Transcriptomic analysis of developing seeds in a wheat (Triticum aestivum L.) mutant RSD32 with reduced seed dormancy.

Seed dormancy, a major factor regulating pre-harvest sprouting, can severely hinder wheat cultivation. Reduced Seed Dormancy 32 (RSD32), a wheat (Triticum aestivum L.) mutant with reduced seed dormancy, is derived from the pre-harvest sprouting tolerant cultivar, 'Norin61'. RSD32 is regulated by a single recessive gene and mutant phenotype expressed in a seed-specific manner. Gene expressions in embryos of 'Norin61' and RSD32 were compared using RNA sequencing (RNA-seq) analysis at different developmental stages of 20, 30, and 40 days after pollination (DAP). Numbers of up-regulated genes in RSD32 are equivalent in all developmental stages. However, down-regulated genes in RSD32 are more numerous on DAP20 and DAP30 than on DAP40. In central components affecting the circadian clock, homologues to the morning-expressed genes are expressed at lower levels in RSD32. However, higher expressions of homologues acting as evening-expressed genes are observed in RSD32. Homologues of Ca2+ signaling pathway related genes are specifically expressed on DAP20 in 'Norin61'. Lower expression is shown in RSD32. These results suggest that RSD32 mutation expresses on DAP20 and earlier seed developmental stages and suggest that circadian clock regulation and Ca2+ signaling pathway are involved in the regulation of wheat seed dormancy.

LARGE GRAIN Encodes a Putative RNA-Binding Protein that Regulates Spikelet Hull Length in Rice.

Grain size is a key determiner of grain weight, one of the yield components in rice (Oryza sativa). Therefore, to increase grain yield, it is important to elucidate the detailed mechanisms regulating grain size. The Large grain (Lgg) mutant, found in the nonautonomous DNA-based active rice transposon1 (nDart1)-tagged lines of Koshihikari, is caused by a truncated nDart1-3 and 355 bp deletion in the 5' untranslated region of LGG, which encodes a putative RNA-binding protein, through transposon display and cosegregation analysis between grain length and LGG genotype in F2 and F3. Clustered regularly interspaced short palindromic repeats/CRISPR-associated 9-mediated knockout and overexpression of LGG led to longer and shorter grains than wild type, respectively, showing that LGG regulates spikelet hull length. Expression of LGG was highest in the 0.6-mm-long young panicle and gradually decreased as the panicle elongated. LGG was also expressed in roots and leaves. These results show that LGG functions at the very early stage of panicle development. Longitudinal cell numbers of spikelet hulls of Lgg, knockout and overexpressed plants were significantly different from those of the wild type, suggesting that LGG might regulate longitudinal cell proliferation in the spikelet hull. RNA-Seq analysis of 1-mm-long young panicles from LGG knockout and overexpressing plants revealed that the expressions of many cell cycle-related genes were reduced in knockout plants relative to LGG-overexpressing plants and wild type, whereas some genes for cell proliferation were highly expressed in knockout plants. Taken together, these results suggest that LGG might be a regulator of cell cycle and cell division in the rice spikelet hull.

Biopsy of recurrent nasolacrimal duct obstruction using sheath-guided dacryoendoscopy.

PURPOSE: The purpose of this article is to present a novel technique, as well the histopathological findings, of dacryoendoscopic guided nasolacrimal duct (NLD) biopsy for recurrent nasolacrimal duct obstruction (NLDO). METHODS: This study involved subjects with recurrent NLDO. Direct endoscopic probing or sheath-guided endoscopic probing was used for the initial intubation in all treated eyes, and the stent had been removed at between 2 and 11 months (mean 3.5 months) post-intubation with dacryoendoscopic confirmation of patency and mucosal regeneration. Biopsy specimens were obtained by scraping the recurrent lesion by sheath advancement. Histopathological examination and immunohistochemical (IHC) staining were performed. RESULTS: In five patients (two males and three females, mean age: 71.2 ± 5.6 years [range: 61-78 years]) with recurrent NLDO, biopsy specimens were obtained from six ducts of six eyes, and stratified epithelium and a mixed inflammatory cell infiltrates were identified. IHC staining was positive for cytokeratin (CK)4 and CK13, and negative for paired box protein Pax-6. CONCLUSIONS: This novel technique enabled a minimally invasive biopsy of the NLD to be obtained, and IHC staining indicated the presence of mucus epithelium, thus suggesting squamous metaplasia of the usual respiratory epithelium which likely occurs secondary to chronic inflammation.

Mechanistic Study of Highly Efficient Direct 1,2-Carboboration of Alkynes with 9-Borafluorenes.

We recently reported a new one-pot transformation of alkynes into 9,10-diarylphenanthrene derivatives, which proceeds through efficient catalyst-free 1,2-carboboration of alkynes with 9-chloro-9-borafluorene (1Cl ), which yields a chlorodibenzoborepin, followed by oxidative deborylation/C-C coupling of the resultant chlorodibenzoborepin. Herein, based on new experimental observations for the catalyst-free 1,2-carboboration by using diphenylacetylenes and 1Br or 1OTf as well as results from theoretical investigations, we show how the substituent on the boron atom of 9-borafluorene affects the reactivity toward alkynes. Kinetic studies indicated that the 1,2-carboboration of diphenylacetylene with the borafluorenes can be described as a second-order reaction. The reaction rates became larger with the increase in the acceptor numbers of the borafluorenes (1Br >1OTf >1Cl ), which was evaluated by the Gutmann-Beckett method based on a Lewis acid/base complexation in solution. Interestingly, thermodynamic parameters obtained experimentally indicated that the term of activation entropy, rather than the term of activation enthalpy, largely contributes to the reaction rate. This experimental result was also supported by DFT calculations. Overall, among the borafluorenes examined, 1Br exhibited the highest reactivity toward a wide variety of substituted diarylacetylenes. Similar to the case of chlorodibenzoborepin, when the dibenzoborepin obtained from 1Br or 1OTf was oxidized by using FeCl3 , an efficient deborylation/C-C coupling took place to give the corresponding 9,10-diarylphenanthrene derivatives in high yields.

Formation of an Isolable Divinylborinium Ion through Twofold 1,2-Carboboration between a Diarylborinium Ion and Diphenylacetylene.

Borinium ions, that is, two-coordinate boron cations, are the most electron-deficient isolable boron compounds. As borinium ions have only four formal valence electrons on boron, they should show a strong tendency to accept electron pairs on the boron atom to fill its valence shell. Thus chemical reactions of borinium ions are expected to give products in which the coordination number of boron is increased from two to three or four. However, contrary to this expectation, we found that the dimesitylborinium ion (Mes2 B+ ) undergoes twofold 1,2-carboboration reactions with two equivalents of diphenylacetylene to yield an unprecedented borinium ion (1+ ) with two substituted vinyl groups on the boron center. NMR spectroscopy and X-ray diffraction analysis of 1+ , together with electronic-structure calculations, revealed that the positive charge is delocalized over the entire π-conjugated system. The fact that the chemical transformation of a borinium ion gives rise to a different borinium ion without a change in the coordination number is remarkable and should provide new insight into the chemistry of the Group 13 elements.

Multicomponent Molecular Puzzles for Photofunction Design: Emission Color Variation in Lewis Acid-Base Pair Crystals Coupled with Guest-to-Host Charge Transfer Excitation.

Simple yet ubiquitous multimolecular assembly systems with color-tunable emissions are realized by cooperative electron donor-acceptor interactions, such as the boron-nitrogen (B-N) dative bond as a Lewis acid-base pair and charge transfer (CT) interactions. These are ternary-component systems consisting of a naphthalenediimide derivative (NDI), tris(pentafluorophenyl)borane (TPFB), and aromatic molecules (guest) with an NDI:TPFB:guest ratio of 1:2:2. The crystal shows guest-dependent color-tunable emissions such as deep blue to orange when a guest molecule of benzene is replaced with other π-conjugated systems. A good correlation between the emission wavelength and ionization potential of the guest and electronic structure calculations indicated that the emission is due to the CT transition from the guest to the NDI. The present study suggests that a rational solution of multcomponent molecular puzzles would be useful for obtaining novel photofunctional solid-state systems.

DNA motion induced by electrokinetic flow near an Au coated nanopore surface as voltage controlled gate.

We used fluorescence microscopy to investigate the diffusion and drift motion of λ DNA molecules on an Au-coated membrane surface near nanopores, prior to their translocation through solid-state nanopores. With the capability of controlling electric potential at the Au surface as a gate voltage, Vgate, the motions of DNA molecules, which are presumably generated by electrokinetic flow, vary dramatically near the nanopores in our observations. We carefully investigate these DNA motions with different values of Vgate in order to alter the densities and polarities of the counterions, which are expected to change the flow speed or direction, respectively. Depending on Vgate, our observations have revealed the critical distance from a nanopore for DNA molecules to be attracted or repelled-DNA's anisotropic and unsteady drifting motions and accumulations of DNA molecules near the nanopore entrance. Further finite element method (FEM) numerical simulations indicate that the electrokinetic flow could qualitatively explain these unusual DNA motions near metal-collated gated nanopores. Finally, we demonstrate the possibility of controlling the speed and direction of DNA motion near or through a nanopore, as in the case of recapturing a single DNA molecule multiple times with alternating current voltages on the Vgate.

Structure and molecular characterization of barley nudix hydrolase genes.

Putative nudix hydrolase (NUDX) genes, which encode amino acid sequences showing homology with those of Arabidopsis NUDXs and conserve nudix motif, were identified from barley. The 14 deduced barley NUDXs (HvNUDX1-14) were classified into established subfamilies, except for 8-oxo-deoxyguanosine 5'-triphosphate (8-oxo-dGTP) pyrophosphohydrolase and mRNA decapping enzyme subfamilies, and three substrate-unknown subfamilies. Drought and UV-C stresses, respectively, up-regulated 7 and 4 HvNUDX genes, but some homologs of Arabidopsis NUDXs showed different responses to abiotic stress. HvNUDX12 gene, belonging to diadenosine tetraphosphates (Ap4A) pyrophosphohydrolase subfamily gene and up-regulated by UV-C, was expressed in Escherichia coli cells. The recombinant protein showed 8-oxo-dGTP, Ap4A, and guanosine-3',5'-tetraphosphate (ppGpp) pyrophosphohydrolase activities, and the suppression of the lacZ amber mutation in a mutT-deficient E. coli cells caused by the incorporation of 8-oxo-GTP into mRNA was prevented to a significant degree. These results suggest that barley NUDXs have unique constitution and response of NUDX to abiotic stress.

Genome-wide expression analysis of reactive oxygen species gene network in Mizuna plants grown in long-term spaceflight.

BACKGROUND: Spaceflight environment have been shown to generate reactive oxygen species (ROS) and induce oxidative stress in plants, but little is known about the gene expression of the ROS gene network in plants grown in long-term spaceflight. The molecular response and adaptation to the spaceflight environment of Mizuna plants harvested after 27 days of cultivation onboard the International Space Station (ISS) were measured using genome-wide mRNA expression analysis (mRNA-Seq). RESULTS: Total reads of transcripts from the Mizuna grown in the ISS as well as on the ground by mRNA-Seq showed 8,258 and 14,170 transcripts up-regulated and down-regulated, respectively, in the space-grown Mizuna when compared with those from the ground-grown Mizuna. A total of 20 in 32 ROS oxidative marker genes were up-regulated, including high expression of four hallmarks, and preferentially expressed genes associated with ROS-scavenging including thioredoxin, glutaredoxin, and alternative oxidase genes. In the transcription factors of the ROS gene network, MEKK1-MKK4-MPK3, OXI1-MKK4-MPK3, and OXI1-MPK3 of MAP cascades, induction of WRKY22 by MEKK1-MKK4-MPK3 cascade, induction of WRKY25 and repression of Zat7 by Zat12 were suggested. RbohD and RbohF genes were up-regulated preferentially in NADPH oxidase genes, which produce ROS. CONCLUSIONS: This large-scale transcriptome analysis revealed that the spaceflight environment induced oxidative stress and the ROS gene network activation in the space-grown Mizuna. Among transcripts altered in expression by space conditions, some were common genes response to abiotic and biotic stress. Furthermore, certain genes were exclusively up-regulated in Mizuna grown on the ISS. Surprisingly, Mizuna grew in space normally, as well as on the ground, demonstrating that plants can acclimate to long-term exposure in the spaceflight environment by reprogramming the expression of the ROS gene network.

Design of ratiometric fluorescent probes based on arene-metal-ion interactions and their application to Cd(II) and hydrogen sulfide imaging in living cells.

Non-coordinative interactions between a metal ion and the aromatic ring of a fluorophore can act as a versatile sensing mechanism for the detection of metal ions with a large emission change of fluorophores. We report the design of fluorescent probes based on arene-metal-ion interactions and their biological applications. This study found that various probes having different fluorophores and metal binding units displayed significant emission redshift upon complexation with metal ions, such as Ag(I), Cd(II), Hg(II), and Pb(II). X-ray crystallography of the complexes confirmed that the metal ions were held in close proximity to the fluorophore to form an arene-metal-ion interaction. Electronic structure calculations based on TDDFT offered a theoretical basis for the sensing mechanism, thus showing that metal ions electrostatically modulate the energy levels of the molecular orbitals of the fluorophore. A fluorescent probe was successfully applied to the ratiometric detection of the uptake of Cd(II) ions and hydrogen sulfide (H2S) in living cells. These results highlight the utility of interactions between arene groups and metal ions in biological analyses.

Aza-crown-ether-appended xanthene: selective ratiometric fluorescent probe for silver(I) ion based on arene-metal ion interaction.

In this Communication, we report on the development of a ratiometric fluorescent probe for silver(I) ions (Ag(I)) based on an arene-metal ion interaction. The probe selectively senses Ag(I) among various metal ions with a large-emission red shift under aqueous conditions, enabling the selective ratiometric detection of Ag(I). X-ray crystallography and NMR analyses reveal that Ag(I) comes into close contact with the fluorophore, which induces a large-emission red shift. The high sensing selectivity of the probe toward Ag(I) might be attributable to the restricted rigid conformation of the cyclic aza crown ether, which exclusively binds Ag(I). In addition to Ag(I) sensing, the Ag(I) complex of the probe is also used for the ratiometric sensing of a cyanide anion (CN(-)), highlighting the utility of the reported probe in fluorescence sensing.

Rice Nudix Hydrolase OsNUDX2 Sanitizes Oxidized Nucleotides.

Nudix hydrolase (NUDX) hydrolyzes 8-oxo-(d)GTP to reduce the levels of oxidized nucleotides in the cells. 8-oxo-(d)GTP produced by reactive oxygen species (ROS) is incorporated into DNA/RNA and mispaired with adenine, causing replicational and transcriptional errors. Here, we identified a rice OsNUDX2 gene, whose expression level was increased 15-fold under UV-C irradiation. The open reading frame of the OsNUDX2 gene, which encodes 776 amino acid residues, was cloned into Escherichia coli cells to produce the protein of 100 kDa. The recombinant protein hydrolyzed 8-oxo-dGTP, in addition to dimethylallyl diphosphate (DMAPP) and isopentenyl diphosphate (IPP), as did Arabidopsis AtNUDX1; whereas the amino acid sequence of OsNUDX2 had 18% identity with AtNUDX1. OsNUDX2 had 14% identity with barley HvNUDX12, which hydrolyzes 8-oxo-dGTP and diadenosine tetraphosphates. Suppression of the lacZ amber mutation caused by the incorporation of 8-oxo-GTP into mRNA was prevented to a significant degree when the OsNUDX2 gene was expressed in mutT-deficient E. coli cells. These results suggest that the different substrate specificity and identity among plant 8-oxo-dGTP-hydrolyzing NUDXs and OsNUDX2 reduces UV stress by sanitizing the oxidized nucleotides.

Distinctive in vitro ATP Hydrolysis Activity of AtVIPP1, a Chloroplastic ESCRT-III Superfamily Protein in Arabidopsis.

Vesicle-inducing protein in plastid 1 (VIPP1), characteristic to oxygenic photosynthetic organisms, is a membrane-remodeling factor that forms homo-oligomers and functions in thylakoid membrane formation and maintenance. The cyanobacterial VIPP1 structure revealed a monomeric folding pattern similar to that of endosomal sorting complex required for transport (ESCRT) III. Characteristic to VIPP1, however, is its own GTP and ATP hydrolytic activity without canonical domains. In this study, we found that histidine-tagged Arabidopsis VIPP1 (AtVIPP1) hydrolyzed GTP and ATP to produce GDP and ADP in vitro, respectively. Unexpectedly, the observed GTPase and ATPase activities were biochemically distinguishable, because the ATPase was optimized for alkaline conditions and dependent on Ca2+ as well as Mg2+, with a higher affinity for ATP than GTP. We found that a version of AtVIPP1 protein with a mutation in its nucleotide-binding site, as deduced from the cyanobacterial structure, retained its hydrolytic activity, suggesting that Arabidopsis and cyanobacterial VIPP1s have different properties. Negative staining particle analysis showed that AtVIPP1 formed particle or rod structures that differed from those of cyanobacteria and Chlamydomonas. These results suggested that the nucleotide hydrolytic activity and oligomer formation of VIPP1 are common in photosynthetic organisms, whereas their properties differ among species.

Distribution of α(IV) collagen chains in the ocular anterior segments of adult mice.

The distribution of the collagen chains from α1(IV) to α6(IV) could serve as a basis for the characterization of type IV collagen. In this study, immunohistochemistry of the ocular anterior segment of adult mice was performed using specific monoclonal antibodies against each chain in the series from α1(IV) to α6(IV). The results show that the components of type IV collagen in vascular basement membranes are α1(IV) and α2(IV) with or without α5(IV) and α6(IV) chains and those in epithelium and muscle basement membranes are α1(IV), α2(IV), α5(IV), and α6(IV) chains. In corneal endothelium, pigmented epithelium of iris and ciliary body, and trabecular meshwork, α3(IV) and α4(IV) chains are also expressed in addition to α1(IV), α2(IV), α5(IV), and α6(IV) chains. Moreover, we investigated the change in molecular composition in ciliary body during postnatal development. α3(IV) and α4(IV) chains were also expressed in addition to α1(IV), α2(IV), α5(IV), and α6(IV) chains in ciliary pigmented epithelium basement membrane from 7 days after birth. This result suggests that the basement membranes gradually change their biochemical features owing to temporal regulation. Taken together, these findings suggest that the different distribution and the developmental expression of α1(IV) to α6(IV) chains are associated with the tissue-specific function of type IV collagen in basement membranes.

A multicolor and ratiometric fluorescent sensing platform for metal ions based on arene-metal-ion contact.

Despite continuous and active development of fluorescent metal-ion probes, their molecular design for ratiometric detection is restricted by the limited choice of available sensing mechanisms. Here we present a multicolor and ratiometric fluorescent sensing platform for metal ions based on the interaction between the metal ion and the aromatic ring of a fluorophore (arene-metal-ion, AM, coordination). Our molecular design provided the probes possessing a 1,9-bis(2'-pyridyl)-2,5,8-triazanonane as a flexible metal ion binding unit attached to a tricyclic fluorophore. This architecture allows to sense various metal ions, such as Zn(II), Cu(II), Cd(II), Ag(I), and Hg(II) with emission red-shifts. We showed that this probe design is applicable to a series of tricyclic fluorophores, which allow ratiometric detection of the metal ions from the blue to the near-infrared wavelengths. X-ray crystallography and theoretical calculations indicate that the coordinated metal ion has van der Waals contact with the fluorophore, perturbing the dye's electronic structure and ring conformation to induce the emission red-shift. A set of the probes was useful for the differential sensing of eight metal ions in a one-pot single titration via principal component analysis. We also demonstrate that a xanthene fluorophore is applicable to the ratiometric imaging of metal ions under live-cell conditions.

Oxidative stress and antioxidant capacity in barley grown under space environment.

The gene expression and enzyme activity of superoxide dismutase, catalase, and ascorbate peroxidase in the space-grown barley were not significantly different from those of the ground-grown barley. Cu2+ reducing and radical scavenging activities in an extract of the space-grown barley were lower than those of the ground-grown barley by 0.7 fold, suggesting that the space environment does not induce oxidative stress, and reduces antioxidant capacity in plants.

An Electronic-structure Informatics Study on the Toxicity of Alkylphenols to Tetrahymena pyriformis.

Alkylphenols (APs) dissolved in water are known to be toxic to animals including humans. In this study, regression models describing the toxicity of the 33 AP molecules were investigated for reproducing and thereby making it possible to predict a quantitative structure-activity relationship (QSAR). For this purpose, we tried to derive regression models for the experimental IGC50 (growth inhibition concentration at 50 %) to Tetrahymena pyriformis by using various descriptor sets consisting of electronic and shape descriptors. By applying the multiple linear regression (MLR) analysis, it was successful to derive a quantitative regression model for the IGC50 values. In this analysis, the size parameters of the molecules were found important, suggesting that bulky molecules should be less toxic. We could also obtain, when the size descriptors were excluded, an MLR model indicating that the electron affinity (EA) should be important, which is consistent with the previous QSAR studies. Through the correlation analysis among the descriptors, it was shown that, in the present set of molecules, EA and a size parameter are highly correlated. Since EA was calculated to be negative, indicating that the related process would be energetically unfavourable, it was concluded that the size of the molecules should be a dominant factor determining IGC50 . This implies that a molecular recognition process would play a critical role in the mode of action for the toxicity.

Two-electron reduction of a Rh-Mo-Rh dithiolato complex to form a triplet ground state associated with a change in CO coordination mode.

We synthesized a dithiolato-bridged heterometal trinuclear complex [{(eta(5)-C(5)Me(5))Rh(S(2)C(6)H(4))}(2)Mo(CO)(2)] (1) in which two rhodadithiolene complex units are bridged by a Mo(CO)(2) moiety. Complex 1 with a Rh(III)-Mo(0)-Rh(III) bond exhibits reversible one-step two-electron reduction with potential inversion. This redox process between 1 and 1(2-) accompanies a reversible structural change, which is an alternation in the CO coordination mode between semibridging and bridging. The ground state of dianion 1(2-) with a Rh(II)-Mo(0)-Rh(II) bond is assigned to spin triplet. These alternations of CO coordination mode and spin state are fully consistent with the density functional theory calculation results. This is the first example of multinuclear metalladithiolene complex which was successful in elucidating a reversible multielectron redox process associated with structural change and spin state change.

trans-cis photoisomerization of azobenzene-conjugated dithiolato-bipyridine platinum(II) complexes: extension of photoresponse to longer wavelengths and photocontrollable tristability.

Azobenzene derivatives modified with dithiolato-bipyridine platinum(II) complexes were synthesized, revealing their highly extended photoresponses to the long wavelength region as well as unique photocontrollable tristability. The absorptions of trans-1 and trans-2 with one azobenzene group on the dithiolene and bipyridine ligands, respectively, cover the range from 300 to 700 nm. These absorptions are ascribed, by means of time-dependent (TD)DFT calculations, to transitions from dithiolene(pi) to bipyridine(pi*), namely, interligand charge transfer (CT), pi-pi*, and n-pi* transitions of the azobenzene unit, and pi-pi* transitions of the bipyridine ligand. In addition, only trans-1 shows distinctive electronic bands, assignable to transitions from the dithiolene(pi) to azobenzene(pi*), defined as intraligand CT. Complex 1 shows photoisomerization behavior opposite to that of azobenzene: trans-to-cis and cis-to-trans conversions proceed with 405 and 312 nm irradiation, which correspond to excitation with the intraligand CT, and pi-pi* bands of the azobenzene and bipyridine units, respectively. In contrast, complex 2 shows photoisomerization similar to that of azobenzene: trans-to-cis and cis-to-trans transformations occur with 365 and 405 nm irradiation, respectively. Irradiation at 578 nm, corresponding to excitation of the interligand CT transitions, results in cis-to-trans conversion of both 1 and 2, which is the longest wavelength ever reported to effect the photoisomerization of the azobenzene group. The absorption and photochromism of 4, which has azobenzene groups on both the dithiolato and bipyridine ligands, have characteristics quite similar to those of 1 and 2, which furnishes 4 with photocontrollable tristability in a single molecule using light at 365, 405, and 578 nm. We also clarified that 1 and 2 have high photoisomerization efficiencies, and good thermal stability of the cis forms. Complexes 3 and 5 have almost the identical photoresponse to those of their positional isomers, complexes 2 and 4.

Localization and expression of serine racemase in Arabidopsis thaliana.

Arabidopsis plants transformed by promoter of A. thaliana serine racemase fused with beta-glucuronidase (GUS) reporter gene showed strong GUS staining in elongating and developing cells such as tip regions of primary and lateral roots, developing leaves, and shoot meristems. RT-PCR and digital northern hybridization showed that expression of the serine racemase gene was not induced by L- and D-serine, light irradiation, biotic and abiotic stresses.