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

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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Molecular bases of morphologically diffused tumors across multiple cancer types

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National Science Review 2022年第11期9卷 65-67页

作者： Dingyun Liu feiyang xing Yueying Wang Jun Xiao Zheng An Ying Xu College of Computer Science and Technology Jilin University Center for Cancer Systems Biology China-Japan Union Hospital of Jilin University School of Life Sciences Jilin University China Computational Systems Biology Lab Department of Biochemistry and Molecular Biology and Institute of BioinformaticsUniversity of Georgia

Diffuse gastric cancer (DGC) and intestinal gastric cancer (IGC) are the two main gastric cancer subtypes [1]. Morphologically, DGC consists of numerous disjoint tiny tumors while IGC forms one or a few solid tumors (Supplementary Supplementary Fig. S1)[1,2]. In-depth studies have discovered that DGCs generally have an ill-defined or missing glandular structure and reduced cell–cell adhesion,

关键词： identification enantioselective semisynthesis (−)-anisomelic acid oral agent anti-SARS-CoV-2

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Synthesis and modification of nanowires anchored on electrodes for electrochemical and electrophysical applications

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Nano Research 2024年第10期17卷 8863-8884页

作者： feiyang Mo Zhitao Chen Nian Liu xing Xie School of Civil and Environmental Engineering Georgia Institute of Technology311 Ferst Drive NWAtlantaGA 30332USA School of Chemical and Biomolecular Engineering Georgia Institute of Technology311 Ferst Drive NWAtlantaGA 30332USA

The integration of nanowires onto electrode surfaces marks a significant advancement over traditional electrode materials,conferring upon nanowire-modified electrodes a vast array of applications within electrochemical and electrophysical *** nanowires used for electrode modification can be catalogized into two distinct types:anchored nanowires and free-standing nanowires.A critical advantage of anchored nanowires lies in their enhanced electrical connectivity with the substrate,which reduces electrode resistance and facilitates charge ***,the anchorage of nanowires onto electrodes provides additional mechanical support,bolstering the structural stability of the nanowire ***,we review the development of anchored nanowires designed for applications in energy storage,electrocatalysis,and electric field treatment(EFT)over the past *** focus on the synthesis and modification strategies employed for anchored nanowires,culminating in the evaluation of these fabrication and enhancement *** this analysis,we aim to furnish comprehensive insights into the preparation of anchored nanowires,guiding the selection of appropriate fabrication processes and subsequent functional modifications.

关键词： electrode modification direct growth etching energy storage electrocatalysis electric field treatment

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A Photocaged Azidosugar for Light-Controlled Metabolic Labeling of Cell-Surface Sialoglycans

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Chinese Journal of Chemistry 2022年第7期40卷 806-812页

作者： Bo Cheng Yi Wan Qi Tang Yifei Du feiyang Xu Zhimin Huang Wei Qin xing Chen College of Chemistry and Molecular Engineering Peking UniversityBeijing 100871China Beijing National Laboratory for Molecular Sciences Peking UniversityBeijing 100871China Peking-Tsinghua Center for Life Sciences Peking UniversityBeijing 100871China Synthetic and Functional Biomolecules Center Peking University Beijing 100871China Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking UniversityBeijing 100871China

The photocaging strategy has been widely used for activating biomolecules and hence regulating the underlying biological processes with high temporal and spatial ***,we integrate this strategy into metabolic glycan labeling,which enables optical-ly-controlled metabolic labeling of cell-surface sialoglycans with azides.N-Azidoacetylmannosamine(ManNAz)is caged with a 4,5-dimethoxy-2-nitrobenzyl(DMNB)group at the anomeric hydroxyl group to block its cellular *** feeding to the cells,irradiation with 365 nm UV light or 405 nm visible light cleaves the photocage and generates ManNAz within the *** is metabolically converted to azido sialic acid,which is then incorporated into cell-surface *** demonstrated spatial and temporal control of this strategy by specifically labeling sialoglycans on a single cell and tracking the metabolism of ManNAz based on light-triggered pulse-chase labeling,*** light-controlled metabolic glycan labeling strategy should facilitate probing of glycosylation in complex biological systems with high spatiotemporal precision.

关键词： Sialic acids Caged compounds Click chemistry Pulse-chase Single cell

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The appliances and prospects of aurum nanomaterials in biodiagnostics, imaging, drug delivery and combination therapy

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Asian Journal of Pharmaceutical Sciences 2019年第4期14卷 349-364页

作者： Dan Yang feiyang Deng Dechun Liu Bo He Bing He xing Tang Qiang Zhang School of Pharmacy Shenyang Pharmaceutical UniversityShenyang 110016China Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems School of Pharmaceutical SciencesPeking UniversityBeijing 100191China State Key Laboratory of Natural and Biomimetic Drugs Peking UniversityBeijing 100191China

Aurum nanomaterials(ANM), combining the features of nanotechnology and metal elements, have demonstrated enormous potential and aroused great attention on biomedical applications over the past few decades. Particularly, their advantages, such as controllable particle size, flexible surface modification, higher drug loading, good stability and biocompatibility, especially unique optical properties, promote the development of ANM in biomedical field. In this review, we will discuss the advanced preparation process of ANM and summarize their recent applications as well as their prospects in diagnosis and therapy. Besides, multi-functional ANM-based theranostic nanosystems will be introduced in details, including radiotherapy(RT), photothermal therapy(PTT), photodynamic therapy(PDT), immunotherapy(IT), and so on.

关键词： Gold nanomaterials Imaging and biodiagnostics Drug delivery Photothermal therapy Immunotherapy Combination therapy

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Mass Spectrometry Analysis of Newly Emerging Coronavirus HCoV-19 Spike Protein and Human ACE2 Reveals Camouflaging Glycans and Unique Post-Translational Modifications

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Engineering 2021年第10期7卷 1441-1451页

作者： Zeyu Sun Keyi Ren xing Zhang Jinghua Chen Zhengyi Jiang Jing Jiang feiyang Ji Xiaoxi Ouyang Lanjuan Li State Key Laboratory for Diagnosis and Treatment of Infectious Diseases National Clinical Research Center for Infectious DiseasesCollaborative Innovation Center for Diagnosis and Treatment of Infectious DiseaseThe First Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhou 310011China Department of Biophysics&Center of Cryo-Electron Microscopy School of MedicineZhejiang UniversityHangzhou 310011China

The coronavirus disease 2019(COVID-19)pandemic has led to worldwide efforts to understand the biological traits of the newly identified human coronavirus(HCoV-19)*** this mass spectrometry(MS)-based study,we reveal that out of 21 possible glycosites in the HCoV-19 spike protein(S protein),20 are completely occupied by N-glycans,predominantly of the oligomannose *** seven glycosylation sites in human angiotensin I converting enzyme 2(hACE2)were found to be completely occupied,mainly by complex ***,glycosylation did not directly contribute to the binding affinity between HCoV-19 S protein and *** post-translational modification(PTM)was identified,including multiple methylated sites in both proteins and multiple sites with hydroxylproline in *** structural models of HCoV-19 S protein and hACE2 were built by adding N-glycan and PTMs to recently published cryogenic electron microscopy *** PTM and glycan maps of HCoV-19 S protein and hACE2 provide additional structural details for studying the mechanisms underlying host attachment and the immune response of HCoV-19,as well as knowledge for developing desperately needed remedies and vaccines.

关键词： N-glycosylation COVID-19 Spike protein hACE2 Structure

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多模型融合投票预标注算法研究

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现代信息科技 2024年第16期8卷 34-38页

作者：吉星陈喆陈飞扬杨文听樊桢珍许丹陕西重型汽车有限公司陕西西安710000

针对标注内容烦琐、耗时等问题,提出一种多模型融合投票预标注方法。在预标注过程中,将Cascade_RCNN、RetinaNet、CondLaneNet三个模型的检测结果进行融合,然后将各个模型生成的坐标结果进行提取、判断、匹配、参数平均、排序等处理,得... 详细信息

针对标注内容烦琐、耗时等问题,提出一种多模型融合投票预标注方法。在预标注过程中,将Cascade_RCNN、RetinaNet、CondLaneNet三个模型的检测结果进行融合,然后将各个模型生成的坐标结果进行提取、判断、匹配、参数平均、排序等处理,得到最终的预标注结果。在公开数据集以及自建数据集上进行多次试验的结果表明,算法能够提高预标注精度,减少标注过程中人工标注工作量,具有较好的效果,验证了该方法的有效性。

关键词：深度学习目标检测车道线检测预标注模型融合

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从体质角度探析叶天士虚劳辨治思路

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天津中医药 2024年第3期41卷 309-312页

作者：刘兴王琦孙鹏程段斐洋莫康华白明华北京中医药大学中医学院北京100029 北京中医药大学国家中医体质与治未病研究院北京100029

虚劳是由多种原因引起的,以脏腑虚损、气血亏虚为主要病机的多种慢性疾病的总称。叶天士重视体质在虚劳形成、病证演变、调护原则、方药运用等方面的作用。虚性体质是导致虚劳发生的根本因素,偏颇体质类型决定了虚劳的不同病证转归。叶... 详细信息

虚劳是由多种原因引起的,以脏腑虚损、气血亏虚为主要病机的多种慢性疾病的总称。叶天士重视体质在虚劳形成、病证演变、调护原则、方药运用等方面的作用。虚性体质是导致虚劳发生的根本因素,偏颇体质类型决定了虚劳的不同病证转归。叶天士创建性地将虚劳调护区别于一般疾病诊治,并结合虚劳患者的体质特点使用血肉有情、柔剂阳药进行调补治疗。文章从体质角度切入,探析叶天士辨治虚劳病的临证思路,佐证了中医辨体论治的重要意义和临床价值,以期为虚劳病的临床诊治提供参考。

关键词：《临证指南医案》叶天士虚劳体质

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电力变压器绝缘成型件的局部放电特性及其绝缘性能综合评价方法

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绝缘材料 2024年第1期57卷 58-67页

作者：刘鑫常文婧张学友田宇高春嘉邢通苏飞洋齐波国网安徽省电力有限公司安徽合肥230001 国网安徽省电力有限公司超高压分公司安徽合肥230000 华北电力大学北京102206

本文搭建了电力变压器绝缘成型件的局部放电特性和闪络特性测试平台,获得了不同绝缘成型件的局部放电起始场强、局部放电起始放电量、局部放电熄灭场强、沿面闪络场强等4个关键绝缘指标的分布规律。结果表明:绝缘成型件的局部放电起始... 详细信息

本文搭建了电力变压器绝缘成型件的局部放电特性和闪络特性测试平台,获得了不同绝缘成型件的局部放电起始场强、局部放电起始放电量、局部放电熄灭场强、沿面闪络场强等4个关键绝缘指标的分布规律。结果表明:绝缘成型件的局部放电起始场强随着电极间距的增大而降低,平行分量下当电极间距从10 mm增大到25 mm时,局部放电起始场强降低了40.6%左右,不同分量下局部放电起始放电量为8.51~13.70 pC;在平行分量下,绝缘撑条和绝缘垫块的局部放电起始场强分别为2.55~2.85 kV/mm和1.43~1.78 kV/mm;在垂直分量下,绝缘撑条和绝缘垫块的局部放电起始场强分别为2.65~3.35 kV/mm和4.31~5.49 kV/mm。不同绝缘成型件表面形貌对其沿面闪络特性影响显著,表面压纹凹槽越密集,尺寸越大,阻碍沿面放电发展的效果越好。基于测试的试样数据库,提出基于熵权法的绝缘成型件综合性能评价方法,利用绝缘成型件放电特性的4个指标以及表观密度、尺寸偏差的离散程度确定不同性能指标的权重,对不同绝缘件进行了综合性能评价,验证了该评价方法的合理性。

关键词：电力变压器绝缘成型件局部放电起始特性闪络特性绝缘性能综合评价方法

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基于无监督机器学习算法的船舶吃水与货量分类量化分析

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上海船舶运输科学研究所学报 2022年第6期45卷 23-28页

作者：刘兴任飞扬韩懿中远海运散货运输有限公司广州510220 上海船舶运输科学研究所有限公司上海200135 中远海运科技股份有限公司上海200135

以中远海运集珍珠海系列姊妹干散货船为研究对象,采用无监督机器学习中的k-Means算法对干散货船的吃水、宣载量和吃水-宣载量进行分类量化分析。根据肘部法则选取最佳簇的数量,明确吃水、宣载量和吃水-宣载量的分类情况;利用线性回归原... 详细信息

以中远海运集珍珠海系列姊妹干散货船为研究对象,采用无监督机器学习中的k-Means算法对干散货船的吃水、宣载量和吃水-宣载量进行分类量化分析。根据肘部法则选取最佳簇的数量,明确吃水、宣载量和吃水-宣载量的分类情况;利用线性回归原理,拟合吃水与宣载量的对应关系。研究结果表明:对于同类干散货船,利用k-Means算法可有效将吃水、宣载量和吃水-宣载量分成3类,方便对干散货船的载货状态进行标识;利用线性回归方法量化出吃水与宣载量之间的关系,决定系数R2趋近于1;通过线性拟合公式计算的宣载量之和与实际宣载量之和相比,误差较小。

关键词： k-Means算法线性回归量化分析吃水宣载量

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