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Mechanism studies of the activation of DNA methyltransferase DNMT1 triggered by histone H3 ubiquitination,revealed by multi-scale molecular dynamics simulations

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Science China(Life Sciences) 2023年第2期66卷 313-323页

作者： Jixue Sun Fei Liu Longxiao Yuan ning-ning Pang Bing Zhu Na Yang State Key Laboratory of Medicinal Chemical Biology College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of TianjinNankai UniversityTianjin 300353China National Laboratory of Biomacromolecules CAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing 100101China

DNMT1 is a DNA methyltransferase that catalyzes and maintains methylation in CpG dinucleotides.It blocks the entrance of DNA into the catalytic pocket via the replication foci targeting sequence(RFTS)domain.Recent studies have shown that an H3-tail-conjugated two-mono-ubiquitin mark(H3Ub2)activates DNMT1 by binding to the RFTS domain.However,the activation mechanism of DNMT1 remains unclear.In this work,we combine various sampling methods of extensive simulations,including conventional molecular dynamics,Gaussian-accelerated molecular dynamics,and coarse-grained molecular dynamics,to elucidate the activation mechanism of DNMT1.Geometric and energy analyses show that binding of H3Ub2 to the RFTS domain of DNMT1 results in the bending of theα4-helix in the RFTS domain at approximately 30°–35°,and the RFTS domain rotates~20°anti-clockwise and moves~3?away from the target recognition domain(TRD).The hydrogen-bonding network at the RFTSTRD interface is significantly disrupted,implying that the RFTS domain is dissociated from the catalytic core,which contributes to activating the auto-inhibited conformation of DNMT1.These results provide structural and dynamic evidence for the role of H3Ub2 in regulating the catalytic activity of DNMT1.

关键词： DNA methyltransferase conformational change molecular dynamics simulation activation molecular mechanism

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Formation of composite hydrogel of carboxymethyl konjac glucomannan/gelatin for sustained release of EGCG

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Food Science and Human Wellness 2022年第5期11卷 1373-1383页

作者： Lin Wang ning zhou Shengxuan Zheng Jie pang Department of Engineering Mechanics Tsinghua UniversityBeijing 100084China Institute of Superlubricity Technology Research Institute of Tsinghua University in ShenzhenShenzhen 518057China College of Food Science Fujian Agriculture and Forestry UniversityFuzhou 350002China

Development of functional bioinspired hydrogels that have good releases control character is necessary for the application of these materials in biomedical engineering.Herein,we report a composite hydrogel prepared from several biocompatible carboxymethyl konjac glucomannan(CKGM)/gelatin(G)/tannic acid(TA)functional nano-hydroxyapatite(TA@n-HA),which has good biodegradability and pH sensitivity.The mechanism of interaction between hydrogels was confirmed by Fourier transform infrared spectroscopy,X-ray diffraction,Scanning electron microscopy and Thermogravimetric analysis.The physico-chemical properties of CKGM/G hydrogels have been significantly improved through the incorporation of TA@n-HA within the matrix.Studies in the sustained release of epigallocatechin gallate(EGCG)demonstrated that the TA@n-HA/CKGM/G hydrogels exhibit not only better pH sensitive properties,but also enhanced biocompatibility and encapsulation in comparison to the matrix devoid of TA@n-HA.Consequently,TA@n-HA/CKGM/G hydrogels using EGCG as a drug release model show the potential for drug delivery.

关键词： Hydrogel Carboxymethyl konjac glucomannan Gelatin Tannic acid Biodegradation Sustained release

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Design and Research of a Portable Tool for Assisting Elderly People Walking

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International Journal of Plant Engineering and Management 2022年第1期27卷 39-52页

作者： WU Daikun pang ning Xi′an Jiaotong Engineering Institute Xi′an 710300China

Based on the serious aging of our country′s population,starting from the impact on the quality of life of the elderly,this paper first analyzes the factors affecting the lives of the elderly,and makes predictions based on my country′s elderly care industry market.After research,a portable tool for assisting elderly people walking is designed,in which electric drive,steering mechanism and seat functions are added by ordinary auxiliary walking tools.Users can sit down and ride when they are tired,mainly including seats and walking functions.The characteristics of its users and various influencing factors are analyzed.The research results can guide the solution of the current portable tools that assist the elderly in walking.

关键词： crutches electric drives steering mechanisms portable

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Preface to Crystalline Porous Materials

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Chinese Journal of Structural Chemistry 2022年第11期41卷 1-2页

作者： Jiandong pang ning Huang Shuai Yuan Jun-Sheng Qin School of Materials Science and Engineering National Institute for Advanced MaterialsTKL of Metal and Molecule-Based Material ChemistryNankai UniversityTianjin300350China MOE Key Laboratory of Macromolecular Synthesis and Functionalization State Key Laboratory of Silicon MaterialsDepartment of Polymer Science and EngineeringZhejiang UniversityHangzhou 310027China State Key Laboratory of Coordination Chemistry School of Chemistry and Chemical EngineeringNanjing UniversityNanjing 210023China State Key Laboratory of Inorganic Synthesis and Preparative Chemistry College of Chemistry and International Center of Future ScienceJilin UniversityChangchun130012China

Novel crystalline porous materials refer to porous materials constructed by linking organic molecule units with coordination bonds, covalent bonds, or supramolecular interactions, mainly including metal-organic frameworks(MOFs), covalent organic frameworks(COFs), metal organic cages(MOCs), and so on. Due to their predictable and designable long-range ordered structures.

关键词： porous Porous linking

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Few-shot text classification by leveraging bi-directional attention and cross-class knowledge

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Science China(Information Sciences) 2021年第3期64卷 33-45页

作者： ning pang Xiang ZHAO Wei WANG Weidong XIAO Deke GUO Science and Technology on Information Engineering Laboratory National University of Defense Technology School of Computer Science and Engineering The University of New South Wales

Few-shot text classification targets at the situation where a model is developed to classify newly incoming query instances after acquiring knowledge from a few support instances. In this paper, we investigate few-shot text classification under a metric-based meta-learning framework. While the representations of the query and support instances are the key to the classification, existing study handles them independently in the text encoding stage. To better describe the classification features, we propose to exploit their interaction with adapted bi-directional attention mechanism. Moreover, distinct from previous approaches that encode different classes individually, we leverage the underlying cross-class knowledge for classification. To this end,we conceive the learning target by incorporating the large margin loss, which is expected to shorten the intra-class distances while enlarging the inter-class distances. To validate the design, we conduct extensive experiments on three datasets, and the experimental results demonstrate that our solution outperforms its state-of-the-art competitors. Detailed analyses also reveal that the bi-directional attention and the cross-class knowledge both contribute to the overall performance.

关键词： text classification meta-learning few-shot learning bi-directional attention cross-class knowledge

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Sensor radiation interception risk control in target tracking

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Defence Technology（防务技术） 2020年第3期16卷 695-704页

作者： Ce pang Gan-lin Shan Wei-ning Ma Gong-guo Xu Army Engineering University Shijiazhuang CampusShijiazhuangHebei050003China

This paper is mainly on the problem of radiation interception risk control in sensor network for target tracking.Firstly,the sensor radiation interception risk is defined as the product of the interception probability and the cost caused by the interception.Secondly,the radiation interception probability model and cost model are established,based on which the calculation method of interception risk can be obtained.Thirdly,a sensor scheduling model of radiation risk control is established,taking the minimum interception risk as the objective function.Then the Hungarian algorithm is proposed to obtain sensor scheduling scheme.Finally,simulation experiments are mad to prove the effectiveness of the methods proposed in this paper,which shows that compared with the sensor radiation interception probability control method,the interception risk control method can keep the sensor scheduling scheme in low risk as well as protect sensors of importance in the sensor network.

关键词： Radio frequency stealth Target tracking Interception probability Interception risk Hungary algorithm

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全国碳市场引入CCER交易及抵销机制的经济影响研究

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气候变化研究进展 2022年第5期18卷 622-636页

作者：张宁庞军中国人民大学环境学院北京100872

基于中国风电及光伏国家核证自愿减排量(CCER)现状及发展趋势,针对CCER供给、抵销和价格形成等关键机制问题,运用电力部门细分的递推动态可计算一般均衡(CGE)模型,模拟了在取消电价补贴的背景下全国碳市场引入风电及光伏CCER交易及抵销... 详细信息

基于中国风电及光伏国家核证自愿减排量(CCER)现状及发展趋势,针对CCER供给、抵销和价格形成等关键机制问题,运用电力部门细分的递推动态可计算一般均衡(CGE)模型,模拟了在取消电价补贴的背景下全国碳市场引入风电及光伏CCER交易及抵销机制的经济影响。研究发现:引入CCER交易及抵销机制会降低碳配额交易价格,并缓解取消电价补贴对风电和光伏电力的负面影响,但也会削弱全国碳市场的碳减排效果,且随着CCER供给总量增加这些作用更明显;全国碳市场引入CCER交易及抵销机制后,碳排放强度较高的控排行业将选择购买更多的CCER,其中火电行业是主要的CCER需求方;未来我国如果不放开CCER项目备案审批则风电行业将是主要受益方,而未来适度放开CCER项目备案审批则风电和光伏行业都将从中受益。因此,全国碳市场在引入CCER交易及抵销机制的同时需从紧设置初始碳配额发放量,并可考虑适时重启CCER项目备案审批工作以更好地促进风电和光伏电力的发展,但允许的CCER清缴比例上限应结合碳减排目标合理设定,以避免对全国碳市场产生较大冲击。

关键词：全国碳市场国家核证自愿减排量(CCER) 风电光伏可计算一般均衡(CGE)模型经济影响

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Evaluation method and optimization strategies of resilience for air&space defense system of systems based on kill network theory and improved self-information quantity

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Defence Technology（防务技术） 2023年第3期21卷 219-239页

作者： Qi Han Bo pang Sen Li ning Li Peng-song Guo Cheng-li Fan Wei-min Li Air Defense and Antimissile School Air Force Engineering UniversityXi’an710051China Graduate School Air Force Engineering UniversityXi’an710051China Information and Navigation School Air Force Engineering UniversityXi’an710077China School of Automation Science and Engineering Xi'an Jiaotong UniversityXi'an710049China

Resilience of air&space defense system of systems(SoSs)is critical to national air defense security.However,the research on it is still scarce.In this study,the resilience of air&space defense SoSs is firstly defined and the kill network theory is established by combining super network and kill chain theory.Two cases of the SoSs are considered:(a)The kill chains are relatively homogenous;(b)The kill chains are relatively heterogenous.Meanwhile,two capability assessment methods,which are based on the number of kill chains and improved self-information quantity,respectively,are proposed.The improved self-information quantity modeled based on nodes and edges can achieve qualitative and quantitative assessment of the combat capability by using linguistic Pythagorean fuzzy sets.Then,a resilient evaluation index consisting of risk response,survivability,and quick recovery is proposed accordingly.Finally,network models for regional air defense and anti-missile SoSs are established respectively,and the resilience measurement results are verified and analyzed under different attack and recovery strategies,and the optimization strategies are also proposed.The proposed theory and method can meet different demands to evaluate combat capability and optimize resilience of various types of air&space defense and similar SoSs.

关键词： network optimization theory

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Optical trapping using transverse electromagnetic(TEM)-like mode in a coaxial nanowaveguide

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Frontiers of Optoelectronics 2021年第4期14卷 399-406页

作者： Yuanhao LOU Xiongjie ning Bei WU Yuanjie pang School of Optical and Electronic Information Wuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan 430074China

Optical traps have emerged as powerful tools for immobilizing and manipulating small particles in three dimensions.Fiber-based optical traps(FOTs)significantly simplify optical setup by creating trapping centers with single or multiple pieces of optical fibers.In addition,they inherit the flexibility and robustness of fiber-optic systems.However,trapping 10-nm-diameter nanoparticles(NPs)using FOTs remains challenging.In this study,we model a coaxial waveguide that works in the optical regime and supports a transverse electromagnetic(TEM)-like mode for NP trapping.Single NPs at waveguide front-end break the symmetry of TEM-like guided mode and lead to high transmission efficiency at far-field,thereby strongly altering light momentum and inducing a large-scale back-action on the particle.We demonstrate,via finite-difference time-domain(FDTD)simulations,that this FOT allows for trapping single 10-nm-diameter NPs at low power.

关键词： fiber-based optical trap(FOT) optical waveguides optical apertures metal nanophotonic structures self-induced back-action plasmonic optical trapping

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Vascular endothelial growth factor A promotes platelet adhesion to collagen Ⅳ and causes early brain injury after subarachnoid hemorrhage

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Neural Regeneration Research 2019年第10期14卷 1726-1733页

作者： Zun-Wei Liu Jun-Jie Zhao Hong-Gang pang Jin-ning Song Department of Renal Transplantation Nephropathy Hospitalthe First Affiliated HospitalMedical College of Xi’an Jiaotong UniversityXi’anShaanxi ProvinceChina Institute of Organ Transplantation Xi’an Jiaotong UniversityXi’anShaanxi ProvinceChina Department of Neurosurgery the First Affiliated HospitalMedical College of Xi’an Jiaotong UniversityXi’anShaanxi ProvinceChina The First Affiliated Hospital Medical College of Xi’an Jiaotong UniversityXi’anShaanxi ProvinceChina

The role of vascular endothelial growth factor A in platelet adhesion in cerebral microvessels in the early stage of subarachnoid hemorrhage remains unclear.In this study,the endovascular puncture method was used to produce a rat model of subarachnoid hemorrhage.Then,30 minutes later,vascular endothelial growth factor A antagonist anti-vascular endothelial growth factor receptor 2 antibody,10μg,was injected into the right ventricle.Immunohistochemistry and western blot assay were used to assess expression of vascular endothelial growth factor A,occludin and claudin-5.Immunohistochemical double labeling was conducted to examine co-expression of GP Ⅰa-Ⅱ integrin and type Ⅳ collagen.TUNEL was used to detect apoptosis in the hippocampus.Neurological score was used to assess behavioral performance.After subarachnoid hemorrhage,the expression of vascular endothelial growth factor A increased in the hippocampus,while occludin and claudin-5 expression levels decreased.Co-expression of GP Ⅰa-Ⅱ integrin and type Ⅳ collagen and the number of apoptotic cells increased,whereas behavioral performance was markedly impaired.After treatment with anti-vascular endothelial growth factor receptor 2 antibody,occludin and claudin-5 expression recovered,while co-expression of GP Ⅰa-Ⅱ integrin and type Ⅳ collagen and the number of apoptotic cells decreased.Furthermore,behavioral performance improved notably.Our findings suggest that increased vascular endothelial growth factor A levels promote platelet adhesion and contribute to early brain injury after subarachnoid hemorrhage.This study was approved by the Biomedical Ethics Committee,Medical College of Xi’an Jiaotong University,China in December 2015.

关键词： nerve regeneration vascular endothelial growth factor A vascular endothelial growth factor receptor 2 subarachnoid hemorrhage brain injuries platelet adhesion collagen blood-brain barrier neural regeneration

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