Search Results 1-20 of 257

  • A simple and dual expression plasmid system in prokaryotic (<i>E. coli</i>) and mammalian cells.  [in Japanese]

    Murakami Manabu , Ohba Takayoshi , Murakami Agnieszka M. , Itagaki Shirou

    … The plasmid (prokaryotic mode) has an efficient selection system for DNA insertion, multiple component genes with rare restriction sites at both ends (termed "units"), and a simple transformation to mammalian expression mode utilizing rare restriction enzymes and re-ligation (deletion step). … With pgMAX system, we made epitope-library of the calcium channel alpha1 subunit (CaV1.2) and found a novel binding site to calcium channel beta2 subunit. …

    Proceedings for Annual Meeting of The Japanese Pharmacological Society 93(0), 3-P-331, 2020

    J-STAGE 

  • Genetic Characterization of a Novel Reassortant H5N6 Avian Influenza Virus Identified from a 10-Year-Old Girl

    Dong Zefeng , Ya Xuerong , Wang Di , Liu Cheng , Shen Qiang , Xia Yu

    … The hemagglutinin (HA) gene of this H5N6 virus belonged to the 2.3.4.4 H5 clade, and the HA linkage peptide of the JSSZ01 strain was RERRRKR↓GLF with multiple basic amino acids. … Q226L and G228S mutations were not observed, but S128P, S137A, and T160A substitutions were identified in the receptor binding sites. …

    Japanese Journal of Infectious Diseases 73(1), 36-43, 2020

    J-STAGE 

  • NMR Analysis on Molecular Interaction of Lignin with Amino Acid Residues of Carbohydrate-Binding Module from Trichoderma reesei Cel7A

    Tokunaga Yuki , Nagata Takashi , Suetomi Takashi , Oshiro Satoshi , Kondo Keiko , Katahira Masato , Watanabe Takashi

    … Nonproductive binding of lignin to cellulolytic enzymes should be avoided for conversion of lignocellulose through enzymatic saccharification. … Although carbohydrate-binding modules (CBMs) of cellulolytic enzymes strongly bind to lignin, the adsorption mechanism at molecular level is still unclear. …

    Scientific Reports (9), 2019-02-13

    IR 

  • ChIP‐Atlas: a data‐mining suite powered by full integration of public ChIP‐seq data

    Oki Shinya , Ohta Tazro , Shioi Go , Hatanaka Hideki , Ogasawara Osamu , Okuda Yoshihiro , Kawaji Hideya , Nakaki Ryo , Sese Jun , Meno Chikara

    … All peak‐call data are integrated to visualize multiple histone modifications and binding sites of transcriptional regulators (TRs) at given genomic loci. … The integrated data can be further analyzed to show TR–gene and TR–TR interactions, as well as to examine enrichment of protein binding for given multiple genomic coordinates or gene names. …

    EMBO Reports 2018(e46255), 1-10, 2018-12-19

    IR 

  • Kinetics of Defluoridation of Aqueous Waste-streams of the Aluminium Industry with a Modified Chelating Resin  [in Japanese]

    ROBSHAW Thomas , TUKRA Sudhir , D. OGDEN Mark

    … Experimental data were found to follow the Ho pseudo 2<sup>nd</sup>-order rate law and the Elovich equation, suggesting that, although multiple uptake mechanisms occurred on heterogeneous binding sites, the process was chemical reaction-controlled. …

    Journal of Ion Exchange 29(3), 104-109, 2018

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  • Using synthetic biology to study gene regulatory evolution

    Justin Crocker , Garth R Ilsley

    … Disentangling and characterizing the components of enhancer activity in multicellular eukaryotic development has proven challenging because enhancers contain activator and repressor binding sites for multiple factors that each exert nuanced, context-dependent control of enhancer activity. …

    Current Opinion in Genetics & Development (47), 91-101, 2017-09-29

    IR 

  • Prediction of the site of CYP3A4 metabolism of tolterodine by molecular dynamics simulation from multiple initial structures of the CYP3A4-tolterodine complex

    Sato Atsuko , Yuki Hitomi , Watanabe Chiduru , Saito Jun-ichi , Konagaya Akihiko , Honma Teruki

    … Predicting the sites of metabolism (SOM) by CYP3A4, as well as the binding modes, for target compounds is important for the design of metabolically more stable drugs. … Precisely predicting the structures of CYP3A4–ligand complexes is enormously challenging owing to the high number of conformational possibilities with its numerous binding substrates. …

    Chem-Bio Informatics Journal 17(0), 38-52, 2017

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  • The role of TDP–43 in ALS pathogenesis  [in Japanese]

    Urushitani Makoto

    … <p>TAR DNA–binding protein 43kDa (TDP–43) is a hallmark protein for amyotrophic lateral sclerosis (ALS), consisting of ubiquitinated and phosphorylated cytosolic inclusions in affected regions, namely TDP–43 proteinopathy. … Multiple cascades, basically causing a loss of these functions, have been proposed as TDP–43–linked ALS pathogenesis ; … Recent knowledge highlights the stress granules as responsible sites of TDP–43 inclusion formation. …

    Neurological Therapeutics 34(2), 72-78, 2017

    J-STAGE  Ichushi Web 

  • Highly Sensitive Fluorescence Quantitative Detection of Mercury in Soil Based on Non-labeled Molecular Beacon and Fluorescent Dye Hoechst 33258

    XIANG Dongshan , ZHAI Kun , SANG Qiuzhang , SHI Boan , YANG Xiaohong

    … In this analytical method, the loop of MB was designed to be a sequence that was complementary to the ssDNA with multiple T-T mismatches, the stem of MB was completely designed as C-G base pairs, and both ends of the MB are not modified by any fluorophore and quencher. … In the presence of Hg<sup>2+</sup>, the MB and ssDNA with multiple T-T mismatches formed a double-stranded nucleic acid (dsDNA) <i>via</i> …

    Analytical Sciences 33(3), 275-279, 2017

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  • The Binding of Silibinin, the Main Constituent of Silymarin, to Site I on Human Serum Albumin

    Yamasaki Keishi , Maruyama Toru , Otagiri Masaki , Sato Hiroki , Minagoshi Saori , Kyubun Karin , Anraku Makoto , Miyamura Shigeyuki , Watanabe Hiroshi , Taguchi Kazuaki , Seo Hakaru

    … In this study, we report on the binding of silibinin to plasma proteins, an issue that has not previously been extensively studied. … Mutual displacement experiments using ligands that primarily bind to sites I and II clearly revealed that silibinin binds tightly and selectively to site I (subsites Ia and/or Ic) of HSA, which is located in subdomain IIA. …

    Biological and Pharmaceutical Bulletin 40(3), 310-317, 2017

    J-STAGE  Ichushi Web 

  • DNA Garden: A Simple Method for Producing Arrays of Stretchable DNA for Single-Molecule Fluorescence Imaging of DNA-Binding Proteins

    Igarashi Chihiro , Murata Agato , Itoh Yuji , Subekti Dwiky Rendra Graha , Takahashi Satoshi , Kamagata Kiyoto

    … Without the need for a microfabricated substrate used for DNA tethering, it facilitates single-molecule investigations of DNA and DNA-binding proteins based on fluorescence microscopic imaging. … The DNA garden was applied to the detection of cleavage sites of restriction enzymes and for the observation of the sliding dynamics of a tumor suppressor, p53, along extended DNA at the single-molecule level. …

    Bulletin of the Chemical Society of Japan 90(1), 34-43, 2017

    J-STAGE 

  • NBS1 and multiple regulations of DNA damage response

    Komatsu Kenshi

    … NBS1, a protein responsible for the radiation-sensitive autosomal recessive disorder Nijmegen breakage syndrome, is one of the first factors to accumulate at sites of DNA double-strand breaks (DSBs). … In this article, we reviewed the functions of these binding proteins and their comprehensive association with NBS1. …

    Journal of Radiation Research 57(S1), i11-i17, 2016-08-16

    IR 

  • Characterization of the expression of the stress-responsive <i>PpERS1</i> gene from peach and analysis of its promoter using transgenic tomato

    Wang Bao-Quan , Liu Ji-Hong , Gong Xiao-Qing , Long Chao-An , Li Guo-Huai

    … Several putative <i>cis</i>-elements were identified in the promoter of <i>PpERS1</i>, including two ethylene-responsive elements (EREs), five W boxes, and four putative binding sites for MYB-type transcription factors. … gene might play important roles in response to multiple stresses via signal transduction mediated by ethylene receptors. …

    Plant Biotechnology 33(5), 383-393, 2016

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  • Cu(II)-Imprinted Chitosan Derivative Containing Carboxyl Groups for the Selective Removal of Cu(II) from Aqueous Solution

    Yoshida Wataru , Oshima Tatsuya , Baba Yoshinari , Goto Masahiro

    … Chitosan was modified with ketoglutaric acid to introduce multiple functional carboxyl groups, which interact with metal cations. … However, desorption of Cu(II) from the imprinted adsorbent was not sufficient because of the strong binding between Cu(II) and the imprinted adsorption sites.</p> …

    JOURNAL OF CHEMICAL ENGINEERING OF JAPAN 49(7), 630-634, 2016

    J-STAGE 

  • Ligand-binding characteristics of feline insulin-binding immunoglobulin G

    SUZUKI Takafumi , NISHII Naohito , TAKASHIMA Satoshi , MATSUBARA Tatsuya , IWASAWA Atsushi , TAKEUCHI Hirofumi , TAHARA Kohei , HACHISU Tatsuyuki , KITAGAWA Hitoshi

    … We purified and fractionated insulin-binding IgGs from cat sera by affinity chromatography and analyzed affinity of insulin-binding IgGs for insulin and their epitopes. … Following the passing of fraction A, which did not bind to insulin, insulin-binding IgGs were eluted into two fractions, B and C, by affinity chromatography using a column fixed with bovine insulin. …

    Journal of Veterinary Medical Science 77(11), 1379-1383, 2015

    J-STAGE  Ichushi Web 

  • Susceptibility to proteases of anti-Tn-antigen MLS128 binding glycoproteins expressed in human colon cancer cells

    Oura Fumie , Yajima Yukiko , Nakata Munehiro , Taniue Kenzui , Akiyama Tetsu , Nakada *Hiroshi , Yamamoto Kazuo , Fujita-Yamaguchi Yoko

    … It must contain multiple cleavage sites for trypsin and thermolysin since these proteases digested 110 kDa GP to MLS128-undetectable small fragments. … It seems to contain cleavage sites for cathepsin D which could cause limited digestion. …

    BioScience Trends 9(1), 49-55, 2015

    J-STAGE  Ichushi Web 

  • Genome-scale identification and characterization of moonlighting proteins

    Khan Ishita , Chen Yuqian , Dong Tiange , Hong Xioawei , Takeuchi Rikiya , Mori Hirotada , Kihara Daisuke

    … Moonlighting proteins perform two or more cellular functions, which are selected based on various contexts including the cell type they are expressed, their oligomerization status, and the binding of different ligands at different sites. … Here, we have developed a computational framework to find moonlighting proteins on a genome scale and identified multiple proteomic characteristics of these proteins. …

    2014-12-11

    IR 

  • Efficient screening of long terminal repeat retrotransposons that show high insertion polymorphism via high-throughput sequencing of the primer binding site

    Monden Yuki , Fujii Nobuyuki , Yamaguchi Kentaro , Ikeo Kazuho , Nakazawa Yoshiko , Waki Takamitsu , Hirashima Keita , Uchimura Yosuke , Tahara Makoto

    … Retrotransposons have been used frequently for the development of molecular markers by using their insertion polymorphisms among cultivars, because multiple copies of these elements are dispersed throughout the genome and inserted copies are inherited genetically. …

    Genome 57(5), 245-252, 2014-06-25

    IR 

  • Use of a Hexasubstituted Benzene Scaffold in the Development of Multivalent HIV-1 Integrase Inhibitors

    Tupchiangmai Wipa , Choksakulporn Saowanaporn , Tewtrakul Supinya , Pianwanit Somsak , Sritana-anant Yongsak

    … The highly directional hexasubstituted benzene moiety was used as the central scaffold to create new human immunodeficiency virus (HIV)-1 integrase inhibitors through the attachment of multiple active groups. …

    Chemical and Pharmaceutical Bulletin 62(8), 754-763, 2014

    J-STAGE  Ichushi Web 

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