Headline News

A new portal site, JBI (Japan alliance for Bioscience Information), has started to support the integrated activities of biological basic databases in Japan

Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University has launched the JBI (Japan alliance for Bioscience Information) portal site in collaboration with National Bioscience Database Center (NBDC), JST; Database Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, ROIS; and DNA Data Bank of Japan (DDBJ), National Institute of Genetics, ROIS. This portal site provides one-stop service of databases and tools which are helpful in various scenes of the life science research.

Visit the website (http://jbioinfo.jp/) for more detail.

Press Release: Calredoxin, a novel protein for promoting efficient photosynthesis

Outline

A group of researchers reports on the structure and function of a novel protein named “Calredoxin”. Calredoxin binds calcium and catalyzes in dependence of its binding, redox reactions, particularly driving the detoxification of harmful oxygen species. The researchers are exploring how this protein functions at the crossroad of calcium- and redox-dependent reactions to promote efficient oxygenic photosynthesis.

Shugoshin forms a specialized chromatin domain at subtelomeres that regulates transcription and replication timing.

A chromosome is composed of structurally and functionally distinct domains. However, the molecular mechanisms underlying the formation of chromatin structure and the function of subtelomeres, the telomere-adjacent regions, remain obscure. Here we report the roles of the conserved centromeric protein Shugoshin 2 (Sgo2) in defining chromatin structure and functions of the subtelomeres in the fission yeast Schizosaccharomyces pombe.

Received the Most-downloaded Publication Award Q3 2015! Closed-cycle cold helium magic-angle spinning for sensitivity-enhanced multi-dimensional solid-state NMR

・Magic-angle spinning (MAS) NMR probe system with a closed-loop helium recirculation.
・Stable MAS for weeks at sample temperature T = 35 K without consuming helium.
・Multi-dimensional MAS NMR at T = 35 K at a low running cost for electricity 16 kW/h.
・An order of magnitude sensitivity gain at T = 40 K and B0 = 16.4 T.

Selective oxidation of 5-hydroxymethylcytosine with micelle incarcerated oxidants to determine it at single base resolution.

5-Methylcytosine (5mC) is oxidized by ten-eleven translocation (TET) enzymes. This process followed by thymine DNA glycosylase is proposed to be the mechanism for methylcytosine demethylation. 5-Hydroxymethylcytosine (5hmC) is one of the most important key oxidative metabolites in the demethylation process, and therefore, simple and accurate method to determine 5hmC at single base resolution is desired. In the present study, we developed a mild catalytic oxidation of 5-hmC using micelle incarcerated oxidants that enables to determine the position of 5hmC at single base resolution.

The RFTS (replication foci targeting sequence) domain of Dnmt1 is not only necessary for replication-coupled maintenance DNA methylation, but also protects genome from aberrant DNA methylation.

In mammals, DNA methylation plays important roles in embryogenesis and terminal differentiation via regulation of the transcription-competent chromatin state. The methylation patterns are propagated to the next generation during replication by maintenance DNA methyltransferase, Dnmt1, in co-operation with Uhrf1.