Development of a genome-wide marker design workflow for onions and its application in target amplicon sequencing-based genotyping.

Onions are one of the most widely cultivated vegetables worldwide; however, the development and utilization of molecular markers have been limited because of the large genome of this plant. We present a genome-wide marker design workflow for onions and its application in a high-throughput genotyping method based on target amplicon sequencing. The efficiency of the method was evaluated by genotyping of F2 populations. In the marker design workflow, unigene and genomic sequence data sets were constructed, and polymorphisms between parental lines were detected through transcriptome sequence analysis. The positions of polymorphisms detected in the unigenes were mapped onto the genome sequence, and primer sets were designed. In total, 480 markers covering the whole genome were selected. By genotyping an F2 population, 329 polymorphic sites were obtained from the estimated positions or the flanking sequences. However, missing or sparse marker regions were observed in the resulting genetic linkage map. We modified the markers to cover these regions by genotyping the other F2 populations. The grouping and order of markers on the linkages were similar across the genetic maps. Our marker design workflow and target amplicon sequencing are useful for genome-wide genotyping of onions owing to their reliability, cost effectiveness, and flexibility.

Functional characterization and vacuolar localization of fructan exohydrolase derived from onion (Allium cepa).

Fructans such as inulin and levan accumulate in certain taxonomic groups of plants and are a reserve carbohydrate alternative to starch. Onion (Allium cepa L.) is a typical plant species that accumulates fructans, and it synthesizes inulin-type and inulin neoseries-type fructans in the bulb. Although genes for fructan biosynthesis in onion have been identified so far, no genes for fructan degradation had been found. In this study, phylogenetic analysis predicted that we isolated a putative vacuolar invertase gene (AcpVI1), but our functional analyses demonstrated that it encoded a fructan 1-exohydrolase (1-FEH) instead. Assessments of recombinant proteins and purified native protein showed that the protein had 1-FEH activity, hydrolyzing the ß-(2,1)-fructosyl linkage in inulin-type fructans. Interestingly, AcpVI1 had an amino acid sequence close to those of vacuolar invertases and fructosyltransferases, unlike all other FEHs previously found in plants. We showed that AcpVI1 was localized in the vacuole, as are onion fructosyltransferases Ac1-SST and Ac6G-FFT. These results indicate that fructan-synthesizing and -degrading enzymes are both localized in the vacuole. In contrast to previously reported FEHs, our data suggest that onion 1-FEH evolved from a vacuolar invertase and not from a cell wall invertase. This demonstrates that classic phylogenetic analysis on its own is insufficient to discriminate between invertases and FEHs, highlighting the importance of functional markers in the nearby active site residues.

Wide-range narrowband multilayer mirror for selecting a single-order harmonic in the photon energy range of 40-70 eV.

An experimental demonstration of a wide-range narrowband multilayer mirror for selecting a single-order high-harmonic (HH) beam from multiple-order harmonics in the photon energy range between 40 eV and 70 eV was carried out. This extreme ultraviolet (XUV) mirror, based on a pair of Zr and Al0.7Si0.3 multilayers, has a reflectivity of 20-35% and contrast of more than 7 with respect to neighboring HHs at angles of incidence from 10 to 56.9 degrees, assuming HHs pumped at 1.55 eV. Thus, specific single-order harmonic beams can be arbitrarily selected from multiple-order harmonics in this photo energy range. In addition, the dispersion for input pulses of the order of 1 fs is negligible. This simple-to-align optical component is useful for the many various applications in physics, chemistry and biology that use ultrafast monochromatic HH beams.

Performance of a ruthenium beam separator used to separate soft x rays from light generated by a high-order harmonic light source.

We describe the design and fabrication of a ruthenium beam separator used to simultaneously attenuate infrared light and reflect soft x rays. Measurements in the infrared and soft x-ray regions showed the beam separator to have a reflectivity of 50%-85% in the wavelength region from 6 to 10 nm at a grazing incidence angle of 7.5 deg and 4.3% at 800 nm and the same angle of grazing incidence, indicating that the amount of attenuation is 0.05-0.09. These results show that this beam separator could provide an effective means for separating IR light from soft x rays in light generated by high-order harmonic generation sources.

A proposal for a collecting mirror assembly for large divergence x-ray sources.

We propose a new type of collecting mirror assembly (CMA) for x rays, which will enable us to build a powerful optical system for collecting x rays from large divergence sources. The CMA consists of several mirror sections connected in series. The angle of each section is designed so that the x rays reflected from it are parallel to the x rays directly incident on the following sections. A simplified CMA structure is designed and applied to the Al-Kα emission line. It is estimated that by using the CMA the number of x rays detected could be increased by a factor of about 2.5.

Identification of an actin-binding site in p47phox an organizer protein of NADPH oxidase.

Actin has been reported to enhance the superoxide-generating activity of neutrophil NADPH oxidase in a cell-free system and to interact with p47phox, a regulatory subunit of the oxidase. In the present study, we searched for an actin-binding site in p47phox by far-western blotting and blot-binding assays using truncated forms of p47phox. The amino-acid sequence 319-337 was identified as an actin-binding site, and a synthetic peptide of this sequence bound to actin. The sequence shows no homology to other known actin-binding motifs. It is located in the autoinhibitory region of p47phox and includes Ser-328, a phosphorylation site essential for unmasking. Although a phosphorylation-mimetic p47phox mutant bound to actin with a lower affinity than the wild type, the same mutant interacted with filamentous actin more efficiently than the wild type. A mutant peptide p47phox (319-337, Ser328Glu) bound to filamentous actin more tightly than to monomer actin. These results suggest that p47phox moves to cortical actin when it becomes unmasked in the cells.