Evolution of ribosomal DNA-derived satellite repeat in tomato genome

Background  

Tandemly repeated DNA, also called as satellite DNA, is a common feature of eukaryotic genomes. Satellite repeats can expand and contract dramatically, which may cause genome size variation among genetically-related species. However, the origin and expansion mechanism are not clear yet and needed to be elucidated.     

A-ring ortho-specific monohydroxylation of daidzein by cytochrome P450s of Nocardia farcinica IFM10152

The bioconversion of the isoflavonoid daidzein using whole cell Nocardia farcinica IFM10152 showed two kinds of major metabolic modifications, i.e. mono-hydroxylation and subsequent O-methylation. The major hydroxylated products of daidzein prior to the O-methylation reaction were 3',4',7-trihydroxyisoflavone (3'-ODI), 4',6,7-trihydroxyisoflavone (6-ODI) and 4',7,8-trihydroxyisoflavone (8-ODI), which are mono-hydroxylated at the ortho position of each hydroxyl group of daidzein. To identify monooxygenases playing a key role in the monohydroxylation of the A-ring of daidzein, all genes of 27 cytochrome P450s from N. farcinica IFM10152 were cloned and transformed into a E. coli BL21 (DE3) host system. By this enzymatic reaction using the mutants and the genome sequence analysis of N. farcinica IFM10152, it was revealed that nfa12130 and nfa33880 P450 genes clustered with their own ferredoxins and ferredoxin reductases (nfa12140+nfa12150 and nfa338870+nfa33860, respectively) are responsible for the hydroxylation of the A-ring of daidzein, and their major reaction products were 6-ODI and 8-ODI, respectively.     

Biosynthesis of dTDP-6-deoxy-beta-D-allose, biochemical characterization of dTDP-4-keto-6-deoxyglucose reductase (GerKI) from Streptomyces sp. KCTC 0041BP

dTDP-6-deoxy-d-allose, an unusual deoxysugar, has been identified as an intermediate in the mycinose biosynthetic pathway of several macrolide antibiotics. In order to characterize the biosynthesis of this deoxysugar, we have cloned and heterologously overexpressed gerK1 in Escherichia coli BL21 (DE3) cells. This gene encodes for a protein with the putative function of a dTDP-4-keto-6-deoxyglucose reductase, which appears to be involved in the dihydrochalcomycin (GERI-155) biosynthesis evidenced by Streptomyces sp KCTC 0041BP. Our results revealed that GerK1 exhibited a specific reductive effect on the 4-keto carbon of dTDP-4-keto-6-deoxy-d-allose, with the hydroxyl group in an axial configuration at the C3 position only. The enzyme catalyzed the conversion of dTDP-4-keto-6-deoxyglucose to dTDP-6-deoxy-beta-D-allose, according to the results of an in vitro coupled enzyme assay, in the presence of GerF (dTDP-4-keto-6-deoxyglucose 3-epimerase). The product was isolated, and its stereochemistry was determined via nuclear magnetic resonance analysis.     

Is insufficient sleep duration associated with suicidal behavior in Korean adolescents?

Sleep and Biological Rhythms - The second leading cause of death among Korean adolescents was suicide in 2014. We assessed the relationship between sleep duration and suicidal behavior (ideation,...     

Computational analysis of the spatiotemporal coordination of polarized PI3K and Rac1 activities in micro-patterned live cells

Polarized molecular activities play important roles in guiding the cell toward persistent and directional migration. In this study, the polarized distributions of the activities of phosphatidylinositol 3-kinase (PI3K) and the Rac1 small GTPase were monitored using chimeric fluorescent proteins (FPs) in cells constrained on micro-patterned strips, with one end connecting to a neighboring cell (junction end) and the other end free of cell-cell contact (free end). The recorded spatiotemporal dynamics of the fluorescent intensity from different cells was scaled into a uniform coordinate system and applied to compute the molecular activity landscapes in space and time. The results revealed different polarization patterns of PI3K and Rac1 activity induced by the growth factor stimulation. The maximal intensity of different FPs, and the edge position and velocity at the free end were further quantified to analyze their correlation and decipher the underlying signaling sequence. The results suggest that the initiation of the edge extension occurred before the activation of PI3K, which led to a stable extension of the free end followed by the Rac1 activation. Therefore, the results support a concerted coordination of sequential signaling events and edge dynamics, underscoring the important roles played by PI3K activity at the free end in regulating the stable lamellipodia extension and cell migration. Meanwhile, the quantification methods and accompanying software developed can provide a convenient and powerful computational analysis platform for the study of spatiotemporal molecular distribution and hierarchy in live cells based on fluorescence images.