Interlaboratory study of DNA extraction from multiple ground samples, multiplex real-time PCR, and multiplex qualitative PCR for individual kernel detection system of genetically modified maize

In many countries, the labeling of grains, feed, and foodstuff is mandatory if the genetically modified (GM) organism content exceeds a certain level of approved GM varieties. We previously developed an individual kernel detection system consisting of grinding individual kernels, DNA extraction from the individually ground kernels, GM detection using multiplex real-time PCR, and GM event detection using multiplex qualitative PCR to analyze the precise commingling level and varieties of GM maize in real sample grains. We performed the interlaboratory study of the DNA extraction with multiple ground samples, multiplex real-time PCR detection, and multiplex qualitative PCR detection to evaluate its applicability, practicality, and ruggedness for the individual kernel detection system of GM maize. DNA extraction with multiple ground samples, multiplex real-time PCR, and multiplex qualitative PCR were evaluated by five laboratories in Japan, and all results from these laboratories were consistent with the expected results in terms of the commingling level and event analysis. Thus, the DNA extraction with multiple ground samples, multiplex real-time PCR, and multiplex qualitative PCR for the individual kernel detection system is applicable and practicable in a laboratory to regulate the commingling level of GM maize grain for GM samples, including stacked GM maize.     

Specific interaction between polyethylenimine and azo dyes carrying hydroxyl groups

The binding of acid azo dyes having phenolic hydroxyl groups such as orange I ( I ), orange II ( II ), chrome violet ( III ), 4-hydroxyazobenzene-4′-sulfonate ( IV ), and 2,4-dihydroxyazobenzene-4′-sulfonate ( V ) by polyethylenimine was studied by equilibrium dialysis and spectroscopic methods. The results obtained indicate that dyes ( III ) and ( V ) with two OH groups are bound much more strongly than dyes ( I ), ( II ), and ( IV ) with one OH group. Also polyethylenimine is far superior to any other polymers which have been examined, including bovine serum albumin, polyvinylpyrrolidone, and poly-L -lysine, in its ability to form complexes with these dyes ( III ) and ( V ). The OH groups involved participate preferentially in complex formation with polyethylenimine. The unusual affinity of polyethylenimine for the dyes carrying OH groups is discussed.     

A numerical study of 3D natural convection in a cube: effects of the horizontal thermal boundary conditions

A high-resolution, three-dimensional finite-difference numerical study of natural convection flows of a viscous fluid in a differentially heated cubical box is reported. The vertical sidewalls of the enclosure are maintained at constant temperatures of different values. The other vertical walls (the end walls) are thermally insulated. For the horizontal walls, two kinds of thermal boundary conditions are specified: adiabatic and perfectly conducting. Computations have been performed for an air-filled cavity for Rayleigh numbers of 10⁵ and 10⁶. The specific effects of the horizontal thermal boundary conditions on the flow structure are examined in detail. In the case of conducting walls, heat transfer through the horizontal walls enhances the convective flow activities. The numerically predicted velocity and temperature profiles in the symmetry planes are consistent with previous experimental measurements and computations.     

Electronic structures of the highest occupied molecular orbital bands of a pentacene ultrathin film

We report the energy dispersions of the highest occupied molecular orbitals (HOMO)-derived bands of a pentacene (Pn) thin film, whose in-plane structure resembles closely that of the ab plane of a low-density bulk Pn phase. Our present photoemission result indicates that the overlap of the pi-orbitals of adjacent Pn molecules is larger than what was expected from theoretical calculations. Further, of the two HOMO-derived bands, the large dispersion width of the band with higher binding energy suggests that this one mainly contributes to the bandlike charge transport in a Pn crystal.     

Polyaniline‐Induced CH Arylation of Arenes with Arenediazonium Salts

A reduced form of polyaniline has been shown to induce direct arylation of an arenediazonium salt with an arene (Gomberg–Bachmann reaction) to give the cross‐coupling product in moderate to good yields under mild conditions. Various arenediazonium salts and arenes, including heteroarenes such as furans, thiophenes, and pyrroles, are employed for the reaction. The most favorable combination of substrates is an electron‐poor arenediazonium salt with an electron‐rich heteroarene. Investigation of the mechanism by reactions with radical scavengers and experiments on kinetic isotope effects indicated the occurrence of a radical chain reaction initiated by one‐electron reduction of an arenediazonium salt by the polyaniline. Only 1 mol % (based on aniline tetramer) of the polyaniline is required for the cross‐coupling reaction to occur. This reaction proceeds under metal‐free conditions and with no need for photonic activation.     

Several contributions to soil compactibility induced by cyclic loading test

To investigate the soil compactibility during the cyclic loading, three different kinds of paddy field soils were prepared so as to clarify interrelationships among stress amplitude ratio, bulk density, soil water content and pore water pressure. The presetting values of specimen include the soil water content(percent dry basis) and bulk density of 25% d.b. and 1.1 Mg/m³ respectively. The relation between the number of cyclic loading and axial strain exhibited an asymptotically increasing trend, converging toward a specific value for each experimental condition. Possible effect caused by elastic–plastic characteristics could be recognized, when axial strain for 0.5 Hz excitation becomes greater than the one of 1.0 Hz under same stress amplitude ratio. When the stress amplitude ratio took 0.1, the absolute value of axial strain of 0.5 Hz was greater than the one of 1.0 Hz, whereas its decreasing trend was recognized in the sequence of silt, clay and silty sand. The qualitative relations between pore water pressure and number of cyclic loading were also examined to scrutinize the effect of effective water pressure to the soil compactibility.     

A free-energy perturbation method based on Monte Carlo simulations using quantum mechanical calculations (QM/MC/FEP method): application to highly solvent-dependent reactions

This study describes the framework of the quantum mechanical (QM)/Monte Carlo (MC)/free‐energy perturbation (FEP) method, a FEP method based on MC simulations using quantum chemical calculations. Because a series of structures generated by interpolating internal coordinates between transition state and reactant did not produce smooth free‐energy profiles, we used structures from the intrinsic reaction coordinate calculations. This method was first applied to the Diels–Alder reaction between methyl vinyl ketone and cyclopentadiene and produced ΔG values of 20.1 and 21.4 kcal mol^?1 in aqueous and methanol solutions, respectively. They are very consistent with the experimentally observed values. The other two applications were the free‐energy surfaces for the Cope elimination of N,N‐dimethyl‐3‐phenylbutan‐2‐amine oxide in aqueous, dimethyl sulfoxide, and tetrahydrofuran solutions, and the Kemp decarboxylation of 6‐hydroxybenzo‐isoxazole‐3‐carboxylic acid in aqueous, dimethyl sulfoxide, and CH₃CN solutions. The calculated activation free energies differed by less than 1.8 kcal mol^?1 from the experimental values for these reactions. Although we used droplet models for the QM/MC/FEP simulations, the calculated results for three reactions are very close to the experimental data. It was confirmed that most of the interactions between the solute and solvents can be described using small numbers of solvent molecules. This is because a few solvent molecules can produce large portions of the solute–solvent interaction energies at the reaction centers. When we confirmed the dependency on the droplet sizes of solvents, the QM/MC/FEP for a large droplet with 106 water molecules produced a ΔG value similar to the experimental values, as well as that for a small droplet with 34 molecules. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Regulation of cellular responses to macroporous inorganic films prepared by the inverse-opal method

Regenerative medicine for repairing damaged body tissues has recently become critically important. Cell culture scaffolds are required for the control of cell attachment, proliferation, and differentiation in in vitro cell cultures. A new strategy to control cell adhesion, morphology, and proliferation was developed by culturing mouse osteoblast-like MC3T3-E1 cells on novel cell culture scaffolds fabricated using ordered nanometer-sized pores (100, 300, 500, and 1000 nm). Results of this study indicate that after 72 h of incubation, the number of cells cultured on a silica film with a pore size of 1000 nm was similar to or slightly lower than that cultured on a non-porous control silica film. Films with 100-500 nm pore sizes, however, resulted in the cell growth inhibition. Morphology of the cultured cells revealed increased elongation and the formation of actin stress fibers was virtually absent on macroporous silica films with 100-500 nm pore size. Vinculin molecules expressed in cells cultured on the non-porous silica films showed many clear focal adhesions, whereas focal contacts were insufficiently formed in cells cultured on macroporous films. The influence of hydroxyapatite (HAp) and alumina scaffolds on the behavior of MC3T3-E1 cells was also evaluated. The proliferation rate of MC3T3-E1 cells cultured on HAp films with 1000 nm pore size was increased to approximately 20% above than that obtained of cells cultured on non-porous HAp films. These results demonstrate that the pore size and constituents of films play a role in controlling the morphology and proliferation rate of MC3T3-E1 cells.     

Theoretical study on singlet oxygen adsorption onto surface of graphene-like aromatic hydrocarbon molecules

Recently, graphene sheet is one of interesting systems to realize novel electronic properties. Especially, interaction between graphene and adsorbed oxygen molecule is very important to control electronic condition. In this paper, we employed some aromatic hydrocarbons as simple systems of graphene sheet and ab initio MO calculations were carried out to investigate inter-molecular interaction. It is found that not triplet but singlet O₂ molecule have potential of chemisorption onto graphene surface. From the calculated potential energy surface (PES) for distance between benzene and O₂ molecules, meta-stable structure is found at about 1.5 Å with potential barrier. In the optimized structure of its meta-stable state, structural strain can be relaxed through bending of planer benzene ring. Its energy is estimated at 70.10 kcal/mol for benzene. We also estimated the strain effects for naphthalene and pyrene molecules as larger case of graphene and they were 80.85 and 72.45 kcal/mol, respectively.