Arginine Arrangement of Bacteriophage λ N‐Peptide Plays a Role as a Core Motif in GNRA Tetraloop RNA Binding

A simple α‐helical N‐model‐peptide was designed to investigate the role of the arginine‐rich motif of bacteriophage λ N‐peptide in selective binding with boxB RNA. The five‐arginine arrangement of native N‐peptide was retained; all other residues were replaced with alanine. In vitro selection of RNA (30 random‐nucleotide region) was carried out with N‐model‐peptide immobilized on a 27 MHz quartz‐crystal microbalance (QCM). Selected RNAs were evaluated on the same QCM plate to obtain binding constants (K_a=10⁷–10⁸ M ^?1). Many selected RNAs contained GNR(N)A‐type loops (similar to the boxB RNA motif recognized by the native N‐peptide). Fragments and minimal RNAs containing the GNRA‐type loop also bound to N‐model‐peptide (K_a=10⁶–10⁷ M ^?1). The RNA recognition specificity of the peptide was studied by changing the “closing” U–A base pair and one base in the tetraloop of the RNA aptamers, and by peptide mutations (18th residue of N‐model‐peptide). It was concluded that the five‐arginine arrangement of the peptide performs selective recognition of the GNRA tetraloop and GNR(N)A pentaloop RNA structures, and that substitution of another functional amino acid residue at the 18th position in N‐peptide adds the recognition ability for a loop‐RNA sequence.     

The coloring of geopolymers by the addition of copper compounds

The development of a new coloring technique is desirable to increase the commercial value of geopolymers. Selected copper compounds, i.e. Cu(OH)₂, CuO, Cu₂O, CuCO₃?Cu(OH)₂?H₂O, CuCl₂?2H₂O and CuSO₄?5H₂O, were added to the initial reactants in order to color the geopolymers in the same manner as naturally occurring minerals. When Cu(OH)₂, CuO and Cu₂O were used, these compounds remained in the geopolymer matrix following hardening of the material. On the contrary, CuCO₃?Cu(OH)₂?H₂O, CuCl₂?2H₂O and CuSO₄?5H₂O were not detected in the final products. XAFS analyses were performed to investigate the local structure of copper in the geopolymers produced. The results showed that the copper spectra of geopolymers incorporating Cu(OH)₂, CuO and Cu₂O correspond to those of pure Cu(OH)₂, CuO and Cu₂O, respectively. However, when CuCO₃?Cu(OH)₂?H₂O, CuCl₂?2H₂O and CuSO₄?5H₂O were added, the copper generated spectra similar to that of the mineral chrysocolla ((Cu, Al)₂H₂Si₂O₅(OH)₄?nH₂O) than the respective copper compounds.     

PCR-free telomerase assay using chronocoulometry coupled with hexaammineruthenium(III) chloride

An electrochemical method based on chronocoulometry coupled with hexaammineruthenium chloride (RuHex) is proposed for simple and rapid assay of telomerase without relying on PCR and gel electrophoresis. Thus, DNA extended by telomerase in extracts of as small as 5-1,000 HeLa cells on the TS primer-immobilized electrodes was quantified successfully. This method is suitable for quick screening of drug candidates which inhibit telomerase. When 10 compounds were tested, the multiplicity of extension (x in (TTAGGG)(x)) varied from 11 to 0, suggesting that there is more than one mechanism of inhibition. IC(50) values of telomerase inhibitors TMPyP4 and PIPER were determined as 5.5 and 15 μM, respectively, though their mechanisms of inhibition are different. This method is capable of discriminating two possible mechanisms of telomerase inhibition: direct binding of inhibitors to telomerase and indirect inhibition through their binding to the quadruplex generated by telomerase. As this method is easy and quick to run, it will be useful for high-throughput screening of drug candidates which inhibit telomerase.     

AgI-coated silver-clad stainless steel hollow waveguides for infrared lightwave transmission and their applications

We fabricated silver iodide (AgI)-coated silver hollow waveguides to transmit a wide range of infrared (IR) light. Silver-clad stainless steel pipes were used as a supporting pipe. Since this type of metallic hollow waveguide has high mechanical strength and heat resistance, it is suitable as a rigid lightwave probe for various applications such as dental or medical laser treatment, IR spectroscopy, thermal radiometry, and laser processing. Considering these applications, we estimated the hollow waveguides with different thicknesses of the AgI layer. By optimizing the AgI layer thickness according to the wavelength of propagating light, we succeeded in efficiently transmitting Er-YAG and CO(2) laser light. We also studied the optical characteristics of a wide range of incoherent light for IR spectroscopy and radiometry applications using these metallic hollow waveguides as lightwave probes.     

Godunov-Type Solution of Curvilinear Shallow-Water Equations

This paper presents details of a second-order accurate Godunov-type numerical model of the two-dimensional conservative hyperbolic shallow-water equations written in a nonorthogonal curvilinear matrix form and discretized using finite volumes. Roe's flux function is used for the convection terms, and a nonlinear limiter is applied to prevent spurious oscillations. Validation tests include frictionless rectangular and circular dam-breaks, an oblique hydraulic jump, jet-forced flow in a circular basin, and vortex shedding from a vertical surface-piercing cylinder. The results indicate that the model accurately simulates sharp fronts, a flow discontinuity between subcritical and supercritical conditions, recirculation in a basin, and unsteady wake flows.     

Acoustic analysis of composite soft materials. I. Characterization of the core and boundary layer from compressibility of core/shell particles dispersed in poly(vinyl chloride)

The sound velocity of butyl acrylate rubber particles modified by poly(methyl methacrylate) in poly(vinyl chloride) was measured as a function of particle concentration. A model for estimating the adiabatic compressibility of the particle and the boundary layer was proposed. From the model, the partial specific adiabatic compressibility of the particles and the rubber core were evaluated. The adiabatic compressibility of the rubber core was estimated as 3.82 × 10⁻¹⁰ Pa⁻¹. The adiabatic compressibility of the poly(methyl methacrylate) shell is discussed based on the modified model. The study indicates that the shell, including the boundary layer between butyl rubber and poly(methyl methacrylate), is perturbed by the butyl acrylate molecules and is so soft as to be comparable to the rubber. © 2001 John Wiley & Sons, Inc. J Appl Polym Sci 81: 2089–2094, 2001     

Reactions between carbon and a reduced C–O–H fluid under diamond-stable HP–HT condition

Reactions between graphitic carbon and a reduced C–O–H fluid were investigated using a mixture of stearic acid C₁₈H₃₆O₂ and oxalic acid dihydrate C₂H₆O₆, as the fluid source at high pressure and temperature (HP–HT) of 7.7 GPa and 1500°C in a platinum sealed capsule. A reduced C–O–H fluid mainly composed of methane and water, was formed by the thermal decomposition of the fluid source before reaching the HP–HT condition. An exchange reaction between carbon and methane occurred and starting carbon was re-crystallized to flaky graphite crystals, but no diamond was formed for the duration up to 24 h. In the experiment for 48 h, octahedral diamond crystals of a few to a few tens of micrometers in size were observed along with the recrystallized graphite. These results show that reduced C–O–H fluid acts as a diamond forming catalyst, although a long incubation time is necessary for diamond formation.     

Characteristic measurement of discharge current injected by the air discharge of an ESD gun onto a ground

An immunity testing method for electrostatic discharge (ESD) is being specified in IEC 61000‐4‐2, in which the contact discharge of an ESD gun is being normally specified. Air discharge testing is known to be a severe immunity test compared to contact discharge testing, while the discharge current injected is not well reproduced. Grasping the behavior of the current injected by the air discharge would be helpful in establishing the worst‐case ESD immunity testing. We previously measured the discharge currents for air discharge testing onto the IEC‐recommended current transducer with a commercially available ESD gun, and showed that there exists a specific relationship of Ip·tr^ξ/V_c=constant (ξ=0.75), between rise time tr and current peak Ip. The current transducer, however, has a frequency‐dependent transfer impedance which should affect the measured current waveform. In this study, we investigated whether the above‐mentioned specific relationship can be obtained for air discharge of an ESD gun onto a ground that assumes a metal enclosure of electronic equipment under test. A method was presented for estimating the discharge current from simultaneously measured magnetic fields with two magnetic field probes regardless of the distance between the gun discharge‐point and the probe position. This method was validated for contact discharge of an ESD gun to an SMA connector. With this method, we estimated the discharge currents injected onto a ground for air discharge testing of an ESD gun with intentionally fast and slow approaches. As a result, we could confirm a specific relationship between rise time tr and current peak Ip of Ip·tr^ξ/V_c=constant with ξ=0.57 independent of charge voltages and gun approaches. © 2007 Wiley Periodicals, Inc. Electr Eng Jpn, 158(4): 51– 59, 2007; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/eej.20454     

Free-Standing Molecularly Thin Amorphous Silica Nanosheets (Small 22/2023)

Recent progress in 2D materials has initiated new fields of molecularly thin amorphous materials with mysterious properties and structures. However, designed synthesis of molecularly thin amorphous silica still remains a challenge; whether free-standing molecularly thin amorphous silica nanosheets can exist is unclear. Here, this issue is addressed by using a new chemical protocol; solid-state surfactant lamellae with ordered alkyl-chain arrangements can serve as superior templates guiding free-standing amorphous silica nanosheets. Simple sonication of the lamellar hybrids allows exfoliation into monolayer amorphous silica nanosheets with 0.9 nm thickness. In addition, the nanosheets show the distinctive feature of high colloidal stability that enables atomic layer engineering of silica nanocoatings and dielectric nanofilms. The approach may shed new light on the properties and applications of old silica.