Adenosine-1,3-diazaphenoxazine derivative for selective base pair formation with 8-oxo-2'-deoxyguanosine in DNA

The selective detection of 8-oxo-2'-deoxyguanosine (8-oxo-dG) in DNA without chemical or enzymatic treatment is an attractive tool for genomic research. We designed and synthesized the non-natural nucleoside analogue, the adenosine-1,3-diazaphenoxazine (Adap) derivative, for selective recognition of 8-oxo-dG in DNA. This study clearly showed that Adap has a highly selective stabilizing effect on the duplex containing the Adap-8-oxo-dG base pair. Furthermore, the fluorescent property of Adap was shown to be useful for the selective detection of 8-oxo-dG in the duplex DNA. To the best of our knowledge, this is the first successful demonstration of a non-natural nucleoside with a high selectivity for 8-oxo-dG in DNA.     

Effects of heme on the thermal stability of mesophilic and thermophilic cytochromes c: comparison between experimental and theoretical results

We have recently proposed a measure of the thermal stability of a protein: the water-entropy gain at 25?°C upon folding normalized by the number of residues, which is calculated using a hybrid of the angle-dependent integral equation theory combined with the multipolar water model and the morphometric approach. A protein with a larger value of the measure is thermally more stable. Here we extend the study to analyses on the effects of heme on the thermal stability of four cytochromes c (PA c(551), PH c(552), HT c(552), and AA c(555)) whose denaturation temperatures are considerably different from one another despite that they share significantly high sequence homology and similar three-dimensional folds. The major conclusions are as follows. For all the four cytochromes c, the thermal stability is largely enhanced by the heme binding in terms of the water entropy. For the holo states, the measure is the largest for AA c(555). However, AA c(555) has the lowest packing efficiency of heme and the apo polypeptide with hololike structure, which is unfavorable for the water entropy. The highest stability of AA c(555) is ascribed primarily to the highest efficiency of side-chain packing of the apo polypeptide itself. We argue for all the four cytochromes c that due to covalent heme linkages, the number of accessible conformations of the denatured state is decreased by the steric hindrance of heme, and the conformational-entropy loss upon folding becomes smaller, leading to an enhancement of the thermal stability. As for the apo state modeled as the native structure whose heme is removed, AA c(555) has a much larger value of the measure than the other three. Overall, the theoretical results are quite consistent with the experimental observations (e.g., at 25?°C the α-helix content of the apo state of AA c(555) is almost equal to that of the holo state while almost all helices are collapsed in the apo states of PA c(551), PH c(552), and HT c(552)).     

One-step production of nanofibrillated bacterial cellulose (NFBC) from waste glycerol using Gluconacetobacter intermedius NEDO-01

A major by-product of biodiesel production is waste glycerol, which has numerous potential applications. In this study, we isolated a novel bacterium capable of producing cellulose from waste glycerol, and identified it as a novel strain (named NEDO-01) of Gluconacetobacter intermedius. Scanning electron microscopy revealed that the morphology of the pellicle produced by NEDO-01 was similar to that of cellulose produced by Gluconacetobacter hansenii ATCC23769. Furthermore, X-ray diffraction and solid-state nuclear magnetic resonance spectroscopic analyses suggested that cellulose produced by NEDO-01 had molecular and crystalline structures similar to those of cellulose produced by ATCC23769. After the optimization of cultivation conditions, NEDO-01 mediated the one-step production of nanofibrillated bacterial cellulose (NFBC) from waste glycerol in a medium supplemented with carboxymethyl cellulose. Transmission electron microscopic analysis revealed that the NFBC was composed of relatively uniform fibers with diameters of approximately 20 nm. NFBC was produced as uniform water suspensions, the yield of which was 3.4 g/L from cultivation in 7.5 L medium in a 10-L jar fermenter. The bioconversion of waste glycerol to NFBC, which has superior fluidity, moldability, and miscibility, has a wide variety of applications, including potential uses in the medical and materials engineering fields.     

Decomposition and Detection of Hydrogen Peroxide Using δ‐MnO2 Thin Film Electrode with Self‐Healing Property

A thin film of δ‐type MnO₂ grown cathodically has been investigated with respect to the ability toward anodic decomposition of H₂O₂ and durability. With polarization at less positive potentials than +0.4 V vs. Ag/AgCl, the film was dissolved exclusively as a result of reduction of Mn⁴⁺ sites in the oxide by H₂O₂ to soluble Mn²⁺. At +0.9 V, MnO₂ remained unchanged and decomposed H₂O₂ in solution. At +0.8 V, the film was once dissolved in the initial stage; however, it was self‐healed via reoxidation of the liberated Mn²⁺ ions. Amperometric flow‐injection analysis of H₂O₂ was carried out with the δ‐MnO₂ film.     

Characteristics of train noise in above-ground and underground stations with side and island platforms

Railway stations can be principally classified by their locations, i.e., above-ground or underground stations, and by their platform styles, i.e., side or island platforms. However, the effect of the architectural elements on the train noise in stations is not well understood. The aim of the present study is to determine the different acoustical characteristics of the train noise for each station style. The train noise was evaluated by (1) the A-weighted equivalent continuous sound pressure level (L_Aeq), (2) the amplitude of the maximum peak of the interaural cross-correlation function (IACC), (3) the delay time (τ₁) and amplitude (?₁) of the first maximum peak of the autocorrelation function. The IACC, τ₁ and ?₁ are related to the subjective diffuseness, pitch and pitch strength, respectively. Regarding the locations, the L_Aeq in the underground stations was 6.4 dB higher than that in the above-ground stations, and the pitch in the underground stations was higher and stronger. Regarding the platform styles, the L_Aeq on the side platforms was 3.3 dB higher than on the island platforms of the above-ground stations. For the underground stations, the L_Aeq on the island platforms was 3.3 dB higher than that on the side platforms when a train entered the station. The IACC on the island platforms of the above-ground stations was higher than that in the other stations.     

Faithful and unfaithful students in time series learning

A model neuron with delay line feedback connections can learna time series generated by another neuron. In the case thatboth neurons have identical transfer functions, a model neuron(student) is capable of reproducing the instruction sequencegenerated by another neuron (teacher), but the parameters arenot uniquely determined by learning a quasi-periodic time series.A student that has completed the learning can be either faithfulor unfaithful, depending on whether it continues mimicking theteacher's time series over a long interval after the learningor whether it departs from the teacher and eventually generatesa time series that bears no resemblance to the teacher's. Inthe case that both neurons have different transfer functions,a student is generally incapable of reproducing the instructionsequence. Each student readjusts its parameters so as to minimizethe mean-squared deviation between the instruction signal andits own output, but this parameter set is not uniquely determined.In this unrealizable learning, the degeneracy among faithfulstudents is lifted and there is no more distinction betweenfaithful and unfaithful students.     

Measurements of Optical Trapping Efficiency for Micron-Sized Dielectric Particles in Various Surrounding Media

The maximum axial trapping efficiency Q_max has been measured in water, ethanol, butanol and octanol for polystyrene latex spheres having a diameter of 2–15μm. The effects of the diameter of the particle as well as the refractive index and the viscosity of surrounding medium have been investigated. For particles of d≥7 μm, Q_max is almost independent of particle size, while it decreases as the diameters decrease to d≦5 μm. It is also noted that Q_max is affected by the viscosity rather than the refractive index of the surrounding medium.     

Morphological study on diffusion‐limited aggregates of poly(ethylene oxide) on alkali halides

When poly(ethylene oxide) was crystallized on a fresh cleavage surface of alkali halides from solution in isoamyl acetate, diffusion‐limited‐aggregate dendrites were formed. Their patterns varied, depending on the kind of substrate on which the poly(ethylene oxide) crystallized: On a KCl substrate, rather ordered dendrites grew with fibrillar crystallites aligning roughly in the 〈110〉_KCl direction, and coarse dendritic clusters formed on NaCl and KBr during the initial stage of their growth. The dendrites grew and matured to sheet the whole surface of alkali halides with a uniform thickness, and subsequently, tetragonal lamellae formed on it through the spiral growth mechanism or the primary nucleation process. Tetragonal lamellar crystals grew with their diagonals parallel to fibrillar crystallites of dendrites. Their orientation did not result from direct, epitaxial contact with the alkali halide substrate but depended on the fibrillar orientation of the underlying sheeted layer. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 2421–2430, 2002     

Novel photocurable monomers: The synthesis of difunctional vinyl ethers with a phosphonate group and difunctional 1‐propenyl ethers with a phosphonate group and their photoinitiated cationic polymerization

Phosphorus‐containing vinyl ether monomers and 1‐propenyl ether monomers were prepared by the regioselective addition reaction of glycidyl vinyl ether (GVE) or 1‐propenyl glycidyl ether with diaryl phosphonates with quaternary onium salts as catalysts. The reaction of GVE with bis(4‐chlorophenyl) phenylphosphonate gave bis[1‐(4‐chlorophenoxy methyl)‐2‐(vinyloxy)ethyl]phenylphosphonate in a 68% yield. The structures of the resulting phosphorus‐containing vinyl ether monomers and 1‐propenyl ether monomers were confirmed by IR and ¹H NMR spectra and elemental analysis. Photoinitiated cationic polymerizations of the resulting phosphorus‐containing vinyl ether monomers and 1‐propenyl ether monomers were investigated with photoacid generators. The polymerization of vinyl ether groups and 1‐propenyl ether groups of the obtained monomers proceeded very smoothly with a sulfonium‐type cationic photoinitiator, bis[4‐(diphenylsulfonio)phenyl]sulfide‐bis(hexafluorophosphate), upon UV irradiation. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 3105–3115, 2005