Application of the Yin-Yang grid to a thermal convection of a Boussinesq fluid with infinite Prandtl number in a three-dimensional spherical shell

A new numerical finite difference code has been developed to solve a thermal convection of a Boussinesq fluid with infinite Prandtl number in a three-dimensional spherical shell. A kind of the overset (Chimera) grid named ``Yin-Yang grid'' is used for the spatial discretization. The grid naturally avoids the pole problems which are inevitable in the latitude-longitude grids. The code is applied to numerical simulations of mantle convection with uniform and variable viscosity. The validity of the Yin-Yang grid for the mantle convection simulation is confirmed

Mechanism of robust circadian oscillation of KaiC phosphorylation in vitro

By incubating the mixture of three cyanobacterial proteins, KaiA, KaiB, and KaiC, with ATP in vitro, Kondo and his colleagues reconstituted the robust circadian rhythm of the phosphorylation level of KaiC (Science, 308; 414-415 (2005)). This finding indicates that protein-protein interactions and the associated hydrolysis of ATP suffice to generate the circadian rhythm. Several theoretical models have been proposed to explain the rhythm generated in this "protein-only" system, but the clear criterion to discern different possible mechanisms was not known. In this paper, we discuss a model based on the two basic assumptions: The assumption of the allosteric transition of a KaiC hexamer and the assumption of the monomer exchange between KaiC hexamers. The model shows a stable rhythmic oscillation of the phosphorylation level of KaiC, which is robust against changes in concentration of Kai proteins. We show that this robustness gives a clue to distinguish different possible mechanisms. We also discuss the robustness of oscillation against the change in the system size. Behaviors of the system with the cellular or subcellular size should shed light on the role of the protein-protein interactions in in vivo circadian oscillation

Sustainable fruit-body formation of edible mycorrhizal Tricholoma species for 3 years in open pot culture with pine seedling hosts

The original publication is available at www.springerlink.comArticleMycoscience. 48(2): 104-108 (2007)journal articl

Overexpression of optineurin E50K disrupts Rab8 interaction and leads to a progressive retinal degeneration in mice

Glaucoma is one of the leading causes of bilateral blindness affecting nearly 8 million people worldwide. Glaucoma is characterized by a progressive loss of retinal ganglion cells (RGCs) and is often associated with elevated intraocular pressure (IOP). However, patients with normal tension glaucoma (NTG), a subtype of primary open-angle glaucoma (POAG), develop the disease without IOP elevation. The molecular pathways leading to the pathology of NTG and POAG are still unclear. Here, we describe the phenotypic characteristics of transgenic mice overexpressing wild-type (Wt) or mutated optineurin (Optn). Mutations E50K, H486R and Optn with a deletion of the first (amino acids 153–174) or second (amino acids 426–461) leucine zipper were used for overexpression. After 16 months, histological abnormalities were exclusively observed in the retina of E50K mutant mice with loss of RGCs and connecting synapses in the peripheral retina leading to a thinning of the nerve fiber layer at the optic nerve head at normal IOP. E50K mice also showed massive apoptosis and degeneration of entire retina, leading to approximately a 28% reduction of the retina thickness. At the molecular level, introduction of the E50K mutation disrupts the interaction between Optn and Rab8 GTPase, a protein involved in the regulation of vesicle transport from Golgi to plasma membrane. Wt Optn and an active GTP-bound form of Rab8 complex were localized at the Golgi complex. These data suggest that alternation of the Optn sequence can initiate significant retinal degeneration in mice

Visualizing the Interconnections Among Climate Risks

It is now widely recognized that climate change affects multiple sectors in virtually every part of the world. Impacts on one sector may influence other sectors, including seemingly remote ones, which we call “interconnections of climate risks.” While a substantial number of climate risks are identified in the Intergovernmental Panel on Climate Change Fifth Assessment Report, there have been few attempts to explore the interconnections between them in a comprehensive way. To fill this gap, we developed a methodology for visualizing climate risks and their interconnections based on a literature survey. Our visualizations highlight the need to address climate risk interconnections in impact and vulnerability studies. Our risk maps and flowcharts show how changes in climate impact natural and socioeconomic systems, ultimately affecting human security, health, and well‐being. We tested our visualization approach with potential users and identified likely benefits and issues. Our methodology can be used as a communication tool to inform decision makers, stakeholders, and the general public of the cascading risks that can be triggered by climate change

Investigation of photoluminescence of Si−O−C(−H) ceramics at an early stage of decarbonization by using high energy excitation

Si−O−C(−H) ceramics with reduced carbon contents were prepared by pyrolyzing polysiloxane particles in hydrogen at temperatures of 750, 800 and 850 °C. Under HeCd laser irradiation (325 nm), the obtained ceramics show broad spectra peaking at 400–415 nm. On the other hand, the excitation on the higher energy region by an ArF excimer laser (193 nm) induces new PL bands located at short wavelength region of 300 and 355 nm. Such high energy PL bands appear prominently in the ceramics synthesized at 750 °C, and are minor in ceramics synthesized at 800 and 850 °C