システム生物学のための統合解析シミュレータ WinBEST-KIT の開発

Previously, I developed the biochemical reaction simulator called WinBEST-KIT (Biochemical Engineering System analyzing Tool-KIT, which runs under Microsoft Windows) for analyzing complicated biochemical reaction systems such as metabolic pathways. WinBEST-KIT provides an integrated simulation environment for experimental researchers in the field of systems biology. One of the most notable features of WinBEST-KIT is that users can very easily customize user-defined reaction step symbols in the graphical user interface. It realizes that users can use their original mathematical kinetic equations for representing unknown kinetic mechanisms as reaction steps in addition to the prepared standard (pre-installed) mathematical kinetic equations such as Michaelis-Menten equation. The problem we must be considered is, however, that the mathematical modeling for the dynamics of the large-scale biochemical reaction systems needs stochastic fluctuation for the several reaction steps. In this study, I developed a new version of WinBEST-KIT that enables users to include the stochastic fluctuation into the customized user-defined reaction step symbols. Therefore, it is possible to include simultaneously both the reaction step symbols in which involve with the stochastic fluctuation and the reaction step symbols in which involve the conventional deterministic reactions, at constructing the model of the biochemical reaction systems to be analyzed with WinBEST-KIT

Bacillus subtilis Cw1Q (previous YjbJ) is a bifunctional enzyme exhibiting muramidase and soluble-lytic transglycosylase activities

CwIQ (previous YjbJ) is one of the putative cell wall hydrolases in Bacillus subtilis. Its domain has an amino acid sequence similar to the soluble-lytic transglycosylase (SLT) of Escherichia coli Slt70 and also goose lysozyme (muramidase). To characterize the enzyme, the domain of CwIQ was cloned and expressed in E. coil. The purified CwIQ protein exhibited cell wall hydrolytic activity. Surprisingly, RP-HPLC, mass spectrometry (MS), and MS/MS analyses showed that CwIQ produces two products, 1,6-anhydro-N-acetylmuramic acid and N-acetylmuramic acid, thus indicating that CwIQ is a bifunctional enzyme. The site-directed mutagenesis revealed that glutamic acid 85 (Glu-85) is an amino acid residue essential to both activities. (C) 2010 Elsevier Inc. All rights reserved.ArticleBIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS. 398(3):606-612 (2010)journal articl

An Explicit Formula of Subblock Occurrences for the p-Adic Expansion

Let b(n,w) be the number of occurrences of subblock w in the p-adic expansion of n ∈ N and set B(N,w)=Σn=0Nb(n,w) for N ∈ N. Properties of the value of B(N,w) were investigated by Prodinger [8] (for p=2) and by Kirschenhofer [3] (for a general p). In this paper we give a simple representation of B(N,w) by means of previous result [5] on the explicit formula of generalized power and exponential sums of digital sums

Identification and Characterization of a Novel Polysaccharide Deacetylase C (PdaC) from Bacillus subtilis

Cell wall metabolism and cell wall modification are very important processes that bacteria use to adjust to various environmental conditions. One of the main modifications is deacetylation of peptidoglycan. The polysaccharide deacetylase homologue, Bacillus subtilis YjeA (renamed PdaC), was characterized and found to be a unique deacetylase. The pdaC deletion mutant was sensitive to lysozyme treatment, indicating that PdaC acts as a deacetylase. The purified recombinant and truncated PdaC from Escherichia coli deacetylated B. subtilis peptidoglycan and its polymer, (-GlcNAc-MurNAc[-L-Ala-D-Glu]-)(n). Surprisingly, RP-HPLC and ESI-MS/MS analyses showed that the enzyme deacetylates N-acetylmuramic acid (MurNAc) not GlcNAc from the polymer. Contrary to Streptococcus pneumoniae PgdA, which shows high amino acid sequence similarity with PdaC and is a zinc-dependent GlcNAc deacetylase toward peptidoglycan, there was less dependence on zinc ion for deacetylation of peptidoglycan by PdaC than other metal ions (Mn2+, Mg2+, Ca2+). The kinetic values of the activity toward B. subtilis peptidoglycan were K-m = 4.8 mM and k(cat) = 0.32 s(-1). PdaC also deacetylated N-acetylglucosamine (GlcNAc) oligomers with a K-m = 12.3 mM and k(cat) = 0.24 s(-1) toward GlcNAc(4). Therefore, PdaC has GlcNAc deacetylase activity toward GlcNAc oligomers and MurNAc deacetylase activity toward B. subtilis peptidoglycan.ArticleJOURNAL OF BIOLOGICAL CHEMISTRY. 287(13):9765-9776 (2012)journal articl

Alteration of intestinal flora by the intake of enzymatic degradation products of adlay (Coix lachryma-jobi L. var. ma-yuen Stapf) with improvement of skin condition

AbstractAdlay has been used as a traditional Chinese medicine and nutrient for its beneficial effects on bowel movements and skin care. This study examined the effect of enzymatic degradation product of adlay, “Super Hatomugi” (SPH) on human skin and the intestinal flora in a randomized, double-blind placebo-controlled study. The subjects were divided into three groups: 500mg SPH, 1000mg SPH, and placebo, taken daily for 4weeks. Hematological and skin condition examinations as well as an analysis of intestinal flora were performed 2weeks before and 10weeks after the start of the SPH intake. Skin condition was improved by SPH intake as revealed by a reduction in the number of nucleated epidermal cells. In addition, an increase in the fecal population of Bacteroidetes followed the SPH intake. These results show the possibility that SPH improves the skin condition and changes the proportions of intestinal flora

Gliosarcoma arising from a fibrillary astrocytoma

We report a 67-year-old woman who was diagnosed with a gliosarcoma at a second operation after diagnosis of a fibrillary astrocytoma 5 months previously. Initially, she underwent a CT-guided stereotactic biopsy. Histological examination showed fibrillary astrocytoma (World Health Organization [WHO] grade II). Loss of heterozygosity (LOH) on 1 p, 10q, and 19q was not detected. She received chemotherapy, but no radiotherapy. Five months after the biopsy, MRI revealed rapid tumor growth. Tissue obtained from partial removal of the tumor revealed gliosarcoma (WHO grade IV), and LOH on 10q and 19q was detected. The history, histopathology, and genetic alterations of this patient are discussed.ArticleJOURNAL OF CLINICAL NEUROSCIENCE. 18(9):1251-1254 (2011)journal articl