Arabidopsis β1,2-xylosyltransferase: substrate specificity and participation in the plant-specific N-glycosylation pathway

β1,2-Xylosyltransferase (XYLT) is a plant-specific glycosyltransferase that contributes to the biosynthesis of N-glycoproteins in plants. However, the specificity of XYLT for N-glycans has not yet been completely clarified. To gain insights into the function of XYLT in the plant N-glycosylation pathway, we examined the acceptor substrate specificity of recombinant Arabidopsis XYLT (AtXYLT) using 2-aminopyridine-labeled N-glycans as the substrates and confirmed the N-glycans of Arabidopsis xylt mutant. Recombinant AtXYLT expressed in insect cells required the β1,2-linked N-acetylglucosamine (GlcNAc) residue at the nonreducing terminus of the α1,3-branched mannose (Man) residue (GlcNAcβ1,2-Manα1,3-Man; GNM3B) for activity. However, AtXYLT showed decreased activity with substrates that contained α1,3-fucose at the chitobiose core-GlcNAc or a terminal GlcNAc at the α1,6-branched Man residue of GlcNAcβ1,2-Man (GlcNAcβ1,2-Manα1,6-Man; GNM3A), whose ratios were 10% and 50% of the optimal substrate, GNM3B, respectively. Moreover, AtXYLT did not show any activity in the transfer of the Xyl residue to N-glycans that contained a mammalian-type β1,4-linked galactose (Gal) residue at the nonreducing terminus of GlcNAcβ1,2-Man. These results indicate that a β1,2-linked GlcNAc residue at the nonreducing terminus of an α1,3-branched Man residue is necessary for AtXYLT activity and that mammalian-type β1,4-linked Gal residue(s) on the same branch completely inhibit(s) the activity. Furthermore, N-glycan analysis showed that approximately 30% of the N-glycans carry the Xyl residue in the wild type. These findings suggest that AtXYLT acts on protein-bound N-glycans prior to α1,3-fucosyltransferase and mannosidase II in planta.     

Laboratory-performance study of quantitative PCR methods to analyze an approved genetically modified maize (Mon810 Line)

A laboratory-performance study was carried out to investigate factors affecting the reliability of the quantitative PCR method to analyze an approved genetically modified (GM) maize (Mon810 line). Test maize powdered samples were prepared as blind samples containing a high (assigned value; 5.45%) or low (assigned value; 0.35%) concentration of the Mon810 line. After confirmation of their homogeneity, they were provided to 27 laboratories participating in the collaborative study. The data were collected from all laboratories and statistically analyzed. Two laboratories, which used a Roche LightCycler (LC), reported significantly high test values. A further examination showed that the LC method is greatly affected by the equipment itself or PCR reagents, resulting in poor repeatability. On the other hand, some laboratories, which used ABI quantitative PCR equipment, reported erroneous test values. In these laboratories, the errors appeared to have been due to inadequate quality and/or yield of DNA. To identify factors affecting the test values, analysis of the measured values for the taxon-specific gene will be useful. Furthermore, the modified silica-gel membrane DNA extraction method made it possible to extract the required amounts of DNA more easily and in a shorter time than before.     

A simple assay for lipid hydroperoxides based on triphenylphosphine oxidation and high-performance liquid chromatography

A simple and sensitive method was developed to measure total hydroperoxides. After the reduction of hydroperoxides with triphenylphosphine (TP) in cyclohexane at 30°C, the amount of triphenylphosphine oxide (TPO) produced is determined by reverse-phase or normal-phase high-performance liquid chromatography (HPLC) in combination with an ultraviolet (UV)-detector by measuring absorption at 220 or 260 nm. TPO was shown to be gener-ated stoichiometrically by reduction of known amounts of either cumene hydroperoxide or methyl 13-hydroper-oxyoctadecadienoate. For various lipids at low levels of oxidation, the peroxide values determined by this method were in good agreement with those obtained by conventional iodometry. The detection limit of TPO in HPLC using absorption at 220 nm was less than 10 pmol. Consequently, total hydroperoxides in lipids at levels corresponding to less than a peroxide value of 1 can be estimated by the TP method on a 10-mg sample.     

Tribological properties of polymer-sheet-adhered metal hybrid gear

A preliminary study was made on the tribology of nylon 66/poly(phenylene ether) polymer sheets adhered to steel gear teeth against a counter steel gear with reference to friction, surface morphology, noise reduction and torque in comparison with a pair of steel gears lubricated with molybdenum grease. Tribological experiments were performed in a gear-testing machine at a rotating speed of 1000 rpm under high torques of the driving and driven gears, recording torque of each gear and noise-frequency profiles. It was found that periodical torque changes in a range of 17–5 N m at 1000 and 3000 cycles (revolutions) turned to 13–8 N m at 5000 cycles, indicating a change to stable cycle and torque conduction, probably due to a plastic surface deformation of the adhered polymer sheet for a smooth contact of pairing teeth. A harsh noise emission in the frequency range of 3–5 kHz was reduced circa 5 dBA as compared with a pair of steel/steel gear. It was found, however, that noise abruptly increased when only one of the adhered polymer sheets was spontaneously removed from the gear surface, probably because of its low adhesive strength against a shear during gear cycle.     

Top-down prepared silicon nanocrystals and a conjugated polymer-based bulk heterojunction: Optoelectronic and photovoltaic applications

Blends consisting of doped silicon nanocrystals (Si-ncs) and two conjugated polymers (poly(3-hexylthiophene) (P3HT) and poly(methoxy ethylexyloxy phenylenevinilene) (MEH PPV)) with improved photostability were fabricated. We show that a top-down approach by electrochemical etching is suitable for preparing doped (boron and phosphorus) freestanding and surfactant-free Si-ncs. The doping of Si-ncs was confirmed by low temperature photoluminescence and electron spin resonance analysis. It is demonstrated that such Si-ncs can be successfully used for the fabrication of room temperature photoluminescent and photosensitive blends. We argue that the luminescence and transport properties of the blends are controlled by the Si-ncs properties and could be assigned to quantum confinement of excitons in nanocrystalites with an energy band gap of ～2 eV. Furthermore, the blending of doped Si-ncs in both conjugated polymers led to the establishment of a bulk heterojunction between the Si-ncs and polymer. The difference in electron affinity and ionization potential between nanocrystals and polymer dissociated the excitons. Those blends showed increased carrier transport and photoconductivity under ambient conditions. It was found that introduction of less defective p-type doped Si-ncs significantly improved overall photostability of the blend. The Si-ncs non-toxicity and easy integration into well-established silicon technologies might bring considerable benefit for hybrid optoelectronic and photovoltaic device development.     

Evolution of cooperative behavior among heterogeneous agents with different strategy representations in an iterated prisoner’s dilemma game

The iterated prisoner’s dilemma (IPD) game has frequently been used to examine the evolution of cooperative behavior among agents. When the effect of representation schemes of IPD game strategies was examined, the same representation scheme was usually assigned to all agents. That is, in the literature, a population of homogeneous agents was usually used in computational experiments. In this article, we focus on a slightly different situation where every agent does not necessarily use the same representation scheme. That is, a population can be a mixture of heterogeneous agents with different representation schemes. In computational experiments, we used binary strings of different lengths (i.e., three-bit and five-bit strings) to represent IPD game strategies. We examined the evolution of cooperative behavior among heterogeneous agents in comparison with the case of homogeneous ones for the standard IPD game with typical payoff values of 0, 1, 3, and 5. Experimental results showed that the evolution of cooperative behavior was slowed down by the use of heterogeneous agents. It was also demonstrated that a faster evolution of cooperative behavior is achieved among majority agents than among minority ones in a heterogeneous population.     

The fabrication method of unsubstituted planar phthalocyanine thin films by a spin-coating technique

We have successfully obtained spin-coated films of unsubstituted planar phthalocyanines (free-base and copper phthalocyanine) from trifluoroacetic acid and chlorobenzene mixed solutions for the first time. The pre-annealed films did not consist of pure phthalocyanines; these films contained the solvent molecules. However, the residual solvent molecules could be removed by annealing at 425 K for 2 h in vacuum. This technique is useful for fabricating unsubstituted planar phthalocyanine thin films.     

Production of microfibrillated cellulose (MFC)-reinforced polylactic acid (PLA) nanocomposites from sheets obtained by a papermaking-like process

The fabrication of cellulose nanofiber-reinforced composites has been so far problematic due to difficulties in obtaining good dispersion of hydrophilic cellulose fibers in a hydrophobic polymer matrix. A new manufacturing process similar to papermaking, which enables the production of thin sheets made of uniformly dispersed microfibrillated cellulose (MFC) with polylactic acid (PLA) fibers was devised, and the composites were obtained by compression molding of the stacked sheets. The process is suitable for adoption at an industrial scale owing to the high yields and fast dewatering times. The measurement of tensile properties revealed that the modulus, strength, and strain at fracture increased linearly with the MFC content. The improvement in toughness was considered one of the key benefits brought by MFC reinforcement.     

Hidden Markov model-based prediction of antigenic peptides that interact with MHC class II molecules

Elucidating the interaction between major histocompatibility complex (MHC) molecules and antigenic peptides is fundamental to better understanding of the processes involved in immune responses and for the development of innovative immunotherapies. In the present study, hidden Markov models (HMM) were combined with the successive state splitting (SSS) algorithm for optimization of the HMM structure, to predict peptide binders to the human MHC class II molecule HLA-DRB1*0101. The predictive performance of our model (S-HMM) was compared with fully connected HMM and artificial neural network (ANN) methods using the relative operating characteristic (ROC) analysis. The S-HMM predictions had values of ROC > or = 0.85 which was at least as good, or better than the comparison methods. In addition, S-HMM is trained on positive data only and does not require exhaustive data preprocessing, such as peptide alignment. Our results demonstrated that S-HMM combines the high accuracy of predictions with the simplicity of implementation and is therefore useful for analyzing MHC class II binding peptides. In particular the S-HMM may be trained using only positive data and, the preprocessing of training data, such as peptide alignment and the selection of binding cores, is not required in this method.