Biomedical subjects

Naoki Kishimoto

Publications and source records attributed to Naoki Kishimoto.

At least 19 recordsLinked to original sources

PubMed2006

Sequential regulation of gibberellin, brassinosteroid, and jasmonic acid biosynthesis occurs in rice coleoptiles to control the transcript levels of anti-microbial thionin genes.

Transcripts of thionin genes encoding antimicrobial peptides were present at a high level in rice coleoptiles just after germination, and decreased to an undetectable level after about 3 d, but this decline was suppressed by co-treatment with gibberellic acid (GA(3)) and brassinolide (BL). The temporal expression patterns of key enzyme genes for the biosyntheses of gibberellins (GAs) and brassinosteroids (BRs) were correlated with the fluctuation of thionin mRNAs. Jasmonic acid (JA) replaced the effect of GA3 and BL, and its change in endogenous level was parallel to that of the thionin genes. These results strongly suggest that thionin gene expression was positively regulated by JA, whose endogenous level was synergistically regulated by GAs and BRs. In contrast, thionin gene expression in etiolated seedlings remained high while the endogenous level of JA was low, suggesting the presence of another signaling pathway in the dark to maintain the thionin level.

Antimicrobial Cationic Peptides↗

PubMed2006

Anisotropic interaction and stereoreactivity in a chemi-ionization process of OCS by collision with He*(2(3)S) metastable atoms.

Ionic-state-resolved collision energy dependence of Penning ionization cross sections for OCS with He*(2(3)S) metastable atoms was measured in a wide collision energy range from 20 to 350 meV. Anisotropic interaction potential for the OCS-He*(2(3)S) system was obtained by comparison of the experimental data with classical trajectory simulations. It has been found that attractive potential wells around the O and S atoms are clearly different in their directions. Around the O atom, the collinear approach is preferred (the well depth is ca. 90 meV), while the perpendicular approach is favored around the S atom (the well depth is ca. 40 meV). On the basis of the optimized potential energy surface and theoretical simulations, stereo reactivity around the O and S atoms was also investigated. The results were discussed in terms of anisotropy of the potential energy surface and the electron density distribution of molecular orbitals to be ionized.

Journal Article↗

PubMed2006

Collision-energy-resolved Penning ionization electron spectroscopy of thiazole and benzothiazole: study of ionic states and anisotropic interactions between a metastable He(23S) atom and hetero cyclic compounds.

Anisotropic interactions between a metastable He(2(3)S) atom and aromatic heterocyclic compounds (thiazole and benzothiazole) as well as their electronic structures were studied by means of collision-energy/electron-energy resolved two-dimensional Penning ionization electron spectroscopy combined with ab initio molecular orbital calculations. Different collision-energy dependence of partial ionization cross sections (CEDPICS) were clearly observed for different ionic states depending on anisotropic extents of molecular orbitals from which an electron is removed. It was found that thiazole and benzothiazole most strongly attract a He(2(3)S) atom around the region where the nitrogen lone pair orbital extends. For another heteroatom, sulfur, it is relatively weak, but a certain attractive interaction was found for the directions perpendicular to the molecular plane. Benzothiazole was shown to widely attract a He(2(3)S) atom in the out-of-plane directions, since the benzene moiety showed a deeper potential well than the five-membered ring. Assignments of the ionic states including shake-up states were also discussed from observed CEDPICS and ab initio molecular orbital calculations. In particular, for the satellite bands, a negative collision energy dependence of the band intensity was well supported by a configuration-interaction calculation that assigns the satellite bands to be the ionization from pi orbitals accompanying pi-pi or n-pi excitations.

Benzothiazoles↗

PubMed2006

Transcriptomic analysis indicates putative metabolic changes caused by manipulation of phosphorus availability in rice leaves.

Plants have developed several strategies for coping with phosphorus (P) deficiency. However, the details of the regulation of gene expression of adaptations to low P are still unclear. Using a cDNA microarray, transcriptomic analyses were carried out of the rice genes regulated by P deficiency and P re-supply to P-deficient plants. The OsPI1 gene, which was isolated as the most significant up-regulated gene under -P conditions, was also the most significant down-regulated gene following P re-supply. Many starch metabolism-related genes, as well as several genes for P(i)-liberating enzymes, were up-regulated by -P treatment, suggesting a homeostatic contribution to the P(i) concentration in leaf tissues. mRNAs for glucanases were also induced by P re-supply: these are suspected to play a role in loosening the cell wall compounds. Most of the genes up-regulated by -P treatment were down-regulated by P re-supply, suggesting that their responses were specific to -P conditions. Conversely, the number of genes up-regulated by P re-supply was also larger following P re-supply than in the -P condition. It is proposed that the genes up-regulated by P re-supply play an important role in P acquisition by P-deficient plants.

Gene Expression Profiling↗

PubMed2006

Probing anisotropic interaction potentials of unsaturated hydrocarbons with He*(2 3S) metastable atom: attractive-site preference of sigma-direction in C2H2 and pi-direction in C2H4.

State-resolved collision energy dependence of Penning ionization cross sections of acetylene (C2H2) and ethylene (C2H4) with He*(2 3S) metastable atoms was observed in a wide collision energy range from 20 to 350 meV. A recently developed discharge nozzle source with a liquid N2 circulator was employed for the measurements in the low-energy range from 20 to 80 meV. Based on classical trajectory calculations for the energy dependence of the partial ionization cross sections, anisotropic potential energy surfaces for the present systems were obtained by optimizing ab initio model potentials for the chemically related systems Li+C2H2 and C2H4. In the case of C2H2, the global minimum was found to be located around the H atom along the molecular axis with a well depth of 48 meV (ca. 1.1 kcal/mol). On the other hand, a dominant attractive well with a depth of 62 meV (ca. 1.4 kcal/mol) was found in the piCC electron region of C2H4. These findings were discussed in connection with orbital interactions between molecular orbitals of the target molecules and atomic orbitals of the metastable atom. It is concluded that sigma-type unoccupied molecular orbitals of C2H2 and a piCC-type highest occupied molecular orbital of C2H4 play a significant role for the attractive-site preference of sigma direction in C2H2 and pi direction in C2H4, respectively.

Journal Article↗

PubMed2006

Collision-energy-resolved penning ionization electron spectroscopy of phenylacetylene and diphenylacetylene by collision with He*(2(3)s) metastable atoms.

Penning ionization of phenylacetylene and diphenylacetylene upon collision with metastable He*(2(3)S) atoms was studied by collision-energy-/electron-energy-resolved two-dimensional Penning ionization electron spectroscopy (2D-PIES). On the basis of the collision energy dependence of partial ionization cross-sections (CEDPICS) obtained from 2D-PIES as well as ab initio molecular orbital calculations for the approach of a metastable atom to the target molecule, anisotropy of interaction between the target molecule and He*(2(3)S) was investigated. For the calculations of interaction potential, a Li(2(2)S) atom was used in place of He*(2(3)S) metastable atom because of its well-known interaction behavior with various targets. The results indicate that attractive potentials localize in the pi regions of the phenyl groups as well as in the pi-conjugated regions of the acetylene group. Although similar attractive interactions were also found by the observation of CEDPICS for ionization of all pi MOs localized at the C[triple bond]C bond, the in-plane regions have repulsive potentials. Rotation of the phenyl groups about the C[triple bond]C bond can be observed for diphenylacetylene because of a low torsion barrier. So the examination of measured PIES was performed taking into consideration the change of ionization energies for conjugated molecular orbitals.

Journal Article↗

PubMed2006

Biosynthesis and secretion of mugineic acid family phytosiderophores in zinc-deficient barley.

Mugineic acid family phytosiderophores (MAs) are metal chelators that are produced in graminaceous plants in response to iron (Fe) deficiency, but current evidence regarding secretion of MAs during zinc (Zn) deficiency is contradictory. Our studies using HPLC analysis showed that Zn deficiency induces the synthesis and secretion of MAs in barley plants. The levels of the HvNAS1, HvNAAT-A, HvNAAT-B, HvIDS2 and HvIDS3 transcripts, which encode the enzymes involved in the synthesis of MAs, were increased in Zn-deficient roots. Studies of the genes involved in the methionine cycle using microarray analysis showed that the transcripts of these genes were increased in both Zn-deficient and Fe-deficient barley roots, probably allowing the plant to meet its demand for methionine, a precursor in the synthesis of MAs. In addition, HvNAAT-B transcripts were detected in Zn-deficient shoots, but not in those that were deficient in Fe. Increased synthesis of MAs in Zn-deficient barley was not due to a deficiency of Fe, because Zn-deficient barley accumulated more Fe than did the control plants, ferritin transcripts were increased in Zn-deficient plants, and Zn deficiency promoted Fe transport from root to shoot. Moreover, analysis using the positron-emitting tracer imaging system (PETIS) confirmed that more 62Zn(II)-MAs than 62Zn2+ were absorbed by the roots of Zn-deficient barley plants. These data suggest that the increased biosynthesis and secretion of MAs arising from a shortage of Zn are not due to an induced Fe deficiency, and that secreted MAs are effective in absorbing Zn from the soil.

Azetidinecarboxylic Acid↗

PubMed2005

Probing the shape and stereochemistry of molecular orbitals in locally flexible aromatic chains: a penning ionization electron spectroscopy and Green's function study of the electronic structure of biphenyl.

We report on the results of an exhaustive study of the interplay between the valence electronic structure, the topology and reactivity of orbitals, and the molecular structure of biphenyl by means of Penning ionization electron spectroscopy in the gas phase upon collision with metastable He*(2(3)S) atoms. The measurements are compared with one-particle Green's function calculations of one-electron and shake-up valence ionization spectra employing the third-order algebraic diagrammatic construction scheme [ADC(3)]. Penning ionization intensities are also analyzed by means of the exterior electron-density model and comparison with photoelectron spectra: in contrast with the lines originating from sigma orbitals, ionization lines belonging to the pi-band system have large Penning ionization cross sections due to their greater extent outside the molecular van der Waals surface. The involved chemi-ionization processes are further experimentally investigated using collision-energy-resolved Penning ionization electron spectroscopy. The cross sections of pi-ionization bands exhibit a markedly negative collision-energy dependence and indicate that the interaction potential that prevails between the molecule and the He*(2(3)S) atom is strongly attractive in the pi-orbital region. On the other hand, the partial ionization cross sections pertaining to sigma-ionization channels are characterized by more limited collision-energy dependencies, as a consequence of rather repulsive interactions within the sigma-orbital region. A comparison of ADC(3) simulations with the Penning ionization electron spectra and UV photoelectron spectra measured by Kubota et al. [Chem. Phys. Lett. 1980, 74, 409] on thin films of biphenyl deposited at 170 and 109 K on copper demonstrates that biphenyl molecules lying at the surface of polycrystalline layers adopt predominantly a planar configuration, whereas within an amorphous sample most molecules have twisted structures similar to those prevailing in the gas phase.

Journal Article↗

PubMed2005

Development of a cooled He*(23S) beam source for measurements of state-resolved collision energy dependence of Penning ionization cross sections: Evidence for a stereospecific attractive well around methyl group in CH3CN.

A low-temperature discharge nozzle source with a liquid-N(2) circulator for He*(2(3)S) metastable atoms has been developed in order to obtain the state-resolved collision energy dependence of Penning ionization cross sections in a low collision energy range from 20 to 80 meV. By controlling the discharge condition, we have made it possible to measure the collision energy dependence of partial ionization cross sections (CEDPICS) for a well-studied system of CH(3)CN+He*(2(3)S) in a wide energy range from 20 to 350 meV. The anisotropic interaction potential energy surface for the present system was obtained starting from an ab initio model potential via an optimization procedure based on classical trajectory calculations for the observed CEDPICS. A dominant attractive well depth was found to be 423 meV (ca. 10 kcal/mol) at a distance of 3.20 A from the center of mass of CH(3)CN in the N-atom side along the CCN axis. In addition, a weak attractive well (ca. 0.9 kcal/mol) surrounding the methyl group (-CH(3)) has been found and ascribed to the interaction between an unoccupied molecular orbital of CH(3)CN and 2s atomic orbital of He*(2(3)S).

Journal Article↗

PubMed2005

Collision-energy-resolved penning ionization electron spectroscopy of HCOOH, CH3COOH, and HCOOCH3 by collision with He*(2(3)S) metastable atoms.

Penning ionization of formic acid (HCOOH), acetic acid (CH3COOH), and methyl formate (HCOOCH3) upon collision with metastable He*(2(3)S) atoms was studied by collision-energy/electron-energy-resolved two-dimensional Penning ionization electron spectroscopy (2D-PIES). Anisotropy of interaction between the target molecule and He*(2(3)S) was investigated based on the collision energy dependence of partial ionization cross sections (CEDPICS) obtained from 2D-PIES as well as ab initio molecular orbital calculations for the access of a metastable atom to the target molecule. For the interaction potential calculations, a Li atom was used in place of He*(2(3)S) metastable atom because of its well-known similarity in interaction with targets. The results indicate that in the studied collision energy range the attractive potential localizes around the oxygen atoms and that the potential well at the carbonyl oxygen atom is at least twice as much as that at the hydroxyl oxygen. Moreover we can notice that attractive potential is highly anisotropic. Repulsive interactions can be found around carbon atoms and the methyl group.

Journal Article↗

PubMed2005

Penning ionization electron spectroscopy of C6H6 by collision with He*(2 3 S) metastable atoms and classical trajectory calculations: optimization of ab initio model potentials.

The potential energy surface of benzene (C(6)H(6)) with a He*(2(3)S) atom was obtained by comparison of experimental data in collision-energy-resolved two-dimensional Penning ionization electron spectroscopy with classical trajectory calculations. The ab initio model interaction potentials for C(6)H(6)+He*(2(3)S) were successfully optimized by the overlap expansion method; the model potentials were effectively modified by correction terms proportional to the overlap integrals between orbitals of the interacting system, C(6)H(6) and He*(2(3)S). Classical trajectory calculations with optimized potentials gave excellent agreement with the observed collision-energy dependence of partial ionization cross sections. Important contributions to corrections were found to be due to interactions between unoccupied molecular orbitals and the He*2s orbital. A C(6)H(6) molecule attracts a He*(2(3)S) atom widely at the region where pi electrons distribute, and the interaction of -80 meV (ca. -1.8 kcal/mol) just cover the carbon hexagon. The binding energy of a C(6)H(6) molecule and a He* atom was 107 meV at a distance of 2.40 A on the sixfold axis from the center of a C(6)H(6) molecule, which is similar to that of C(6)H(6)+Li and is much larger than those of the C(6)H(6)+[He,Ne,Ar] systems.

Journal Article↗

PubMed2004

Collision-energy-resolved Penning ionization electron spectroscopy of bromomethanes (CH3Br, CH2Br2, and CHBr3) by collision with He*(2(3)S) metastable atoms.

Ionization of bromomethanes (CH3Br, CH2Br2, and CHBr3) upon collision with metastable He*(2(3)S) atoms has been studied by means of collision-energy-resolved Penning ionization electron spectroscopy. Lone-pair (nBr) orbitals of Br4p characters have larger ionization cross sections than sigma(C-Br) orbitals. The collision-energy dependence of the partial ionization cross sections shows that the interaction potential between the molecule and the He*(2(3)S) atom is highly anisotropic around CH3Br or CH2Br2, while isotropic attractive interactions are found for CHBr3. Bands observed at electron energies of approximately 2 eV in the He*(2(3)S) Penning ionization electron spectra (PIES) of CH2Br2 and CHBr3 have no counterpart in ultraviolet (He I) photoionization spectra and theoretical (third-order algebraic diagrammatic construction) one-electron and shake-up ionization spectra. Energy analysis of the processes involved demonstrates that these bands and further bands overlapping with sigma(C-Br) or piCH2 levels are related to autoionization of dissociating (He+ - Br-) pairs. Similarly, a band at an electron energy of approximately 1 eV in the He*(2(3)S) PIES spectra of CH3Br has been ascribed to autoionizing Br** atoms released by dissociation of (unidentified) excited states of the target molecule. A further autoionization (S) band can be discerned at approximately 1 eV below the lone-pair nBr bands in the He*(2(3)S) PIES spectrum of CHBr3. This band has been ascribed to the decay of autoionizing Rydberg states of the target molecule (M**) into vibrationally excited states of the molecular ion. It was found that for this transition, the interaction potential that prevails in the entrance channel is merely attractive.

Journal Article↗

PubMed2004

Collision-energy-resolved Penning ionization electron spectroscopy of p-benzoquinone: study of electronic structure and anisotropic interaction with He(*)(2 (3)S) metastable atoms.

Collision energy dependence of partial ionization cross sections (CEDPICS) of p-benzoquinone with He(*)(2 (3)S) metastable atoms indicates that interaction potentials between p-benzoquinone and He(*)(2 (3)S) are highly anisotropic in the studied collision energy range (100-250 meV). Attractive interactions were found around the C==O groups for in-plane and out-of-plane directions, while repulsive interactions were found around CH bonds and the benzenoid ring. Assignment of the first four ionic states of p-benzoquinone and an analogous methyl-substituted compound was examined with CEDPICS and anisotropic distributions of the corresponding two nonbonding oxygen orbitals (n(O) (+),n(O) (-)) and two pi(CC) orbitals (pi(CC) (+),pi(CC) (-)). An extra band that shows negative CEDPICS was observed at ca. 7.2 eV in Penning ionization electron spectrum.

Journal Article↗

PubMed2004

An overlap expansion method for improving ab initio model potentials: anisotropic intermolecular potentials of N2, CO, and C2H2 with He*(2(3)S).

An overlap expansion method is proposed for improving ab initio model potentials. Correction terms are expanded in terms of overlap integrals between orbitals of the interacting system. The method is used to improve ab initio model potentials for N2+He*(2(3)S), CO+He*(2(3)S), and C2H2+He*(2(3)S). Physical meanings of the optimization are elucidated in terms of target orbitals. Correction terms are found to be dominated by the components of HOMO, LUMO, next-HOMO, and next-LUMO on the target molecule. The present overlap expansion method using a limited number of correction terms related to frontier orbitals provides an efficient and intuitive approach for construction of highly anisotropic intermolecular interaction potentials.

Journal Article↗

PubMed2004

The Rice PIPELINE: a unification tool for plant functional genomics.

The Rice Genome Research Project in Japan performs genome sequencing and comprehensive expression profiling, constructs genetic and physical maps, collects full-length cDNAs and generates mutant lines, all aimed at improving the breeding of the rice plant as a food source. The National Institute of Agrobiological Sciences in Tsukuba, Japan, has accumulated numerous rice biological resources and has already successfully produced a high-quality genome sequence, a high-density genetic map with 3000 markers, 30,000 full-length cDNAs, over 700 expression profiles with a 9000 cDNA microarray and 15,000 flanking sequences with Tos17 insertions in about 3765 mutant lines from about 50,000 transposon insertion lines. These resources are available in the public domain. A new unification tool for functional genomics, called Rice PIPELINE, has also been developed for the dynamic collection and compilation of genomics data (genome sequences, full-length cDNAs, gene expression profiles, mutant lines, cis elements) from various databases. The mission of Rice PIPELINE is to provide a unique scientific resource that pools publicly available rice genomic data for search by clone sequence, clone name, GenBank accession number, or keyword. The web-based form of Rice PIPELINE is available at http://cdna01.dna.affrc.go.jp/PIPE/.

Computational Biology↗

PubMed2004

The virescent-2 mutation inhibits translation of plastid transcripts for the plastid genetic system at an early stage of chloroplast differentiation.

The rice virescent-2 mutant (v(2)) is temperature conditional and develops chlorotic, chloroplast-deficient leaves at the restrictive temperature. In the v(2) mutant, plastid-encoded proteins involved in photosynthesis and plastid transcriptional regulation were not detectable at any time during chloroplast differentiation. However, the plastid transcripts for these two classes of proteins behaved differently in the mutant, with those for the plastid transcription/translation apparatus accumulating to wild-type levels and those for photosynthetic apparatus being suppressed. Polysome analysis showed that translation of the plastid transcripts encoding the plastid transcription/translation apparatus was blocked at an early stage of chloroplast differentiation. Accumulation of transcripts of nuclear-encoded photosynthetic genes, such as cab and rbcS, was strongly suppressed in the mutant at later stages of chloroplast differentiation, whereas transcripts of genes for the plastid transcription apparatus, such as OsRpoTp and OsSIG2A, accumulated to abnormally high levels at these stages. These results suggest that activation of the plastid translation machinery at an early stage of chloroplast differentiation is important for triggering the transmission of information about plastid developmental state to the nucleus, which in turn is required for the induction of nuclear-encoded chloroplast proteins at later stages of chloroplast differentiation.

Cell Differentiation↗

PubMed2004

cDNA microarray analysis of rice anther genes under chilling stress at the microsporogenesis stage revealed two genes with DNA transposon Castaway in the 5'-flanking region.

Rice is most chilling sensitive at the onset of microspore release. Chilling treatment at this stage causes male sterility. The gene expression profile during the microspore development process under chilling stress was revealed using a microarray that included 8,987 rice cDNAs. As many as 160 cDNAs were up- or down-regulated by chilling during the microspore release stage. RT-PCR analysis of 5 genes confirmed the microarray results. We identified 3 novel genes whose expression levels were remarkably changed by chilling in rice anther. A new cis element that includes a DNA transposon Castaway sequence was found in the 5' upstream region of two genes which were conspicuously down-regulated by chilling temperatures in rice anther.

5' Flanking Region↗

PubMed2003

Genomics approach to abscisic acid- and gibberellin-responsive genes in rice.

We used an 8987-EST collection to construct a cDNA microarray system with various genomics information (full-length cDNA, expression profile, high accuracy genome sequence, phenotype, genetic map, and physical map) in rice. This array was used as a probe to hybridize target RNAs prepared from normally grown callus of rice and from callus treated for 6 hr or 3 days with the hormones abscisic acid (ABA) or gibberellin (GA). We identified 509 clones, including many clones that had never been annotated as ABA-or GA-responsive. These genes included not only ABA- or GA-responsive genes but also genes responsive to other physiological conditions such as pathogen infection, heat shock, and metal ion stress. Comparison of ABA- and GA-responsive genes revealed antagonistic regulation for these genes by both hormones except for one defense-related gene, thionin. The gene for thionin was up-regulated by both hormone treatments for 3 days. The upstream regions of all the genes that were regulated by both hormones had cis-elements for ABA and GA response. We performed a clustering analysis of genes regulated by both hormones and various expression profiles that showed three notable clusters (seed tissues, low temperature and sugar starvation, and thionin-gene related). A comparison of the cis-elements for hormone response genes between rice and Arabidopsis thaliana, we identified cis-elements for dehydration-stress response or for expression of amylase gene as Arabidopsis gene-specific or rice gene-specific, respectively.

Abscisic Acid↗