Prediction of ferroelectricity-driven Berry curvature enabling charge- and spin-controllable photocurrent in tin telluride monolayers

In symmetry-broken crystalline solids, pole structures of Berry curvature (BC) can emerge, and they have been utilized as a versatile tool for controlling transport properties. For example, the monopole component of the BC is induced by the time-reversal symmetry breaking, and the BC dipole arises from a lack of inversion symmetry, leading to the anomalous Hall and nonlinear Hall effects, respectively. Based on first-principles calculations, we show that the ferroelectricity in a tin telluride monolayer produces a unique BC distribution, which offers charge- and spin-controllable photocurrents. Even with the sizable band gap, the ferroelectrically driven BC dipole is comparable to those of small-gap topological materials. By manipulating the photon handedness and the ferroelectric polarization, charge and spin circular photogalvanic currents are generated in a controllable manner. The ferroelectricity in group-IV monochalcogenide monolayers can be a useful tool to control the BC dipole and the nonlinear optoelectronic responses

The catalytic core of DEMETER guides active DNA demethylation in Arabidopsis.

The Arabidopsis DEMETER (DME) DNA glycosylase demethylates the maternal genome in the central cell prior to fertilization and is essential for seed viability. DME preferentially targets small transposons that flank coding genes, influencing their expression and initiating plant gene imprinting. DME also targets intergenic and heterochromatic regions, but how it is recruited to these differing chromatin landscapes is unknown. The C-terminal half of DME consists of 3 conserved regions required for catalysis in vitro. We show that this catalytic core guides active demethylation at endogenous targets, rescuing dme developmental and genomic hypermethylation phenotypes. However, without the N terminus, heterochromatin demethylation is significantly impeded, and abundant CG-methylated genic sequences are ectopically demethylated. Comparative analysis revealed that the conserved DME N-terminal domains are present only in flowering plants, whereas the domain architecture of DME-like proteins in nonvascular plants mainly resembles the catalytic core, suggesting that it might represent the ancestral form of the 5mC DNA glycosylase found in plant lineages. We propose a bipartite model for DME protein action and suggest that the DME N terminus was acquired late during land plant evolution to improve specificity and facilitate demethylation at heterochromatin targets

Interaction and ordering of vacancy defects in NiO

By using a first-principles method employing the local density approximation plus Hubbard parameter approach, we study point defects in NiO and interactions between them. The defect states associated with nickel or oxygen vacancies are identified within the energy gap. It is found that nickel vacancies introduce shallow levels in the density of states for the spin direction opposite to that of the removed Ni atom, while the oxygen vacancy creates more localized in-gap states. The interaction profiles between vacancies indicate that specific defect arrangements are strongly favored for both nickel and oxygen vacancies. In the case of nickel vacancies, defect ordering in a simple-cubic style is found to be most stable, leading to a half-metallic behavior. The ionized oxygen vacancies also show a tendency toward clustering, more strongly than neutral pairs. The microscopic origin of vacancy clustering is understood based on overlap integrals between defect states. © 2008 The American Physical Society.open343

Revealing biomass heterosis in the allodiploid xBrassicoraphanus, a hybrid between Brassica rapa and Raphanus sativus, through integrated transcriptome and metabolites analysis

Background Heterosis is biologically important but the molecular basis of the phenomenon is poorly understood. We characterized intergeneric hybrids between B. rapa cv. Chiifu and R. sativus cv. WK10039 as an extreme example of heterosis. Taking advantage of clear heterosis phenotypes and the genetic distance between parents, we performed transcriptome and metabolite analysis to decipher the molecular basis of heterosis. Results The heterosis was expressed as fresh weight in the field and as inflorescence stem length in the glass house. Flowering time, distributed as a normal segregating population, ranged from the early flowering of one parent to the late flowering of the other, in contrast to the homogeneous flowering time in a typical F1 population, indicating unstable allelic interactions. The transcriptome and metabolome both indicated that sugar metabolism was altered, suggesting that the change in metabolism was linked to the heterosis. Because alleles were not shared between the hybridized genomes, classic models only partly explain this heterosis, indicating that other mechanisms are involved. Conclusion The differential expression of genes for primary and secondary metabolism, along with the altered metabolite profiles, suggests that heterosis could involve a change in balance between primary and secondary metabolism.This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Ministry of Science and ICT (2016R1D1A1B03930431 and 2013R1A1A2058687 to GY) and by NextGeneration BioGreen 21 Program (PJ013262 to HJH) Rural Development Administration (RDA), Korea. The funding agencies were not involved in the experimental design, collection and interpretation of data, and in preparation of the manuscript

Phonon mediated ultrafast spin relaxation of a valley-polarized electron in monolayer MoS2

The excited state of a particularly selected spin- and valley-polarized electron is gathering growing interest in terms of the coupling between different degrees of freedom and also in the perspective novel device functionality. The measurement of monolayer of MoS2 is quite much matured, and the time scales of spin relaxation, inter-valley scattering, intra-valley scattering, and electron-hole recombination have been analyzed through circularly polarized pump-prove experiments. The spin relaxation is believed to occur within 100 fs which is distinctly faster than all the other degrees of freedom. Here, we use the real-time propagation time-dependent density functional theory (rtp-TDDFT) method to investigate the microscopic origin of the spin dynamics. We present that the specific phonon, that breaks the mirror symmetry of 2H-phase of MoS2, sharply causes the precession of spins through the strong spin-orbit interaction. Thus the incoherent population of such phonons can cause the temperature-dependent relaxation of the spin polarization. We also discuss the general effect of oscillating magnetic field carried by phonons in the strong spin-orbit coupled solid system

A genetic characterization of Korean waxy maize (Zea mays L.) landraces having flowering time variation by RNA sequencing

Maize is the second-most produced crop in the Korean peninsula and has been continuously cultivated since the middle of the 16th century, when it was originally introduced from China. Even with this extensive cultivation history, the diversity and properties of Korean landraces have not been investigated at the nucleotide sequence level. We collected 12 landraces with various flowering times and performed RNA-seq in the early vegetative stage. The transcriptomes of 12 Korean landraces have been analyzed for their genetic variations in coding sequence and genetic relationships to other maize germplasm. The Korean landraces showed specific genetic characteristics and were closely related to a Chinese inbred line. Flowering-time related gene profiles pointed to multiple causes for the variation of flowering time within Korean landraces; the profiles revealed significant positive and negative correlations among genes, allowing us to infer possible mechanisms for flowering time variation in maize. Our results demonstrate the value of transcriptome-based genetic and gene expression profiles for information on possible breeding resources, which is particularly needed in Korean waxy landraces.Y

MYB1 transcription factor is a candidate responsible for red root skin in radish (Raphanus sativus L.).

Root skin color is one of the economically important traits in radish (Raphanus sativus), and the pigmentation in red skin varieties is largely attributable to anthocyanin accumulation. Pelargonidin was found as a major anthocyanin pigment accumulated in the sub-epidermal layer of red radish roots. In the 20 F2 population generated from the F1 with red root skins, root skins with red and white colors segregated in a 3:1 ratio. Additionally, a test cross between a red F3 individual and a white skin individual gave rise to 1:1 segregation of red and white, indicating that the root skin color of radish is determined by a single locus and red color is dominant over white. We performed association mapping for root skin color using SNPs obtained from RNA-seq analysis. Segregation analysis on the 152 F3 test-cross population revealed an RsMyb1 transcription factor as a candidate gene to determine root skin color. A PCR marker based on the polymorphism within 2 kb of RsMyb1 was developed and tested on 12 and 152 individuals from F2 and F3 test cross populations, respectively, and red and white root skin colors were completely distinguished corresponding to the genotypes. Expression levels of RsMyb1 in red or purple root cultivars were significantly higher than in white root cultivars. These findings suggest that RsMyb1 is a crucial determinant for anthocyanin biosynthesis in radish roots, and the molecular marker developed in this study will be useful for marker-assisted selection for red skin individuals at early seedling stages

Dynamic changes in DNA methylation occur in TE regions and affect cell proliferation during leaf-to-callus transition in Arabidopsis

Plant somatic cells can be reprogrammed into pluripotent cell mass, called callus, through a two-step in vitro tissue culture method. Incubation on callus-inducing medium triggers active cell proliferation to form a pluripotent callus. Notably, DNA methylation is implicated during callus formation, but a detailed molecular process regulated by DNA methylation remains to be fully elucidated. Here, we compared genome-wide DNA methylation profiles between leaf and callus tissues in Arabidopsis using whole-genome bisulphite-sequencing. Global distribution of DNA methylation showed that CHG methylation was increased, whereas CHH methylation was reduced especially around transposable element (TE) regions during the leaf-to-callus transition. We further analysed differentially expressed genes around differentially methylated TEs (DMTEs) during the leaf-to-callus transition and found that genes involved in cell cycle regulation were enriched and also constituted a coexpression gene network along with pluripotency regulators. In addition, a conserved DNA sequence analysis for upstream cis-elements led us to find a putative transcription factor associated with cell fate transition. CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) was newly identified as a regulator of plant regeneration, and consistently, the cca1lhy mutant displayed altered phenotypes in callus proliferation. Overall, these results suggest that DNA methylation coordinates cell cycle regulation during callus formation, and CCA1 may act as a key upstream coordinator at least in part in the processes.N

Decreased Expression of Cell Adhesion Molecule 4 in Gastric Adenocarcinoma and Its Prognostic Implications

Cell adhesion molecule 4 (CADM4) is a novel tumor suppressor candidate. The prognostic implications of CADM4 in gastric cancer have not been conclusively elucidated. Therefore, we evaluated the clinicopathological significance and prognostic value of CADM4 expression in a large series of patients with gastric adenocarcinoma. Immunohistochemical staining for CADM4 was performed on 534 gastric adenocarcinomas. We evaluated the associations between CADM4 expression and the clinicopathological and molecular characteristics of the adenocarcinomas. The prognostic effect of CADM4 expression was evaluated by survival analyses. Low CADM4 expression was significantly associated with young age (p = 0.046), aggressive histological type (p < 0.001), high pT category (p < 0.001), nodal metastasis (p < 0.001), high stage (p = 0.002), lymphovascular invasion (p = 0.001), and perineural invasion (p = 0.001). Low CADM4 expression was more frequently observed in tumors without human epidermal growth factor receptor 2 (HER2) amplification (p = 0.002). Low CADM4 expression was associated with worse overall survival (p = 0.007) and recurrence-free survival (p = 0.005) in the survival analyses. Low CADM4 expression was associated with aggressive clinicopathological features and poor clinical outcomes. CADM4 can act as a tumor suppressor in gastric adenocarcinoma and can be considered a prognostic biomarker