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Previous studies have reported that PID2, which encodes a B-lectin receptor-like kinase, is a key gene in the resistance of rice to Magnaporthe oryzae strain ZB15. However, the PID2-mediated downstream signalling events remain largely unknown. The U-box E3 ubiquitin ligase OsPIE3 (PID2-interacting E3) was isolated and confirmed to play key roles in PID2-mediated rice blast resistance. Yeast two-hybrid analysis showed that the armadillo repeat region of OsPIE3 is required for its interaction with PID2. Further investigation demonstrated that OsPIE3 can modify the subcellular localisation of PID2, thus promoting its nuclear recruitment from the plasma membrane for protein degradation in the ubiquitin-proteasome system. Site-directed mutagenesis of a conserved cysteine site (C230S) within the U-box domain of OsPIE3 reduces PID2 translocation and ubiquitination. Genetic analysis suggested that OsPIE3 loss-of-function mutants exhibited enhanced resistance to M. oryzae isolate ZB15, whereas mutants with overexpressed OsPIE3 exhibited reduced resistance. Furthermore, the OsPIE3/PID2 double mutant displayed a similar blast phenotype to that of the PID2 single mutant, suggesting that OsPIE3 is a negative regulator and functions along with PID2 in blast disease resistance. Our findings confirm that the E3 ubiquitin ligase OsPIE3 is necessary for PID2-mediated rice blast disease resistance regulation.

Zinc (Zn) and cerium (Ce) modified hierarchical ZSM-5 (HZ) catalysts were prepared by incipient wetness impregnation, and their catalytic performances in methanol to aromatics reaction were evaluated in a fixed-bed reactor operating at 400°C under 0.1 MPa and WHSV of 1.0 h−1. The structure, acidity, and state of Zn species of the Zn/Ce modified HZ catalysts were investigated via several characterization techniques, including XRD, NH3-TPD, H2-TPR, nitrogen adsorption, and XPS. The results showed that the aromatization activity of 2 wt% Zn-modified HZ (2% Zn/HZ) could be significantly enhanced by loading 0.6 wt% Ce, which was mainly attributed to the increase in surface ZnOH+ species. Moreover, it was found that Ce inhibited pore blockage caused by Zn. Consequently, compared to 2% Zn/HZ, 2% Zn-0.6% Ce/HZ exhibited higher aromatic selectivity and longer catalyst lifetime.

The rapid accumulation of molecular data motivates development of innovative approaches to computationally characterize sequences, structures and functions of biological and chemical molecules in an efficient, accessible and accurate manner. Notwithstanding several computational tools that characterize protein or nucleic acids data, there are no one-stop computational toolkits that comprehensively characterize a wide range of biomolecules. We address this vital need by developing a holistic platform that generates features from sequence and structural data for a diverse collection of molecule types. Our freely available and easy-to-use iFeatureOmega platform generates, analyzes and visualizes 189 representations for biological sequences, structures and ligands. To the best of our knowledge, iFeatureOmega provides the largest scope when directly compared to the current solutions, in terms of the number of feature extraction and analysis approaches and coverage of different molecules. We release three versions of iFeatureOmega including a webserver, command line interface and graphical interface to satisfy needs of experienced bioinformaticians and less computer-savvy biologists and biochemists. With the assistance of iFeatureOmega, users can encode their molecular data into representations that facilitate construction of predictive models and analytical studies. We highlight benefits of iFeatureOmega based on three research applications, demonstrating how it can be used to accelerate and streamline research in bioinformatics, computational biology, and cheminformatics areas. The iFeatureOmega webserver is freely available at http://ifeatureomega.erc.monash.edu and the standalone versions can be downloaded from https://github.com/Superzchen/iFeatureOmega-GUI/ and https://github.com/Superzchen/iFeatureOmega-CLI/.

Background Grain size and chalkiness is a critical agronomic trait affecting rice yield and quality. The application of transcriptomics to rice has widened the understanding of complex molecular responsive mechanisms, differential gene expression, and regulatory pathways under varying conditions. Similarly, metabolomics has also contributed drastically for rice trait improvements. As master regulators of plant growth and development, phys influence seed germination, vegetative growth, photoperiodic flowering, shade avoidance responses. OsPHYB can regulate a variety of plant growth and development processes, but little is known about the roles of rice gene OsPHYB in modulating grain development. Results In this study, rice phytochrome B (OsPHYB) was edited using CRISPR/Cas9 technology. We found that OsPHYB knockout increased rice grain size and chalkiness, and increased the contents of amylose, free fatty acids and soluble sugar, while the gel consistency and contents of proteins were reduced in mutant grains. Furthermore, OsPHYB is involved in the regulation of grain size and chalk formation by controlling cell division and complex starch grain morphology. Transcriptomic analysis revealed that loss of OsPHYB function affects multiple metabolic pathways, especially enhancement of glycolysis, fatty acid, oxidative phosphorylation, and antioxidant pathways, as well as differential expression of starch and phytohormone pathways. An analysis of grain metabolites showed an increase in the free fatty acids and lysophosphatidylcholine, whereas the amounts of sugars, alcohols, amino acids and derivatives, organic acids, phenolic acids, alkaloids, nucleotides and derivatives, and flavonoids decreased, which were significantly associated with grain size and chalk formation. Conclusions Our study reveals that, OsPHYB plays an important regulatory role in the growth and development of rice grains, especially grain size and chalkiness. Furthermore, OsPHYB regulates grain size and chalkiness formation by affecting gene metabolism interaction network. Thus, this study not only revealed that OsPHYB plays a vital role in regulating grain size and chalkiness of rice but reveal new functions and highlighted the importance and value of OsPHYB in rice grain development and provide a new strategy for yield and quality improvement in rice breeding.

In the deep drawing forming process of wheel disks, the wall thickness at the rounded corners tends to be thinned. Using DEFORM software analysis, two stages of the deep drawing forming process are used to study the wheel disk forming. A finite element model of deep drawing and forming was established based on the theoretical analysis of the deep drawing and forming process. The stress and strain field distribution during the forming process of the circular blank was simulated and analyzed. The analysis shows that different punch feed rates and friction coefficients greatly influence the thinning rate and forming load of the wheel forming. The thinning rate reached 15.4% when the punch feed rate was 180 mm/s. The maximum forming load increases with the increase of friction coefficient, and the total forming load reaches 424 kN when the friction coefficient is 0.20. The effect of r p /t 0 and r d /t 0 on the wall thickness of the second pass forming was also analyzed. The results show that when r p /t 0 is 1.6~2.4 and rd/t0 is 2~3, the minimum wall thickness is larger, ΔX is also the smallest, and the forming quality is the best. The optimal set of parameters was obtained: punch feed rate of 120 mm/s, friction coefficient of 0.12, and r p /t 0 of 2.4. Physical tests were conducted on the self-designed forming machine, and the results were consistent with the simulation results, which verified the feasibility of the forming solution.

The phytochrome-interacting factor-like gene OsPIL15 negatively regulates grain size and 1000-grain weight, but its regulatory effect on rice quality traits is unknown. Here, knock-down, knock-out, and over-expression of OsPIL15 transgenic rice lines were used to investigate the effects of OsPIL15 on rice yield and quality traits. The results showed that knock-down or knock-out of OsPIL15 increased grain length and width, chalkiness, amylose content, glutenin and globulin content, and total protein content but reduced amylopectin content, total starch content, prolamin and albumin content, and gel consistency. Over-expression of OsPIL15 showed the opposite results, except for the reduction of prolamin content. Although OsPIL15 changed the grain size and weight, it had no effect on grain length/width ratio, brown rice rate, and milled rice rate. KEGG pathway enrichment analysis of differentially expressed genes between transgenic lines and wild type showed that OsPIL15 mainly regulated genes related to ribosome, metabolic pathways, and biosynthesis of secondary metabolites. Gene expression analysis showed that RNAi transgenic lines decreased OsCIN2 and OsSUS1 expression and increased OsGBSSI, OsSSI, OsAPGL2, and OsAPGL3 expression level, while over-expression of OsPIL15 increased OsCIN2, OsSUS1, OsSUS6, and OsSSI and decreased OsSSIIa, OsSSIIc, and OsAPGL2 expression level. These results revealed that OsPIL15 plays an important role in rice grain development. In addition to grain shape, OsPIL15 also regulates chalkiness, starch content, protein content, and gel consistency. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11032-022-01311-x.

Cytokinin oxidase/dehydrogenases (CKXs) are key enzymes that degrade cytokinins (CTKs) and play an essential role in plant growth and development. The present study analyzed the phenotypic and physiological characteristics of OsCKX2 overexpressing (OE) and knockout (KO) rice plants after exposure to phosphate (Pi) deficiency and the transcriptome and metabolome to investigate the function of OsCKX2 in response to Pi deficiency. OsCKX2 KO plants demonstrated higher endogenous CTK levels than wild-type (WT) under Pi deficiency. Further analysis indicated more robust tolerance of OsCKX2 KO plants to Pi deficiency, which exhibited higher phosphorus concentration, larger shoot biomass, and lesser leaf yellowing under Pi deficiency; whereas the opposite was observed for OsCKX2 OE plants. Transcriptome and metabolome analyses revealed that overexpression of OsCKX2 downregulated the transcriptional levels of genes related to Pi transporters, membrane lipid metabolism, and glycolysis, and reduced the consumption of metabolites in membrane lipid metabolism and glycolysis. On the contrary, knockout of OsCKX2 upregulated the expression of Pi transporters, and increased the consumption of metabolites in membrane lipid metabolism and glycolysis. These results indicated that OsCKX2 impacted Pi uptake, recycling, and plant growth via Pi transporters, phospholipid hydrolysis, and glycolysis under Pi deficiency. Overall, OsCKX2 negatively regulated Pi deficiency tolerance by modulating CTKs in rice.

Upland rice is an ecotype adapted to dry culture system. In this study, changes in germination characteristics and transcriptome of germinating seeds exposed to 15% polyethylene glycol (PEG) were investigated using upland rice genotype IRAT109. PEG reduced germination potential and inhibited growth of seed radicle and plumule. Under PEG stress, gibberellic acid (GA) content decreased and abscisic acid (ABA) content increased. Transcriptome analysis revealed that 1270 genes were differentially expressed between stressed and non-stressed seeds. Approximately, 56.46% of differentially expressed genes (DEGs) were up-regulated and 43.54% of DEGs were down-regulated under PEG stress. Gene Ontology (GO) analysis categorized 1149 DEGs into 52 functional groups and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis assigned 123 DEGs to 54 pathways. A large number of DEGs related to GA signal transduction, ABA biosynthesis and signal transduction, and defense response pathways were upregulated. Results indicated that genes related with GA signal transduction and ABA play important role in germination under drought stress. Findings of this study are highly useful to understand the molecular mechanism of germination and provide candidate genes for molecular breeding in dry direct-seeded rice. © 2019 Friends Science Publishers

Portable nuclear magnetic resonance (NMR) instruments are widely used in many fields. However, the large volume, low uniformity and end effect limits the application of portable NMR instruments. In order to improve the uniformity and compensate the end effect, a Halbach structure with 9-layer permanent magnet is proposed, which is optimized by axially adjusting the magnet height based on the Halbach array principle and Quality factor (Q) is introduced to represent the magnetic field uniformity at both ends of the central cylinder region. Each layer consists of 16 permanent magnets with trapezoidal cross section and the total volume is Φ240 × 141.8 mm. Through simulation, it is found that the final magnetic flux density is 1.09 T and the uniformity is 418 ppm in the central region (Φ20 × 20 mm) of the optimized structure. The proposed structure has the advantages of small size, compactness in structure and homogeneity, which is very suitable for portable NMR systems.

© 2019 IEEE. The key to dynamic pressure calibration is the generation of sinusoidal pressure signals. This paper uses a liquid-gas two-phase piston sinusoidal pressure generator for generating higher frequency pressure signals. The design of the contraction section has a large effect on the sinusoidal pressure generator. The flow field characteristics of the contraction section were simulated by Fluent simulation software. We analyze the frequency response, exit velocity distribution and axial pressure distribution of different contraction curves, then select the appropriate contraction curve and verify it by experiment. The simulation work in this paper provides a reference for the design of liquid-gas two-phase high-frequency sinusoidal pressure generator.

The primers used in the paper. (DOCX 14 kb)

Predicted targets of OsmiR159 by psRobot and their expressions detected by RNAseq. (DOCX 15 kb)

Phylogenetic analysis of the targets of OsmiR159 and AtmiR159. (DOCX 54 kb)

Awnness is a key trait in rice domestication, yet no studies have been conducted on fine mapping or association mapping of the rice awn gene. In this study, we investigated the awnness and genotype of a core collection of 303 cultivated rice varieties and a BC5F2 segregating population of 200 individuals. Combining association and linkage analyses, we mapped the awnness related genes to chromosome 4. Primary association analysis using 24 SSR markers revealed five loci significantly associated with awnness on chromosome 4. The associated markers cover previously identified regions. Fine association mapping was conducted using another 29 markers within a 4-Mb region, covering the associated marker in34, which is close to the awn gene Awn4.1. Seven associated markers were revealed, distributed over an 870-kb region. Combining the fine association mapping and linkage analysis of awnness in the 200 BC5F2 segregating population, we finally identified a 330-kb region as the candidate region for Awn4.1. The results indicate that combining association mapping and linkage mapping provides an efficient and precise approach to both genome-wide mapping and fine mapping of rice genes.

Phosphorous (P) deficiency is a major restraint factor for crop production and plants have developed several mechanisms to adapt to low P stress. In this study, a set of 271 introgression lines (ILs) were used to characterize the responses of seedlings to low P availability and to identify QTLs for root traits, biomass, and plant height under P-deficiency and P-sufficiency conditions. Plant height, total dry weight, shoot dry weight, and root number were inhibited under P-deficiency, whereas maximum root length (MRL) and root-shoot ratio (RS) were induced by P-deficiency stress. Relative MRL (RMRL, the ratio of MRL under P-deficiency to MRL under P-sufficiency condition) and relative RS (RRS) were used to evaluate P-deficiency tolerance at the seedling stage. A total of 24 additive QTLs and 29 pairs of epistatic QTLs were detected, but only qRN4 was detected in both conditions. This suggested that different mechanisms may exist in both P supply levels. QTLs for adaptive traits (RMRL, RRS, RRV, and RRDW) and qRN4 consistently expressed to increase trait stability may contribute to P-deficiency tolerance. Twelve intervals were cluster regions of QTLs for P-deficiency tolerance, and one QTL (qRRS8) showed pleiotropic effects on P-deficiency tolerance and drought tolerance. These interesting QTLs can be used in marker-assisted breeding through the target ILs.

We have previously reported the presence of feline immunodeficiency virus (FIV)-specific, major histocompatibility complex (MHC)-restricted cytolytic T lymphocytes (CTL) in experimentally FIV-infected cats. However, the fine specificity of the CTL and the role of individual FIV proteins in inducing FIV-specific CTL responses remain unknown. In this study, we examined the in vitro induction and activity of FIV p24 capsid-specific CTL obtained from cats that had been experimentally infected with FIV Petaluma for 30 to 56 months. An amphotropic murine retrovital vector was used to generate transgenic primary feline T lymphoblasts that expressed the FIV capsid protein. When the autologous capsid-transduced T cells were used in vitro to stimulate CTL responses from peripheral blood mononuclear cells of chronically infected cats, MHC-restricted lysis of virus-infected target cells was observed. The majority of the CTL expressed CD8, and depletion of this population, but not CD4 cells, effectively diminished the CTL activity. When the autologous capsid-transduced T cells were used as target cells, lysis by capsid-induced effectors was not observed. Analysis of capsid-transduced T cell clones revealed a variable and low level of capsid expression among the clones. This study demonstrates the potential for using retroviral vectors as a means of inducing CTL effector cells that will specifically kill lentivirus-infected cells during lentiviral infection.

Introgression lines (ILs) are valuable materials for identifying quantitative trait loci (QTLs), evaluating genetic interactions, and marker assisted breeding. A set of 430 ILs (BC 5 F 3 ) containing segments from upland tropical japonica cultivar IRAT109 in a lowland temperate japonica cultivar Yuefu background were developed. One hundred and seventy-six polymorphic markers were used to identify introgressed segments. No segment from IRAT109 was found in 160 lines. Introgressed segments of the other 270 lines covered 99.1% of the donor genome. The mean number of introgressed donor segments per individual was 3.3 with an average length of 14.4 cM. QTL analysis was conducted on basal root thickness (BRT) of the 270 ILs grown under irrigated lowland, upland and hydroponic conditions. A total of 22 QTLs affecting BRT were identified, six QTLs ( qBRT3.1 , qBRT3.2 , qBRT6.1 , qBRT8.2 , qBRT9.1 , and qBRT9.2 ) were consistently expressed under at least two environments (location and water regime), and qBRT7.2 was a new BRT QTL identified under lowland conditions. IL255 containing qBRT9.1 showed an increase of 10.09% and 7.07% BRT over cultivar Yuefu when grown under upland and lowland conditions, respectively. Using a population of 304 F 2:3 lines derived from the cross IL255×Yuefu, qBRT9.1 was validated and mapped to a 1.2 cM interval between RM24271 and RM566. The presence of qBRT9.1 explained 12% of BRT variation. The results provide upland rice ILs and BRT QTLs for analyzing the genetic basis of drought resistance, detecting favorable genes from upland rice, and rice drought resistance breeding.

A recombinant DNA probe with specificity for the 3′ end of genomic RNA from the Ark 99 strain of infectious bronchitis virus (IBV) was found to hybridize with extracted RNA of three strains with the Ark serotype, as well as the Mass41, Holl52, Gray, JMK, Conn, Fla and SE17 strains of IBV. Viral infection was detected in the cytoplasm of chicken embryo kidney cells inoculated with Mass41, Ark99, SE17 or two recent field isolates of IBV using in situ cytohybridization and a biotinylated probe. In vivo infections were detected in individual cells of tracheas and lungs 2, 4, and 6 days after inoculation of chicks with Mass41 and Ark99. In situ hybridization of Ark99 infected tissue sections using 32P-dATP labelled probe indicated that more viral replication was present in the trachea on day 4 than either days 2 or 6; whereas more viral RNA was found in the lungs on day 6 than days 2 or 4 after inoculation.

Retroviruses must bypass the tight coupling of splicing and nuclear export of mRNA in their replication cycle because unspliced genomic RNA and incompletely spliced mRNA must be exported to the cytoplasm for packaging or translation. This process is mediated by a cis-acting constitutive transport element (CTE) for simple retroviruses and by the trans-acting viral protein Rev in concert with its response element (RRE) for complex retroviruses (e.g., HIV). Recently, we identified RNA helicase A (RHA) as a potential cellular cofactor for CTE. Here, we report that RHA also plays a role in Rev/RRE-mediated gene expression and HIV replication. RHA binds weakly to HIV-1 RRE independently of Rev. Overexpression of RHA, but not of an RHA mutant lacking helicase activity, increased both Rev/RRE- and CTE-dependent gene expression and the levels of unspliced HIV mRNA. Microinjection of antibodies to RHA into nuclei dramatically inhibited both CTE- and Rev-dependent gene expression in human cells. Exogenous RHA cDNA, but not the mutant RHA, rescued this inhibition. We propose that RHA is required to release both CTE- and RRE-containing mRNA from spliceosomes before completion of splicing, thus freeing them for nuclear export.

The core polyprotein of feline immunodeficiency virus (FIV) was expressed in primary feline T-lymphocytes using a retroviral vector. These cells were used as antigen-presenting stimulator cells (APSC) for the in vitro induction of cytotoxic T-lymphocytes (CTL) from feline peripheral blood mononuclear cells (PBMC). CTL from 4 cats chronically infected with the Petaluma strain of FIV specifically lysed autologous FIV-infected targets in an MHC-restricted manner. The CD8 phenotype of more than 70% of the induced effector cells (97% for cells from one cat) was consistent with MHC class I-restricted cytotoxicity. In addition, it was possible to detect low levels of core polyprotein-specific lysis from effector cells of two of the FIV-infected cats. When observed, the level of lysis, measured as a percentage of specific 111 In release, was lower for the transgenic gag -expressing targets than for FIV-infected targets. The difference in killing may reflect the low level of core polyprotein expressed in the transgenic cells compared with FIV-infected cells. FIV-specific CTL were not detected in either PBMC stimulated with cells transduced by a retroviral vector without the FIV gag sequence or PBMC from an uninfected cat stimulated with autologous transgenic APSC. The detection of FIV-specific CTL from infected cats following stimulation with transgenic APSC suggests a role for retroviral vectors in determining CTL specific for individual lentiviral proteins in protective immunity.