Subject:
alcohols; fluorides; glycosylation; isomerization; sieves
Abstract:
... A completely β-selective glycosylation that does not rely on neighboring group participation is described. The novelty of this work is the design of the glycosyl donor locked into the axial-rich form by the o-xylylene bridge between the 3-O and 6-O of d-glucopyranose. The synthesized 2,4-di-O-benzyl-3,6-O-(o-xylyene)glucopyranosyl fluoride could efficiently react with various alcohols in a SnCl₂–A ...
DOI:
10.1021/ja301480g

10. Composition and physiological function of the chloroplast NADH dehydrogenase‐like complex in Marchantia polymorpha

Author:
Nishimura, Yoshiki,   et al.   ; Ueda, Minoru; Kuniyoshi, Tetsuki; Yamamoto, Hiroshi; Sugimoto, Kazuhiko; Ishizaki, Kimitsune; Kohchi, Takayuki; Shikanai, Toshiharu;     Show all 8 Authors
Source:
plant journal 2012 v.72 no.4 pp. 683-693
ISSN:
0960-7412
Subject:
Arabidopsis; Marchantia polymorpha; NAD (coenzyme); chlorophyll; chloroplasts; electron transfer; fluorescence; gel electrophoresis; genes; light intensity; molecular weight; mosses and liverworts; photosystem I; prediction; thallus
Abstract:
... The chloroplast NADH dehydrogenase‐like (NDH) complex mediates cyclic electron transport and chloro‐respiration and consists of five sub‐omplexes, which in angiosperms further associate with photosystem I (PSI) to form a super‐complex. In Marchantia polymorpha, 11 plastid‐encoded subunits and all the nuclear‐encoded subunits of the A, B, membrane and ferredoxin‐binding sub‐complexes are conserved. ...
DOI:
10.1111/j.1365-313X.2012.05115.x
PubMed:
22862786

11. Correlation between phosphorylation ratios by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis and radioactivities by radioactive assay

Author:
Katayama, Yoshiki,   et al.   ; Tsuchiya, Akira; Asai, Daisuke; Kang, Jeong-Hun; Mori, Takeshi; Niidome, Takuro;     Show all 6 Authors
Source:
Analytical biochemistry 2012 v.421 no.2 pp. 773-775
ISSN:
0003-2697
Subject:
amino acids; correlation; desorption; ionization; matrix-assisted laser desorption-ionization mass spectrometry; monitoring; phosphorylation
Abstract:
... To investigate the correlation between the counts per minute (CPM) by radioactivity assay and the phosphorylation ratio by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI–TOF MS) analysis, we prepared 136 peptide substrates. The correlation coefficient of phosphorylation ratios to CPM was 0.77 for all samples. However, the more the numbers of positively charged ...
DOI:
10.1016/j.ab.2011.08.035

12. Crystal structure analysis of the translation factor RF3 (release factor 3)

Author:
Higuchi, Yoshiki,   et al.   ; Kihira, Kiyohito; Shimizu, Yoshihiro; Shomura, Yasuhito; Shibata, Naoki; Kitamura, Masaya; Nakagawa, Atsushi; Ueda, Takuya; Ochi, Kozo;     Show all 9 Authors
Source:
FEBS letters 2012 v.586 no.20 pp. 3705-3709
ISSN:
0014-5793
Subject:
bacteria; crystal structure; guanosine; guanosinetriphosphatase; stress response; translation (genetics)
Abstract:
... The bacterial translational GTPases release factor RF3 promotes translation termination by recycling RF1 or RF2. Here, we present the crystal structures of RF3 complexed with GDP and guanosine 3′,5′-(bis)diphosphate (ppGpp) at resolutions of 1.8 and 3.0Å, respectively. ppGpp is involved in the so-called “stringent response” of bacteria. ppGpp binds at the same site as GDP, suggesting that GDP and ...
DOI:
10.1016/j.febslet.2012.08.029

13. DDM1 (Decrease in DNA Methylation) genes in rice (Oryza sativa)

Author:
Habu, Yoshiki,   et al.   ; Higo, Hiromi; Tahir, Muhammad; Takashima, Kazuya; Miura, Asuka; Watanabe, Koichi; Tagiri, Akemi; Ugaki, Masashi; Ishikawa, Ryuji; Eiguchi, Mitsugu; Kurata, Nori; Sasaki, Takuji; Richards, Eric; Takano, Makoto; Kishimoto, Naoki; Kakutani, Tetsuji;     Show all 16 Authors
Source:
Molecular genetics and genomics 2012 v.287 no.10 pp. 785-792
ISSN:
1617-4615
Subject:
Arabidopsis thaliana; DNA methylation; Oryza sativa; amino acid sequences; complementary DNA; epigenetics; gene expression regulation; genes; genomics; growth and development; loci; mutants; plant growth; rice; transposons
Abstract:
... Regulation of cytosine methylation in the plant genome is of pivotal in determining the epigenetic states of chromosome regions. Relative tolerance of plant to deficiency in cytosine methylation provides unparalleled opportunities to study the mechanism for regulation of cytosine methylation. The Decrease in DNA Methylation 1 (DDM1) of Arabidopsis thaliana is one of the best characterized plant ep ...
DOI:
10.1007/s00438-012-0717-5

14. Deposition by the 2011 Tohoku-oki tsunami on coastal lowland controlled by beach ridges near Sendai, Japan

Author:
Sato, Yoshiki,   et al.   ; Takashimizu, Yasuhiro; Urabe, Atsushi; Suzuki, Koji;     Show all 4 Authors
Source:
Sedimentary geology 2012 v.282 pp. 124-141
ISSN:
0037-0738
Subject:
agricultural soils; subsidence; suspended sediment; tsunamis; glass; surveys; seawater; soil erosion; sand; earthquakes; silt; Bacillariophyceae; Japan
Abstract:
... A study of the 2011 Tohoku-oki tsunami deposits on the coastal lowland of the Sendai Plain, Japan was carried out along a shore-perpendicular survey line in the Arahama area. Field descriptions and tsunami water depth measurements were complemented by sedimentary analyses, including grain size, grain fabric and diatom analysis. The tsunami deposits show a generally fining-inland trend along the 3. ...
DOI:
10.1016/j.sedgeo.2012.07.004

15. Determination of bismuth in open ocean waters by inductively coupled plasma sector-field mass spectrometry after chelating resin column preconcentration

Author:
Sohrin, Yoshiki,   et al.   ; Norisuye, Kazuhiro;     Show all 2 Author
Source:
Analytica chimica acta 2012 v.727 pp. 71-77
ISSN:
0003-2670
Subject:
bismuth; detection limit; mass spectrometry; nitric acid; seawater
Abstract:
... A novel low-blank method is described for the analysis of bismuth in seawater based on preconcentration using an ethylenediaminetriacetic acid chelating resin column followed by determination with inductively coupled plasma sector-field mass spectrometry (ICPSFMS). A sample is siphoned into and drains through the column with the flow rate being kept constant by using a flotation device. Bi in 250m ...
DOI:
10.1016/j.aca.2012.03.042

16. Domain Swapping of the Heme and N-Terminal α-Helix in Hydrogenobacter thermophilus Cytochrome c552 Dimer

Author:
Higuchi, Yoshiki,   et al.   ; Hayashi, Yugo; Nagao, Satoshi; Osuka, Hisao; Komori, Hirofumi; Hirota, Shun;     Show all 6 Authors
Source:
Biochemistry 2012 v.51 no.43 pp. 8608-8616
ISSN:
1520-4995
Subject:
Hydrogenobacter; absorption; amino acids; circular dichroism spectroscopy; cytochrome c; dimerization; dissociation; enthalpy; entropy; ethanol; heme; horses; protein subunits; redox potential; thermal stability
Abstract:
... Oxidized horse cytochrome c (cyt c) has been shown to oligomerize by domain swapping its C-terminal helix successively. We show that the structural and thermodynamic properties of dimeric Hydrogenobacter thermophilus (HT) cytochrome c₅₅₂ (cyt c₅₅₂) and dimeric horse cyt c are different, although both proteins belong to the cyt c superfamily. Optical absorption and circular dichroism spectra of oxi ...
DOI:
10.1021/bi3011303

17. Early growth stage of a large delta — Transformation from estuarine-platform to deltaic-progradational conditions (the northeastern Mekong River Delta, Vietnam)

Author:
Saito, Yoshiki,   et al.   ; Hanebuth, Till J.J.; Proske, Ulrike; Nguyen, Van Lap; Ta, Thi Kim Oanh;     Show all 5 Authors
Source:
Sedimentary geology 2012 v.261-262 pp. 108-119
ISSN:
0037-0738
Subject:
developmental stages; river deltas; sea level; sediments; subsidence; Mekong River; Vietnam
Abstract:
... The initial growth stage of a river delta can be defined either as the beginning geomorphologic expansion of the river-dominated coastal lowland or as the starting basinward-directed progradation of the geological/stratigraphic delta body. Differentiating between these two perspectives is necessary for understanding the sensitive reaction of a deltaic system to dynamic changes in sea-level and sed ...
DOI:
10.1016/j.sedgeo.2012.03.014

18. Effect of Bisecting GlcNAc and Core Fucosylation on Conformational Properties of Biantennary Complex-Type N-Glycans in Solution B

Author:
Yamaguchi, Yoshiki,   et al.   ; Nishima, Wataru; Miyashita, Naoyuki; Sugita, Yuji; Re, Suyong;     Show all 5 Authors
Source:
The Journal of physical chemistry 2012 v.116 no.29 pp. 8504-8512
ISSN:
1520-5207
Subject:
fucose; glycoproteins; glycosidic linkages; hydrogen bonding; models; molecular dynamics; nuclear magnetic resonance spectroscopy
Abstract:
... The introduction of bisecting GlcNAc and core fucosylation in N-glycans is essential for fine functional regulation of glycoproteins. In this paper, the effect of these modifications on the conformational properties of N-glycans is examined at the atomic level by performing replica-exchange molecular dynamics (REMD) simulations. We simulate four biantennary complex-type N-glycans, namely, unmodifi ...
DOI:
10.1021/jp212550z

19. Evaluation of vertical cell fluidity in a multilayered sheet of skeletal myoblasts

Author:
Sawa, Yoshiki,   et al.   ; Kino-oka, Masahiro; Ngo, Trung Xuan; Nagamori, Eiji; Takezawa, Yasunori; Miyake, Yasuki; Saito, Atsuhiro; Shimizu, Tatsuya; Okano, Teruo; Taya, Masahito;     Show all 10 Authors
Source:
Journal of bioscience and bioengineering 2012 v.113 no.1 pp. 128-131
ISSN:
1389-1723
Subject:
confocal laser scanning microscopy; diffusivity; fibroblasts; myoblasts
Abstract:
... The procedure for fabricating a multilayered cell sheet has been developed by combining multiple sheets using a thermo-responsive surface and stamp system. Confocal laser scanning microscopy revealed that the fluidity of a multilayered sheet of skeletal myoblasts could be estimated as vertical diffusivity and changed upon addition of dermal fibroblasts. ...
DOI:
10.1016/j.jbiosc.2011.09.001

20. Exposure to 1-bromopropane induces microglial changes and oxidative stress in the rat cerebellum

Author:
Murakumo, Yoshiki,   et al.   ; Subramanian, Kaviarasan; Mohideen, Sahabudeen Sheik; Suzumura, Akio; Asai, Naoya; Takahashi, Masahide; Jin, Shijie; Zhang, Lingyi; Huang, Zhenlie; Ichihara, Sahoko; Kitoh, Junzoh; Ichihara, Gaku;     Show all 12 Authors
Source:
Toxicology 2012 v.302 no.1 pp. 18-24
ISSN:
0300-483X
Subject:
cerebellum; humans; immunohistochemistry; neuroglia; neurotoxicity; nitric oxide; oxidative stress; rats; reactive oxygen species; reproductive toxicology; solvents; thiobarbituric acid-reactive substances
Abstract:
... 1-Bromopropane (1-BP), an alternative to ozone-depleting solvents, is reported to exhibit neurotoxicity and reproductive toxicity in animals and humans. However, the underlying mechanism of the toxicity remains elusive. This study was designed to identify the microglial changes and oxidative stress in the central nervous system (CNS) after 1-BP exposure. Four groups of Wistar-ST rats (n=12 each) w ...
DOI:
10.1016/j.tox.2012.07.006