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Single-cell network analysis reveals gene expression programs for Arabidopsis root development and metabolism

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Plant Communications 2024年第8期5卷 32-49页

作者： Ershang Han Zhenxing Geng Yue Qin Yuewei Wang shisong ma MOE Key Laboratory for Cellular Dynamics School of Life SciencesDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaInnovation Academy for Seed DesignChinese Academy of SciencesHefei 230027China School of Data Science University of Science and Technology of ChinaHefei 230027China

Single-cell RNA-sequencing datasets of Arabidopsis roots have been generated,but related comprehensive gene co-expression network analyses are *** conducted a single-cell gene co-expression network analysis with publicly available scRNA-seq datasets of Arabidopsis roots using a SingleCellGGM *** analysis identified 149 gene co-expression modules,which we considered to be gene expression programs(GEPs).By examining their spatiotemporal expression,we identified GEPs specifically expressed in major root cell types along their developmental *** GEPs define gene programs regulating root cell development at different stages and are enriched with relevant developmental *** examples,a GEP specific for the quiescent center(QC)contains 20 genes regulating QC and stem cell niche homeostasis,and four GEPs are expressed in sieve elements(SEs)from early to late developmental stages,with the early-stage GEP containing 17 known SE developmental *** also identified GEPs for metabolic pathways with cell-type-specific expression,suggesting the existence of cell-type-specific metabolism in *** the GEPs,we discovered and verified a columellaspecific gene,NRL27,as a regulator of the auxin-related root gravitropism *** analysis thus systematically reveals GEPs that regulate Arabidopsis root development and metabolism and provides ample resources for root biology studies.

关键词： single-cell RNA sequencing single-cell gene co-expression network analysis gene expression program Arabidopsis root development NRL27 gravitropism

Stomatal maturomics:hunting genes regulating guard cell maturation and function formation from single-cell transcriptomes

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Journal of Genetics and Genomics 2024年第11期51卷 1286-1299页

作者： Yuming Peng Yi Liu Yifan Wang Zhenxing Geng Yue Qin shisong ma MOE Key Laboratory for Cellular Dynamics School of Life SciencesDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaInnovation Academy for Seed DesignChinese Academy of SciencesHefeiAnhui 230027China School of Data Science University of Science and Technology of ChinaHefeiAnhui 230027China School of Quantum Information Future Technology Henan Key Laboratory of Quantum Materials and Quantum EnergyHenan UniversityKaifengHenan 450046China

Stomata play critical roles in gas exchange and immunity to *** many genes regulating early stomatal development up to the production of young guard cells(GCs)have been identified in Arabidopsis,much less is known about how young GCs develop into mature functional *** we perform a maturomics study on stomata,with“maturomics”defined as omics analysis of the maturation process of a tissue or *** develop an integrative scheme to analyze three public stomata-related single-cell RNAseq datasets and identify a list of 586 genes that are specifically up-regulated in all three datasets during stomatal maturation and function *** list,termed sc_586,is enriched with known regulators of stomatal maturation and *** validate the reliability of the dataset,we selected two candidate G2-like transcription factor genes,MYS1 and MYS2,to investigate their roles in *** two genes redundantly regulate the size and hoop rigidity of mature GCs,and the mys1 mys2 double mutants cause mature GCs with severe defects in regulating their stomatal *** together,our results provide a valuable list of genes for studying GC maturation and function formation.

关键词： Stomata maturomics Hoop rigidity Stomatal aperture Single-cell analysis G2-like transcription factors MYS1 MYS2

Decoding transcriptional regulation via a human gene expression predictor

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Journal of Genetics and Genomics 2023年第5期50卷 305-317页

作者： Yuzhou Wang Yu Zhang Ning Yu Bingyan Li Jiazhen Gong Yide Mei Jianqiang Bao shisong ma The First Affiliated Hospital of USTC Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui 230027China MOE Key Laboratory for Cellular Dynamics School of Life SciencesDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaInnovation Academy for Seed DesignChinese Academy of SciencesHefeiAnhui 230027China School of Data Science University of Science and Technology of ChinaHefeiAnhui 230027China

Transcription factors(TFs)regulate cellular activities by controlling gene expression,but a predictive model describing how TFs quantitatively modulate human transcriptomes is *** construct a universal human gene expression predictor named EXPLICIT-Human and utilize it to decode transcriptional *** the expression of 1613 TFs,the predictor reconstitutes highly accurate transcriptomes for samples derived from a wide range of tissues and *** broad applicability of the predictor indicates that it recapitulates the quantitative relationships between TFs and target genes ubiquitous across *** interacting TF-target gene pairs are extracted from the predictor and enable downstream inference of TF regulators for diverse pathways involved in development,immunity,metabolism,and stress response.A detailed analysis of the hematopoiesis process reveals an atlas of key TFs regulating the development of different hematopoietic cell lineages,and a portion of these TFs are conserved between humans and *** results demonstrate that our method is capable of delineating the TFs responsible for fate *** to other existing tools,EXPLICIT-Human shows a better performance in recovering the correct TF regulators.

关键词： Gene expression predictor Gene regulatory network Graphical Gaussian model Gene module Human Mouse

EXPLICIT-Kinase:A gene expression predictor for dissecting the functions of the Arabidopsis kinome

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Journal of Integrative Plant Biology 2022年第7期64卷 1374-1393页

作者： Yuming Peng Wanzhu Zuo Hui Zhou Fenfen Miao Yu Zhang Yue Qin Yi Liu Yu Long shisong ma MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics School of Life SciencesUniversity of Science and Technology of ChinaInnovation Academy for Seed DesignChinese Academy of SciencesHefei 230027China State Key Laboratory of Crop Stress Adaptation and Improvement School of Life SciencesHenan UniversityKaifeng 475001China State Key Laboratory for Plant Molecular Genetics Center of Excellence for Molecular Plant SciencesChinese Academy ofSciencesShanghai 200032China School of Data Science University of Science and Technology of ChinaHefei 230027China

Protein kinases regulate virtually all cellular processes,but it remains challenging to determine the functions of all protein kinases,collectively called the“kinome”,in any *** developed a computational approach called EXPLICIT-Kinase to predict the functions of the Arabidopsis *** the activities of many kinases can be regulated transcriptionally,their gene expression patterns provide clues to their functions.A universal gene expression predictor for Arabidopsis was constructed to predict the expression of 30,172 nonkinase genes based on the expression of 994 *** model reconstituted highly accurate transcriptomes for diverse Arabidopsis *** identified the significant kinases as predictor kinases for predicting the expression of Arabidopsis genes and ***,these predictor kinases were often regulators of related pathways,as exemplified by those involved in cytokinesis,tissue development,and stress *** analyses revealed that portions of these predictor kinases are shared and conserved between Arabidopsis and *** an example,we identified a conserved predictor kinase,RAF6,from a stomatal movement *** verified that RAF6 regulates stomatal *** can directly interact with SLAC1,a key anion channel for stomatal closure,and modulate its channel *** approach enables a systematic dissection of the functions of the Arabidopsis kinome.

关键词： kinase kinome predictor

De novo assembly of a Chinese soybean genome

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Science China(Life Sciences) 2018年第8期61卷 871-884页

作者： Yanting Shen Jing Liu Haiying Geng Jixiang Zhang Yucheng Liu Haikuan Zhang Shilai Xing Jianchang Du shisong ma Zhixi Tian State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 China Provincial Key Laboratory of Agrobiology Institute of Crop Germplasm and Biotechnology Jiangsu Academy of Agricultural Sciences Nanjing 210014 China School of Life Sciences University of Science and Technology of China Hefei 230027 China Berry Genomics Corporation Beijing 100015 China University of Chinese Academy of Sciences Beijing 100039 China

Soybean was domesticated in China and has become one of the most important oilseed crops. Due to bottlenecks in their introduction and dissemination, soybeans from different geographic areas exhibit extensive genetic diversity. Asia is the largest soybean market; therefore, a high-quality soybean reference genome from this area is critical for soybean research and ***, we report the de novo assembly and sequence analysis of a Chinese soybean genome for "Zhonghuang 13" by a combination of SMRT, Hi-C and optical mapping data. The assembled genome size is 1.025 Gb with a contig N50 of 3.46 Mb and a scaffold N50 of 51.87 Mb. Comparisons between this genome and the previously reported reference genome(cv. Williams82) uncovered more than 250,000 structure variations. A total of 52,051 protein coding genes and 36,429 transposable elements were annotated for this genome, and a gene co-expression network including 39,967 genes was also established. This high quality Chinese soybean genome and its sequence analysis will provide valuable information for soybean improvement in the future.

关键词： de novo soybean genome Zhonghuang 13 Gmax_ZH13 structure variation gene co-expression network

6-Phosphogluconate dehydrogenase 2 bridges the OPP and shikimate pathways to enhance aromatic amino acid production in plants

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Science China(Life Sciences) 2024年第11期67卷 2488-2498页

作者： Qian Tang Yuxin Huang Zhuanglin Shen Linhui Sun Yang Gu Huiqing He Yanhong Chen Jiahai Zhou Limin Zhang Cuihuan Zhao shisong ma Yunhai Li Jie Wu Qiao Zhao Shenzhen Key Laboratory of Synthetic Genomics Guangdong Provincial Key Laboratory of Synthetic GenomicsKey Laboratory of Quantitative Synthetic BiologyShenzhen Institute of Synthetic BiologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China Center for Plant Biology School of Life SciencesTsinghua UniversityBeijing 100084China University of Chinese Academy of Sciences Beijing 100049China CAS Key Laboratory for Quantitative Engineering Biology Shenzhen Institute of Synthetic BiologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China Key Laboratory of Quantitative Synthetic Biology Shenzhen Institute of Synthetic BiologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China Key Laboratory of Agricultural Microbiology of Heilongjiang Province Northeast Agricultural UniversityHarbin 150030China State Key Laboratory of Plant Cell and Chromosome Engineering CAS Centre for Excellence in Molecular Plant BiologyInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijing 100101China MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics School of Life SciencesUniversity of Science and Technology of ChinaInnovation Academy for Seed DesignChinese Academy of SciencesHefei 230027China

The oxidative pentose phosphate(OPP)pathway provides metabolic intermediates for the shikimate pathway and directs carbon flow to the biosynthesis of aromatic amino acids(AAAs),which serve as basic protein building blocks and precursors of numerous metabolites essential for plant ***,genetic evidence linking the two pathways is largely *** this study,we identified 6-phosphogluconate dehydrogenase 2(PGD2),the rate-limiting enzyme of the cytosolic OPP pathway,through suppressor screening of arogenate dehydrogenase 2(adh2)in *** data indicated that a single amino acid substitution at position 63(glutamic acid to lysine)of PGD2 enhanced its enzyme activity by facilitating the dissociation of products from the active site of PGD2,thus increasing the accumulation of AAAs and partially restoring the defective phenotype of *** analysis indicated that the point mutation occurred in a well-conserved amino acid *** with different amino acids at this conserved site of PGDs confer diverse catalytic activities,thus exhibiting distinct AAAs producing *** findings uncover the genetic link between the OPP pathway and AAAs biosynthesis through *** gain-of-function point mutation of PGD2 identified here could be considered as a potential engineering target to alter the metabolic flux for the production of AAAs and downstream compounds.

关键词： plant metabolism aromatic amino acids oxidative pentose phosphate pathway shikimate pathway 6-phosphogluconate dehydrogenase

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十八胺法在新建超临界机组停运保护中的应用

热力发电 2010年第10期39卷 100-103,111页

作者：孙小军桑俊珍马世松莫宗宝河北省电力研究院河北石家庄050021 神华河北国华沧东发电有限责任公司河北沧州061110

以神华河北国华黄骅发电厂超临界机组为例,介绍新建超临界机组蒸汽吹管后十八胺法停运保护的保护范围、加药设备、加药条件、注意事项、加药过程、效果检查以及机组整套起动期间的冷热态冲洗情况和凝结水精处理的投运时机等。停运后的... 详细信息

以神华河北国华黄骅发电厂超临界机组为例,介绍新建超临界机组蒸汽吹管后十八胺法停运保护的保护范围、加药设备、加药条件、注意事项、加药过程、效果检查以及机组整套起动期间的冷热态冲洗情况和凝结水精处理的投运时机等。停运后的检查及机组起动过程的冷热态冲洗结果表明,所形成的保护膜憎水性显著且硫酸铜点滴试验时间长,冷态和热态冲洗过程中十八胺含量和铁含量合格快,十八胺停运保护方法取得了良好的停运保护效果。

关键词：十八胺超临界机组停运保护冲洗凝结水精处理

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330MW锅炉再热汽温偏低的技术改造

江苏电机工程 2015年第4期34卷 74-75,78页

作者：马士松陈国华江苏新海发电有限公司江苏连云港222023

江苏某发电有限公司330 MW机组锅炉再热蒸汽温度长期低于设计值,除了影响机组运行经济性,严重时也会造成汽轮机末级叶片冲蚀。通过在低温再热器垂直段区域增加部分受热面,再热蒸汽温度能够达到或超过设计水平,在为企业带来丰厚经济效益... 详细信息

江苏某发电有限公司330 MW机组锅炉再热蒸汽温度长期低于设计值,除了影响机组运行经济性,严重时也会造成汽轮机末级叶片冲蚀。通过在低温再热器垂直段区域增加部分受热面,再热蒸汽温度能够达到或超过设计水平,在为企业带来丰厚经济效益的同时,也解决了低温再热器磨损问题,提高了机组运行的安全、经济水平,减轻了环境污染。

关键词：锅炉再热蒸汽温度低温再热器改造

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回转式空气预热器漏风控制系统改造

发电设备 2015年第4期29卷 284-287页

作者：马士松李建荣宋艳江苏新海发电有限公司江苏连云港222023 上海发电设备成套设计研究院上海200240

介绍了1 000 MW发电机组中空气预热器漏风控制系统(LCS)的工作原理,分析了LCS在运行中存在的问题,提出了综合改造措施并进行了论证。实践结果表明:经过改造,该空气预热器LCS运行正常,漏风率减小,实现了节能降耗的目的。

关键词：回转式空气预热器漏风控制系统机械式传感器激光测距节能降耗