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Multi-omics analysis reveals the evolutionary origin of diterpenoid alkaloid biosynthesis pathways in Aconitum

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Journal of Integrative Plant Biology 2023年第10期65卷 2320-2335页

作者： dake Zhao Ya Zhang Huanxing Ren Yana Shi Ding Dong Zonghang Li Guanghong Cui Yong Shen Zongmin Mou Edward JKennelly Luqi Huang Jue Ruan Suiyun chen Diqiu Yu Yupeng Cun School of Ecology and Environmental Science Yunnan UniversityKunming 650500China Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural SciencesShenzhen 518000China Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders Pediatric Research InstituteMinistry of Education Key Laboratory of Child Development and DisordersNational Clinical Research Center for Child Health and DisordersChina International Science and Technology Cooperation Base of Child Development and Critical DisordersChildren's Hospital of Chongqing Medical UniversityChongqing 400014China Germplasm Bank of Wild Species Kunming Institute of BotanyChinese Academy of SciencesKunming 650201China Faculty of Life Science and Technology Kunming University of Science and TechnologyKunming 650500China National Resource Center for Chinese Materia Medica Chinese Academy of Chinese Medical SciencesBeijing 100700China College of Agriculture and Biotechnology Yunnan Agricultural UniversityKunming 650201China Department of Biological Sciences Lehman CollegeCity University of New YorkBronx 10468New YorkUSA Graduate Center City University of New YorkBronx 10468New YorkUSA State Key Laboratory for Conservation and Utilization of Bio‐resources in Yunnan Yunnan UniversityKunming 650500China

Diterpenoid alkaloids(DAs) have been often utilized in clinical practice due to their analgesic and anti-infammatory properties. Natural DAs are prevalent in the family Ranunculaceae, notably in the Aconitum genus. Nevertheless, the evolutionary origin of the biosynthesis pathway responsible for DA production remains *** this study, we successfully assembled a highquality, pseudochromosome-level genome of the DA-rich species Aconitum vilmorinianum(***)(5.76 Gb). An A. vilmorinianumspecific whole-genome duplication event was discovered using comparative genomic analysis,which may aid in the evolution of the DA biosynthesis pathway. We identified several genes involved in DA biosynthesis via integrated genomic, transcriptomic, and metabolomic analyses. These genes included enzymes encoding target ent-kaurene oxidases and aminotransferases, which facilitated the activation of diterpenes and insertion of nitrogen atoms into diterpene skeletons, thereby mediating the transformation of diterpenes into DAs. The divergence periods of these genes in A. vilmorinianum were further assessed, and it was shown that two major types of genes were involved in the establishment of the DA biosynthesis pathway. Our integrated analysis offers fresh insights into the evolutionary origin of DAs in *** as well as suggestions for engineering the biosynthetic pathways to obtain desired DAs.

关键词： Aconitum vilmorinianum acute toxicity biosynthetic pathway diterpenoid alkaloid evolutionary origin genome assembly

Microbial ingress and in vitro degradation enhanced by glucose on bioabsorbable Mg-Li-Ca alloy

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Bioactive Materials 2020年第4期5卷 902-916页

作者： Ling-Yu Li Zhuang-Zhuang Han Rong-Chang Zeng Wei-chen Qi Xiao-Fan Zhai Yi Yang Yun-Tian Lou Tingyue Gu dake Xu Ji-Zhou Duan Corrosion Laboratory for Light Metals College of Material Science and EngineeringShandong University of Science and TechnologyQingdao266590China Institute of Oceanology Chinese Academy of SciencesQingdao266590China Shenyang National Laboratory for Materials Science Northeastern UniversityShenyang110819China School of Materials Science and Engineering Zhengzhou UniversityZhengzhou450002China Department of Chemical&Biomolecular Engineering Russ College of Engineering and TechnologyOhio UniversityAthensOH45701-2979USA

Biodegradable magnesium alloys are challenging to be implanted in patients with hyperglycemia and diabetes.A hypothesis is suggested that glucose accelerates microbial ingress and in vitro degradation of Mg-Li-Ca *** resistance and mechanical properties was demonstrated using electrochemical,hydrogen evolution and tensile *** bacteria from Hank's solution were isolated via 16S rRNA gene *** results revealed that Mg-1Li-1Ca alloy exhibited different responses to Hank's solution with and without *** solution acidity was ascribed to Microbacterium hominis and Enterobacter xiangfangensis,indicating that glucose promoted microbial activity and degradation and deterioration in mechanical property of Mg-1Li-1Ca alloy.

关键词： Glucose Magnesium Bacteria Biomaterial Biodegradation

Bioactive extracellular matrix scaffolds engineered with proangiogenic proteoglycan mimetics and loaded with endothelial progenitor cells promote neovascularization and diabetic wound healing

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Bioactive Materials 2022年第4期7卷 460-473页

作者： Siqi He Tanaya Walimbe Hongyuan chen Kewa Gao Priyadarsini Kumar Yifan Wei dake Hao Ruiwu Liu Diana L.Farmer Kit S.Lam Jianda Zhou Alyssa Panitch Aijun Wang Department of Burns and Plastic Surgery The Third Xiangya Hospital of Central South UniversityChina Department of Surgery UC DavisUnited States Department of Biomedical Engineering UC DavisUnited States Department of Biochemistry and Molecular Medicine UC DavisUnited States Institute for Pediatric Regenerative Medicine Shriners Hospitals for Children Northern CaliforniaUnited States

Diabetic ischemic wound treatment remains a critical clinical *** plays a significant role in wound healing during all stages of the tissue repair *** that enhance angiogenesis and neovascularization and improve ischemic pathology may promote the healing of poor wounds,particularly diabetic wounds in highly ischemic *** previously identified a cyclic peptide LXW7 that specifically binds to integrinαvβ3 on endothelial progenitor cells(EPCs)and endothelial cells(ECs),activates vascular endothelial growth factor(VEGF)receptors,and promotes EC growth and *** this study,we designed and synthesized a multi-functional pro-angiogenic molecule by grafting LXW7 and collagen-binding peptides(SILY)to a dermatan sulfate(DS)glycosaminoglycan backbone,named LXW7-DS-SILY,and further employed this multi-functional molecule to functionalize collagen-based extracellular matrix(ECM)*** confirmed that LXW7-DS-SILY modification significantly promoted EPC attachment and growth on the ECM scaffolds in vitro and supported EPC survival in vivo in the ischemic *** applied in an established Zucker Diabetic Fatty(ZDF)rat ischemic skin flap model,LXW7-DS-SILY-functionalized ECM scaffolds loaded with EPCs significantly improved wound healing,enhanced neovascularization and modulated collagen fibrillogenesis in the ischemic ***,this study provides a promising novel treatment to accelerate diabetic ischemic wound healing,thereby reducing limb amputation and mortality of diabetic patients.

关键词： Diabetic ischemic wound ECM scaffold Endothelial progenitor cells Neovascularization Wound healing

基于蚁群算法的客运站到发线运用计划编制方法

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西南交通大学学报 2008年第2期43卷 153-158页

作者：吕红霞何大可陈韬西南交通大学交通运输学院四川成都610031 西南交通大学信息科学与技术学院四川成都610031

建立了客运站到发线使用的0-1规划模型,并用蚁群算法求解.用理论最优目标函数值与目标函数值的比值表达信息素,用列车使用到发线权值的倒数表达启发式信息,用2-opt的方法实现局部搜索.为提高解的性能和算法的收敛速度,按所处时段的列车... 详细信息

建立了客运站到发线使用的0-1规划模型,并用蚁群算法求解.用理论最优目标函数值与目标函数值的比值表达信息素,用列车使用到发线权值的倒数表达启发式信息,用2-opt的方法实现局部搜索.为提高解的性能和算法的收敛速度,按所处时段的列车密集程度和对其它列车的影响程度由大到小排序,再按该顺序求解.用哈尔滨站的实际数据验证了提出的方法的有效性.

关键词：到发线运用计划 0-1规划蚁群算法铁路客运站

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后来企业自主创新能力的内涵和影响因素分析

经济社会体制比较 2006年第2期 17-22页

作者：徐大可陈劲浙江大学管理学院

提高自主创新能力,是发展中国家后来企业提高国际竞争力的中心环节。本文在界定后来企业自主创新内涵的基础上,分析了后来企业自主创新能力的维度和影响因素,提出了一个分析后来企业自主创新能力发展的框架模型,并通过浙江赐富集团的案... 详细信息

提高自主创新能力,是发展中国家后来企业提高国际竞争力的中心环节。本文在界定后来企业自主创新内涵的基础上,分析了后来企业自主创新能力的维度和影响因素,提出了一个分析后来企业自主创新能力发展的框架模型,并通过浙江赐富集团的案例进行了说明。

关键词：后来企业自主创新

Common Postzygotic Mutational Signatures in Healthy Adult Tissues Related to Embryonic Hypoxia

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Genomics, Proteomics & Bioinformatics 2022年第1期20卷 177-191页

作者： Yaqiang Hong dake Zhang Xiangtian Zhou Aili chen Amir Abliz Jian Bai Liang Wang Qingtao Hu Kenan Gong Xiaonan Guan Mengfei Liu Xinchang Zheng Shujuan Lai Hongzhu Qu Fuxin Zhao Shuang Hao Zhen Wu Hong Cai Shaoyan Hu Yue Ma Junting Zhang Yang Ke Qian-Fei Wang Wei chen Changqing Zeng CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China Beijing Advanced Innovation Centre for Biomedical Engineering Key Laboratory for Biomechanics and Mechanobiology of Ministry of EducationSchool of Biological Science and Medical EngineeringBeihang UniversityBeijing 100191China Tsinghua-Peking Center for Life Sciences School of Life SciencesTsinghua UniversityBeijing 100084China School of Optometry and Ophthalmology and Eye Hospital Wenzhou Medical UniversityWenzhou 325035China The State Key Laboratory of Optometry Ophthalmology and Vision ScienceWenzhou 325035China Key Laboratory of Carcinogenesis and Translational Research(MOE) Laboratory of GeneticsPeking University Cancer Hospital&InstituteBeijing 100142China Skull Base and Brainstem Tumor Division Department of NeurosurgeryBeijing Tian Tan HospitalCapital Medical UniversityBeijing 100050China China National Clinical Research Center for Neurological Diseases Beijing 100050China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China Department of Hematology and Oncology Children’s Hospital of Soochow UniversitySuzhou 215025China Institute of Biophysics Chinese Academy of SciencesBeijing 100101China Collaborative Innovation Center for Genetics and Development Shanghai 200438China University of Chinese Academy of Sciences Beijing 100049China

Postzygotic mutations are acquired in normal tissues throughout an individual’s lifetime and hold clues for identifying mutagenic ***,we investigated postzygotic mutation spectra of healthy individuals using optimized ultra-deep exome sequencing of the time-series samples from the same volunteer as well as the samples from different *** blood,sperm,and muscle cells,we resolved three common types of mutational *** A and B represent clocklike mutational processes,and the polymorphisms of epigenetic regulation genes influence the proportion of signature B in mutation ***,signature C,characterized by C>T transitions at GpCpN sites,tends to be a feature of diverse normal *** of this type are likely to occur early during embryonic development,supported by their relatively high allelic frequencies,presence in multiple tissues,and decrease in occurrence with *** none of the public datasets for tumors feature this signature,except for 19.6%of samples of clear cell renal cell carcinoma with increased activation of the hypoxia-inducible factor 1(HIF-1)signaling ***,the accumulation of signature C in the mutation profile was accelerated in a human embryonic stem cell line with drug-induced activation of HIF-1α.Thus,embryonic hypoxia may explain this novel signature across multiple normal *** study suggests that hypoxic condition in an early stage of embryonic development is a crucial factor inducing C>T transitions at GpCpN sites;and individuals’genetic background may also influence their postzygotic mutation profiles.

关键词： Postzygotic mutation Mutational signature Healthy individual Embryonic development Hypoxia

Single-cell technologies:From research to application

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The Innovation 2022年第6期3卷 92-108页

作者： Lu Wen Guoqiang Li Tao Huang Wei Geng Hao Pei Jialiang Yang Miao Zhu Pengfei Zhang Rui Hou Geng Tian Wentao Su Jian chen dake Zhang Pingan Zhu Wei Zhang Xiuxin Zhang Ning Zhang Yunlong Zhao Xin Cao Guangdun Peng Xianwen Ren Nan Jiang Caihuan Tian Zi-Jiang chen Biomedical Pioneering Innovation Centre(BIOPIC) Peking UniversityBeijing 100871China Bio-Med Big Data Center CAS Key Laboratory of Computational BiologyShanghai Institute of Nutrition and HealthChinese Academy of SciencesShanghai 200031China School of Chemical Engineering and Technology Sun Yat-Sen UniversityZhuhai 519082China Mozhuo Biotech(Zhejiang)Co. Ltd.TongxiangJiaxing 314500China Geneis(Beijing)Co. Ltd.Beijing 100102China Guangzhou Institutes of Biomedicine and Health Chinese Academy of SciencesGuangzhou 510530China Department of Medical Oncology Zhongshan HospitalFudan UniversityShanghai 200032China School of Food Science and Technology Dalian Polytechnic UniversityDalian 116034China State Key Laboratory of Transducer Technology Aerospace Information Research InstituteChinese Academy of SciencesBeijing 100190China Key Laboratory of Biomechanics and Mechanobiology Ministry of EducationBeijing Advanced Innovation Center for Biomedical EngineeringSchool of Engineering MedicineBeihang UniversityBeijing 100083China Department of Mechanical Engineering City University of Hong KongHong Kong 999077China Chongqing Institute of Green and Intelligent Technology Chinese Academy of SciencesChongqing 400714China Center of Peony Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Flower Crops(North China)Key Laboratory of Biology and Genetic Improvement of Horticultural CropsMinistry of Agriculture and Rural AffairsBeijing 100081China Department of Hepatic Surgery Fudan University Shanghai Cancer CenterShanghai 200032China Advanced Technology Institute University of SurreyGuildfordSurreyGU27XHUK National Physical Laboratory TeddingtonMiddlesex TW110LWUK Institute of Clinical Science Zhongshan HospitalFudan UniversityShanghai 200032China West China School of Basic Medical Sciences&Forensic Medicine Sichuan UniversityChengdu 610041China Jinfeng Laboratory Chongqing 401329China Center for Reproduc

In recent years,more and more single-cell technologies have been developed.A vast amount of single-cell omics data has been generated by large projects,such as the Human Cell Atlas,the Mouse Cell Atlas,the Mouse RNA Atlas,the Mouse ATAC Atlas,and the Plant Cell *** on these single-cell big data,thousands of bioinformatics algorithms for quality control,clustering,cell-type annotation,developmental inference,cell-cell transition,cell-cell interaction,and spatial analysis are *** powerful experimental single-cell technology and state-of-the-art big data analysis methods based on artificial intelligence,the molecular landscape at the single-cell level can be revealed.

关键词： Atlas landscape application

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超声成像系统中自适应动态滤波器的设计

传感技术学报 2010年第1期23卷 78-81页

作者：李鹏陈裕泉胡大可郑音飞浙江大学生物医学工程系杭州310027 浙江大学电子科学技术及仪器系杭州310027

在传统超声成像的动态滤波器设计中,需首先按线性声场模型计算出近场及远场回波的中心频率,据此确定出动态滤波器在接收过程中各段的滤波器系数。但这种方式有许多与实际不符的假设,这造成了动态滤波器并不能很好的匹配真实回波,降低了... 详细信息

在传统超声成像的动态滤波器设计中,需首先按线性声场模型计算出近场及远场回波的中心频率,据此确定出动态滤波器在接收过程中各段的滤波器系数。但这种方式有许多与实际不符的假设,这造成了动态滤波器并不能很好的匹配真实回波,降低了图像的分辨率及灵敏度。为了解决这个问题,文章设计了一种自适应的动态滤波器,利用FFT变换,实时的分析各小段真实回波的频率特性,根据真实回波的频率特性选择不同的动态滤波器系数。实验证明,此种方法能够在保持图像的分辨率的同时提高图像的灵敏度。

关键词：超声自适应动态滤波器分辨率灵敏度

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种用油菜籽干燥的现状及发展趋势(英文)

农业工程学报 2012年第S2期28卷 309-315页

作者：杨玲杨明金陈建李云伍吴达科西南大学工程技术学院重庆400715

油菜籽是世界第三大植物油和第二大蛋白粉来源。油菜籽的干燥和储存工艺影响种子的生理特性和作物产量。该文在分析种用油菜籽干燥要求的基础上,对油菜籽干燥的应用现状、研究现状和设备开发现状进行了综述,在此基础上对种用油菜籽干燥... 详细信息

油菜籽是世界第三大植物油和第二大蛋白粉来源。油菜籽的干燥和储存工艺影响种子的生理特性和作物产量。该文在分析种用油菜籽干燥要求的基础上,对油菜籽干燥的应用现状、研究现状和设备开发现状进行了综述,在此基础上对种用油菜籽干燥的发展趋势进行了展望,指出:种用油菜籽干燥的研究工作应围绕干燥工艺对种子生理特性的影响、干燥过程传热传质特性、干燥过程控制和优化、CFD的应用和新型干燥技术的实验研究等方面开展;种用油菜籽干燥设备的开发应解决中小型油菜籽干燥机和小区作业干燥机的需求,并对油菜籽通用干燥设备进行参数和过程控制优化,以大幅改进其总体性能。

关键词：农业机械干燥种子干燥工艺干燥特性油菜籽生理特性种用