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Xu P, Huang S, Zhai X, Fan Y, Li X, Yang H, Cao Y, Fan G. N6-methyladenosine modification changes during the recovery processes for Paulownia witches' broom disease under the methyl methanesulfonate treatment. PLANT DIRECT 2023; 7:e508. [PMID: 37426893 PMCID: PMC10325887 DOI: 10.1002/pld3.508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 05/05/2023] [Accepted: 06/04/2023] [Indexed: 07/11/2023]
Abstract
Phytoplasmas induce diseases in more than 1000 plant species and cause substantial ecological damage and economic losses, but the specific pathogenesis of phytoplasma has not yet been clarified. N 6-methyladenosine (m6A) is the most common internal modification of the eukaryotic Messenger RNA (mRNA). As one of the species susceptible to phytoplasma infection, the pathogenesis and mechanism of Paulownia has been extensively studied by scholars, but the m6A transcriptome map of Paulownia fortunei (P. fortunei) has not been reported. Therefore, this study aimed to explore the effect of phytoplasma infection on m6A modification of P. fortunei and obtained the whole transcriptome m6A map in P. fortunei by m6A-seq. The m6A-seq results of Paulownia witches' broom (PaWB) disease and healthy samples indicate that PaWB infection increased the degree of m6A modification of P. fortunei. The correlation analysis between the RNA-seq and m6A-seq data detected that a total of 315 differentially methylated genes were predicted to be significantly differentially expressed at the transcriptome level. Moreover, the functions of PaWB-related genes were predicted by functional enrichment analysis, and two genes related to maintenance of the basic mechanism of stem cells in shoot apical meristem were discovered. One of the genes encodes the receptor protein kinase CLV2 (Paulownia_LG2G000076), and the other gene encodes the homeobox transcription factor STM (Paulownia_LG15G000976). In addition, genes F-box (Paulownia_LG17G000760) and MSH5 (Paulownia_LG8G001160) had exon skipping and mutually exclusive exon types of alternative splicing in PaWB-infected seedling treated with methyl methanesulfonate, and m6A modification was found in m6A-seq results. Moreover, Reverse Transcription-Polymerase Chain Reaction (RT-PCR) verified that the alternative splicing of these two genes was associated with m6A modification. This comprehensive map provides a solid foundation for revealing the potential function of the mRNA m6A modification in the process of PaWB. In future studies, we plan to verify genes directly related to PaWB and methylation-related enzymes in Paulownia to elucidate the pathogenic mechanism of PaWB caused by phytoplasma invasion.
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Affiliation(s)
- Pingluo Xu
- Institute of PaulowniaHenan Agricultural UniversityZhengzhouP. R. China
| | - Shunmou Huang
- Institute of PaulowniaHenan Agricultural UniversityZhengzhouP. R. China
| | - Xiaoqiao Zhai
- Key Laboratory of Forest Germplasm Resources Protection and Improved Variety Selection in Henan ProvinceHenan Province Academy of ForestryZhengzhouP. R. China
| | - Yujie Fan
- Institute of PaulowniaHenan Agricultural UniversityZhengzhouP. R. China
- College of ForestryHenan Agricultural UniversityZhengzhouP. R. China
| | - Xiaofan Li
- Institute of PaulowniaHenan Agricultural UniversityZhengzhouP. R. China
| | - Haibo Yang
- Institute of PaulowniaHenan Agricultural UniversityZhengzhouP. R. China
| | - Yabing Cao
- Institute of PaulowniaHenan Agricultural UniversityZhengzhouP. R. China
| | - Guoqiang Fan
- Institute of PaulowniaHenan Agricultural UniversityZhengzhouP. R. China
- College of ForestryHenan Agricultural UniversityZhengzhouP. R. China
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2
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Battogtokh D, Tyson JJ. Nucleation of stem cell domains in a bistable activator-inhibitor model of the shoot apical meristem. CHAOS (WOODBURY, N.Y.) 2022; 32:093117. [PMID: 36182391 DOI: 10.1063/5.0093841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/03/2022] [Indexed: 06/16/2023]
Abstract
Shoot apical meristems (SAMs) give rise to all above-ground tissues of a plant. Expansion of meristematic tissue is derived from the growth and division of stem cells that reside in a central zone of the SAM. This reservoir of stem cells is maintained by expression of a transcription factor WUSCHEL that is responsible for the development of stem cells in the central zone. WUSCHEL expression is self-activating and downregulated by a signaling pathway initiated by CLAVATA proteins, which are upregulated by WUSCHEL. This classic activator-inhibitor network can generate localized patterns of WUSCHEL activity by a Turing instability provided certain constraints on reaction rates and diffusion constants of WUSCHEL and CLAVATA are satisfied, and most existing mathematical models of nucleation and confinement of stem cells in the SAM rely on Turing's mechanism. However, Turing patterns have certain properties that are inconsistent with observed patterns of stem cell differentiation in the SAM. As an alternative mechanism, we propose a model for stem cell confinement based on a bistable-switch in WUSCHEL-CLAVATA interactions. We study the bistable-switch mechanism for pattern formation in a spatially continuous domain and in a discrete cellularized tissue in the presence of a non-uniform field of a rapidly diffusing hormone. By comparing domain formation by Turing and bistable-switch mechanisms in these contexts, we show that bistable switching provides a superior account of nucleation and confinement of the stem cell domain under reasonable assumptions on reaction rates and diffusion constants.
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Affiliation(s)
- Dorjsuren Battogtokh
- Department of Biological Sciences, Virginia Polytechnic Institute & State University, Blacksburg, Virginia 24061, USA
| | - John J Tyson
- Department of Biological Sciences, Virginia Polytechnic Institute & State University, Blacksburg, Virginia 24061, USA
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3
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Nimmakayala P, Lopez-Ortiz C, Shahi B, Abburi VL, Natarajan P, Kshetry AO, Shinde S, Davenport B, Stommel J, Reddy UK. Exploration into natural variation for genes associated with fruit shape and size among Capsicum chinense collections. Genomics 2021; 113:3002-3014. [PMID: 34229041 DOI: 10.1016/j.ygeno.2021.06.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/07/2021] [Accepted: 06/30/2021] [Indexed: 11/28/2022]
Abstract
Phenotype diversity within cultivated Capsicum chinense is particularly evident for fruit shape and size. We used this diversity in C. chinense to further unravel the genetic mechanisms underlying fruit shape variation in pepper and related Solanaceous species. We identified candidate genes for C. chinense fruit shape, explored their contribution to population structure, and characterized their potential function in pepper fruit shape. Using genotyping by sequencing, we identified 43,081 single nucleotide polymorphisms (SNPs) from diverse collections of C. chinense. Principal component, neighbor-joining tree, and population structure analyses resolved 3 phylogenetically robust clusters associated with fruit shapes. Genome-wide association study (GWAS) was used to identify associated genomic regions with various fruit shape traits obtained from image analysis with Tomato Analyzer software. In our GWAS, we selected 12 SNPs associated with locule number trait and 8 SNP markers associated with other fruit shape traits such as perimeter, area, obovoid, ellipsoid and morphometrics (5y, 6y and 7y). The SNPs in CLAVATA1, WD-40, Auxin receptor, AAA type ATPase family protein, and RNA polymerase III genes were the major markers identified for fruit locule number from our GWAS results. Furthermore, we found SNPs in tetratricopeptide-repeat thioredoxin-like 3, enhancer of ABA co-receptor 1, subunit of exocyst complex 8 and pleiotropic drug resistance proteins associated with various fruit shape traits. CLAVATA1, WD-40 and Auxin receptor genes are known genes that affect tomato fruit shape. In this study, we used Arabidopsis thaliana T-DNA insertion knockout mutants and expression profiles for functional characterization of newly identified genes and to understand their role in fruit shape.
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Affiliation(s)
- Padma Nimmakayala
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Carlos Lopez-Ortiz
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Bhagarathi Shahi
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Venkata L Abburi
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Purushothaman Natarajan
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Arjun Ojha Kshetry
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Suhas Shinde
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Brittany Davenport
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - John Stommel
- Genetic Improvement of Fruits and Vegetables Laboratory, USDA, ARS, Beltsville MD-20705, USA
| | - Umesh K Reddy
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA.
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4
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Liu Z, Shpak ED, Hong T. A mathematical model for understanding synergistic regulations and paradoxical feedbacks in the shoot apical meristem. Comput Struct Biotechnol J 2020; 18:3877-3889. [PMID: 33335685 PMCID: PMC7720093 DOI: 10.1016/j.csbj.2020.11.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 01/22/2023] Open
Abstract
The shoot apical meristem (SAM) is the primary stem cell niche in plant shoots. Stem cells in the SAM are controlled by an intricate regulatory network, including negative feedback between WUSCHEL (WUS) and CLAVATA3 (CLV3). Recently, we identified a group of signals, Epidermal Patterning Factor-Like (EPFL) proteins, that are produced at the peripheral region and are important for SAM homeostasis. Here, we present a mathematical model for the SAM regulatory network. The model revealed that the SAM uses EPFL and signals such as HAIRY MERISTEM from the middle in a synergistic manner to constrain both WUS and CLV3. We found that interconnected negative and positive feedbacks between WUS and CLV3 ensure stable WUS expression in the SAM when facing perturbations, and the positive feedback loop also maintains distinct cell populations containing WUS on and CLV3 on cells in the apical-basal direction. Furthermore, systematic perturbations of the parameters revealed a tradeoff between optimizations of multiple patterning features. Our results provide a holistic view of the regulation of SAM patterning in multiple dimensions. They give insights into how Arabidopsis integrates signals from lateral and apical-basal axes to control the SAM patterning, and they shed light into design principles that may be widely useful for understanding regulatory networks of stem cell niche.
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Affiliation(s)
- Ziyi Liu
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN, United States
| | - Elena D. Shpak
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN, United States
| | - Tian Hong
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN, United States
- National Institute for Mathematical and Biological Synthesis, Knoxville, TN, United States
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5
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Bucksch A, Atta-Boateng A, Azihou AF, Battogtokh D, Baumgartner A, Binder BM, Braybrook SA, Chang C, Coneva V, DeWitt TJ, Fletcher AG, Gehan MA, Diaz-Martinez DH, Hong L, Iyer-Pascuzzi AS, Klein LL, Leiboff S, Li M, Lynch JP, Maizel A, Maloof JN, Markelz RJC, Martinez CC, Miller LA, Mio W, Palubicki W, Poorter H, Pradal C, Price CA, Puttonen E, Reese JB, Rellán-Álvarez R, Spalding EP, Sparks EE, Topp CN, Williams JH, Chitwood DH. Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences. FRONTIERS IN PLANT SCIENCE 2017; 8:900. [PMID: 28659934 PMCID: PMC5465304 DOI: 10.3389/fpls.2017.00900] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 05/12/2017] [Indexed: 05/21/2023]
Abstract
The geometries and topologies of leaves, flowers, roots, shoots, and their arrangements have fascinated plant biologists and mathematicians alike. As such, plant morphology is inherently mathematical in that it describes plant form and architecture with geometrical and topological techniques. Gaining an understanding of how to modify plant morphology, through molecular biology and breeding, aided by a mathematical perspective, is critical to improving agriculture, and the monitoring of ecosystems is vital to modeling a future with fewer natural resources. In this white paper, we begin with an overview in quantifying the form of plants and mathematical models of patterning in plants. We then explore the fundamental challenges that remain unanswered concerning plant morphology, from the barriers preventing the prediction of phenotype from genotype to modeling the movement of leaves in air streams. We end with a discussion concerning the education of plant morphology synthesizing biological and mathematical approaches and ways to facilitate research advances through outreach, cross-disciplinary training, and open science. Unleashing the potential of geometric and topological approaches in the plant sciences promises to transform our understanding of both plants and mathematics.
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Affiliation(s)
- Alexander Bucksch
- Department of Plant Biology, University of Georgia, AthensGA, United States
- Warnell School of Forestry and Natural Resources, University of Georgia, AthensGA, United States
- Institute of Bioinformatics, University of Georgia, AthensGA, United States
| | | | - Akomian F. Azihou
- Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-CalaviCotonou, Benin
| | - Dorjsuren Battogtokh
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, BlacksburgVA, United States
| | - Aly Baumgartner
- Department of Geosciences, Baylor University, WacoTX, United States
| | - Brad M. Binder
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, KnoxvilleTN, United States
| | | | - Cynthia Chang
- Division of Biology, University of Washington, BothellWA, United States
| | - Viktoirya Coneva
- Donald Danforth Plant Science Center, St. LouisMO, United States
| | - Thomas J. DeWitt
- Department of Wildlife and Fisheries Sciences–Department of Plant Pathology and Microbiology, Texas A&M University, College StationTX, United States
| | - Alexander G. Fletcher
- School of Mathematics and Statistics and Bateson Centre, University of SheffieldSheffield, United Kingdom
| | - Malia A. Gehan
- Donald Danforth Plant Science Center, St. LouisMO, United States
| | | | - Lilan Hong
- Weill Institute for Cell and Molecular Biology and Section of Plant Biology, School of Integrative Plant Sciences, Cornell University, IthacaNY, United States
| | - Anjali S. Iyer-Pascuzzi
- Department of Botany and Plant Pathology, Purdue University, West LafayetteIN, United States
| | - Laura L. Klein
- Department of Biology, Saint Louis University, St. LouisMO, United States
| | - Samuel Leiboff
- School of Integrative Plant Science, Cornell University, IthacaNY, United States
| | - Mao Li
- Department of Mathematics, Florida State University, TallahasseeFL, United States
| | - Jonathan P. Lynch
- Department of Plant Science, The Pennsylvania State University, University ParkPA, United States
| | - Alexis Maizel
- Center for Organismal Studies, Heidelberg UniversityHeidelberg, Germany
| | - Julin N. Maloof
- Department of Plant Biology, University of California, Davis, DavisCA, United States
| | - R. J. Cody Markelz
- Department of Plant Biology, University of California, Davis, DavisCA, United States
| | - Ciera C. Martinez
- Department of Molecular and Cell Biology, University of California, Berkeley, BerkeleyCA, United States
| | - Laura A. Miller
- Program in Bioinformatics and Computational Biology, The University of North Carolina, Chapel HillNC, United States
| | - Washington Mio
- Department of Mathematics, Florida State University, TallahasseeFL, United States
| | - Wojtek Palubicki
- The Sainsbury Laboratory, University of CambridgeCambridge, United Kingdom
| | - Hendrik Poorter
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, JülichGermany
| | | | - Charles A. Price
- National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, KnoxvilleTN, United States
| | - Eetu Puttonen
- Department of Remote Sensing and Photogrammetry, Finnish Geospatial Research Institute, National Land Survey of FinlandMasala, Finland
- Centre of Excellence in Laser Scanning Research, National Land Survey of FinlandMasala, Finland
| | - John B. Reese
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, KnoxvilleTN, United States
| | - Rubén Rellán-Álvarez
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV)Irapuato, Mexico
| | - Edgar P. Spalding
- Department of Botany, University of Wisconsin–Madison, MadisonWI, United States
| | - Erin E. Sparks
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, NewarkDE, United States
| | | | - Joseph H. Williams
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, KnoxvilleTN, United States
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6
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Bucksch A, Atta-Boateng A, Azihou AF, Battogtokh D, Baumgartner A, Binder BM, Braybrook SA, Chang C, Coneva V, DeWitt TJ, Fletcher AG, Gehan MA, Diaz-Martinez DH, Hong L, Iyer-Pascuzzi AS, Klein LL, Leiboff S, Li M, Lynch JP, Maizel A, Maloof JN, Markelz RJC, Martinez CC, Miller LA, Mio W, Palubicki W, Poorter H, Pradal C, Price CA, Puttonen E, Reese JB, Rellán-Álvarez R, Spalding EP, Sparks EE, Topp CN, Williams JH, Chitwood DH. Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences. FRONTIERS IN PLANT SCIENCE 2017. [PMID: 28659934 DOI: 10.3389/978-2-88945-297-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The geometries and topologies of leaves, flowers, roots, shoots, and their arrangements have fascinated plant biologists and mathematicians alike. As such, plant morphology is inherently mathematical in that it describes plant form and architecture with geometrical and topological techniques. Gaining an understanding of how to modify plant morphology, through molecular biology and breeding, aided by a mathematical perspective, is critical to improving agriculture, and the monitoring of ecosystems is vital to modeling a future with fewer natural resources. In this white paper, we begin with an overview in quantifying the form of plants and mathematical models of patterning in plants. We then explore the fundamental challenges that remain unanswered concerning plant morphology, from the barriers preventing the prediction of phenotype from genotype to modeling the movement of leaves in air streams. We end with a discussion concerning the education of plant morphology synthesizing biological and mathematical approaches and ways to facilitate research advances through outreach, cross-disciplinary training, and open science. Unleashing the potential of geometric and topological approaches in the plant sciences promises to transform our understanding of both plants and mathematics.
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Affiliation(s)
- Alexander Bucksch
- Department of Plant Biology, University of Georgia, AthensGA, United States
- Warnell School of Forestry and Natural Resources, University of Georgia, AthensGA, United States
- Institute of Bioinformatics, University of Georgia, AthensGA, United States
| | | | - Akomian F Azihou
- Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-CalaviCotonou, Benin
| | - Dorjsuren Battogtokh
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, BlacksburgVA, United States
| | - Aly Baumgartner
- Department of Geosciences, Baylor University, WacoTX, United States
| | - Brad M Binder
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, KnoxvilleTN, United States
| | | | - Cynthia Chang
- Division of Biology, University of Washington, BothellWA, United States
| | - Viktoirya Coneva
- Donald Danforth Plant Science Center, St. LouisMO, United States
| | - Thomas J DeWitt
- Department of Wildlife and Fisheries Sciences-Department of Plant Pathology and Microbiology, Texas A&M University, College StationTX, United States
| | - Alexander G Fletcher
- School of Mathematics and Statistics and Bateson Centre, University of SheffieldSheffield, United Kingdom
| | - Malia A Gehan
- Donald Danforth Plant Science Center, St. LouisMO, United States
| | | | - Lilan Hong
- Weill Institute for Cell and Molecular Biology and Section of Plant Biology, School of Integrative Plant Sciences, Cornell University, IthacaNY, United States
| | - Anjali S Iyer-Pascuzzi
- Department of Botany and Plant Pathology, Purdue University, West LafayetteIN, United States
| | - Laura L Klein
- Department of Biology, Saint Louis University, St. LouisMO, United States
| | - Samuel Leiboff
- School of Integrative Plant Science, Cornell University, IthacaNY, United States
| | - Mao Li
- Department of Mathematics, Florida State University, TallahasseeFL, United States
| | - Jonathan P Lynch
- Department of Plant Science, The Pennsylvania State University, University ParkPA, United States
| | - Alexis Maizel
- Center for Organismal Studies, Heidelberg UniversityHeidelberg, Germany
| | - Julin N Maloof
- Department of Plant Biology, University of California, Davis, DavisCA, United States
| | - R J Cody Markelz
- Department of Plant Biology, University of California, Davis, DavisCA, United States
| | - Ciera C Martinez
- Department of Molecular and Cell Biology, University of California, Berkeley, BerkeleyCA, United States
| | - Laura A Miller
- Program in Bioinformatics and Computational Biology, The University of North Carolina, Chapel HillNC, United States
| | - Washington Mio
- Department of Mathematics, Florida State University, TallahasseeFL, United States
| | - Wojtek Palubicki
- The Sainsbury Laboratory, University of CambridgeCambridge, United Kingdom
| | - Hendrik Poorter
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, JülichGermany
| | | | - Charles A Price
- National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, KnoxvilleTN, United States
| | - Eetu Puttonen
- Department of Remote Sensing and Photogrammetry, Finnish Geospatial Research Institute, National Land Survey of FinlandMasala, Finland
- Centre of Excellence in Laser Scanning Research, National Land Survey of FinlandMasala, Finland
| | - John B Reese
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, KnoxvilleTN, United States
| | - Rubén Rellán-Álvarez
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV)Irapuato, Mexico
| | - Edgar P Spalding
- Department of Botany, University of Wisconsin-Madison, MadisonWI, United States
| | - Erin E Sparks
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, NewarkDE, United States
| | | | - Joseph H Williams
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, KnoxvilleTN, United States
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7
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Battogtokh D, Tyson JJ. A Bistable Switch Mechanism for Stem Cell Domain Nucleation in the Shoot Apical Meristem. FRONTIERS IN PLANT SCIENCE 2016; 7:674. [PMID: 27242874 PMCID: PMC4876614 DOI: 10.3389/fpls.2016.00674] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/02/2016] [Indexed: 05/22/2023]
Affiliation(s)
- Dorjsuren Battogtokh
- Department of Theoretical Physics, The Institute of Physics and Technology, Mongolian Academy of SciencesUlaanbaatar, Mongolia
- Department of Biological Sciences, Virginia Polytechnic and State UniversityBlacksburg, VA, USA
- *Correspondence: Dorjsuren Battogtokh
| | - John J. Tyson
- Department of Biological Sciences, Virginia Polytechnic and State UniversityBlacksburg, VA, USA
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8
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Battogtokh D. Domain nucleation and confinement in agent-controlled bistable systems. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:032713. [PMID: 25871150 DOI: 10.1103/physreve.91.032713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Indexed: 05/13/2023]
Abstract
We report a mechanism of pattern formation in growing bistable systems coupled indirectly. A modified Fujita et al. model is studied as an example of a reaction-diffusion system of nondiffusive activator and inhibitor molecules immersed in the medium of a fast diffusive agent. Here we show that, as the system grows, a new domain nucleates spontaneously in the area where the local level of the agent becomes critical. Newly nucleated domains are stable and the pattern formation is different from Turing's mechanism in monostable systems. Domains are spatially confined by the agent even if the activator and inhibitor molecules diffuse. With the spatial extension of the system, a larger domain may undergo a wave number instability, and the concentrations of active molecules within the neighboring elements of a domain can become sharply different. The mechanism reported in this work could be generic for pattern formation systems involving multistability, growth, and indirect coupling.
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Affiliation(s)
- Dorjsuren Battogtokh
- The Institute of Physics and Technology, Mongolian Academy of Sciences, Ulaanbaatar 51, Mongolia and Department of Biological Sciences, Virginia Polytechnic and State University, Blacksburg, Virginia 24061, USA
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9
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Voß U, Bishopp A, Farcot E, Bennett MJ. Modelling hormonal response and development. TRENDS IN PLANT SCIENCE 2014; 19:311-9. [PMID: 24630843 PMCID: PMC4013931 DOI: 10.1016/j.tplants.2014.02.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 02/05/2014] [Accepted: 02/07/2014] [Indexed: 05/20/2023]
Abstract
As our knowledge of the complexity of hormone homeostasis, transport, perception, and response increases, and their outputs become less intuitive, modelling is set to become more important. Initial modelling efforts have focused on hormone transport and response pathways. However, we now need to move beyond the network scales and use multicellular and multiscale modelling approaches to predict emergent properties at different scales. Here we review some examples where such approaches have been successful, for example, auxin-cytokinin crosstalk regulating root vascular development or a study of lateral root emergence where an iterative cycle of modelling and experiments lead to the identification of an overlooked role for PIN3. Finally, we discuss some of the remaining biological and technical challenges.
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Affiliation(s)
- Ute Voß
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Anthony Bishopp
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Etienne Farcot
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham, LE12 5RD, UK; School of Mathematical Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Malcolm J Bennett
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham, LE12 5RD, UK.
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10
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Nikolaev SV, Zubairova US, Penenko AV, Mjolsness ED, Shapiro BE, Kolchanov NA. Model of structuring the stem cell niche in shoot apical meristem of Arabidopsis thaliana. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2013; 452:316-9. [PMID: 24150656 DOI: 10.1134/s0012496613050104] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Indexed: 01/21/2023]
Affiliation(s)
- S V Nikolaev
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
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11
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Shapiro BE, Meyerowitz EM, Mjolsness E. Using cellzilla for plant growth simulations at the cellular level. FRONTIERS IN PLANT SCIENCE 2013; 4:408. [PMID: 24137172 PMCID: PMC3797531 DOI: 10.3389/fpls.2013.00408] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 09/26/2013] [Indexed: 05/23/2023]
Abstract
Cellzilla is a two-dimensional tissue simulation platform for plant modeling utilizing Cellerator arrows. Cellerator describes biochemical interactions with a simplified arrow-based notation; all interactions are input as reactions and are automatically translated to the appropriate differential equations using a computer algebra system. Cells are represented by a polygonal mesh of well-mixed compartments. Cell constituents can interact intercellularly via Cellerator reactions utilizing diffusion, transport, and action at a distance, as well as amongst themselves within a cell. The mesh data structure consists of vertices, edges (vertex pairs), and cells (and optional intercellular wall compartments) as ordered collections of edges. Simulations may be either static, in which cell constituents change with time but cell size and shape remain fixed; or dynamic, where cells can also grow. Growth is controlled by Hookean springs associated with each mesh edge and an outward pointing pressure force. Spring rest length grows at a rate proportional to the extension beyond equilibrium. Cell division occurs when a specified constituent (or cell mass) passes a (random, normally distributed) threshold. The orientation of new cell walls is determined either by Errera's rule, or by a potential model that weighs contributions due to equalizing daughter areas, minimizing wall length, alignment perpendicular to cell extension, and alignment perpendicular to actual growth direction.
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Affiliation(s)
- Bruce E. Shapiro
- Department of Mathematics, California State UniversityNorthridge, CA, USA
- Biological Network Modeling Center, CaltechPasadena, CA, USA
| | | | - Eric Mjolsness
- Department of Computer Science, University of CaliforniaIrvine, CA, USA
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12
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Fujita H, Kawaguchi M. Pattern formation by two-layer Turing system with complementarysynthesis. J Theor Biol 2013; 322:33-45. [DOI: 10.1016/j.jtbi.2013.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 12/06/2012] [Accepted: 01/11/2013] [Indexed: 10/27/2022]
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13
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Roeder AHK, Tarr PT, Tobin C, Zhang X, Chickarmane V, Cunha A, Meyerowitz EM. Computational morphodynamics of plants: integrating development over space and time. Nat Rev Mol Cell Biol 2011; 12:265-73. [PMID: 21364682 PMCID: PMC4128830 DOI: 10.1038/nrm3079] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The emerging field of computational morphodynamics aims to understand the changes that occur in space and time during development by combining three technical strategies: live imaging to observe development as it happens; image processing and analysis to extract quantitative information; and computational modelling to express and test time-dependent hypotheses. The strength of the field comes from the iterative and combined use of these techniques, which has provided important insights into plant development.
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Affiliation(s)
- Adrienne H. K. Roeder
- Division of Biology 156-29, California Institute of Technology, 1200 E.
California Blvd., Pasadena, CA 91125, , (626)
395-6895, FAX (626) 449-0756
| | - Paul T. Tarr
- Division of Biology 156-29, California Institute of Technology, 1200 E.
California Blvd., Pasadena, CA 91125, , (626)
395-6895, FAX (626) 449-0756
| | - Cory Tobin
- Division of Biology 156-29, California Institute of Technology, 1200 E.
California Blvd., Pasadena, CA 91125, , (626) 395-4936,
FAX (626) 449-0756
| | - Xiaolan Zhang
- Division of Biology 156-29, California Institute of Technology, 1200 E.
California Blvd., Pasadena, CA 91125, , (626)
395-8438, FAX (626) 449-0756
| | - Vijay Chickarmane
- Division of Biology 156-29, California Institute of Technology, 1200 E.
California Blvd., Pasadena, CA 91125, , (626)
395-6895, FAX (626) 449-0756
| | - Alexandre Cunha
- Center for Advanced Computing Research MC 158-79, California Institute of
Technology, 1200 E. California Blvd., Pasadena, CA 91125,
, (626) 395-8031
| | - Elliot M. Meyerowitz
- Division of Biology 156-29, California Institute of Technology, 1200 E.
California Blvd., Pasadena, CA 91125, , (626)
395-6889, FAX (626) 449-0756
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14
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Fujita H, Toyokura K, Okada K, Kawaguchi M. Reaction-diffusion pattern in shoot apical meristem of plants. PLoS One 2011; 6:e18243. [PMID: 21479227 PMCID: PMC3066213 DOI: 10.1371/journal.pone.0018243] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 03/01/2011] [Indexed: 01/04/2023] Open
Abstract
A fundamental question in developmental biology is how spatial patterns are self-organized from homogeneous structures. In 1952, Turing proposed the reaction-diffusion model in order to explain this issue. Experimental evidence of reaction-diffusion patterns in living organisms was first provided by the pigmentation pattern on the skin of fishes in 1995. However, whether or not this mechanism plays an essential role in developmental events of living organisms remains elusive. Here we show that a reaction-diffusion model can successfully explain the shoot apical meristem (SAM) development of plants. SAM of plants resides in the top of each shoot and consists of a central zone (CZ) and a surrounding peripheral zone (PZ). SAM contains stem cells and continuously produces new organs throughout the lifespan. Molecular genetic studies using Arabidopsis thaliana revealed that the formation and maintenance of the SAM are essentially regulated by the feedback interaction between WUSHCEL (WUS) and CLAVATA (CLV). We developed a mathematical model of the SAM based on a reaction-diffusion dynamics of the WUS-CLV interaction, incorporating cell division and the spatial restriction of the dynamics. Our model explains the various SAM patterns observed in plants, for example, homeostatic control of SAM size in the wild type, enlarged or fasciated SAM in clv mutants, and initiation of ectopic secondary meristems from an initial flattened SAM in wus mutant. In addition, the model is supported by comparing its prediction with the expression pattern of WUS in the wus mutant. Furthermore, the model can account for many experimental results including reorganization processes caused by the CZ ablation and by incision through the meristem center. We thus conclude that the reaction-diffusion dynamics is probably indispensable for the SAM development of plants.
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Affiliation(s)
- Hironori Fujita
- Division of Symbiotic Systems, National Institute for Basic Biology, National Institute for Natural Sciences, Okazaki, Japan.
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