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Transcriptomic Analysis Reveals the Formation Mechanism of Anthocyanins Light-Independent Synthesis in Chrysanthemum

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Phyton-International Journal of Experimental Botany 2024年第7期93卷 1599-1621页

作者： Fangye Liu Jiaping Qu Yajun Li Jiawei Fan Yumeng Cui Jingwen Wu Xueqi Gu Xia Li He Huang beijing Advanced Innovation Center for Tree Breeding by Molecular Design Beijing Key Laboratory of Ornamental Plants Germplasm Innovation&Molecular BreedingNational Engineering Research Center for FloricultureBeijing Laboratory of Urban and Rural Ecological EnvironmentKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Education MinistrySchool of Landscape ArchitectureBeijing Forestry UniversityBeijing100083China Urban Construction School Beijing City UniversityBeijing100083China

Chrysanthemum×morifolium is a horticultural crop which plays a vital role in theﬂower industry with signiﬁ-cant economic value and has a cultivation history of over three thousand years in *** accumulation of anthocyanins is always affected by ***,we revealed that anthocyanin accumulation is highly dependent on light in‘2021135’genotype chrysanthemum,while it is light-independent in‘2001402’genotype ***,no literature has been reported regarding the non-photosensitive chrysanthemum in anthocya-nins light-independent synthesis *** the phenotype analysis of 44 F1 generations,we found that light-independence is a dominant trait which can be stable inherited by *** transcriptome of the rayﬂorets of‘2021135’and‘2001402’under light and bagging treatment were sequenced and *** on weighted gene co-expression network analysis(WGCNA),K-means analysis,and Real-Time Quantitative Poly-merase Chain Reaction(RT-qPCR)analysis,16 genes were highly correlated with the anthocyanin *** anthocyanin content of rayﬂorets treated with different light-quality conditions indicated that blue light signiﬁ-cantly affected anthocyanin *** Yeast one-hybrid analysis,CmBIC1.1 and CmBIC1.2 can directly regulate the anthocyanin structural gene *** our study,we revealed the important characteristics of light-independent anthocyanin synthesis in chrysanthemums and screened regulatory factors in light-depen-dent and light-independent anthocyanin synthesis *** results laid the groundwork for subsequent ana-lysis of the molecular mechanism involved in the light-independent synthesis of anthocyanins in chrysanthemums.

关键词： Chrysanthemum non-photosensitive transcriptome anthocyanin biosynthesis

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Natural Disaster Risk Monitoring for Immovable Cultural Relics Based on Digital Twin

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Journal of Geodesy and Geoinformation science 2024年第1期7卷 90-104页

作者： LI Bolun DONG Youqiang QIAO Yunfei HOU Miaole WEN Caihuan The International Joint Laboratory of Safety and Energy Conservation for Ancient Buildings Beijing University of Civil Engineering and ArchitectureBeijing 102616China China Cultural Heritage Information and Consulting Center Beijing 100029China Hebei Institute of Geological Surveying and Mapping Langfang 065000China

Natural disaster risk monitoring is an important task for disaster prevention and *** the case of immovable cultural relics,however,the feedback mechanism,risk factors,monitoring logic,and monitoring indicators of natural disaster risk monitoring are *** to achieve intelligent perception and monitoring of natural disaster risk for immovable cultural relics has always been a focus and a challenge for *** on the analysis of the concepts and issues related to the natural disaster risk of immovable cultural relics,this paper proposes a framework for natural disaster risk monitoring for immovable cultural relics based on the digital *** framework focuses on risk monitoring,including the physical entities of natural disaster risk for immovable cultural relics,monitoring indicators,and virtual entity construction.A platform for monitoring the natural disaster risk of immovable cultural relics is *** the Puzhou Ancient City Site as a test bed,the proposed concept can be used for monitoring the natural disaster risk of immovable cultural relics at different scales.

关键词： immovable cultural relics natural disaster risk digital twin risk monitoring

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Cognitive impairment in cerebral small vessel disease induced by hypertension

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Neural Regeneration Research 2024年第7期19卷 1454-1462页

作者： Weipeng Wei Denglei Ma Lin Li Lan Zhang Department of Pharmacy Xuanwu Hospital of Capital Medical UniversityBeijingChina beijing Geriatric Medical Research Center Beijing Engineering Research Center for Nervous System DrugsNational Center for Neurological DisordersNational Clinical Research Center for Geriatric DiseasesBeijingChina

Hypertension is a primary risk factor for the progression of cognitive impairment caused by cerebral small vessel disease,the most common cerebrovascular *** r,the causal relationship between hypertension and cerebral small vessel disease remains *** has substantial negative impacts on brain health and is recognized as a risk factor for cerebrovascular *** hypertension and lifestyle factors are associated with risks for stro ke and dementia,and cerebral small vessel disease can cause dementia and *** is the main driver of cerebral small vessel disease,which changes the structure and function of cerebral vessels via various mechanisms and leads to lacunar infarction,leukoaraiosis,white matter lesions,and intracerebral hemorrhage,ultimately res ulting in cognitive decline and demonstrating that the brain is the to rget organ of *** review updates our understanding of the pathogenesis of hypertensioninduced cerebral small vessel disease and the res ulting changes in brain structure and function and declines in cognitive *** also discuss drugs to treat cerebral small vessel disease and cognitive impairment.

关键词： blood-brain barrier cerebral small vessel disease cognitive impairment dementia endothelial dysfunction enlarged perivascular space hypertension lacunar infarction neuroinflammation treatment white matter high signal intensity

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Distributed Region Tracking and Perimeter Surveillance for Second-Order Multi-Agent Systems in Star-Shaped Sets

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Journal of Systems science & Complexity 2024年第5期37卷 1995-2020页

作者： SHANG Juan MO Lipo MI Rongxin CAO Xianbing School of Mathematics and Statistics Beijing Technology and Business University The Department of Foundation Shijiazhuang Institute of Railway Technology School of Computer and Artificial Intelligence Beijing Technology and Business University Research Centre for Agri-Product Quality Traceability Beijing Technology and Business University Coordination Center of China National Computer Network Emergency Response Technical Team

This paper investigates region tracking and perimeter surveillance of second-order multi-agent systems, where all agents move within a star-shaped set. First, by coordination transformations,the region tracking problem is converted from the star-shaped sets to a circular region. The authors employ communication and collaboration to complete region tracking and perimeter surveillance tasks,and then revert back to the star-shaped set by using inverse transformations. Second, the authors propose a distributed control strategy based on attractive and interaction potential functions, under which all agents can quickly track a given circular region and move around the perimeter. Finally,the authors validate the effectiveness and performance advantages of the proposed method through simulation experiments.

关键词： Distributed control multi-agent systems star-shaped sets target tracking

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Distributed Heterogeneous Multi-Agent Optimization with Stochastic Sub-Gradient

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Journal of Systems science & Complexity 2024年第4期37卷 1470-1487页

作者： HU Haokun MO Lipo CAO Xianbing School of Mathematics and Statistics Central South UniversityChangsha 410083China School of Mathematics and Statistics Beijing Technology and Business UniversityBeijing 100048China Research Centre for Agri-Product Quality Traceability Beijing Technology and Business UniversityBeijing 100048China School of Computer and Artificial Intelligence Beijing Technology and Business UniversityBeijing 100048China China Food Flavor and Nutrition Health Innovation Center Beijing Technology and Business UniversityBeijing 100048China

This paper studies the optimization problem of heterogeneous networks under a timevarying *** agent only accesses to one local objective function,which is *** improved algorithm with noisy measurement of local objective functions' sub-gradients and additive noises among information exchanging between each pair of agents is designed to minimize the sum of objective functions of all *** weaken the effect of these noises,two step sizes are introduced in the control *** graph theory,stochastic analysis and martingale convergence theory,it is proved that if the sub-gradients are uniformly bounded,the sequence of digraphs is balanced and the union graph of all digraphs is joint strongly connected,then the designed control protocol can force all agents to find the global optimal point almost *** last,the authors give some numerical examples to verify the effectiveness of the stochastic sub-gradient algorithms.

关键词： Communication noises distributed stochastic optimization heterogeneous networks subgradient measurement noises

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Proteomic Stratification of Prognosis and Treatment Options for Small Cell Lung Cancer

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Genomics, Proteomics & Bioinformatics 2024年第2期22卷 81-92页

作者： Zitian Huo Yaqi Duan Dongdong Zhan Xizhen Xu Nairen Zheng Jing Cai Ruifang Sun Jianping Wang Fang Cheng Zhan Gao Caixia Xu Wanlin Liu Yuting Dong Sailong Ma Qian Zhang Yiyun Zheng Liping Lou Dong Kuang Qian Chu Jun Qin Guoping Wang Yi Wang Institute of Pathology Tongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan 430030China Department of Pathology School of Basic MedicineTongji Medical CollegeHuazhong University of Science and TechnologyWuhan 430030China National Health Commission Key Laboratory of Respiratory Diseases Tongji HosptialTongji Medical CollegeHuazhong University of Science and TechnologyWuhan 430030China beijing Pineal Diagnostics Co. Ltd.Beijing 102206China Department of Oncology Tongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan 430030China State Key Laboratory of Proteomics Beijing Proteome Research CenterNational Center for Protein Sciences(Beijing)Beijing Institute of LifeomicsBeijing 102206China Institution of Pathology The First Affiliated Hospital of Henan UniversityKaifeng 475001China Department of Tumor Biobank Shanxi Cancer HospitalTaiyuan 030013China Chongqing Key Laboratory of Big Data for Bio Intelligence School of BioinformationChongqing University of Posts and TelecommunicationsChongqing 400065China

Small cell lung cancer(SCLC)is a highly malignant and heterogeneous cancer with limited therapeutic options and prognosis prediction ***,we analyzed formalin-fixed,paraffin-embedded(FFPE)samples of surgical resections by proteomic profiling,and stratified SCLC into three proteomic subtypes(S-I,S-II,and S-III)with distinct clinical outcomes and chemotherapy *** proteomic subtyping was an independent prognostic factor and performed better than current tumor–node–metastasis or Veterans Administration Lung Study Group staging *** subtyping results could be further validated using FFPE biopsy samples from an independent cohort,extending the analysis to both surgical and biopsy *** signatures of the S-II subtype in particular suggested potential benefits from *** overexpressed proteins in S-III,the worst prognostic subtype,allowed us to nominate potential therapeutic targets,indicating that patient selection may bring new hope for previously failed clinical ***,analysis of an independent cohort of SCLC patients who had received immunotherapy validated the prediction that the S-II patients had better progression-free survival and overall survival after first-line ***,our study provides the rationale for future clinical investigations to validate the current findings for more accurate prognosis prediction and precise treatments.

关键词： Small cell lung cancer Proteomics Prognosis Chemotherapy response Immunotherapy

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Understanding the factors influencing cloud-core vertical accelerations during deep convection formation in the WRF model

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Atmospheric and Oceanic science Letters 2024年第3期17卷 1-7页

作者： Na Li Jin Wang Lingkun Ran Lei Yin Xiba Tang Yuchen Liu Institute of Atmospheric Physics Chinese Academy of SciencesBeijingChina Guizhou Meteorological Bureau GuiyangChina University of Chinese Academy of sciences BeijingChina Nanjing University of Posts and Telecommunications NanjingChina Yunnan Key Laboratory of Meteorological Disasters and Climate Resources in the Great Mekong Subregion Yunnan UniversityKunmingChina

本文将扰动气压利用一个线性诊断关系代替,重新推导了WRF模式框架地形追随坐标系下的垂直动量方程,建立了垂直加速与对流触发(DCI)影响因子(如温度,水汽等)的直接联系.研究发现,DCI过程与对流核垂直加速相关,三维副散,扰动位势在垂直方... 详细信息

本文将扰动气压利用一个线性诊断关系代替,重新推导了WRF模式框架地形追随坐标系下的垂直动量方程,建立了垂直加速与对流触发(DCI)影响因子(如温度,水汽等)的直接联系.研究发现,DCI过程与对流核垂直加速相关,三维副散,扰动位势在垂直方向的二阶非均匀性,扰动位温垂直梯度,比湿及其垂直梯度,水凝物拖曳,均是能够直接影响垂直加速和对流触发的物理因子,这些量与模式基本预报量相关,通过解析基本预报量对对流发展的直接影响,可能有助于理解模式对DCI过程预测失败的原因.

关键词：垂直加速深对流垂直速度冰雹

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DNA methylation clocks for estimating biological age in Chinese cohorts

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Protein & Cell 2024年第8期15卷 575-593页

作者： Zikai Zheng Jiaming Li Tianzi Liu Yanling Fan Qiao-Cheng Zhai Muzhao Xiong Qiao-Ran Wang Xiaoyan Sun Qi-Wen Zheng Shanshan Che Beier jiang Quan Zheng Cui Wang Lixiao Liu Jiale Ping Si Wang Dan-Dan Gao Jinlin Ye Kuan Yang Yuesheng Zuo Shuai Ma Yun-GuiYang Jig Qu Feng Zhang Peilin Jia Guang-Hui Liu Weiqi Zhang CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China University of Chinese Academy of sciences Beijing 100049China CAS Key Laboratory of Computational Biology Shanghai Institute of Nutrition and HealthChinese Academy of SciencesShanghai 200031China Division of Orthopaedics Quzhou Affliated Hospital of Wenzhou Medical UniversityQuzhou 324000China The Joint Innovation Center for Engineering in Medicine Quzhou Affliated Hospital of Wenzhou Medical UniversityQuzhou 324000China Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric DisordersXuanwu Hospital Capital Medical UniversityBeijing 100053China Aging Translational Medicine Center International Center for Aging and CancerXuanwu HospitalCapital Medical UniversityBeijing 100053China Aging Biomarker Consortium Beijing 100101China State Key Laboratory of Membrane Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Key Laboratory of Organ Regeneration and Reconstruction Institute of ZoologyChinese Academy of SciencesBeijing 100101China nstitute for Stem Cell and Regeneration Chinese Academy of SciencesBeijing 100101China beijing Institute for Stem Cell and Regenerative Medicine Beijing 100101China State Key Laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China National Genomics Data Center Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China

Epigenetic clocks are accurate predictors of human chronological age based on the analysis of DNA methylation(DNAm)at specific CpG ***,a systematic comparison between DNA methylation data and other omics datasets has not yet been ***,available DNAm age predictors are based on datasets with limited ethnic *** address these knowledge gaps,we generated and analyzed DNA methylation datasets from two independent Chinese cohorts,revealing age-related DNAm ***,a DNA methylation aging clock(iCAS-DNAmAge)and a group of DNAm-based multi-modal clocks for Chinese individuals were developed,with most of them demonstrating strong predictive capabilities for chronological *** clocks were further employed to predict factors influencing aging *** DNAm aging clock,derived from multi-modal aging features(compositeAge-DNAmAge),exhibited a close association with multi-omics changes,lifestyles,and disease status,underscoring its robust potential for precise biological age *** findings offer novel insights into the regulatory mechanism of age-related DNAm changes and extend the application of the DNAm clock for measuring biological age and aging pace,providing the basis for evaluating aging intervention strategies.

关键词： DNA methylation aging clock aging age prediction

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Single-cell omics:experimental workflow,data analyses and applications

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science China Life sciences 2024年

作者： Fengying Sun Haoyan Li Dongqing Sun Shaliu Fu Lei Gu Xin Shao Qinqin Wang Xin Dong Bin Duan Feiyang Xing Jun Wu Minmin Xiao Fangqing Zhao Jing-Dong J.Han Qi Liu Xiaohui Fan Chen Li Chenfei Wang Tieliu Shi Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biology the Institute of Biomedical Sciences and School of Life Sciences East China Normal University beijing Institutes of Life science Chinese Academy of Sciences Peking-Tsinghua Center for Life sciences Academy for Advanced Interdisciplinary Studies Center for Quantitative Biology (CQB) Peking University Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases Women’s Hospital Zhejiang University School of Medicine Key Laboratory of Advanced Theory and Application in Statistics and Data science-MOE School of Statistics East China Normal University Shanghai 200062 China Department of Clinical Laboratory the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City) Pharmaceutical Informatics Institute College of Pharmaceutical Sciences Zhejiang University Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University) Ministry of Education Orthopaedic Department Tongji Hospital Bioinformatics Department School of Life Sciences and Technology Tongji University Frontier science Center for Stem Cells School of Life Sciences and Technology Tongji University Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East Hospital Bioinformatics Department School of Life Sciences and Technology Tongji University Research Institute of Intelligent Computing Zhejiang Lab Shanghai Research Institute for Intelligent Autonomous Systems Center for Single-cell Omics School of Public Health Shanghai Jiao Tong University School of Medicine National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River Delta Zhejiang University

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome,proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.

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CRL2^(APPBP2)-mediated TSPYL2 degradation counteracts human mesenchymal stem cell senescence

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science China(Life sciences) 2024年第3期67卷 460-474页

作者： Daoyuan Huang Qian Zhao Kuan Yang Jinghui Lei Ying Jing Hongyu Li Chen Zhang Shuai Ma Shuhui Sun Yusheng Cai Guibin Wang Jing Qu Weiqi Zhang Si Wang Guang-Hui Liu Advanced Innovation Centerfor Human Brain Protection National Clinical Research Centerfor Geriatric DisordersXuanwu Hospital Capital Medical UniversityBeijing 100053China State Key Laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Aging Translational MedicineCenter International Centerfor Aging and CancerBejing Municipal GeriatricMedical Research CenterXuanwu HospitalCapital Medical UniversityBeijing 100053China State Key Laboratory of Membrane Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of sciences Beijing 100049China beijing Institute for Stem Cell and Regenerative Medicine Beijing100101China CAS Key Laboratory of Genomic and Precision Medicine Bejing Institute of Genomics and China National Center for BioinformationChinese Academy of SciencesBeijing 100101China Institute for Stem Cell and Regeneration CASBeijing 100101China The Fifth People's Hospital of Chongqing Chongqing 400062China Sino-Danish Cllege University of Chinese Academy of SciencesBeijing101408China National Laboratory of Biomacromolecules CAS Center for Excelence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing100101China State Key Laboratory of Proteomics Beijing Proteome Research CenterNational Center for Protein Sciences(Beijing)Beijing Institute of LifeomicsBeijing 102206China

Cullin-RING E3 ubiquitin ligases(CRLs),the largest family of multi-subunit E3 ubiquitin ligases in eukaryotic cells,represent core cellular machinery for executing protein degradation and maintaining ***,we asked what roles Cullin proteins play in human mesenchymal stem cell(hMSC)homeostasis and *** this end,we conducted a comparative aging phenotype analysis by individually knocking down Cullin members in three senescence models:replicative senescent hMSCs,Hutchinson-Gilford Progeria Syndrome hMSCs,and Werner syndrome *** all family members,we found that CUL2 deficiency rendered hMSCs the most susceptible to *** investigate CUL2-specific underlying mechanisms,we then applied CRISPR/Cas9-mediated gene editing technology to generate CUL2-deficient human embryonic stem cells(hESCs).When we differentiated these into h MSCs,we found that CUL2 deletion markedly accelerates hMSC ***,we identified that CUL2 targets and promotes ubiquitin proteasome-mediated degradation of TSPYL2(a known negative regulator of proliferation)through the substrate receptor protein APPBP2,which in turn downregulates one of the canonical aging marker-P21^(waf1/cip1),and thereby delays *** work provides important insights into how CRL2^(APPBP2)-mediated TSPYL2 degradation counteracts hMSC senescence,providing a molecular basis for directing intervention strategies against aging and aging-related diseases.

关键词： Cullins stem cell senescence aging proteostasis ubiquitination APPBP2 TSPYL2

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