Mapping of Protein-Protein Interaction Sites in the Plant-Type [2Fe-2S] Ferredoxin

Knowing the manner of protein-protein interactions is vital for understanding biological events. The plant-type [2Fe-2S] ferredoxin (Fd), a well-known small iron-sulfur protein with low redox potential, partitions electrons to a variety of Fd-dependent enzymes via specific protein-protein interactions. Here we have refined the crystal structure of a recombinant plant-type Fd I from the blue green alga Aphanothece sacrum (AsFd-I) at 1.46 Å resolution on the basis of the synchrotron radiation data. Incorporating the revised amino-acid sequence, our analysis corrects the 3D structure previously reported; we identified the short α-helix (67-71) near the active center, which is conserved in other plant-type [2Fe-2S] Fds. Although the 3D structures of the four molecules in the asymmetric unit are similar to each other, detailed comparison of the four structures revealed the segments whose conformations are variable. Structural comparison between the Fds from different sources showed that the distribution of the variable segments in AsFd-I is highly conserved in other Fds, suggesting the presence of intrinsically flexible regions in the plant-type [2Fe-2S] Fd. A few structures of the complexes with Fd-dependent enzymes clearly demonstrate that the protein-protein interactions are achieved through these variable regions in Fd. The results described here will provide a guide for interpreting the biochemical and mutational studies that aim at the manner of interactions with Fd-dependent enzymes

Sunlight Photocatalyzed Regioselective β‐Alkylation and Acylation of Cyclopentanones.

Visible light induced direct β-C–H/C–C conversion of cyclopentanones was accomplished by using tetrabutylammonium decatungstate, TBADT, as the photocatalyst

Radium isotopes in Na-Cl type groundwater from the Japan Sea side of Japan, Central Japan

[研究報告

Electron Microscopy Observation of Biomineralization within Wood Tissues of Kurogaki

Interactions between minerals and microorganisms play a crucial role in living wood tissues. However, living wood tissues have never been studied in the field. Fortunately, we found several kurogaki (black persimmon; Diospyros kaki) trees at Tawara in Kanazawa, Ishikawa, Japan. Here, we report the characterization of kurogaki based on scanning electron microscopy equipped with energy-dispersive spectroscopy (SEM-EDS) and transmission electron microscopy (TEM), associated with inductively coupled plasma-mass spectrometry (ICP-MS) analyses, X-ray fluorescence analyses (XRF) and X-ray powder diffraction (XRD) analyses. This study aims to illustrate the ability of various microorganisms associated with biominerals within wood tissues of kurogaki, as shown by SEM-EDS elemental content maps and TEM images. Kurogaki grows very slowly and has extremely hard wood, known for its striking black and beige coloration, referred to as a “peacock pattern”. However, the scientific data for kurogaki are very limited. The black “peacock pattern” of the wood mainly comprises cellulose and high levels of crystal cristobalite. As per the XRD results, the black taproot contains mineralized 7 Å clays (kaolinite), cellulose, apatite and cristobalite associated with many microorganisms. The chemical compositions of the black and beige portions of the black persimmon tree were obtained by ICP-MS analyses. Particular elements such as abundant Ca, Mg, K, P, Mn, Ba, S, Cl, Fe, Na, and Al were concentrated in the black region, associated with Pb and Sr elements. SEM-EDS semi-qualitative analyses of kurogaki indicated an abundance of P and Ca in microorganisms in the black region, associated with Pb, Sr, S, Mn, and Mg elements. On the other hand, XRF and XRD mineralogical data showed that fresh andesite, weathered andesite, and the soils around the roots of kurogaki correlate with biomineralization of the black region in kurogaki roots, showing clay minerals (kaolinite) and cristobalite formation. In conclusion, we describe how the biominerals in the black region in the cellulose within wood tissues grow chemically and biologically in the sap under the conditions associated with the beige portions of the taproot. This can explain why the crystals produce the “peacock pattern” in the kurogaki formed during the year. We conclude that kurogaki microbiota are from bacteria in the andesitic weathered soil environment, which produce silicification. In other words, the patterned portions of kurogaki consist of silicified wood

Preparatory acoustic emission activity of hydraulic fracture in granite with various viscous fluids revealed by deep learning technique

To investigate the influence of fluid viscosity on the fracturing process, we conducted hydraulic fracturing experiments on Kurokami-jima granite specimens with resins of various viscosities. We monitored the acoustic emission (AE) activity during fracturing and estimated the moment tensor (MT) solutions for 54 727 AE events using a deep learning technique. We observed the breakdown at 14–22 MPa of borehole pressure, which was dependent on the viscosity, as well as two preparatory phases accompanying the expansion of AE-active regions. The first expansion phase typically began at 10–30 per cent of the breakdown pressure, where AEs occurred three-dimensionally surrounding the wellbore and their active region expanded with time towards the external boundaries of the specimen. The MT solutions of these AEs corresponded to crack-opening (tensile) events in various orientations. The second expansion phase began at 90–99 per cent of the breakdown pressure. During this phase, a new planar AE distribution emerged from the borehole and expanded along the maximum compression axis, and the focal mechanisms of these AEs corresponded to the tensile events on the AE-delineating plane. We interpreted that the first phase was induced by fluid penetration into pre-existing microcracks, such as grain boundaries, and the second phase corresponded to the main fracture formation. Significant dependences on fluid viscosity were observed in the borehole pressure at the time of main fracture initiation and in the speed of the fracture propagation in the second phase. The AE activity observed in the present study was fairly complex compared to that observed in previous experiments conducted on tight shale samples. This difference indicates the importance of the interaction between the fracturing fluid and pre-existing microcracks in the fracturing process

Study on Operating Principle of Cockcroft-Walton Circuit to Produce Plasmas Using High-Voltage Discharge

The basis of the operating principle of Cockcroft-Walton (CW) circuit, which produces a high-voltage, is studied using a simulator of an electrical circuit. The CW circuit experimentally contributed to the breakthrough of nuclear physics for the development of a particle accelerator. High-voltage discharges play an important role not only in producing plasmas but are also applicable in a wide variety of fields. However, studies on the operating principle of CW circuits are not sufficient, though improvement and application of it have been studied. Through our studies, we have found that a part of electrical charge stored in the capacitors remains, the output value of the voltage can be expressed in recurrence formula, and more time is needed for boosting circuits that have higher number of steps. Furthermore, we studied combinations between frequencies of alternating current and capacitance in a capacitor in order to boost effectively

Crystal Structures of the Quinone Oxidoreductase from Thermus thermophilus HB8 and Its Complex with NADPH: Implication for NADPH and Substrate Recognition

The crystal structures of the ζ-crystalline-like soluble quinone oxidoreductase from Thermus thermophilus HB8 (QOR(Tt)) and of its complex with NADPH have been determined at 2.3- and 2.8-Å resolutions, respectively. QOR(Tt) is composed of two domains, and its overall fold is similar to the folds of Escherichia coli quinone oxidoreductase (QOR(Ec)) and horse liver alcohol dehydrogenase. QOR(Tt) forms a homodimer in the crystal by interaction of the βF-strands in domain II, forming a large β-sheet that crosses the dimer interface. High thermostability of QOR(Tt) was evidenced by circular dichroic measurement. NADPH is located between the two domains in the QOR(Tt)-NADPH complex. The disordered segment involved in the coenzyme binding of apo-QOR(Tt) becomes ordered upon NADPH binding. The segment covers an NADPH-binding cleft and may serve as a lid. The 2′-phosphate group of the adenine of NADPH is surrounded by polar and positively charged residues in QOR(Tt), suggesting that QOR(Tt) binds NADPH more readily than NADH. The putative substrate-binding site of QOR(Tt), unlike that of QOR(Ec), is largely blocked by nearby residues, permitting access only to small substrates. This may explain why QOR(Tt) has weak p-benzoquinone reduction activity and is inactive with such large substrates of QOR(Ec) as 5-hydroxy-1,4-naphthoquinone and phenanthraquinone