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Items: 1 to 50 of 92

1.

Autopolyploidization, geographic origin, and metabolome evolution in Arabidopsis thaliana.

Vergara F, Rymen B, Kuwahara A, Sawada Y, Sato M, Hirai MY.

Am J Bot. 2017 Jun;104(6):905-914. doi: 10.3732/ajb.1600419. Epub 2017 Jun 16.

2.
3.
4.

Succinate and Lactate Production from Euglena gracilis during Dark, Anaerobic Conditions.

Tomita Y, Yoshioka K, Iijima H, Nakashima A, Iwata O, Suzuki K, Hasunuma T, Kondo A, Hirai MY, Osanai T.

Front Microbiol. 2016 Dec 21;7:2050. doi: 10.3389/fmicb.2016.02050. eCollection 2016.

5.

Investigation of kinetic-order sensitivities in metabolic reaction networks.

Yamada M, Iwanaga M, Sriyudthsak K, Hirai MY, Shiraishi F.

J Theor Biol. 2017 Feb 21;415:32-40. doi: 10.1016/j.jtbi.2016.12.001. Epub 2016 Dec 7.

PMID:
27939412
6.

Changes in trans-S-1-Propenyl-l-cysteine Sulfoxide and Related Sulfur-Containing Amino Acids during Onion Storage.

Kamata Y, Aoyagi M, Sawada Y, Nakabayashi R, Hirai MY, Saito K, Imai S.

J Agric Food Chem. 2016 Nov 30;64(47):9063-9071. Epub 2016 Nov 16.

PMID:
27933869
7.

Expression of Flavone Synthase II and Flavonoid 3'-Hydroxylase Is Associated with Color Variation in Tan-Colored Injured Leaves of Sorghum.

Mizuno H, Yazawa T, Kasuga S, Sawada Y, Kanamori H, Ogo Y, Hirai MY, Matsumoto T, Kawahigashi H.

Front Plant Sci. 2016 Nov 21;7:1718. eCollection 2016.

8.

A new parametric method to smooth time-series data of metabolites in metabolic networks.

Miyawaki A, Sriyudthsak K, Hirai MY, Shiraishi F.

Math Biosci. 2016 Dec;282:21-33. doi: 10.1016/j.mbs.2016.09.011. Epub 2016 Sep 28.

PMID:
27693302
9.

The Minimum Open Reading Frame, AUG-Stop, Induces Boron-Dependent Ribosome Stalling and mRNA Degradation.

Tanaka M, Sotta N, Yamazumi Y, Yamashita Y, Miwa K, Murota K, Chiba Y, Hirai MY, Akiyama T, Onouchi H, Naito S, Fujiwara T.

Plant Cell. 2016 Nov;28(11):2830-2849. Epub 2016 Oct 19.

10.

Primary Metabolism during Biosynthesis of Secondary Wall Polymers of Protoxylem Vessel Elements.

Ohtani M, Morisaki K, Sawada Y, Sano R, Uy AL, Yamamoto A, Kurata T, Nakano Y, Suzuki S, Matsuda M, Hasunuma T, Hirai MY, Demura T.

Plant Physiol. 2016 Nov;172(3):1612-1624. Epub 2016 Sep 6.

11.

Anionic metabolite biosynthesis enhanced by potassium under dark, anaerobic conditions in cyanobacteria.

Ueda S, Kawamura Y, Iijima H, Nakajima M, Shirai T, Okamoto M, Kondo A, Hirai MY, Osanai T.

Sci Rep. 2016 Aug 31;6:32354. doi: 10.1038/srep32354.

12.

Mathematical Modeling and Dynamic Simulation of Metabolic Reaction Systems Using Metabolome Time Series Data.

Sriyudthsak K, Shiraishi F, Hirai MY.

Front Mol Biosci. 2016 May 3;3:15. doi: 10.3389/fmolb.2016.00015. eCollection 2016. Review.

13.

PASMet: a web-based platform for prediction, modelling and analyses of metabolic systems.

Sriyudthsak K, Mejia RF, Arita M, Hirai MY.

Nucleic Acids Res. 2016 Jul 8;44(W1):W205-11. doi: 10.1093/nar/gkw415. Epub 2016 May 12.

14.

Understanding Sugar Catabolism in Unicellular Cyanobacteria Toward the Application in Biofuel and Biomaterial Production.

Osanai T, Iijima H, Hirai MY.

Subcell Biochem. 2016;86:511-23. doi: 10.1007/978-3-319-25979-6_20. Review.

PMID:
27023248
15.

The Sorghum Gene for Leaf Color Changes upon Wounding (P) Encodes a Flavanone 4-Reductase in the 3-Deoxyanthocyanidin Biosynthesis Pathway.

Kawahigashi H, Kasuga S, Sawada Y, Yonemaru J, Ando T, Kanamori H, Wu J, Mizuno H, Momma M, Fujimoto Z, Hirai MY, Matsumoto T.

G3 (Bethesda). 2016 May 3;6(5):1439-47. doi: 10.1534/g3.115.026104.

16.

Chemical Assignment of Structural Isomers of Sulfur-Containing Metabolites in Garlic by Liquid Chromatography-Fourier Transform Ion Cyclotron Resonance-Mass Spectrometry.

Nakabayashi R, Sawada Y, Aoyagi M, Yamada Y, Hirai MY, Sakurai T, Kamoi T, Rowan DD, Saito K.

J Nutr. 2016 Feb;146(2):397S-402S. doi: 10.3945/jn.114.202317. Epub 2016 Jan 13.

PMID:
26764333
17.

Modification of photosynthetic electron transport and amino acid levels by overexpression of a circadian-related histidine kinase hik8 in Synechocystis sp. PCC 6803.

Kuwahara A, Arisaka S, Takeya M, Iijima H, Hirai MY, Osanai T.

Front Microbiol. 2015 Oct 20;6:1150. doi: 10.3389/fmicb.2015.01150. eCollection 2015.

18.

Genetic manipulation of a metabolic enzyme and a transcriptional regulator increasing succinate excretion from unicellular cyanobacterium.

Osanai T, Shirai T, Iijima H, Nakaya Y, Okamoto M, Kondo A, Hirai MY.

Front Microbiol. 2015 Oct 6;6:1064. doi: 10.3389/fmicb.2015.01064. eCollection 2015.

19.

Changes in primary metabolism under light and dark conditions in response to overproduction of a response regulator RpaA in the unicellular cyanobacterium Synechocystis sp. PCC 6803.

Iijima H, Shirai T, Okamoto M, Kondo A, Hirai MY, Osanai T.

Front Microbiol. 2015 Aug 26;6:888. doi: 10.3389/fmicb.2015.00888. eCollection 2015.

20.

Determination of growth stages and metabolic profiles in Brachypodium distachyon for comparison of developmental context with Triticeae crops.

Onda Y, Hashimoto K, Yoshida T, Sakurai T, Sawada Y, Hirai MY, Toyooka K, Mochida K, Shinozaki K.

Proc Biol Sci. 2015 Jul 22;282(1811). pii: 20150964. doi: 10.1098/rspb.2015.0964.

21.

Seawater cultivation of freshwater cyanobacterium Synechocystis sp. PCC 6803 drastically alters amino acid composition and glycogen metabolism.

Iijima H, Nakaya Y, Kuwahara A, Hirai MY, Osanai T.

Front Microbiol. 2015 Apr 22;6:326. doi: 10.3389/fmicb.2015.00326. eCollection 2015.

22.

One day of nitrogen starvation reveals the effect of sigE and rre37 overexpression on the expression of genes related to carbon and nitrogen metabolism in Synechocystis sp. PCC 6803.

Nakaya Y, Iijima H, Takanobu J, Watanabe A, Hirai MY, Osanai T.

J Biosci Bioeng. 2015 Aug;120(2):128-34. doi: 10.1016/j.jbiosc.2014.12.020. Epub 2015 Jan 29.

PMID:
25641577
23.

Ectopic expression of myo-inositol 3-phosphate synthase induces a wide range of metabolic changes and confers salt tolerance in rice.

Kusuda H, Koga W, Kusano M, Oikawa A, Saito K, Hirai MY, Yoshida KT.

Plant Sci. 2015 Mar;232:49-56. doi: 10.1016/j.plantsci.2014.12.009. Epub 2014 Dec 18.

PMID:
25617323
24.

rre37 Overexpression alters gene expression related to the tricarboxylic acid cycle and pyruvate metabolism in Synechocystis sp. PCC 6803.

Iijima H, Watanabe A, Takanobu J, Hirai MY, Osanai T.

ScientificWorldJournal. 2014;2014:921976. doi: 10.1155/2014/921976. Epub 2014 Dec 28.

25.

A U-system approach for predicting metabolic behaviors and responses based on an alleged metabolic reaction network.

Sriyudthsak K, Sawada Y, Chiba Y, Yamashita Y, Kanaya S, Onouchi H, Fujiwara T, Naito S, Voit EO, Shiraishi F, Hirai MY.

BMC Syst Biol. 2014;8 Suppl 5:S4. doi: 10.1186/1752-0509-8-S5-S4. Epub 2014 Dec 12.

26.

Alteration of cyanobacterial sugar and amino acid metabolism by overexpression hik8, encoding a KaiC-associated histidine kinase.

Osanai T, Shirai T, Iijima H, Kuwahara A, Suzuki I, Kondo A, Hirai MY.

Environ Microbiol. 2015 Jul;17(7):2430-40. doi: 10.1111/1462-2920.12715. Epub 2015 Jan 27.

PMID:
25403325
27.

Expression level of a flavonoid 3'-hydroxylase gene determines pathogen-induced color variation in sorghum.

Mizuno H, Yazawa T, Kasuga S, Sawada Y, Ogata J, Ando T, Kanamori H, Yonemaru J, Wu J, Hirai MY, Matsumoto T, Kawahigashi H.

BMC Res Notes. 2014 Oct 27;7:761. doi: 10.1186/1756-0500-7-761.

28.

Metabolomic analysis reveals rewiring of Synechocystis sp. PCC 6803 primary metabolism by ntcA overexpression.

Osanai T, Oikawa A, Iijima H, Kuwahara A, Asayama M, Tanaka K, Ikeuchi M, Saito K, Hirai MY.

Environ Microbiol. 2014 Oct;16(10):3304-17. doi: 10.1111/1462-2920.12554. Epub 2014 Aug 29.

PMID:
25039649
29.

NblA1/A2-Dependent Homeostasis of Amino Acid Pools during Nitrogen Starvation in Synechocystis sp. PCC 6803.

Kiyota H, Hirai MY, Ikeuchi M.

Metabolites. 2014 Jun 30;4(3):517-31. doi: 10.3390/metabo4030517.

30.

Engineering of cyanobacteria for the photosynthetic production of limonene from CO2.

Kiyota H, Okuda Y, Ito M, Hirai MY, Ikeuchi M.

J Biotechnol. 2014 Sep 20;185:1-7. doi: 10.1016/j.jbiotec.2014.05.025. Epub 2014 Jun 4.

PMID:
24905149
31.

PENDISC: a simple method for constructing a mathematical model from time-series data of metabolite concentrations.

Sriyudthsak K, Iwata M, Hirai MY, Shiraishi F.

Bull Math Biol. 2014 Jun;76(6):1333-51. doi: 10.1007/s11538-014-9960-8. Epub 2014 May 7.

32.

Pathway-level acceleration of glycogen catabolism by a response regulator in the cyanobacterium Synechocystis species PCC 6803.

Osanai T, Oikawa A, Numata K, Kuwahara A, Iijima H, Doi Y, Saito K, Hirai MY.

Plant Physiol. 2014 Apr;164(4):1831-41. doi: 10.1104/pp.113.232025. Epub 2014 Feb 12.

33.

Rre37 stimulates accumulation of 2-oxoglutarate and glycogen under nitrogen starvation in Synechocystis sp. PCC 6803.

Joseph A, Aikawa S, Sasaki K, Teramura H, Hasunuma T, Matsuda F, Osanai T, Hirai MY, Kondo A.

FEBS Lett. 2014 Jan 31;588(3):466-71. doi: 10.1016/j.febslet.2013.12.008. Epub 2013 Dec 24.

34.

Estimation of kinetic parameters in an S-system equation model for a metabolic reaction system using the Newton-Raphson method.

Iwata M, Sriyudthsak K, Hirai MY, Shiraishi F.

Math Biosci. 2014 Feb;248:11-21. doi: 10.1016/j.mbs.2013.11.002. Epub 2013 Nov 27.

PMID:
24291302
35.

Promotion of chloroplast proliferation upon enhanced post-mitotic cell expansion in leaves.

Kawade K, Horiguchi G, Ishikawa N, Hirai MY, Tsukaya H.

BMC Plant Biol. 2013 Sep 28;13:143. doi: 10.1186/1471-2229-13-143.

36.

Disarming the jasmonate-dependent plant defense makes nonhost Arabidopsis plants accessible to the American serpentine leafminer.

Abe H, Tateishi K, Seo S, Kugimiya S, Hirai MY, Sawada Y, Murata Y, Yara K, Shimoda T, Kobayashi M.

Plant Physiol. 2013 Nov;163(3):1242-53. doi: 10.1104/pp.113.222802. Epub 2013 Sep 10.

37.

Pleiotropic effect of sigE over-expression on cell morphology, photosynthesis and hydrogen production in Synechocystis sp. PCC 6803.

Osanai T, Kuwahara A, Iijima H, Toyooka K, Sato M, Tanaka K, Ikeuchi M, Saito K, Hirai MY.

Plant J. 2013 Nov;76(3):456-65. doi: 10.1111/tpj.12310. Epub 2013 Sep 19.

38.

Novel bioresources for studies of Brassica oleracea: identification of a kale MYB transcription factor responsible for glucosinolate production.

Araki R, Hasumi A, Nishizawa OI, Sasaki K, Kuwahara A, Sawada Y, Totoki Y, Toyoda A, Sakaki Y, Li Y, Saito K, Ogawa T, Hirai MY.

Plant Biotechnol J. 2013 Oct;11(8):1017-27. doi: 10.1111/pbi.12095. Epub 2013 Jul 30.

39.

Increased bioplastic production with an RNA polymerase sigma factor SigE during nitrogen starvation in Synechocystis sp. PCC 6803.

Osanai T, Numata K, Oikawa A, Kuwahara A, Iijima H, Doi Y, Tanaka K, Saito K, Hirai MY.

DNA Res. 2013 Dec;20(6):525-35. doi: 10.1093/dnares/dst028. Epub 2013 Jul 15.

40.

Capillary electrophoresis-mass spectrometry reveals the distribution of carbon metabolites during nitrogen starvation in Synechocystis sp. PCC 6803.

Osanai T, Oikawa A, Shirai T, Kuwahara A, Iijima H, Tanaka K, Ikeuchi M, Kondo A, Saito K, Hirai MY.

Environ Microbiol. 2014 Feb;16(2):512-24. doi: 10.1111/1462-2920.12170. Epub 2013 Jun 25.

PMID:
23796428
41.

Novel insights into the function of Arabidopsis R2R3-MYB transcription factors regulating aliphatic glucosinolate biosynthesis.

Li Y, Sawada Y, Hirai A, Sato M, Kuwahara A, Yan X, Hirai MY.

Plant Cell Physiol. 2013 Aug;54(8):1335-44. doi: 10.1093/pcp/pct085. Epub 2013 Jun 20.

PMID:
23792303
42.

ANGUSTIFOLIA3 signaling coordinates proliferation between clonally distinct cells in leaves.

Kawade K, Horiguchi G, Usami T, Hirai MY, Tsukaya H.

Curr Biol. 2013 May 6;23(9):788-92. doi: 10.1016/j.cub.2013.03.044. Epub 2013 Apr 18.

43.

SS-mPMG and SS-GA: tools for finding pathways and dynamic simulation of metabolic networks.

Katsuragi T, Ono N, Yasumoto K, Altaf-Ul-Amin M, Hirai MY, Sriyudthsak K, Sawada Y, Yamashita Y, Chiba Y, Onouchi H, Fujiwara T, Naito S, Shiraishi F, Kanaya S.

Plant Cell Physiol. 2013 May;54(5):728-39. doi: 10.1093/pcp/pct052. Epub 2013 Apr 9.

PMID:
23574698
44.

Plant lipidomics based on hydrophilic interaction chromatography coupled to ion trap time-of-flight mass spectrometry.

Okazaki Y, Kamide Y, Hirai MY, Saito K.

Metabolomics. 2013 Mar;9(Suppl 1):121-131. Epub 2011 May 31.

45.

A new class of plant lipid is essential for protection against phosphorus depletion.

Okazaki Y, Otsuki H, Narisawa T, Kobayashi M, Sawai S, Kamide Y, Kusano M, Aoki T, Hirai MY, Saito K.

Nat Commun. 2013;4:1510. doi: 10.1038/ncomms2512.

46.

Combination of liquid chromatography-Fourier transform ion cyclotron resonance-mass spectrometry with 13C-labeling for chemical assignment of sulfur-containing metabolites in onion bulbs.

Nakabayashi R, Sawada Y, Yamada Y, Suzuki M, Hirai MY, Sakurai T, Saito K.

Anal Chem. 2013 Feb 5;85(3):1310-5. doi: 10.1021/ac302733c. Epub 2013 Jan 17.

PMID:
23327693
47.

Identification of a metabolic reaction network from time-series data of metabolite concentrations.

Sriyudthsak K, Shiraishi F, Hirai MY.

PLoS One. 2013;8(1):e51212. doi: 10.1371/journal.pone.0051212. Epub 2013 Jan 10.

48.

PRIMe Update: innovative content for plant metabolomics and integration of gene expression and metabolite accumulation.

Sakurai T, Yamada Y, Sawada Y, Matsuda F, Akiyama K, Shinozaki K, Hirai MY, Saito K.

Plant Cell Physiol. 2013 Feb;54(2):e5. doi: 10.1093/pcp/pcs184. Epub 2013 Jan 3.

49.

Integrated LC-MS/MS system for plant metabolomics.

Sawada Y, Hirai MY.

Comput Struct Biotechnol J. 2013 May 23;4:e201301011. doi: 10.5936/csbj.201301011. eCollection 2013. Review.

50.

Changes in mRNA stability associated with cold stress in Arabidopsis cells.

Chiba Y, Mineta K, Hirai MY, Suzuki Y, Kanaya S, Takahashi H, Onouchi H, Yamaguchi J, Naito S.

Plant Cell Physiol. 2013 Feb;54(2):180-94. doi: 10.1093/pcp/pcs164. Epub 2012 Dec 4.

PMID:
23220693

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