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Peroxidase-like active Cu-ZIF-8 with rich copper(I)-nitrogen sites for excellent antibacterial performances toward drug-resistant bacteria

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Nano Research 2024年第8期17卷 7427-7435页

作者： Xiaoze Wang Hui Wang Jingkun Zhang Ning Han Wenjun Ma Donghai Zhang Mingshui Yao Xianliang Wang Yunfa Chen State key laboratory of Mesoscience and Engineering Institute of Process EngineeringChinese Academy of SciencesBeijing 100190China University of the Chinese Academy of Sciences Beijing 100049China laboratory of Theoretical and computational Nanoscience CAS Key Laboratory of Nanosystem and Hierarchial FabricationCAS Center for Excellence in NanoscienceNational Center for Nanoscience and TechnologyBeijing 100190China China CDC key laboratory of Environment and Population Health National Institute of Environmental HealthChinese Center for Disease Control and PreventionBeijing 100021China

Bacterial pathogens pose a serious threat to human health,and there is an urgent need to develop highly effective antibacterial materials to eliminate the increasingly serious contamination of drug-resistant ***,a Cu-doped ZIF-8 particle with unsaturated copper exhibits high peroxidase-like activity.99.998%antibacterial efficiency against *** can be achieved for 30 min at a low concentration of 50μg·mL^(−1),as well as complete sterilization against ***(up to 8 log).99.999%antibacterial efficiency against Methicillin-resistant Staphylococcus aureus can be achieved,performing orders of magnitude higher than *** mechanism shows that the unsaturated Cu-Nx sites are enzyme-like active centers,which could promote the consumption of bacteria reducing substances by H_(2)O_(2),and the generated*OH further aggravates bacterial oxidative stress and membrane *** importantly,the oxidation activity of adsorbed oxygen species on Cu-ZIF-8 is enhanced by charge transfer and structural changes between the ligand and copper center like natural ***-doped ZIF-8 with peroxidase-like activity shows great potential in antibacterial application and the revealed catalytic mechanism is helpful for understanding the high antibacterial activity of nanoparticles with Cu-Nx sites.

关键词： Cu-doped ZIF-8 peroxidase-like reactive oxygen species(ROS) catalytic mechanism antibacterial activity

Understanding the cooperative effects in the catalysis of homodimeric fluoroacetate dehalogenase

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Science China Chemistry 2024年第7期67卷 2382-2391页

作者： Ke-Wei Chen Jia-Nan Chen Jun Zhang Chao Wang Tian-Yu Sun Yun-Dong Wu key laboratory of computational Chemistry and Drug Design State Key Laboratory of Chemical OncogenomicSchool of Chemical Biology and BiotechnologyPeking University Shenzhen Graduate SchoolShenzhen 518055China Institute of Chemical biology Shenzhen Bay LaboratoryShenzhen 518132China College of Chemistry and Molecular Engineering Peking UniversityBeijing 100871China Changping laboratory Beijing 102200China

Fluoroacetate dehalogenases(FAcD),a homodimeric enzyme,catalyzes the conversion of fluoroacetic acid to glycolic acid(GoA).It has been proved that the enzyme has a half-of-the-site ***,its catalytic(C)subunit converts the first substrate to a covalent intermediate;then,the non-catalytic(NC)subunit binds a second substrate and promotes the conversion of the intermediate in the C subunit into the final *** the release of the product,the C subunit becomes the NC subunit,and the previous NC subunit becomes the C *** elucidate the detailed mechanism behind this cooperative catalysis,we have conducted microsecond-scale MD simulations along the reaction *** simulations indicate that the substrate in the NC subunit induces W185 and Y141 adopting an open conformation in the C *** opening of W185(C)facilitates the entry of catalytic water,enhancing the catalytic activity for product formation,while the opening of Y141(C)creates an unfavorable environment for product binding,promoting its *** interaction network analysis reveals that the substrate in the NC subunit can induce conformational changes through a conserved water chain at the interface.

关键词： enzyme catalysis molecular dynamics cooperative effect pre-reaction state

Universal Machine Learning Kohn–Sham Hamiltonian for Materials

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Chinese Physics Letters 2024年第7期41卷 95-110页

作者：钟阳于宏宇杨吉辉郭星宇向红军龚新高 key laboratory of computational Physical Sciences(Ministry of Education) Institute of Computational Physical SciencesState Key Laboratory of Surface Physicsand Department of PhysicsFudan UniversityShanghai 200433China Shanghai Qi Zhi Institute Shanghai 200030China

While density functional theory(DFT)serves as a prevalent computational approach in electronic structure calculations,its computational demands and scalability limitations ***,leveraging neural networks to parameterize the Kohn-Sham DFT Hamiltonian has emerged as a promising avenue for accelerating electronic structure *** advancements,challenges such as the necessity for computing extensive DFT training data to explore each new system and the complexity of establishing accurate machine learning models for multi-elemental materials still *** these hurdles,this study introduces a universal electronic Hamiltonian model trained on Hamiltonian matrices obtained from first-principles DFT calculations of nearly all crystal structures on the Materials *** demonstrate its generality in predicting electronic structures across the whole periodic table,including complex multi-elemental systems,solid-state electrolytes,Moir´e twisted bilayer heterostructure,and metal-organic ***,we utilize the universal model to conduct high-throughput calculations of electronic structures for crystals in GNoME datasets,identifying 3940 crystals with direct band gaps and 5109 crystals with flat *** offering a reliable efficient framework for computing electronic properties,this universal Hamiltonian model lays the groundwork for advancements in diverse fields,such as easily providing a huge data set of electronic structures and also making the materials design across the whole periodic table possible.

关键词： Hamiltonian utilize twisted

Hot versus cold subduction initiation

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National Science Review 2024年第2期11卷 101-102页

作者： Zhong-Hai Li key laboratory of computational Geodynamics College of Earth and Planetary SciencesUniversity of Chinese Academy of Sciences

In the framework of plate tectonics, subduction initiation(SI) indicates the birth of a plate convergent boundary, which is a key point of plate tectonics and Wilson's cycle; however, its dynamic process is not well c... 详细信息

关键词： DRIVEN CRUST

Pleistocene glaciation advances the cryptic speciation of Stellera chamaejasme *** a major biodiversity hotspot

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Journal of Integrative Plant biology 2024年第6期66卷 1192-1205页

作者： Santosh Kumar Rana Hum Kala Rana Jacob BLandis Tianhui Kuang Juntong Chen Hengchang Wang Tao Deng Charles C.Davis Hang Sun cas key laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201China Arkansas Biosciences Institute Arkansas State UniversityJonesboroArkansas 72401USA School of Integrative Plant Science Section of Plant Biology and the L.H.Bailey HortoriumCornell UniversityIthacaNew York 14853USA BTI computational biology Center Boyce Thompson InstituteIthacaNew York 14853USA cas key laboratory of Plant Germplasm Enhancement and Specialty Agriculture Chinese Academy of SciencesWuhan Botanical GardenWuhan 430074China Department of Organismic and Evolutionary biology HerbariaHarvard UniversityCambridgeMassachusetts 02138USA

The mountains of Southwest China comprise a significant large mountain range and biodiversity hotspot imperiled by global climate *** high species diversity in this mountain system has long been attributed to a complex set of factors,and recent large-scale macroevolutionary investigations have placed a broad timeline on plant diversification that stretches from 10 million years ago(Mya)to the *** our increasing understanding of the temporal mode of speciation,finer-scale populationlevel investigations are lacking to better refine these temporal trends and illuminate the abiotic and biotic influences of cryptic *** is largely due to the dearth of organismal sampling among closely related species and populations,spanning the incredible size and topological heterogeneity of this *** study dives into these evolutionary dynamics of speciation using genomic and ecomorphological data of Stellera chamaejasme *** identified four previously unrecognized cryptic species having indistinct morphological traits and large metapopulation of evolving lineages,suggesting a more recent diversification(~2.67-0.90 Mya),largely influenced by Pleistocene glaciation and biotic *** factors likely influenced allopatric speciation and advocated cyclical warming–cooling episodes along elevational gradients during the *** study refines the evolutionary timeline to be much younger than previously implicated and raises the concern that projected future warming may influence the alpine species diversity,necessitating increased conservation efforts.

关键词： cryptic speciation glacial-interglacial Hengduan Mountains north-south migration Stellera chamaejasme

Dynamics of perinuclear actin ring regulating nuclear morphology

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Applied Mathematics and Mechanics(English Edition) 2024年第8期45卷 1415-1428页

作者： Haoxiang YANG Houbo SUN Jinghao SHEN Hao WU Hongyuan JIANG cas key laboratory of Mechanical Behavior and Design of Materials Department of Modern MechanicsUniversity of Science and Technology of ChinaHefei 230026China

Cells are capable of sensing and responding to the extracellular mechanical microenvironment via the actin *** vivo,tissues are frequently subject to mechanical forces,such as the rapid and significant shear flow encountered by vascular endothelial ***,the investigations about the transient response of intracellular actin networks under these intense external mechanical forces,their intrinsic mechanisms,and potential implications are very ***,we observe that when cells are subject to the shear flow,an actin ring structure could be rapidly assembled at the periphery of the *** gain insights into the mechanism underlying this perinuclear actin ring assembly,we develop a computational model of actin *** demonstrate that this perinuclear actin ring assembly is triggered by the depolymerization of cortical actin,Arp2/3-dependent actin filament polymerization,and myosin-mediated actin network ***,we discover that the compressive stress generated by the perinuclear actin ring could lead to a reduction in the nuclear spreading area,an increase in the nuclear height,and a decrease in the nuclear *** present model thus explains the mechanism of the perinuclear actin ring assembly under external mechanical forces and suggests that the spontaneous contraction of this actin structure can significantly impact nuclear morphology.

关键词： mechanical force actin dynamics perinuclear actin ring compressive stress nucleus

Uncertain knowledge graph embedding:an effective method combining multi-relation and multi-path

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Frontiers of Computer Science 2024年第3期18卷 73-89页

作者： Qi LIU Qinghua ZHANG Fan ZHAO Guoyin WANG key laboratory of Tourism Multisource Data Perception and Decision Ministry of Culture and TourismChongqing University of Posts and TelecommunicationsChongqing 400065China Chongqing key laboratory of computational Intelligence Chongqing University of Posts and TelecommunicationsChongqing 400065China Chongqing key laboratory of Big Data Intelligent Computing Chongqing University of Posts and TelecommunicationsChongqing 400065China

Uncertain Knowledge Graphs(UKGs)are used to characterize the inherent uncertainty of knowledge and have a richer semantic structure than deterministic knowledge *** research on the embedding of UKG has only recently begun,Uncertain Knowledge Graph Embedding(UKGE)model has a certain effect on solving this ***,there are still unresolved *** the one hand,when reasoning the confidence of unseen relation facts,the introduced probabilistic soft logic cannot be used to combine multi-path and multi-step global information,leading to information *** the other hand,the existing UKG embedding model can only model symmetric relation facts,but the embedding problem of asymmetric relation facts has not be *** address the above issues,a Multiplex Uncertain Knowledge Graph Embedding(MUKGE)model is proposed in this ***,to combine multiple information and achieve more accurate results in confidence reasoning,the Uncertain ResourceRank(URR)reasoning algorithm is ***,the asymmetry in the UKG is *** embed asymmetric relation facts of UKG,a multi-relation embedding model is ***,experiments are carried out on different datasets via 4 tasks to verify the effectiveness of *** results of experiments demonstrate that MUKGE can obtain better overall performance than the baselines,and it helps advance the research on UKG embedding.

关键词： knowledge representation uncertain knowledge graph multi-relation embedding uncertain reasoning

Mitigating growth-stress tradeoffs via elevated TOR signaling in rice

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Molecular Plant 2024年第2期17卷 240-257页

作者： Wei Li Jiaqi Liu Zeqi Li Ruiqiang Ye Wenzhen Chen Yuqing Huang Yue Yuan Yi Zhang Huayi Hu Peng Zheng Zhongming Fang Zeng Tao Shiyong Song Ronghui Pan Jian Zhang Jumim Tu Jen Sheen Hao Du State key laboratory of Rice biology College of Agriculture and BiotechnologyZhejiang UniversityYu-Hang-Tang Road No.866Hangzhou 310058China ZJU-Hangzhou Global Scientific and Technological Innovation Center Zhejiang UniversityHangzhou 311215China Hainan Institute of Zhejiang University Sanya 572025China National key laboratory of Plant Molecular Genetics CASCenter for Excellence in Molecular Plant SciencesShanghai lnstitute of Plant Physiology and EcologyChineseAcademy of SciencesShanghai 200032China key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region(Ministry of Education) College of Agricultural SciencesGuizhouUniversityGuiyang 550025China State key laboratory of Rice biology and Breeding China National Rice Research InstituteHangzhou 311400China Department of Molecular biology and Center for computational and Integrative biology Massachusetts General Hospitaland Department of GeneticsHarvard Medical SchoolBostonMA02114USA

Rice production accounts for approximately half of the freshwater resources utilized in agriculture,result-ing in greenhouse gas emissions such as methane(CH4)from flooded paddy *** address this chal-lenge,environmentally friendly and cost-effective water-saving techniques have become widely adopted in rice ***,the implementation of water-saving treatments(WsTs)in paddy-field rice has been associated with a substantial yield loss of up to 50%as well as a reduction in nitrogen use efficiency(NUE).In this study,we discovered that the target of rapamycin(TOR)signaling pathway is compromised in rice under *** profiling-coupled transcriptome sequencing(polysome-seq)analysis unveiled a substantial reduction in global translation in response to WST associated with the downregulation of TOR ***,biochemical,and genetic analyses revealed new insights into the impact of the positive TOR-S6K-RPS6 and negative TOR-MAF1 modules on translation repression under ***,ammonium exhibited a greater ability to alleviate growth constraints under WsT by enhancing TOR signaling,which simultaneously promoted uptake and utilization of ammonium and nitrogen *** further demonstrated that TOR modulates the ammonium transporter AMT1;1 as well as the amino acid permease APP1 and dipeptide transporter NPF7.3 at the translational level through the 5'untranslated ***,these findings reveal that enhancing TOR signaling could mitigate rice yield penalty due to WST by regulating the processes involved in protein synthesis and *** study will contribute to the breeding of new rice varieties with increased water and fertilizer utilization efficiency.

关键词： target of rapamycin TOR water-saving rice low-carbon agriculture drought nitrogen use efficiency NUE

A Comprehensive Overview of CFN From a Commonsense Perspective

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Machine Intelligence Research 2024年第2期21卷 239-256页

作者： Ru Li Yunxiao Zhao Zhiqiang Wang Xuefeng Su Shaoru Guo Yong Guan Xiaoqi Han Hongyan Zhao key laboratory of computational Intelligence and Chinese Information Processing of Ministry of Education School of Computer and Information TechnologyShanxi UniversityTaiyuan 030006China

Chinese FrameNet(CFN)is a scenario commonsense knowledge base(CKB)that plays an important role in research on Chinese language *** is based on the theory of frame semantics and English FrameNet(FN).The CFN knowledge base contains a wealth of scenario commonsense knowledge,including frames,frame elements,and frame relations,as well as annotated instances with rich scenario-related labels on Chinese sentences and *** this paper,we conduct a comprehensive overview of CFN from a commonsense perspective,covering topics such as scenario commonsense representation,CFN resources,and its *** also summarize recent breakthroughs and identify future research ***,we introduce the concept of scenario commonsense,including its definitions,examples,and representation methods,with a focus on the relationship between scenario commonsense and the frame concept in *** addition,we provide a comprehensive overview of CFN resources and their applications,highlighting the newly proposed frame-based discourse representation and a human-machine collaboration framework for expanding the CFN ***,we explore emerging topics such as expanding the CFN resource,improving the interpretability of machine reading comprehension,and using scenario CKBs for text generation.

关键词： Chinese FrameNet(CFN) commonsense scenario commonsense frame knowledge