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Takashi Matsumoto

Publications and source records attributed to Takashi Matsumoto.

At least 19 recordsLinked to original sources
PubMed2007

Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene.

Increased seed production has been a common goal during the domestication of cereal crops, and early cultivators of barley (Hordeum vulgare ssp. vulgare) selected a phenotype with a six-rowed spike that stably produced three times the usual grain number. This improved yield established barley as a founder crop for the Near Eastern Neolithic civilization. The barley spike has one central and two lateral spikelets at each rachis node. The wild-type progenitor (H. vulgare ssp. spontaneum) has a two-rowed phenotype, with additional, strictly rudimentary, lateral rows; this natural adaptation is advantageous for seed dispersal after shattering. Until recently, the origin of the six-rowed phenotype remained unknown. In the present study, we isolated vrs1 (six-rowed spike 1), the gene responsible for the six-rowed spike in barley, by means of positional cloning. The wild-type Vrs1 allele (for two-rowed barley) encodes a transcription factor that includes a homeodomain with a closely linked leucine zipper motif. Expression of Vrs1 was strictly localized in the lateral-spikelet primordia of immature spikes, suggesting that the VRS1 protein suppresses development of the lateral rows. Loss of function of Vrs1 resulted in complete conversion of the rudimentary lateral spikelets in two-rowed barley into fully developed fertile spikelets in the six-rowed phenotype. Phylogenetic analysis demonstrated that the six-rowed phenotype originated repeatedly, at different times and in different regions, through independent mutations of Vrs1.

Base Sequence↗
PubMed2007

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is approximately 32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene.

Arabidopsis↗
PubMed2007

Regulatory role of RsgI in sigI expression in Bacillus subtilis.

The sigma gene, sigI, of Bacillus subtilis belongs to the group IV heat-shock response genes and has many orthologues in the bacterial phylum Firmicutes. The B. subtilis sigI gene is considered to constitute an operon with rsgI (regulation of sigI, formerly ykrI). As little is known about either the structure and function of the sigI-rsgI operon or the SigI regulons, the role of RsgI in heat-inducible transcription of the sigI-rsgI operon was investigated, using Northern analysis and a heat-stable beta-galactosidase reporter assay. Heat-inducible, SigI-dependent transcription of the sigI-rsgI operon was stimulated greatly by disrupting rsgI. Yeast two-hybrid analysis showed direct interaction between the N-terminal portion of the presumed RsgI protein and SigI. Without RsgI function, induction of transcription of the sigI-rsgI operon upon transient heat stress depended on dnaK activity. However, transcription of the operon was induced during growth at prolonged higher temperature even without DnaK function. Without RsgI function, sigI-rsgI operon transcription was induced after the end of growth independent of any temperature shift in a sporulation medium and toward the end of growth in a rich complex medium. Furthermore, glucose addition resulted in a strong suppression of sigI-rsgI transcription. Therefore it is hypothesized that transcription of the sigI-rsgI operon of B. subtilis is negatively regulated by the putative transmembrane protein RsgI, which moderates SigI's sensitivity to heat shock or nutritional stress.

Bacillus subtilis↗
PubMed2006

Isolated electrodeless high-frequency quartz crystal microbalance for immunosensors.

This paper presents a contactless technique to measure shear bulk wave resonance frequencies of an isolated quartz crystal in a flow cell. The line antenna placed outside the cell generates and detects the resonance frequencies in a wireless-electrodeless manner. It is revealed that this mechanism relies on the quasistatic electric field. A 0.3-mm-thick AT-cut quartz was used, and its overtone resonance frequencies up to 80 MHz were measured in liquids. Exact vibrational analysis was carried out for a triple-layered resonator system consisting of the adsorbed material layer, the electrode film, and the quartz plate. It predicts higher frequency sensitivity to the adsorbed material at higher modes when the electrode layer is removed. The 13th overtone (72-MHz resonance frequency) was used to detect human immunoglobulin G with concentrations between 0.1 and 20 microg/mL captured by protein A immobilized on one side of the crystal. The real-time measurement of the frequency response yielded the equilibrium constant KA=5.21 x 10(7) M(-1).

Biosensing Techniques↗
PubMed2006

Focusing of light by negative refraction in a photonic crystal slab superlens on silicon-on-insulator substrate.

We experimentally demonstrate the light focusing by negative refraction in a photonic crystal slab superlens at wavelengths lambda of 1.26-1.42 microm. The photonic crystal slab was fabricated on silicon-on-insulator substrate with an interface structure optimized for low reflection and diffraction losses. The light focusing in the photonic crystal slab was clearly observed through the intentional out-of-plane radiation or scattering of guided light in the slab. The minimum focused spot width was limited to 1.8 microm(1.4 lambda) owing to aberrations. The focusing characteristics were in good agreement with those obtained from photonic band and finite-difference time-domain analyses.

Journal Article↗
PubMed2006

Crystal structures of a multidrug transporter reveal a functionally rotating mechanism.

AcrB is a principal multidrug efflux transporter in Escherichia coli that cooperates with an outer-membrane channel, TolC, and a membrane-fusion protein, AcrA. Here we describe crystal structures of AcrB with and without substrates. The AcrB-drug complex consists of three protomers, each of which has a different conformation corresponding to one of the three functional states of the transport cycle. Bound substrate was found in the periplasmic domain of one of the three protomers. The voluminous binding pocket is aromatic and allows multi-site binding. The structures indicate that drugs are exported by a three-step functionally rotating mechanism in which substrates undergo ordered binding change.

Bacterial Outer Membrane Proteins↗
PubMed2006

Dodecamethoxy- and hexaoxotricyclobutabenzene: synthesis and characterization.

We report herein the syntheses of dodecamethoxytricyclobutabenzene (TCBB) 1 and hexaoxo-TCBB 2, a class of molecules with structural and theoretical interest. The preparation is based on the 3-fold [2 + 2] cycloadditions of benzyne and ketene silyl acetals (KSAs), where the selectively protected 2-iodophloroglucinol derivative served as a synthetic equivalent of benztriyne I, allowing rapid and regioselective annulation of fully functionalized four-membered rings. Structural study on the former compound showed that the C-C bond lengths in the central benzene ring were essentially the same.

Journal Article↗
PubMed2006

Sequence comparison of distal and proximal ribosomal DNA arrays in rice (Oryza sativa L.) chromosome 9S and analysis of their flanking regions.

Rice (Oryza sativa ssp. japonica cv. Nipponbare) harbors a ribosomal RNA gene (rDNA) cluster in the nucleolar-organizing region at the telomeric end of the short arm of chromosome 9. We isolated and sequenced two genomic clones carrying rice rDNA fragments from this region. The rice rDNA repeat units could be classified into three types based on length, which ranged from 7,928 to 8,934 bp. This variation was due to polymorphism in the number of 254-bp subrepeats in the intergenic spacer (IGS). Polymerase chain reaction (PCR) analysis suggested that the rDNA units in rice vary widely in length and that the copy number of the subrepeats in the IGS ranges from 1 to 12 in the rice genome. PCR and Southern blot analyses showed that most rDNA units have three intact and one truncated copies of the subrepeats in the IGS, and distal (telomere-side) rDNA units have more subrepeats than do proximal (centromere-side) ones. Both genomic clones we studied contained rDNA-flanking DNA sequences of either telomeric repeats (5'-TTTAGGG-3') or a chromosome-specific region, suggesting that they were derived from the distal or proximal end, respectively, of the rDNA cluster. A similarity search indicated that retrotransposons appeared more frequently in a 500-kb portion of the proximal rDNA-flanking region than in other subtelomeric regions or sequenced regions of the genome. This study reveals the repetitive nature of the telomeric end of the short arm of chromosome 9, which consists of telomeric repeats, an rDNA array, and a retrotransposon-rich chromosomal region.

Base Sequence↗
PubMed2006

Detection of 6-nitrotryptophan in proteins by Western blot analysis and its application for peroxynitrite-treated PC12 cells.

We have previously reported on the formation of 6-nitrotryptophan by the reaction of reactive nitrogen species with a tryptophan residue in human Cu, Zn-superoxide dismutase (SOD) (F. Yamakura et al., J. Biochem. 138 (2005) 57-69). Here, we report on the preparation of anti-6-nitrotryptophan antiserum by using synthesized 6-nitrotryptophan-conjugated keyhole limpet hemocyanin as an antigen and the purification of the antibody by using a 6-nitrotryptophan-conjugated affinity column. The purified antibody was immunoreactive with 6-nitrotryptophan residue containing Cu, Zn-SOD but not immunoreactive with Cu, Zn-SOD, Mn-SOD, bovine serum albumin, and 3-nitrotyrosine residue containing Mn-SOD. Nitro group of 6-nitrotryptophan was reduced by sodium hydrosulfite to form 6-aminotryptophan as a major product. The reduced 6-nitrotryptophan residues lost its immunoreactivity with the antibody. We detected different immunoreactive bands between using antibody for 6-nitrotryptophan residues and that for 3-nitrotyrosine residues in crude extracts of neuron-like PC12 cells treated with peroxynitrite by a Western blot analysis. Western blot analysis for two-dimensional gel electrophoresis showed nine intensively stained immunoreactive spots for 6-nitrotryptophan residues in the peroxynitrite-treated PC12 cells, which were subjected to trypsin digestion and LC-ESI-MS/MS analysis. We identified M2 pyruvate kinase, elongation factor 2, mitochondrial aconitase, pyruvate carboxylase, and heat shock protein HSP90alpha as candidates for 6-nitrotryptophan residues containing proteins, with peptide coverage over 10%, in crude extracts of peroxynitrite-treated PC12 cells.

Animals↗
PubMed2006

Poly-oxygenated tricyclobutabenzenes via repeated [2 + 2] cycloaddition of benzyne and ketene silyl acetal.

Described herein is a synthesis of highly functionalized tricyclobutabenzenes, a class of molecules of structural and theoretical interest. The preparation is based on the repeated [2 + 2] cycloadditions of benzyne and ketene silyl acetals (KSAs), where two types of regioselectivity enable discrimination of the functionalities on the four-membered rings. By these steps, we were able to prepare poly-oxygenated octamethoxytricyclobutabenzene and its hydrolyzed tetra-oxo derivatives. Structural study on the latter compound showed the interesting properties related to the strained four-membered ring.

Journal Article↗
PubMed2006

Sequencing and characterization of telomere and subtelomere regions on rice chromosomes 1S, 2S, 2L, 6L, 7S, 7L and 8S.

Telomeres, which are important for chromosome maintenance, are composed of long, repetitive DNA sequences associated with a variety of telomere-binding proteins. We characterized the organization and structure of rice telomeres and adjacent subtelomere regions on the basis of cytogenetic and sequence analyses. The length of the rice telomeres ranged from 5.1 to 10.8 kb, as revealed by both fibre-fluorescent in situ hybridization and terminal restriction-fragment assay. Physical maps of the chromosomal ends were constructed from a fosmid library. This facilitated sequencing of the telomere regions of chromosomes 1S, 2S, 2L, 6L, 7S, 7L and 8S. The resulting sequences contained conserved TTTAGGG telomere repeats, which indicates that the physical maps partly covered the telomere regions of the respective chromosome arms. These repeats were organized in the order of 5'-TTTAGGG-3' from the chromosome-specific region, except in chromosome 7S, in which seven inverted copies also existed in tandem array. Analysis of the telomere-flanking regions revealed the occurrence of deletions, insertions, or chromosome-specific substitutions of single nucleotides within the repeat sequences at the junction between the telomere and subtelomere. The sequences of the 500-kb regions of the seven chromosome ends were analysed in detail. A total of 598 genes were predicted in the telomeric regions. In addition, repetitive sequences derived from various kinds of retrotransposon were identified. No significant evidence for segmental duplication could be detected within or among the subtelomere regions. These results indicate that the rice chromosome ends are heterogeneous in both sequence and characterization.

Base Sequence↗
PubMed2006

[Evaluation of immunochromatographic test kits for food allergens using processed food models].

It has been mandatory to label five allergenic substances (AS; egg, milk, wheat, buckwheat and peanut) in all processed foods, since April 2002 in Japan. Two kinds of ELISA kits have been provided as screening test kits for the Japanese official method. The kits have many advantages but some disadvantages, i.e., the kits are not necessarily suitable for daily monitoring in food manufacturing plants, because they require various analytical equipments and the use of complicated procedures. To overcome these drawbacks, we have developed other diagnostic kits based on immunochromatography that should enable more rapid and simple screening for food allergens. Then we examined the performance of these immunochromatographic test kits (IC kits) in terms of sensitivity, repeatability and cross-reactivity to AS proteins in 11 kinds of food models with various heating conditions and physical properties. We also examined processed food models including AS protein of constant concentration, using the IC kits and ELISA kits, and compared the results. The IC kits detected AS proteins at 5 microg/g in the extracts from processed food models, and provided highly reproducible results. Cross-reactivity among the AS proteins was not observed. The results obtained using the IC kits showed performance equivalent to that of the ELISA kits we examined in unheating processed food models including AS proteins of constant concentration. The IC kits should be more suitable for daily monitoring in food manufacturing plants.

Allergens↗
PubMed2006

[A case of quadruple cancers of esophagus, stomach, lung and buccal mucosa improving the quality of life by loco-regional cancer therapy].

The patient is an 86-year-old man who was presented with right submandibular mass and tarry stool. He was diagnosed having right buccal carcinoma with right cervical lymph node metastasis, gastric cancer with double lesions, and suspected right superior lung cancer by endoscopy and computed tomography. We started with an operation for the right buccal carcinoma. After the operation, superficial-esophageal carcinoma was found. Due to his old age and a lack of physical strength in the operation, we performed an endoscopic mucosal resection for esophageal cancer and argon plasma coagulation for gastric cancer. Symptomatic therapy was only performed for lung cancer. He died from lung cancer 18 months later. However, he had a good quality of life during the progress without recurrence, and the gastric cancer was also controllable without symptoms. It was difficult to decide the treatment for duplicated multiple organ cancers caused by numerous factors such as in our case. We assume that patient's quality of life is the most appropriate factor to be considered in selecting the treatment for elderly patients.

Aged, 80 and over↗
PubMed2005

Random sheared fosmid library as a new genomic tool to accelerate complete finishing of rice (Oryza sativa spp. Nipponbare) genome sequence: sequencing of gap-specific fosmid clones uncovers new euchromatic portions of the genome.

The International Rice Genome Sequencing Project has recently announced the high-quality finished sequence that covers nearly 95% of the japonica rice genome representing 370 Mbp. Nevertheless, the current physical map of japonica rice contains 62 physical gaps corresponding to approximately 5% of the genome, that have not been identified/represented in the comprehensive array of publicly available BAC, PAC and other genomic library resources. Without finishing these gaps, it is impossible to identify the complete complement of genes encoded by rice genome and will also leave us ignorant of some 5% of the genome and its unknown functions. In this article, we report the construction and characterization of a tenfold redundant, 40 kbp insert fosmid library generated by random mechanical shearing. We demonstrated its utility in refining the physical map of rice by identifying and in silico mapping 22 gap-specific fosmid clones with particular emphasis on chromosomes 1, 2, 6, 7, 8, 9 and 10. Further sequencing of 12 of the gap-specific fosmid clones uncovered unique rice genome sequence that was not previously reported in the finished IRGSP sequence and emphasizes the need to complete finishing of the rice genome.

Base Sequence↗
PubMed2005

Wireless electrodeless piezomagnetic biosensor with an isolated nickel oscillator.

This study presents a fundamental concept of piezomagnetic biochemical sensor driven in a wireless-electrodeless manner. A stepped cylindrical rod of nickel is used as the oscillator, which traps the vibrational energy of axially-polarized surface-shear waves in the central part, where the diameter is slightly larger. A meander-line coil surrounding the oscillator with an air gap can cause and detect the resonant vibrations of the surface-shear waves via the piezomagnetic effect. The resonant frequency of the trapped-mode resonance is continuously measured to detect human immunoglobulin G (IgG). It decreased by 0.08% when a solution containing IgG was injected into the glass cell where the oscillator was placed alone. This oscillator is useful for fundamental studies of various biochemical reactions in a closed system in different environmental gases and different pressures.

Biosensing Techniques↗