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Method for the extraction of circulating nucleic acids based on MOF reveals cell-free RNA signatures in liver cancer

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National science Review 2024年第1期11卷 94-106页

作者： Yuqing Sun Haixin Yu Shaoqing Han Ruoxi Ran Ying Yang Yongling Tang Yuhao Wang Wenhao Zhang Heng Tang Boqiao Fu Boshi Fu Xiaocheng Weng Song-Mei Liu Hexiang Deng Shuang Peng Xiang Zhou College of Chemistry and Molecular Sciences Key Laboratory of Biomedical Polymers-Ministry of Education Wuhan University Department of Digestive Surgical Oncology Union Hospital Tongji Medical College Huazhong University of Science and Technology Cancer Center Union HospitalTongji Medical CollegeHuazhong University of Science and Technology Department of Clinical Laboratory Center for Gene Diagnosis and Program of Clinical Laboratory Zhongnan Hospital of Wuhan University College of Chemistry and Materials Science Hubei Engineering University Department of Pharmacology School of Pharmacy China Medical University Taikang Center for Life and Medical Sciences Wuhan University Department of Hematology Zhongnan Hospital of Wuhan University

Cell-free RNA(cf RNA) allows assessment of health, status, and phenotype of a variety of human organs and is a potential biomarker to non-invasively diagnose numerous diseases. Nevertheless, there is a lack of highly efficient and bias-free cf RNA isolation technologies due to the low abundance and instability of cf ***, we developed a reproducible and high-efficiency isolation technology for different types of cell-free nucleic acids(containing cf RNA and viral RNA) in serum/plasma based on the inclusion of nucleic acids by metal-organic framework(MOF) materials, which greatly improved the isolation efficiency and was able to preserve RNA integrity compared with the most widely used research kit method. Importantly, the quality of cf RNA extracted by the MOF method is about 10-fold that of the kit method, and the MOF method isolates more than three times as many different RNA types as the kit method. The whole transcriptome mapping characteristics of cf RNA in serum from patients with liver cancer was described and a cf RNA signature with six cf RNAs was identified to diagnose liver cancer with high diagnostic efficiency(area under curve = 0.905 in the independent validation cohort) using this MOF method. Thus, this new MOF isolation technique will advance the field of liquid biopsy, with the potential to diagnose liver cancer.

关键词： MOF circulating cell-free RNA biomarker liver cancer diagnosis

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Culture-free identification of fast-growing cyanobacteria cells by Raman-activated gravity-driven encapsulation and sequencing

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Synthetic and Systems Biotechnology 2023年第4期8卷 708-715页

作者： Jinyu Cui Rongze Chen Huili Sun Yingyi Xue Zhidian Diao Jingyun Song Xiaohang Wang Jia Zhang Chen Wang Bo Ma Jian Xu Guodong Luan Xuefeng Lu Key Laboratory of Biofuels Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesNo.189 Songling RoadQingdao266101China Shandong Energy Institute Qingdao266101China Qingdao New Energy Shandong Laboratory Qingdao266101China College of Life Science University of Chinese Academy of SciencesBeijingChina Dalian National Laboratory for Clean Energy Dalian116023China Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina

By directly converting solar energy and carbon dioxide into biobased products,cyanobacteria are promising chassis for photosynthetic *** make cyanobacterial photosynthetic biosynthesis technology economically feasible on industrial scales,exploring and engineering cyanobacterial chassis and cell factories with fast growth rates and carbon fixation activities facing environmental stresses are of great *** simplify and accelerate the screening for fast-growing cyanobacteria strains,a method called Individual Cyanobacteria Vitality Tests and Screening(iCyanVS)was *** show that the ^(13)C incorporation ratio of carotenoids can be used to measure differences in cell growth and carbon fixation rates in individual cyanobacterial cells of distinct genotypes that differ in growth rates in bulk cultivations,thus greatly accelerating the process screening for fastest-growing *** feasibility of this approach is further demonstrated by phenotypically and then genotypically identifying individual cyanobacterial cells with higher salt tolerance from an artificial mutant library via Raman-activated gravity-driven encapsulation and ***,this method should find broad applications in growth rate or carbon intake rate based screening of cyanobacteria and other photosynthetic cell factories.

关键词： Cyanobacteria Single-cell Raman microspectroscopy Stable isotope probing Carotenoids Identification

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The single-cell transcriptomic landscape of the topological differences in mammalian auditory receptors

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science China(life sciences) 2024年第11期67卷 2398-2410页

作者： Xiangyu Ma Xin Chen Yuwei Che Siyao Zhu Xinlin Wang Shan Gao Jiheng Wu Fanliang Kong Cheng Cheng Yunhao Wu Jiamin Guo Jieyu Qi Renjie Chai State Key Laboratory of Bioelectronics Department of Otolaryngology Head and Neck SurgeryZhongda HospitalSchool of Life Sciences and TechnologyAdvanced Institute for Life and HealthJiangsu Province High-Tech Key Laboratory for Bio-Medical ResearchSoutheast UniversityNanjing 210096China School of Engineering Vanderbilt UniversityNashville 37240USA Department of Otolaryngology-Head and Neck Surgery Affiliated Drum Tower Hospital of Nanjing University Medical SchoolJiangsu Provincial Key Medical Discipline(Laboratory)Nanjing 210096China Research Institute of Otorhinolaryngology Nanjing 210096China Department of Neurology Aerospace Center HospitalSchool of Life SciencesBeijing Institute of TechnologyBeijing 100081China Advanced Technology Research Institute Beijing Institute of TechnologyBeijing 100081China Co-innovation Center of Neuroregeneration Nantong UniversityNantong 226001China Department of Otolaryngology Head and Neck Surgery Sichuan Provincial People’s HospitalUniversity of Electronic Science and Technology of ChinaChengdu 610072China Southeast University Shenzhen Research Institute Shenzhen 518063China

Mammalian hair cells(HCs)are arranged spirally along the cochlear axis and correspond to different frequency *** as primary sound detectors,HCs spatially segregate component frequencies into a topographical *** display significant diversity in anatomical and physiological characteristics,yet little is known about the organization of the cochleotopic map of HCs or the molecules involved in this *** single-cell RNA sequencing,we determined the distinct molecular profiles of inner hair cells and outer hair cells,and we identified numerous position-dependent genes that were expressed as *** identified genes such as Ptn,Rxra,and Nfe2l2 were found to be associated with *** employed the SCENIC algorithm to predict the transcription factors that potentially shape these tonotopic ***,we confirmed that Nfe2l2,a tonotopy-related transcription factor,is critical in mice for sensing low-tomedium sound frequencies in *** analysis of cell-cell communication revealed potential receptor-ligand networks linking inner hair cells to spiral ganglion neurons,including pathways such as BDNF-Ntrk and PTN-Scd4,which likely play essential roles in tonotopic ***,these findings suggest that molecular gradients serve as the organizing principle for maintaining the selection of sound frequencies by HCs.

关键词： tonotopic axis hair cell auditory receptor scRNA-seq

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Medicago2035:Genomes,functional genomics,and molecular breeding

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Molecular Plant 2025年第2期18卷 219-244页

作者： Qinyi Ye Chuanen Zhou Hao Lin Dong Luo Divya Jain Maofeng Chai Zhichao Lu Zhipeng Liu Sonali Roy Jiangli Dong Zeng-Yu Wang Tao Wang College of Biological Sciences China Agricultural UniversityBeijing 100193China The Key Laboratory of Plant Development and Environmental Adaptation Biology Ministry of EducationShandong Key Laboratory of Precision Molecular Crop Design and BreedingSchool of Life SciencesShandong UniversityQingdao 266237China Biotechnology Research Institute Chinese Academy of Agricultural SciencesBeijing 100081China College of Animal Science and Technology Guangxi Key Laboratory of Animal BreedingDisease Control and PreventionGuangxi Grass StationGuangxi UniversityNanning 530004China College of Agriculture Tennessee State UniversityNashvilleTN 37209USA Shandong Key Laboratory for Germplasm Innovation of Saline-Alkaline Tolerant Grasses and Trees Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River DeltaCollege of Grassland ScienceQingdao Agricultural UniversityQingdao 266109China College of Pastoral Agriculture Science and Technology State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystemsLanzhou UniversityLanzhou 730020China

Medicago,a genus in the Leguminosae or Fabaceae family,includes the most globally significant forage crops,notably alfalfa(Medicago sativa).Its close diploid relative Medicago truncatula serves as an exemplary model plant for investigating legume growth and development,as well as symbiosis with *** the past decade,advances in Medicago genomics have significantly deepened our understanding of the molecular regulatory mechanisms that underlie various *** this review,we comprehensively summarize research progress on Medicago genomics,growth and development(including compound leaf development,shoot branching,flowering time regulation,inflorescence development,floral organ development,and seed dormancy),resistance to abiotic and biotic stresses,and symbiotic nitrogen fixation with rhizobia,as well as molecular *** propose avenues for molecular biology research on Medicago in the coming decade,highlighting those areas that have yet to be investigated or that remain ambiguous.

关键词： Medicago alfalfa legume model functional genomics nodule symbiosis molecular breeding

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Large-scale data-driven and physics-based models offer insights into the relationships among the structures,dynamics,and functions of chromosomes

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Journal of Molecular Cell Biology 2023年第6期15卷 11-24页

作者： Cibo Feng Jin Wang Xiakun Chu Advanced Materials Thrust Function HubThe Hong Kong University of Science and Technology(Guangzhou)Guangzhou 511400China Green e Materials Laboratory The Hong Kong University of Science and Technology(Guangzhou)Guangzhou 511400China College of Physics Jilin UniversityChangchun 130012China Department of Chemistry and Physics The State University of New York at Stony BrookStony BrookNY 11794USA Division of Life Science The Hong Kong University of Science and TechnologyHong Kong SAR 999077China Guangzhou Municipal Key Laboratory of Materials Informatics The Hong Kong University of Science and Technology(Guangzhou)Guangzhou 511400China

The organized three-dimensional chromosome architecture in the cell nucleus provides scaffolding for precise regulation of gene *** the cell changes its identity in the cell-fate decision-making process,extensive rearrangements of chromo-some structures occur accompanied by large-scale adaptations of gene expression,underscoring the importance of chromosome dynamics in shaping genome *** the last two decades,rapid development of experimental methods has provided unprecedented data to characterize the hierarchical structures and dynamic properties of *** parallel,these enormous data offer valuable opportunities for developing quantitative computational ***,we review a variety of large-scale polymer models developed to investigate the structures and dynamics of *** from the underlying modeling strategies,these approaches can be classified into data-driven(‘top-down’)and physics-based(‘bottom-up’)*** discuss their contributions to offering valuable insights into the relationships among the structures,dynamics,and functions of chromosomes and propose the perspective of developing data integration approaches from different experimental technologies and multidisciplinary theoretical/simulation methods combined with different modeling strategies.

关键词： 4D genome data-driven model physics-based model structure-function relationships cell-fate decision struc-tural changes chromosome dynamics

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Discoidin domain receptor 1 as a potent therapeutic target in solid tumors

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hlife 2024年第9期2卷 454-466页

作者： Shaheen Bibi Weihong Zeng Peiyi Zheng Seyed Majid Mousavi Mehmandousti Tengchuan Jin Department of Obstetrics and Gynecology The First Affiliated Hospital of USTCDivision of Life Sciences and MedicineCenter for Advanced Interdisciplinary Science and Biomedicine of IHMUniversity of Science and Technology of ChinaAnhuiChina Laboratory of Structural Immunology The CAS Key Laboratory of Innate Immunity and Chronic DiseaseSchool of Basic Medical SciencesDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaAnhuiChina Institute of Health and Medicine Hefei Comprehensive National Science CenterAnhuiChina Biomedical Sciences and Health Laboratory of Anhui Province University of Science&Technology of ChinaAnhuiChina Clinical Research Hospital of Chinese Academy of Sciences(Hefei) University of Science and Technology of ChinaAnhuiChina

Despite signiﬁcant discoveries in basic cancer research and improvements in treatment options and clinical outcomes,cancer remains a major public health concern ***,the main focus of cancer research is the signaling pathways that are crucial for cell survival,cell proliferation,and cell *** aberrant expression of proteins involved in these signaling pathways often leads to abnormal cell growth,cell metastasis,and invasion of healthy *** such protein is discoidin domain receptor 1(DDR1)which belongs to the family of receptor tyrosine kinases(RTKs)and is activated upon collagen binding,as a result,downstream signaling pathways are stimulated which are responsible for cell survival,cell growth,adhesion,extracellular matrix remodeling,and cell ***1 is found to have abnormally elevated expression in various solid tumors,implying a critical role in cancer ***-tional cancer treatment involves the use of cytotoxic drugs,chemotherapy,radiotherapy,and surgery,which do not pro-vide long-term survival and often result in cancer *** small-molecule kinase inhibitors have been synthesized against RTKs including DDR1 and have been highly efﬁcacious in tumor *** recently,targeting the DDR1 extracellular domain(ECD)has garnered much attention from researchers,as inhibiting the DDR1-collagen binding has been attributed to maximizing the likelihood of the combined cytotoxic effect of both immune cells and tar-geted *** review focuses on the structure,function,activation,and signaling partners of DDR1,its role in different solid tumors,andﬁnally discusses about designing more DDR1 non-kinase inhibitors as promising therapeutic strategies against DDR1-driven tumors.

关键词： discoidin domain receptor 1(DDR1) signaling pathway solid tumors non-kinase inhibitors

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Fast reconstruction and optical-sectioning three-dimensional structured illumination microscopy

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The Innovation 2025年第3期6卷 50-58,49页

作者： Ruijie Cao Yaning Li Wenyi Wang Yunzhe Fu Xiaoyu Bu Dilizhatai Saimi Jing Sun Xichuan Ge Shan Jiang Yuru Pei Baoxiang Gao Zhixing Chen Meiqi Li Peng Xi Department of Biomedical Engineering College of Future TechnologyPeking UniversityBeijing 100871China National Biomedical Imaging Center College of Future TechnologyPeking UniversityBeijing 100871China China Academy of Space Technology Beijing Institute of Space Mechanics and ElectricityBeijing 100094China Airy Technologies Co. Ltd.Beijing 100081China Key Laboratory of Analytical Science and Technology of Hebei Province College of Chemistry and Materials ScienceHebei UniversityBaoding 071002China College of Future Technology Institute of Molecular MedicineNational Biomedical Imaging CenterBeijing Key Laboratory of Cardiometabolic Molecular MedicinePeking UniversityBeijing 100871China Institute of Biomedical Engineering Beijing Institute of Collaborative InnovationBeijingChina Key Laboratory of Machine Perception(MOE) Department of Machine IntelligencePeking UniversityBeijing 100871China Peking-Tsinghua Center for Life Science Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijing 100871China School of Life Sciences Peking UniversityBeijing 100871China

Three-dimensional structured illumination microscopy(3DSIM)is a popular method for observing subcellular/cellular structures or animal/plant tissues with gentle phototoxicity and 3D ***,its time-consuming reconstruction process poses challenges for high-throughput imaging and real-time ***,traditional 3DSIM typically requires more than six z layers for successful reconstruction and is susceptible to defocused *** poses a great gap between single-layer 2DSIM and 6-layer 3DSIM,and limits the observation of thicker *** address these limitations,we developed FO-3DSIM,a novel method that integrates spatial-domain reconstruction with optical-sectioning ***-3DSIM enhances reconstruction speed by up to 855.7 times with superior performance with limited z layers and under high defocused *** retains the high-fidelity,low-photon reconstruction capabilities of our previously proposed *** fast reconstruction and optical sectioning,we achieved large field-of-view(FOV)3D super-resolution imaging of mouse kidney actin,covering a region of 0.453 mm×0.453 mm×2.75μm within 23 min of acquisition and 13 min of *** real-time performance was demonstrated in live actin imaging with *** approach reduces photodamage through limited z layer reconstruction,allowing the observation of ER tubes with just three *** anticipate that FO-3DSIM will pave the way for near real-time,large FOV 6D imaging,encompassing xyz super-resolution,multi-color,long-term,and polarization imaging with less photodamage,removed defocused backgrounds,and reduced reconstruction time.

关键词： gentle phototoxicity phototoxicity high throughput imaging fast reconstruction real time observation optical sectioning three dimensional structured illumination microscopy reconstruction process

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Strength performance simulation and testing of pontoon component cabin 2

Strength performance simulation and testing of pontoon compo...

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2023 2nd International Conference on Aerospace and Control Engineering, ICoACE 2023

作者： Yang, Li Sun, Libing Zhu, Yuanchun Feng, Zhijie Zhang, Dongxiao Emergency Rescue Technology R&D Department Hangyu Life-Saving Equipment Co. Ltd. Hubei Xiangyang441100 China Key Laboratory of Aviation Science and Technology for Aviation Protection and Lifesaving Technology Hubei Xiangyang441100 China

The helicopter emergency flotation system consists of a buoy installation mechanism, a high-pressure gas bottle, and an electronic control starting device. The buoy assembly cabin is an important part of the buoy installation mechanism. During the flotation test, openings and cracks appeared in the pontoon assembly cabin due to insufficient strength. To avoid the occurrence of openings and cracks, methods such as rounding corners at the locations of openings and cracks, carbon fiber cross-laying technology, and changing cross-sections at stress concentration locations are adopted. The improved method was applied to the buoy cabin of the emergency flotation system, and the damage coefficient in the front and back states was simulated. The simulation results showed that the damage coefficient was reduced by 59%. After the improved cabin was subjected to the emergency flotation system flotation test, the openings and cracks in the pontoon assembly cabin disappeared, indicating that the improvement method was effective and could improve the strength and performance of the cabin. © Published under licence by IOP Publishing Ltd.

关键词： Flotation

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Synergy in Rice Immunity:Exploring Strategies of Coordinated Disease Defense Through Receptor-Like Kinases and Receptor-Like Cytoplasmic Kinases

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Rice science 2024年第6期31卷 643-658页

作者： PEI Mengtian CAO Yingying XIE Xuze CAO Ying CHEN Jia ZHANG Xi WANG Zonghua LU Guodong ZHANG Shenghang State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops Fujian Agriculture and Forestry UniversityFuzhou 350002China Fujian Key Laboratory of Aptamers Technology Fuzhou General Teaching Hospital(the 900th Hospital)Fujian Medical UniversityFuzhou 350002China Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering National Observations and Research Station for Wetland Ecosystems of the Yangtze EstuaryInstitute of Biodiversity Science and Institute of Eco-ChongmingSchool of Life SciencesFudan UniversityShanghai 200433China

Receptor-like kinases(RLKs)and receptor-like cytoplasmic kinases(RLCKs)play an indispensable role in the perception and transmission of extracellular signals in *** rice,these kinases actively participate in immune responses against a variety of pathogens,including fungi,bacteria,and ***,research on the specific response mechanisms and the spectrum of different kinase activities against various pathogens remains *** review provides an in-depth and comprehensive overview of the types and functions of RLKs and RLCKs involved in disease resistance,emphasizing the central role of certain RLKs and RLCKs in the plant immune *** kinases can recognize specific molecular patterns of pathogens and rapidly initiate an immune response in ***,the activity and functional regulation of these key kinases are tightly controlled by various post-translational modifications,such as phosphorylation and *** meticulous regulation ensures that the rice immune system's response is both precise and timely,effectively balancing the intensity of the immune response and preventing potential issues caused by either hyperactivity or *** synthesizing current research findings,this review not only broadens our understanding of the role of RLKs and RLCKs in plant immunity but also provides new perspectives and strategies for future research on disease resistance breeding in *** studies are expected to delve deeper into the signaling networks and regulatory mechanisms of these kinases,exploring their potential in agricultural production to develop rice varieties with enhanced disease resistance.

关键词： receptor-like kinase receptor-like cytoplasmic kinase pathogen-associated molecular pattern genetic breeding

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The high quality genome of potherb mustard Xuecai(Brassica juncea ***)provides new insights into leaf shape variation

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Journal of Integrative Agriculture 2025年第4期24卷 1461-1476页

作者： Shuangping Heng Mengdi Cui Xiaolin Li Shaoheng Zhang Guangzhi Mao Feng Xing Zhengjie Wan Jing Wen Jinxiong Shen Tingdong Fu College of Life Sciences Institute for Conservation and Utilization of Agro-Bioresources in Dabie MountainsXinyang Normal UniversityXinyang 464000China College of Horticulture and Forestry National Key Laboratory for Germplasm Innovation&Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhan 430070China College of Plant Science and Technology National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan 430070China

The potherb mustard Xuecai(XC)cultivar is a cruciferous vegetable that is popular either fresh or *** to the deep notches in the edges of leaves in mustard XC,this plant can be said to have multipinnately lobed *** net photosynthesis of lobed leaves is significantly greater than that of simple ***,the molecular mechanism of leaf shape variation has not been ***,we used HiFi and Hi-C data to assemble the XC *** genome was 961.72 Mb in size,with a contig N50 value of 6.565 *** XC genome was compared with four previously sequenced mustard genomes,and the genomic collinearity regions,SNPs,and indels were *** BjRCO genes were found on chromosome(Chr.)A10 in potherb mustard XC when the BjRCO gene locus was compared against other sequenced *** *** duplication was found to contribute to the BjRCO gene copy *** transcript expression of BjRCO genes was greater in multipinnately lobed leaves than in sawtooth-like ***,these findings indicate that both the greater copy number and the expression level of BjRCO genes regulate leaf shape from simple to complex in *** editing of the BjRCO gene from XC changed the leaf shape from multipinnately lobed to *** high-quality XC genome sequence not only provides new insight into *** leaf-type genomics but also helps in deciphering leaf shape *** study provides insights into the variation and evolution of important traits in Brassica plants through a comparative analysis of the sequenced genomes.

关键词： Brassica juncea genome sequence multipinnately lobed leaves BjRCO gene editing

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