Showing papers by "Nagoya University published in 2008"

The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants

Abstract: We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.

The Sixth Data Release of the Sloan Digital Sky Survey

Abstract: This paper describes the Sixth Data Release of the Sloan Digital Sky Survey. With this data release, the imaging of the northern Galactic cap is now complete. The survey contains images and parameters of roughly 287 million objects over 9583 deg(2), including scans over a large range of Galactic latitudes and longitudes. The survey also includes 1.27 million spectra of stars, galaxies, quasars, and blank sky ( for sky subtraction) selected over 7425 deg2. This release includes much more stellar spectroscopy than was available in previous data releases and also includes detailed estimates of stellar temperatures, gravities, and metallicities. The results of improved photometric calibration are now available, with uncertainties of roughly 1% in g, r, i, and z, and 2% in u, substantially better than the uncertainties in previous data releases. The spectra in this data release have improved wavelength and flux calibration, especially in the extreme blue and extreme red, leading to the qualitatively better determination of stellar types and radial velocities. The spectrophotometric fluxes are now tied to point-spread function magnitudes of stars rather than fiber magnitudes. This gives more robust results in the presence of seeing variations, but also implies a change in the spectrophotometric scale, which is now brighter by roughly 0.35 mag. Systematic errors in the velocity dispersions of galaxies have been fixed, and the results of two independent codes for determining spectral classifications and red-shifts are made available. Additional spectral outputs are made available, including calibrated spectra from individual 15 minute exposures and the sky spectrum subtracted from each exposure. We also quantify a recently recognized underestimation of the brightnesses of galaxies of large angular extent due to poor sky subtraction; the bias can exceed 0.2 mag for galaxies brighter than r = 14 mag.

Widespread translational inhibition by plant miRNAs and siRNAs.

Abstract: High complementarity between plant microRNAs (miRNAs) and their messenger RNA targets is thought to cause silencing, prevalently by endonucleolytic cleavage. We have isolated Arabidopsis mutants defective in miRNA action. Their analysis provides evidence that plant miRNA-guided silencing has a widespread translational inhibitory component that is genetically separable from endonucleolytic cleavage. We further show that the same is true of silencing mediated by small interfering RNA (siRNA) populations. Translational repression is effected in part by the ARGONAUTE proteins AGO1 and AGO10. It also requires the activity of the microtubule-severing enzyme katanin, implicating cytoskeleton dynamics in miRNA action, as recently suggested from animal studies. Also as in animals, the decapping component VARICOSE (VCS)/Ge-1 is required for translational repression by miRNAs, which suggests that the underlying mechanisms in the two kingdoms are related.

The Milky Way Tomography with SDSS. I. Stellar Number Density Distribution

Abstract: Using the photometric parallax method we estimate the distances to ~48 million stars detected by the Sloan Digital Sky Survey (SDSS) and map their three-dimensional number density distribution in the Galaxy. The currently available data sample the distance range from 100 pc to 20 kpc and cover 6500 deg2 of sky, mostly at high Galactic latitudes (|b| > 25). These stellar number density maps allow an investigation of the Galactic structure with no a priori assumptions about the functional form of its components. The data show strong evidence for a Galaxy consisting of an oblate halo, a disk component, and a number of localized overdensities. The number density distribution of stars as traced by M dwarfs in the solar neighborhood (D < 2 kpc) is well fit by two exponential disks (the thin and thick disk) with scale heights and lengths, bias corrected for an assumed 35% binary fraction, of H1 = 300 pc and L1 = 2600 pc, and H2 = 900 pc and L2 = 3600 pc, and local thick-to-thin disk density normalization ρthick(R☉)/ρthin(R☉) = 12% . We use the stars near main-sequence turnoff to measure the shape of the Galactic halo. We find a strong preference for oblate halo models, with best-fit axis ratio c/a = 0.64, ρH ∝ r−2.8 power-law profile, and the local halo-to-thin disk normalization of 0.5%. Based on a series of Monte Carlo simulations, we estimate the errors of derived model parameters not to be larger than ~20% for the disk scales and ~10% for the density normalization, with largest contributions to error coming from the uncertainty in calibration of the photometric parallax relation and poorly constrained binary fraction. While generally consistent with the above model, the measured density distribution shows a number of statistically significant localized deviations. In addition to known features, such as the Monoceros stream, we detect two overdensities in the thick disk region at cylindrical galactocentric radii and heights (R,Z) ~ (6.5,1.5) kpc and (R,Z) ~ (9.5,0.8) kpc and a remarkable density enhancement in the halo covering over 1000 deg2 of sky toward the constellation of Virgo, at distances of ~6-20 kpc. Compared to counts in a region symmetric with respect to the l = 0° line and with the same Galactic latitude, the Virgo overdensity is responsible for a factor of 2 number density excess and may be a nearby tidal stream or a low-surface brightness dwarf galaxy merging with the Milky Way. The u − g color distribution of stars associated with it implies metallicity lower than that of thick disk stars and consistent with the halo metallicity distribution. After removal of the resolved overdensities, the remaining data are consistent with a smooth density distribution; we detect no evidence of further unresolved clumpy substructure at scales ranging from ~50 pc in the disk to ~1-2 kpc in the halo.

The genome of the model beetle and pest Tribolium castaneum.

Abstract: Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short-germ development. Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.

Unconventional Pairing Originating from the Disconnected Fermi Surfaces of Superconducting LaFeAsO 1-x F x

Abstract: For a newly discovered iron-based high ${T}_{c}$ superconductor ${\mathrm{LaFeAsO}}_{1\ensuremath{-}x}{\mathrm{F}}_{x}$, we have constructed a minimal model, where inclusion of all five Fe $d$ bands is found to be necessary. The random-phase approximation is applied to the model to investigate the origin of superconductivity. We conclude that the multiple spin-fluctuation modes arising from the nesting across the disconnected Fermi surfaces realize an extended $s$-wave pairing, while $d$-wave pairing can also be another candidate.

Aspects of Immune Dysfunction in End-stage Renal Disease

Abstract: End-stage renal disease (ESRD) is associated with significantly increased morbidity and mortality resulting from cardiovascular disease (CVD) and infections, accounting for 50% and 20%, respectively, of the total mortality in ESRD patients. It is possible that these two complications are linked to alterations in the immune system in ESRD, as uremia is associated with a state of immune dysfunction characterized by immunodepression that contributes to the high prevalence of infections among these patients, as well as by immunoactivation resulting in inflammation that may contribute to CVD. This review describes disorders of the innate and adaptive immune systems in ESRD, underlining the specific role of ESRD-associated disturbances of Toll-like receptors. Finally, based on the emerging links between the alterations of immune system, CVD, and infections in ESRD patients, it emphasizes the potential role of the immune dysfunction in ESRD as an underlying cause for the high mortality in this patient population and the need for more studies in this area.

Class of viable modified f(R) gravities describing inflation and the onset of accelerated expansion

Abstract: A general approach to viable modified f(R) gravity is developed in both the Jordan and the Einstein frames. A class of exponential, realistic modified gravities is introduced and investigated with care. Special focus is made on step-class models, most promising from the phenomenological viewpoint and which provide a natural way to classify all viable modified gravities. One- and two-step models are explicitly considered, but the analysis is extensible to N-step models. Both inflation in the early universe and the onset of recent accelerated expansion arise in these models in a natural, unified way. Moreover, it is demonstrated that models in this category easily pass all local tests, including stability of spherical body solution, nonviolation of Newton's law, and generation of a very heavy positive mass for the additional scalar degree of freedom.

Traffic jams without bottlenecks—experimental evidence for the physical mechanism of the formation of a jam

Abstract: A traffic jam on a highway is a very familiar phenomenon. From the physical viewpoint, the system of vehicular flow is a non-equilibrium system of interacting particles (vehicles). The collective effect of the many-particle system induces the instability of a free flow state caused by the enhancement of fluctuations, and the transition to a jamming state occurs spontaneously if the average vehicle density exceeds a certain critical value. Thus, a bottleneck is only a trigger and not the essential origin of a traffic jam. In this paper, we present the first experimental evidence that the emergence of a traffic jam is a collective phenomenon like 'dynamical' phase transitions and pattern formation

Functional genomic screen reveals genes involved in lipid-droplet formation and utilization

Abstract: Eukaryotic cells store neutral lipids in cytoplasmic lipid droplets enclosed in a monolayer of phospholipids and associated proteins. These dynamic organelles serve as the principal reservoirs for storing cellular energy and for the building blocks for membrane lipids. Excessive lipid accumulation in cells is a central feature of obesity, diabetes and atherosclerosis, yet remarkably little is known about lipid-droplet cell biology. Here we show, by means of a genome-wide RNA interference (RNAi) screen in Drosophila S2 cells that about 1.5% of all genes function in lipid-droplet formation and regulation. The phenotypes of the gene knockdowns sorted into five distinct phenotypic classes. Genes encoding enzymes of phospholipid biosynthesis proved to be determinants of lipid-droplet size and number, suggesting that the phospholipid composition of the monolayer profoundly affects droplet morphology and lipid utilization. A subset of the Arf1-COPI vesicular transport proteins also regulated droplet morphology and lipid utilization, thereby identifying a previously unrecognized function for this machinery. These phenotypes are conserved in mammalian cells, suggesting that insights from these studies are likely to be central to our understanding of human diseases involving excessive lipid storage.

Gene silencing in cancer by histone H3 lysine 27 trimethylation independent of promoter DNA methylation

Abstract: Epigenetic silencing in cancer cells is mediated by at least two distinct histone modifications, polycomb-based histone H3 lysine 27 trimethylation (H3K27triM) and H3K9 dimethylation. The relationship between DNA hypermethylation and these histone modifications is not completely understood. Using chromatin immunoprecipitation microarrays (ChIP-chip) in prostate cancer cells compared to normal prostate, we found that up to 5% of promoters (16% CpG islands and 84% non-CpG islands) were enriched with H3K27triM. These genes were silenced specifically in prostate cancer, and those CpG islands affected showed low levels of DNA methylation. Downregulation of the EZH2 histone methyltransferase restored expression of the H3K27triM target genes alone or in synergy with histone deacetylase inhibition, without affecting promoter DNA methylation, and with no effect on the expression of genes silenced by DNA hypermethylation. These data establish EZH2-mediated H3K27triM as a mechanism of tumor-suppressor gene silencing in cancer that is potentially independent of promoter DNA methylation.

Mutation in triangulated categories and rigid Cohen–Macaulay modules

Abstract: We introduce the notion of mutation of n-cluster tilting subcategories in a triangulated category with Auslander–Reiten–Serre duality. Using this idea, we are able to obtain the complete classifications of rigid Cohen–Macaulay modules over certain Veronese subrings.

IL23 differentially regulates the Th1/Th17 balance in ulcerative colitis and Crohn’s disease

Abstract: Background: A novel T helper (Th) cell lineage, Th17, that exclusively produces the proinflammatory cytokine interleukin 17 (IL17) has been reported to play important roles in various inflammatory diseases. IL23 is also focused upon for its potential to promote Th17. Here, the roles of the IL23/IL17 axis in inflammatory bowel diseases such as ulcerative colitis (UC) and Crohn’s disease (CD) were investigated. Methods: Mucosal samples were obtained from surgically resected specimens (controls, n = 12; UC, n = 17; CD, n = 22). IL17 production by isolated peripheral blood (PB) and lamina propria (LP) CD4 + cells was examined. Quantitative PCR amplification was performed to determine the mRNA expression levels of IL17, interferon γ (IFNγ), IL23 receptor (IL23R) and retinoic acid-related orphan receptor γ (RORC) in LP CD4 + cells, and IL12 family members, such as IL12p40, IL12p35 and IL23p19, in whole mucosal specimens. The effects of exogenous IL23 on IL17 production by LP CD4 + cells were also examined. Results: IL17 production was higher in LP CD4 + cells than in PB. Significant IL17 mRNA upregulation in LP CD4 + cells was found in UC, while IFNγ was increased in CD. IL23R and RORC were upregulated in LP CD4 + cells isolated from both UC and CD. IL17 production was significantly increased by IL23 in LP CD4 + cells from UC but not CD. Upregulated IL23p19 mRNA expression was correlated with IL17 in UC and IFNγ in CD. Conclusions: IL23 may play important roles in controlling the differential Th1/Th17 balance in both UC and CD, although Th17 cells may exist in both diseases.

Resumming Cosmological Perturbations via the Lagrangian Picture: One-loop Results in Real Space and in Redshift Space

Abstract: We develop a new approach to study the nonlinear evolution in the large-scale structure of the Universe both in real space and in redshift space, extending the standard perturbation theory of gravitational instability. Infinite series of terms in standard Eulerian perturbation theory are resummed as a result of our starting from a Lagrangian description of perturbations. Delicate nonlinear effects on scales of the baryon acoustic oscillations are more accurately described by our method than the standard one. Our approach differs from other resummation techniques recently proposed, such as the renormalized perturbation theory, etc., in that we use simple techniques and thus resulting equations are undemanding to evaluate, and in that our approach is capable of quantifying the nonlinear effects in redshift space. The power spectrum and correlation function of our approach are in good agreement with numerical simulations in literature on scales of baryon acoustic oscillations. Especially, nonlinear effects on the baryon acoustic peak of the correlation function are accurately described both in real space and in redshift space. Our approach provides a unique opportunity to analytically investigate the nonlinear effects on baryon acoustic scales in observable redshift space, which is requisite in constraining the nature of dark energy, the curvature of the Universe, etc., by redshift surveys.

The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access.

Abstract: We analyzed global gene expression in Arabidopsis in response to various hormones and in related experiments as part of the AtGenExpress project. The experimental agents included seven basic phytohormones (auxin, cytokinin, gibberellin, brassinosteroid, abscisic acid, jasmonate and ethylene) and their inhibitors. In addition, gene expression was investigated in hormone-related mutants and during seed germination and sulfate starvation. Hormone-inducible genes were identified from the hormone response data. The effects of each hormone and the relevance of the gene lists were verified by comparing expression profiles for the hormone treatments and related experiments using Pearson's correlation coefficient. This approach was also used to analyze the relationships among expression profiles for hormone responses and those included in the AtGenExpress stress-response data set. The expected correlations were observed, indicating that this approach is useful to monitor the hormonal status in the stress-related samples. Global interactions among hormones-inducible genes were analyzed in a pairwise fashion, and several known and novel hormone interactions were detected. Genome-wide transcriptional gene-to-gene correlations, analyzed by hierarchical cluster analysis (HCA), indicated that our data set is useful for identification of clusters of co-expressed genes, and to predict the functions of unknown genes, even if a gene's function is not directly related to the experiments included in AtGenExpress. Our data are available online from AtGenExpressJapan; the results of genome-wide HCA are available from PRIMe. The data set presented here will be a versatile resource for future hormone studies, and constitutes a reference for genome-wide gene expression in Arabidopsis.

Crystal structure of squid rhodopsin

Abstract: Invertebrate phototransduction uses an inositol-1,4,5-trisphosphate signalling cascade in which photoactivated rhodopsin stimulates a Gq-type G protein, that is, a class of G protein that stimulates membrane-bound phospholipase Cβ. The same cascade is used by many G-protein-coupled receptors, indicating that invertebrate rhodopsin is a prototypical member. Here we report the crystal structure of squid (Todarodes pacificus) rhodopsin at 2.5 A resolution. Among seven transmembrane α-helices, helices V and VI extend into the cytoplasmic medium and, together with two cytoplasmic helices, they form a rigid protrusion from the membrane surface. This peculiar structure, which is not seen in bovine rhodopsin, seems to be crucial for the recognition of Gq-type G proteins. The retinal Schiff base forms a hydrogen bond to Asn 87 or Tyr 111; it is far from the putative counterion Glu 180. In the crystal, a tight association is formed between the amino-terminal polypeptides of neighbouring monomers; this intermembrane dimerization may be responsible for the organization of hexagonally packed microvillar membranes in the photoreceptor rhabdom. The rhodopsins found in the invertebrate eye are light-activated G-protein-coupled receptors, whose activity is coupled to Gq-type G-proteins. Midori Murakami and Tsutomu Kouyama now report the crystal structure of squid rhodopsin, at 2.5 A, in which a putative G-protein-binding site is resolved. The newly obtained structure could help explain one of the novel properties of the invertebrate eye, the ability to detect the direction of the polarization plane of visible light. Invertebrate rhodopsins are light-activated G-protein-coupled receptors, whose activity is coupled to Gq-type G-proteins. This paper reports the crystal structure of squid rhodopsin, at 2.5 A, in which a putative G-protein-binding site is resolved.

Arabidopsis CLV3 peptide directly binds CLV1 ectodomain.

Abstract: CLV1, which encodes a leucine-rich repeat receptor kinase, and CLV3, which encodes a secreted peptide, function in the same genetic pathway to maintain stem cell populations in Arabidopsis shoot apical meristem. Here, we show biochemical evidence, by ligand binding assay and photoaffinity labeling, that the CLV3 peptide directly binds the CLV1 ectodomain with a dissociation constant of 17.5 nM. The CLV1 ectodomain also interacts with the structurally related CLE peptides, with distinct affinities depending on the specific amino acid sequence. Our results provide direct evidence that CLV3 and CLV1 function as a ligand-receptor pair involved in stem cell maintenance.

Non-cell-autonomous control of vascular stem cell fate by a CLE peptide/receptor system

Abstract: Land plants evolved a long-distance transport system of water and nutrients composed of the xylem and phloem, both of which are generated from the procambium- and cambium-comprising vascular stem cells. However, little is known about the molecular mechanism of cell communication governing xylem–phloem patterning. Here, we show that a dodecapeptide (HEVHypSGHypNPISN; Hyp, 4-hydroxyproline), TDIF (tracheary element differentiation inhibitory factor), is secreted from the phloem and suppresses the differentiation of vascular stem cells into xylem cells through a leucine-rich repeat receptor-like kinase (LRR-RLK). TDIF binds in vitro specifically to the LRR-RLK, designated TDR (putative TDIF receptor), whose expression is restricted to procambial cells. However, the combined analysis of TDIF with a specific antibody and the expression profiles of the promoters of two genes encoding TDIF revealed that TDIF is synthesized mainly in, and secreted from, the phloem and its neighboring cells. The observation that TDIF is capable of promoting proliferation of procambial cells while suppressing xylem differentiation suggests that this small peptide functions as a phloem-derived, non-cell-autonomous signal that controls stem cell fate in the procambium. Our results indicate that we have discovered a cell communication system governing phloem–xylem cross-talk.

Neuroepithelial progenitors undergo LGN-dependent planar divisions to maintain self-renewability during mammalian neurogenesis

Abstract: Neuroepithelial progenitors undergo LGN-dependent planar divisions to maintain self-renewability during mammalian neurogenesis

Thyrotrophin in the pars tuberalis triggers photoperiodic response

Abstract: Molecular mechanisms regulating animal seasonal breeding in response to changing photoperiod are not well understood. Rapid induction of gene expression of thyroid-hormone-activating enzyme (type 2 deiodinase, DIO2) in the mediobasal hypothalamus (MBH) of the Japanese quail (Coturnix japonica) is the earliest event yet recorded in the photoperiodic signal transduction pathway. Here we show cascades of gene expression in the quail MBH associated with the initiation of photoinduced secretion of luteinizing hormone. We identified two waves of gene expression. The first was initiated about 14 h after dawn of the first long day and included increased thyrotrophin (TSH) beta-subunit expression in the pars tuberalis; the second occurred approximately 4 h later and included increased expression of DIO2. Intracerebroventricular (ICV) administration of TSH to short-day quail stimulated gonadal growth and expression of DIO2 which was shown to be mediated through a TSH receptor-cyclic AMP (cAMP) signalling pathway. Increased TSH in the pars tuberalis therefore seems to trigger long-day photoinduced seasonal breeding.

Intrinsic spin Hall effect and orbital Hall effect in 4 d and 5 d transition metals

Abstract: We study the intrinsic spin Hall conductivity (SHC) in various $5d$ transition metals (Ta, W, Re, Os, Ir, Pt, and Au) and $4d$ transition metals (Nb, Mo, Tc, Ru, Rh, Pd, and Ag) based on the Naval Research Laboratory tight-binding model, which enables us to perform quantitatively reliable analysis. In each metal, the obtained intrinsic SHC is independent of resistivity in the low resistive regime $(\ensuremath{\rho}l50\phantom{\rule{0.3em}{0ex}}\ensuremath{\mu}\ensuremath{\Omega}\phantom{\rule{0.2em}{0ex}}\mathrm{cm})$ whereas it decreases in proportion to ${\ensuremath{\rho}}^{\ensuremath{-}2}$ in the high resistive regime. In the low resistive regime, the SHC takes a large positive value in Pt and Pd, both of which have approximately nine $d$ electrons per ion $({n}_{d}=9)$. On the other hand, the SHC takes a large negative value in Ta, Nb, W, and Mo, where ${n}_{d}l5$. In transition metals, a conduction electron acquires the trajectory-dependent phase factor that originates from the atomic wave function. This phase factor, which is reminiscent of the Aharonov--Bohm phase, is the origin of the SHC in paramagnetic metals and that of the anomalous Hall conductivity in ferromagnetic metals. Furthermore, each transition metal shows huge and positive $d$-orbital Hall conductivity (OHC), independent of the strength of the spin-orbit interaction. Since the OHC is much larger than the SHC, it will be possible to realize an orbitronics device made of transition metals.

Assessing the dynamics of dissolved organic matter (DOM) in coastal environments by excitation emission matrix fluorescence and parallel factor analysis (EEM-PARAFAC)

Abstract: The distributions of fluorescent components in dissolved organic matter (DOM) from Ise Bay, Japan, were determined by excitation emission matrix (EEM) fluorescence spectroscopy combined with parallel factor analysis (PARAFAC). Three terrestrial humic-like, one marine humic-like, and three non-humic-like fluorescent components were identified by PARAFAC, and the environmental dynamics of individual fluorescent components in the bay area were evaluated. The observed linear relationships between salinity and abundance of two of the three humic-like components in the bay area indicate a terrestrial origin and conservative mixing behavior of these components. On the other hand, nonconservative mixing for the other terrestrial and the marine humic-like components was observed, indicating that the sources of these were other than solely riverine inputs. Thus, in addition to riverine sources, this terrestrial humic-like component may receive inputs from biogeochemical reworking of terrestrial DOM and/or particulate organic matter, while the most likely sources for the marine humic-like component are estuarine biological activity and/or microbial reworking of plankton-derived DOM. From the spatial distributions in the bay area as well as their relationships with salinity, two of the non-humic-like components were suggested to be of autochthonous estuarine origin and likely represent biologically labile components. Microbial degradation processes were suggested to be important factors driving the dynamics of another non-humic-like component. This study exemplifies the potential applicability of EEM-PARAFAC in studies of fluorescent DOM dynamics in estuaries.

Observation of a Resonancelike Structure in the π +- ψ ' Mass Distribution in Exclusive B→Kπ +- ψ ' Decays

Abstract: Reference EPFL-ARTICLE-154575doi:10.1103/PhysRevLett.100.142001View record in Web of Science Record created on 2010-11-05, modified on 2017-12-10

Regulation of Rice NADPH Oxidase by Binding of Rac GTPase to Its N-Terminal Extension

Abstract: Reactive oxygen species (ROS) produced by NADPH oxidase play critical roles in various cellular activities, including plant innate immunity response. In contrast with the large multiprotein NADPH oxidase complex of phagocytes, in plants, only the homologs of the catalytic subunit gp91phox and the cytosolic regulator small GTPase Rac are found. Plant homologs of the gp91phox subunit are known as Rboh (for respiratory burst oxidase homolog). Although numerous Rboh have been isolated in plants, the regulation of enzymatic activity remains unknown. All rboh genes identified to date possess a conserved N-terminal extension that contains two Ca2+ binding EF-hand motifs. Previously, we ascertained that a small GTPase Rac (Os Rac1) enhanced pathogen-associated molecular pattern–induced ROS production and resistance to pathogens in rice (Oryza sativa). In this study, using yeast two-hybrid assay, we found that interaction between Rac GTPases and the N-terminal extension is ubiquitous and that a substantial part of the N-terminal region of Rboh, including the two EF-hand motifs, is required for the interaction. The direct Rac–Rboh interaction was supported by further studies using in vitro pull-down assay, a nuclear magnetic resonance titration experiment, and in vivo fluorescence resonance energy transfer (FRET) microscopy. The FRET analysis also suggests that cytosolic Ca2+ concentration may regulate Rac–Rboh interaction in a dynamic manner. Furthermore, transient coexpression of Os Rac1 and rbohB enhanced ROS production in Nicotiana benthamiana, suggesting that direct Rac–Rboh interaction may activate NADPH oxidase activity in plants. Taken together, the results suggest that cytosolic Ca2+ concentration may modulate NADPH oxidase activity by regulating the interaction between Rac GTPase and Rboh.

Chiral HPLC for efficient resolution of enantiomers

Abstract: Resolution of racemic compounds is one of the potential ways of obtaining both enantiomers. Among several resolution techniques in the past few decades, direct enantioseparation by high-performance liquid chromatography (HPLC) has significantly advanced, and a large number of chiral stationary phases (CSPs) for HPLC have been developed using both chiral small molecules and polymers with chiral recognition abilities. In this tutorial review, after describing the brief history and general view of CSPs, special emphasis will be placed on the studies involving the development and application of polysaccharide-based CSPs in our group.

Single- and Double-Stranded Helical Polymers: Synthesis, Structures, and Functions

Abstract: Biological macromolecules, such as DNA and proteins, possess a unique and specific ordered structure, such as a right-handed double helix or a single alpha-helix. Those structures direct the sophisticated functions of these molecules in living systems. Inspired by biological helices, chemists have worked to synthesize polymers with controlled helicity, not only to mimic the biological helices but also to realize their functions. Although numerous synthetic polymers that fold into a single-handed helix have been reported, double-stranded helical polymers are almost unavailable except for a few oligomers. In addition, the exact structures of most helical polymers remain obscure. Therefore, the development of a conceptually new method for constructing double-stranded helical polymers and a reliable method for unambiguously determining the helical structures are important and urgent challenges in this area. In this Account, we describe the recent advances in the synthesis, structures, and functions of single- and double-stranded helical polymers from our group and others and provide a brief historical overview of synthetic helical polymers. We found unique macromolecules that fold into a preferred-handed helix through noncovalent bonding interactions with specific chiral guests. During the noncovalent helicity induction process, these guest molecules significantly amplified chirality in a dynamic helical polymer. During the intensive exploration of the helicity induction mechanism, we observed an unusual macromolecular helical memory in dynamic helical polymers. Furthermore, we found that rigid-rod helical poly(phenylacetylene)s and poly(phenyl isocyanide)s showing a cholesteric or smectic liquid crystal self-assemble to form two-dimensional crystals with a controlled helical conformation on solid substrates upon exposure to solvent vapors. We visualized their helical structures including the helical pitch and handedness by atomic force microscopy (AFM). We propose a modular strategy to construct complementary double helices by employing chiral amidinium-carboxylate salt bridges with m-terphenyl backbones. The double-stranded helical structures were characterized by circular dichroism in solution and X-ray diffraction of the crystals or the direct AFM observations. Serendipitously, we found that oligoresorcinols self-assemble into well-defined double helices resulting from interstrand aromatic stacking in water. These oligoresorcinols bound cyclic and linear oligosaccharides in water to form rotaxanes and hetero-double helices, respectively. The examples presented in this Account demonstrate the notable progress in the synthesis and structural determination of helical polymers including single- and double-stranded helices. Not only do we better understand the principle underlying the generation of helical conformations, but we have also used the knowledge of these unique helical structures to develop novel helical polymers with specific functions.

Genetic approaches to crop improvement: responding to environmental and population changes.

Abstract: Crop production is threatened by global climate change, and recent demands for crops to produce bio-fuels have started to affect the worldwide supply of some of the most important foods. How can we support a growing human population in such circumstances? One potential solution is the improvement of crops to increase yield from both irrigated and non-irrigated lands, and to create novel varieties that are more tolerant to environmental stresses. Recent progress has been made in the isolation and functional analyses of genes controlling yield and tolerance to abiotic stresses. In addition, promising new methods are being developed for identifying additional genes and variants of interest and putting these to practical use in crop improvement.