The catalytic core of DEMETER guides active DNA demethylation in <i>Arabidopsis</i>

Zhang, Changqing,Hung, Yu-Hung,Rim, Hyun Jung,Zhang, Dapeng,Frost, Jennifer M.,Shin, Hosub,Jang, Hosung,Liu, Fang,Xiao, Wenyan,Iyer, Lakshminarayan M.,Aravind, L.,Zhang, Xiang-Qian,Fischer, Robert L. National Academy of Sciences 2019 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.116 No.35

<P><B>Significance</B></P><P>Flowering plants reproduce via a unique double-fertilization event, producing the zygote and the nutritive endosperm. The genome of the central cell, the precursor of the endosperm, undergoes extensive demethylation prior to fertilization. This epigenetic reconfiguration, directed by the DEMETER (DME) glycosylase at thousands of loci in <I>Arabidopsis</I>, differentiates the epigenetic landscapes of parental genomes and establishes parent of origin-specific expression of many imprinted genes in endosperm essential for seed development. However, how DME is targeted to various locations remains unknown. Here we show that the multidomain DME is organized into 2 functional regions: the C-terminal region, which guides localization and catalysis, and the N-terminal region, which likely recruits chromatin remodelers to facilitate demethylation within heterochromatin.</P><P>The <I>Arabidopsis</I> 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 <I>dme</I> 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.</P>

Heritable Epigenetic Variation and its Potential Applications for Crop Improvement

( Changqing Zhang ),( Tzung Fu Hsieh ) 한국육종학회 2013 Plant Breeding and Biotechnology Vol.1 No.4

Phenotypic variation within organisms is driven primarily by genetic diversity. However, there is a growing appreciation that epigenetic variation, resulting from a multitude of diverse chemical modifications to the DNA and chromatin, can have profound effects on phenotype. Heritable epigenetic marks persist through meiosis and can be stably transmitted to the next generation, resulting in transgenerational epigenetic inheritance. Importantly, when epigenetic changes occur near coding genes, affecting their transcriptional state, heritable epigenetic variation can result in heritable phenotypic variation. Large-scale interrogation of epigenome inheritance in Arabidopsis has revealed that spontaneous variation in DNA methylation occurs at a rate that is orders of magnitude greater than genetic mutation, indicating the key importance of epigenetic variation during evolution. Thus, there is a potential for epigenetics to play a role in crop improvement, including regulation of trans gene expression and creation of novel epialleles. Here, we review cases of naturally occurring and genetically induced epialleles, and discuss how the studies from two epigenetic populations are rapidly increasing our understanding of epigenetic diversity.

Earthquake response analysis of series reactor

Changqing Bai,Qingyu Xu,Hongyan Zhang 국제구조공학회 2005 Structural Engineering and Mechanics, An Int'l Jou Vol.21 No.6

Vibration reliability sensitivity analysis of general system with correlation failure modes

Changqing Su,Yimin Zhang,Qunchao Zhao 대한기계학회 2011 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.25 No.12

The vibration problem of the general system is the main object of research. The material properties and geometry of general system are random parameters because of the manufacturing environment, technical conditions, manufacturing and installation errors, multiphase materials, features and other factors. According to the relation criterion that the difference between the natural frequency and the driving frequency of general systems is not beyond a specific value, the vibration reliability mode and vibration reliability of general systems are defined considering the correlation of the multi-order natural frequency and the random characteristics of structure size and material, and the vibration reliability analysis method for avoiding the resonant is carried out. The second-order joint failure probability is obtained by using the numerical integration method. Based on the reliability design theory and sensitivity analysis method, the vibration reliability sensitivity of the general system with correlation failure modes is extensively discussed and a numerical method for vibration reliability sensitivity design is presented. The variation regularities of vibration reliability sensitivity are obtained and the effects of random parameters on vibration reliability of the general system are studied. The presented method provided the theoretic basis for the reliability design of the general system. A numerical example demonstrated that the proposed method is effective.

Four active monomers from Moutan Cortex exert inhibitory effects against oxidative stress by activating Nrf2/Keap1 signaling pathway

Baoshun Zhang,Deqing Yu,Nanxuan Luo,Changqing Yang,Yurong Zhu 대한생리학회-대한약리학회 2020 The Korean Journal of Physiology & Pharmacology Vol.24 No.5

Paeonol, quercetin, β-sitosterol, and gallic acid extracted from Moutan Cortex had been reported to possess anti-oxidative, anti-inflammatory, and antitumor activities. This work aimed to illustrate the potential anti-oxidative mechanism of monomers in human liver hepatocellular carcinoma (HepG2) cells-induced by hydrogen peroxide (H₂O₂) and to evaluate whether the hepatoprotective effect of monomers was independence or synergy in mice stimulated by carbon tetrachloride (CCl₄). Monomers protected against oxidative stress in HepG2 cells in a doseresponse manner by inhibiting the generation of reactive oxygen species, increasing total antioxidant capacity, catalase and superoxide dismutase (SOD) activities, and activating the antioxidative pathway of nuclear factor E2-related factor 2/Kelchlike ECH-associated protein 1 (Nrf2/Keap1) signaling pathway. We found that the in vitro antioxidant capacities of paeonol and quercetin were better than those of -sitosterol and gallic acid. Furthermore, paeonol apparently diminished the levels of alanine transaminase and aspartate aminotransferase, augmented the contents of glutathione and SOD, promoted the expressions of Nrf2 and heme oxygenase-1 proteins in mice stimulated by CCl₄. In HepG2 cells, paeonol, quercetin, β-sitosterol, and gallic acid play a defensive role against H₂O₂-induced oxidative stress through activating Nrf2/Keap1 pathway, indicating that these monomers have anti-oxidative properties. Totally, paeonol and quercetin exerted anti-oxidative and hepatoprotective effects, which is independent rather than synergy.

Earthquake response analysis of series reactor

Bai, Changqing,Xu, Qingyu,Zhang, Hongyan Techno-Press 2005 Structural Engineering and Mechanics, An Int'l Jou Vol.21 No.6

A direct transfer substructure method is presented in this paper for analyzing the dynamic characteristics and the seismic random responses of a series reactor. This method combines the concept of FRF (frequency response function) and the transfer matrix algorithm with the substructure approach. The inner degrees of freedom of each substructure are eliminated in the process of reconstruction and the computation cost is reduced greatly. With the convenient solution procedure, the dynamic characteristics analysis of the structure is valid and efficient. Associated with the pseudo excitation algorithm, the direct transfer substructure method is applied to investigating the seismic random responses of the series reactor. The numerical results demonstrate that the presented method is efficient and practicable in engineering. Finally, a precise time integration method is employed in performing a time-history analysis on the series reactor under El Centro and Taft earthquake waves.

Stochastic finite element modeling and response analysis of rotor systems with random properties under random loads

Hongyan Zhang,Changqing Bai,Yijun Mao 대한기계학회 2015 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.29 No.8

Random properties and random loads are highly important in rotor dynamic analysis because they cause system dynamic responses tobehave randomly. In this paper, a stochastical finite element of rotating shaft based on Timosheko beam theory is proposed for rotor systemmodeling, in which material and geometric random properties are considered one-dimensional stochastic field functions. A randomresponse analytical method is developed to determine the statistics of the dynamic responses of stochastical rotor systems under randomloads. The numerically obtained whirl speed of a turbopump rotor system is compared with the test data to validate the proposed model,and good agreement is observed. Linear and nonlinear turbopump rotor systems are employed to compare the results obtained from theproposed model and the Monte Carlo simulation. The numerically predicted results, which coincide well with Monte Carlo simulationdata, demonstrate the feasibility and efficiency of the proposed stochastic model and method for actual rotor system analysis and design.

Nonpolar a-plane n-ZnO/i-ZnO/p-AlGaN heterojunction light emitting diode

Jun ZHANG,Jingwen CHEN,Feng WU,Shuai WANG,Hanling LONG,Shida DU,Jiangnan DAI,Changqing CHEN 한국진공학회 2016 한국진공학회 학술발표회초록집 Vol.2016 No.8

Complete genome and phylogenetic analysis of bovine papillomavirus type 15 in Southern Xinjiang dairy cow

Hu, Jianjun,Zhang, Wanqi,Chauhan, Surinder Singh,Shi, Changqing,Song, Yumeng,Zhao, Yubing,Wang, Zhehong,Cheng, Long,Zhang, Yingyu The Korean Society of Veterinary Science 2020 Journal of Veterinary Science Vol.21 No.2

Background: Bovine papilloma is a neoplastic disease caused by bovine papillomaviruses (BPVs), which were recently divided into 5 genera and at least 24 genotypes. Objectives: The complete genome sequence of BPV type 15 (BPV Aks-02), a novel putative BPV type from skin samples from infected cows in Southern Xinjiang China, was determined by collecting warty lesions, followed by DNA extraction and amplicon sequencing. Methods: DNA was analyzed initially by polymerase chain reaction (PCR) using the degenerate primers FAP59 and FAP64. The complete genome sequences of the BPV Aks-02 were amplified by PCR using the amplification primers and sequencing primers. Sequence analysis and phylogenetic analysis were performed using bio-informatic software. Results: The nucleotide sequence of the L1 open reading frame (ORF) of BPV Aks-02 was 75% identity to the L1 ORF of BPV-9 reference strain from GenBank. The complete genome consisted of 7,189 base pairs (G + C content of 42.50%) that encoded 5 early (E8, E7, E1, E2, and E4) and 2 late (L1 and L2) genes. The E7 protein contained a consensus CX₂CX₂₉CX₂C zinc-binding domain and a LxCxE motif. Among the different members of this group, the percentages of the complete genome and ORFs (including 5 early and 2 late ORFs) sequence identity of BPV Aks-02 were closer to the genus Xipapillomavirus 1 of the Xipapillomavirus genus. Phylogenetic analysis and sequence similarities based on the L1 ORF of BPV Aks-02 revealed the same cluster. Conclusions: The results suggest that BPV type (BPV Aks-02) clustered with members of the Xipapillomavirus genus as BPV 15 and were closely related to Xipapillomavirus 1.

Dynamics, Stability, and Cooperative Formation Control of Magnetic Sail-Based Planetary Displaced Orbits

Lei Zhao,Changqing Yuan,Ling Gao,Chengxi Zhang 한국항공우주학회 2023 International Journal of Aeronautical and Space Sc Vol.24 No.2

The aim of this paper is to analyze dynamic characteristics and stability of magnetic sail-based planetary displaced orbits, and the feasibility of using a magnetic sail as an advanced propellantless control technology for formation flying around elliptic planetary displaced orbits (EPDOs). The thrust can be obtained from the momentum exchange between solar wind and an artificial magnetic field. First, the requirements of a magnetic sail for generating and maintaining a planetary circular displaced orbit is discussed including the value of attitude angles and characteristic acceleration. Based on different orbital periods, the circular displaced orbits are divided into three types and their linear stability is analyzed. For elliptical orbits, the conditions required to maintain an EPDO are investigated and the dynamical models of magnetic sail formation system are established. A finite time coordinated control algorithms relying on the protocols formulated on an undirected communication graph is proposed to achieve synchronized formation tracking rapidly while enhancing the robustness of formation system due to information interaction between spacecraft. Several numerical simulations are conducted to demonstrate that spacecraft formation can be effectively controlled by the proposed propellantless propulsion system.