Identification of an endonuclease and N-adenine methyltransferase from Ureaplasma parvum SV3F4 strain.

Here, we report a novel endonuclease and N-adenine DNA methyltransferase (mA methyltransferase) in the Ureaplasma parvum SV3F4 strain. Our previous study found that the SV3F4 strain carries 17 unique genes, which are not encoded in the two previously reported U. parvum serovar 3 strain, OMC-P162 and ATCC 700970.

Volatile profiling of fruits of 17 mango cultivars by HS-SPME-GC/MS combined with principal component analysis.

Headspace solid-phase microextraction combined with gas chromatography/mass spectrometry is one of the strongest tools for comprehensive analysis of volatile compounds and has been used to analyze aromatic components of mango and investigate its varietal characteristics. In this study, profiling of aroma compounds in 17 mango cultivars, grown in the same green house to exclude the effect of environmental factors, was conducted and the patterns were subjected to principal component analysis (PCA) to identify the relationship between the aroma components and cultivars. Fifty-nine different volatile constituents were detected from the blends of these 17 mango cultivars.

Promotion of lipopeptide antibiotic production by sp. IA in the presence of rice husk biochar.

The purpose of this study is to isolate the beneficial microorganisms whose growth is promoted in the presence of charcoal materials. We successfully isolated strain IA, whose growth is promoted on an agar plate with charcoal materials, and identified it as a novel strain of the sp. The growth of strain IA in the liquid medium was promoted by the addition of both activated charcoal (AC) and rice husk biochar (RHB).

Metabolomic analysis of primary metabolites in citrus leaf during defense responses.

Mechanical damage is one of the unavoidable environmental stresses to plant growth and development. Plants induce a variety of reactions which defend against natural enemies and/or heal the wounded sites. Jasmonic acid (JA) and salicylic acid (SA), defense-related plant hormones, are well known to be involved in induction of defense reactions and play important roles as signal molecules.

Isolation and characterization of wound-induced compounds from the leaves of Citrus hassaku.

Citrus plants are world widely cultivated as horticultural tree crops, and nowadays their pharmacological activities have been well studied. Since research of defense responses in citrus plants have been mainly focused on the post-harvested fruits because of their commercial importance, defense mechanisms during their developmental stages have not been well understood. In the present study, two wound-induced compounds were isolated from leaves of Citrus hassaku, and their structures were elucidated by high-resolution electron spray ionization mass spectra (HRESIMS) and nuclear magnetic resonance (NMR) analyses.

Metabolic changes in Citrus leaf volatiles in response to environmental stress.

Citrus plants are well known as a rich source of VOCs, and several have important roles in defense responses. However, how VOCs are regulated in response to environmental stress is not yet well understood. In this study, we investigated dynamic changes of VOCs present in leaves of seven Citrus species (Citrus sinensis, C.

Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L.

The whole genome of Jatropha curcas was sequenced, using a combination of the conventional Sanger method and new-generation multiplex sequencing methods. Total length of the non-redundant sequences thus obtained was 285 858 490 bp consisting of 120 586 contigs and 29 831 singlets. They accounted for ~95% of the gene-containing regions with the average G + C content was 34.

Stimulated Raman scattering microscope with shot noise limited sensitivity using subharmonically synchronized laser pulses.

We propose and demonstrate the use of subharmonically synchronized laser pulses for low-noise lock-in detection in stimulated Raman scattering (SRS) microscopy. In the experiment, Yb-fiber laser pulses at a repetition rate of 38 MHz are successfully synchronized to Ti:sapphire laser pulses at a repetition rate of 76 MHz with a jitter of <8 fs by a two-photon detector and an intra-cavity electro-optic modulator. By using these pulses, high-frequency lock-in detection of SRS signal is accomplished without high-speed optical modulation.

Structure and functional characterization of Vibrio parahaemolyticus thermostable direct hemolysin.

Thermostable direct hemolysin (TDH) is a major virulence factor of Vibrio parahaemolyticus that causes pandemic foodborne enterocolitis mediated by seafood. TDH exists as a tetramer in solution, and it possesses extreme hemolytic activity. Here, we present the crystal structure of the TDH tetramer at 1.

Enzymatic production of (-)-indolactam V by LtxB, a cytochrome P450 monooxygenase.

The P450 cytochrome monooxygenase gene, ltxB, was cloned and overexpressed in Escherichia coli as a 6xHis-tagged protein. The resulting recombinant LtxB was purified by Ni-NTA affinity chromatography and characterized biochemically. Purified LtxB demonstrated typical cytochrome P450 spectroscopic properties including substrate-induced transition from a low-spin (lambdamax=414 nm) to high-spin state (lambdamax=386 nm) upon incubation with N-methyl-L-valyl-L-tryptophanol.

Label-free imaging by stimulated parametric emission microscopy reveals a difference in hemoglobin distribution between live and fixed erythrocytes.

We demonstrate that stimulated parametric emission (SPE) microscopy enables label-free, 3-D visualization of internal hemoglobin distribution of live mouse and chicken erythrocytes with high sensitivity. Change in hemoglobin distribution in chicken erythrocytes before and after ethanol fixation is clearly visualized.

Development of an enzyme activity screening system for beta-glucosidase-displaying yeasts using calcium alginate micro-beads and flow sorting.

Recent reports on high-speed affinity screening systems for yeast cells using flow cytometry have not been adapted to screening yeast cells that display hydrolyzing enzymes, since the fluorescent molecules which are released from fluoresceinated substrate diffuse into solution after enzymatic reaction. In this research, yeast cells displaying beta-glycosidase were individually captured in micro-sized calcium alginate beads by using the newly developed reverse micelle method to prevent diffusion of hydrolyzed fluorescent substrates. By adopting flow sorting to these captured cells, active cells were successfully enriched about 82-fold from a mixed suspension with negative controls.

Analysis and experimental assessment of the sensitivity of stimulated Raman scattering microscopy.

We theoretically show that the shot-noise-limited sensitivity of stimulated Raman scattering (SRS) microscopy, which enables high-contrast vibrational imaging, is similar to that of coherent anti-Stokes Raman scattering microscopy. We experimentally confirm that the sensitivity of our SRS microscope is lower than the shot-noise limit only by <15 dB, which indicates that the high-sensitivity of SRS microscopy is readily available.

Bioactive beads-mediated transformation of rice with large DNA fragments containing Aegilops tauschii genes.

Transformation with large DNA molecules enables multiple genes to be introduced into plants simultaneously to produce transgenic plants with complex phenotypes. In this study, a large DNA fragment (ca. 100 kb) containing a set of Aegilops tauschii hardness genes was introduced into rice plants using a novel transformation method, called bioactive beads-mediated transformation.

High-resolution spatial and temporal analysis of phytoalexin production in oats.

The production of oat (Avena sativa L.) phytoalexins, avenanthramides, occurs in response to elicitor treatment with oligo-N-acetylchitooligosaccharides. In this study, avenanthramides production was investigated by techniques that provide high spatial and temporal resolution in order to clarify the process of phytoalexin production at the cellular level.

Transient gene expression in guard cell chloroplasts of tobacco using ArF excimer laser microablation.

In this paper, we report a novel method for delivering genes into chloroplasts of tobacco cells using laser microablation. The plasmid pLD200-GFP was introduced into chloroplasts of Nicotiana tabacum cv. Xanthi guard cells and transient GFP expression was detected in the chloroplasts after 2-3 d of incubation.

Line-scanning microscopy for time-gated and spectrally resolved fluorescence imaging.

Laser-scanning fluorescence microscopy for efficient acquisition of time-gated and spectrally resolved fluorescence images was developed based on line illumination of the laser beam and detection of the fluorescence image through a slit. In this optical arrangement, the fluorescence image was obtained by scanning only one axis perpendicular to the excitation line, and the acquisition time was significantly reduced compared with conventional laser-scanning confocal microscopy. A multidimensional fluorescence dataset consisting of fluorescence intensities as a function of x-position, y-position, fluorescence wavelength, and delay time after photoexcitation was analyzed and decomposed based on the parallel factor analysis model.

Improvement of transformation efficiency by bioactive-beads-mediated gene transfer using DNA-lipofectin complex as entrapped genetic material.

The efficiency of bioactive-beads-mediated plant transformation was improved using DNA-lipofectin complex as the entrapped genetic material instead of naked DNA used in the conventional method. In the improved method, beads aggregated and formed clusters around the protoplasts resulting in a 4-fold higher transformation efficiency than that by the conventional method.

Single cell-based analysis of torenia petal pigments by a combination of ArF excimer laser micro sampling and nano-high performance liquid chromatography (HPLC)-mass spectrometry.

The molecular constituents of the petal pigments of the Torenia plant (Torenia hybrida) were analyzed on a single-cell basis by a combination of newly developed laser-microsampling and nano-flow liquid chromatography-electro spray ionization mass spectrometry (LC-ESIMS) techniques. Our method should provide a facile method for obtaining precise metabolic profiles of each cell in a single plant tissue.

Highly sensitive spectral interferometric four-wave mixing microscopy near the shot noise limit and its combination with two-photon excited fluorescence microscopy.

We present spectral interferometric four-wave mixing (FWM) microscopy with a nearly shot-noise limited sensitivity and with the capability of separating FWM signals from fluorescence signals. We analyze the requirements for obtaining the shot-noise limited sensitivity and experimentally achieve the sensitivity that is only 4-dB lower than the shot-noise limit. Moreover, we show that only FWM signals can be extracted through the Fourier filtering even when the FWM spectrum is overlapped and overwhelmed by the fluorescence spectrum.

A novel gene delivery system in plants with calcium alginate micro-beads.

We have produced micrometer-sized calcium alginate beads referred to as "bio-beads" that encapsulate plasmid DNA molecules carrying a reporter gene. In order to evaluate the efficiency of the bio-beads in mediating genetic transfection, protoplasts isolated from cultured tobacco cells (BY-2) were transfected with bio-beads containing a plasmid that carries the modified green fluorescent protein gene CaMV35S-sGFP. With the bio-beads treatment, approximately ten-fold higher GFP expression was observed after 24 h incubation compared to that with the conventional method using a naked plasmid solution.

A novel microsurgery method for intact plant tissue at the single cell level using ArF excimer laser microprojection.

A novel microsurgery technique for the partial removal of rigid cell-walls in intact plant tissue is established. Using a size-variable slit, an ArF excimer laser was microprojected on the surface of the targeted cell, and this method enabled the area- and depth-controllable processing of the cortical structure of plant cells including the cuticle and cell wall layer. In epidermal cells of all tested plants, viabilities of more than 90% were retained 24 h after irradiation.

Isolation and characterization of a cDNA encoding phytochrome A in the non-photosynthetic parasitic plant, Orobanche minor Sm.

In this study, the isolation and characterization of a phytochrome A (PHYA) homologous cDNA (OmPHYA) in the non-photosynthetic holoparasitic plant Orobanche minor are described. The present findings provide the first report of the presence of a PHYA homolog in the holoparasite. This study found that OmPHYA is of similar size to the other PHYAs of green plants and shows 72, 77, and 77% amino acid sequence identity with PHYA in Arabidopsis, potato, and tobacco respectively.

Biosynthetic pathway for the C45 polyprenol, solanesol, in tobacco.

Feeding experiments were independently performed with [1-13C]deoxy-D-xylulose triacetate and (RS)-[2-13C]mevalonolactone in the tobacco plant. The labeling pattern for solanesol was elucidated to reveal that the isoprene moiety of solanesol would be derived from deoxy-xylulose. The result strongly suggests that tobacco solanesol is biosynthesized via the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway.

Flower color modulations of Torenia hybrida by downregulation of chalcone synthase genes with RNA interference.

Suppression of biosynthetic genes involved in flower color formation is an important approach for obtaining target flower colors. Here we report that flower color of the garden plant Torenia hybrida was successfully modulated by RNA interference (RNAi) against a gene of chalcone synthase (CHS), a key enzyme for anthocyanin and flavonoid biosynthesis. By using each of the coding region and the 3'-untranslated region of the CHS mRNA as an RNAi target, exhaustive and gene-specific gene silencing were successfully induced, and the original blue flower color was modulated to white and pale colors, respectively.