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Science China(Life Sciences) 2024年第7期67卷 1338-1367页

作者： Chunli Chen Yuxin Hu Momoko Ikeuchi yuling jiao Kalika Prasad Ying Hua Su Jun Xiao Lin Xu Weibing Yang Zhong Zhao Wenkun Zhou Yun Zhou Jian Gao Jia-Wei Wang National Key Laboratory for Germplasm Innovation&Utilization of Horticultural Crops Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China College of Life Science and Technology Huazhong Agricultural UniversityWuhan 430070China Key Laboratory of Plant Molecular Physiology Institute of BotanyChinese Academy of Sciences(CAS)China National Botanical GardenBeijing 100093China Division of Biological Sciences Graduate School of Science and TechnologyNara Institute of Science and TechnologyNara 630-0192Japan State Key Laboratory of Protein and Plant Gene Research School of Life SciencesPeking UniversityBeijing 100871China Peking-Tsinghua Center for Life Sciences Center for Quantitative BiologyAcademy for Advanced Interdisciplinary StudiesPeking UniversityBeijing 100871China Indian Institute of Science Education and Research Pune 411008IndiaThiruvananthapuram 695551India State Key Laboratory of Wheat Improvement College of Life SciencesShandong Agricultural UniversityTai’an 271018China Sino-German Joint Research Center on Agricultural Biology Shandong Agricultural UniversityTai’an 271018China Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental Biology(IGDB)CASBeijing 100101China CAS-JIC Centre of Excellence for Plant and Microbial Science(CEPAMS) IGDBCASBeijing 100101China National Key Laboratory of Plant Molecular Genetics CEMPSInstitute of Plant Physiology and Ecology(SIPPE)CASShanghai 200032China CEPAMS SIPPECASShanghai 200032China Hefei National Laboratory for Physical Sciences at the Microscale CEMPSSchool of Life SciencesDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefei 230027China State Key Laboratory of Plant Environmental Resilience College of Biological SciencesChina Agricultural UniversityBeijing 100193China Department of Botany and Plant Pathology and Center for Plant Biology Purdue UniversityWest Lafayette 47907USA School of Life Science and Technology Shang

Plants or tissues can be regenerated through various *** animal regeneration,cell totipotency and pluripotency are the molecular basis of plant *** systematic studies on Arabidopsis thaliana gradually unravel the fundamental mechanisms and principles underlying plant ***,plant hormones,cell division,epigenetic remodeling,and transcription factors play crucial roles in reprogramming somatic cells and reestablishing meristematic *** research on basal non-vascular plants and monocot crops has revealed that plant regeneration differs among species,with various plant species using distinct mechanisms and displaying significant differences in regenerative *** multi-omics studies at the single-cell level,tracking plant regeneration processes in real-time,and deciphering the natural variation in regenerative capacity will ultimately help understand the essence of plant regeneration,improve crop regeneration efficiency,and contribute to future crop design.

关键词： apical meristem model species regeneration phytohormone plant cell reprogramming somatic embryogenesis

Improved Analysis of PINNs:Alleviate the CoD for Compositional Solutions

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Annals of Applied Mathematics 2023年第3期39卷 239-263页

作者： yuling jiao Xiliang Lu Jerry Zhijian Yang Cheng Yuan Pingwen Zhang School of Mathematics and Statistics Wuhan UniversityWuhanHubei 430072China Hubei Key Laboratory of Computational Science Wuhan UniversityWuhanHubei 430072China School of Mathematical Sciences Peking UniversityBeijing 100871China

In this paper,we present an improved analysis of the Physics Informed Neural Networks(PINNs)method for solving second-order elliptic *** assuming an intrinsic sparse structure in the underlying solution,we provide a convergence rate analysis that can overcome the curse of dimensionality(CoD).Specifically,using some approximation theory in Sobolev space together with the multivariate Faa di Bruno formula,we first derive the approximation error for composition functions with a small degree of freedom in each compositional ***,by integrating several results on the statistical error of neural networks,we obtain a refined convergence rate analysis for PINNs in solving elliptic equations with compositional *** also demonstrate the benefits of the intrinsic sparse structure with two simple numerical examples.

关键词： Composition function deep neural network approximation

A Posteriori Error Analysis of a P2-CDG Space-Time Finite Element Method for the Wave Equation

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Numerical Mathematics(Theory,Methods and Applications) 2022年第3期15卷 662-678页

作者： yuling Guo Jianguo Huang College of Science University of Shanghai for Science and TechnologyShanghai 200093China School of Mathematical Sciences and MOE-LSC Shanghai Jiao Tong UniversityShanghai 200240China

This paper develops a posteriori error bound for a space-time finite element method for the linear wave *** standard P_(l)conforming element is used for the spatial discretization and a P_(2)-CDG method is applied for the time *** essential ingredients in the a posteriori error analysis are the twice time reconstruction functions and the C^(1)(J)-smooth elliptic reconstruction,which lead to reliable a posteriori error bound in view of the energy *** an outcome,a time adaptive algorithm is proposed with the error equidistribution *** experiments are reported to illustrate the performance of the a posteriori error bound and the validity of the adaptive algorithm.

关键词： P_(2)-CDG wave equations a posteriori error estimate

Mechanism Analysis of Pore Water Pressure Fluctuation During Clay Precompression Consolidation

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World Journal of Engineering and Technology 2024年第4期12卷 987-995页

作者： Yueqin Wu Dengheng Zheng Chenglong jiao Siying Xie Qiaojing Li Yingyi Tan yuling Tu Guangzhou Railway Polytechnic Guangzhou China

Pore water pressure fluctuations are an inherent phenomenon during the consolidation process of clayey foundations, and understanding its mechanism is crucial for comprehending the consolidation process and addressing issues such as drainage blockage during consolidation. This study investigates the consolidation behavior of clay, particularly focusing on pore water pressure fluctuations during the consolidation process of dredged marine sedimentary mud from Daya Bay, Guangdong Province. Given the prevalent use of clay in large-scale construction projects in southern China, understanding the factors influencing pore water pressure is crucial for optimizing consolidation times and improving construction efficacy. Using a custom vacuum preloading model, the research explores the impact of sodium hydroxide on the bound water content and its subsequent effects on pore water pressure dynamics. Experimental findings reveal a distinct inflection point in pore water pressure dissipation, suggesting that particle migration and bound water interactions contribute to the observed fluctuations. These results provide valuable insights for enhancing engineering applications in clay consolidation and mitigating drainage issues, ultimately informing construction practices and reducing project timelines.

关键词： Clay Consolidation Pore Water Pressure Bound Water

考虑随机需求和时间约束LIRP联合协同优化

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西南交通大学学报 2020年第5期55卷 963-970页

作者：焦玉玲张林静邢小翠吉林大学交通学院吉林长春130022

针对多节点多层次多功能的供应链管理中整体效益亟待提高的问题,结合某连锁超市的单一供应商、多分销中心、多零售店所构成二级分销网络,建立以系统总成本和供货时间为目标的多目标选址-库存-路径问题(location-inventory-routing probl... 详细信息

针对多节点多层次多功能的供应链管理中整体效益亟待提高的问题,结合某连锁超市的单一供应商、多分销中心、多零售店所构成二级分销网络,建立以系统总成本和供货时间为目标的多目标选址-库存-路径问题(location-inventory-routing problem,LIRP)集成规划模型.利用线性加权法将其转化为单目标规划模型,提出遗传算法和节约里程法相结合的两阶段启发式算法并求解模型,第1阶段用遗传算法求解选址-库存问题,第2阶段用节约里程算法求解车辆路径规划问题.并结合某连锁超市实例,对不同总成本权重下的不同决策方案的分销网络进行LIRP集成优化,优化后的系统方案比原文献的总里程减少了3606.9 km,系统总成本减小了6526.2元,缺货成本降低了124.6元,只有19.7元,验证了模型和算法的有效性.

关键词：二级分销网络选址模型车辆路径库存两阶段启发式算法遗传算法节约里程法

Plant multiscale networks:charting plant connectivity by multi-level analysis and imaging techniques

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Science China(Life Sciences) 2021年第9期64卷 1392-1422页

作者： Xi Zhang Yi Man Xiaohong Zhuang Jinbo Shen Yi Zhang Yaning Cui Meng Yu Jingjing Xing Guangchao Wang Na Lian Zijian Hu Lingyu Ma Weiwei Shen Shunyao Yang Huimin Xu Jiahui Bian Yanping Jing Xiaojuan Li Ruili Li Tonglin Mao yuling jiao Sodmergen Haiyun Ren Jinxing Lin Beijing Advanced Innovation Center for Tree Breeding by Molecular Design Beijing Forestry UniversityBeijing 100083China College of Biological Sciences and Biotechnology Beijing Forestry UniversityBeijing 100083China School of Life Sciences Centre for Cell&Developmental Biology and State Key Laboratory of AgrobiotechnologyThe Chinese University of Hong KongHong Kong 999077China State Key Laboratory of Subtropical Silviculture Zhejiang A&F UniversityHangzhou 311300China Key Laboratory of Cell Proliferation and Regulation Biology Ministry of EducationCollege of Life ScienceBeijing Normal UniversityBeijing 100875China Key Laboratory of Plant Stress Biology School of Life SciencesHenan UniversityKaifeng 457004China College of Biological Sciences China Agricultural UniversityBeijing 100193China State Key Laboratory of Plant Physiology and Biochemistry Department of Plant SciencesCollege of Biological SciencesChina Agricultural UniversityBeijing 100193China State Key Laboratory of Plant Genomics Institute of Genetics and Developmental BiologyChinese Academy of Sciencesand National Center for Plant Gene ResearchBeijing 100101China Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation College of Life SciencesPeking UniversityBeijing 100871China

In multicellular and even single-celled organisms,individual components are interconnected at multiscale levels to produce enormously complex biological networks that help these systems maintain homeostasis for development and environmental *** biology studies initially adopted network analysis to explore how relationships between individual components give rise to complex biological *** analysis has been applied to dissect the complex connectivity of mammalian brains across different scales in time and space in The Human Brain *** plant science,network analysis has similarly been applied to study the connectivity of plant components at the molecular,subcellular,cellular,organic,and organism *** of these multiscale networks contributes to our understanding of how genotype determines *** this review,we summarized the theoretical framework of plant multiscale networks and introduced studies investigating plant networks by various experimental and computational *** next discussed the currently available analytic methodologies and multi-level imaging techniques used to map multiscale networks in ***,we highlighted some of the technical challenges and key questions remaining to be addressed in this emerging field.

关键词： multiscale network connectivity cytoskeleton membrane contact site organelle interaction multicellularity connectome cytoarchitecture topological analysis multi-level imaging techniques

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WUSCHEL介导的固有免疫:植物干细胞抵御病毒侵害的新机制

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植物学报 2020年第5期55卷 537-540页

作者：杜斐焦雨铃中国科学院种子创新研究院遗传与发育生物学研究所国家植物基因研究中心(北京)植物基因组学国家重点实验室北京100101 中国科学院大学北京100049

植物茎顶端分生组织干细胞是具有持续分化潜能的细胞团,是植物体地上部所有组织和器官的来源。由于植物行固着生长模式,其无法通过移动来趋利避害,因此保护植物干细胞免受病毒和其它病原体侵害对于植物正常生长发育至关重要。尽管人们... 详细信息

植物茎顶端分生组织干细胞是具有持续分化潜能的细胞团,是植物体地上部所有组织和器官的来源。由于植物行固着生长模式,其无法通过移动来趋利避害,因此保护植物干细胞免受病毒和其它病原体侵害对于植物正常生长发育至关重要。尽管人们很早就观察到植物茎顶端干细胞区域与其它部位相比具有极强的抗病毒特性,但很长时间以来对于植物干细胞如何抵御病毒侵染却知之甚少。近日,中国科学技术大学赵忠团队阐明了拟南芥(Arabidopsis thaliana)茎顶端干细胞通过WUS蛋白介导的固有免疫反应抵御病毒侵害的机制。WUS能被黄瓜花叶病毒诱导表达,并抑制病毒在茎尖中央区和周边区积累。WUS通过直接抑制S-腺苷-L-甲硫氨酸依赖的甲基转移酶(SAM MTase)基因的转录,影响rRNA的加工和核糖体的稳定性,使病毒蛋白质合成受阻,从而阻止病毒的复制与传播。该研究揭示了植物体的一种保守且广谱抗病毒策略,具有重要的理论意义和应用价值。

关键词：拟南芥干细胞 WUS MTase rRNA 蛋白质合成

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染色质免疫共沉淀实验方法

植物学报 2020年第4期55卷 475-480页

作者：王泓力焦雨铃中国科学院遗传与发育生物学研究所植物基因组学国家重点实验室北京100101 中国科学院大学北京100049

染色质免疫共沉淀(ChIP)技术是一种检测蛋白质与DNA结合的实验技术。该方法可以先进行样品交联,然后将蛋白质与DNA复合物进行随机DNA切断,再借助免疫学方法特异性富集与目的蛋白相结合的DNA片段,从而检测转录因子等目的蛋白质与DNA的结... 详细信息

染色质免疫共沉淀(ChIP)技术是一种检测蛋白质与DNA结合的实验技术。该方法可以先进行样品交联,然后将蛋白质与DNA复合物进行随机DNA切断,再借助免疫学方法特异性富集与目的蛋白相结合的DNA片段,从而检测转录因子等目的蛋白质与DNA的结合情况,鉴定基因启动子或其它DNA结合位点。该方法同时也可应用于研究基因组特定位点的组蛋白修饰情况。该文介绍了依赖交联固定的常规免疫共沉淀(X-ChIP),以及适用于10~3细胞级别微量实验材料的基于微球菌核酸酶非交联免疫共沉淀(ULI-NChIP)具体操作过程和注意事项。

关键词：染色质免疫共沉淀基于微球菌核酸酶非交联免疫共沉淀

Boosting wheat functional genomics via an indexed EMS mutant library of KN9204

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Plant Communications 2023年第4期4卷 58-76页

作者： Dongzhi Wang Yongpeng Li Haojie Wang Yongxin Xu Yiman Yang Yuxin Zhou Zhongxu Chen Yuqing Zhou Lixuan Gui Yi Guo Chunjiang Zhou Wenqiang Tang Shuzhi Zheng Lei Wang Xiulin Guo Yingjun Zhang Fa Cui Xuelei Lin yuling jiao Yuehui He Junming Li Fei He Xigang Liu Jun Xiao Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China Ministry of Education Key Laboratory of Molecular and Cellular Biology Hebei Key Laboratory of Molecular and Cellular BiologyCollege of Life SciencesHebei Normal UniversityHebei Collaboration Innovation Center for Cell SignalingShijiazhuang 050024China Center for Agricultural Resources Research Institute of Genetics and Development BiologyChinese Academy of SciencesShijiazhuang 050022China University of Chinese Academy of Sciences Beijing 100049China Department of Life Science TcuniIncChengdu 610000China State Key Laboratory of Protein and Plant Gene Research Peking-Tsinghua Center for Life SciencesSchool of Life SciencesCenter for Quantitative BiologyPeking UniversityBeijing 100871China State Key Laboratory of Protein and Plant Gene Research School of Advanced Agricultural SciencesPeking-Tsinghua Center for Life SciencesPeking UniversityBeijing 100871China Plant Genetic Engineering Center of Hebei Province Institute of Biotechnology and Food ScienceHebei Academy of Agriculture and Forestry SciencesShijiazhuang 050051China Institute ofCereal and OilCrops Hebei Academy of Agriculture and Forestry SciencesLaboratory of CropGenetics andBreeding ofHebeiShijiazhuang 050035China Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong College of AgricultureLudong UniversityYantai 264025China Centre of Excellence for Plant and Microbial Science(CEPAMS) JIC-CASBeijing 100101China

A better understanding of wheat functional genomics can improve targeted breeding for better agronomic traits and environmental ***,the lack of gene-indexed mutants and the low transformation efficiency of wheat limit in-depth gene functional studies and genetic manipulation for *** this study,we created a library for KN9204,a popular wheat variety in northern China,with a reference genome,transcriptome,and epigenome of different tissues,using ethyl methyl sulfonate(EMS)*** library contains a vast developmental diversity of critical tissues and transition *** capture sequencing of 2090 mutant lines using KN9204 genome-designed probes revealed that 98.79%of coding genes had mutations,and each line had an average of 1383 EMS-type *** identified new allelic variations for crucial agronomic trait-related genes such as Rht-D1,Q,TaTB1,and *** tested 100 lines with severemutations in 80 NAC transcription factors(TFs)under drought and salinity stress and identified 13 lines with altered *** analysis of three lines using transcriptome and chromatin accessibility data revealed hundreds of direct NAC targets with altered transcription patterns under salt or drought stress,including SNAC1,DREB2B,CML16,and ZFP182,factors known to respond to abiotic ***,we have generated and indexed a KN9204 EMS mutant library that can facilitate functional genomics research and offer resources for genetic manipulation of wheat.

关键词： wheat exome capture sequencing EMS mutagenesis functional genomics