<Preliminary>A Role of Oxalic Acid in Acid Hydrolysis of Non-Phenolic β-O-4 Type Lignin Carbohydrate Complexes (LCC) Model Compounds

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<Preliminary>An Enzymatic Study of an Oxalate Producing System in Relation to the Glyoxylate Cycle in White-rot Fungus Phanerochaete chrysosporium

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MUCHA: multiple chemical alignment algorithm to identify building block substructures of orphan secondary metabolites

[Background]In contrast to the increasing number of the successful genome projects, there still remain many orphan metabolites for which their synthesis processes are unknown. Metabolites, including these orphan metabolites, can be classified into groups that share the same core substructures, originated from the same biosynthetic pathways. It is known that many metabolites are synthesized by adding up building blocks to existing metabolites. Therefore, it is proposed that, for any given group of metabolites, finding the core substructure and the branched substructures can help predict their biosynthetic pathway. There already have been many reports on the multiple graph alignment techniques to find the conserved chemical substructures in relatively small molecules. However, they are optimized for ligand binding and are not suitable for metabolomic studies. [Results]We developed an efficient multiple graph alignment method named as MUCHA (Multiple Chemical Alignment), specialized for finding metabolic building blocks. This method showed the strength in finding metabolic building blocks with preserving the relative positions among the substructures, which is not achieved by simply applying the frequent graph mining techniques. Compared with the combined pairwise alignments, this proposed MUCHA method generally reduced computational costs with improving the quality of the alignment. [Conclusions]MUCHA successfully find building blocks of secondary metabolites, and has a potential to complement to other existing methods to reconstruct metabolic networks using reaction patterns

エノキの組織培養と不定根の誘導

エノキ (Celtis sinensis Pers. var, japonica Nakai) の成木の新枝よりナフタレン酢酸 (NAA) 1. 0mg/ℓ, 6-ベンジルアミノプリン (BAP) 0. 1mg/ℓを含むイオン強度を半分にした改変 Murashige-Skoog (MS) 培地を用い緑色カルスを誘導した。このカルスの生育は早く, プランテックスを用いて25℃で2, 500luxの照光下培養した場合, 9週間で絶乾重量が9倍になった。このカルスを0. 5mg/ℓのNAAと1. 0mg/ℓのBAPを含む改変MS培地を用いて暗黒下培養したところ, 67％の率で根が誘導された。A green compact callus was induced from sterilized shoots of Japanese hackberry (Celtis sinensis Pers. var. japonica Nakai) on a Murashige-Skoog medium supplemented with 1.0mg/ ℓ 1-naphthaleneacetic acid (NAA) and 0.1 mg/ ℓ 6-benzylaminopurine (BAP). The callus grew fast on this medium in PLANTEX to attain 9 fold amount of dry weight at 9 weeks incubation at 25℃ with a continuous illumination of 2, 500 lux. Roots were regenerated from the callus after incubation for 4 weeks under dark at hormonal combination of 0.5mg/ ℓ NAA and 1.0 mg/ ℓ BAP at a relatively high frequency of 67%

KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data

Correlations of gene-to-gene co-expression and metabolite-to-metabolite co-accumulation calculated from large amounts of transcriptome and metabolome data are useful for uncovering unknown functions of genes, functional diversities of gene family members and regulatory mechanisms of metabolic pathway flows. Many databases and tools are available to interpret quantitative transcriptome and metabolome data, but there are only limited ones that connect correlation data to biological knowledge and can be utilized to find biological significance of it. We report here a new metabolic pathway database, KaPPA-View4 (http://kpv.kazusa.or.jp/kpv4/), which is able to overlay gene-to-gene and/or metabolite-to-metabolite relationships as curves on a metabolic pathway map, or on a combination of up to four maps. This representation would help to discover, for example, novel functions of a transcription factor that regulates genes on a metabolic pathway. Pathway maps of the Kyoto Encyclopedia of Genes and Genomes (KEGG) and maps generated from their gene classifications are available at KaPPA-View4 KEGG version (http://kpv.kazusa.or.jp/kpv4-kegg/). At present, gene co-expression data from the databases ATTED-II, COXPRESdb, CoP and MiBASE for human, mouse, rat, Arabidopsis, rice, tomato and other plants are available

<Preliminary>Lignin Peroxidase-Catalyzed Oxidation of a β-O-4 Model Compound of Lignin Carbohydrate Complex

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木材腐朽モデル系におけるシュウ酸の生化学的役割と新規シュウ酸生成酵素グリオキシル酸脱水素酵素の性質

京都大学0048新制・課程博士博士(農学)甲第7591号農博第1030号新制||農||773(附属図書館)学位論文||H11||N3226(農学部図書室)UT51-99-D208京都大学大学院農学研究科林産工学専攻(主査)教授 島田 幹夫, 教授 桒原 正章, 教授 中坪 文明学位規則第4条第1項該当Doctor of Agricultural ScienceKyoto UniversityDA

<Preliminary>A Possible Intramolecular Electron Transfer Pathway of Glyoxylate Dehydrogenase in a Brown-rot Fungus Tyromyces palustris

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