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

Science China Life Sciences 2025年第1期68卷 5-102页

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 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 SciencesZhejiang University Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University) Ministry of EducationOrthopaedic DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji University Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Research Institute of Intelligent Computing Zhejiang Lab Shanghai Research Institute for Intelligent Autonomous Systems Center for Single-cell Omics School of Public HealthShanghai Jiao Tong University School of Medicine National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang University Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal University Beijing Institutes of Life Science Chinese Academy of Sciences Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology (CQB)Peking University Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases Women's HospitalZhejiang University School of Medicine Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of StatisticsEast China Normal 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 sc RNA-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.

关键词： single-cell sequencing genome epigenome proteomics metabolomics multimodal spatial transcriptomics CRISPR screening

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De novo synthesis of atropisomeric benzofurans via Cu/SPDO complex catalyzed asymmetric formal [3 + 2] annulation

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Science China Chemistry 2025年第1期68卷 174-180页

作者： fan-xiao Meng Xing-Yu Wang Ka Lu Ju-Song Yang Fu-Min Zhang Ai-Jun Ma Bao Du Yong-Qiang Tu State Key Laboratory of Applied Organic Chemistry College of Chemistry and Chemical Engineering Lanzhou University School of Chemistry and Chemical Engineering Shanghai Jiao Tong University School of Biotechnology and Health Sciences Wuyi University

Herein, the de novo synthesis of atropisomeric benzofurans through the Cu/spirocyclic-pyrrolidine-oxazoline(SPDO) complex catalyze asymmetric formal [3 + 2] cycloaddition between quinones and ynamides is explored, producing a range of structurally diverse axially chiral benzofurans in satisfactory yields with good to excellent enantioselectivities. Furthermore, density functional theory calculations were applied to explain the possible reaction mechanism.

关键词： benzofuran atropisomers novel de novo synthetic strategy asymmetric formal [3 + 2] cycladdition Cu/SPDO complex DFT calculations

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Development of a general circumferentially nonuniform heat transfer fuel rod model for subchannel analysis and application to helical fuel rods

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Science China Technological Sciences 2025年

作者： Junsen FU Junlong LI xiaowen WANG Qi ZHANG Yao xiao Hanyang gu School of Mechanical Engineering Shanghai Jiao Tong University Key Laboratory of Nuclear Power Systems and Equipment of the Ministry of Education Shanghai Jiao Tong University National Key Laboratory of Nuclear Reactor Technology Nuclear Power Institute of China State Key Laboratory of Nuclear Power Safety Technology and Equipment Shanghai Jiao Tong University

The subchannel analysis method is one of the most crucial transient safety analysis methods in the thermal design of nuclear reactors. The nonuniformity of circumferential heat transfer is slight in conventional pressurized water reactor (PWR)cores, but it is significant in advanced reactors with wire-wrapped or helical fuel rods. Predicting circumferentially nonuniform heat transfer behavior can be challenging owing to the complex geometry of helical fuel rods. In this study, a general circumferentially nonuniform heat transfer fuel rod (GCNF) model is developed to predict the fuel central temperature and circumferential heat flux and wall temperature. This model incorporates a refined two-dimensional fuel conduction model and circumferential nonuniform shape factor, addressing the dual factors contributing to the circumferential nonuniformity of helical fuel rods. An empirical correlation for the nonuniform shape factor is developed based on the computational fluid dynamics (CFD) results, and it is implemented to the subchannel code. The newly developed model is applied to a helical fuel annulus and validated by comparing the prediction results with CFD data. The maximum wall temperature predicted by the code is 1.15°C lower than the value calculated through CFD. In terms of the heat flux, the maximum value at the inner corner is22 kW lower than that obtained from the CFD prediction. The accurate prediction of circumferentially nonuniform heat transfer in helical fuel, concerning the surface heat flux and cladding temperature, addresses existing shortcomings in helical fuel subchannel analysis methods. Additionally, the capability to predict the fuel central temperature is essential for the safety analysis to determine whether fuel rods are melting. The generality of the model framework allows it to be used for the prediction of circumferential nonuniform heat transfer behavior in other types of fuel assemblies.

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Integration of perioperative features and intragraft TCF7L2 expression to predict lipid metabolic disorder in liver transplant recipients

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Science China Life Sciences 2025年第1期68卷 297-299页

作者： Junbin Zhou Rongli Wei guanghan fan Zhengxing Lian Xuanyu Zhang Linsong Tang Zhetuo Qi Haiyang Xie Shusen Zheng Qiang Wei xiao Xu Department of Hepatobiliary and Pancreatic Surgery People's Hospital of LishuiAffiliated Lishui Hospital of Wenzhou Medical UniversityThe First Affiliated Hospital of Lishui University NHFPC Key Laboratory of Combined Multi-Organ Transplantation Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province Department of Hepatobiliary and Pancreatic SurgeryHangzhou First People's Hospital Department of Hepatobiliary and Pancreatic Surgery The First Affiliated HospitalZhejiang University School of Medicine Department of Urology The Second Affiliated HospitalZhejiang University School of Medicine Department of Hepatobiliary and Pancreatic Surgery Department of Liver TransplantationShulan (Hangzhou) Hospital Hangzhou Medical College Zhejiang University School of Medicine

Dear Editor, Liver transplantation(LT) is the only curative therapy for patients with endstage liver disease(He et al., 2023; Ling et al., 2022). Post-transplant hypertriglyceridemia(PTHT), which has an incidence of up to 32.8% in 6 months after LT, is one of the major post-transplant complications(Toshima et al., 2020).

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Identification of a dual functional betulinic acid analog for the treatment of osteoarthritis by phenotypic screening

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Science China Life Sciences 2025年第1期68卷 300-302页

作者： Ze-Min Lin Mai Xiang Wen-Hui Wei Shu-Hui fan Li Chen Jie Wang xiao-Qian Yang Chun-Hao Yang Shi-Jun He Jian-Ping Zuo Laboratory of Immunopharmacology State Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of Sciences School of Pharmacy University of Chinese Academy of Sciences School of Pharmacy Nanjing University of Chinese Medicine State Key Laboratory of Drug Research Department of Medicinal ChemistryShanghai Institute of Materia MedicaChinese Academy of Sciences Innovation Research Institute of Traditional Chinese Medicine Shanghai University of Traditional Chinese Medicine Experiment Center for Science and Technology Shanghai University of Traditional Chinese Medicine

Dear Editor, Phenotypic drug discovery, which observes compound effects on physiology,has given way to targeting specific molecules, but has revived by using modern methods to find drugs based on therapeutic outcomes in disease models(Vincent et al., 2022). Osteoarthritis(OA) is a prevalent chronic joint disorder, primarily affecting knee joints, with osteoclast activation due to low-grade inflammation resulting in increased bone resorption and structural changes in the joint(Katz et al.,2021).

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Synthesis of chiral phosphine derivatives through a copper（I）-catalyzed desymmetric SNAr reaction

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Science China Chemistry 2025年

作者： Shuai Zhang Pei-Zhi Liu Yan-Bo Li Qi Zhang Jun-Zhao xiao Yi-fan Wang Tian-Yu Wei Jia-Wei Jiang Ye Wang Qian Peng Liang Yin Key Laboratory of Fluorine and Nitrogen Chemistry and Advanced Materials Shanghai Institute of Organic Chemistry University of Chinese Academy of Sciences Chinese Academy of Sciences State Key Laboratory of Elemento-Organic Chemistry and Tianjin Key Laboratory of Biosensing and Molecular Recognition College of Chemistry Frontiers Science Center for New Organic Matter Nankai University Haihe Laboratory of Sustainable Chemical Transformations

Axially chiral phosphines are a class of extremely important ligands in asymmetric catalysis. Herein, an unprecedented copper（I）-catalyzed asymmetric SNAr reaction with HP（S）R2is uncovered, which delivers a series of axially chiral phosphine derivatives in high yields with excellent enantioselectivity. Furthermore, the diastereoselective reaction with the kinetic resolution of racemic HP（S）ArR proceeds smoothly, providing the products with moderate diastereoselectivity and excellent enantioselectivity. Control experiments indicate that HP（S）Ph2is much more active than HPPh2and HP（O）Ph2as the pronucleophile in the present reaction. It is found that the SNAr reaction （the first SNAr） proceeds in a desymmetric manner, providing the desired chiral products while a continued SNAr reaction （the second SNAr） slightly occurs in a kinetic resolution manner in the present catalytic system, which enhances the ee of the desired chiral products. DFTcalculations support a concerted reaction pathway rather than a step-wise mechanism. Finally, axially chiral olefin-phosphines produced by the present method work as suitable ligands in Pdcatalyzed asymmetric allylic substitution with C-, N-, and O-nucleophiles and Rh-catalyzed asymmetric addition of arylboronic acid to benzil.

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Pathological Changes in Heroin-induced Spongiform Leukoencephalopathy and Therapeutic Effect of Comprehensive Rehabilitation： A Follow-up Study （Abstract）

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Journal of Acupuncture and Tuina Science 2005年第4期3卷 11-11页

作者： xiao Xue-chang CHU xiao-fan gu Kun-yi DONG Jia-zheng SU xiao-lin ZHOU Ci-xiong SUO Ping ZHAO Hong-wen CHEN Zuo-wei

Objective： To explore the pathological mechanism and effective comprehensive rehabilitation protocol of heroin-induced spongiform leukoencephalopathy （HSLE）. Method： Four patients with HSLE received comprehensive rehabilitation treatment including medication with dexametasone, encephalon polytide, cytidine diphosphate choline, and Vitamin B, intravascular irradiation with low-energy laser, hyperbaric treatment, balance training, acupuncture, and psychological consultation, etc and the therapeutic effects were observed to formulate the optimal comprehensive rehabilitation treatment protocol. Results： Clinical assessment was performed 10 weeks after treatment, which yielded significant improvement in cognition, psychology, linguistic ability, balance, as well as walking and ability to perform daily activities. The scores of Changguchun scale were 9, 8, 28 and 26 respectively before treatment for the 4 cases, while 35, 32, 35 and 35 respectively after treatment. The symptoms of drug abstinence, addiction and desire disappeared in case 1 and 2. Linguistic abilities were improved in 3 patients. In balance response examination, patient 1 scored 18 after treatment vs 3 before treatment, and the other 3 patients scored 20 vs 7, 16 vs 10, and 17 vs 11 respectively. The MBI scores for activity of daily life were 95 after treatment vs 35 before treatment in case 1, 100 vs 40 in case 2, 90 vs 30 in case 3, and 95 vs 40 in case 4. Conclusion： Comprehensive rehabilitation benefits the recovery of patients with HSLE. The pathological mechanism of HSLE involves not only the central nervous demyelination and immune response, but also cerebral ischemia and hypoxia.

关键词：海洛因海绵组织治疗方法脑疾病复原治疗

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Catalytic decomposition of methane to produce hydrogen:A review

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Journal of Energy Chemistry 2021年第7期30卷 415-430页

作者： Zeyu fan Wei Weng Jing Zhou Dong gu Wei xiao School of Resource and Environmental Sciences Hubei International Scientiﬁc and Technological Cooperation Base of Sustainable Resource and EnergyWuhan UniversityWuhan 430072HubeiChina College of Chemistry and Molecular Sciences Hubei Key Laboratory of Electrochemical Power SourcesWuhan UniversityWuhan 430072HubeiChina The Institute for Advanced Studies Wuhan UniversityWuhan 430072HubeiChina

The increasing demands of hydrogen and the recent discovery of large reserves of methane have prompted the conversion of methane to *** challenges raised by intensive CO_(2) emission from the traditional conversion of methane have provoked emission-free hydrogen production from *** catalytic decomposition of methane(CDM) to produce hydrogen and advanced carbon hence comes into consideration due to the short process and environmental *** many researchers have made considerable progress in CDM research on the laboratory scale,CDM is still in its infancy in *** history of its development,fundamental mechanisms,and recent research progress in catalysts and catalytic systems are herein *** problems of catalytic interface degradation are reviewed,focusing on deactivation from coke deposition in the CDM *** introduction of a liquid phase interface which can in-situ remove carbon products provides a new strategy for this ***,the challenges and prospects for future research into novel CDM catalysts or catalyst systems are included.

关键词： Hydrogen production Methane decomposition Metal-based catalysts Carbon-based catalysts Liquid catalyst

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Corrosion Behavior of Selective Laser Melted AISi10Mg Alloy in NaCl Solution and Its Dependence on Heat Treatment

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Acta Metallurgica Sinica(English Letters) 2020年第3期33卷 327-337页

作者： Xin-Hui gu Jun-Xi Zhang xiao-Lei fan Lai-Chang Zhang Shanghai Key Laboratory of Material Protection and Advanced Material in Electric Power Shanghai University of Electric PowerShanghai 200090China School of Engineering Edith Cowan University270 Joondalup DriveJoondalupPerthWA 6027Australia

This work investigates the corrosion behavior of AlSilOMg alloy produced by selective laser melting(SLM) and the counterparts heat-treated at 450-550℃in 3.5 wt% NaCl *** measurements and weight loss tests together with microstructural characterizations were *** SLM-produced alloy displays a microstructure with a continuous network of Si particles,exhibiting superior corrosion *** heat treatment,the Si particles are coarsened and isolated and A1 matrix dissolves into their surrounding area,thereby degrading the corrosion resistance ***,the corrosion resistance of AlSilOMg alloy degrades with increasing the heat treatment temperature.

关键词： Aluminum Selective laser melting XRD Electrochemistry Pitting corrosion

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Thermophoresis effects on gas-particle phases flow behaviors in entrained flow coal gasifier using Eulerian model

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Chinese Journal of Chemical Engineering 2017年第6期25卷 712-721页

作者： Chao Dai fan gu School of Energy and Environment Southeast University Nanjing 210096 China

A numerical model based on the Eulerian–Eulerian two-fluid approach is used to simulate the gasification of coal char inside an entrained flow gasifier. In this model, effects of thermophoresis of coal char particles are thoroughly investigated. The thermophoresis is due to the gas temperature gradient caused by absorpted heat of coal char gasification. This work, firstly, calculates the gas temperature gradient and thermophoretic force at1100 °C,1200 °C,1300 °C and 1400 °C wall temperatures. Then, the changes of particle volume fraction and velocity in the gasifier are studied in the simulation with thermophoresis or not. The results indicate that considering the particle thermophoresis has some effects on the calculation of particle volume fraction in the gasifier, especially at wall temperature of 1400 °C, and the maximum particle volume fraction variance ratio reaches up to 1.38% on wall surface of the gasifier. These effects are mainly caused by large gas temperature gradient along the radial direction of the gasifier. For the particle velocity, the changes are small but can be observable along radial direction of the gasifier, which has good agreement with the distributions of radial gas temperature gradient and thermophoretic force. These changes above may have certain effects on gasification reaction rates in this Eulerian model. So the change of gasification reaction rates in the simulation with thermophoresis or not is studied finally.

关键词： Gasification Thermophoresis Eulerian model Two-phase flow

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