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Rodriguez-Maroto G, Catalán P, Nieto C, Prat S, Ares S. Mathematical Modeling of Photo- and Thermomorphogenesis in Plants. Methods Mol Biol 2024; 2795:247-261. [PMID: 38594544 DOI: 10.1007/978-1-0716-3814-9_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Increased day lengths and warm conditions inversely affect plant growth by directly modulating nuclear phyB, ELF3, and COP1 levels. Quantitative measures of the hypocotyl length have been key to gaining a deeper understanding of this complex regulatory network, while similar quantitative data are the foundation for many studies in plant biology. Here, we explore the application of mathematical modeling, specifically ordinary differential equations (ODEs), to understand plant responses to these environmental cues. We provide a comprehensive guide to constructing, simulating, and fitting these models to data, using the law of mass action to study the evolution of molecular species. The fundamental principles of these models are introduced, highlighting their utility in deciphering complex plant physiological interactions and testing hypotheses. This brief introduction will not allow experimentalists without a mathematical background to run their own simulations overnight, but it will help them grasp modeling principles and communicate with more theory-inclined colleagues.
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Affiliation(s)
- Gabriel Rodriguez-Maroto
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
- Department of Mathematics, Universidad Carlos III de Madrid, Madrid, Spain
| | - Pablo Catalán
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain.
- Department of Mathematics, Universidad Carlos III de Madrid, Madrid, Spain.
| | - Cristina Nieto
- Centro Nacional de Biotecnologia (CNB), CSIC, Madrid, Spain
- Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), CSIC, Madrid, Spain
| | - Salomé Prat
- Centro Nacional de Biotecnologia (CNB), CSIC, Madrid, Spain
- Centro de Investigación en Agrigenomica (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Saúl Ares
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain.
- Centro Nacional de Biotecnologia (CNB), CSIC, Madrid, Spain.
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2
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Banwarth-Kuhn M, Rodriguez K, Michael C, Ta CK, Plong A, Bourgain-Chang E, Nematbakhsh A, Chen W, Roy-Chowdhury A, Reddy GV, Alber M. Combined computational modeling and experimental analysis integrating chemical and mechanical signals suggests possible mechanism of shoot meristem maintenance. PLoS Comput Biol 2022; 18:e1010199. [PMID: 35727850 PMCID: PMC9249181 DOI: 10.1371/journal.pcbi.1010199] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 07/01/2022] [Accepted: 05/12/2022] [Indexed: 11/19/2022] Open
Abstract
Stem cell maintenance in multilayered shoot apical meristems (SAMs) of plants requires strict regulation of cell growth and division. Exactly how the complex milieu of chemical and mechanical signals interact in the central region of the SAM to regulate cell division plane orientation is not well understood. In this paper, simulations using a newly developed multiscale computational model are combined with experimental studies to suggest and test three hypothesized mechanisms for the regulation of cell division plane orientation and the direction of anisotropic cell expansion in the corpus. Simulations predict that in the Apical corpus, WUSCHEL and cytokinin regulate the direction of anisotropic cell expansion, and cells divide according to tensile stress on the cell wall. In the Basal corpus, model simulations suggest dual roles for WUSCHEL and cytokinin in regulating both the direction of anisotropic cell expansion and cell division plane orientation. Simulation results are followed by a detailed analysis of changes in cell characteristics upon manipulation of WUSCHEL and cytokinin in experiments that support model predictions. Moreover, simulations predict that this layer-specific mechanism maintains both the experimentally observed shape and structure of the SAM as well as the distribution of WUSCHEL in the tissue. This provides an additional link between the roles of WUSCHEL, cytokinin, and mechanical stress in regulating SAM growth and proper stem cell maintenance in the SAM.
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Affiliation(s)
- Mikahl Banwarth-Kuhn
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, California, United States of America
- Department of Applied Mathematics, University of California, Merced, California, United States of America
- Department of Mathematics, University of California, Riverside, California, United States of America
| | - Kevin Rodriguez
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, California, United States of America
- Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America
- Center for Plant Cell Biology, University of California, Riverside, California, United States of America
- Institute for Integrative Genome Biology, University of California, Riverside, California, United States of America
| | - Christian Michael
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, California, United States of America
- Department of Mathematics, University of California, Riverside, California, United States of America
| | - Calvin-Khang Ta
- Computer Science and Engineering Department, University of California, Riverside, California, United States of America
| | - Alexander Plong
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, California, United States of America
- Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America
- Center for Plant Cell Biology, University of California, Riverside, California, United States of America
- Institute for Integrative Genome Biology, University of California, Riverside, California, United States of America
| | - Eric Bourgain-Chang
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, California, United States of America
- Department of Mathematics, University of California, Riverside, California, United States of America
| | - Ali Nematbakhsh
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, California, United States of America
- Department of Mathematics, University of California, Riverside, California, United States of America
| | - Weitao Chen
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, California, United States of America
- Department of Mathematics, University of California, Riverside, California, United States of America
| | - Amit Roy-Chowdhury
- Computer Science and Engineering Department, University of California, Riverside, California, United States of America
- Department of Electrical and Computer Engineering, University of California, Riverside, California, United States of America
| | - G. Venugopala Reddy
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, California, United States of America
- Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America
- Center for Plant Cell Biology, University of California, Riverside, California, United States of America
- Institute for Integrative Genome Biology, University of California, Riverside, California, United States of America
- * E-mail: (GVR); (MA)
| | - Mark Alber
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, California, United States of America
- Department of Mathematics, University of California, Riverside, California, United States of America
- * E-mail: (GVR); (MA)
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3
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Jangveladze T, Kiguradze Z, Gagoshidze M, Nikolishvili M. Stability and convergence of the variable directions difference scheme for one nonlinear two-dimensional model. INT J BIOMATH 2015. [DOI: 10.1142/s1793524515500576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The system of two-dimensional nonlinear partial differential equations is considered. This system describes the vein formation in meristematic tissues of young leaves. Variable directions difference scheme is constructed and investigated. Absolute stability regarding space and time steps of scheme is shown. The convergence statement for the constructed scheme is proved. Rate of convergence is given. Various numerical experiments are carried out and results of some of them are considered in this paper. Comparison of numerical experiments with the results of the theoretical investigation is given too.
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Affiliation(s)
- Temur Jangveladze
- Ilia Vekua Institute of Applied Mathematics of Ivane Javakhishvili Tbilisi State University, 2 University Street, 0186 Tbilisi, Georgia
- Georgian Technical University, 77 Kostava Ave., 0175 Tbilisi, Georgia
| | - Zurab Kiguradze
- Ilia Vekua Institute of Applied Mathematics of Ivane Javakhishvili Tbilisi State University, 2 University Street, 0186 Tbilisi, Georgia
| | - Mikheil Gagoshidze
- Sokhumi State University, 12 Politkovskaya Street, 0186 Tbilisi, Georgia
| | - Maia Nikolishvili
- Ivane Javakhishvili Tbilisi State University, 2 University Street, 0186 Tbilisi, Georgia
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4
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Parent B, Tardieu F. Can current crop models be used in the phenotyping era for predicting the genetic variability of yield of plants subjected to drought or high temperature? JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:6179-89. [PMID: 24948682 DOI: 10.1093/jxb/eru223] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A crop model with genetic inputs can potentially simulate yield for a large range of genotypes, sites, and years, thereby indicating where and when a given combination of alleles confers a positive effect. We discuss to what extent current crop models, developed for predicting the effects of climate or cultivation techniques on a reference genotype, are adequate for ranking yields of a large number of genotypes in climatic scenarios with water deficit or high temperatures. We compare here the algorithms involved in 19 crop models. Marked differences exist in the representation of the combined effects of temperature and water deficit on plant development, and in the coordination of these effects with biomass production. The current literature suggests that these differences have a small impact on the yield prediction of a reference genotype because errors on the effects of different traits compensate each other. We propose that they have a larger impact if the crop model is used in a genetic context, because the model has to account for the genetic variability of studied traits. Models with explicit genetic inputs will be increasingly feasible because model parameters corresponding to each genotype can now be measured in phenotyping platforms for large plant collections. This will in turn allow prediction of parameter values from the allelic composition of genotypes. It is therefore timely to adapt crop models to this new context to simulate the allelic effects in present or future climatic scenarios with water or heat stresses.
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Affiliation(s)
- Boris Parent
- INRA, UMR759 Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, Place Viala, F-34060 Montpellier, France
| | - François Tardieu
- INRA, UMR759 Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, Place Viala, F-34060 Montpellier, France
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5
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Sozzani R, Busch W, Spalding EP, Benfey PN. Advanced imaging techniques for the study of plant growth and development. TRENDS IN PLANT SCIENCE 2014; 19:304-10. [PMID: 24434036 PMCID: PMC4008707 DOI: 10.1016/j.tplants.2013.12.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 11/29/2013] [Accepted: 12/11/2013] [Indexed: 05/07/2023]
Abstract
A variety of imaging methodologies are being used to collect data for quantitative studies of plant growth and development from living plants. Multi-level data, from macroscopic to molecular, and from weeks to seconds, can be acquired. Furthermore, advances in parallelized and automated image acquisition enable the throughput to capture images from large populations of plants under specific growth conditions. Image-processing capabilities allow for 3D or 4D reconstruction of image data and automated quantification of biological features. These advances facilitate the integration of imaging data with genome-wide molecular data to enable systems-level modeling.
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Affiliation(s)
- Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Wolfgang Busch
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Edgar P Spalding
- Department of Botany, University of Wisconsin, Madison, WI 53706 USA
| | - Philip N Benfey
- Department of Biology, Duke Center for Systems Biology, and Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA.
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6
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7
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Abstract
The use of computational techniques increasingly permeates developmental biology, from the acquisition, processing and analysis of experimental data to the construction of models of organisms. Specifically, models help to untangle the non-intuitive relations between local morphogenetic processes and global patterns and forms. We survey the modeling techniques and selected models that are designed to elucidate plant development in mechanistic terms, with an emphasis on: the history of mathematical and computational approaches to developmental plant biology; the key objectives and methodological aspects of model construction; the diverse mathematical and computational methods related to plant modeling; and the essence of two classes of models, which approach plant morphogenesis from the geometric and molecular perspectives. In the geometric domain, we review models of cell division patterns, phyllotaxis, the form and vascular patterns of leaves, and branching patterns. In the molecular-level domain, we focus on the currently most extensively developed theme: the role of auxin in plant morphogenesis. The review is addressed to both biologists and computational modelers.
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Affiliation(s)
| | - Adam Runions
- Department of Computer Science, University of Calgary, Calgary, AB T2N 1N4, Canada
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8
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Kahlen K, Stützel H. Modelling photo-modulated internode elongation in growing glasshouse cucumber canopies. THE NEW PHYTOLOGIST 2011; 190:697-708. [PMID: 21251000 DOI: 10.1111/j.1469-8137.2010.03617.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
• Growing glasshouse plant canopies are exposed to natural fluctuations in light quantity, and the dynamically changing canopy architecture induces local variations in light quality. This modelling study aimed to analyse the importance of both light signals for an accurate prediction of individual internode lengths. • We conceptualized two model approaches for estimating final internode lengths (FILs). The first one is only photosynthetically active radiation (PAR)-sensitive and ignores canopy architecture, whereas the second approach uses a functional-structural growth model for considering variations in both PAR and red : far-red (R : FR) ratio (L-Cucumber). Internode lengths measured in three experiments were used for model parameterization and evaluation. • The overall trends for the simulated FILs using the exclusively PAR-sensitive model approach were already in line with the measured FILs, but they underestimated FILs at higher ranks. L-Cucumber provided considerably better FIL predictions under various light conditions and canopy architectures. • Both light signals are needed for an accurate estimation of the FILs, and only L-Cucumber is able to consider R : FR signals from the growing canopy. Yet this study highlights the significance of the PAR signal for predicting FILs as neighbour effects increase, which indicates a potential role of photosynthate signalling in internode elongation.
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Affiliation(s)
- Katrin Kahlen
- Institute of Biological Production Systems, Leibniz Universität Hannover, Hannover, Germany.
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9
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Moulia B, Der Loughian C, Bastien R, Martin O, Rodríguez M, Gourcilleau D, Barbacci A, Badel E, Franchel G, Lenne C, Roeckel-Drevet P, Allain JM, Frachisse JM, de Langre E, Coutand C, Fournier-Leblanc N, Julien JL. Integrative Mechanobiology of Growth and Architectural Development in Changing Mechanical Environments. MECHANICAL INTEGRATION OF PLANT CELLS AND PLANTS 2011. [DOI: 10.1007/978-3-642-19091-9_11] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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10
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Dumas C. Plant development: a new old story. C R Biol 2010; 333:392-3. [PMID: 20371114 DOI: 10.1016/j.crvi.2010.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Christian Dumas
- UMR5667 CNRS-INRA-ENS, reproduction et développement des plantes, Ecole normale supérieure de Lyon, université de Lyon, 46 allée d'Italie, Lyon cedex 07, France
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11
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Zazímalová E, Murphy AS, Yang H, Hoyerová K, Hosek P. Auxin transporters--why so many? Cold Spring Harb Perspect Biol 2010; 2:a001552. [PMID: 20300209 PMCID: PMC2829953 DOI: 10.1101/cshperspect.a001552] [Citation(s) in RCA: 253] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Interacting and coordinated auxin transporter actions in plants underlie a flexible network that mobilizes auxin in response to many developmental and environmental changes encountered by these sessile organisms. The independent but synergistic activity of individual transporters can be differentially regulated at various levels. This invests auxin transport mechanisms with robust functional redundancy and added auxin flow capacity when needed. An evolutionary perspective clarifies the roles of the different transporter groups in plant development. Mathematical and functional analysis of elements of auxin transport makes it possible to rationalize the relative contributions of members of the respective transporter classes to the localized auxin transport streams that then underlie both preprogrammed developmental changes and reactions to environmental stimuli.
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Affiliation(s)
- Eva Zazímalová
- Institute of Experimental Botany AS CR, Rozvojová 263, CZ-165 02 Prague 6, Czech Republic.
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12
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Koornneef M, Meinke D. The development of Arabidopsis as a model plant. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 61:909-21. [PMID: 20409266 DOI: 10.1111/j.1365-313x.2009.04086.x] [Citation(s) in RCA: 220] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Twenty-five years ago, Arabidopsis thaliana emerged as the model organism of choice for research in plant biology. A consensus was reached about the need to focus on a single organism to integrate the classical disciplines of plant science with the expanding fields of genetics and molecular biology. Ten years after publication of its genome sequence, Arabidopsis remains the standard reference plant for all of biology. We reflect here on the major advances and shared resources that led to the extraordinary growth of the Arabidopsis research community. We also underscore the importance of continuing to expand and refine our detailed knowledge of Arabidopsis while seeking to appreciate the remarkable diversity that characterizes the plant kingdom.
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Affiliation(s)
- Maarten Koornneef
- Department of Plant Breeding and Genetics at the Max Planck Institute for Plant Breeding Research, Carl-von Linné Weg 10, Cologne, Germany.
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13
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Chickarmane V, Roeder AH, Tarr PT, Cunha A, Tobin C, Meyerowitz EM. Computational morphodynamics: a modeling framework to understand plant growth. ANNUAL REVIEW OF PLANT BIOLOGY 2010; 61:65-87. [PMID: 20192756 PMCID: PMC4120954 DOI: 10.1146/annurev-arplant-042809-112213] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Computational morphodynamics utilizes computer modeling to understand the development of living organisms over space and time. Results from biological experiments are used to construct accurate and predictive models of growth. These models are then used to make novel predictions that provide further insight into the processes involved, which can be tested experimentally to either confirm or rule out the validity of the computational models. This review highlights two fundamental challenges: (a) to understand the feedback between mechanics of growth and chemical or molecular signaling, and (b) to design models that span and integrate single cell behavior with tissue development. We review different approaches to model plant growth and discuss a variety of model types that can be implemented to demonstrate how the interplay between computational modeling and experimentation can be used to explore the morphodynamics of plant development.
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Affiliation(s)
- Vijay Chickarmane
- Division of Biology, California Institute Technology, Pasadena, California 91125
| | - Adrienne H.K. Roeder
- Division of Biology, California Institute Technology, Pasadena, California 91125
- Center for Integrative Study of Cell Regulation, California Institute Technology, Pasadena, California 91125
| | - Paul T. Tarr
- Division of Biology, California Institute Technology, Pasadena, California 91125
| | - Alexandre Cunha
- Center for Advanced Computing Research, California Institute Technology, Pasadena, California 91125
- Center for Integrative Study of Cell Regulation, California Institute Technology, Pasadena, California 91125
| | - Cory Tobin
- Division of Biology, California Institute Technology, Pasadena, California 91125
| | - Elliot M. Meyerowitz
- Division of Biology, California Institute Technology, Pasadena, California 91125
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14
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Petersson SV, Johansson AI, Kowalczyk M, Makoveychuk A, Wang JY, Moritz T, Grebe M, Benfey PN, Sandberg G, Ljung K. An auxin gradient and maximum in the Arabidopsis root apex shown by high-resolution cell-specific analysis of IAA distribution and synthesis. THE PLANT CELL 2009; 21:1659-68. [PMID: 19491238 PMCID: PMC2714926 DOI: 10.1105/tpc.109.066480] [Citation(s) in RCA: 330] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Revised: 05/04/2009] [Accepted: 05/12/2009] [Indexed: 05/18/2023]
Abstract
Local concentration gradients of the plant growth regulator auxin (indole-3-acetic acid [IAA]) are thought to instruct the positioning of organ primordia and stem cell niches and to direct cell division, expansion, and differentiation. High-resolution measurements of endogenous IAA concentrations in support of the gradient hypothesis are required to substantiate this hypothesis. Here, we introduce fluorescence-activated cell sorting of green fluorescent protein-marked cell types combined with highly sensitive mass spectrometry methods as a novel means for analyses of IAA distribution and metabolism at cellular resolution. Our results reveal the presence of IAA concentration gradients within the Arabidopsis thaliana root tip with a distinct maximum in the organizing quiescent center of the root apex. We also demonstrate that the root apex provides an important source of IAA and that cells of all types display a high synthesis capacity, suggesting a substantial contribution of local biosynthesis to auxin homeostasis in the root tip. Our results indicate that local biosynthesis and polar transport combine to produce auxin gradients and maxima in the root tip.
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Affiliation(s)
- Sara V Petersson
- Department of Forest Genetics, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden
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15
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Cvrcková F, Lipavská H, Zárský V. Plant intelligence: why, why not or where? PLANT SIGNALING & BEHAVIOR 2009; 4:394-9. [PMID: 19816094 PMCID: PMC2676749 DOI: 10.4161/psb.4.5.8276] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Accepted: 02/24/2009] [Indexed: 05/09/2023]
Abstract
The concept of plant intelligence, as proposed by Anthony Trewavas, has raised considerable discussion. However, plant intelligence remains loosely defined; often it is either perceived as practically synonymous to Darwinian fitness, or reduced to a mere decorative metaphor. A more strict view can be taken, emphasizing necessary prerequisites such as memory and learning, which requires clarifying the definition of memory itself. To qualify as memories, traces of past events have to be not only stored, but also actively accessed. We propose a criterion for eliminating false candidates of possible plant intelligence phenomena in this stricter sense: an "intelligent" behavior must involve a component that can be approximated by a plausible algorithmic model involving recourse to stored information about past states of the individual or its environment. Re-evaluation of previously presented examples of plant intelligence shows that only some of them pass our test.
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Affiliation(s)
- Fatima Cvrcková
- Department of Plant Physiology, Faculty of Sciences, Charles University, Praha, Czech Republic.
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16
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Micol JL. Leaf development: time to turn over a new leaf? CURRENT OPINION IN PLANT BIOLOGY 2009; 12:9-16. [PMID: 19109050 DOI: 10.1016/j.pbi.2008.11.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Revised: 10/30/2008] [Accepted: 11/01/2008] [Indexed: 05/18/2023]
Abstract
Molecular cloning of mutations affecting the morphology of plant leaves has proven to be useful for the causal analysis of leaf development. Studies of leaf mutants have produced a wealth of biologically meaningful information on the genes that participate in leaf initiation, leaf polarity specification and maintenance, and leaf expansion and maturation. The availability of collections of gene-indexed insertional mutants, automated platforms for high-throughput imaging, and new morphometry software is making genome-wide leaf phenomics possible and complements classical forward genetics approaches. Large-scale phenomic studies will further our understanding, among others, of two intriguing phenomena that recently reentered the leaf scenario. One is the unexpected relationship between translation and leaf dorsoventrality, recently confirmed by the severe abaxialization of double mutants involving loss-of-function alleles of the developmental selector genes AS1 and AS2 and some genes encoding ribosomal proteins. The second unexplained phenomenon is the compensatory cell enlargement experienced by some leaf mutants, in which a reduced cell number is compensated by their increased cell size compared with the wild type. This compensation suggests that cell cycling and cell enlargement are integrated in leaf primordia via cell-to-cell communication.
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Affiliation(s)
- José Luis Micol
- División de Genética and Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, Elche, Alicante, Spain.
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17
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Potters G, Pasternak TP, Guisez Y, Jansen MAK. Different stresses, similar morphogenic responses: integrating a plethora of pathways. PLANT, CELL & ENVIRONMENT 2009; 32:158-69. [PMID: 19021890 DOI: 10.1111/j.1365-3040.2008.01908.x] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Exposure of plants to mild chronic stress can cause induction of specific, stress-induced morphogenic responses (SIMRs). These responses are characterized by a blockage of cell division in the main meristematic tissues, an inhibition of elongation and a redirected outgrowth of lateral organs. Key elements in the ontogenesis of this phenotype appear to be stress-affected gradients of reactive oxygen species (ROS), antioxidants, auxin and ethylene. These gradients are present at the the organismal level, but are integrated on the cellular level, affecting cell division, cell elongation and/or cell differentiation. Our analysis of the literature indicates that stress-induced modulation of plant growth is mediated by a plethora of molecular interactions, whereby different environmental signals can trigger similar morphogenic responses. At least some of the molecular interactions that underlie morphogenic responses appear to be interchangeable. We speculate that this complexity can be viewed in terms of a thermodynamic model, in which not the specific pathway, but the achieved metabolic state is biologically conserved.
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Affiliation(s)
- Geert Potters
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
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18
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NPY genes and AGC kinases define two key steps in auxin-mediated organogenesis in Arabidopsis. Proc Natl Acad Sci U S A 2008; 105:21017-22. [PMID: 19075219 DOI: 10.1073/pnas.0809761106] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Auxin is an essential regulator of plant organogenesis. Most key genes in auxin biosynthesis, transport, and signaling belong to gene families, making it difficult to conduct genetic analysis of auxin action in plant development. Herein we report the functional analysis of several members of 2 gene families (NPY/ENP/MAB4 genes and AGC kinases) in auxin-mediated organogenesis and their relationships with the YUC family of flavin monooxygenases that are essential for auxin biosynthesis. We show that 5 NPY genes (NPY1 to NPY5) and 4 AGC kinases (PID, PID2, WAG1, and WAG2) have distinct, yet overlapping, expression patterns. Disruption of NPY1 does not cause obvious defects in organogenesis, but npy1 npy3 npy5 triple mutants failed to make flower primordia, a phenotype that is also observed when AGC kinase PID is compromised. Inactivation of YUC1 and YUC4 in npy1 background also phenocopies npy1 npy3 npy5 and pid. Simultaneous disruption of PID and its 3 closest homologs (PID2, WAG1, and WAG2) completely abolishes the formation of cotyledons, which phenocopies npy1 pid double mutants and yuc1 yuc4 pid triple mutants. Our results demonstrate that NPY genes and AGC kinases define 2 key steps in a pathway that controls YUC-mediated organogenesis in Arabidopsis.
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Billoud B, Le Bail A, Charrier B. A stochastic 1D nearest-neighbour automaton models early development of the brown alga Ectocarpus siliculosus. FUNCTIONAL PLANT BIOLOGY : FPB 2008; 35:1014-1024. [PMID: 32688850 DOI: 10.1071/fp08036] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Accepted: 07/25/2008] [Indexed: 06/11/2023]
Abstract
Early development of the filamentous brown alga Ectocarpus siliculosus (Dillwyn) Lyngbye involves two cell types that are arranged in a polymorphic, but constrained, pattern. The present study aimed to decipher the cellular processes responsible for the establishment of this pattern. Thorough observations characterised five different events of division and differentiation that occurred during the early development. The hypothesis that a local control is responsible for these processes was tested. To do so, Ectomat, a stochastic automaton in which each cell only interacts with its closest neighbour(s), was created. The probabilities for the five events were adjusted to fit to the observations. Simulations with Ectomat reconstructed most of the essential properties of the sporophyte development, in terms of cell-type proportion, relative position and growth dynamics. The whole organism properties emerged by applying local transition rules. In conclusion, no global position information system was required at this development stage. Randomly occurring cell events, driven by simple contact interactions, are sufficient to account for the early filament development and establishment of the cell-type pattern of E. siliculosus.
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Affiliation(s)
- Bernard Billoud
- UPMC Univ Paris 06, Atelier de Bioinformatique, MB1202, F75005 Paris, France
| | - Aude Le Bail
- UPMC Univ Paris 06, UMR7139 Végétaux marins et biomolécules, Station Biologique, F29682 Roscoff cedex, France
| | - Bénédicte Charrier
- UPMC Univ Paris 06, UMR7139 Végétaux marins et biomolécules, Station Biologique, F29682 Roscoff cedex, France
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Falkenberg B, Witt I, Zanor MI, Steinhauser D, Mueller-Roeber B, Hesse H, Hoefgen R. Transcription factors relevant to auxin signalling coordinate broad-spectrum metabolic shifts including sulphur metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2008; 59:2831-46. [PMID: 18596113 PMCID: PMC2486478 DOI: 10.1093/jxb/ern144] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Revised: 04/22/2008] [Accepted: 04/28/2008] [Indexed: 05/18/2023]
Abstract
A systems approach has previously been used to follow the response behaviour of Arabidopsis thaliana plants upon sulphur limitation. A response network was reconstructed from a time series of transcript and metabolite profiles, integrating complex metabolic and transcript data in order to investigate a potential causal relationship. The resulting scale-free network allowed potential transcriptional regulators of sulphur metabolism to be identified. Here, three sulphur-starvation responsive transcription factors, IAA13, IAA28, and ARF-2 (ARF1-Binding Protein), all of which are related to auxin signalling, were selected for further investigation. IAA28 overexpressing and knock-down lines showed no major morphological changes, whereas IAA13- and ARF1-BP-overexpressing plants grew more slowly than the wild type. Steady-state metabolite levels and expression of pathway-relevant genes were monitored under normal and sulphate-depleted conditions. For all lines, changes in transcript and metabolite levels were observed, yet none of these changes could exclusively be linked to sulphur stress. Instead, up- or down-regulation of the transcription factors caused metabolic changes which in turn affected sulphur metabolism. Auxin-relevant transcription factors are thus part of a complex response pattern to nutrient starvation that serve as coordinators of the metabolic shifts driving sulphur homeostasis rather then as direct effectors of the sulphate assimilation pathway. This study provides the first evidence ever presented that correlates auxin-related transcriptional regulators with primary plant metabolism.
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Affiliation(s)
- Bettina Falkenberg
- Max-Planck-Institut fuer Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, 14424 Potsdam, Germany
| | - Isabell Witt
- Max-Planck-Institut fuer Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, 14424 Potsdam, Germany
| | - Maria Inés Zanor
- Max-Planck-Institut fuer Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, 14424 Potsdam, Germany
| | - Dirk Steinhauser
- Max-Planck-Institut fuer Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, 14424 Potsdam, Germany
| | - Bernd Mueller-Roeber
- Universität Potsdam, Institut fuer Biochemie und Biologie, Karl-Liebknecht-Str. 24–25, Haus 20, 14476 Potsdam-Golm, Germany
| | - Holger Hesse
- Max-Planck-Institut fuer Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, 14424 Potsdam, Germany
- To whom correspondence should be addressed. E-mail:
| | - Rainer Hoefgen
- Max-Planck-Institut fuer Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, 14424 Potsdam, Germany
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Thomas H. Systems biology and the biology of systems: how, if at all, are they related? THE NEW PHYTOLOGIST 2008; 177:11-15. [PMID: 18078470 DOI: 10.1111/j.1469-8137.2007.02313.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Affiliation(s)
- Howard Thomas
- Institute of Biological Science, Edward Llwyd Building, Aberystwyth University, Ceredigion SY23 3DA, UK (tel +44 1970 628768; fax +44 1970 622350; email )
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Kramer EM. Computer models of auxin transport: a review and commentary. JOURNAL OF EXPERIMENTAL BOTANY 2008; 59:45-53. [PMID: 17431022 DOI: 10.1093/jxb/erm060] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
With the recent proliferation of computer models of auxin transport, it is important that plant biologists understand something about these techniques and how to evaluate them. The paper begins with a brief introduction to the parts of a computer model, followed by a discussion of the limitations of the most common auxin modelling technique. Lastly, several recent models of organ initiation in the shoot apical meristem (i.e. phyllotaxis) are reviewed. The cell and molecular biology of phyllotaxis is now understood well enough that computer models can go beyond a simple 'proof of principle' and start to provide insights into gene function.
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Affiliation(s)
- Eric M Kramer
- Physics Department, Simon's Rock College, Great Barrington, MA 01230, USA.
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Hennig L. Patterns of beauty--omics meets plant development. TRENDS IN PLANT SCIENCE 2007; 12:287-93. [PMID: 17580122 DOI: 10.1016/j.tplants.2007.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2007] [Revised: 04/17/2007] [Accepted: 05/31/2007] [Indexed: 05/15/2023]
Abstract
Developmental biology aims to identify mechanisms that govern cell proliferation and differentiation in the body plan formation of multicellular organisms. In the past, developmental biologists described how anatomy and morphology are established during ontogenesis, and developmental geneticists identified many developmental regulators. In contrast to the traditional approaches that mostly focus on one or a few genes at a time, highly parallel profiling technologies have been developed for use in biological research over the past decade. Such parallel profiling technologies probe many genes, transcripts, proteins or metabolites at once. In this review, I discuss the growing impact of transcriptomics, proteomics, metabolomics and modelling on plant developmental biology. Novel profiling technologies will not make traditional gene-centred approaches obsolete but should instead complement forward developmental genetics.
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Affiliation(s)
- Lars Hennig
- Institute of Plant Sciences & Zurich-Basel Plant Science Center, ETH Zurich, LFW E17, CH-8092 Zurich, Switzerland.
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Omelyanchuk NA, Mironova VV, Zalevsky EM, Shamov IS, Poplavsky AS, Podkolodny NL, Ponomaryov DK, Nikolaev SV, Mjolsness ED, Meyerowitz EM, Kolchanov NA. A systems approach to morphogenesis in Arabidopsis thaliana: I. AGNS database. Biophysics (Nagoya-shi) 2006. [DOI: 10.1134/s0006350906070165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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