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Single-cell transcriptome analysis reveals widespread monoallelic gene expression in individual rice mesophyll cells

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Science Bulletin 2017年第19期62卷 1304-1314页

作者： yingying Han Xiao Chu Haopeng Yu ying-ke ma Xiu-Jie Wang Wenfeng Qian Yuling Jiao State key Laboratory of Plant Genomics Institute of Genetics and Developmental BiologyChinese Academy of Sciences University of Chinese Academy of Sciences Department of Biological Chemistry School of MedicineUniversity of California key Laboratory of Genetic Network Biology Institute of Genetics and Developmental BiologyChinese Academy of Sciences Beijing Institute of Genomics Chinese Academy of Sciences

Monoallelic gene expression refers to the phenomenon that all transcripts of a gene in a cell are expressed from only one of the two alleles in a diploid organism. Although monoallelic gene expression has been occasionally reported with bulk transcriptome analysis in plants, how prevalent it is in individual plant cells remains unknown. Here, we developed a single-cell RNA-seq protocol in rice and investigated allelic expression patterns in mesophyll cells of indica （93-11 ） and japonica （Nipponbare） inbred lines, as well as their F1 reciprocal hybrids. We observed pervasive monoallelic gene expression in individual mesophyll cells, which could be largely explained by stochastic and independent transcription of two alleles. By con- trast, two mechanisms that were proposed previously based on bulk transcriptome analyses, parent-of- origin effects and allelic repression, were not well supported by our data. Furthermore, monoallelically expressed genes exhibited a number of characteristics, such as lower expression levels, narrower H3K4me3/H3K9acJH3K27me3 peaks, and larger expression divergences between 93-11 and Nipponbare. Taken together, the development of a single-cell RNA-seq protocol in this study offers us an excellent opportunity to investigate the origins and prevalence of monoallelic gene expression in plant cells.

关键词： Monoallelic gene expressionSingle-cell RNA-seqRice mesophyll cellsIndependent allelic expression

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Computational identification of endogenous target mimics for microRNAs in plants and introduction to a plant small RNA analysis toolbox

Computational identification of endogenous target mimics for...

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第十四届全国植物基因组学大会

作者： Huajun Wu Zhimin Wang ying-ke ma Meng Wang Xiujie Wang State key Laboratory of Plant Genomics Institute of Genetics and Developmental BiologyChinese Academy of Sciences

Target mimicry is a recently identified regulatory mechanism for microRNA(miRNA) functions in plants in which the decoy RNAs bind to miRNAs via complementary sequences and therefore block the interaction between miRNA... 详细信息

关键词： target mimicry endogenous microRNA target mimic(eTM) small RNA analysis small RNA biogenesis degradome

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珍芪滴眼液熏蒸疗法对干眼的短期疗效

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眼科 2016年第5期25卷 347-350页

作者：张海娟黄蓉张俊秀武宇影马科首都医科大学附属北京同仁医院北京同仁眼科中心北京市眼科研究所眼科学与视觉科学北京市重点实验室 100005

目的观察珍芪滴眼液熏蒸疗法对干眼的疗效。设计前瞻性、随机、开放、阳性滴眼液平行对照的临床试验。研究对象 2013-2015年北京同仁医院眼科门诊干眼患者96例,平均年龄(60.95±12.22)岁。方法 96例受试者随机分为试验组与对照组,各48... 详细信息

目的观察珍芪滴眼液熏蒸疗法对干眼的疗效。设计前瞻性、随机、开放、阳性滴眼液平行对照的临床试验。研究对象 2013-2015年北京同仁医院眼科门诊干眼患者96例,平均年龄(60.95±12.22)岁。方法 96例受试者随机分为试验组与对照组,各48例。两组均给予玻璃酸钠滴眼液,每日4次,每次1滴。在此基础上,试验组使用珍芪滴眼液熏蒸疗法,每天1次,每次20分钟。对照组给予珍芪滴眼液点眼,每日4次,每次1滴。观察用药4周受试者干眼症状及体征改善情况。主要指标总有效率(临床显效+有效)、症状总分、Schirmer I试验(schirmer I test,SIt)、泪膜破裂时间(break-up time,BUT)、角膜荧光素染色评分。结果治疗前试验组与对照组在症状总分、SIt、BUT、角膜荧光素染色计分上均无显著性差异。治疗4周试验组总有效率(81.25%)明显高于对照组(62.50%)(P=0.041)。治疗4周时试验组BUT为(7.53±3.78)s,对照组为(6.08±2.99)s,试验组明显高于对照组(P=0.041)。症状总分试验组为1.92±1.99,对照组为2.32±2.30,试验组明显低于对照组(P=0.031)。结论珍芪滴眼液熏蒸疗法能有效治疗干眼,在玻璃酸钠滴眼液的基础上,该疗法优于珍芪滴眼液点眼治疗。

关键词：干眼中药熏蒸按摩

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psRobot:a web-based meta-analysis toolbox for plant small RNA

psRobot:a web-based meta-analysis toolbox for plant small RN...

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2011全国植物生物学研讨会

作者： Hua-Jun Wu,ying-ke ma,Meng Wang and Xiu-Jie Wang~* The State key Laboratory of Plant Genomics,Center for Molecular Systems Biology,Institute of Genetics and Developmental Biology,Chinese Academy of Sciences,Beijing 100101

Small RNAs(smRNAs) in plants,mainly consisting of miRNAs and siRNAs, play an important role in both transcriptional regulation and post transcriptional *** the rapid development of the next-generation sequencing technology, a large number of small RNA deep sequencing data have been *** is developed to meet the growing demands for user-friendly small RNA analysis tools. Web-based psRobot has two major functions:stem-loop smRNA prediction and srnRNA target ***-loop smRNA prediction estimates the biogenesis of the queried small RNAs by structural and functional *** analysis

关键词： small RNA stem-loop prediction target prediction meta-analysis

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The complex roles of m^(6)A modifications in neural stem cell proliferation, differentiation, and self-renewal and implications for memory and neurodegenerative diseases

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Neural Regeneration Research 2025年第6期20卷 1582-1598页

作者： Yanxi Li Jing Xue Yuejia ma ke Ye Xue Zhao Fangliang Ge Feifei Zheng Lulu Liu Xu Gao Dayong Wang Qing Xia Department of Biochemistry and Molecular Biology College of Basic Medical SciencesHarbin Medical UniversityHarbinHeilongjiang ProvinceChina College of Basic Medical Sciences Harbin Medical UniversityHarbinHeilongjiang ProvinceChina Basic Medical Institute Heilongjiang Academy of Medical SciencesHarbinHeilongjiang ProvinceChina key Laboratory of Heilongjiang Province for Genetically Modified Animals Harbin Medical UniversityHarbinHeilongjiang ProvinceChina Translational Medicine Research and Cooperation Center of Northern China Heilongjiang Academy of Medical SciencesHarbinHeilongjiang ProvinceChina Dongzhimen Hospital Beijing University of Chinese MedicineBeijingChina

N6-methyladenosine(m^(6)A), the most prevalent and conserved RNA modification in eukaryotic cells, profoundly influences virtually all aspects of mRNA metabolism. mRNA plays crucial roles in neural stem cell genesis and neural regeneration, where it is highly concentrated and actively involved in these processes. Changes in m^(6)A modification levels and the expression levels of related enzymatic proteins can lead to neurological dysfunction and contribute to the development of neurological diseases. Furthermore, the proliferation and differentiation of neural stem cells, as well as nerve regeneration, are intimately linked to memory function and neurodegenerative diseases. This paper presents a comprehensive review of the roles of m^(6)A in neural stem cell proliferation, differentiation, and self-renewal, as well as its implications in memory and neurodegenerative diseases. m^(6)A has demonstrated divergent effects on the proliferation and differentiation of neural stem cells. These observed contradictions may arise from the time-specific nature of m^(6)A and its differential impact on neural stem cells across various stages of development. Similarly, the diverse effects of m^(6)A on distinct types of memory could be attributed to the involvement of specific brain regions in memory formation and recall. Inconsistencies in m^(6)A levels across different models of neurodegenerative disease, particularly Alzheimer's disease and Parkinson's disease, suggest that these disparities are linked to variations in the affected brain regions. Notably, the opposing changes in m^(6)A levels observed in Parkinson's disease models exposed to manganese compared to normal Parkinson's disease models further underscore the complexity of m^(6)A's role in neurodegenerative processes. The roles of m^(6)A in neural stem cell proliferation, differentiation, and self-renewal, and its implications in memory and neurodegenerative diseases, appear contradictory. These inconsistencies may be a

关键词： Alzheimer's disease cell self-renewal central nervous system memory microglia nerve regeneration neurodegenerative diseases neurogenesis RNA methylation

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深度学习赋能波束管理:现状、挑战与机遇

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中山大学学报（自然科学版）（中英文） 2025年第1期64卷 40-50页

作者：王昭诚马可清华大学电子工程系北京100084

随着载波频率的不断提高和大规模天线阵列的广泛部署,基于模拟移相器的波束赋形成为下一代无线通信的标志性技术之一。此时,波束管理被用于获取和维护基站和用户端具有最大接收功率的最优波束对,以保障可靠的无线通信服务。传统波束管... 详细信息

随着载波频率的不断提高和大规模天线阵列的广泛部署,基于模拟移相器的波束赋形成为下一代无线通信的标志性技术之一。此时,波束管理被用于获取和维护基站和用户端具有最大接收功率的最优波束对,以保障可靠的无线通信服务。传统波束管理方法往往依赖于海量搜索。同时,传统数学模型无法全面的、准确刻画非线性的波束的内在关联和高维无线环境特征,因而难以取得令人满意的波束增益性能。近年来,得益于深度学习强大的自适应拟合能力,深度学习赋能波束管理得到了国内外广泛关注。本文总结了深度学习赋能波束管理的研究进展,并展望了未来的研究方向。首先,阐述了深度学习应用于波束管理的典型场景和潜在优势;随后,从空/时/频域切入,讨论当前深度学习赋能波束管理的主要研究路线和代表性工作;最后,面向更大规模的无线网络、更多元的波束管理功能和更鲁棒的深度学习模型,阐述未来的研究挑战与机遇。

关键词：深度学习波束管理空域时域频域

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An Emergency Blood Allocation Approach Considering Blood Group Compatibility in Disaster Relief Operations

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International Journal of Disaster Risk Science 2019年第1期10卷 74-88页

作者： Zu-Jun ma ke-Ming Wang ying Dai School of management Yangtze University Institute for Logistics and Emergency management School of Economics and Management Southwest Jiaotong University School of Information Science and Technology Southwest Jiaotong University

Large-scale sudden-onset disasters may cause massive injuries and thus place great pressure on the emergency blood supplies of local blood banks. When blood is in short supply, blood products gathered urgently to a local blood center should be appropriately allocated to blood banks in the affected area. Moreover, ABO/Rh(D) compatibilities among blood groups must be considered during emergency situations. To minimize the total unmet demand of blood products considering the optimal ABO/Rh(D)-compatible blood substitution scheme, a mixed integer programming model is developed and solved efficiently by using a greedy heuristic algorithm. Finally, a numerical example derived from the emergency blood supply scenario of the Wenchuan Earthquake is presented to verify the proposed model and algorithm. The results show that considering ABO/Rh(D)-compatible blood substitution can remarkably increase the efficiency of emergency blood allocation while lowering blood shortage, and the preference order of possible ABO/Rh(D)-compatible substitutions has an influence on the allocation solution.

关键词： Blood group compatibility Blood substitution Disaster relief Emergency blood allocation Greedy heuristic algorithm

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Influences of initial porosity,stress triaxiality and Lode parameter on plastic deformation and ductile fracture

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Acta Mechanica Solida Sinica 2017年第5期30卷 493-506页

作者： ying-Song ma Dong-Zhi Sun Florence Andrieux ke-Shi Zhang College of Civil Engineering and Architecture Guangxi UniversityKey Lab of Disaster Prevention and Structural SafetyGuangxi Key Lab Disaster Prevention and Engineering SafetyNanning 530004China Department of Mining Engineering Shanxi Datong UniversityDatong 037003China Fraunhofer Institute for Mechanics of materials IWM Woehlerstrasse 1179108 FreiburgGermany

Local mechanical properties in aluminum cast components are inhomogeneous as a con- sequence of spatial distribution of microstructure, e.g., porosity, inclusions, grain size and arm spacing of secondary dendrites. In this work, the effect of porosity is investigated. Cast components contain voids with different sizes, forms, orientations and distributions. This is approximated by a porosity distribution in the following. The aim of this paper is to in- vestigate the influence of initial porosity, stress triaxiality and Lode parameter on plastic deformation and ductile fracture. A micromechanical model with a spherical void located at the center of the matrix material, called the representative volume element （RVE）, is de- veloped. Fully periodic boundary conditions are applied to the RVE and the values of stress triaxiality and Lode parameter are kept constant during the entire course of loading. For this purpose, a multi-point constraint （MPC） user subroutine is developed to prescribe the loading. The results of the RVE model are used to establish the constitutive equations and to further investigate the influences of initial porosity, stress triaxiality and Lode parameter on elastic constant, plastic deformation and ductile fracture of an aluminum die castin~ alloy.

关键词： Stress triaxialityLode parameterVoidDuctile fractureRVE

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西双版纳热带森林地表径流场设计的研究

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水土保持学报 1999年第S1期11卷 56-60页

作者：刘玉洪张克映马友鑫沙丽清刘文杰中国科学院西双版纳热带植物园昆明650223

讨论了西双版纳地区热带雨林、橡胶林和无林旷地地表径流场的选择与设计。

关键词：西双版纳热带森林地表径流场设计

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Features and distribution patterns of Chinese endemic seed plant species

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Journal of Systematics and Evolution 2011年第2期49卷 81-94页

We compiled and identified a list of Chinese endemic seed plant species based on a large number of published references and expert reviews. The characters of these seed plant species and their distribution patterns were described at length. China is rich in endemic seed plants, with a total of 14 939 species (accounting for 52.1% of its total seed plant species) belonging to 1584 genera and 191 families. Temperate families and genera have a significantly higher proportion of endemism than cosmopolitan and tropical ones. The most primitive and derived groups have significantly higher endemism than the other groups. The endemism of tree, shrub, and liana or vine is higher than that of total species; in contrast, the endemism of herb is lower than that of total species. Geographically, these Chinese endemic plants are mainly distributed in Yunnan and Sichuan provinces, southwest China. Species richness and proportion of these endemic plants decrease with increased latitude and have a unimodal response to altitude. The peak value of proportion of endemism is at higher altitudes than that of total species and endemic species richness. The proportions of endemic shrub, liana or vine, and herb increase with altitude and have a clear unimodal curve. In contrast, the proportion of tree increases with altitude, with a sudden increase at ～4000 m and has a completely different model. To date, our study provides the most comprehensive list of Chinese endemic seed plant species and their basic composition and distribution features.

关键词： biodiversity conservation distribution pattern endemism flora of China seed plants.

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