Updated on 2022/12/21

写真a

 
OHTA Jun
 
Organization
Faculty of Medicine, Dentistry and Pharmaceutical Sciences Assistant Professor
Position
Assistant Professor
External link

Degree

  • Doctor ( 1989   Okayama University )

Research Interests

  • amino acid

  • medical biochemistry (medical chemistry in general)

  • pathobiochemistry (pathological medical chemistry)

  • chemoinformatics

  • bioinformatics

  • metabolism

  • metabolic network

  • cysteine

  • glutathione

Research Areas

  • Life Science / Medical biochemistry

  • Life Science / Pathological biochemistry

  • Informatics / Life, health and medical informatics

Education

  • Okayama University   大学院・医学研究科   生理系・生化学専攻

    1985.4 - 1989.3

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    Country: Japan

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  • Okayama University    

    - 1989

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  • Okayama University   医学部   医学科

    1979.4 - 1985.3

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    Country: Japan

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  • Okayama University    

    - 1985

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Research History

  • Okayama University   学術研究院・医歯薬学域   Assistant Professor

    2021.4

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  • Okayama University   大学院・医歯薬学総合研究科   Assistant Professor

    2007.4 - 2021.3

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  • Okayama University   大学院・医歯薬学総合研究科   Research Assistant

    2005.4 - 2007.3

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  • - Assistant Professor,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences,Okayama University

    2004

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  • Okayama University   大学院・医歯学総合研究科   Research Assistant

    2001.4 - 2005.3

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  • Cornell University   Visiting Fellow

    1994.5 - 1995.3

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  • Okayama University   Medical School   Research Assistant

    1989.4 - 2001.3

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Professional Memberships

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Papers

  • A novel variant of the Calvin–Benson cycle bypassing fructose bisphosphate Reviewed

    Jun Ohta

    Scientific Reports   12   3984   2022.3

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    DOI: 10.1038/s41598-022-07836-7

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  • Single-atom Tracing in a Model Network of Carbohydrate Metabolism and Pathway Selection Reviewed

    OHTA Jun

    IPSJ Transactions on Bioinformatics   11   1 - 13   2018.6

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    Authorship:Lead author, Last author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.2197/ipsjtbio.11.1

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  • Connectivity matrix method for analyses of biological networks and its application to atom-level analysis of a model network of carbohydrate metabolism Reviewed

    J. Ohta

    IEE PROCEEDINGS SYSTEMS BIOLOGY   153 ( 5 )   372 - 374   2006.9

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    Authorship:Lead author, Last author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:INSTITUTION ENGINEERING TECHNOLOGY-IET  

    An approach for analysis of biological networks is proposed. In this approach, named the connectivity matrix (CM) method, all the connectivities of interest are expressed in a matrix. Then, a variety of analyses are performed on GNU Octave or Matlab. Each node in the network is expressed as a row vector or numeral that carries information defining or characterising the node itself Information about connectivity itself is also expressed as a row vector or numeral. Thus, connection of node n(1) to node n(2) through edge e is expressed as [n(1), n(2), e], a row vector formed by the combination of three row vectors or numerals, where n(1), n(2) and e indicate two different nodes and one connectivity, respectively. All the connectivities in any given network are expressed as a matrix, CM, each row of which corresponds to one connectivity. Using this CM method, intermetabolite atom-level connectivity is investigated in a model metabolic network composed of the reactions for glycolysis, oxidative decarboxylation of pyruvate, citric acid cycle, pentose phosphate pathway and gluconeogenesis.

    DOI: 10.1049/ip-syb:20060018

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  • Cysteine dioxygenase and gamma-glutamylcysteine synthetase activities in primary cultured hepatocytes respond to sulfur amino acid supplementation in a reciprocal manner Reviewed

    J Ohta, YH Kwon, MH Stipanuk

    AMINO ACIDS   19 ( 3-4 )   705 - 728   2000

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    Hepatocytes were cultured for 3 days as spheroids (aggregates) or as monolayers in basal medium and in sulfur amino acid-supplemented media. Cultured hepatocytes had low levels of cysteine dioxygenase (CDO) activity and normal levels of gamma -glutamylcysteine synthetase (GCS) and cysteine-sulfinate decarboxylase (CSDC) activities compared to freshly isolated cells. CDO activity increased and GCS activity decreased in a dose-response manner in cells cultured in either methionine- or cysteine-supplemented media. CSDC activity was not significantly affected by methionine supplementation. Changes in CDO and GCS were associated with changes in cysteine catabolism to taurine plus sulfate and in synthesis of glutathione, respectively. These responses are similar to those observed in liver of intact rats fed diets supplemented with sulfur amino acids. A near-maximal response of CDO or GCS activity was observed when the medium contained 1.0 mmol/L of methionine plus cyst(e)ine. Changes in CDO and GCS activities did not appear to be mediated by changes in the intracellular glutathione concentration. Cultured hepatocytes offer a useful model for further studies of cysteine metabolism and its regulation in response to sulfur amino acid availability.

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  • Formation of gamma-glutamylpropargylglycylglycine from propargylglycine in human blood and erythrocytes Reviewed

    N Nagamine, J Ohta, N Masuoka, H Kodama, T Ubuka

    ACTA MEDICA OKAYAMA   53 ( 1 )   19 - 25   1999.2

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    Authorship:Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:OKAYAMA UNIV MED SCHOOL  

    gamma-Glutamylpropargylglycylglycine (gamma-Glu-PPG-Gly) was isolated as a metabolite of propargyl-glycine (2-amino-4-pentynoic acid, a natural and synthetic inhibitor of cystathionine gamma-lyase) from human blood incubated with D,L-propargylglycine in the presence of L-glutamate and glycine, and identified by fast-atom-bombardment mass spectrometry, indicating that human blood can metabolize propargylglycine to gamma-Glu-PPG-Gly. When whole blood was incubated with 2mM D,L-propargylglycine in the presence of 10 mM L-glutamate and 10 mM glycine at 37 degrees C for 16 h, 0.094 +/- 0.013 mu mol of gamma-Glu-PPG-Gly was formed per mi of whole blood. When erythrocytes were incubated under the same conditions for 16 h, 0.323 +/- 0.060 mu mol of gamma-Glu-PPG-Gly was formed per mi of erythrocytes, suggesting a large contribution of erythrocytes to gamma-Glu-PPG-Gly formation in whole blood. The apparent K-m value of gamma-Glu-PPG-Gly formation in human erythrocytes for D,L-propargylglycine was 0.32 mM. The observed rate of gamma-Glu-PPG-Gly formation and the K-m value for D,L-propargylglycine suggest that metabolism of propargylglycine to gamma-Glu-PPG-Gly can play a definite biological role in human subjects who are loaded with propargylglycine.

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  • A new metabolite of propargylglycine, gamma-glutamylpropargylglycylglycine, in liver of D,L-propargylglycine-administered rats Reviewed

    J Ohta, T Ubuka, H Kodama, K Sugahara, N Nagamine

    BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS   1334 ( 2-3 )   240 - 246   1997.3

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    Authorship:Lead author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:ELSEVIER SCIENCE BV  

    A new metabolite of propargylglycine (2-amino-4-pentynoic acid, a natural and synthetic inhibitor of cystathionine gamma-lyase) was isolated from liver of rats intraperitoneally administered D,L-propargylglycine with ion-exchange chromatography, and identified as a glutathione analogue, N-[N-gamma-glutamyl(propargylglycyl)]glycine (gamma-Glu-PPG-Gly), by fast-atom-bombardment-mass spectrometry and reactions of the compound including acid hydrolysis, carboxypeptidase reaction, and gamma-glutamyltranspeptidase reaction. The content of gamma-Glu-PPG-Gly in rat liver increased dose-dependently with the increase of D,L-propargylglycine. When the dose of D,L-propargylglycine was 50 mg/kg of body weight, the increase of gamma-Glu-PPG-Gly was proportional to the time after the administration of D,L-propargylglycine, up to 8 h, and then gradually decreased to about 50% of the maximum at 24 h, where the maximum level of gamma-Glu-PPG-Gly at 8 h was 1.15+/-0.08 mu mol/g of liver. The propargylglycine moiety of gamma-Glu-PPG-Gly in rat liver at 14 h after the administration of D,L-propargylglycine corresponded to 2-7% of the propargylglycine administered when the dose of D,L-propargylglycine was 3.125-200 mg/kg of body weight. The present results indicate that gamma-Glu-PPG-Gly is a major intermediate of propargylglycine metabolism in rat liver. The structural resemblance between glutathione and gamma-Glu-PPG-Gly suggests a possible involvement of propargylglycine and gamma-Glu-PPG-Gly as cysteine and glutathione analogues, respectively, in sulfur amino-acid metabolism.

    DOI: 10.1016/S0304-4165(96)00100-6

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  • INCREASE IN CYSTATHIONINE CONTENT IN RAT-LIVER MITOCHONDRIA AFTER D,L-PROPARGYLGLYCINE ADMINISTRATION Reviewed

    J OHTA, T UBUKA, H KODAMA, K SUGAHARA, K YAO, N MASUOKA, M KINUTA

    AMINO ACIDS   9 ( 2 )   111 - 122   1995

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    Intraperitoneal administration of D,L-propargylglycine to rats resulted in an increase in the cystathionine content of whole liver and liver mitochondria. Cystathionine in mitochondria was identified by amino acid analysis, thin layer chromatography, high-voltage paper electrophoresis and liquid chromatography-mass spectrometry. The cystathionine content of whole liver was 5.37 +/- 1.59 mu mol per g of fresh liver at 14 h after the administration of 50 mg of D,L-propargylglycine per kg of body weight, while 0.07 +/- 0.02 mu mol of cystathionine per g of fresh liver was detected in the control rats. The cystathionine content of liver mitochondria from both groups of rats was 9.40 +/- 1.20 and 0.19 +/- 0.04 nmol of cystathionine per mg of protein, respectively. The mitochondrial cystathionine increased dose-dependently with the increase of D,L-propargylglycine administered. The increase was proportional to the time after the administration up to 12 h, and then decreased. The increase of cystathionine in the liver mitochondria was linearly proportional to that in the whole liver. These results suggest that cystathionine in liver mitochondria is in an equilibrium with that in the cytosol.

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  • Exploring for metabolic pathways based on stoichiometry

    OHTA Jun

    IPSJ SIG Technical Reports   2022-BIO-70 ( 59 )   1 - 3   2022.6

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  • Non-branched linear substructures in stoichiometric metabolic network structures of elementary flux mode type pathways

    OHTA Jun

    IPSJ SIG Technical Reports   2022-BIO-69 ( 10 )   1 - 4   2022.3

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  • Number of symmetries of stoichiometric metabolic network structure variant of elementary flux mode type pathway

    OHTA Jun

    IPSJ SIG Technical Reports   2021-BIO-68 ( 4 )   1 - 3   2021.11

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  • Stoichiometric metabolic network structure as a snapshot of the state of formation and utilization of metabolite molecules in elementary flux mode type pathway

    OHTA Jun

    IPSJ SIG Technical Reports   2021-BIO-66 ( 22 )   1 - 7   2021.6

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  • Calculation of stoichiometric metabolic network structure of elementary flux mode type metabolic pathway: Optimization of algorithm for difference judgement between calculated network structures

    OHTA Jun

    IPSJ SIG Technical Reports   2021-BIO-65 ( 4 )   1 - 8   2021.3

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  • Calculation of stoichiometric metabolic network structure of elementary flux mode type metabolic pathway: Acceleration of difference judgement between calculated network structures

    OHTA Jun

    IPSJ SIG Technical Reports   2020-BIO-64 ( 5 )   1 - 7   2020.11

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  • Accelerating calculation of stoichiometrically balanced metabolite-level network structure of elementary flux mode type metabolic pathway

    OHTA Jun

    IPSJ SIG Technical Reports   2020-BIO-63 ( 1 )   1 - 7   2020.8

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  • Calculation of stoichiometrically balanced metabolite-level network structure of elementary flux mode type metabolic pathway

    OHTA Jun

    IPSJ SIG Technical Reports   2020-BIO-62 ( 3 )   1 - 6   2020.6

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  • Complete atomic-level mapping of elementary flux mode-type metabolic pathways through metabolites with symmetry

    OHTA Jun

    IPSJ SIG Technical Report   2020-BIO-61 ( 9 )   1 - 8   2020.3

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  • Acceleration of complete atomic-level mapping of elementary flux mode-type metabolic pathways

    OHTA Jun

    IPSJ SIG Technical Report   2019-BIO-60 ( 6 )   1 - 7   2019.11

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  • Complete atomic-level mapping of elementary flux mode type pathways in metabolic networks

    OHTA Jun

    IPSJ SIG Technical Report   2019-BIO-59 ( 2 )   1 - 6   2019.9

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  • Computation of atomic-level pathways for complete biosynthesis in metabolic networks

    OHTA Jun

    IPSJ SIG Technical Report   2019-BIO-58 ( 59 )   1 - 6   2019.6

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  • Convergence of isotopomer distribution simulation in metabolic networks

    OHTA Jun

    IPSJ SIG Technical Report   2019-BIO-57 ( 1 )   1 - 6   2019.3

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  • Simulation of time course change of isotope distribution in metabolic networks

    OHTA Jun

    IPSJ SIG Technical Report   2018-BIO-56 ( 5 )   1 - 6   2018.12

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  • EMU tracing: listing all the elementary metabolite units (EMU) which can be formed from source EMUs through a given metabolic network

    OHTA Jun

    IPSJ SIG Technical Report   2018-BIO-55 ( 6 )   1 - 7   2018.9

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  • Isotopomer tracing: listing all the isotopomers synthesizable from source isotopomers through a given metabolic network

    OHTA Jun

    IPSJ SIG Technical Report   2018-BIO-54 ( 48 )   1 - 6   2018.6

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  • Different effect of diastereoisomers of L-cystathionine sulfoxide on the stimulus coupled responses of human neutrophils Reviewed

    Yosei Shimazaki, Jianying Zhang, Hiroshi Wakiguchi, Takanobu Kurashige, Yasuhiro Sagara, Noriyoshi Masuoka, Jun Ohta, Toshihiko Ubuka, Hiroyuki Kodama

    Biochemical and Biophysical Research Communications   247 ( 2 )   387 - 391   1998.6

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Academic Press Inc.  

    The priming effect of L-cystathionine sulfoxide, which is one of the unusual cystathionine metabolites found in the urine of patients with cystathioninuria, on the stimulus-induced superoxide generation by human neutrophils was examined. The synthetic L-cystathionine sulfoxide significantly enhanced the superoxide generations induced by N-formyl-methionyl-leucyl-phenylalanine [fMLP], opsonized zymosan [OZ], arachidonic acid [AA], and phorbol 12-myristate 13-acetate [PMA]. Then the synthetic L-cystathionine sulfoxide was separated into two diastereoisomers, CS-I and CS-II, which showed a peak at 76 and 83 min on chromatogram by amino acid analyzer, respectively. CS-I enhanced the superoxide generations induced by AA and PMA but not those induced by fMLP and OZ. On the contrary, CS-II enhanced the superoxide generations induced by fMLP and OZ but not those induced by AA and PMA. The superoxide generation induced by PMA with CS-I was suppressed by H-7 and was enhanced by genistein, while that by fMLP with CS-II was suppressed by genistein and was enhanced by H-7.

    DOI: 10.1006/bbrc.1998.8796

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  • Characterization of hydrogen peroxide removal activities in mouse hemolysates: catalase activity and hydrogen peroxide removal activity by hemoglobin Reviewed

    N Masuoka, M Wakimoto, J Ohta, K Ishii, T Nakano

    BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE   1361 ( 2 )   131 - 137   1997.8

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    Hydrogen peroxide removal activities in normal and acatalasemic mouse hemolysates were examined to determine the optimal temperature of catalase. From thermal stability of the removal activities in hemolysates, the removal activities were divided into two activities. The removal activity deactivated at lower temperature was catalase, and the 50% inactivation was observed after 10 min incubation at 47.2 +/- 0.5 degrees C for normal hemolysates and 34.0 +/- 0.8 degrees C for acatalasemic ones. The removal activity deactivated at a higher temperature remained after the addition of sodium azide, and the 50% inactivation was observed at 63.5 +/- 1.4 degrees C. After separation of the removal activities by carboxymethyl-cellulose column chromatography, the removal activity deactivated at higher temperature was attributed to the activity by hemoglobin. From Lineweaver-Burk plot analysis of the removal rates by hemoglobin at 37 degrees C, the Michaelis constant for hydrogen peroxide and the maximum velocity were 201 +/- 53 mu M and 5.37 +/- 1.39 mu mol/s per g of Hb, respectively. Removal rates by hemoglobin in mouse hemolysates at 37 degrees C in 70 mu M hydrogen peroxide were 1.32 +/- 0.12 mu mol/s per g of Hb. Catalase activity (k/g Hb: rate constant related to the hemoglobin content) in normal mouse hemolysates was 104 +/- 12 at 25 degrees C and 117 +/- 10 at 37 degrees C, and that in acatalasemic hemolysates was 10.5 +/- 1.7 at 25 degrees C. These results indicate that activity of hydrogen peroxide removal by hemoglobin is substantial and the activity in acatalasemic hemolysates is predominant at low concentration of hydrogen peroxide. (C) 1997 Elsevier Science B.V.

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  • Identification of S-[2-carboxy-1-(1H-imidazol-4-yl)ethyl]-3-mercaptopyruvic acid with a metabolic intermediate between S-[2-carboxy-1-(1H-imidazol-4-yl)ethyl]-L-cysteine and S-[2-carboxy-1-(1H-imidazol-4-yl)ethyl]-3-mercaptolactic acid Reviewed

    M Kinuta, H Shimizu, N Masuoka, J Ohta, WB Yao, T Ubuka

    AMINO ACIDS   13 ( 2 )   163 - 169   1997

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    S-[2-Carboxy-1-(1H-imidazol-4-yl)ethyl]-3-mercaptopyruvic acid (I) was chemically synthesized in 15% yield by incubating a reaction mixture of trans-urocanic acid and 3-fold excess of 3-mercaptopyruvic acid at 45 degrees C for 6 days. The synthesized compound was characterized by fast-atom-bombardment mass spectrometry and high-voltage paper electrophoresis. Compound I was identified with a product of an enzymatic reaction of S-[2-carboxy-1-(1H-imidazol-4-yl)ethyl]-L-cysteine (II) with rat liver homogenate in a phosphate buffer, pH 7.4. Compound I was degraded to S-[2-carboxy-1-(1H-imidazol-4-yl)ethyl]-3-mercaptolactic acid (III), a compound previously found in human urine [Kinuta et al. (1994) Biochem J 297: 475-478], by incubation with rat liver homogenate. From these results, we suggest that compound I is a metabolic intermediate for the formation of compound III from compound II. The present pathway follows a formation of compound II from S-[2-carboxy-1-(1H-imidazol-4-yl)ethyl]gluthathione [Kinuta et al. (1993) Biochim Biophys Acta 1157: 192-198], a proposed metabolite of L-histidine.

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  • Taurine production in rat primary hepatocytes Reviewed

    J Ohta, MH Stipanuk

    TAURINE 2   403   69 - 71   1996

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    Authorship:Lead author   Language:English   Publishing type:Research paper (international conference proceedings)   Publisher:PLENUM PRESS DIV PLENUM PUBLISHING CORP  

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  • INCREASE IN TISSUE CYSTEINE LEVEL AND EXCRETION OF SULFATE AND TAURINE AFTER INTRAGASTRIC ADMINISTRATION OF L-2-OXOTHIAZOLIDINE-4-CARBOXYLATE IN RATS Reviewed

    S YAMADA, T ABE, J OHTA, N MASUOKA, T UBUKA

    AMINO ACIDS   8 ( 1 )   37 - 45   1995

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    Five mmol of L-2-oxothiazolidine-4-carboxylate (OTC)/kg of body weight was administered into the stomach of rats, and cysteine levels in tissues and sulfate and taurine excreted in the urine were determined. The cysteine (plus cystine expressed as cysteine) concentration in the liver increased to 170-200% of the original level at 30 min and that in the blood to 160% at 60 min after the OTC administration. These high levels were maintained until 8 h after the administration and decreased gradually thereafter. Excretion of sulfate and taurine increased after the OTC administration and the increase corresponded to 26% and 15%, respectively, of the OTC administered. These findings suggest that at least about 40% of the OTC administered into the stomach was taken up and converted to cysteine, which was metabolized to sulfate and taurine.

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  • HIGH-PERFORMANCE LIQUID-CHROMATOGRAPHIC DETERMINATION OF TAURINE AND HYPOTAURINE USING 3,5-DINITROBENZOYL CHLORIDE AS DERIVATIZING REAGENT Reviewed

    N MASUOKA, K YAO, M KINUTA, J OHTA, M WAKIMOTO, T UBUKA

    JOURNAL OF CHROMATOGRAPHY B-BIOMEDICAL APPLICATIONS   660 ( 1 )   31 - 35   1994.10

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    A method for the determination of taurine and hypotaurine in biological samples involving the preparation of their 3,5-dinitrobenzoyl derivatives followed by HPLC was established. Taurine and hypotaurine in aqueous media were reacted with 3,5-dinitrobenzoyl chloride in the presence of triethylamine to prepare 3,5-dinitrobenzoyl derivatives. These derivatives were separated on a C-18 reversed-phase column and detected by recording the absorbance at 254 nm. Derivatives of taurine and hypotaurine were obtained in yields of 91.4 +/- 3.3 and 85.6 +/- 2.6%, respectively. The calibration graphs for taurine and hypotaurine were linear between 2.5 and 500 mu M with correlation coefficients of 0.999. The method was applied to the determination of taurine and hypotaurine in human and rat urine and blood and in rat liver and heart.

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  • Inhibition of sulfate-forming activity in rat liver mitochondria by (aminooxy)acetate Reviewed

    T. Teraoka, J. Ohta, T. Abe, H. Inoue, T. Ubuka

    Amino Acids   5 ( 2 )   245 - 251   1993.6

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    The effect of (aminooxy)acetate, an inhibitor of aminotransferases, on the sulfate formation from l-cysteine and l-cysteinesulfinate in rat liver mitochondria was studied. Incubation of 10 mM l-cysteine with rat liver mitochondria at 37°C in the presence of 10 mM 2-oxoglutarate and 10 mM glutathione resulted in the formation of 4.60 and 1.52 μmol of sulfate and thiosulfate, respectively, per 60 min per mitochondria obtained from 1 g of liver. Under the same conditions sulfate formation from l-cysteinesulfinate was 24.96 μmol, but thiosulfate was not formed. The addition of (aminooxy)acetate at 2 mM or more completely inhibited the sulfate and thiosulfate formation from l-cysteine and the sulfate formation from l-cysteinesulfinate. These findings support our previous conclusion that cysteine transamination and 3-mercaptopyruvate pathway (MP pathway) are involved in the sulfate formation from l-cysteine in rat liver mitochondria (Ubuka et al., 1992). © 1993 Springer-Verlag.

    DOI: 10.1007/BF00805987

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  • ASSAY OF SIALIDASE ACTIVITY USING ION-EXCHANGE CHROMATOGRAPHY AND ACIDIC NINHYDRIN REACTION Reviewed

    K YAO, T UBUKA, N MASUOKA, M KINUTA, J OHTA, T TERAOKA, S FUTANI

    JOURNAL OF CHROMATOGRAPHY-BIOMEDICAL APPLICATIONS   581 ( 1 )   11 - 15   1992.10

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    A new assay method for sialidase (EC 3.2.1.18) activity using ion-exchange chromatography and acidic ninhydrin reaction has been developed. Fetuin, 4-methylumbelliferyl-N-acetylneuraminic acid (MUB-NANA), gangliosides and N-acetylneuramin-lactose were examined as substrates. Free sialic acid liberated from these substrates by sialidase reaction was isolated with a Dowex 1-X8 column (trifluoroacetate form, 1.5 cm x 0.5 cm I.D.) and determined by acidic ninhydrin reaction. Among the substrates tested. MUB-NANA was the best in the present method. N-Acetylneuramin-lactose could not be used as the substrate, because it was not separated from liberated sialic acid under the conditions used. The recovery of N-acetylneuraminic acid was above 88%, and the sensitivity of the method was 20 nmol in 300 mul of the reaction mixture. The method was applied to the sialidase assay during its purification from rat skeletal muscle, and a Michaelis constant of 1.15 mM was obtained with MUB-NANA as the substrate. The method using the acidic ninhydrin reaction was simple and exhibited good reproducibility.

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  • l-Cysteine metabolism via 3-mercaptopyruvate pathway and sulfate formation in rat liver mitochondria Reviewed

    T. Ubuka, J. Ohta, W. B. Yao, T. Abe, T. Teraoka, Y. Kurozumi

    Amino Acids   2 ( 1-2 )   143 - 155   1992.2

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    We have studied the 3-mercaptopyruvate pathway (transamination pathway) of l-cysteine metabolism in rat liver mitochondria. l-Cysteine and other substrates at 10 mM concentration were incubated with mitochondrial fraction at pH 8.4, and sulfate and thiosulfate were determined by ion chromatography. When l-cysteine alone was incubated, sulfate formed was 0.7 μmol per mitochondria from one g of liver per 60 min. Addition of 2-oxoglutarate and GSH resulted in more than 3-fold increase in sulfate formation, and thiosulfate was formed besides sulfate. The sum (A + 2B) of sulfate (A) and thiosulfate (B) formed was approximately 7-times that with l-cysteine alone. Incubation with 3-mercaptopyruvate resulted in sulfate and thiosulfate formation, and sulfate was formed with thiosulfate. These reactions were stimulated with glutathione. Sulfate formation from l-cysteinesulfinate and 2-oxoglutarate was not enhanced by glutathione and thiosulfate was not formed. These findings indicate that l-cysteine was metabolized and sulfate was formed through 3-mercaptopyruvate pathway in mitochondria. © 1992 Springer-Verlag.

    DOI: 10.1007/BF00806085

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  • CHEMICAL S-THIOLATION OF REDUCED RIBONUCLEASE-A WITH GLUTATHIONE AND CYSTEINE Reviewed

    T UBUKA, J OHTA, N MASUOKA, T ABE, T TERAOKA, WB YAO, YQ CHAO

    FRONTIERS AND NEW HORIZONS IN AMINO ACID RESEARCH   595 - 598   1992

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  • S-[2-Carboxy-1-(1 H-imidazol-4-yl)ethyl]cysteine in normal human urine Reviewed

    M. Kinuta, N. Masuoka, K. Yao, J. Ohta, S. Yoshida, S. Futani, T. Ubuka

    Amino Acids   1 ( 2 )   259 - 262   1991.6

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    A compound, which had the same mobility on a high-voltage paper electrophoretogram and the same RF value on a thin-layer chromatogram as those of S-[2-carboxy-1-(1 H-imidazol-4-yl)ethyl]cysteine (I), was partially purified from human urine by ion-exchange column chromatography. The compound gave a signal at m/z 260 on its FAB mass spectrum, which was assigned as MH+ of compound I. These results suggest that the urinary compound is compound I and it is a physiological precursor of 3-[(carboxymethyl)thio]-3-(1 H-imidazol-4-yl)propanoic acid [Kinuta et al., (1991) Biochem J 275: 617-621]. © 1991 Springer-Verlag.

    DOI: 10.1007/BF00806924

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  • ISOLATION AND CHARACTERIZATION OF 3-[(CARBOXYMETHYL)THIO]-3-(1H-IMIDAZOL-4-YL)PROPANOIC ACID FROM HUMAN URINE AND PREPARATION OF ITS PROPOSED PRECURSOR, S-[2-CARBOXY-1-(1H-IMIDAZOL-4-YL)ETHYL]CYSTEINE Reviewed

    M KINUTA, K YAO, N MASUOKA, J OHTA, T TERAOKA, T UBUKA

    BIOCHEMICAL JOURNAL   275   617 - 621   1991.5

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    3-[(Carboxymethyl)thio]-3-(1 H-imidazol-4-yl)propanoic acid (I) was isolated from healthy human urine by using ion-exchange column chromatography, and characterized by physicochemical analysis involving i.r., m.s. and n.m.r. spectrometrices as well as chemical synthesis. The urinary content was 0.04-0.07-mu-mol/l. Compound (I) was synthesized by the addition of mercaptoacetic acid to urocanic acid. In order to establish the origin of the compound, S-[2-carboxyl-(1 H-imidazol-4-yl)ethyl]cysteine (II) and S-[2-carboxy-1-(1 H-imidazol-4-yl)ethyl]glutathione (III) were produced by similar reactions of urocanic acid with cysteine and GSH respectively. The yield of compound (II) was markedly increased by sunlight irradiation of the reaction mixture or by the use of cis-urocanic acid rather than the trans isomer. Incubation of compound (II) with rat liver homogenate in a phosphate buffer, pH 7.40, formed a major and some minor products of enzymic degradation, one of which was identified with compound (I). Exposure of rats to the sunlight for 2 days resulted in increase of the epidermal content of trans-urocanic acid from the normal value of 0.38 to 1.70-mu-g/mg wet wt. of skin, accompanied by formation de novo of the epidermal cis isomer. After sunlight irradiation, the content of the trans isomer decreased at a constant rate of 0.03-mu-g/mg wet wt. of skin per day, whereas the cis isomer was eliminated more quickly, having a phase of rapid decrease in the early period. From these results we suggest that compound (I) may participate in the metabolism of urocanic acid and natural thiol compounds such as cysteine and GSH.

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  • FORMATION OF SULFATE FROM L-CYSTEINE IN RAT-LIVER MITOCHONDRIA Reviewed

    T UBUKA, S YUASA, J OHTA, N MASUOKA, K YAO, M KINUTA

    ACTA MEDICA OKAYAMA   44 ( 2 )   55 - 64   1990.4

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  • VISUALIZATION OF SIALOGLYCOPROTEINS IN POLYACRYLAMIDE GELS BY ACIDIC NINHYDRIN REACTION Reviewed

    K YAO, T UBUKA, N MASUOKA, M KINUTA, J OHTA, K ISHINO

    ACTA MEDICA OKAYAMA   44 ( 2 )   65 - 70   1990.4

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  • REDUCTION OF 3-MERCAPTOPYRUVATE IN RAT-LIVER IS CATALYZED BY LACTATE-DEHYDROGENASE Reviewed

    J OHTA, T UBUKA

    ACTA MEDICA OKAYAMA   43 ( 2 )   89 - 95   1989.4

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:OKAYAMA UNIV MED SCHOOL  

    DOI: 10.18926/AMO/30871

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Books

  • IMAC, Inter- and Intra-Metabolite Atom-level Connectivity Database (2003-)

    2003年からインターネット上に公開しているデータベースである。随時データを更新追加している。  2003 

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  • Taurine production in rat primary hepatocytes

    Jun Ohta, Martha Stipanuk( Role: Joint author ,  pp.69-71)

    Advances in experimental medicine and biology, vol. 403 Taurine2 : basic and clinical aspects, Plenum Press  1996 

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MISC

  • Stoichiometric Metabolic-Network Generation from Given Metabolites Reviewed

    Jun Ohta

    The Proceedings of the 2008 Annual Conference of the Japanese Society for Bioinformatics   P064-1-P064-2   2008

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  • A Strategy for Metabolic Pathway Prediction: Generation of Metabolic Networks by Network Expansion Reviewed

    Jun Ohta

    The Proceedings of the 2007 Annual Conference of the Japanese Society for Bioinformatics   P018-1-P018-2   2007

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  • Visualization of Metabolic Networks as Networks of Atoms by Pajek: An Application of Connectivity Matrix Method Reviewed

    Jun Ohta

    Genome Informatics, Volume 17 Poster and Software demonstrations, 17th International Conference on Genome Informatics   P146   2006

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  • 原子のネットワークとしての代謝ネットワークと社会的ネットワークの類似性について 自分が原子になったと考えてみる

    太田潤

    日本ソフトウェア科学会研究会資料 JWEIN2006 講演論文集   2006

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  • Theoretical Analysis of Metabolic Networks: Attempt to Express Topological Position of Individual Atoms in a Given Network Reviewed

    Jun Ohta

    16th International Conference on Genome InformaticsPoster and Software demonstrations   2005

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  • Toward Complete Structural Analyses of Metabolic Networks: Prototype Data Format for Describing Both Inter- and Intra-Metabolite Atom-level Connectivities

    Ohta J

    Proceedings for 5th International Conference on Systems Biology   141-141   2004

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  • Data Format for Computational Analysis of Intermetabolite Atom-level Connectivity in Metabolic Networks

    Ohta J

    Molecular & Cellular Proteomics   2,9,830-830   2003

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  • Metabolic fluxes giving atomic level pathways calculated by single-atom tracing

    OHTA Jun

    IPSJ SIG Technical Report   2022-BIO-72 ( 9 )   1 - 1   2022.11

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  • What metabolic maps and metabolic pathway diagrams represent

    OHTA Jun

    IPSJ SIG Technical Report   2022-BIO-71 ( 4 )   1 - 1   2022.9

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  • COVID-19感染者間の関係のPajekによる可視化

    太田 潤

    情報処理学会研究報告   2021-BIO-67 ( 5 )   1 - 1   2021.9

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  • Single-atom tracing in a model network of carbohydrate metabolism and pathway selection

    OHTA Jun

    IPSJ SIG Technical Report   2018-BIO-53 ( 6 )   1 - 6   2018.3

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  • Strategy for Exploring Metabolic Pathways: Generation of Hypothetical Metabolic Network. Reviewed

    Ohta J

    J Comput Sci Syst Biol   8 ( 1 )   55 - 58   2015

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  • Attempt of stoichiometric extension of amino acid metabolism-related model metabolic network

    Jun Ohta

    AMINO ACIDS   37 ( 1 )   95 - 95   2009.7

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  • IMAC, Inter- And Intra-Metabolite Atom-Level Connectivity Database

    Jun Ohta

    IFMBE (ISSN 1727-1983, ISBN 3-540-36839-6 Springer Berlin Heidelberg New York)   Volume 14, 4131-4131   2006

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  • A new dipeptide, O-phosphoserylethanolamine isolated from Agkistroden blomhoffi (mamushi) Reviewed

    N Masuoka, JY Zhang, L Partoo, J Ohta, K Sasaki, H Ebinuma, H Kodama

    ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS   407 ( 2 )   184 - 188   2002.11

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    Language:English   Publisher:ACADEMIC PRESS INC ELSEVIER SCIENCE  

    A new dipeptide was isolated from several tissues of Agkistroden blomhoffi (mamushi: a venomous snake in Japan), using ion-exchange resins and thin-layer chromatography. It was identified as O-phosphoserylethanolamine by mass spectrometry and comparison with synthetic compounds using several methods. This compound was contained in several mamushi tissues including the liver, heart, brain, bile, and muscle. The concentrations of O-phosphoserylethanolamine in the liver, brain, muscle, skin, heart, and bile were 7.17 +/- 3.11, 16.98 +/- 4.25, 37.37 +/- 7.88, 37.56 +/- 8.97, 23.93 +/- 6.11, and 22.21 +/- 5.76 mumol/g, respectively. (C) 2002 Elsevier Science (USA). All rights reserved.

    DOI: 10.1016/S0003-9861(02)00485-X

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  • Cdk5/p35 regulates neurotransmitter release through phosphorylation and downregulation of P/Q-type voltage-dependent calcium channel activity Reviewed

    K Tomizawa, J Ohta, M Matsushita, A Moriwaki, ST Li, K Takei, H Matsui

    JOURNAL OF NEUROSCIENCE   22 ( 7 )   2590 - 2597   2002.4

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    Cyclin-dependent kinase 5 (Cdk5) is a proline-directed serine/ threonine kinase with close structural homology to the mitotic Cdks. The complex of Cdk5 and p35, the neuron-specific regulatory subunit of Cdk5, plays important roles in brain development, such as neuronal migration and neurite outgrowth. Moreover, Cdk5 is thought to be involved in the promotion of neurodegeneration in Alzheimer's disease.
    Cdk5 is abundant in mature neurons; however, its physiological functions in the adult brain are unknown. Here we show that Cdk5/p35 regulates neurotransmitter release in the presynaptic terminal. Both Cdk5 and p35 were abundant in the synaptosomes. Roscovitine, a specific inhibitor of Cdk5 in neurons, induced neurotransmitter release from the synaptosomes in response to membrane depolarization and enhanced the EPSP slopes in rat hippocampal slices. The electrophysiological study using each specific inhibitor of the voltage-dependent calcium channels (VDCCs) and calcium imaging revealed that roscovitine enhanced Ca2+ influx from the P/Q-type VDCC. Moreover, Cdk5/p25 phosphorylated the intracellular loop connecting domains II and III (LII-III) between amino acid residues 724 and 981 of isoforms cloned from rat brain of the alpha(1A) subunit of P/Q-type Ca2+ channels. The phosphorylation inhibited the interaction of LII-III with SNAP-25 and synaptotagmin I, which were plasma membrane soluble N-ethylmaleimide- sensitive factor attachment protein (SNAP) receptor (SNARE) proteins and were required for efficient neurotransmitter release. These results strongly suggest that Cdk5/p35 inhibits neurotransmitter release through the phosphorylation of P/Q-type VDCC and downregulation of the channel activity.

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  • Determination of S-[2-carboxy-1-(1H-imidazol-4-yl)ethyl]glutathione, a novel metabolite of L-histidine, in tissue extracts from sunlight-irradiated rat by capillary electrophoresis Reviewed

    M Kinuta, J Ohta, H Yamada, K Kinuta, T Abe, SA Li, A Otsuka, A Nakanishi, K Takei

    ELECTROPHORESIS   22 ( 16 )   3365 - 3370   2001.10

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    Exposure of the skin to sunlight results in an increase in the content of epidermal Urocanic acid, a key metabolite Of L-histidine, and some portions of the metabolite penetrate into the body fluid. S-[2-Carboxy-1 -(1H-imidazol-4-yl)ethyl]glutathione (GS(CIE)), an adduct of glutathione and urocanic acid, was proposed to be an origin of a urinary compound, S-[2-carboxy-1-(1H-imidazol-4-yl)ethyl]-L-cysteine (Cys(CIE)). Various catabolites of Cys(CIE) were also isolated from human urine previously. However, no direct evidence to show the existence of GS(CIE) as a biological material had been found. By using capillary electrophoresis, the glutathione adduct has now been found in the extracts of rat tissues from the kidney, liver, skin and blood when the rat was kept under conditions of sunlight irradiation after the fur on the dorsal skin had been clipped. On the other hand, no or a trace of GS(CIE) was determined in rat tissue extracts when the animal was kept indoor in usual manner. The glutathione adduct was isolated from the kidney extract of the sunlight-irradiated rat using ion-exchangers and high-voltage paper electrophoresis, and determined by fast-atom-bombardment mass spectrometry. These results indicate that GS(CIE) formation actually occurs in the body and that the formation is accelerated by exposing the rat to sunlight irradiation. From these findings, we propose an alternative pathway of histidine metabolism which is initiated by the adduction of urocanic acid to glutathione to form GS(CIE) and terminates with the formation of the urinary compounds via Cys(CIE).

    DOI: 10.1002/1522-2683(200109)22:16<3365::AID-ELPS3365>3.0.CO;2-M

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  • Reciprocal regulation of cysteine dioxygenase (CDO) and gamma-glutamylcysteine synthetase (gamma GCS) in rat hepatocytes.

    YH Kwon, DL Bella, J Ohta, MH Stipanuk

    FASEB JOURNAL   10 ( 3 )   2724 - 2724   1996.3

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Presentations

  • What metabolic maps and metabolic pathway diagrams represent

    OHTA Jun

    2022.9.12 

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  • Enumerating pathways for producing ribose 5-phosphate from glucose through glycolytic reactions and non-oxidative pentose-phosphate-pathway reactions without using atomic level information

    OHTA Jun

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    Event date: 2021.11.3 - 2021.11.5

    Language:Japanese   Presentation type:Poster presentation  

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  • Pajekを使う

    太田 潤

    第25回オープンバイオ研究会  2021.3.13 

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    Event date: 2021.3.13

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  • Complexity of pathways for forming ribose 5-phosphate from glycolytic metabolites through non-oxidative pentose-phosphate-pathway reactions

    OHTA Jun

    2020.12.2 

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    Event date: 2020.12.2 - 2020.12.4

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  • Enumerating pathways for producing ribose 5-phosphate from glucose through glycolytic reactions and non-oxidative pentose-phosphate-pathway reactions using atomic level information

    OHTA Jun

    2020.9.16 

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  • Metabolic fluxes giving atomic level pathways calculated by single-atom tracing

    OHTA Jun

    2022.11.29 

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    Event date: 2022.11.29

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  • Exploring for metabolic pathways based on stoichiometry

    OHTA Jun

    2022.6.29 

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    Event date: 2022.6.27 - 2022.6.29

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  • Non-branched linear substructures in stoichiometric metabolic network structures of elementary flux mode type pathways

    OHTA Jun

    2022.3.10 

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    Event date: 2022.3.10

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  • Calvin-Benson回路の反応によるリブロース1,5-ビスリン酸新規生成:Rubiscoを6回利用する原子レベル経路

    太田 潤

    第16回日本ゲノム微生物学会年会  2022.3.2 

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    Event date: 2022.3.2 - 2022.3.4

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  • Atomic level pathway for glyceraldehyde 3-phosphate formation through "transaldolase variant" of Calvin-Benson cycle

    OHTA Jun

    2021.12.2 

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    Event date: 2021.12.1 - 2021.12.3

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  • Number of symmetries of stoichiometric metabolic network structure variant of elementary flux mode type pathway

    OHTA Jun

    2021.11.30 

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  • COVID-19感染者間の関係のPajekによる可視化

    太田 潤

    情報処理学会「第67回バイオ情報学研究会(SIGBIO)」  2021.9.30 

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  • Stoichiometric metabolic network structure as a snapshot of the state of formation and utilization of metabolite molecules in elementary flux mode type pathway

    OHTA Jun

    2021.6.30 

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  • Calculation of stoichiometric metabolic network structure of elementary flux mode type metabolic pathway: Optimization of algorithm for difference judgement between calculated network structures

    OHTA Jun

    2021.3.11 

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  • Calvin-Benson回路の反応によるCO2からのリブロース1,5-ビスリン酸新規生成の原子レベル経路

    太田 潤

    第15回日本ゲノム微生物学会年会  2021.3.4 

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    Event date: 2021.3.4 - 2021.3.6

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  • Calculation of stoichiometric metabolic network structure of elementary flux mode type metabolic pathway: Acceleration of difference judgement between calculated network structures

    OHTA Jun

    2020.12.7 

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  • Accelerating calculation of stoichiometrically balanced metabolite-level network structure of elementary flux mode type metabolic pathway

    OHTA Jun

    2020.9.4 

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  • Calculation of stoichiometrically balanced metabolite-level network structure of elementary flux mode type metabolic pathway

    OHTA Jun

    2020.6.29 

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    Event date: 2020.6.29

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  • 原子レベル情報を用いる化学量論的に釣り合った生合成代謝経路算出

    太田 潤

    第61回日本生化学会中国・四国支部例会  2020.6.10 

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    Event date: 2020.5.23 - 2020.7

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  • 生命科学系公共データベースによる実習を立案した経験

    太田 潤

    第24回オープンバイオ研究会  2020.3.14 

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    Event date: 2020.3.14

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  • 合流する生合成代謝経路の算出

    太田 潤

    第70回 人工知能学会 分子生物情報研究会(SIG-MBI)  2020.3.13 

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  • Complete atomic-level mapping of elementary flux mode-type metabolic pathways through metabolites with symmetry

    OHTA Jun

    2020.3.13 

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    Event date: 2020.3.12 - 2020.3.13

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  • 化学量論的に釣り合った生合成代謝経路の原子レベルマッピング:その応用

    太田 潤

    第14回日本ゲノム微生物学会年会  2020.3.7 

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  • Acceleration of complete atomic-level mapping of elementary flux mode-type metabolic pathways

    OHTA Jun

    2019.12.2 

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  • Atomic-level pathways for nonoxidative formation of ribose 5-phosphate by pentose phosphate pathway reactions

    OHTA Jun

    2019.12 

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  • 代謝ネットワークにおけるelementary flux mode型経路の完全原子レベルマッピング

    太田 潤

    情報処理学会「第59回バイオ情報学研究会(SIGBIO)」  2019.9.8 

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  • Incorporation of carbon atoms of the acetyl moiety of acetyl-CoA into metabolites in an in silico model network of carbohydrate metabolism

    OHTA Jun

    2019.9 

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  • Pathways for oxygen atoms of glucose to carbon dioxide in a model network of carbohydrate metabolism

    SAWAE Seigo, OHTA Jun

    2019.9 

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  • Transketolase-like protein 1の代謝機能に関する13C代謝フラックス解析によるエビデンスの検討

    太田 潤

    第7回がんと代謝研究会  2019.8.2 

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  • Computation of atomic-level pathways for complete biosynthesis in metabolic networks

    2019.6.19 

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  • In silico 糖質代謝モデルネットワークにおける acetyl-CoA の acetyl部分の炭素のグルコースへのグルコース非産生的取込

    太田 潤

    第60回日本生化学会 中国・四国支部例会  2019.5.18 

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  • ノードの二項関係リストから所属ネットワーク別のノードリストを作成する

    太田 潤

    第23回オープンバイオ研究会  2019.3.10 

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  • “原子=人”とみてみることから垣間見える代謝ネットワークと社会的ネットワークの比喩的類似性

    太田 潤

    第68回 人工知能学会 分子生物情報研究会(SIG-MBI)  2019.3.9 

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  • Convergence of isotopomer distribution simulation in metabolic networks

    OHTA Jun

    2019.3.8 

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  • メタノール利用反応を含む 糖質代謝モデルネットワークにおける メタノールからのグルコース完全合成

    太田 潤

    第13回日本ゲノム微生物学会年会  2019.3.6 

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  • 代謝ネットワーク:特定原料代謝産物からの目的代謝産物完全合成の可能性

    太田 潤

    JSBi九州地域部会セミナー@福岡市  2018.12.17 

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  • Simulation of time course change of isotope distribution in metabolic networks

    OHTA Jun

    2018.12.14 

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  • Incorporation of acetyl moiety carbons of acetyl-CoA into glucose through a model network of carbohydrate metabolism

    OHTA Jun

    2018.11 

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  • EMU tracing: listing all the elementary metabolite units (EMU) which can be formed from source EMUs through a given metabolic network

    OHTA Jun

    2018.9.18 

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  • Isotopomer tracing approach to investigate pathways for complete glucose synthesis from methanol through a model network of carbohydrate metabolism including reactions for methanol utilization

    OHTA Jun

    2018.9 

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  • Octave/Matlab上での生化学反応のbrute force生成の試み-4本の結合が切断される場合について

    大槻和平, 太田潤

    第7回生命医薬情報学連合大会(IIBMP2018)  2018.9 

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  • Isotopomer tracing: listing all the isotopomers synthesizable from source isotopomers through a given metabolic network

    OHTA Jun

    2018.6 

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  • 代謝ネットワークのsingle-atom tracingにより計算される経路の働きの指標について

    太田 潤

    JSBi九州地域部会セミナー鹿児島2018  2018.5.25 

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  • Listing atom-level pathways in a model network of carbohydrate metabolism and calculating their stoichiometric balances

    OHTA Jun

    2018.5 

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  • 生物ネットワーク情報の行列表現について

    太田 潤

    第22回オープンバイオ研究会  2018.3.9 

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  • 新代謝経路発見のための仮想代謝ネットワーク生成について

    太田 潤

    第65回 人工知能学会 分子生物情報研究会(SIG-MBI)  2018.3.8 

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  • メタノール利用反応を含む糖質代謝モデルネットワークにおけるメタノールからグルコースへの経路の検討

    太田 潤

    第12回日本ゲノム微生物学会年会  2018.3 

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  • 糖質代謝モデルネットワーク上のsingle-atom tracingによる経路計算と経路選択

    太田 潤

    情報処理学会「第53回バイオ情報学研究会(SIGBIO)」  2018.3 

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  • Generation of hypothetical reactions from a set of metabolites based on stoichiometry International conference

    OHTA Jun

    APBC 2018(The Sixteenth Asia Pacific Bioinformatics Conference)  2018.1 

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  • Interconversion between atom mapping matrices and connectivity matrices

    OHTA Jun

    ConBio2017  2017.12 

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  • 代謝ネットワークのsingle-atom tracingにより計算される経路の生化学的意味について

    太田 潤

    日本バイオインフォマティクス学会(JSBi)九州地域部会セミナー @宮崎  2017.10 

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  • 代謝ネットワーク:原子ネットワーク構造と化学結合間のつながりによるネットワーク構造

    太田 潤

    JSBi 九州地域部会セミナー2017  2017.3 

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  • Stereochemistry of the propargylglycine moiety in gamma-glutamylpropargylglycine formed from propargylglycine in baker's yeast

    OHTA Jun

    2016.11 

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  • Classification of hypothetical metabolic networks

    OHTA Jun

    2015.12 

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  • Atomic tracing between carbon atoms in glucose in a model network of carbohydrate metabolism

    OHTA Jun

    2014.11 

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  • Toward Manipulating Biochemical Reactions on Octave/Matlab International conference

    HYODO Yuki, OHTA Jun

    Metabolomics 2014: The 10th International Conference of the Metabolomics Society  2014.6 

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  • IMAC, Inter- And Intra-Metabolite Atom-Level Connectivity Database

    太田 潤

    第85回日本生化学会大会  2012.12 

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  • Study on generation of hypothetical metabolic networks for prediction of uni

    OHTA Jun

    2010.12 

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  • Attempt of stoichiometric extension of amino acid metabolism-related model metabolic network International conference

    OHTA Jun

    11th International Congress on Amino Acids, Peptides and Proteins  2009.8 

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  • 代謝ネットワークを原子ネットワークとみる考え方から“合成的”代謝ネットワーク研究へ

    太田 潤

    第9回日本蛋白質科学会年会  2009.5 

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  • 新代謝経路探索のための化学量論的代謝ネットワーク拡張

    太田 潤

    第3回日本ゲノム微生物学会年会  2009.3 

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  • コンピュータ上での生化学反応生成から代謝ネットワーク研究へ

    太田 潤

    JSBi システムバイオロジー研究会  2009.1 

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  • Manipulating Biochemical Reactions on Octave/Matlab International conference

    HYODO Yuki, OHTA Jun

    The 19th International Conference on Genome Informatics (GIW2008)  2008.12 

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  • A strategy for generation of hypothetical metabolic networks based on melabolome information and stoichiometry

    OHTA Jun

    2008.12 

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  • Generation of hypothetical metabolic networks for pathway prediction

    OHTA Jun

    2008.10 

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  • Atom network view of metabolic networks and its potential

    OHTA Jun

    2008.9 

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  • Strategy for exploring new metabolic pathways: Generation of hypothetical metabolic networks International conference

    OHTA Jun

    IECA2008 (International E. Coli allianace)  2008.9 

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  • Concept of metabolic networks as atom networks and generation of metabolic networks by network expansion International conference

    OHTA Jun

    ICSB2008 (International Conference on Systems Biology)  2008.8 

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  • 代謝ネットワークにおけるノードの「機能」とネットワーク内での「位置」の関係に関する研究

    太田 潤

    第2回日本ゲノム微生物学会年会  2008.3 

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  • Metabolic networks as atom networks and balanced reaction pattern

    OHTA Jun

    2007.12 

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  • Concept of metabolic networks as atom networks International conference

    OHTA Jun

    Nishinomiya-Yukawa International & Interdisciplinary Symposium 2007, What is Life? Yukawa Institute for Theoretical Physics, Kyoto University  2007.10 

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  • Visualization of atom network structure of metabolic networks by Pajek

    OHTA Jun

    2007.10 

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  • A Strategy for Metabolic Pathway Prediction: Generation of Metabolic Networks Using Balanced Reaction Pattern International conference

    OHTA Jun

    The Seventh International Workshop on Bioinformatics and Systems Biology  2007.7 

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  • Connectivity matrix method and atom mapping matrices International conference

    OHTA Jun

    Second FEBS Advanced Course on Systems Biology: From Molecules To Life  2007.3 

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  • 生物ネットワーク情報の行列表現とその代謝ネットワークへの応用

    太田 潤

    第1回日本ゲノム微生物学会年会  2007.3 

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  • Visualization of Metabolic Networks as Networks of Atoms by Pajek: An Application of Connectivity Matrix Method International conference

    OHTA Jun

    The 17th International Conference on Genome Informatics (GIW2006)  2006.12 

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  • Metabolic Networks: Connectivity Matrix-Based Isotopomer Analysis on Matlab/Octave International conference

    OHTA Jun

    The 7th International Conference on Systems Biology  2006.10 

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  • Attempt to express topological position of individual metabolites in the whole metabolic network of Escherichia coli. International conference

    OHTA Jun

    IECA2006, 3rd International E.Coli Alliance Conference on Systems Biology  2006.10 

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  • 原子のネットワークとしての代謝ネットワークと社会的ネットワークの類似性について 自分が原子になったと考えてみる

    太田 潤

    日本ソフトウェア科学会 ネットワークが創発する知能研究会 第2回国内ワークショップ  2006.9 

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  • Connectivity matrix method for analyses of biological networks and its application to atom-level analysis of a model network of carbohydrate metabolism International conference

    OHTA Jun

    12th BTK meeting, Systems Biology: Redefining Biothermokinetics, International Study Group on Systems Biology  2006.9 

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  • ネットワークを構成するノードの「機能」とネットワーク内での「位置」の関係の研究に向けて

    太田 潤

    日本バイオインフォマティクス学会 システムバイオロジー研究会サテライトミーティング In 秋田  2006.8.31 

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  • IMAC, Inter- And Intra-Metabolite Atom-Level Connectivity Database International conference

    OHTA Jun

    World Congress on Medical Physics and Biomedical Engineering 2006  2006.8 

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  • Connectivity Matrix 法によるネットワーク解析 - 原子レベル代謝ネットワーク解析への応用 -

    太田 潤

    日本バイオインフォマティクス学会・夏の学校  2006.8 

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  • Application of Connectivity Matrix Method to Atom-level Analysis of Metabolic Networks: Calculation of Paths Connecting Two Metabolites

    OHTA Jun

    CBI2006, Integration of Chem-Bio-Pharma Informatics for Rational Drug Development and e-ADMET, Chem-Bio Informatics Society  2006.7 

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  • Atom-level and Metabolite-level Analyses of Metabolic Networks using Matlab and Octave International conference

    OHTA Jun

    20th IUBMB International Congress of Biochemistry and Molecular Biology and 11th FAOBMB Congress  2006.6 

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  • 化学構造を含む原子レベル代謝ネットワーク全構造の記述と解析

    太田 潤

    文部科学省研究費補助金・特定領域研究ゲノム「4領域」第8回ワークショップ 微生物ゲノム研究のフロンティア  2006.3 

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  • Octave, Matlabを用いる代謝ネットワークの研究

    太田 潤

    日本バイオインフォマティクス学会 第9回システムバイオロジー研究会  2006.1.18 

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  • Theoretical Analysis of Metabolic Networks: Attempt to Express Topological Position of Individual Atoms in a Given Network International conference

    OHTA Jun

    The 16th International Conference on Genome Informatics (GIW2005)  2005.12 

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  • Development of "connectivity matrix" method for theoretical analyses of metabolic networks

    OHTA Jun

    第78回日本生化学会大会  2005.10 

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  • 数値計算ソフトOctave/Matlabを用いる原子レベルでの代謝ネットワークの研究

    太田 潤

    第一回 プロテイン・インフォマティクスワークショップ in 九州  2005.10 

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  • "Connectivity Matrix" Method: Analysis of Metabolic Networks on GNU Octave/Matlab International conference

    OHTA Jun

    SYMBIONIC COURSE 2005: Methods, Data Handling and Standards in Neuronal Systems Biology  2005.8 

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  • ネットワーク構造の記述法の開発

    太田 潤

    日本バイオインフォマティクス学会・夏の学校  2005.8 

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  • Matlab/GNU Octave as a Platform for Analyses of Metabolic Networks

    OHTA Jun

    CBI学会2005年大会, Chem-Bio Informatics in the Post-Genome Era, Chem-Bio Informatics Society  2005.8 

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  • "Connectivity matrix" method for theoretical analyses of metabolic networks International conference

    OHTA Jun

    Metabolomics 2005, The First Annual Meeting of the Metabolomics Society  2005.6 

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  • Connectivity matrix for describing all the atom-level connectivities in a given metabolic network and its use for analysis of the network structure International conference

    OHTA Jun

    First FEBS Advanced Course on Systems Biology: From Molecules & Modeling To Cells  2005.3 

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  • Metabolic Networks: Use of Matrix Expression for Structural Analyses

    OHTA Jun

    第27回日本分子生物学会年会  2004.12 

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  • Atom-level Analysis of Metabolic Networks Consisting of Multiple Compartments

    OHTA Jun

    2004.10 

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  • Toward Complete Structural Analyses of Metabolic Networks: Prototype Data Format for Describing Both Inter- and Intra-Metabolite Atom-level Connectivities International conference

    OHTA Jun

    5th International Conference on Systems Biology  2004.10 

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  • Structural analyses of metabolic networks using GNU Octave

    OHTA Jun

    CBI学会2004年大会, New Technologies for Drug Design and Discovery in the Post-Genome Era, Chem-Bio Informatics Society  2004.7 

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  • Atom-level Analysis of Metabolic Networks using GNU Octave and IMAC, A Database of Inter-Metabolite Atom-level Connectivity Invited International conference

    OHTA Jun

    IECA2004, 2nd International E.Coli Alliance Conference on Systems Biology  2004.6 

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  • Intermetabolite atom-level connectivity in metabolic network Pathways from 6 carbon atoms of D-Glucose to CO2 in a model network of carbohydrate metabolism

    OHTA Jun

    2003.10 

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  • Data Format for Computational Analysis of Intermetabolite Atom-level Connectivity in Metabolic Networks International conference

    OHTA Jun

    HUPO 2nd Annual & IUBMB XIX World Congress  2003.10 

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  • A Role of Gamma-Glutamylcysteine Synthetase in Propargylglycine Metabolism International conference

    OHTA Jun

    HUPO 2nd Annual & IUBMB XIX World Congress  2003.10 

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  • 代謝ネットワークの構造解析:Intermetabolite atom-level connectivityを表現するformat

    太田 潤

    CBI2003 情報計算化学生物学会2003年大会  2003.9 

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  • Intermetabolite atom-level connectivity in a model metabolic network of carbohydrate metabolism International conference

    OHTA Jun

    IECA2003, First IECA Conference on Systems Biology of E. Coli  2003.6 

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  • ラット初代培養肝細胞によるシステイン代謝調節に関する研究

    太田 潤, Young Hye Kwon, Martha, H. Stipanuk

    第44回日本生化学会中国・四国支部例会  2003.5 

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  • プロパルギルグリシン投与ラット肝臓ミトコンドリア内のγ―グルタミルプロパルギルグリシルグリシン

    太田 潤

    第75回日本生化学会大会  2002.10 

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  • 赤血球による過酸化水素の分解について 8.ヘモグロビンによる分解

    益岡典芳, 太田潤, 汪達紘, 竹居孝二, 中野琢, 児玉裕敬

    第74回日本生化学会大会  2001.10 

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  • 酵母におけるプロパルギルグリシンのγ-グルタミルプロパルギルグリシンへの代謝

    太田 潤

    第74回日本生化学会大会  2001.10 

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  • Amanita pseudoporphyriaおよびAmanita abruptaに含まれる非タンパク性アミノ酸、プロパルギルグリシンの哺乳動物におけるグルタチオン類似体への代謝

    太田 潤

    平成13年度日本菌学会関東支部年次大会(日本大学薬学部)  2001.4.21 

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Works

Research Projects

  • Theoretical study on structure-function relationship in metabolic networks

    2002

    Ordinary Research 

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    Grant type:Competitive

    I am making an atom-level database of metabolism and performing theoretical study on structure-function relationship in metabolic networks.

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  • Biochemistry of non-protein amino acids

    1994

    Ordinary Research 

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    Grant type:Competitive

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  • Biochemistry of Sulfur Amino Acids

    1985

    Ordinary Research 

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    Grant type:Competitive

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