Publications by authors named "Hiroshi Yamagishi"

37 Publications

Intraspecific variations of the cytoplasmic male sterility genes and in Brassica maurorum and Moricandia arvensis, and the specificity of the mRNA processing.

Genome 2021 Jun 15. Epub 2021 Jun 15.

Dept. Biotech., Fac. Eng., Kyoto Sangyo Univ., Motoyama, Kamigamo, Kyoto, Kyoto, Japan, 603-8555;

The mitochondrial gene co-transcribed with and causes cytoplasmic male sterility in crops, is widely distributed across wild species and genera of . However, intraspecific variations in the presence of have not yet been studied, and the mechanisms for the wide distribution of the gene remain unclear. We analyzed the presence and sequence variations of in two wild species, and . After polymerase chain reaction amplification of the 5' region of and the coding sequence of , we determined the DNA sequences. and showed variations for the presence of or () both between and within accessions, and were not fixed to the mitochondrial type having the male sterile genes. Sequencing of the amplicons clarified that has instead of . Sequencing also indicated mitochondrial heteroplasmy in the two species; particularly, in , one plant possessed both the and sequences. The results suggested that substoichiometric shifting of the mitochondrial genomes leads to the acquisition or loss of . Furthermore, fertility restorer genes of the two species were involved in the processing of the mRNA of the male sterility genes at different sites.
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http://dx.doi.org/10.1139/gen-2021-0011DOI Listing
June 2021

Robust Angular Anisotropy of Circularly Polarized Luminescence from a Single Twisted-Bipolar Polymeric Microsphere.

J Am Chem Soc 2021 Jun 4;143(23):8772-8779. Epub 2021 Jun 4.

Department of Materials Science, Faculty of Pure and Applied Sciences, and Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan.

It has long been surmised that the circular polarization of luminescence (CPL) emitted by a chiral molecule or a molecular assembly should vary with the direction in which the photon is emitted. Despite its potential utility, this anisotropic CPL has not yet been demonstrated at the level of single molecules or supramolecular assemblies. Here we show that conjugated polymers bearing chiral side chains self-assemble into solid microspheres with a twisted bipolar interior, which are formed via liquid-liquid phase separation and subsequent condensation into a cholesteric lyotropic liquid crystalline mesophase. The resultant microspheres, when dispersed in methanol, exhibit CPL with a value as high as 0.23. The microspheres are mechanically robust enough to be handled with a microneedle under ambient conditions, allowing comprehensive examination of the angular anisotropy of CPL. The single microsphere is found to exhibit distinct angularly anisotropic birefringence and CPL with up to ∼0.5 in the equatorial plane, which is 2.5-fold greater than that along the polar axis. Such optically anisotropic solid materials are important for the application to next-generation microlight-emitting and visualizing devices as well as for fundamental optics studies of chiral light-matter interaction.
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http://dx.doi.org/10.1021/jacs.1c03185DOI Listing
June 2021

A single nucleotide substitution in the coding region of Ogura male sterile gene, orf138, determines effectiveness of a fertility restorer gene, Rfo, in radish.

Mol Genet Genomics 2021 May 26;296(3):705-717. Epub 2021 Mar 26.

Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo, Kita, Kyoto, 603-8555, Japan.

Cytoplasmic male sterility (CMS) observed in many plants leads defect in the production of functional pollen, while the expression of CMS is suppressed by a fertility restorer gene in the nuclear genome. Ogura CMS of radish is induced by a mitochondrial orf138, and a fertility restorer gene, Rfo, encodes a P-type PPR protein, ORF687, acting at the translational level. But, the exact function of ORF687 is still unclear. We found a Japanese variety showing male sterility even in the presence of Rfo. We examined the pollen fertility, Rfo expression, and orf138 mRNA in progenies of this variety. The progeny with Type H orf138 and Rfo showed male sterility when their orf138 mRNA was unprocessed within the coding region. By contrast, all progeny with Type A orf138 were fertile though orf138 mRNA remained unprocessed in the coding region, demonstrating that ORF687 functions on Type A but not on Type H. In silico analysis suggested a specific binding site of ORF687 in the coding region, not the 5' untranslated region estimated previously, of Type A. A single nucleotide substitution in the putative binding site diminishes affinity of ORF687 in Type H and is most likely the cause of the ineffectiveness of ORF687. Furthermore, fertility restoration by RNA processing at a novel site in some progeny plants indicated a new and the third fertility restorer gene, Rfs, for orf138. This study clarified that direct ORF687 binding to the coding region of orf138 is essential for fertility restoration by Rfo.
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http://dx.doi.org/10.1007/s00438-021-01777-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8144145PMC
May 2021

Appearance of male sterile and black radishes in the progeny of cross between and .

Breed Sci 2020 Dec 5;70(5):637-641. Epub 2020 Nov 5.

Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo, Kita, Kyoto 603-8555, Japan.

In addition to Ogura cytoplasmic male sterility (CMS), which is used extensively for F hybrid seed production in Brassicaceae crops, two other CMS systems, NWB CMS and DCGMS, have also been identified. The causal gene for the latter two CMS systems has been identified as a novel chimeric gene, . We previously reported that is specific to black radish cultivars and that it is present in line 'RS-5' of ; however, the sequence in 'RS-5' differed from that of black radish cultivars. Though, with an sequence identical to that found in black radish cultivars was recently identified. We therefore sought to determine whether the gene in line 'RS-5' induces CMS in radishes. We crossed 'RS-5' as a female parent with a cultivated radish, 'Uchiki-Gensuke', as a male parent, and examined the gross plant morphology and pollen fertility of the resulting progeny. The F population contained both male sterile plants and plants with black roots. The findings showed that contains two types of genes that induce CMS, and that the origin of black radishes could be attributed to having gene.
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http://dx.doi.org/10.1270/jsbbs.20081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7878931PMC
December 2020

Fluorescence Switchable Conjugated Polymer Microdisk Arrays by Cosolvent Vapor Annealing.

Polymers (Basel) 2021 Jan 15;13(2). Epub 2021 Jan 15.

Department of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8573, Ibaraki, Japan.

Depositing minute light emitters into a regular array is a basic but essential technique in display technology. However, conventional lithographic methodologies involve multistep and energy-consuming processes. Here, we develop a facile method in which organic and polymeric fluorescent dyes spontaneously aggregate to form a patterned microarray. We find that a thin film of fluorescent π-conjugated polymer transforms into micrometer-sized aggregates when exposed to binary organic vapor at ambient temperature. The arrayed microaggregates can be formed over the whole substrate surface when using a quartz substrate that is prepatterned with regular hydrophilic boxes and hydrophobic grids. The resultant microarray is applicable to optical memories and displays when photoswitchable fluorophores are doped into the polymer matrix.
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http://dx.doi.org/10.3390/polym13020269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7829903PMC
January 2021

Molecular simulation on the stability and adsorption properties of choline-based ionic liquids/IRMOF-1 hybrid composite for selective HS/CO capture.

J Hazard Mater 2020 11 28;399:123008. Epub 2020 May 28.

Division of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8573, Japan.

The compatibility and performance of an Isoreticular Metal-Organic Frameworks (IRMOF-1) impregnated with choline-based ionic liquids (ILs) for selective adsorption of HS/CO, were studied by molecular dynamics (MD) simulation. Cholinium alanate ([Chl][Ala]) was nominated as the suitable IL for impregnation into IRMOF-1, consistent with the low RMSD values (0.546 nm, 0.670 nm, 0.776 nm) at three IL/IRMOF-1 w/w ratios (W = 0.4, 0.8, and 1.2). The [Chl] and [Ala] ion pair was located preferentially around the carboxylate group within the IRMOF-1 framework, with the latter interacting strongly with the host than the [Chl]. Results of radius of gyration (Rg) and root mean square displacement (RMSD) revealed that a ratio of 0.4 w/w of IL/IRMOF-1 (Rg = 1.405 nm; RMSD = 0.546 nm) gave the best conformation to afford an exceptionally stable IL/IRMOF-1 composite. It was discovered that the IL/IRMOF-1 composite was more effective in capturing HS and CO compared to pristine IRMOF-1. The gases adsorbed in higher quantities in the IL/IRMOF-1 composite phase compared to the bulk phase, with a preferential adsorption for HS, as shown by the uppermost values of adsorption ( [Formula: see text] = 17.954 mol L bar) and an adsorption selectivity ( [Formula: see text] = 43.159) at 35 IL loading.
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http://dx.doi.org/10.1016/j.jhazmat.2020.123008DOI Listing
November 2020

Facile light-initiated radical generation from 4-substituted pyridine under ambient conditions.

Chem Commun (Camb) 2020 Jun;56(51):6937-6940

Department of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan.

Photochemical reactions that generate stable radical species under ambient conditions find unique applications in materials science. Here we present a facile photogeneration of a stable radical species from a 4-substituted pyridine derivative in the presence of water and air at room temperature. The radical generation reaction accompanies a visible colour change to green and is repeatable multiple times.
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http://dx.doi.org/10.1039/d0cc02538kDOI Listing
June 2020

Single-Crystalline Optical Microcavities from Luminescent Dendrimers.

Angew Chem Int Ed Engl 2020 Jul 20;59(31):12674-12679. Epub 2020 May 20.

Department of Materials Science, Faculty of Pure and Applied Sciences, and, Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8573, Japan.

Microcrystallites are promising minute mirrorless laser sources. A variety of luminescent organic compounds have been exploited along this line, but dendrimers have been inapplicable owing to their fragility and extremely poor crystallinity. Now, a dendrimer family that overcomes these difficulties is presented. First-, second-, and third-generation carbazole (Cz) dendrimers with a carbon-bridged oligo(phenylenevinylene) (COPV2) core (GnCOPV2, n=1-3) assemble to form microcrystals. The COPV2 cores align uni/bidirectionally in the crystals while the Cz units in G2- and G3COPV2 align omnidirectionally. The dendrons work as light-harvesting antennas that absorb non-polarized light and transfer it to the COPV2 core, from which a polarized luminescence radiates. Furthermore, these crystals act as laser resonators, where the lasing thresholds are strongly coupled with the crystal morphology and the orientation of COPV2, which is in contrast with the conventional amorphous dendrimers.
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http://dx.doi.org/10.1002/anie.202000712DOI Listing
July 2020

Self-assembly of lattices with high structural complexity from a geometrically simple molecule.

Science 2018 Sep;361(6408):1242-1246

Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.

Here we report an anomalous porous molecular crystal built of C-H···N-bonded double-layered roof-floor components and wall components of a segregatively interdigitated architecture. This complicated porous structure consists of only one type of fully aromatic multijoint molecule carrying three identical dipyridylphenyl wedges. Despite its high symmetry, this molecule accomplishes difficult tasks by using two of its three wedges for roof-floor formation and using its other wedge for wall formation. Although a C-H···N bond is extremely labile, the porous crystal maintains its porosity until thermal breakdown of the C-H···N bonds at 202°C occurs, affording a nonporous polymorph. Though this nonporous crystal survives even at 325°C, it can retrieve the parent porosity under acetonitrile vapor. These findings show how one can translate simplicity into ultrahigh complexity.
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http://dx.doi.org/10.1126/science.aat6394DOI Listing
September 2018

Multichromosomal structure of the onion mitochondrial genome and a transcript analysis.

Mitochondrion 2019 05 10;46:179-186. Epub 2018 Jul 10.

Plant Organelle Genome Research Center, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto 603-8555, Japan; Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto 603-8555, Japan. Electronic address:

The structures of plant mitochondrial genomes are more complex than those of animals. One of the reasons for this is that plant mitochondrial genomes typically have many long and short repeated sequences and intra- and intermolecular recombination may create various DNA molecules in this organelle. Recombination may sometimes create a novel gene that causes cytoplasmic male sterility (CMS). The onion has several cytoplasm types, with some causing CMS while others do not. The complete mitochondrial genome sequence of the onion was reported for an inbred line with CMS-S cytoplasm; however, the number of differences between onion strains remains unclear, and studies on purified mitochondrial DNA (mtDNA) have not yet been performed. Furthermore, analyses of transcripts in the mitochondrial genome have not been conducted. In the present study, we examined the mitochondrial genome of the onion variety "Momiji-3" (Allium cepa L.) possessing CMS-S-type cytoplasm using next-generation sequencing (NGS). The "Momiji-3" mitochondrial genome mainly exists as three circles as a result of recombination through repeated sequences and we herein succeeded for the first time in visualizing its structure using pulsed field gel electrophoresis (PFGE). The ability to clarify the structure of the mitochondrial genome is rare in plant mitochondria; therefore, "Momiji-3" represents a good example for elucidating complex plant mitochondrial genomes. We also mapped transcript data to the mitochondrial genome in order to identify the RNA-editing positions in all gene-coding regions and estimate the expression levels of genes. We identified 635 editing positions in gene-coding regions. Start and stop codons were created by RNA editing in six genes (nad1, nad4L, atp6, atp9, ccmFC, and orf725). The transcript amounts of novel open reading frames (ORFs) were all markedly lower than those of functional genes. These results suggest that a new functional gene was not present in the mitochondrial genome of "Momiji-3", and that the candidate gene for CMS is orf725, as previously reported.
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http://dx.doi.org/10.1016/j.mito.2018.05.001DOI Listing
May 2019

Complete mitochondrial genome sequences of (Chinese cabbage and mizuna), and intraspecific differentiation of cytoplasm in and .

Breed Sci 2017 Sep 28;67(4):357-362. Epub 2017 Jul 28.

Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo, Motoyama, Kita, Kyoto 603-8555, Japan.

The complete sequence of the mitochondrial genome was determined for two cultivars of . After determining the sequence of a Chinese cabbage variety, 'Oushou hakusai', the sequence of a mizuna variety, 'Chusei shiroguki sensuji kyomizuna', was mapped against the sequence of Chinese cabbage. The precise sequences where the two varieties demonstrated variation were ascertained by direct sequencing. It was found that the mitochondrial genomes of the two varieties are identical over 219,775 bp, with a single nucleotide polymorphism (SNP) between the genomes. Because is the maternal species of an amphidiploid crop species, , the distribution of the SNP was observed both in and . While the mizuna type SNP was restricted mainly to cultivars of mizuna (japonica group) in , the mizuna type was widely distributed in . The finding that the two species have these SNP types in common suggests that the nucleotide substitution occurred in wild before both mitotypes were domesticated. It was further inferred that the interspecific hybridization between and took place twice and resulted in the two mitotypes of cultivated .
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http://dx.doi.org/10.1270/jsbbs.17023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5654463PMC
September 2017

Redox-Responsive Molecular Systems and Materials.

Adv Mater 2017 Jul 19;29(25). Epub 2016 Dec 19.

Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.

Redox reactions can alter the electronic, optical, and magnetic properties of molecules and their ensembles by adding or removing electrons. Here, the developments made over the past 10 years using molecular events are discussed, such as assembly/disassembly, transformation of ensembles, geometric changes, and molecular motions that are designed to be redox-responsive. Considerable progress has occurred in the application of these events to the realization of electronic memory, color displays, actuators, adhesives, and drug delivery. In these cases, systems behave in either a highly or a poorly correlated manner depending on the number of redox-active units involved, based on the method of integration. One of the great advantages of redox-responsive devices and materials is that they have the potential to be readily integrated into existing electronic technologies.
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http://dx.doi.org/10.1002/adma.201603888DOI Listing
July 2017

Metal-Organic Nanotube with Helical and Propeller-Chiral Motifs Composed of a C10-Symmetric Double-Decker Nanoring.

J Am Chem Soc 2015 Jun 11;137(24):7628-31. Epub 2015 Jun 11.

†Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.

Coassembly of an achiral ferrocene-cored tetratopic pyridyl ligand (FcL) with AgBF4 in CH2Cl2/MeCN (7:3 v/v) containing chiral Bu4N(+) (+)- or (-)-menthylsulfate (MS*(-)) results in the formation of an "optically active" metal-organic nanotube (FcNT) composed of a C10-symmetric double-decker nanoring featuring 10 FcL units and 20 Ag(+) ions. The circular dichroism spectrum of FcNT along with its 2D X-ray diffraction (2D XRD) pattern indicates that the constituent metal-organic nanorings in FcNT stack one-handed helically on top of each other. A crystal structure of the dimeric double-decker model complex (Ag2(FcL')2) from a ditopic ferrocene ligand (FcL') and AgBF4 allowed for confirming the binding of MS*(-) onto the Ag(+) center of the complex. The results of detailed spectroscopic studies indicate that in its double-decker aromatic arrays, FcNT possibly possesses propeller-chiral twists in addition to the helically chiral structure, where the former is considerably more dynamic than the latter. Notably, both chiral structural motifs responded nonlinearly to an enantiomeric excess of MS*(-) (majority rule) though with no stereochemical influence on one another.
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http://dx.doi.org/10.1021/jacs.5b04386DOI Listing
June 2015

Complete mitochondrial genome sequence of black mustard (Brassica nigra; BB) and comparison with Brassica oleracea (CC) and Brassica carinata (BBCC).

Genome 2014 Nov 13;57(11-12):577-82. Epub 2015 Feb 13.

Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo, Kita, Kyoto 603-8555, Japan.

Crop species of Brassica (Brassicaceae) consist of three monogenomic species and three amphidiploid species resulting from interspecific hybridizations among them. Until now, mitochondrial genome sequences were available for only five of these species. We sequenced the mitochondrial genome of the sixth species, Brassica nigra (nuclear genome constitution BB), and compared it with those of Brassica oleracea (CC) and Brassica carinata (BBCC). The genome was assembled into a 232 145 bp circular sequence that is slightly larger than that of B. oleracea (219 952 bp). The genome of B. nigra contained 33 protein-coding genes, 3 rRNA genes, and 17 tRNA genes. The cox2-2 gene present in B. oleracea was absent in B. nigra. Although the nucleotide sequences of 52 genes were identical between B. nigra and B. carinata, the second exon of rps3 showed differences including an insertion/deletion (indel) and nucleotide substitutions. A PCR test to detect the indel revealed intraspecific variation in rps3, and in one line of B. nigra it amplified a DNA fragment of the size expected for B. carinata. In addition, the B. carinata lines tested here produced DNA fragments of the size expected for B. nigra. The results indicate that at least two mitotypes of B. nigra were present in the maternal parents of B. carinata.
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http://dx.doi.org/10.1139/gen-2014-0165DOI Listing
November 2014

Cytoplasmic male sterility in Brassicaceae crops.

Breed Sci 2014 May;64(1):38-47

National Research Centre of Plant Biotechnology , New Delhi 10012 , India.

Brassicaceae crops display strong hybrid vigor, and have long been subject to F1 hybrid breeding. Because the most reliable system of F1 seed production is based on cytoplasmic male sterility (CMS), various types of CMS have been developed and adopted in practice to breed Brassicaceae oil seed and vegetable crops. CMS is a maternally inherited trait encoded in the mitochondrial genome, and the male sterile phenotype arises as a result of interaction of a mitochondrial CMS gene and a nuclear fertility restoring (Rf) gene. Therefore, CMS has been intensively investigated for gaining basic insights into molecular aspects of nuclear-mitochondrial genome interactions and for practical applications in plant breeding. Several CMS genes have been identified by molecular genetic studies, including Ogura CMS from Japanese radish, which is the most extensively studied and most widely used. In this review, we discuss Ogura CMS, and other CMS systems, and the causal mitochondrial genes for CMS. Studies on nuclear Rf genes and the cytoplasmic effects of alien cytoplasm on general crop performance are also reviewed. Finally, some of the unresolved questions about CMS are highlighted.
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http://dx.doi.org/10.1270/jsbbs.64.38DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4031109PMC
May 2014

The complete mitochondrial genome sequence of Brassica oleracea and analysis of coexisting mitotypes.

Curr Genet 2014 Nov 12;60(4):277-84. Epub 2014 Jun 12.

Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita, Kyoto, 603-8555, Japan,

The complete mitochondrial genome sequences of Brassica species have provided insight into inter- and intraspecific variation of plant mitochondrial genomes. However, the size of mitochondrial genome sequenced for Brassica oleracea hitherto does not match to its physical mapping data. This fact led us to investigate B. oleracea mitochondrial genome in detail. Here we report novel B. oleracea mitochondrial genome, derived from var. capitata, a cabbage cultivar ''Fujiwase''. The genome was assembled into a 219,952-bp circular sequence that is comparable to the mitochondrial genomes of other Brassica species (ca. 220-232 kb). This genome contained 34 protein-coding genes, 3 rRNA genes and 17 tRNA genes. Due to absence of a large repeat (140 kb), the mitochondrial genome of ''Fujiwase'' is clearly smaller than the previously reported mitochondrial genome of B. oleracea accession ''08C717'' (360 kb). In both mitotypes, all genes were identical, except cox2-2, which was present only in the Fujiwase type. At least two rearrangement events via large and small repeat sequences have contributed to the structural differences between the two mitotypes. PCR-based marker analysis revealed that the Fujiwase type is predominant, whereas the 08C717 type coexists at low frequency in all B. oleracea cultivars examined. Intraspecific variations in the mitochondrial genome in B. oleracea may occur because of heteroplasmy, coexistence of different mitotypes within an individual, and substoichiometric shifting. Our data indicate that the Fujiwase-type genome should be used as the representative genome of B. oleracea.
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http://dx.doi.org/10.1007/s00294-014-0433-2DOI Listing
November 2014

Manipulation of discrete nanostructures by selective modulation of noncovalent forces.

Science 2014 May 10;344(6183):499-504. Epub 2014 Apr 10.

Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.

Covalent organic synthesis commonly uses the strategy of selective bond cleavage and formation. If a similar approach can be applied stepwisely to noncovalent synthesis, more exotic or challenging nanostructures might become achievable. Here, we report that ferrocene-based tetratopic pyridyl ligands, which can dynamically change their geometry by means of thermal rotation of their cyclopentadienyl rings in solution, assemble with AgBF4 into discrete metal-organic nanotubes with large and uniform diameters. The nanotubes can be cut into metal-organic nanorings through selective attenuation of the inter-nanoring interaction via ferrocene oxidation. The resultant nanorings can be transferred onto inorganic substrates electrostatically or allowed to reassemble to form the original nanotube by the reductive neutralization of their oxidized ferrocene units.
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http://dx.doi.org/10.1126/science.1252120DOI Listing
May 2014

A possible breakage of linkage disequilibrium between mitochondrial and chloroplast genomes during Emmer and Dinkel wheat evolution.

Genome 2013 Apr 8;56(4):187-93. Epub 2013 Apr 8.

The 31st Laboratory, Department of Bioresources and Environmental Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan.

In wheat (Triticum) and Aegilops, chloroplast and mitochondrial genomes have been studied for over three decades to clarify the phylogenetic relationships among species, and most of the maternal lineages of polyploid species have been clarified. Mitochondrial genomes of Emmer (tetraploid with nuclear genome AABB) and Dinkel (hexaploid with AABBDD) wheat are classified into two different types, VIIa and VIIb, by the presence-absence of the third largest HindIII fragment (named H3) in the mitochondrial DNA. Although the mitochondrial genome in the genera often provides useful information to clarify the phylogenetic relationship among closely related species, the phylogenetic significance of this dimorphism has yet not been clarified. In this study, to facilitate analysis using a large number of accessions, a sequence characterized amplified region (SCAR) marker that distinguishes the type VIIb mitochondrial genome from type VIIa was first developed. Mitochondrial genome type was determined for each of 30 accessions of wild and cultivated Emmer wheat and 25 accessions of Dinkel wheat. The mitochondrial genome type for each accession was compared with the plastogroup that had been determined using chloroplast microsatellite markers. Unexpectedly, the distribution of mitochondrial genome type was not in accordance with that of the plastogroups, suggesting occasional paternal leakage of either the mitochondrial or chloroplast genome during speciation and differentiation of Emmer and Dinkel wheat. An alternative possibility that substoichiometric shifting is involved in the observed dimorphism of the mitochondrial genome is also discussed.
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http://dx.doi.org/10.1139/gen-2012-0153DOI Listing
April 2013

A complete mitochondrial genome sequence of Ogura-type male-sterile cytoplasm and its comparative analysis with that of normal cytoplasm in radish (Raphanus sativus L.).

BMC Genomics 2012 Jul 31;13:352. Epub 2012 Jul 31.

31 Laboratory, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto 603-8555, Japan.

Background: Plant mitochondrial genome has unique features such as large size, frequent recombination and incorporation of foreign DNA. Cytoplasmic male sterility (CMS) is caused by rearrangement of the mitochondrial genome, and a novel chimeric open reading frame (ORF) created by shuffling of endogenous sequences is often responsible for CMS. The Ogura-type male-sterile cytoplasm is one of the most extensively studied cytoplasms in Brassicaceae. Although the gene orf138 has been isolated as a determinant of Ogura-type CMS, no homologous sequence to orf138 has been found in public databases. Therefore, how orf138 sequence was created is a mystery. In this study, we determined the complete nucleotide sequence of two radish mitochondrial genomes, namely, Ogura- and normal-type genomes, and analyzed them to reveal the origin of the gene orf138.

Results: Ogura- and normal-type mitochondrial genomes were assembled to 258,426-bp and 244,036-bp circular sequences, respectively. Normal-type mitochondrial genome contained 33 protein-coding and three rRNA genes, which are well conserved with the reported mitochondrial genome of rapeseed. Ogura-type genomes contained same genes and additional atp9. As for tRNA, normal-type contained 17 tRNAs, while Ogura-type contained 17 tRNAs and one additional trnfM. The gene orf138 was specific to Ogura-type mitochondrial genome, and no sequence homologous to it was found in normal-type genome. Comparative analysis of the two genomes revealed that radish mitochondrial genome consists of 11 syntenic regions (length >3 kb, similarity >99.9%). It was shown that short repeats and overlapped repeats present in the edge of syntenic regions were involved in recombination events during evolution to interconvert two types of mitochondrial genome. Ogura-type mitochondrial genome has four unique regions (2,803 bp, 1,601 bp, 451 bp and 15,255 bp in size) that are non-syntenic to normal-type genome, and the gene orf138 was found to be located at the edge of the largest unique region. Blast analysis performed to assign the unique regions showed that about 80% of the region was covered by short homologous sequences to the mitochondrial sequences of normal-type radish or other reported Brassicaceae species, although no homology was found for the remaining 20% of sequences.

Conclusions: Ogura-type mitochondrial genome was highly rearranged compared with the normal-type genome by recombination through one large repeat and multiple short repeats. The rearrangement has produced four unique regions in Ogura-type mitochondrial genome, and most of the unique regions are composed of known Brassicaceae mitochondrial sequences. This suggests that the regions unique to the Ogura-type genome were generated by integration and shuffling of pre-existing mitochondrial sequences during the evolution of Brassicaceae, and novel genes such as orf138 could have been created by the shuffling process of mitochondrial genome.
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http://dx.doi.org/10.1186/1471-2164-13-352DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3473294PMC
July 2012

[How to tell a patient the truth?--a case report from a psycho-oncology outpatient clinic].

Gan To Kagaku Ryoho 2009 Sep;36(9):1511-4

Dept. of Psychiatry, Kansai Denryoku Hospital.

Depression and anxiety are common psychiatric syndromes in the cancer population, but are not always managed very well due to the barriers to psychiatric consultation in Japan. We have tried to care for cancer patients with depression or anxiety through our psycho-oncology outpatient clinic. We have found that some anxiety in cancer patients derives from miscommunications between patients and physicians in charge because physicians do not tell the conditions of diseases clearly to patients. Needless to say, physicians should learn the communication skills regarding breaking bad news but we would like to emphasize the importance of smooth communication among health care professionals through this case report which makes us reconsider how we should have told the patient the truth (the time for stopping anti-cancer treatment, prognosis and so on) to a patient.
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September 2009

Introduction of transformed chloroplasts from tobacco into petunia by asymmetric cell fusion.

Plant Cell Rep 2009 Nov 2;28(11):1633-40. Epub 2009 Sep 2.

Department of Biotechnology, Kyoto Sangyo University, Japan.

Plastid engineering technique has been established only in Nicotiana tabacum, and the widespread application is severely limited so far. In order to exploit a method to transfer the genetically transformed plastomes already obtained in tobacco into other plant species, somatic cell fusion was conducted between a plastome transformant of tobacco and a cultivar of petunia (Petunia hybrida). A tobacco strain whose plastids had been transformed with aadA (a streptomycin/spectinomycin adenylyltransferase gene) and mdar [a gene for monodehydroascorbate reductase (MDAR)] and a petunia variety, 'Telstar', were used as cell fusion partners. An efficient regeneration system from the protoplasts of both the parents, and effectiveness of selection for the aadA gene with spectinomycin were established before the cell fusion. In addition, the influence of UV irradiation on the callus development from the protoplasts and shoot regeneration of tobacco was investigated. Protoplasts were cultured after cell fusion treatment with polyethylene glycol, and asymmetric somatic cybrids were selected using the aadA gene as a marker. Although many shoots of tobacco that had escaped the UV irradiation regenerated, several shoots possessing the morphology of petunia and the resistance to spectinomycin were obtained. Molecular analyses of the petunia type regenerants demonstrated that they had the nuclear and mitochondrial genomes derived from petunia besides the chloroplasts of tobacco transformed with aadA and mdar. Furthermore, it was ascertained that mdar was transcribed in the somatic cybrids. The results indicate the success in intergeneric transfer of transformed plastids of tobacco into petunia.
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http://dx.doi.org/10.1007/s00299-009-0763-6DOI Listing
November 2009

A novel Rf gene controlling fertility restoration of Ogura male sterility by RNA processing of orf138 found in Japanese wild radish and its STS markers.

Genome 2009 Jun;52(6):495-504

Department of Biotechnology, Faculty of Engineering, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto 603-8555, Japan.

To reveal the molecular and genetic mechanism of fertility restoration in Ogura male sterility in Japanese wild radish (Raphanus sativus var. hortensis f. raphanistroides), we investigated fertility restoration of a plant that lacks the dominant type of orf687, a previously identified fertility restorer gene. A total of 100 F2 plants were made from the cross between a male-sterile strain with the Ogura cytoplasm, 'MS-Gensuke', and a Japanese wild radish plant. Segregation of pollen fertility in the F2 plants led us to assume that 2 dominant complementary genes controlled the fertility restoration of the plants. However, the fertility of 27 of 59 male-fertile plants was not completely restored, resulting in a group of plants with partial male fertility. Northern blot analysis of the CMS-associated gene orf138 indicated that one restorer allele (termed Rft) was involved in the processing of orf138 RNA. Rapid amplification of cDNA ends (RACE) and subsequent Northern blot analysis confirmed that the orf138 transcript lost a 5' part of the coding region of the orf138 gene in the restored plants. The accumulation of ORF138 protein was significantly reduced by Rft, but trace amounts of the protein were recognized in both partially male-fertile and male-sterile plants with Rft. The relationship of pollen fertility and segregation of co-dominant sequence tagged site (STS) markers in the F2 generation suggested that the penetrance of Rft was so low that Rft needs suitable conditions to function sufficiently for the complete restoration of fertility.
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http://dx.doi.org/10.1139/g09-026DOI Listing
June 2009

Inhibition of chalcone synthase expression in anthers of Raphanus sativus with Ogura male sterile cytoplasm.

Ann Bot 2008 Oct 14;102(4):483-9. Epub 2008 Jul 14.

Department of Biotechnology, Kyoto-Sangyo University, Kyoto 603-8555, Japan.

Background And Aims: Expression of the mitochondrial gene orf138 causes Ogura cytoplasmic male sterility (CMS) in Raphanus sativus, but little is known about the mechanism by which CMS takes place. A preliminary microarray experiment revealed that several nuclear genes concerned with flavonoid biosynthesis were inhibited in the male-sterile phenotype. In particular, a gene for one of the key enzymes for flavonoid biosynthesis, chalcone synthase (CHS), was strongly inhibited. A few reports have suggested that the inhibition of CHS causes nuclear-dependent male sterile expression; however, there do not appear to be any reports elucidating the effect of CHS on CMS expression. In this study, the expression patterns of the early genes in the flavonoid biosynthesis pathway, including CHS, were investigated in normal and male-sterile lines.

Methods: In order to determine the aberrant stage for CMS expression, the characteristics of male-sterile anthers are observed using light and transmission electron microscopy for several stages of flower buds. The expression of CHS and the other flavonoid biosynthetic genes in the anthers were compared between normal and male-sterile types using real time RT-PCR.

Key Results: Among the flavonoid biosynthetic genes analysed, the expression of CHS was strongly inhibited in the later stages of anther development in sterility cytoplasm; accumulation of putative naringenin derivatives was also inhibited.

Conclusions: These results show that flavonoids play an important role in the development of functional pollen, not only in nuclear-dependent male sterility, but also in CMS.
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http://dx.doi.org/10.1093/aob/mcn116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2701772PMC
October 2008

Developmental changes in heart photosensitivity of the isopod crustacean Ligia exotica.

Zoolog Sci 2007 Mar;24(3):273-6

Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan.

During juvenile development, the cardiac pacemaker of the isopod crustacean Ligia exotica is transferred from the myocardium to the cardiac ganglion of the neurogenic heart. In adult, light stimulus decreases the beat frequency of the heart. To elucidate developmental changes in the photosensitivity of the juvenile Ligia heart, we examined the effect of a light stimulus on the semi-isolated heart of juveniles at various developmental stages by the recording membrane potential of the myocardium. We also examined the effect of hyperpolarizing current injection into the myocardium, because this causes different effects on the beat frequency between myogenic and neurogenic hearts. In newly hatched juveniles, beat frequency decreased upon current injection but exhibited no response to white light. In contrast, 10 days after hatching, beat frequency did not change upon current injection, but decreased in response to white light. The heart photoresponse of juveniles was reversibly eliminated by application of tetrodotoxin, which changes the heartbeat from neurogenic to myogenic by suppressing cardiac ganglion activity. The proportion of juveniles exhibiting a heart photoresponse increased gradually up to 100% during the period between 3 and 10 days after hatching. The results suggest that the heart photoresponse of L. exotica appears in association with transfer of the cardiac pacemaker from the myocardium to the cardiac ganglion during juvenile development.
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http://dx.doi.org/10.2108/zsj.24.273DOI Listing
March 2007

Photosensitive neurogenic heart of the isopod crustacean Ligia exotica.

Proc Biol Sci 2006 Oct;273(1600):2535-40

Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.

The heart of animals is regulated through the central nervous system in response to external sensory stimuli. We found, however, that the adult neurogenic heart of the isopod crustacean Ligia exotica has photosensitivity. The beat frequency of the isolated heart decreased in response to a light stimulus. Magnitude of the response was stimulus intensity dependent and the heartbeat frequency decreased to less than 80% of the dark value during illumination of the white light with an intensity of 6.0 mW cm-2. The spectral sensitivity curve of the heart photoresponse peaked at a wavelength around 520 nm. In response to 530 nm monochromatic light, the relationship between light intensity and response magnitude was linear and the threshold intensity was 7.26 x 1012 quanta cm-2 s-1. Bursting activity of the cardiac ganglion, which is located in the heart and acts as the cardiac pacemaker deceased in frequency in response to illumination by white light. This fact suggests that the heart photoresponse of L. exotica results from the photosensitivity of the cardiac ganglion neurons. The photoresponse of the heart therefore contributes to regulation of cardiac output in addition to other regulatory systems.
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http://dx.doi.org/10.1098/rspb.2006.3625DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1634909PMC
October 2006

Rice plant development: from zygote to spikelet.

Plant Cell Physiol 2005 Jan 19;46(1):23-47. Epub 2005 Jan 19.

Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, 113-865 Japan.

Rice is becoming a model plant in monocotyledons and a model cereal crop. For better understanding of the rice plant, it is essential to elucidate the developmental programs of the life cycle. To date, several attempts have been made in rice to categorize the developmental processes of some organs into substages. These studies are based exclusively on the morphological and anatomical viewpoints. Recent advancement in genetics and molecular biology has given us new aspects of developmental processes. In this review, we first describe the phasic development of the rice plant, and then describe in detail the developmental courses of major organs, leaf, root and spikelet, and specific organs/tissues. Also, for the facility of future studies, we propose a staging system for each organ.
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http://dx.doi.org/10.1093/pcp/pci501DOI Listing
January 2005

Cloning and characterization of a novel radish protein kinase which is homologous to fungal cot-I like and animal Ndr protein kinases.

Genes Genet Syst 2004 Oct;79(5):283-91

Department of Biotechnology, Faculty of Engineering, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto 603-8555, Japan.

According to the similarity of the amino acid sequences in their catalytic domains, eukaryotic protein kinases have been classified into the five main groups: 'AGC', 'CaMK', 'CMGC', 'PTK' and 'other'. The AGC group, represented by the cyclic nucleotide-dependent kinases (PKA and PKG), the calcium-phospholipid-dependent kinases (PKC) and the ribosomal S6 protein kinases, are poorly characterized in plants except for a few cases. In this study, in order to gain a better understanding of plant protein kinases in the AGC group, three cDNAs encoding novel protein kinases, RsNdr1 and RsNdr2a/b, were cloned from radish and characterized by molecular and biochemical methods. The deduced amino acid sequences of RsNdr1 and RsNdr2a/b contained all 12 conserved catalytic subdomains which are characteristic of the eukaryotic Ser/Thr protein kinases. A cell lysate from E. coli overexpressing RsNdr1 fusion protein had protein kinase activity toward a conventional protein substrate (myelin basic protein), whereas that from E. coli harboring a fusion plasmid encoding kinase-dead RsNdr1 or RsNdr2 did not show any protein kinase activity. A phylogenetic tree for 17 protein kinases from various organisms showed that the RsNdrs are more closely related to the protein kinases in a particular subgroup of the 'AGC' (fungal cot1-like and animal Ndr kinases) than to the authentic 'AGC' protein kinases, such as PKA, PKC or ribosomal S6 kinase.
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http://dx.doi.org/10.1266/ggs.79.283DOI Listing
October 2004

Developmental changes in dopamine modulation of the heart in the isopod crustacean Ligia exotica: reversal of chronotropic effect.

Zoolog Sci 2004 Sep;21(9):917-22

Institute of Biological Sciences, University of Tsukuba, Ibaraki, Japan.

Developmental changes in dopamine modulation of the heart were examined in the isopod crustacean Ligia exotica. The Ligia cardiac pacemaker is transferred from the myocardium to the cardiac ganglion during juvenile development and the heartbeat changes from myogenic to neurogenic. In the myogenic heart of early juveniles, dopamine affected the myocardium and caused a decrease in the frequency and an increase in the duration of the myocardial action potential, resulting in negative chronotropic (decrease in beat frequency) and positive inotropic (increase in contractile force) effects on the heart. Contrastingly, in the heart of immature adults just after juvenile development, dopamine caused effects of adult type, positive chronotropic and positive inotropic effects on the heart affecting the cardiac ganglion and myocardium. During the middle and late juvenile stages, dopamine caused individually a negative or a positive chronotropic effect on the heart. These results suggest that the chronotropic effect of dopamine on the Ligia heart is reversed from negative to positive in association with the cardiac pacemaker transfer from the myocardium to the cardiac ganglion during juvenile development.
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http://dx.doi.org/10.2108/zsj.21.917DOI Listing
September 2004

[Concepts in atypical psychoses].

Seishin Shinkeigaku Zasshi 2004 ;106(3):338-41

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July 2004
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