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首页 > 过刊浏览>2022年第38卷第8期 >2798-2810. DOI:10.13345/j.cjb.220127
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植物多细胞网络分析研究进展
作者:
基金项目:

国家重点研发计划(2016YFD0100504)；国家自然科学基金(31571584,31370317)；重庆市自然科学基金(cstc2013jcyjA80016)


Advances in the plant multicellular network analysis
Author:
  • SHI Bore

    SHI Bore

    Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, College of Life Sciences, Southwest University, Chongqing 400715, China;Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), Southwest University, Chongqing 400715, China
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  • HUANG Xiaoping

    HUANG Xiaoping

    Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, College of Life Sciences, Southwest University, Chongqing 400715, China;Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), Southwest University, Chongqing 400715, China
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  • FU Xiurong

    FU Xiurong

    Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, College of Life Sciences, Southwest University, Chongqing 400715, China;Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), Southwest University, Chongqing 400715, China
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  • WANG Bangjun

    WANG Bangjun

    Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, College of Life Sciences, Southwest University, Chongqing 400715, China;Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), Southwest University, Chongqing 400715, China
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  • 摘要
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    摘要:

    多细胞网络分析是一种可用于分析细胞空间结构的方法。器官的功能是由组成它们的细胞决定的，细胞空间排列赋予了器官更高层面的功能。目前关于植物细胞的空间排列结构是如何影响器官的机理仍然知之甚少。通过对植株进行3D扫描提取细胞网络模型用于多细胞网络分析，可深入揭示植物发育机制，并为人工合成植物多细胞系统提供参考。本文回顾了多细胞模型的发展历程，总结了多细胞网络分析的流程，并阐述了多细胞网络分析在植物生长发育中的发展与应用。此外，本文还对植物多细胞网络分析未来的发展趋势进行了展望。

    Abstract:

    Multicellular network analysis is a method for topological properties analysis of cells. The functions of organs are determined by their inner cells. The arrangement of cells within organs endows higher-order functionality through a structure-function relationship, though the organizational properties of these multicellular configurations remain poorly understood. Multicellular network analysis with multicellular models established by 3D scanning of plants, will further discover the plant development mechanism, and provide clues for synthesizing plant multicellular systems. In this paper, we review the development of multicellular models, summarize the process of multicellular network analysis, and describe the development and application of multicellular network analysis in plants. In addition, this review also provides perspective on future development of plant multicellular network analysis.

    参考文献
    [1] 张晨阳,武耀康,徐显皓,等.工业微生物代谢网络模型的研究进展及应用.生物工程学报, 2021, 37(3):860-873.Zhang CY, Wu YK, Xu XH, et al.Current status and future perspectives of metabolic network models of industrial microorganisms.Chin J Biotech, 2021, 37(3):860-873(in Chinese).
    [2] Zhang X, Man Y, Zhuang XH, et al.Plant multiscale networks:charting plant connectivity by multi-level analysis and imaging techniques.Sci China Life Sci, 2021, 64(9):1392-1422.
    [3] Gosak M, Markovič R, Dolenšek J, et al.Network science of biological systems at different scales:a review.Phys Life Rev, 2018, 24:118-135.
    [4] Cortes-Poza Y, Padilla-Longoria P, Alvarez-Buylla E.Spatial dynamics of floral organ formation.J Theor Biol, 2018, 454:30-40.
    [5] Kaur A, Chitre A, Wanjale K, et al.Recognition of protein network for bioinformatics knowledge analysis using support vector machine.Biomed Res Int, 2022, 2022:2273648.
    [6] Rellán-Álvarez R, Lobet G, Lindner H, et al.GLO-Roots:an imaging platform enabling multidimensional characterization of soil-grown root systems.Elife, 2015, 4:e07597.
    [7] Cabin Z, Derieg NJ, Garton A, et al.Non-pollinator selection for a floral homeotic mutant conferring loss of nectar reward in Aquilegia coerulea.Curr Biol, 2022, 32(6):1332-1341.
    [8] Birnbaum KD, Otegui MS, Bailey-Serres J, et al.The plant cell atlas:focusing new technologies on the kingdom that nourishes the planet.Plant Physiol, 2022, 188(2):675-679.
    [9] Green PB.Cell morphogenesis.Annu Rev Plant Physiol, 1969, 20:365-394.
    [10] Davies J.Using synthetic biology to explore principles of development.Development, 2017, 144(7):1146-1158.
    [11] Cajal S, Ramòn Y.Histologie du système nerveux de l'Homme et des vertébrés.Paris:Maloine Press, 1911:887-890.
    [12] Chalfie M, Sulston JE, White JG, et al.The neural circuit for touch sensitivity in Caenorhabditis elegans.J Neurosci, 1985, 5(4):956-964.
    [13] Sporns O, Tononi G, Kötter R.The human connectome:a structural description of the human brain.PLoS Comput Biol, 2005, 1(4):e42.
    [14] Ryan K, Lu ZY, Meinertzhagen IA.The CNS connectome of a tadpole larva of Ciona intestinalis(L.) highlights sidedness in the brain of a chordate sibling.eLife, 2016, 5:e16962.
    [15] Bullmore E, Sporns O.Complex brain networks:graph theoretical analysis of structural and functional systems.Nat Rev Neurosci, 2009, 10(3):186-198.
    [16] DeFelipe J.From the connectome to the synaptome:an epic love story.Science, 2010, 330(6008):1198-1201.
    [17] Queller DC, Strassmann JE.Beyond society:the evolution of organismality.Philos Trans R Soc Lond B Biol Sci, 2009, 364(1533):3143-3155.
    [18] Montenegro-Johnson TD, Stamm P, Strauss S, et al.Digital single-cell analysis of plant organ development using 3DCellAtlas.Plant Cell, 2015, 27(4):1018-1033.
    [19] Kurihara D, Mizuta Y, Nagahara S, et al.Optical clearing of plant tissues for fluorescence imaging.J Vis Exp, 2022(179):e63428.
    [20] Jackson MD, Xu H, Duran-Nebreda S, et al.Topological analysis of multicellular complexity in the plant hypocotyl.eLife, 2017, 6:e26023.
    [21] Montenegro-Johnson T, Strauss S, Jackson MDB, et al.3DCellAtlas Meristem:a tool for the global cellular annotation of shoot apical meristems.Plant Methods, 2019, 15:33.
    [22] Barabási AL PM.Network Science.Cambridge, UK:Cambridge University Press, 2016
    [23] Gibson MC, Patel AB, Nagpal R, et al.The emergence of geometric order in proliferating metazoan epithelia.Nature, 2006, 442(7106):1038-1041.
    [24] Heller D, Hoppe A, Restrepo S, et al.EpiTools:an open-source image analysis toolkit for quantifying epithelial growth dynamics.Dev Cell, 2016, 36(1):103-116.
    [25] Newman MEJ.Networks:an introduction, Oxford,UK:Oxford University Press, 2010
    [26] Bassel GW.Multicellular systems biology:quantifying cellular patterning and function in plant organs using network science.Mol Plant, 2019, 12(6):731-742.
    [27] Di Laurenzio L, Wysocka-Diller J, Malamy JE, et al.The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root.Cell, 1996, 86(3):423-433.
    [28] Avena-Koenigsberger A, Goñi J, Solé R, et al.Network morphospace.J R Soc Interface, 2015, 12(103):20140881.
    [29] Ollé-Vila A, Duran-Nebreda S, Conde-Pueyo N, et al.A morphospace for synthetic organs and organoids:the possible and the actual.Integr Biol (Camb), 2016, 8(4):485-503.
    [30] Dissmeyer N, Weimer AK, Pusch S, et al.Control of cell proliferation, organ growth, and DNA damage response operate independently of dephosphorylation of the Arabidopsis Cdk1 homolog CDKA;1.Plant Cell, 2009, 21(11):3641-3654.
    [31] Yang C, Sofroni K, Wijnker E, et al.The Arabidopsis Cdk1/Cdk2 homolog CDKA;1 controls chromosome axis assembly during plant meiosis.EMBO J, 2020, 39(3):e101625.
    [32] Weimer AK, Nowack MK, Bouyer D, et al.Retinoblastoma related1 regulates asymmetric cell divisions in Arabidopsis.Plant Cell, 2012, 24(10):4083-4095.
    [33] Hardtke CS, Berleth T.The Arabidopsis gene MONOPTEROS encodes a transcription factor mediating embryo axis formation and vascular development.EMBO J, 1998, 17(5):1405-1411.
    [34] Schlereth A, Möller B, Liu WL, et al.MONOPTEROS controls embryonic root initiation by regulating a mobile transcription factor.Nature, 2010, 464(7290):913-916.
    [35] Treml BS, Winderl S, Radykewicz R, et al.The gene ENHANCER OF PINOID controls Cotyledon development in the Arabidopsis embryo.Development, 2005, 132(18):4063-4074.
    [36] Yoshida S, Barbier De Reuille P, Lane B, et al.Genetic control of plant development by overriding a geometric division rule.Dev Cell, 2014, 29(1):75-87.
    [37] Zhang ZJ, Runions A, Mentink RA, et al.A WOX/auxin biosynthesis module controls growth to shape leaf form.Curr Biol, 2020, 30(24):4857-4868.e6.
    [38] Duckett CM, Grierson C, Linstead P, et al.Clonal relationships and cell patterning in the root epidermis of Arabidopsis.Development, 1994, 120(9):2465-2474.
    [39] Jackson MDB, Duran-Nebreda S, Kierzkowski D, et al.Global topological order emerges through local mechanical control of cell divisions in the Arabidopsis shoot apical meristem.Cell Syst, 2019, 8(1):53-65.e3.
    [40] Kierzkowski D, Runions A, Vuolo F, et al.A growth-based framework for leaf shape development and diversity.Cell, 2019, 177(6):1405-1418.e17.
    [41] Dong Y, Majda M,Šimura J, et al.HEARTBREAK controls post-translational modification of INDEHISCENT to regulate fruit morphology in Capsella.Curr Biol, 2020, 30(19):3880-3888.e5.
    [42] Doursat R, Sayama H, Michel O.Mophogenetic engineering:Toward Programmable Complex Systems.2013th ed.Berlin:Springer Press, 2012..
    [43] Wolf DM, Arkin AP.Motifs, modules and games in bacteria.Curr Opin Microbiol, 2003, 6(2):125-134.
    [44] Boyle PM, Silver PA.Harnessing nature's toolbox:regulatory elements for synthetic biology.J R Soc Interface, 2009, 6(Suppl 4):S535-S546.
    [45] Glass DS, Riedel-Kruse IH.A synthetic bacterial cell-cell adhesion toolbox for programming multicellular morphologies and patterns.Cell, 2018, 174(3):649-658.e16.
    [46] Weber W, Daoud-El Baba M, Fussenegger M.Synthetic ecosystems based on airborne inter-and intrakingdom communication.Proc Natl Acad Sci USA, 2007, 104(25):10435-10440.
    [47] Maharbiz MM.Synthetic multicellularity.Trends Cell Biol, 2012, 22(12):617-623.
    [48] Solé R, Ollé-Vila A, Vidiella B, et al.The road to synthetic multicellularity.Curr Opin Syst Biol, 2018, 7:60-67.
    [49] Ivanchenko MG, Zhu JS, Wang BJ, et al.The cyclophilin A DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation.Development, 2015, 142(4):712-721.
    [50] Galvan-Ampudia CS, Cerutti G, Legrand J, et al.Temporal integration of auxin information for the regulation of patterning.Elife, 2020, 9:e55832.
    [51] Boehm CR, Pollak B, Purswani N, et al.Synthetic botany.Cold Spring Harb Perspect Biol, 2017, 9(7):a023887.
    [52] Liu Y, Yang MY, Deng YX, et al.High-spatial-resolution multi-omics sequencing via deterministic barcoding in tissue.Cell, 2020, 183(6):1665-1681.e18.
    [53] Bai T, Xu J, Zhang Z, et al.Context-aware learning for cancer cell nucleus recognition in pathology images.Bioinformatics, 2022:2022Mar21;btac167.
    [54] Kipf T N, Welling M.Semi-supervised classification with graph convolutional networks.2016, arXiv:1609.02907.
    [55] Xia KK, Sun HX, Li J, et al.The single-cell stereo-seq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leaves.Dev Cell, 2022, 57:1-12.
    [56] Von Mering C, Krause R, Snel B, et al.Comparative assessment of large-scale data sets of protein-protein interactions.Nature, 2002, 417(6887):399-403.
    [57] Du F, Jiao Y.Mechanical control of plant morphogenesis:concepts and progress.Curr Opin Plant Biol, 2020, 57:16-23.
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施般若,黄小萍,付秀荣,王邦俊. 植物多细胞网络分析研究进展[J]. 生物工程学报, 2022, 38(8): 2798-2810

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  • 收稿日期:2022-02-22
  • 在线发布日期: 2022-08-25
  • 出版日期: 2022-08-25
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