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哺乳动物单细胞研究技术的现状与未来
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作者 姜文倩 田亚茸 +1 位作者 左锐 林峻 《生物工程学报》 CAS CSCD 北大核心 2019年第1期27-39,共13页
近年来,生命科学和医学的基础研究已深入到单细胞阶段。单细胞研究为揭示生命活动的基本规律、探索细胞异质性、提高对疾病发病机制的认识等提供了重要的线索和依据,同时,单细胞技术已被应用于日常实践中,如法医学和临床生殖医学。单细... 近年来,生命科学和医学的基础研究已深入到单细胞阶段。单细胞研究为揭示生命活动的基本规律、探索细胞异质性、提高对疾病发病机制的认识等提供了重要的线索和依据,同时,单细胞技术已被应用于日常实践中,如法医学和临床生殖医学。单细胞研究中使用的技术也在不断变化,并越来越复杂。文中主要介绍单细胞分离技术,包括手工挑取、激光捕获显微切割和微流控技术,以及单细胞中DNA、RNA和蛋白质分析方法的各种技术。此外,文中总结了近年来生命科学和医学领域的主要单细胞研究成果,讨论了单细胞相关技术和研究的不足,并介绍了其未来的发展方向。 展开更多
关键词 单细胞 激光捕获显微切割 微流控 单细胞基因组测序 单细胞转录组测序
Single-cell Analysis of CAR-T Cell Activation Reveals A Mixed TH1/TH2 Response Independent of Differentiation
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作者 Iva Xhangolli Burak Dura +3 位作者 GeeHee Lee Dongjoo Kim Yang Xiao Rong Fan 《基因组蛋白质组与生物信息学报:英文版》 CAS CSCD 2019年第2期129-139,共11页
The activation mechanism of chimeric antigen receptor (CAR)-engineered T cells may differ substantially from T cells carrying native T cell receptor,but this difference remains poorly understood. We present the first ... The activation mechanism of chimeric antigen receptor (CAR)-engineered T cells may differ substantially from T cells carrying native T cell receptor,but this difference remains poorly understood. We present the first comprehensive portrait of single-cell level transcriptional and cyto-kine signatures of anti-CD19/4-1BB/CD28/CD3ζ CAR-T cells upon antigen-specific stimulation. Both CD4+helper T (TH) cells and CD8+cytotoxic CAR-T cells are equally effective in directly killing target tumor cells and their cytotoxic activity is associated with the elevation of a range of TH1 and TH2 signature cytokines,e.g.,interferon γ,tumor necrotic factor α,interleukin 5 (IL5),and IL13,as confirmed by the expression of master transcription factor genes TBX21 and GATA3. However,rather than conforming to stringent TH1 or TH2 subtypes,single-cell analysis reveals that the predominant response is a highly mixed TH1/TH2 function in the same cell. The reg-ulatory T cell activity,although observed in a small fraction of activated cells,emerges from this hybrid TH1/TH2 population. Granulocyte-macrophage colony stimulating factor (GM-CSF) is pro-duced from the majority of cells regardless of the polarization states,further contrasting CAR-T to classic T cells. Surprisingly,the cytokine response is minimally associated with differentiation status,although all major differentiation subsets such as na?ve,central memory,effector memory,and effector are detected. All these suggest that the activation of CAR-engineered T cells is a canon-ical process that leads to a highly mixed response combining both type 1 and type 2 cytokines together with GM-CSF,supporting the notion that polyfunctional CAR-T cells correlate with objective response of patients in clinical trials. This work provides new insights into the mechanism of CAR activation and implies the necessity for cellular function assays to characterize the quality of CAR-T infusion products and monitor therapeutic responses in patients. 展开更多
关键词 SINGLE-CELL TRANSCRIPTOMICS SINGLE-CELL PROTEOMICS CAR-T T cell activation
Single-cell analyses identify distinct and intermediate states of zebrafish pancreatic islet development
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作者 Chong-Jian Lu Xiao-Ying Fan +12 位作者 Yue-Feng Guo Zhen-Chao Cheng Ji Dong Jin-Zi Chen Lian-Yan Li Mei-Wen Wang Ze-Kai Wu Fei Wang Xiang-Jun Tong Ling-Fei Luo Fu-Chou Tang Zuo-Yan Zhu Bo Zhang 《分子细胞生物学报:英文版》 SCIE CAS CSCD 2019年第6期435-447,共13页
Pancreatic endocrine islets are vital for glucose homeostasis. However, the islet developmental trajectory and its regulatory network are not well understood. To define the features of these specification and differen... Pancreatic endocrine islets are vital for glucose homeostasis. However, the islet developmental trajectory and its regulatory network are not well understood. To define the features of these specification and differentiation processes, we isolated individual islet cells from TgBAC(neurod1:EGFP) transgenic zebrafish and analyzed islet developmental dynamics across four different embryonic stages using a single-cell RNA-seq strategy. We identified proliferative endocrine progenitors, which could be further categorized by different cell cycle phases with the G1/S subpopulation displaying a distinct differentiation potential. We identified endocrine precursors, a heterogeneous intermediate-state population consisting of lineage-primed alpha, beta and delta cells that were characterized by the expression of lineage-specific transcription factors and relatively low expression of terminally differentiation markers. The terminally differentiated alpha, beta, and delta cells displayed stage-dependent differentiation states, which were related to their functional maturation. Our data unveiled distinct states, events and molecular features during the islet developmental transition, and provided resources to comprehensively understand the lineage hierarchy of islet development at the single-cell level. 展开更多
关键词 SINGLE-CELL RNA-seq ZEBRAFISH pancreas ISLET precursor CELL PROGENITOR CELL
Current challenges and solutions of de novo assembly
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作者 Xingyu Liao Min Li +3 位作者 You Zou Fang-Xiang Wu Yi-Pan Jianxin Wang 《中国电气与电子工程前沿:英文版》 CSCD 2019年第2期90-109,共20页
Background:Next-generation sequencing (NGS) technologies have fostered an unprecedented proliferation of highthroughput sequencing projects and a concomitant development of novel algorithms for the assembly of short r... Background:Next-generation sequencing (NGS) technologies have fostered an unprecedented proliferation of highthroughput sequencing projects and a concomitant development of novel algorithms for the assembly of short reads.However,numerous technical or computational challenges in de novo assembly still remain,although many new ideas and solutions have been suggested to tackle the challenges in both experimental and computational settings.Results:In this review,we first briefly introduce some of the major challenges faced by NGS sequence assembly.Then,we analyze the characteristics of various sequencing platforms and their impact on assembly results.After that,we classify de novo assemblers according to their frameworks (overlap graph-based,de Bruijn graph-based and string graph-based),and introduce the characteristics of each assembly tool and their adaptation scene.Next,we introduce in detail the solutions to the main challenges of de novo assembly of next generation sequencing data,single-cell sequencing data and single molecule sequencing data.At last,we discuss the application of SMS long reads in solving problems encountered in NGS assembly.Conclusions:This review not only gives an overview of the latest methods and developments in assembly algorithms,but also provides guidelines to determine the optimal assembly algorithm for a given input sequencing data type. 展开更多
关键词 next-generation SEQUENCING SINGLE-CELL SEQUENCING SINGLE-MOLECULE SEQUENCING de novo assembly algorithms
光镊技术在生命科学研究中的应用现状 预览
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作者 李银妹 王浩威 龚雷 《生物学杂志》 CAS CSCD 北大核心 2019年第3期1-8,共8页
光镊技术发明30年来,在生命科学领域中的应用取得了开创性成果,促进了生物物理学的发展。2018年光镊发明人A.Ashkin获得了诺贝尔物理学奖,再次激发了社会对光镊技术的关注。光镊能够主动操控微观粒子如细胞,还能对操控力进行定量测量,... 光镊技术发明30年来,在生命科学领域中的应用取得了开创性成果,促进了生物物理学的发展。2018年光镊发明人A.Ashkin获得了诺贝尔物理学奖,再次激发了社会对光镊技术的关注。光镊能够主动操控微观粒子如细胞,还能对操控力进行定量测量,在生物医学领域有其独特的用处。从生物应用视角来讨论光镊技术,希望通过重温光镊技术的特点和功能,为生物学家遴选科学问题和样品设计做铺垫。介绍生物学家能方便掌握的单光镊操控应用实例,致力于普及和推进已有的研究成果。重点讨论物理生物交叉研究的特点,分析光镊技术研究单细胞、单分子中涉及的技术瓶颈。结合实验室的工作介绍光镊技术的研究进展和仪器应用现状,展望该领域未来发展方向和前景。 展开更多
关键词 光镊技术 物理生物交叉 单细胞 单分子
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A case study on the detailed reproducibility of a Human Cell Atlas project
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作者 Kui Hua Xuegong Zhang 《中国电气与电子工程前沿:英文版》 CSCD 2019年第2期162-169,共8页
Background:Reproducibility is a defining feature of a scientific discovery.Reproducibility can be at different levels for different types of study.The purpose of the Human Cell Atlas (HCA) project is to build maps of ... Background:Reproducibility is a defining feature of a scientific discovery.Reproducibility can be at different levels for different types of study.The purpose of the Human Cell Atlas (HCA) project is to build maps of molecular signatures of all human cell types and states to serve as references for future discoveries.Constructing such a complex reference atlas must involve the assembly and aggregation of data from multiple labs,probably generated with different technologies.It has much higher requirements on reproducibility than individual research projects.To add another layer of complexity,the bioinformatics procedures involved for single-cell data have high flexibility and diversity.There are many factors in the processing and analysis of single-cell RNA-seq data that can shape the final results in different ways.Methods:To study what levels of reproducibility can be reached in current practices,we conducted a detailed reproduction study for a well-documented recent publication on the atlas of human blood dendritic cells as an example to break down the bioinformatics steps and factors that are crucial for the reproducibility at different levels.Results:We found that the major scientific discovery can be well reproduced after some efforts,but there are also some differences in some details that may cause uncertainty in the future reference.This study provides a detailed case observation on the on-going discussions of the type of standards the HCA community should take when releasing data and publications to guarantee the reproducibility and reliability of the future atlas.Conclusion:Current practices of releasing data and publications may not be adequate to guarantee the reproducibility of HCA.We propose building more stringent guidelines and standards on the information that needs to be provided along with publications for projects that evolved in the HCA program. 展开更多
关键词 HUMAN CELL ATLAS REPRODUCIBILITY single CELL BIOINFORMATICS
毕赤酵母液滴微流控高通量筛选方法的建立与应用
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作者 吕彤 涂然 +2 位作者 袁会领 刘浩 王钦宏 《生物工程学报》 CAS CSCD 北大核心 2019年第7期1317-1325,共9页
巴斯德毕赤酵母是当前应用最为方便和广泛的外源蛋白表达系统之一,为了进一步提高其表达外源蛋白的能力,文中建立了基于液滴微流控的毕赤酵母高通量筛选方法,并以木聚糖酶融合荧光蛋白为例,筛选获得木聚糖酶表达和分泌能力提高的突变株... 巴斯德毕赤酵母是当前应用最为方便和广泛的外源蛋白表达系统之一,为了进一步提高其表达外源蛋白的能力,文中建立了基于液滴微流控的毕赤酵母高通量筛选方法,并以木聚糖酶融合荧光蛋白为例,筛选获得木聚糖酶表达和分泌能力提高的突变株。通过PCR扩增得到木聚糖酶xyn5基因和绿色荧光蛋白gfp基因融合片段,并克隆到毕赤酵母表达载体pPIC9K中构建出木聚糖酶融合绿色荧光蛋白的质粒pPIC9K-xyn5-gfp,电转化至毕赤酵母GS115中得到表达木聚糖酶和绿色荧光蛋白的毕赤酵母SG菌株。该菌株经过常压室温等离子体诱变后进行单细胞液滴包埋,液滴培养24h后进行微流控筛选,获得高表达木聚糖酶的突变菌株,进而用于下一轮的诱变突变库构建和筛选。以此类推,经过5轮液滴微流控筛选,获得一株高产菌株SG-m5,其木聚糖酶活为149.17U/mg,较出发菌株提升300%,分泌外源蛋白的能力较出发菌株提高160%。文中建立的毕赤酵母单细胞液滴微流控高通量筛选方法能达到每小时10万菌株的筛选通量,筛选百万级别的菌株库仅需10h,消耗荧光试剂体积100μL,对比传统的微孔板筛选方法降低试剂成本近百万倍,为高效、低成本筛选获得表达和分泌外源蛋白能力提高的毕赤酵母提供了一条新途径。 展开更多
关键词 毕赤酵母 液滴微流控 高通量筛选 单细胞 外源蛋白表达 蛋白分泌
水基流延技术及其在固体氧化物燃料电池上的应用 预览
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作者 罗凌虹 刘邵帅 程亮 《陶瓷学报》 CAS 北大核心 2019年第2期139-147,共9页
本文以氧化铝基板的水系流延为例论述了水基流延的技术的要点以及该成型技术在制备平板式中温固体氧化物燃料电池(solid oxide of fuel cell, SOFC)单电池上的应用。
关键词 水系流延 SOFC 单电池 工艺
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Single-event upset prediction in static random access memory cell account for parameter variations
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作者 Mingxue HUO Guoliang MA +6 位作者 Bin ZHOU Liyi XIAO Chunhua QI Yanqing ZHANG Jianning MA Yinghun PIAO Tianqi WANG 《中国科学:信息科学(英文版)》 SCIE EI CSCD 2019年第6期177-179,共3页
Dear editor,As technology downscales, the impact of process variations (PVs) becomes a harmful problem,which significantly affects the integrated circuit(IC) performance (1)The transistor parameters can be significant... Dear editor,As technology downscales, the impact of process variations (PVs) becomes a harmful problem,which significantly affects the integrated circuit(IC) performance (1)The transistor parameters can be significantly affected by the lithography,random dopant fluctuations (RDFs), surface-state charge, gate depletion, and line edge roughness[1, 2]. 展开更多
关键词 SEU Single-event upset PREDICTION in static random access memory CELL ACCOUNT for parameter VARIATIONS
Extensive exploration of T cell heterogeneity in cancers by single cell sequencing 预览
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作者 Xiaofang Wang Yangqiu Li 《中国癌症研究:英文版》 SCIE CAS CSCD 2019年第2期410-418,共9页
Human T cells are a highly heterogeneous population and can recognize a wide variety of antigens by their T cell receptors(TCRs). Tumor cells display a large repertoire of antigens that serve as potential targets for ... Human T cells are a highly heterogeneous population and can recognize a wide variety of antigens by their T cell receptors(TCRs). Tumor cells display a large repertoire of antigens that serve as potential targets for recognition,thus making T cells in the tumor micro-environment more complicated. Making a connection between TCRs and the transcriptional information of individual T cells will be interesting for investigating clonal expansion within T cell populations under pathologic conditions. Advances in single cell RNA-sequencing(scRNA-seq) have allowed for comprehensive analysis of T cells. In this review, we briefly describe the research progress on tumor microenvironment T cells using single cell RNA sequencing, and then discuss how scRNA-seq can be used to resolve immune system heterogeneity in health and disease. Finally, we point out future directions in this field and potential for immunotherapy. 展开更多
关键词 T cells tumor MICRO-ENVIRONMENT SINGLE-CELL RNA-sequencing
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Bioactive A-ring rearranged limonoids from the root barks of Walsura robusta
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作者 Faliang An Xiaobing Wang +2 位作者 Minghua Yang Jun Luo Lingyi Kong 《药学学报:英文版》 CSCD 2019年第3期545-556,共12页
Screening active natural products, rapid identification, and accurate isolation are of great important for modern natural lead compounds discovery1. We hereby reported the isolation of seven new neotecleanin-type limo... Screening active natural products, rapid identification, and accurate isolation are of great important for modern natural lead compounds discovery1. We hereby reported the isolation of seven new neotecleanin-type limonoids(1–7), seven new limonoids with 5-oxatricyclo[5.4.0.11,4]hendecane ring system(8–14), and two new precursors(15–16) together with four known limonoids(17–20) from the root barks of Walsura robusta. Their structures, including their absolute configurations, were elucidated based on analyses of HR-ESI-MS, 1D/2D NMR, ECD spectrum calculations and singlecrystal X-ray diffraction techniques. Compounds 2, 8, 9, 11, 13, 14, 18 showed significant anti-inflammatory activities in LPS-induced RAW 264.7 cell line, BV2 microglial cells, and Propionibacterium acnes-stimulated THP-1 human monocytic cells. Walrobsin M(11) exhibited anti-inflammatory activity with IC50 value of 7.9670.36 μmol/L, and down-regulated phosphorylation levels of ERK and p38 in a dose-dependent manner. 展开更多
关键词 Walsura ROBUSTA LIMONOID Neotecleanin-type ECD spectrum calculation SINGLE-CRYSTAL X-ray diffraction ANTI-INFLAMMATORY activity PROPIONIBACTERIUM acnes THP-1 human monocytic cell
基于单细胞三维形态学体外分析重楼皂苷I的人红细胞毒性
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作者 肖文海 杨政伟 李远 《中国输血杂志》 CAS 2019年第4期334-338,共5页
目的从单细胞三维形态学角度上体外分析重楼皂苷I(PPI)的人红细胞毒性。方法将浓度为0.78-50μg/mL的PPI和人红细胞在37℃下震荡孵育3h作为实验组,以未经PPI处理的人红细胞作为实验对照;通过相对红细胞溶血率和红细胞沉降实验分析PPI红... 目的从单细胞三维形态学角度上体外分析重楼皂苷I(PPI)的人红细胞毒性。方法将浓度为0.78-50μg/mL的PPI和人红细胞在37℃下震荡孵育3h作为实验组,以未经PPI处理的人红细胞作为实验对照;通过相对红细胞溶血率和红细胞沉降实验分析PPI红细胞溶血活性;通过激光三维显微成像技术检测红细胞三维形态学图像,并分析相关三维形态学参数。结果 PPI红细胞溶血活性存在浓度依赖性,EC50值为3.92μg/mL;随着PPI浓度增大,红细胞形态先后经历轻微膨胀、出芽状结构形成、膜缺失到薄片状细胞膜结构的改变过程,PPI浓度达到6.25μg/mL时红细胞结构完全被破坏;与对照组相比,0.78μg/mL和1.56μg/mL PPI处理后红细胞平均高度、最大高度、表面积和体积均显著增大(P<0.01),3.125μg/mL PPI处理后上述参数显著降低(P<0.01),PPI处理后红细胞周长(1.56μg/mL PPI处理除外)和水平费雷特直径变化则无统计学意义(P>0.05)。结论本研究建立了单细胞三维形态学可视化分析方法将有利于加深PPI和人红细胞间的相互作用认知,促进PPI临床开发和应用。 展开更多
关键词 重楼皂苷I 红细胞 细胞毒性 单细胞 三维形态学
SSCC:A Novel Computational Framework for Rapid and Accurate Clustering Large-scale Single Cell RNA-seq Data
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作者 Xianwen Ren Liangtao Zheng Zemin Zhang 《基因组蛋白质组与生物信息学报:英文版》 CAS CSCD 2019年第2期201-210,共10页
Clustering is a prevalent analytical means to analyze single cell RNA sequencing (scRNA-seq) data but the rapidly expanding data volume can make this process computationally challenging. New methods for both accurate ... Clustering is a prevalent analytical means to analyze single cell RNA sequencing (scRNA-seq) data but the rapidly expanding data volume can make this process computationally challenging. New methods for both accurate and efficient clustering are of pressing need. Here we proposed Spearman subsampling-clustering-classification (SSCC),a new clustering framework based on random projection and feature construction,for large-scale scRNA-seq data. SSCC greatly improves clustering accuracy,robustness,and computational efficacy for various state-of-the-art algorithms benchmarked on multiple real datasets. On a dataset with 68,578 human blood cells,SSCC achieved 20%improvement for clustering accuracy and 50-fold acceleration,but only consumed 66%memory usage,compared to the widelyused software package SC3. Compared to k-means,the accuracy improvement of SSCC can reach 3-fold. An R implementation of SSCC is available at https://github.com/Japrin/sscClust. 展开更多
关键词 Single cell RNA-SEQ CLUSTERING SUBSAMPLING Classification
Call for Papers Special Issue on “Single-cell Omics Analysis”
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《基因组蛋白质组与生物信息学报:英文版》 CAS CSCD 2019年第2期222-223,共2页
The cell has been primarily studied as a part of its bulk population for decades until recent breakthroughs in single-cell omics technologies. The study of the seemingly isogenic cellular populations often buries dive... The cell has been primarily studied as a part of its bulk population for decades until recent breakthroughs in single-cell omics technologies. The study of the seemingly isogenic cellular populations often buries diverse cellular characteristics. Even in cells with the same cellular history,heterogeneity inherently arises due to the stochastic fluctuation of gene expression during transcription and translation or noises in signaling pathways. These hidden cell-to-cell variations can be paramount in the diagnosis and treatment of disease. For instance,the heterogeneity in tumor cells is crucial in understanding tumor initiation,progression,metastasis,and therapeutic response. A very small subpopulation of cells that may confer the most resistance in a preclinical drug test could be responsible for tumor relapse in patients after treatment. Thus,as medicine becomes more and more personalized,there is a greater desire to more accurately represent and understand single cells and the distinct subpopulations. 展开更多
关键词 PAPERS Special ISSUE SINGLE-CELL OMICS ANALYSIS a part of its BULK population
Real-time observation of dynamic heterogeneity of gold nanorods on plasma membrane with darkfield microscopy
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作者 Feng Ge Jianfeng Xue +2 位作者 Zonghua Wang Bin Xiong Yan He 《中国科学:化学英文版》 SCIE EI CAS CSCD 2019年第8期1072-1081,共10页
The plasma membrane possesses a complicated structure, on which the protein clusters are randomly but orderly distributed to maintain the regular morphology and function of cells. Investigating the detailed dynamic be... The plasma membrane possesses a complicated structure, on which the protein clusters are randomly but orderly distributed to maintain the regular morphology and function of cells. Investigating the detailed dynamic behaviors of nanoparticles(NPs) on cytomembrane is of great importance to understand cellular mechanisms and advance the bio-nano technologies for drug delivery, photothermal therapy, immunotherapy, etc. In this work, to study the dynamic heterogeneous interactions between NPs and cell membrane with high resolution, we established a simple method to efficiently track the translational and rotational diffusion of individual gold nanorods(AuNRs) on cell membranes. This method is based on that an anisotropic AuNR appears as a colored spot under a darkfield microscope(DFM) equipped with a color camera. While obtaining its lateral position, the polar angle of the AuNR can be calculated simultaneously from intensity difference between the R and G channels. Careful analysis shows that the lateral motion of single AuNRs do not follow normal Brownian diffusion, which could be attributed to their hop diffusion in the dynamically varying picket-fence structure of the live cell membrane. Furthermore, 4 different rotationtranslation patterns of the AuNR are observed due to spatiotemporal heterogeneity of the cytomembrane. This simple but robust method for simultaneously obtaining the location and orientation of anisotropic plasmonic nanoparticles could be further applied to the analysis of complicated biological and biomedical processes. 展开更多
关键词 single PARTICLE TRACKING gold NANORODS NANOPARTICLE cell interaction darkfield MICROSCOPY
Dgcr8 deletion in the primitive heart uncovered novel microRNA regulating the balance of cardiac-vascular gene program
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作者 Xi Chen Lin Wang +8 位作者 Rujin Huang Hui Qiu Peizhe Wang Daren Wu Yonglin Zhu Jia Ming Yangming Wang Jianbin Wang Jie Na 《蛋白质与细胞:英文版》 SCIE CAS CSCD 2019年第5期327-346,共20页
Primitive mammalian heart transforms from a single tube to a four-chambered muscular organ during a short developmental window.We found that knocking out global microRNA by deleting Dgcr8 microprocessor in Mespl cardi... Primitive mammalian heart transforms from a single tube to a four-chambered muscular organ during a short developmental window.We found that knocking out global microRNA by deleting Dgcr8 microprocessor in Mespl cardiovascular progenitor cells lead to the formation of extremely dilated and enlarged heart due to defective cardiomyocyte(CM)differentiation.Transcriptome analysis revealed unusual upregulation of vascular gene expression in Dgcr8 cKO hearts.Single cell RNA sequencing study further confirmed the increase of angiogenesis genes in single Dgcr8 cKO CM.We also performed global microRNA profiling of E9.5 heart for the first time,and identified that miR-541 was transiently highly expressed in E9.5 hearts.Interestingly,introducing miR-541 back into microRNA-free CMs partially rescued their defects,downregulated angiogenesis genes and significantly upregulated cardiac genes.Moreover,miR-541 can target Ctgf and inhibit endothelial function.Our results suggest that micro-RNAs are required to suppress abnormal angiogenesis gene program to maintain CM differentiation. 展开更多
关键词 MICRORNA Dgcr8 Cardiovascular PROGENITOR cells miRNA-541 Single cell RNA sequencing
Characterization and validation of somatic mutation spectrum to reveal heterogeneity in gastric cancer by single cell sequencing
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作者 Lihua Peng Rui Xing +20 位作者 Dongbing Liu Li Bao Wenxiang Cheng Hongyi Wang Yuan Yu Xiaofeng Liu Lu Jiang Yan Wu Zhongxue An Qiaoyi Liang Ryong Nam Kim Young Kee Shin Huanming Yang Jian Wang Jun Yu Xiuqing Zhang Xun Xu Jiaan Yang Kui Wu Shida Zhu Youyong Lu 《科学通报:英文版》 SCIE EI CSCD 2019年第4期236-244,共9页
Gastric cancer (GC) is a highly heterogeneons disease with multiple cellular types and poor prognosis. However, the cellular evolution and molecular basis of GC at the in dividual intra-tumor level has not bee n well ... Gastric cancer (GC) is a highly heterogeneons disease with multiple cellular types and poor prognosis. However, the cellular evolution and molecular basis of GC at the in dividual intra-tumor level has not bee n well dem on strated. We performed single-cell whole exome sequencing to detect somatic singlenucleotide variants (SNVs) and significantly mutated genes (SMGs) among 34 tumor cells and 9 normal cells from a patient w让h GC. The Complete Prediction for Protein Conformation (CPPC) approach directly predicting the folding con formation of the protein 3D structure with Protein Folding Shape Code, combined with functional experiments were used to confirm the characterization of mutated SMGs in GC cells. We ide ntified 201 somatic SNVs, in eluding 117 non-sy nony mous mutations in GC cells. Further analysis idenrified 24 significant mutated genes (SMGs) in single cells, for which a single amino acid change might affect protein conforniation. Among them, two genes (CDC27 and FLG) that were mutated only in single cells but not in the corresponding tumor tissue, were recurrently present in another GC tissue cohort, and may play a potential role to promote carcinogenesis, as confirmed by functional characterization. Our findings showed a mutational landscape of GC at intra-tumor level for the first time and provided opportunities for understanding the heterogeneity and individualized target therapy for this disease. 展开更多
关键词 Gastric cancer SINGLE-CELL whole EXOME SEQUENCING SNV SIGNIFICANT mutated gene HETEROGENEITY
单晶钙钛矿的制备及应用研究进展
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作者 高娟 冀婷 +3 位作者 李国辉 范明明 郝玉英 崔艳霞 《微纳电子技术》 北大核心 2019年第3期169-176,共8页
近年来,钙钛矿材料由于其带隙可调、吸收系数高、成本低等优势在国际上备受瞩目。其中,单晶钙钛矿具有优于多晶钙钛矿的光学、电学特性,成为制备高性能光电器件的理想材料。从钙钛矿的基本分子组成和化学结构出发,介绍了单晶钙钛矿的基... 近年来,钙钛矿材料由于其带隙可调、吸收系数高、成本低等优势在国际上备受瞩目。其中,单晶钙钛矿具有优于多晶钙钛矿的光学、电学特性,成为制备高性能光电器件的理想材料。从钙钛矿的基本分子组成和化学结构出发,介绍了单晶钙钛矿的基本光学和电学特性,指出了块状、薄片/薄膜和纳米结构有机-无机杂化单晶钙钛矿的制备方法,总结了它们在光电探测器、太阳电池、光泵浦激光和辐射探测中的应用。最后,对单晶钙钛矿当前研究中所面临的挑战及未来的发展进行展望,指出开发低成本、高稳定性、无毒的单晶钙钛矿光电器件有望加速其商业化进程。 展开更多
关键词 钙钛矿 单晶 光电探测器 太阳电池 激光 辐射探测
A glimpse of endocrine pancreas development from single-cell analyses
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作者 Ce Gao Jinrong Peng 《分子细胞生物学报:英文版》 SCIE CAS CSCD 2019年第6期433-434,共2页
Diabetes is a global public health concern in the 21st century. According to the report in the International Diabetes Federation Diabetes Atlas in 2015, 415 million adults suffer from diabetes globally. Although consi... Diabetes is a global public health concern in the 21st century. According to the report in the International Diabetes Federation Diabetes Atlas in 2015, 415 million adults suffer from diabetes globally. Although considerable progress has made in the treatment of diabetes, such as insulin administration, researchers are still looking for alternative therapeutic approaches, e.g. islet transplantation from cadaveric donors, for its radical cure. However, this approach is limited due to the scarcity of donors and availability of islet cells. 展开更多
关键词 endocrine pancreas DEVELOPMENT SINGLE-CELL ANALYSES International DIABETES FEDERATION DIABETES Atlas
BRIF-Seq: Bisulfite-Converted Randomly Integrated Fragments Sequencing at the Single-Cell Level
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作者 Xiang Li Lu Chen +3 位作者 Qinghua Zhang Yonghao Sun Qing Li Jianbing Yan 《分子植物:英文版》 SCIE CAS CSCD 2019年第3期438-446,共9页
Single-cell bisulfite sequencing (scBS-seq) was developed to assess DNA methylation heterogeneity in human and mouse. However, the reads are under-represented in regions with high DNA methylation, because these region... Single-cell bisulfite sequencing (scBS-seq) was developed to assess DNA methylation heterogeneity in human and mouse. However, the reads are under-represented in regions with high DNA methylation, because these regions are usually fragmented into long segments and are seldom sequenced on the lllumina plat. form. To reduce the read distribution bias and maximize the use of these long segments, we developed bisulfite-converted randomly integrated fragments sequencing (BRIF-seq), a method with high rates of read mapping and genome coverage. Single microspore of maize, which has a highly methylated and repetitive genome, was used to perform BRIF.seq. High coverage of the haploid genome was obtained to evaluate the methylation states of CG, CHG, and CHH (H = A, C, or T). Compared with scBS-seq, BRIF-seq produced reads that were distributed more evenly across the genome, including regions with high DNA methylation. Surprisingly, the methylation rates among the four microspores within one tetrad were similar, but differed significantly among tetrads, suggesting that non-simultaneous methylation reprogramming could occur among tetrads. Similar levels of heterogeneity, which often occur in lowcopy regions, were detected in different genetic backgrounds. These results suggest that BRIF-seq can be applied for single-cell methylome analysis of any species with diverse genetic backgrounds. 展开更多
关键词 SINGLE-CELL methylome WHOLE-GENOME AMPLIFICATION REPROGRAMMING
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