Metabolomics and differential gene expression in anthocyanin chemo-varietal forms of Perilla frutescens

We have investigated metabolite profiles and gene expression in two chemo-varietal forms, red and green forms, of Perilla frutescens var. crispa. Striking difference in anthocyanin content was observed between the red and green forms. Anthocyanin, mainly malonylshisonin, was highly accumulated in the leaves of the red form but not in the green form. Less obvious differences were also observed in the stems. However, there was no remarkable difference in the contents and patterns of flavones and primary metabolites such as inorganic anions, organic anions and amino acids. These results suggest that only the regulation of anthocyanin production, but not that of other metabolites, differs in red and green forms. Microscopic observation and immunohistochemical studies indicated that the epidermal cells of leaves and stems are the sites of accumulation of anthocyanins and localization of anthocyanidin synthase protein. By differential display of mRNA from the leaves of red and green forms, we could identify several genes encoding anthocyanin-biosynthetic enzymes and presumptive regulatory proteins. The possible regulatory network leading to differential anthocyanin accumulation in a form-specific manner is discussed.     

Differential gene expression profiles of red and green forms of Perilla frutescens leading to comprehensive identification of anthocyanin biosynthetic genes

Differential screening by PCR-select subtraction was carried out for cDNAs from leaves of red and green perilla, two chemovarietal forms of Perilla frutescens regarding anthocyanin accumulation. One hundred and twenty cDNA fragments were selected as the clones preferentially expressed in anthocyanin-accumulating red perilla over the nonaccumulating green perilla. About half of them were the cDNAs encoding the proteins related presumably to phenylpropanoid-derived metabolism. The cDNAs encoding glutathione S-transferase (GST), PfGST1, and chalcone isomerase (CHI), PfCHI1, were further characterized. The expression of PfGST1 in an Arabidopsis thaliana tt19 mutant lacking the GST-like gene involved in vacuole transport of anthocyanin rescued the lesion of anthocyanin accumulation in tt19, indicating a function of PfGST1 in vacuole sequestration of anthocyanin in perilla. The recombinant PfCHI1 could stereospecifically convert naringenin chalcone to (2S)-naringenin. PfGST1 and PfCHI1 were preferentially expressed in the leaves of red perilla, agreeing with the accumulation of anthocyanin and expression of other previously identified genes for anthocyanin biosynthesis. These results suggest that the genes of the whole anthocyanin biosynthetic pathway are regulated in a coordinated manner in perilla.     

Clustering cancer gene expression data: a comparative study

Background  

The use of clustering methods for the discovery of cancer subtypes has drawn a great deal of attention in the scientific community. While bioinformaticians have proposed new clustering methods that take advantage of characteristics of the gene expression data, the medical community has a preference for using "classic" clustering methods. There have been no studies thus far performing a large-scale evaluation of different clustering methods in this context.     

A comparative study of discriminating human heart failure etiology using gene expression profiles

Background  

Human heart failure is a complex disease that manifests from multiple genetic and environmental factors. Although ischemic and non-ischemic heart disease present clinically with many similar decreases in ventricular function, emerging work suggests that they are distinct diseases with different responses to therapy. The ability to distinguish between ischemic and non-ischemic heart failure may be essential to guide appropriate therapy and determine prognosis for successful treatment. In this paper we consider discriminating the etiologies of heart failure using gene expression libraries from two separate institutions.     

Synaptonemal complex alterations in X-irradiated and in oestrogen-treated mice: a comparative study.

Synaptonemal complexes (SCs) were analysed in male NMRI mice either X-irradiated or treated with oestradiol benzoate (E2B). Animals 30 days old underwent a single X-ray exposure of either 5, 7.5 or 10 Gy and were killed at different times after exposure, i.e., 24 h, 1, 4, 12 and 16 weeks. E2B was injected daily to adult mice from day 30 to day 60 or up to day 90 of age. Oestradiol was also administered during the neonatal period and animals were examined on days 28, 60 and 90 of age. Different SC alterations were found in X-irradiated and in E2B-treated mice. SC lesions were rare in oestrogen-treated adult mice. Among SC anomalies, asynapsis and fragmentation of SC were common lesions. However, the former was more frequent in E2B-treated mice, whereas the latter was more frequent in X-irradiated mice. Quadri- or multi-valents, bridges between bivalents, rings and loops were exclusively encountered in the latter, whereas heterotelomeric associations seemed to be specific in E2B-treated animals. The mechanisms of the different SC lesions are discussed.     

Cytokinin-induced gene expression in cultured green cells of Nicotiana tabacum identified by fluorescent differential display

The cell growth and plastid development of cultured green tobacco cells were maintained by the phytohormone cytokinin. After subculture into cytokinin-free medium, when cytokinin treatment was resumed, physiological changes induced by cytokinin were analyzed. Changes in chlorophyll biosynthesis and photosynthetic gene expression were observed 1 week after cytokinin induction, and changes in cell growth were observed 2 weeks after cytokinin induction. Two cytokinin-induced genes (cig) were isolated from these cells using the fluorescent differential display technique. Northern analysis confirmed that expression of these cig was induced by both natural and synthetic cytokinins. The expression of cig1 was also induced by abscisic acid, and its cDNA sequence was similar to the proline dehydrogenase gene. The expression of cig2 is specific to cytokinin and is not induced by other phytohormones. The amino acid sequence encoded by cig2 is similar to the GDP/GTP exchange factor eIF2B, which regulates translation initiation. The expression of these cig suggests a complex induction system involving cytokinin and other phytohormones.