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Plant, Cell & Environment

Cover image for Vol. 36 Issue 9

Special Issue: Models in Plant Sciences

September 2013

Volume 36, Issue 9

Pages 1573–1750

  1. Editorial

    1. Top of page
    2. Editorial
    3. Reviews
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      Special issue on plant computational biology (pages 1573–1574)

      STEVE LONG and MARK STITT

      Version of Record online: 5 AUG 2013 | DOI: 10.1111/pce.12162

  2. Reviews

    1. Top of page
    2. Editorial
    3. Reviews
    1. You have free access to this content
      On improving the communication between models and data (pages 1575–1585)

      MICHAEL C. DIETZE, DAVID S. LEBAUER and ROB KOOPER

      Version of Record online: 3 JAN 2013 | DOI: 10.1111/pce.12043

      The potential for model-data synthesis is growing in importance as we enter an era of ‘big data’, greater connectivity, and faster computation. Realizing this potential requires that the research community broaden its perspective about how and why they interact with models. We provide a review and perspective on the statistics and informatics of model-data fusion in plant biology. Overall we promote a community-based paradigm to model-data synthesis and highlight some of the tools and techniques that facilitate this approach.

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      Modelling the reaction mechanism of ribulose-1,5-bisphosphate carboxylase/oxygenase and consequences for kinetic parameters (pages 1586–1596)

      GUILLAUME TCHERKEZ

      Version of Record online: 4 FEB 2013 | DOI: 10.1111/pce.12066

      The chemical mechanism of Rubisco is at the heart of photosynthetic metabolism since it dictates the rate of carboxylation. Here, advantage is taken of chemical formalism to give general equations describing carboxylation velocity, specificity and isotope effects. The limits of these and uncertainties on intrinsic chemical events are discussed so as to appreciate possibilities of optimization.

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      Network analysis for gene discovery in plant-specialized metabolism (pages 1597–1606)

      YASUHIRO HIGASHI and KAZUKI SAITO

      Version of Record online: 21 FEB 2013 | DOI: 10.1111/pce.12069

      Network analysis depicts biological systems and behaviours from omics data, enabling us to extract biological meaning and predict gene function. Genes involved in specialized metabolism are often co-ordinately regulated at the transcriptional level. We review advances in gene co-expression and gene-to-metabolite network analysis in Arabidopsis and non-model plant species from a viewpoint of gene discovery in plant specialized metabolism.

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      Hydrogen sulfide: environmental factor or signalling molecule? (pages 1607–1616)

      MIROSLAV LISJAK, TIHANA TEKLIC, IAN D. WILSON, MATTHEW WHITEMAN and JOHN T. HANCOCK

      Version of Record online: 26 FEB 2013 | DOI: 10.1111/pce.12073

      This paper highlights the effects of hydrogen sulfide on plants, and discusses the evidence that this gas can be considered as a signalling molecule. Plants can be shown to generate hydrogen sulfide and respond to it, with recent work pointing to the possibility that hydrogen sulfide may modify protein thiol groups. This would mean that hydrogen sulfide may be in competition with reactive oxygen species and nitric oxide in its potential signalling role.

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      Steady-state models of photosynthesis (pages 1617–1630)

      SUSANNE VON CAEMMERER

      Version of Record online: 22 APR 2013 | DOI: 10.1111/pce.12098

      In the challenge to increase photosynthetic rate per leaf area steady state models of photosynthesis provide not only tools for gas exchange analysis but also for thought experiments that can explore photosynthetic pathway changes. These include redirecting photorespiratory CO2 , inserting bicarbonate pumps into C3 chloroplasts or inserting C4 photosynthesis into rice. Here a number of models derived from the C3 model by Farquhar, von Caemmerer and Berry are discussed and compared.

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      Modelling metabolic CO2 evolution – a fresh perspective on respiration (pages 1631–1640)

      LEE J. SWEETLOVE, THOMAS C. R. WILLIAMS, C. Y. MAURICE CHEUNG and R. GEORGE RATCLIFFE

      Version of Record online: 6 MAY 2013 | DOI: 10.1111/pce.12105

      Although respiration is a major contributor to the net exchange of CO 2 between plants and the atmosphere, it would be desirable to take a holistic view of the network when modelling the process and to consider all the potential contributors to light-independent CO 2 balance. We argue that flux balance analysis of genome-scale metabolic models offers a practicable tool for predictive modelling of net CO 2 evolution. This is supported by the encouraging agreement that has been found between the experimental results obtained by metabolic flux analysis and the predictions of flux balance analysis. While there is scope for further improvement, particularly in the way in which flux balance analysis handles cell maintenance costs, its power is already sufficient to make useful predictions about the impact of environmental factors on CO 2 production by plant tissues.

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      Modelling C3 photosynthesis from the chloroplast to the ecosystem (pages 1641–1657)

      CARL J. BERNACCHI, JUSTIN E. BAGLEY, SHAWN P. SERBIN, URSULA M. RUIZ-VERA, DAVID M. ROSENTHAL and ANDY VANLOOCKE

      Version of Record online: 14 MAY 2013 | DOI: 10.1111/pce.12118

      The mechanistically based leaf photosynthesis model has played a major role in defining the path toward scientific understanding of photosynthetic carbon uptake and the role of photosynthesis on regulating the earth's climate and biogeochemical systems. This review summarizes the photosynthesis model, including its continued development and applications. We also review the implications these developments have on quantifying photosynthesis at a wide range of spatial and temporal scales, and discuss the model's role in determining photosynthetic responses to changes in environmental conditions.

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      Putting mechanisms into crop production models (pages 1658–1672)

      KENNETH J. BOOTE, JAMES W. JONES, JEFFREY W. WHITE, SENTHOLD ASSENG and JON I. LIZASO

      Version of Record online: 22 MAY 2013 | DOI: 10.1111/pce.12119

      Crop simulation models integrate multiple ecophysiological processes and can account for effects of genetics, environment and crop management. This paper reviews the level of mechanistic detail in crop production models relative to phenology, leaf area growth, assimilation, and reproductive growth, including efforts to incorporate genetic information to characterize cultivar differences. We highlight improvements needed in the prediction of elevated temperature stress on reproductive fertility, CO2 effects on transpiration, and simulation of root growth and nutrient uptake under stressful edaphic conditions. Improved representation of mechanisms are needed to better connect crop growth to genetics and to improve simulations relating to soil fertility, soil water-logging, and pest damage.

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      Physiological mechanisms in plant growth models: do we need a supra-cellular systems biology approach? (pages 1673–1690)

      HENDRIK POORTER, NIELS P. R. ANTEN and LEO F. M. MARCELIS

      Version of Record online: 10 JUN 2013 | DOI: 10.1111/pce.12123

      Growth models play an important role in structuring our knowledge on the myriad of interactions that plants have with their environment, on the many internal feed-forwards and feed-backs that occur while they grow and adjust themselves, and on the way the physiological responses can be scaled up from lower to higher integration levels. In this review we discuss the level of physiological mechanism that is included in various groups of plant models, and the mechanisms that are neglected. We conclude that we should acquire more insight into the trade-offs that may occur between the various physiological processes and plant organs and provide suggestions how to advance here.

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      Modelling stomatal conductance in response to environmental factors (pages 1691–1699)

      THOMAS N. BUCKLEY and KEITH A. MOTT

      Version of Record online: 27 JUN 2013 | DOI: 10.1111/pce.12140

      In this study, the ZmPIS gene with a maize ubiquitin promoter was introduced into maize (Zea mays L.) inbred line DH4866 by an Agrobacterium-mediated method to explore the function of the ZmPIS gene in the response of maize to drought stress. The overexpression of ZmPIS in maize resulted in significantly elevated levels of most phospholipids, galactolipids in leaves compared with those in WT and markedly up-regulated expression of some genes involved in the phospholipids metabolism pathway and the ABA biosynthesis pathway after drought stress. Consistent with these results, the drought stress tolerance of the ZmPIS sense transgenic plants were enhanced significantly compared to WT maize plants. These results imply that ZmPIS regulate the plant response to drought stress through altering membrane lipid composition and increasing ABA synthesis in maize.

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      Predictive modelling of complex agronomic and biological systems (pages 1700–1710)

      JOOST J. B. KEURENTJES, JAAP MOLENAAR and BAS J. ZWAAN

      Version of Record online: 4 JUL 2013 | DOI: 10.1111/pce.12156

      Predictive modelling of biological systems is becoming increasingly important in modern plant biology. Much progress has been made in time but for many purposes it remains unclear what methods are most appropriate. Especially the type of models and the kind of data that need to feed these models deserve special attention. Transparency in experimental design and model development can, therefore, assist in better congruence between biologists and modellers.

      Corrected by:

      Erratum: Erratum

      Vol. 36, Issue 10, 1910, Version of Record online: 3 SEP 2013

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      e-photosynthesis: a comprehensive dynamic mechanistic model of C3 photosynthesis: from light capture to sucrose synthesis (pages 1711–1727)

      XIN-GUANG ZHU, YU WANG, DONALD R. ORT and STEPHEN P. LONG

      Version of Record online: 19 NOV 2012 | DOI: 10.1111/pce.12025

      Although the process of photosynthesis from light capture to carbohydrate synthesis has been largely known for some time, a complete dynamic process model representing each discrete step has been lacking. e-Photosynthesis described here provides this platform and is shown to reproduce in silico, quantitatively and qualitatively, responses of leaf gas exchange, electron transport, chlorophyll fluorescence and biochemical fluxes observed in vivo. The model provides a design engineering tool for selecting targets in a system of over 100 potential targets and many thousands of permutations.

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      Computational modelling of the BRI1 receptor system (pages 1728–1737)

      G. WILMA VAN ESSE, KLAUS HARTER and SACCO C. DE VRIES

      Version of Record online: 12 MAR 2013 | DOI: 10.1111/pce.12077

      BRI1 mediated brassinosteroid signaling in Arabidopsis is suitable for mathematical modeling approaches. This can be helpful to position the components of the BR signalosome and to understand and interpret its complex biological output. The focus of this review is on a number of recent modeling studies. Future developments will require additional quantitative data, to be generated using fluorescently labeled reporters.

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      Analysis of metabolic flux using dynamic labelling and metabolic modelling (pages 1738–1750)

      A. R. FERNIE and J. A. MORGAN

      Version of Record online: 14 MAR 2013 | DOI: 10.1111/pce.12083

      Diverse approaches have been developed in order to analyse metabolic fluxes. These can be broadly divided into stationary methods which require that the system under study is at isotopic as well as metabolic steady state and instationary methods for which only metabolic steady state is a pre-requisite. Here we review the use of instationary methods to interrogate plant metabolism and its regulation.

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