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Fukushima A.,RIKEN | Kusano M.,RIKEN | Kusano M.,Kihara Institute for Biological Research
Frontiers in Plant Science

Metabolomics has grown greatly as a functional genomics tool, and has become an invaluable diagnostic tool for biochemical phenotyping of biological systems. Over the past decades, a number of databases involving information related to mass spectra, compound names and structures, statistical/mathematical models and metabolic pathways, and metabolite profile data have been developed. Such databases complement each other and support efficient growth in this area, although the data resources remain scattered across the World Wide Web. Here, we review available metabolome databases and summarize the present status of development of related tools, particularly focusing on the plant metabolome. Data sharing discussed here will pave way for the robust interpretation of metabolomic data and advances in plant systems biology. © 2013 Fukushima and Kusano. Source

Kawakami H.,Akita Prefectural University | Yokoyama M.,Kihara Institute for Biological Research | Takagi K.,Shiseido Co. | Ogawa S.,Shiseido Co. | And 3 more authors.
In Vitro Cellular and Developmental Biology - Plant

The stress-induced α-ketol derivative of linolenic acid, identified in Lemna paucicostata as 9-hydroxy-10-oxo-12(Z),15(Z)-octadecadienoic acid (KODA), is involved in the enhancement of flower formation and the breaking of dormancy. Swertia japonica is an important bitter stomachic, and its adventitious roots contain xanthones, which are antioxidant compounds. Here, we demonstrate that KODA enhanced redifferentiation of adventitious roots from calli of S. japonica. Moreover, the effect of KODA was confirmed in liquid culture and the redifferentiation of adventitious roots was increased more than in solid culture. Conversely, KODA suppressed the biosynthesis of xanthone diglycoside, which suggests that KODA maintained the roots in an immature state under our culture conditions. © 2015, The Society for In Vitro Biology. Source

Kamoshida G.,Hoshi University | Ogawa T.,Yokohama City University | Ogawa T.,Kihara Institute for Biological Research | Oyanagi J.,Yokohama City University | And 10 more authors.
Clinical and Experimental Metastasis

Macrophages infiltrating tumor tissues (tumor-associated macrophages, TAM) affect the malignant behaviors of tumor cells. We previously reported that monocytes were differentiated into TAM-like cells secreting matrix metalloproteinase (MMP)-9 by co-culture with tumor cells, and that cell adhesion to extracellular matrix (ECM) proteins played a critical role in the differentiation. In this study, we found that the monocyte differentiation was promoted by laminin-332 (laminin-5), a major epithelial ECM component. We also demonstrated that the proteolytic processing of the γ2 chain of laminin-332 was essential for its activity but that the N-terminal short arm of the γ2 chain inhibited MMP-9 secretion. These results indicate that the activity of laminin-332 for monocyte differentiation is dynamically regulated by the proteolytic processing of the γ2 chain. © Springer Science+Business Media 2013. Source

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