Two dominant genes in barley (Hordeum vulgare L.) complementarily encode perfect resistance to Japanese soil-borne wheat mosaic virus.

Japanese soil-borne wheat mosaic virus (Furovirus) is a damaging pathogen of wheat and barley. This virus can survive in the soil for several decades, so the deployment of resistant cultivars represents the only practical control measure. Here, a genetic analysis has identified two regions of the barley genome-one on chromosome 2H and the other on chromosome 3H-as harboring gene(s) encoding resistance to this virus. The joint presence of both loci, termed Jmv1 and Jmv2, made the plants essentially immune, with resistance being dominant over susceptibility at each locus. Phylogenetic analysis showed that the virus is not closely related to the type Furovirus species Soil-borne wheat mosaic virus. There was a difference between the RNA1- and RNA2-based phylogenies of the virus species in Furovirus implying the independent segregation of the virus subgenomes.

A genetic analysis of the resistance in barley to Soil-borne wheat mosaic virus.

Soil-borne wheat mosaic virus (SBWMV), a ubiquitous pathogen commonly encountered in temperate regions of the Northern hemisphere, can damage a number of economically important cereal crops, notably wheat and barley. Given that the plasmodiophorid cercozoan Polymyxa graminis, which acts as the vector of SBWMV, can survive in the soil for many decades, the only feasible control measure is the deployment of resistant cultivars. Here, a quantitative trait locus (QTL) approach was taken to characterize the genetic basis of the SBWMV resistance exhibited by the barley cultivar Haruna Nijo. The analysis revealed that between 33% and 41% of the variation for the measure chosen to represent resistance was under the control of a gene(s) mapping to a region at the distal end of the short arm of chromosome 2H. In contrast to most of the genes known to encode resistance to soil-borne mosaic viruses, the allele specifying resistance was dominant over those present in a susceptible genotype.

Understanding hydrogen-bonding structures of molecular crystals via electron and NMR nanocrystallography.

Understanding hydrogen-bonding networks in nanocrystals and microcrystals that are too small for X-ray diffractometry is a challenge. Although electron diffraction (ED) or electron 3D crystallography are applicable to determining the structures of such nanocrystals owing to their strong scattering power, these techniques still lead to ambiguities in the hydrogen atom positions and misassignments of atoms with similar atomic numbers such as carbon, nitrogen, and oxygen. Here, we propose a technique combining ED, solid-state NMR (SSNMR), and first-principles quantum calculations to overcome these limitations. The rotational ED method is first used to determine the positions of the non-hydrogen atoms, and SSNMR is then applied to ascertain the hydrogen atom positions and assign the carbon, nitrogen, and oxygen atoms via the NMR signals for 1H, 13C, 14N, and 15N with the aid of quantum computations. This approach elucidates the hydrogen-bonding networks in L-histidine and cimetidine form B whose structure was previously unknown.

Scanning Electron Microscopy (SEM) Energy Dispersive X-ray Spectroscopy (EDS) Mapping and In-situ Observation of Carbonization of Culms of Bambusa Multiplex.

Green culms of bamboo and charcoal of Bambusa multiplex were investigated by scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS) mapping. A dynamic observation of the initial stage of carbonization was also performed in-situ by heating a radial longitudinal section of the bamboo culm at a rate of 20°C/min up to 500°C. EDS mapping of the green bamboo culms detected Si signals in the harder cells such as the epidermis (Ep), cortex (Cor) and vascular bundle sheath (Bs) and between these cells as silicon oxide particles. Appreciable morphological change of the cells occurred in a temperature range of about 300-400°C due to the decomposition of cellulose that is the main component of the bamboo cells. The charcoal of the bamboo culm has a skin layer which originates from the Ep and Cor and the main central cylinder with many openings that originate from the expanded xylem and phloem holes. During carbonization, the Si atoms in the Ep and Cor were segregated as thin silicon oxide layers onto both the sides of the skin layer and the Si included in the Bs fibers and parenchyma cells accumulated near the walls of the openings.

Structural investigations on green culms and charcoal of Bambusa multiplex.

Green culms of Bambusa multiplex and the bamboo charcoal carbonized from the green culms at 700°C have been studied by means of X-ray diffraction, X-ray fluorescent element analysis, analytical scanning electron microscopy, and analytical scanning transmission electron microscopy (STEM), aiming at industrial applications as raw materials for functional devices and substances. It is revealed that the green culms and the charcoal contain a significant amount of Si, in particular, ∼18 wt % in the skin. The green culms comprise amorphous and crystalline celluloses. The charcoal has a so-called amorphous structure which is composed of randomly distributed carbon nanotubes and fibers. The growth of Ag-doped activated charcoal powders that were produced by two different methods using this charcoal powder has also been studied.

Solid-state NMR meets electron diffraction: determination of crystalline polymorphs of small organic microcrystalline samples.

A combination of solid-state NMR (ssNMR) and electron diffraction (ED) has been used to determine the crystalline polymorphs in small-organic microcrystalline molecules. Although 13C cross-polarization magic angle spinning (CPMAS) is a widely used method for determining crystalline polymorphs, even in a mixture, it sometimes fails if the molecular conformations are similar. On the other hand, ED can, in principle, differentiate crystalline forms with different lattice parameters, even when they have very similar molecular conformations. However, its application is usually limited to inorganic molecules only. This is because the ED measurements of organic molecules are very challenging due to degradation of the sample by electron irradiation. We overcame these difficulties by the use of 1H double-quantum/single-quantum correlation experiments at very fast magic angle spinning, together with ED observations under mild electron irradiation. The experiments were demonstrated on L-histidine samples in L-histidine·HCl·H2O, orthorhombic L-histidine and monoclinic L-histidine.

Draft genome sequence of an inbred line of Chenopodium quinoa, an allotetraploid crop with great environmental adaptability and outstanding nutritional properties.

Chenopodium quinoa Willd. (quinoa) originated from the Andean region of South America, and is a pseudocereal crop of the Amaranthaceae family. Quinoa is emerging as an important crop with the potential to contribute to food security worldwide and is considered to be an optimal food source for astronauts, due to its outstanding nutritional profile and ability to tolerate stressful environments. Furthermore, plant pathologists use quinoa as a representative diagnostic host to identify virus species. However, molecular analysis of quinoa is limited by its genetic heterogeneity due to outcrossing and its genome complexity derived from allotetraploidy. To overcome these obstacles, we established the inbred and standard quinoa accession Kd that enables rigorous molecular analysis, and presented the draft genome sequence of Kd, using an optimized combination of high-throughput next generation sequencing on the Illumina Hiseq 2500 and PacBio RS II sequencers. The de novo genome assembly contained 25 k scaffolds consisting of 1 Gbp with N50 length of 86 kbp. Based on these data, we constructed the free-access Quinoa Genome DataBase (QGDB). Thus, these findings provide insights into the mechanisms underlying agronomically important traits of quinoa and the effect of allotetraploidy on genome evolution.

The Birth of a Black Rice Gene and Its Local Spread by Introgression.

The origin and spread of novel agronomic traits during crop domestication are complex events in plant evolution. Wild rice (Oryza rufipogon) has red grains due to the accumulation of proanthocyanidins, whereas most cultivated rice (Oryza sativa) varieties have white grains induced by a defective allele in the Rc basic helix-loop-helix (bHLH) gene. Although the events surrounding the origin and spread of black rice traits remain unknown, varieties with black grains due to anthocyanin accumulation are distributed in various locations throughout Asia. Here, we show that the black grain trait originated from ectopic expression of the Kala4 bHLH gene due to rearrangement in the promoter region. Both the Rc and Kala4 genes activate upstream flavonol biosynthesis genes, such as chalcone synthase and dihydroflavonol-4-reductase, and downstream genes, such as leucoanthocyanidin reductase and leucoanthocyanidin dioxygenase, to produce the respective specific pigments. Genome analysis of 21 black rice varieties as well as red- and white-grained landraces demonstrated that black rice arose in tropical japonica and its subsequent spread to the indica subspecies can be attributed to the causal alleles of Kala4. The relatively small size of genomic fragments of tropical japonica origin in some indica varieties indicates that refined introgression must have occurred by natural crossbreeding in the course of evolution of the black trait in rice.

Three-dimensional chemical mapping by EFTEM-TomoJ including improvement of SNR by PCA and ART reconstruction of volume by noise suppression.

Electron tomography is becoming one of the most used methods for structural analysis at nanometric scale in biological and materials sciences. Combined with chemical mapping, it provides qualitative and semiquantitative information on the distribution of chemical elements on a given sample. Due to the current difficulties in obtaining three-dimensional (3D) maps by energy-filtered transmission electron microscopy (EFTEM), the use of 3D chemical mapping has not been widely adopted by the electron microscopy community. The lack of specialized software further complicates the issue, especially in the case of data with a low signal-to-noise ratio (SNR). Moreover, data interpretation is rendered difficult by the absence of efficient segmentation tools. Thus, specialized software for the computation of 3D maps by EFTEM needs to include optimized methods for image series alignment, algorithms to improve SNR, different background subtraction models, and methods to facilitate map segmentation. Here we present a software package (EFTEM-TomoJ, which can be downloaded from http://u759.curie.fr/fr/download/softwares/EFTEM-TomoJ), specifically dedicated to computation of EFTEM 3D chemical maps including noise filtering by image reconstitution based on multivariate statistical analysis. We also present an algorithm named BgART (for background removing algebraic reconstruction technique) allowing the discrimination between background and signal and improving the reconstructed volume in an iterative way.

Performances of an 80-200 kV microscope employing a cold-FEG and an aberration-corrected objective lens.

The performances of a newly developed 80-200 kV cold field emission gun (CFEG) transmission electron microscope (TEM) integrating a spherical aberration corrector for a TEM image-forming lens have been evaluated. To begin, we show that the stability of both emission and probe currents makes use of this new CFEG much friendlier. The energy spread of electrons emitted from the CFEG has been measured as a function of emission current and shows a very last 0.26 eV energy resolution at 200 kV and even 0.23 eV at 80 kV. The combination of the CFEG and the CEOS™ aberration corrector, associated with enhanced mechanical and electrical stabilities of this new microscope, allows reaching an information transfer below 75 pm at 200 and 80 pm at 80 kV. This unseen resolution at 200 kV has allowed us to study the structure of CoPt nanoparticles by observing direct images of their atomic arrangement along the high indexes zone axis. We have evidenced the presence of defects in these nanostructures that are not parallel to the electron beam. The precise stoichiometry of two iron oxides, FeO and Fe2O3, has been determined from an analysis of iron valence state that was obtained from a direct analysis of EELS fine structures spectrum of the two oxides.

The bHLH Rac Immunity1 (RAI1) Is Activated by OsRac1 via OsMAPK3 and OsMAPK6 in Rice Immunity.

The Rac/Rop GTPase OsRac1 plays an essential role in rice immunity. However, the regulatory genes acting downstream of OsRac1 are largely unknown. We focused on the RAI1 gene, which is up-regulated in suspension cells expressing a constitutively active form of OsRac1. RAI1 encodes a putative basic helix-loop-helix transcription factor. A microarray analysis of cells transformed with an inducible RAI1 construct showed increased expression of PAL1 and OsWRKY19 genes after induction, suggesting that these genes are regulated by RAI1. This was confirmed using RAI1 T-DNA activation-tagged and RNA interference lines. The PAL1 and OsWRKY19 genes were also up-regulated by sphingolipid and chitin elicitors, and the RAI1 activation-tagged plants had increased resistance to a rice blast fungus. These results indicated that RAI1 is involved in defense responses in rice. RAI1 interacted with OsMAPK3 and OsMAPK6 proteins in vivo and in vitro. Also, RAI1 was phosphorylated by OsMAPK3/6 and OsMKK4-dd in vitro. Overexpression of OsMAPK6 and/or OsMAPK3 together with OsMKK4-dd increased PAL1 and OsWRKY19 expression in rice protoplasts. Therefore, the regulation of PAL1 and OsWRKY19 expression by RAI1 could be controlled via an OsMKK4-OsMAPK3/6 cascade. Co-immunoprecipitation assays indicated that OsMAPK3 and OsRac1 occur in the same complex as OsMAPK6. Taken together, our results indicate that RAI1 could be regulated by OsRac1 through an OsMAPK3/6 cascade. In this study, we have identified RAI1 as the first transcription factor acting downstream of OsRac1. This work will help us to understand the immune system regulated by OsRac1 in rice and its orthologs in other plant species.

LAX PANICLE2 of rice encodes a novel nuclear protein and regulates the formation of axillary meristems.

Aerial architecture in higher plants is dependent on the activity of the shoot apical meristem (SAM) and axillary meristems (AMs). The SAM produces a main shoot and leaf primordia, while AMs are generated at the axils of leaf primordia and give rise to branches and flowers. Therefore, the formation of AMs is a critical step in the construction of plant architecture. Here, we characterized the rice (Oryza sativa) lax panicle2 (lax2) mutant, which has altered AM formation. LAX2 regulates the branching of the aboveground parts of a rice plant throughout plant development, except for the primary branch in the panicle. The lax2 mutant is similar to lax panicle1 (lax1) in that it lacks an AM in most of the lateral branching of the panicle and has a reduced number of AMs at the vegetative stage. The lax1 lax2 double mutant synergistically enhances the reduced-branching phenotype, indicating the presence of multiple pathways for branching. LAX2 encodes a nuclear protein that contains a plant-specific conserved domain and physically interacts with LAX1. We propose that LAX2 is a novel factor that acts together with LAX1 in rice to regulate the process of AM formation.

Signal peptide peptidases are expressed in the shoot apex of rice, localized to the endoplasmic reticulum.

Signal peptide peptidase (SPP) is a multi-transmembrane aspartic proteinase involved in regulated intramembrane proteolysis, which is implicated in fundamental life processes such as immunological response, cell signaling, tissue differentiation, and embryogenesis. In this study, we identified two rice SPPs: OsSPP1 and OsSPP2. Green fluorescent protein-fused OsSPP1 and OsSPP2 were localized to the ER in cultured plant cells. In situ hybridization showed that OsSPPs were strongly expressed in vegetative shoot apex, young panicle, developing panicle, and the early developing florets. Undifferentiated cells, which have the potential to differentiate into all of the aerial parts of the plant are presented in the shoot apex. OsSPPs are located in both the undifferentiated cells, and the early differentiated cells at the shoot apex. These results suggest that rice SPPs have an important function in differentiation and development at the shoot apex. The expression of the shoot apex and ER localization is equal to dicot Arabidopsis thaliana, and will have common crucial roles in plant.

Expression level of ABERRANT PANICLE ORGANIZATION1 determines rice inflorescence form through control of cell proliferation in the meristem.

Two types of branches, rachis branches (i.e. nonfloral) and spikelets (i.e. floral), are produced during rice (Oryza sativa) inflorescence development. We previously reported that the ABERRANT PANICLE ORGANIZATION1 (APO1) gene, encoding an F-box-containing protein orthologous to Arabidopsis (Arabidopsis thaliana) UNUSUAL FLORAL ORGANS, suppresses precocious conversion of rachis branch meristems to spikelets to ensure generation of certain number of spikelets. Here, we identified four dominant mutants producing an increased number of spikelets and found that they are gain-of-function alleles of APO1. The APO1 expression levels are elevated in all four mutants, suggesting that an increase of APO1 activity caused the delay in the program shift to spikelet formation. In agreement with this result, ectopic overexpression of APO1 accentuated the APO1 gain-of-function phenotypes. In the apo1-D dominant alleles, the inflorescence meristem starts to increase in size more vigorously than the wild type when switching to the reproductive development phase. This alteration in growth rate is opposite to what is observed with the apo1 mutants that have a smaller inflorescence meristem. The difference in meristem size is caused by different rates of cell proliferation. Collectively, these results suggest that the level of APO1 activity regulates the inflorescence form through control of cell proliferation in the meristem.

Two-Step Regulation of LAX PANICLE1 Protein Accumulation in Axillary Meristem Formation in Rice.

Axillary meristem (AM) formation is an important determinant of plant architecture. In rice (Oryza sativa), LAX PANICLE1 (LAX1) function is required for the generation of AM throughout the plant's lifespan. Here, we show a close relationship between AM initiation and leaf development; specifically, the plastochron 4 (P4) stage of leaf development is crucial for the proliferation of meristematic cells. Coincident with this, LAX1 expression starts in the axils of leaves at P4 stage. LAX1 mRNA accumulates in two to three layers of cells in the boundary region between the initiating AM and the shoot apical meristem. In lax1 mutants, the proliferation of meristematic cells is initiated but fails to progress into the formation of AM. The difference in sites of LAX1 mRNA expression and its action suggests non-cell-autonomous characteristics of LAX1 function. We found that LAX1 protein is trafficked to AM in a stage- and direction-specific manner. Furthermore, we present evidence that LAX1 protein movement is required for the full function of LAX1. Thus, we propose that LAX1 protein accumulates transiently in the initiating AM at P4 stage by a strict regulation of mRNA expression and a subsequent control of protein trafficking. This two-step regulation is crucial to the establishment of the new AM.

Growth and structural properties of CuAg and CoPt bimetallic nanoparticles.

Core/shell CuAg and alloyed CoPt have been synthesized using two vapor phase deposition techniques. For CuAg prepared by Thermal Evaporation (TE), the size and the morphology of the Cu cores are the key parameters to promote the formation of the core/shell arrangement. For CoPt synthesized by Pulsed Laser Deposition (PLD), the growth kinetics of nanoparticles, depending on the deposition rate, the substrate nature and the temperature, controls the nanoparticle morphology. The competition between the growth and the ordering kinetics governs the nanoparticle structure. By reducing the growth kinetics, as-grown L1(0) ordered nanoparticles are obtained according to the bulk phase diagram.

Measurement of electric potential distributions around FEG-emitters by electron holography.

An evaluation technique for field emission guns (FEG-emitters) was established by using electron holography. For performing electron holography under an applied voltage, a specimen holder with the capabilities of three-directional motion as well as voltage application was developed. An unused Schottky emitter and a used emitter that had failed after operating for about 10,000 h were selected for this study. By visualizing the electric potential distributions around the emitters, it was clarified that a change in the edge shape of the emitter led to the change in the strength of the electric field. The observations revealed that electron holography can be applied to evaluate the performances of the various emitters.

Cubic crystal protein inclusions in the neodermis of the pancreatic fluke, Eurytrema pancreaticum, and Eurytrema coelomaticum.

Light microscopy of Eurytrema pancreaticum and Eurytrema coelomaticum collected from cattle in Japan, China, Thailand, and Brazil showed many cubic crystal inclusions in the neodermis (tegument) of all flukes. The crystal inclusions were histochemically positive for protein. Scanning electron microscopy showed many cubic protrusions containing cubic crystal protein inclusions on the surface of the neodermis. Transmission electron microscopy showed that cubic crystal protein inclusions appeared in the perikarya of subtegumental parts, passed through the cytoplasmic bridge, moved into the syncytial neodermal cytoplasm, and then protruded from, and finally separated from, the neodermal cytoplasm. Cubic crystal protein inclusions were hexahedral with each side 2-18 microm long. High-resolution microscopy of ultrathin sections of crystal inclusions showed a lattice fringe at spacings of about 0.52 nm by using a filtering processing. Diffractograms were obtained by Fourier transform of the images. The lattice structure of the crystal protein inclusions was shown by inverse Fourier transform, indicating that the cubic crystal protein inclusions were single crystals. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis estimated the molecular weight of protein in the cubic crystal inclusion as 36.6 kDa. Energy-dispersive X-ray spectroscopy proved that the cubic crystal protein inclusions were composed of protein and sulfur.

A novel subunit structure of Clostridium botulinum serotype D toxin complex with three extended arms.

The botulinum neurotoxins (BoNTs) are the most potent toxins known in nature, causing the lethal disease known as botulism in humans and animals. The BoNTs act by inhibiting neurotransmitter release from cholinergic synapses. Clostridium botulinum strains produce large BoNTs toxin complexes, which include auxiliary non-toxic proteins that appear not only to protect BoNTs from the hostile environment of the digestive tract but also to assist BoNT translocation across the intestinal mucosal layer. In this study, we visualize for the first time a series of botulinum serotype D toxin complexes using negative stain transmission electron microscopy (TEM). The complexes consist of the 150-kDa BoNT, 130-kDa non-toxic non-hemagglutinin (NTNHA), and three kinds of hemagglutinin (HA) subcomponents: 70-kDa HA-70, 33-kDa HA-33, and 17-kDa HA-17. These components assemble sequentially to form the complex. A novel TEM image of the mature L-TC revealed an ellipsoidal-shaped structure with "three arms" attached. The "body" section was comprised of a single BoNT, a single NTNHA and three HA-70 molecules. The arm section consisted of a complex of HA-33 and HA-17 molecules. We determined the x-ray crystal structure of the complex formed by two HA-33 plus one HA-17. On the basis of the TEM image and biochemical results, we propose a novel 14-mer subunit model for the botulinum toxin complex. This unique model suggests how non-toxic components make up a "delivery vehicle" for BoNT.

A role of OsGA20ox1 , encoding an isoform of gibberellin 20-oxidase, for regulation of plant stature in rice.

Gibberellin (GA) 20-oxidase (GA20ox) is a key enzyme that normally catalyzes the penultimate steps in GA biosynthesis. One of the GA20ox genes in rice (Oryza sativa L.), OsGA20ox2 ( SD1 ), is well known as the "Green Revolution gene", and loss-of function mutation in this locus causes semi-dwarfism. Another GA20ox gene, OsGA20ox1, has also been identified, but its contribution to plant stature has remained unclear because no suitable mutants have been available. We isolated a mutant, B142, tagged with a T-DNA containing three CaMV 35S promoters, which showed a tall, GA-overproduction phenotype. The final stature of the B142 mutant reflects internode overgrowth and is approximately twice that of its wild-type parent. This mutant responds to application of both GA3 and a GA biosynthesis inhibitor, indicating that it is a novel tall mutant of rice distinct from GA signaling mutants such as slr1 . The integrated T-DNAs, which contain three CaMV 35S promoters, are located upstream of the OsGA20ox1 open reading frame (ORF) in the B142 mutant genome. Analysis of mRNA and the endogenous GAs reveal that biologically active GA level is increased by up-regulation of the OsGA20ox1 gene in B142. Introduction of OsGA20ox1 cDNA driven by 35S promoter into the wild type phenocopies the morphological characteristics of B142. These results indicate that the elongated phenotype of the B142 mutant is caused by up-regulation of the OsGA20ox1 gene. Moreover, the final stature of rice was reduced by specific suppression of the OsGA20ox1 gene expression. This result indicates that not only OsGA20ox2 but also OsGA20ox1 affects plant stature.