DWT1/DWL2 act together with OsPIP5K1 to regulate plant uniform growth in rice

•Uniform growth of the main shoot and tillers significantly influences rice plant architecture and grain yield. The WUSCHEL‐related homeobox transcription factor DWT1 is a key regulator of this important agronomic trait, disruption of which causes enhanced main shoot dominance and tiller dwarfism by an unknown mechanism. •Here, we have used yeast‐two‐hybrid screening to identify OsPIP5K1, a member of the rice phosphatidylinositol‐4‐phosphate 5‐kinase family, as a protein that interacts with DWT1. Cytological analyses confirmed that DWT1 induces accumulation of OsPIP5K1 and its product PI(4,5)P2, a phosphoinositide secondary messenger, in nuclear bodies. •Mutation of OsPIP5K1 compounds the dwarf dwt1 phenotype but abolishes the main shoot dominance. Conversely, overexpression of OsPIP5K1 partially rescues dwt1 developmental defects. Furthermore, we showed that DWL2, the homologue of DWT1, is also able to interact with OsPIP5K1 and shares partial functional redundancy with DWT1 in controlling rice uniformity. •Overall, our data suggest that nuclear localised OsPIP5K1 acts with DWT1 and/or DWL2 to coordinate the uniform growth of rice shoots, likely to be through nuclear phosphoinositide signals, and provides insights into the regulation of rice uniformity via a largely unexplored plant nuclear signalling pathway

Formalization of Function Matrix Theory in HOL

Function matrices, in which elements are functions rather than numbers, are widely used in model analysis of dynamic systems such as control systems and robotics. In safety-critical applications, the dynamic systems are required to be analyzed formally and accurately to ensure their correctness and safeness. Higher-order logic (HOL) theorem proving is a promise technique to match the requirement. This paper proposes a higher-order logic formalization of the function vector and the function matrix theories using the HOL theorem prover, including data types, operations, and their properties, and further presents formalization of the differential and integral of function vectors and function matrices. The formalization is implemented as a library in the HOL system. A case study, a formal analysis of differential of quadratic functions, is presented to show the usefulness of the proposed formalization

Ellipticity-dependent sequential over-barrier ionization of cold rubidium

We perform high-resolution measurements of momentum distribution on Rb$^{n+}$ recoil ions up to charge state $n=4$, where laser-cooled rubidium atoms are ionized by femtosecond elliptically polarized lasers with the pulse duration of 35 fs and the intensity of 3.3$\times$10$^{15}$ W/cm$^2$ in the over-barrier ionization (OBI) regime. The momentum distributions of the recoil ions are found to exhibit multi-band structures as the ellipticity varies from the linear to circular polarizations. The origin of these band structures can be explained quantitatively by the classical OBI model and dedicated classical trajectory Monte Carlo simulations with Heisenberg potential. Specifically, with back analysis of the classical trajectories, we reveal the ionization time and the OBI geometry of the sequentially released electrons, disentangling the mechanisms behind the tilted angle of the band structures. These results indicate that the classical treatment can describe the strong-field multiple ionization processes of alkali atoms

Methylation of CYP1A1 and VKORC1 promoter associated with stable dosage of warfarin in Chinese patients

Objective To investigate the association between DNA methylation and the stable warfarin dose through genome-wide DNA methylation analysis and pyrosequencing assay. Method This study included 161 patients and genome-wide DNA methylation analysis was used to screen potential warfarin dose-associated CpGs through Illumina Infinium HumanMethylation 450 K BeadChip; then, the pyrosequencing assay was used to further validate the association between the stable warfarin dose and alterations in the methylation of the screened CpGs. GenomeStudio Software and R were used to analyze the differentially methylated CpGs. Results The methylation levels of CpGs surrounding the xenobiotic response element (XRE) within the CYP1A1 promoter, differed significantly between the different dose groups (P  0, P < 0.05) with an increase in the stable dose of warfarin. At the VKORC1 promoter, two CpGs methylation levels were significantly different between the differential dose groups (P < 0.05), and one CpG (Chr16: 31106793) presented a significant negative correlation (r <  0, P <  0.05) among different dose (low, medium, and high) groups. Conclusion This is a novel report of the methylation levels of six CpGs surrounding the XRE within the CYP1A1 promoter and one differential CpG at the VKORC1 promoter associated with stable warfarin dosage; these methylation levels might be applied as molecular signatures for warfarin

Molecular analysis of phosphomannomutase (PMM) genes reveals a unique PMM duplication event in diverse Triticeae species and the main PMM isozymes in bread wheat tissues

BACKGROUND: Phosphomannomutase (PMM) is an essential enzyme in eukaryotes. However, little is known about PMM gene and function in crop plants. Here, we report molecular evolutionary and biochemical analysis of PMM genes in bread wheat and related Triticeae species. RESULTS: Two sets of homoeologous PMM genes (TaPMM-1 and 2) were found in bread wheat, and two corresponding PMM genes were identified in the diploid progenitors of bread wheat and many other diploid Triticeae species. The duplication event yielding PMM-1 and 2 occurred before the radiation of diploid Triticeae genomes. The PMM gene family in wheat and relatives may evolve largely under purifying selection. Among the six TaPMM genes, the transcript levels of PMM-1 members were comparatively high and their recombinant proteins were all enzymatically active. However, PMM-2 homoeologs exhibited lower transcript levels, two of which were also inactive. TaPMM-A1, B1 and D1 were probably the main active isozymes in bread wheat tissues. The three isozymes differed from their counterparts in barley and Brachypodium distachyon in being more tolerant to elevated test temperatures. CONCLUSION: Our work identified the genes encoding PMM isozymes in bread wheat and relatives, uncovered a unique PMM duplication event in diverse Triticeae species, and revealed the main active PMM isozymes in bread wheat tissues. The knowledge obtained here improves the understanding of PMM evolution in eukaryotic organisms, and may facilitate further investigations of PMM function in the temperature adaptability of bread wheat

Giant All-Optical Modulation of Second-Harmonic Generation Mediated by Dark Excitons.

All-optical control of nonlinear photonic processes in nanomaterials is of significant interest from a fundamental viewpoint and with regard to applications ranging from ultrafast data processing to spectroscopy and quantum technology. However, these applications rely on a high degree of control over the nonlinear response, which still remains elusive. Here, we demonstrate giant and broadband all-optical ultrafast modulation of second-harmonic generation (SHG) in monolayer transition-metal dichalcogenides mediated by the modified excitonic oscillation strength produced upon optical pumping. We reveal a dominant role of dark excitons to enhance SHG by up to a factor of ∼386 at room temperature, 2 orders of magnitude larger than the current state-of-the-art all-optical modulation results. The amplitude and sign of the observed SHG modulation can be adjusted over a broad spectral range spanning a few electronvolts with ultrafast response down to the sub-picosecond scale via different carrier dynamics. Our results not only introduce an efficient method to study intriguing exciton dynamics, but also reveal a new mechanism involving dark excitons to regulate all-optical nonlinear photonics

Complex 3D microfluidic architectures formed by mechanically guided compressive buckling.

Microfluidic technologies have wide-ranging applications in chemical analysis systems, drug delivery platforms, and artificial vascular networks. This latter area is particularly relevant to 3D cell cultures, engineered tissues, and artificial organs, where volumetric capabilities in fluid distribution are essential. Existing schemes for fabricating 3D microfluidic structures are constrained in realizing desired layout designs, producing physiologically relevant microvascular structures, and/or integrating active electronic/optoelectronic/microelectromechanical components for sensing and actuation. This paper presents a guided assembly approach that bypasses these limitations to yield complex 3D microvascular structures from 2D precursors that exploit the full sophistication of 2D fabrication methods. The capabilities extend to feature sizes <5 μm, in extended arrays and with various embedded sensors and actuators, across wide ranges of overall dimensions, in a parallel, high-throughput process. Examples include 3D microvascular networks with sophisticated layouts, deterministically designed and constructed to expand the geometries and operating features of artificial vascular networks

Identification of LncRNA Linc00513 Containing Lupus-Associated Genetic Variants as a Novel Regulator of Interferon Signaling Pathway

Systemic lupus erythematosus (SLE) is a complex autoimmune disease characterized by augmented type I interferon signaling. High-throughput technologies have identified plenty of SLE susceptibility single-nucleotide polymorphisms (SNPs) yet the exact roles of most of them are still unknown. Functional studies are principally focused on SNPs in the coding regions, with limited attention paid to the SNPs in non-coding regions. Long non-coding RNAs (lncRNAs) are important players in shaping the immune response and show relationship to autoimmune diseases. In order to reveal the role of SNPs located near SLE related lncRNAs, we performed a transcriptome profiling of SLE patients and identified linc00513 as a significantly over expressed lncRNA containing functional SLE susceptibility loci in the promoter region. The risk-associated G allele of rs205764 and A allele of rs547311 enhanced linc00513 promoter activity and related to increased expression of linc00513 in SLE. We also identified linc00513 to be a novel positive regulator of type I interferon pathway by promoting the phosphorylation of STAT1 and STAT2. Elevated linc00513 expression positively correlated with IFN score in SLE patients. Linc00513 expression was higher in active disease patients than those inactive ones. In conclusion, our data identify two functional promoter variants of linc00513 that contribute to increased level of linc00513 and confer susceptibility on SLE. The study provides new insights into the genetics of SLE and extends the role of lncRNAs in the pathogenesis of SLE