Kodama T

References (12)

Title : Phenolic derivatives with anti-acetylcholinesterase inhibitory activities from Galeola nudifolia in Vietnam - Minh_2023_Chem.Biodivers__e202301482
Author(s) : Minh K , Nakashima Y , Kodama T , Lee YE , Nguyen HM , Ikumi N , Morita H
Ref : Chem Biodivers , :e202301482 , 2023
Abstract : A new phenolic derivative, galeomalate A (1), together with five known structurally related compounds (2-6), was isolated from the ethyl acetate extract of Galeola nudifolia collected in Vietnam. The structures were elucidated by various spectroscopic methods, including 1D and 2D NMR, HR-ESI-TOF-MS, and CD data, and chemical conversion of the sugar moiety. All isolated compounds possessed acetylcholinesterase (AChE) inhibitory activities in a dose-dependent manner. Among them, compounds 2 and 3 exhibited the first and second highest inhibitory activity on AChE with IC50 values of 122.13 and 125.49 microM, respectively. Compounds 1 and 4-6 inhibited the AChE activity by mixed modes of action comprising competitive and non-competitive modes, whereas 2 and 3 exerted their inhibitory activities in a competitive manner. Molecular docking analyses suggested that the phenyl-beta-D-glucopyranoside unit of 2 and 3 bound to the active site of AChE for the competitive inhibitory activities, while the mixed inhibitory activity of 4 was due to the two binding patterns in the active-site and the active-site entrance of AChE. Furthermore, the docking studies indicated that 1, 5, and 6 would inhibit AChE in a mixed inhibitory manner by adopting three distinct binding patterns of the additional phenyl-beta-D-glucopyranoside unit at the active-site entrance.
ESTHER : Minh_2023_Chem.Biodivers__e202301482
PubMedSearch : Minh_2023_Chem.Biodivers__e202301482
PubMedID: 37899310

Title : Fatal Poisoning with Both Dichlorvos and Phenthoate - Nara_2018_J.Forensic.Sci_63_1928
Author(s) : Nara A , Yamada C , Kodama T , Saka K , Takagi T
Ref : J Forensic Science , 63 :1928 , 2018
Abstract : Organophosphates are widely used as pesticides. However, organophosphates are occasionally orally ingested to commit suicide. In this case, a man in his late 80s committed suicide by ingesting both dichlorvos and phenthoate. Autopsy findings revealed a characteristic volatile odor from his mouth, stomach, lungs, liver, and kidneys. The esophageal mucosa was denatured and had lost elasticity. Serum cholinesterase activity was 9 IU/L. Toxicological analyses performed using high-performance liquid chromatography-tandem mass spectrometry revealed that dichlorvos concentrations in the left and right cardiac blood samples were 11.6 and 4.6 mug/mL, respectively. Phenthoate concentrations in the left and right cardiac blood samples were 5.8 and 0.51 mug/mL, respectively. The total amounts of dichlorvos and phenthoate in the stomach were 7.35 and 4.55 g, respectively. The case history, autopsy findings, and toxicological analyses indicated that the cause of death was acute fatal poisoning after oral ingestion of both dichlorvos and phenthoate.
ESTHER : Nara_2018_J.Forensic.Sci_63_1928
PubMedSearch : Nara_2018_J.Forensic.Sci_63_1928
PubMedID: 29601635

Title : 2,3-Butandione 2-monoxime inhibits skeletal myosin II by accelerating ATP cleavage - Komatsu_2017_Biochem.Biophys.Res.Commun_490_849
Author(s) : Komatsu H , Koseki Y , Kanno T , Aoki S , Kodama T
Ref : Biochemical & Biophysical Research Communications , 490 :849 , 2017
Abstract : 2,3-Butandione 2-monoxime (BDM) is a widely used myosin inhibitor with an unclear mode of action. In this report, we investigated the mechanism of BDM oxime group nucleophilic reactivity on the phosphoester bond of ATP. BDM increased the ATPase activity of skeletal myosin subfragment 1 (S1) under conditions in which ATP cleavage is the rate-limiting step (K(+), EDTA-ATPase activity of native S1 and Mg(2+)-ATPase activity of trinitrophenylated S1 and partially unfolded S1). Furthermore, the effect of BDM on the S1-bound adenosine 5'-(beta,gamma-imido) triphosphate (AMPPNP) (31)P NMR spectrum suggests that BDM changes the microenvironment around the phosphorus atoms of myosin-bound nucleotide. A computational search for the BDM-binding site in the adenosine 5'-[gamma-thio] triphosphate (myosin-ATPgammaS) complex predicted that BDM is located adjacent to the nucleotide on myosin. Therefore, we propose that the BDM oxime group catalytically assists in ATP cleavage, thereby enhancing the ATPase activity of myosin in a manner analogous to pralidoxime-mediated reactivation of organophosphate-inactivated acetylcholinesterase. This is the first study suggesting that oxime provides catalytic assistance for ATP cleavage by an ATP-hydrolyzing enzyme.
ESTHER : Komatsu_2017_Biochem.Biophys.Res.Commun_490_849
PubMedSearch : Komatsu_2017_Biochem.Biophys.Res.Commun_490_849
PubMedID: 28648599

Title : Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli - Ogura_2009_Proc.Natl.Acad.Sci.U.S.A_106_17939
Author(s) : Ogura Y , Ooka T , Iguchi A , Toh H , Asadulghani M , Oshima K , Kodama T , Abe H , Nakayama K , Kurokawa K , Tobe T , Hattori M , Hayashi T
Ref : Proc Natl Acad Sci U S A , 106 :17939 , 2009
Abstract : Among the various pathogenic Escherichia coli strains, enterohemorrhagic E. coli (EHEC) is the most devastating. Although serotype O157:H7 strains are the most prevalent, strains of different serotypes also possess similar pathogenic potential. Here, we present the results of a genomic comparison between EHECs of serotype O157, O26, O111, and O103, as well as 21 other, fully sequenced E. coli/Shigella strains. All EHECs have much larger genomes (5.5-5.9 Mb) than the other strains and contain surprisingly large numbers of prophages and integrative elements (IEs). The gene contents of the 4 EHECs do not follow the phylogenetic relationships of the strains, and they share virulence genes for Shiga toxins and many other factors. We found many lambdoid phages, IEs, and virulence plasmids that carry the same or similar virulence genes but have distinct evolutionary histories, indicating that independent acquisition of these mobile genetic elements has driven the evolution of each EHEC. Particularly interesting is the evolution of the type III secretion system (T3SS). We found that the T3SS of EHECs is composed of genes that were introduced by 3 different types of genetic elements: an IE referred to as the locus of enterocyte effacement, which encodes a central part of the T3SS; SpLE3-like IEs; and lambdoid phages carrying numerous T3SS effector genes and other T3SS-related genes. Our data demonstrate how E. coli strains of different phylogenies can independently evolve into EHECs, providing unique insights into the mechanisms underlying the parallel evolution of complex virulence systems in bacteria.
ESTHER : Ogura_2009_Proc.Natl.Acad.Sci.U.S.A_106_17939
PubMedSearch : Ogura_2009_Proc.Natl.Acad.Sci.U.S.A_106_17939
PubMedID: 19815525
Gene_locus related to this paper: ecoli-Aes , ecoli-rutD , ecoli-bioh , ecoli-C2429 , ecoli-C4836 , ecoli-d7xp23 , ecoli-dlhh , ecoli-entf , ecoli-fes , ecoli-mhpc , ecoli-pldb , ecoli-ptrb , ecoli-yafa , ecoli-yaim , ecoli-ybff , ecoli-ycfp , ecoli-ycjy , ecoli-yeiG , ecoli-YFBB , ecoli-yghX , ecoli-yhet , ecoli-yiel , ecoli-yjfp , ecoli-YNBC , ecoli-ypfh , ecoli-ypt1 , ecoli-yqia , ecoli-Z1341 , ecoli-Z1930 , ecoli-Z2445 , ecoli-YfhR , yerpe-YBTT

Title : Human homolog of NOTUM, overexpressed in hepatocellular carcinoma, is regulated transcriptionally by beta-catenin\/TCF - Torisu_2008_Cancer.Sci_99_1139
Author(s) : Torisu Y , Watanabe A , Nonaka A , Midorikawa Y , Makuuchi M , Shimamura T , Sugimura H , Niida A , Akiyama T , Iwanari H , Kodama T , Zeniya M , Aburatani H
Ref : Cancer Sci , 99 :1139 , 2008
Abstract : The Drosophila Notum gene, which is regulated by the Wingless pathway, encodes a secreted hydrolase that modifies heparan sulfate proteoglycans. In comparative analysis of the gene expression profiles in primary human hepatocellular carcinomas (HCC) and normal organs, we observed that the human ortholog of Drosophila Notum was overexpressed markedly in a subset of HCC, but expressed rarely in adult normal tissues. Immunoblotting confirmed the overexpression of NOTUM protein in 12 of 40 primary HCC cases (30%). High levels of NOTUM protein were significantly associated with intracellular (nuclear or cytoplasmic) accumulation of beta-catenin protein: all 10 HCC with high intracellular beta-catenin also had high NOTUM expression, whereas only 2 of 30 cases (6.7%) without intracellular beta-catenin had high NOTUM expression (P < 0.00001). NOTUM expression in HepG2 cells was downregulated significantly by induction of a dominant-negative mutant of TCF4, a beta-catenin partner. In vivo binding of the beta-catenin/TCF complex to the NOTUM promoter was demonstrated by chromatin immunoprecipitation in HepG2 and SW480 cells, where canonical Wnt signaling is activated constitutively. These findings provide evidence that NOTUM is a novel target of beta-catenin/TCF4 and is upregulated in Wnt/beta-catenin signaling-activated HCC.
ESTHER : Torisu_2008_Cancer.Sci_99_1139
PubMedSearch : Torisu_2008_Cancer.Sci_99_1139
PubMedID: 18429952

Title : Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice - Kikuchi_2003_Science_301_376
Author(s) : Kikuchi S , Satoh K , Nagata T , Kawagashira N , Doi K , Kishimoto N , Yazaki J , Ishikawa M , Yamada H , Ooka H , Hotta I , Kojima K , Namiki T , Ohneda E , Yahagi W , Suzuki K , Li CJ , Ohtsuki K , Shishiki T , Otomo Y , Murakami K , Iida Y , Sugano S , Fujimura T , Suzuki Y , Tsunoda Y , Kurosaki T , Kodama T , Masuda H , Kobayashi M , Xie Q , Lu M , Narikawa R , Sugiyama A , Mizuno K , Yokomizo S , Niikura J , Ikeda R , Ishibiki J , Kawamata M , Yoshimura A , Miura J , Kusumegi T , Oka M , Ryu R , Ueda M , Matsubara K , Kawai J , Carninci P , Adachi J , Aizawa K , Arakawa T , Fukuda S , Hara A , Hashizume W , Hayatsu N , Imotani K , Ishii Y , Itoh M , Kagawa I , Kondo S , Konno H , Miyazaki A , Osato N , Ota Y , Saito R , Sasaki D , Sato K , Shibata K , Shinagawa A , Shiraki T , Yoshino M , Hayashizaki Y , Yasunishi A
Ref : Science , 301 :376 , 2003
Abstract : We collected and completely sequenced 28,469 full-length complementary DNA clones from Oryza sativa L. ssp. japonica cv. Nipponbare. Through homology searches of publicly available sequence data, we assigned tentative protein functions to 21,596 clones (75.86%). Mapping of the cDNA clones to genomic DNA revealed that there are 19,000 to 20,500 transcription units in the rice genome. Protein informatics analysis against the InterPro database revealed the existence of proteins presented in rice but not in Arabidopsis. Sixty-four percent of our cDNAs are homologous to Arabidopsis proteins.
ESTHER : Kikuchi_2003_Science_301_376
PubMedSearch : Kikuchi_2003_Science_301_376
PubMedID: 12869764
Gene_locus related to this paper: orysa-Q852M6 , orysa-Q8GSE8 , orysa-Q9FYP7 , orysa-Q5JLP6 , orysa-Q8H5P5 , orysa-Q7F1Y5 , orysa-cbp3 , orysa-Q6YSZ8 , orysa-Q8S5X5 , orysa-Q8LIG3 , orysa-Q7F1B1 , orysa-Q9FW17 , orysa-Q337C3 , orysa-Q84QZ6 , orysa-Q84QY7 , orysa-Q6ZDG5 , orysa-Q658B2 , orysa-Q8H3R3 , orysa-Q5SNH3 , orysa-q2qnj4 , orysa-q2qyi1 , orysa-Q4VWY7 , orysa-q5smv5 , orysa-q5z901 , orysa-Q5ZBI5 , orysa-q6atz0 , orysa-q6i5q3 , orysj-q6yse8 , orysa-q6z8b1 , orysa-q6z995 , orysa-q7x7y5 , orysa-q7xkj9 , orysa-q7xr63 , orysa-q7xsq2 , orysa-q7xts6 , orysa-Q8LQS5 , orysa-Q8W3C6 , orysa-q53m20 , orysa-q67iz3 , orysa-q67j02 , orysa-q67j05 , orysa-q67j09 , orysa-q67j10 , orysa-q67tv0 , orysa-q67uz1 , orysa-q69xr2 , orysa-q69y21 , orysa-q75hy2 , orysa-q75i01 , orysa-q688m8 , orysa-q688m9 , orysa-Q6H8G1 , orysi-b8a7e7 , orysi-b8bfe5 , orysj-cgep , orysj-q0djj0 , orysj-q0jaf0 , orysj-q5jl22 , orysj-q6h7q9 , orysj-q6yvk6 , orysj-q7f8x1 , orysj-q10j20 , orysj-q10ss2 , orysj-q69uw6

Title : [Recent findings on local anesthetics] - Kitagawa_2001_Masui_50_S71
Author(s) : Kitagawa N , Kodama T , Totoki T
Ref : Masui , 50 :S71 , 2001
Abstract :
ESTHER : Kitagawa_2001_Masui_50_S71
PubMedSearch : Kitagawa_2001_Masui_50_S71
PubMedID: 11871107

Title : Cloning and characterization of genes involved in the degradation of dibenzofuran by Terrabacter sp. strain DBF63. -
Author(s) : Kasuga K , Nojiri H , Yamane H , Kodama T , Omori T
Ref : J Ferment Bioeng , 84 :387 , 1997
Gene_locus related to this paper: 9mico-q3mnp3 , tersp-DBFC

Title : Inverse relationship between serum cholinesterase activity and the administration of cyclophosphamide: an index of cyclophosphamide therapy [see comments] - Imai_1994_Nephrol.Dial.Transplant_9_1240
Author(s) : Imai H , Kodama T , Yasuda T , Nakamoto Y , Miura AB
Ref : Nephrol Dial Transplant , 9 :1240 , 1994
Abstract : To determine whether serum cholinesterase activity can be a monitoring index of cyclophosphamide therapy in patients with steroid-resistant glomerulopathy, we compared the cholinesterase activity of 37 patients who received a combined therapy that included the use of cyclophosphamide, prednisolone, antiplatelet drugs, and anticoagulant drugs, with the cholinesterase activity of 25 patients who received prednisolone therapy that excluded cyclophosphamide from the combined therapy. In the prednisolone and the combined groups, cholinesterase activity declined as shown in the following formula: Y = 371-26.4 x log(X): (r2 = 0.28), Y = 444-147.7 x log(X): (r2 = 0.95), respectively. (Y: cholinesterase activity, X: the day after treatment). In the combined therapy group, the prevalence of adverse reactions following treatment in the subgroup below 200 U/l of cholinesterase activity was significantly greater (P < 0.01) than that in the subgroup above 200 U/l of cholinesterase activity. However, there was no significant difference (P < 0.25) in the prevalence of adverse reactions between the subgroups with more or less than 184 U/l of cholinesterase activity following treatment. These results suggest the importance of not going below 200 U/l of cholinesterase activity after treatment when the normal cholinesterase activity range is between 300 and 760 U/l (e.g. less than 65% of the lowest value of the normal range of other hospitals) in order to eliminate the hazards of cyclophosphamide to the patients with steroid-resistant glomerulopathy.
ESTHER : Imai_1994_Nephrol.Dial.Transplant_9_1240
PubMedSearch : Imai_1994_Nephrol.Dial.Transplant_9_1240
PubMedID: 7816283

Title : Structure, organization, and chromosomal mapping of the human macrophage scavenger receptor gene - Emi_1993_J.Biol.Chem_268_2120
Author(s) : Emi M , Asaoka H , Matsumoto A , Itakura H , Kurihara Y , Wada Y , Kanamori H , Yazaki Y , Takahashi E , Lepert M , Jean-Marc Lalouel JM , Kodama T , Mukai T
Ref : Journal of Biological Chemistry , 268 :2120 , 1993
Abstract : Macrophage scavenger receptors (MSR) mediate the binding, internalization, and processing of a wide range of negatively charged macromolecules. Functional MSR are trimers of two C-terminally different subunits that contain six functional domains. We have cloned an 80-kilobase human MSR gene and localized it to band p22 on chromosome 8 by fluorescent in situ hybridization and by genetic linkage using three common restriction fragment length polymorphisms. The human MSR gene consists of 11 exons, and two types of mRNAs are generated by alternative splicing from exon 8 to either exon 9 (type II) or to exons 10 and 11 (type I). The promoter has a 23-base pair inverted repeat with homology to the T cell element. Exon 1 encodes the 5'-untranslated region followed by a 12-kilobase intron which separates the transcription initiation and the translation initiation sites. Exon 2 encodes a cytoplasmic domain, exon 3, a transmembrane domain, exons 4 and 5, an alpha-helical coiled-coil, and exons 6-8, a collagen-like domain. The position of the gap in the coiled coil structure corresponds to the junction of exons 4 and 5. These results show that the human MSR gene consists of a mosaic of exons that encodes the functional domains. Furthermore, the specific arrangement of exons played a role in determining the structural characteristics of functional domains.
ESTHER : Emi_1993_J.Biol.Chem_268_2120
PubMedSearch : Emi_1993_J.Biol.Chem_268_2120
PubMedID: 8093617
Gene_locus related to this paper: human-LPL

Title : Familial plasma lecithin: cholesterol acyltransferase deficiency. A new family with partial LCAT activity - Sakuma_1982_Acta.Med.Scand_212_225
Author(s) : Sakuma M , Akanuma Y , Kodama T , Yamada N , Murata S , Murase T , Itakura H , Kosaka K
Ref : Acta Med Scand , 212 :225 , 1982
Abstract : A 43-year-old woman and her 47-year-old brother were studied because of corneal opacity. They showed a marked decrease in plasma high density lipoproteins (HDL) and a decrease in the ester ratio of plasma total cholesterol. Discoidal particles were found in the HDL2 fraction (d 1.063-1.125). A marked heterogeneity of low density lipoproteins was disclosed in both patients by electron microscopy. Apoprotein analysis revealed an increase in apo E and a decrease in apo A-I and A-II in both patients. These abnormalities were similar to the data reported in other cases with hereditary lecithin : cholesterol acyltransferase (LCAT) deficiency. However, several interesting dissimilarities have been disclosed as compared with the previously reported cases. Neither patient had proteinuria, and their kidney functions were within the normal limits. The ester ratios of plasma cholesterol of both patients were the highest among the cases reported thus far. Their plasma LCAT activities were 14.4 and 15% of the normal mean values determined by Glomset-Wright's common-substrate method. The enzyme activities determined by Stokke-Norum's self-substrate method were 40.2 and 29% respectively. These results may indicate that this inherited disorder is not characterized by absence of plasma LCAT or presence of inhibitory factors in plasma, but by the presence of partially inactive LCAT in patients' plasma.
ESTHER : Sakuma_1982_Acta.Med.Scand_212_225
PubMedSearch : Sakuma_1982_Acta.Med.Scand_212_225
PubMedID: 7148518

Title : Familial lecithin-cholesterol acyltransferase deficiency in a Japanese family: evidence for functionally defective enzyme in homozygotes and obligate heterozygotes - Albers_1982_Hum.Genet_62_82
Author(s) : Albers JJ , Chen CH , Adolphson JL , Sakuma M , Kodama T , Akanuma Y
Ref : Hum Genet , 62 :82 , 1982
Abstract : Lecithin-cholesterol acyltransferase (LCAT) mass and activity were measured in a Japanese family with familial LCAT deficiency. The two LCAT-deficient subjects had LCAT mass approximately 40-46% of normal (2.65 and 2.31 micrograms/ml respectively, as compared with normal levels of 5.76 +/- 0.95 microgram/ml in 19 Japanese subjects) and enzyme activity less than 10% of normal (9.1 and 8.3 nmol/h/ml respectively, as compared with normal levels of 100 nmol/h/ml). All obligate heterozygotes examined, including the father of the two LCAT-deficient subjects, and all five children of the deficient subjects had LCAT mass approximately 72-80% of the normal LCAT mass (4.12, 4.38, 4.45, 4.48, 4.49, 4.61 micrograms/ml, respectively) and LCAT activity approximately half normal (51.9, 52.4, 54.2, 56.6, and 57.2 nmol/h/ml). We conclude that the two LCAT-deficient subjects of this family have functionally defective enzyme. Furthermore, the data suggest that the plasma of the obligate heterozygotes contain both normal and functionally defective enzymes.
ESTHER : Albers_1982_Hum.Genet_62_82
PubMedSearch : Albers_1982_Hum.Genet_62_82
PubMedID: 7152525