Occurrence,horizontal transfer and degeneration of VDE intein family in Saccharomycete yeasts

VDE is a homing endonuclease gene originally discovered as an intervening element in VMA1s of Saccharomyces cerevisiae. There have been two independent subfamilies of VDE, one from S. cerevisiae strain X2180-1A and the other from Saccharomyces sp. DH1-1A in the host VMA1 gene, and they share the identity of 96.3%. In order to search the occurrence, intra/interspecies transfer and molecular degeneration of VDE, complete sequences of VMA1 in 10 strains of S. cerevisiae, eight species of saccharomycete yeasts, Candida glabrata and Kluyveromyces lactis were determined. We found that six of 10 S. cerevisiae strains contain VDEs 99.7-100% identical to that of the strain X2180-1A, one has no VDE, whereas the other three harbour VDEs 100% identical to that of the strain DH1-1A. S. carlsbergensis has two VMA1s, one being 99.8% identical to that of the strain X2180-1A with VDE 100% identical to that of the strain DH1-1A and the other containing the same VMA1 in S. pastorianus with no VDE. This and other evidence indicates that intra/interspecies transmissions of VDEs have occurred among saccharomycete yeasts. Phylogenetic analyses of VMA1 and VDE suggest that the S. cerevisiae VDEs had branched earlier than other VDEs from an ancestral VDE and had invaded into the host loci as relatively late events. The two VDEs seemed to degenerate in individual host loci, retaining their splicing capacity intact. The degeneration of the endonuclease domains was distinct and, if compared, its apparent rate was much faster than that of the protein-splicing domains.     

An aqueous suspension system for phospholipase D-mediated synthesis of PS without toxic organic solvent

Enzymatic synthesis of PS by phospholipase D (PLD)-mediated transphosphatidylation in an aqueous media was investigated. The purpose of this study was to establish a novel synthetic method where no toxic organic solvents were used. An attempt to react soybean lecithin (simply dispersed in an aqueous buffer) with an aqueous solution of l-serine and PLD was unsuccessful, giving only 20% of PS. By contrast, a suspension of lecithin adsorbed on fine powders such as silica was effectively converted into PS in an aqueous solution of l-serine and PLD. After screening various powders for use as the lecithin adsorbent, calcium sulfate was found to be the best with respect to lecithin conversion. In addition, calcium sulfate did not require prior adsorption of lecithin (i.e., the reaction proceeded effectively simply by adding the powder to an aqueous mixture of lecithin, l-serine, and PLD). With this “aqueous suspension system” of calcium sulfate, up to 180 mg/mL lecithin was completely converted, resulting in more than 80% PS in 24 h. The synthesized PS could easily be recovered from the powder by extracting with a mixture of n-hexane, ethanol, and diluted HCl.     

Modification of cleanup methods for dioxin analysis in green leafy vegetables and comparison of packing methods for a multi-layer silica gel column

To determine polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs) and coplanar polychlorinated biphenyls (Co-PCBs) in green leafy vegetables, the cleanup method was modified, and packing methods for a multi-layer silica gel column were compared in food samples. First, the additional cleanup was examined for a mono-ortho PCBs fraction obtained by alumina column chromatography from spinach extract. Small solids such as rough crystals that remained after concentration of the mono-ortho PCBs fraction were identified as long-chain hydrocarbons from leaf epicuticular wax by GC/MS. Cleanup using an activated carbon silica gel column with n-hexane as the washing solvent was effective. Next, multi-layer silica gel columns packed by wet packing and dry packing were compared using komatsuna, salmon and butter as samples. The columns prepared by both methods gave similar values at each isomeric concentration level and showed similar efficiency with favorable recoveries.     

Synthesis of Hadamard transformers by use of multimode interference optical waveguides

We propose a synthesis method of optical Hadamard transformer using multimode interference (MMI) couplers. By using the signal transfer matrix of 2 x 2, 4 x 4, and 8 x 8 MMI couplers, we show that sum and difference units of input signals can be synthesized. An interchange unit of two signals can also be synthesized. One synthesis method of Hadamard transformers is a combination of only 2 x 2 units, and the other is a combination of N x N(N > or = 4) units as well as 2 x 2 units. The design examples of operation units are shown, and the size and the output power of Hadamard transformers are estimated.     

Force estimation via physical properties of air cushion for the control of a human-cooperative robot: basic experiments

For the control of a human-cooperative robot (HCR) using a soft material, we aim to verify, in this study, the usefulness of force estimation via physical properties of an air cushion. First, the physical model of the air cushion was represented by an air cylinder with a piston, which is subject to constraint by nonlinear elasticity. Second, the elastic properties of the air cushion were examined under the assumption that it can be formulated by a function of pneumatic pressure. The force applied to the air cushion was next estimated on the basis of the physical model, and the HCR was successfully controlled according to the estimated force.     

Photorefractive device using self-assembled monolayer coated indium-tin-oxide electrodes

Photorefractive (PR) performances of methyl-substituted poly(triarylamine) (PTAA)-based PR device were demonstrated using chemically modified electrodes (CMEs) of self-assembled monolayer (SAM) coated indium-tin-oxide (ITO) electrodes. The SAM-ITO electrodes successfully suppressed dark current which blocks the formation of space-charge field and also causes the dielectric breakdown. The PR device consisted of composite of PTAA, 4-azacycloheptylbenzylidenemalononitrile (7-DCST), N-ethylcarbazole (ECz), and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) sandwiched between the SAM-ITO electrodes. The PR devices showed the PR performances: optical gain Γ, refractive index Δn, diffraction efficiency η, response time τ, sensitivity S, phase shift Φ, trap-limited field E_q, number density of traps N_T, and space-charge field E_SC. The remarkable response time of 11.3 ms was achieved at the low electric field of 20 V μm⁻¹, which was comparable to the response time of high-definition television (HDTV) quality of 16 ms. Our approach will widen the usage of higher mobility materials to photorefractive field and give us more favorable materials to achieve the best performance of photorefractivity in the future.     

Thermal and optical properties of epoxy/zirconia hybrid materials synthesized via in situ polymerization

Epoxy/zirconia hybrid materials were synthesized from a bisphenol-A type epoxy resin, zirconium-tetra-n-propoxide and acetic acid via in situ polymerization. Acetic acid was used to control the hydrolysis and condensation reaction of the zirconium-tetra-n-propoxide. As a result, the zirconia produced by the in situ polymerization was uniformly dispersed into the epoxy matrix on a nano scale or less, and the hybrid materials exhibited an excellent optical transparency. With the increasing zirconia contents, the storage modulus in the rubbery region increased and the peak area of tanδ in the glass transition temperature region decreased. These results indicate that their heat resistance of the hybrid materials could be improved by hybridization with zirconia. Furthermore, the refractive indices of the hybrid materials were significantly improved with the increasing zirconia contents.     

Influence of the methyl group on the dielectric constant of boron carbon nitride films containing it

LSI interconnect insulators made using low dielectric constant (low-k) materials are required for high performance devices with a small RC delay. We investigated a boron carbon nitride film containing the methyl group (Me–BCN) using tris-di-methyl-amino-boron (TMAB: B[N(CH₃)₂]₃) gas as a low-k material. In addition, we studied the influence of the methyl group on the dielectric constant (k-value) and the properties of the Me–BCN films. It was found that the k-value of the Me–BCN films decreases with increasing number of C–H bonds due to the methyl group (CH₃). The number of O–H bonds due to water incorporation is suppressed by increasing the number of C–H bonds. Consequently, we suggested that a lower k-value can be realized by the suppression of water invasion by a hydrophobic surface due to methyl bonds. Thus, the control of the methyl group is important to achieve a low-k material using Me–BCN films.     

Water wettability/non-wettability of polymer materials by molecular orbital studies

The water wettability and non-wettability onto various kinds of polymers, which have so far been macroscopically described by the water contact angle, were investigated using the molecular orbital theory. An atomistic model consisting of an H₂O molecule and a selected polymer crystal surface was analyzed in the isolated and the physisorbed states. The degree of interaction between the water molecule and the polymer surface was evaluated by considering the change of Mulliken charge at the oxygen site in the water molecule, and also the work of adhesion during the physisorption process. Such energetic quantities for several polymers were compared with the macroscopic water wettability/non-wettability. We found fairly good agreement between these approaches for the highly non-wettability polymers.     

Characterization of polystyrene-binding peptides (PS-tags) for site-specific immobilization of proteins

In this study, we characterized polystyrene-binding peptides (PS-tags) that possess a specific binding affinity for hydrophilic polystyrene (phi-PS) plates. Both the FITC-labeled PS19-1 (RAFIASRRIKRP) and PS19-6 (RIIIRRIRR) peptides showed strong binding affinity for commercially available hydrophilic, but not hydrophobic, PS plates in the presence of the non-ionic surfactant Tween 20. The dissociation constants (K_d) of the PS19-1 and PS19-6 peptides for the hydrophilic PS-A plate were 169 and 86 nM, respectively, and the K_d of both peptides increased with the concentration of NaCl or urea. Based on adsorption yield and residual activity of glutathione S-transferase (GST) after fusion with the PS19-6 peptide or its variants, it was found that the basic amino acid in the PS-tags, i.e., Arg was essential for the strong binding affinity of PS-tags in both the peptide and peptide-fused protein forms The aliphatic amino acids in PS19-6 and PS19-6L, such as Ile or Leu, were also effective. Thus, a series of PS-tags that possess this unusual feature, especially the peptides PS19-6 (RIIIRRIRR) and PS19-6L (RLLLRRLRR), are potential candidate affinity peptide tags for site-specific immobilization of proteins onto hydrophilic PS plates, which show potential as solid supports for protein-based biochips.