Systematic transient assays of promoter activities for leaf-specific genes identified by gene-expression profiling with cDNA microarrays in Arabidopsis thaliana

We identified 85 genes highly expressed in leaves using an Arabidopsis cDNA microarray. A vector, pRAB5, was designed to allow cloning and assaying of the promoters. Fifty-one promoters from the selected genes were cloned and then assayed using a microprojectile bombardment and dual luciferase reporter assay system. This system allowed efficient systematic assays of promoter activity.     

Efficient construction of cDNA microarrays utilizing normalized cDNA libraries of Arabidopsis thaliana

We have demonstrated the utility of normalization for efficient cDNA microarray preparation using Arabidopsis as a model. Nonredundant cDNAs including 5722 species were efficiently collected from random 7914 expressed sequence tags (ESTs) in four normalized cDNA libraries. The prepared microarrays were successfully used to monitor gene expression. These methodologies should be applicable to the study of other species in plant biotechnology.     

Novel episomal vectors and a highly efficient transformation procedure for the fission yeast Schizosaccharomyces japonicus

Schizosaccharomyces japonicus is a fission yeast for which new genetic tools have recently been developed. Here, we report novel plasmid vectors with high transformation efficiency and an electroporation method for Sz. japonicus. We isolated 44 replicating segments from 12 166 transformants of Sz. japonicus genomic fragments and found a chromosomal fragment, RS1, as a new replicating sequence that conferred high transformation activity to Sz. japonicus cells. This sequence was cloned into a pUC19 vector with ura4⁺ of Sz. pombe (pSJU11) or the kan gene on the kanMX6 module (pSJK11) as selection markers. These plasmids transformed Sz. japonicus cells in the early‐log phase by electroporation at a frequency of 123 cfu/µg for pSJK11 and 301 cfu/µg for pSJU11, which were higher than previously reported autonomously replicating sequences. Although a portion of plasmids remained in host cells by integration into the chromosome via RS1 segment, the plasmids could be recovered from transformants. The plasmid copy number was estimated to be 1.88 copies per cell by Southern blot analysis using a Sz. pombe ura4⁺ probe. The plasmid containing ade6⁺ suppressed the auxotrophic growth of the ade6‐domE mutant, indicating that the plasmid would be useful for suppressor screening and complementation assays in Sz. japonicus. Furthermore, pSJU11 transformed Sz. pombe cells with the same frequency as the pREP2 plasmid. This study is a report to demonstrate practical use of episomal plasmid vectors for genetic research in Sz. japonicus. RS1 has been submitted to the DDBJ/EMBL/GenBank database (Accession No. AB547343). Copyright © 2010 John Wiley & Sons, Ltd.     

Effect of light intensity and frequency of flashing light from blue light emitting diodes on astaxanthin production by Haematococcus pluvialis

Flashing light from blue light emitting diodes is an effective method for the reduction of energy consumption in the bioproduction of astaxanthin by Haematococcus pluvialis. We investigated the effects of light intensity and frequency on the final astaxanthin concentration in bioproduction by H. pluvialis grown mixotrophically. The final astaxanthin concentration under illumination with flashing light, with frequencies ranging from 25 to 200 Hz, was dependent on the light intensity and on the duty cycle and was equivalent, or higher, in comparison with that under illumination with continuous light at the same incident intensity. The light intensity determined the maximum attainable concentration of astaxanthin under continuous illumination. Under illumination with flashing light, the ratio of the final astaxanthin concentration to the maximum concentration at a specific light intensity was correlated to the duty cycle in the frequency range from 25 to 200 Hz. The effect of lower frequencies on enhanced astaxanthin production under flashing light was also studied; at levels as low as 1 Hz, higher final astaxanthin concentrations were observed under flashing light compared to concentrations attained under continuous light.     

Mechanism of the Photofading of Stilbene–fluorescent Dyes. Contribution of Singlet Oxygen to the Photofading of 4, 4‘–Bisacetamidostilbene

Self—sensitized and Rose Bengal—sensitized photo—oxidation of 4, 4′-bisacetamidostilbene (BAAS) in solution gives p—acetamidobenzaldehyde and p—acetamidobenzoic acid via the reaction of singlet oxygen with the trans isomer (la). The rate of the photo—oxidation is retarded in the presence of effective singlet oxygen quenchers. On the other hand, cls—BAAS (lb) is more stable to visible light under the conditions of Rose Bengal—sensitized photo—oxidation than trans—stilbene.     

Novel Components of the Sex Pheromones Produced by Emerald Moths: Identification,Synthesis, and Field Evaluation

The subfamily Geometrinae (Lepidoptera: Geometridae) includes many species called emerald moths. Based on our recent finding of novel polyenyl compounds, including a double bond at the 12-position from two geometrine species, Hemithea tritonaria and Thalassodes immissaria intaminata, (6Z,9Z,12Z)-6,9,12-trienes and (3Z,6Z,9Z,12Z)-3,6,9,12-tetraenes with a C₁₇–C₂₀ straight chain were synthesized and analyzed by GC-MS. The 6,9,12-trienes, which were prepared by a double Wittig reaction between two alkanals and an ylide derived from (Z)-1,6-diiodo-3-hexene, characteristically produced fragment ions at m/z 79, 150, and M–98. The 3,6,9,12-tetraenes, which were prepared by a coupling between (Z)-3-alkenal and an ylide derived from (3Z,6Z)-1-iodo-3,6-nonadiene, showed fragment ions at m/z 79, 148, and M–96. These diagnostic ions were useful to distinguish these compounds from other known polyenyl pheromones, such as 4,6,9- and 6,9,11-trienes and 1,3,6,9-tetraenes. With reference to the GC-MS data, pheromone extracts of other species in Geometrinae inhabiting the Iriomote Islands were analyzed, and the 6,9,12-trienes were identified in the pheromone gland extracts of Pamphlebia rubrolimbraria rubrolimbraria and Maxates versicauda microptera. Furthermore, a field evaluation of the synthetic polyenes in a mixed forest of Tokyo revealed the following new male attractants for emerald moths: Idiochlora ussuriaria by a C₁₇ 6,9,12-triene and Jodis lactearia by a C₂₀ 3,6,9,12-tetraene, indicating the characteristic chemical structures of Geometrinae pheromones. On the other hand, through reexamination of the pheromone extract of H. tritonaria, (3E,6E)-α-farnesene was identified as an electrophysiologically active component in addition to the C₁₇ 6,9,12-triene. The binary mixture attracted more males than the single component lure baited with the triene in the Iriomote Islands.     

Fischer–Tropsch synthesis over Co–SiO2 catalysts prepared by the sol–gel method

Fischer–Tropsch synthesis was carried out in slurry phase over uniformly dispersed Co–SiO₂ catalysts prepared by the sol–gel method. When 0.01–1 wt.% of noble metals were added to the Co–SiO₂ catalysts, a high and stable catalytic activity was obtained over 60 h of the reaction at 503 K and 1 MPa. The addition of noble metals increased the reducibility of surface Co on the catalysts, without changing the particle size of Co metal significantly. High dispersion of metallic Co species stabilized on SiO₂ was responsible for stable activity. The uniform pore size of the catalysts was enlarged by varying the preparation conditions and by adding organic compounds such as N,N-dimethylformamide and formamide. Increased pore size resulted in decrease in CO conversion and selectivity for CO₂, a byproduct, and an increase in the olefin/paraffin ratio of the products. By modifying the surface of wide pore silica with Co–SiO₂ prepared by the sol–gel method, a bimodal pore structured catalyst was prepared. The bimodal catalyst showed high catalytic performance with reducing the amount of the expensive sol–gel Co–SiO₂.     

Structural Analysis of the Complex between Penta-EF-Hand ALG-2 Protein and Sec31A Peptide Reveals a Novel Target Recognition Mechanism of ALG-2

ALG-2, a 22-kDa penta-EF-hand protein, is involved in cell death, signal transduction, membrane trafficking, etc., by interacting with various proteins in mammalian cells in a Ca²⁺-dependent manner. Most known ALG-2-interacting proteins contain proline-rich regions in which either PPYPXnYP (type 1 motif) or PXPGF (type 2 motif) is commonly found. Previous X-ray crystal structural analysis of the complex between ALG-2 and an ALIX peptide revealed that the peptide binds to the two hydrophobic pockets. In the present study, we resolved the crystal structure of the complex between ALG-2 and a peptide of Sec31A (outer shell component of coat complex II, COPII; containing the type 2 motif) and found that the peptide binds to the third hydrophobic pocket (Pocket 3). While amino acid substitution of Phe⁸⁵, a Pocket 3 residue, with Ala abrogated the interaction with Sec31A, it did not affect the interaction with ALIX. On the other hand, amino acid substitution of Tyr¹⁸⁰, a Pocket 1 residue, with Ala caused loss of binding to ALIX, but maintained binding to Sec31A. We conclude that ALG-2 recognizes two types of motifs at different hydrophobic surfaces. Furthermore, based on the results of serial mutational analysis of the ALG-2-binding sites in Sec31A, the type 2 motif was newly defined.     

Prediction of a New Ligand-Binding Site for Type 2 Motif based on the Crystal Structure of ALG-2 by Dry and Wet Approaches

ALG-2 is a penta-EF-hand Ca(2+)-binding protein and interacts with a variety of intracellular proteins. Two types of ALG-2-binding motifs have been determined: type 1, PXYPXnYP (X, variable; n = 4), in ALIX and PLSCR3; type 2, PXPGF, in Sec31A and PLSCR3. The previously solved X-ray crystal structure of the complex between ALG-2 and an ALIX peptide containing type 1 motif showed that the peptide binds to Pocket 1 and Pocket 2. Co-crystallization of ALG-2 and type 2 motif-containing peptides has not been successful. To gain insights into the molecular basis of type 2 motif recognition, we searched for a new hydrophobic cavity by computational algorithms using MetaPocket 2.0 based on 3D structures of ALG-2. The predicted hydrophobic pocket designated Pocket 3 fits with N-acetyl-ProAlaProGlyPhe-amide, a virtual penta-peptide derived from one of the two types of ALG-2-binding sites in PLSCR3 (type 2 motif), using the molecular docking software AutoDock Vina. We investigated effects of amino acid substitutions of the predicted binding sites on binding abilities by pulldown assays using glutathione-S-transferase -fused ALG-2 of wild-type and mutant proteins and lysates of cells expressing green fluorescent protein -fused PLSCR3 of wild-type and mutants. Substitution of either L52 with Ala or F148 with Ser of ALG-2 caused loss of binding abilities to PLSCR3 lacking type 1 motif but retained those to PLSCR3 lacking type 2 motif, strongly supporting the hypothesis that Pocket 3 is the binding site for type 2 motif.     

Sequence analysis of poly(ethylene/1,4-cyclohexanedimethylene terephthalate) copolymer using H and C NMR

The triad-level sequence analysis of poly(ethylene/1,4-cyclohexanedimethylene terephthalate) copolymer was reported in a solvent system of o-chlorophenol/deuterated chloroform mixture (50/50 v/v) at 80 °C using 600 MHz ¹H NMR. The well-resolved alcoholic CH₂ proton peak of the glycol units was observed, which made the detailed sequence analysis possible. The peaks of the cis- and trans-forms of the 1,4-cyclohexanedimethylene glycol units were split into the triad sequence in the chain and could be assigned by a comparison of the spectra with those of homopolymers and by an additional two-dimensional heteronuclear multiple bond correlation observation. The triad sequence distributions centered on 1,4-cyclohexanedimethylene glycol units were determined, which was independent of the cis- and trans-forms of the units and controlled according to Bernoullian statistics.