1
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Kong S, Zhu M, Roeder AHK. Self-organization underlies developmental robustness in plants. Cells Dev 2024:203936. [PMID: 38960068 DOI: 10.1016/j.cdev.2024.203936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/26/2024] [Accepted: 06/26/2024] [Indexed: 07/05/2024]
Abstract
Development is a self-organized process that builds on cells and their interactions. Cells are heterogeneous in gene expression, growth, and division; yet how development is robust despite such heterogeneity is a fascinating question. Here, we review recent progress on this topic, highlighting how developmental robustness is achieved through self-organization. We will first discuss sources of heterogeneity, including stochastic gene expression, heterogeneity in growth rate and direction, and heterogeneity in division rate and precision. We then discuss cellular mechanisms that buffer against such noise, including Paf1C- and miRNA-mediated denoising, spatiotemporal growth averaging and compensation, mechanisms to improve cell division precision, and coordination of growth rate and developmental timing between different parts of an organ. We also discuss cases where such heterogeneity is not buffered but utilized for development. Finally, we highlight potential directions for future studies of noise and developmental robustness.
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Affiliation(s)
- Shuyao Kong
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Mingyuan Zhu
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Adrienne H K Roeder
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
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2
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Red Light Resets the Expression Pattern, Phase, and Period of the Circadian Clock in Plants: A Computational Approach. BIOLOGY 2022; 11:biology11101479. [PMID: 36290383 PMCID: PMC9598827 DOI: 10.3390/biology11101479] [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: 09/05/2022] [Revised: 10/02/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022]
Abstract
Simple Summary Progress in computational biology has provided a comprehensive understanding of the dynamics of the plant circadian clock. Previously proposed models of the plant circadian clock have intended to model its entrainment using white-light/dark cycles. However, these models have failed to take into account the effect of light quality on circadian rhythms, which has been experimentally observed. In this work, we developed a computational approach to characterizing the effects of light quality on plant circadian rhythms. The results demonstrated that red light can reset the expression patterns, phases, and periods of clock component genes. The circadian period, amplitude, and phase can be co-optimized for high-quality and efficient breeding. Abstract Recent research in the fields of biochemistry and molecular biology has shown that different light qualities have extremely different effects on plant development, and optimizing light quality conditions can speed up plant growth. Clock-regulated red-light signaling, can enhance hypocotyl elongation, and increase seedling height and flower and fruit productivity. In order to investigate the effect of red light on circadian clocks in plants, a novel computational model was established. The expression profiles of the circadian element CCA1 from previous related studies were used to fit the model. The simulation results were validated by the expression patterns of CCA1 in Arabidopsis, including wild types and mutants, and by the phase shifts of CCA1 after red-light pulse. The model was used to further explore the complex responses to various photoperiods, such as the natural white-light/dark cycles, red/white/dark cycles, and extreme 24 h photoperiods. These results demonstrated that red light can reset the expression pattern, period, and phase of the circadian clock. Finally, we identified the dependence of phase shifts on the length of red-light pulse and the minimum red-light pulse length required for producing an observable phase shift. This work provides a promising computational approach to investigating the response of the circadian clock to other light qualities.
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3
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Abstract
Circadian clocks are important to much of life on Earth and are of inherent interest to humanity, implicated in fields ranging from agriculture and ecology to developmental biology and medicine. New techniques show that it is not simply the presence of clocks, but coordination between them that is critical for complex physiological processes across the kingdoms of life. Recent years have also seen impressive advances in synthetic biology to the point where parallels can be drawn between synthetic biological and circadian oscillators. This review will emphasize theoretical and experimental studies that have revealed a fascinating dichotomy of coupling and heterogeneity among circadian clocks. We will also consolidate the fields of chronobiology and synthetic biology, discussing key design principles of their respective oscillators.
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Affiliation(s)
- Chris N Micklem
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK.,The Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CH3 0HE, UK
| | - James C W Locke
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
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4
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Zhang R, Gonze D. Stochastic simulation of a model for circadian rhythms in plants. J Theor Biol 2021; 527:110790. [PMID: 34087270 DOI: 10.1016/j.jtbi.2021.110790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/09/2021] [Accepted: 05/27/2021] [Indexed: 11/29/2022]
Abstract
Circadian clocks allow living organisms to anticipate and adapt to the daily variations of the environment. The interlocked feedback loops of the transcription factors network in the plant clock generate oscillations with expression peaks at specific times of the day. In this work, we explore the effect of molecular noise on the behavior of the plant circadian clock through numerical simulations. The influence of system size, photoperiod, and mutations of clock genes on the robustness of the oscillations are discussed. Our simulations show that the oscillations remain robust when the mRNA and protein levels are in the range of a few hundreds molecules. Entrainment by light-dark cycles enhances the robustness compared to constant conditions. Multiple light inputs and inter-cellular coupling also contribute to the robustness of the oscillations. The comparison between deterministic and stochastic simulations of single and double mutants shows that stochasticity does not qualitatively affect the behaviour of mutants but that they do not have the same robustness to noise. Finally, the model shows that noise can induce transitions between two limit cycles in a birhythmic clock mutant.
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Affiliation(s)
- Ruqiang Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Didier Gonze
- Unité de Chronobiologie Théorique, Faculté des Sciences, Université Libre de Bruxelles (ULB), Brussels, Belgium.
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5
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Autran D, Bassel GW, Chae E, Ezer D, Ferjani A, Fleck C, Hamant O, Hartmann FP, Jiao Y, Johnston IG, Kwiatkowska D, Lim BL, Mahönen AP, Morris RJ, Mulder BM, Nakayama N, Sozzani R, Strader LC, ten Tusscher K, Ueda M, Wolf S. What is quantitative plant biology? QUANTITATIVE PLANT BIOLOGY 2021; 2:e10. [PMID: 37077212 PMCID: PMC10095877 DOI: 10.1017/qpb.2021.8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 05/03/2023]
Abstract
Quantitative plant biology is an interdisciplinary field that builds on a long history of biomathematics and biophysics. Today, thanks to high spatiotemporal resolution tools and computational modelling, it sets a new standard in plant science. Acquired data, whether molecular, geometric or mechanical, are quantified, statistically assessed and integrated at multiple scales and across fields. They feed testable predictions that, in turn, guide further experimental tests. Quantitative features such as variability, noise, robustness, delays or feedback loops are included to account for the inner dynamics of plants and their interactions with the environment. Here, we present the main features of this ongoing revolution, through new questions around signalling networks, tissue topology, shape plasticity, biomechanics, bioenergetics, ecology and engineering. In the end, quantitative plant biology allows us to question and better understand our interactions with plants. In turn, this field opens the door to transdisciplinary projects with the society, notably through citizen science.
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Affiliation(s)
- Daphné Autran
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - George W. Bassel
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Eunyoung Chae
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Daphne Ezer
- The Alan Turing Institute, London, United Kingdom
- Department of Statistics, University of Warwick, Coventry, United Kingdom
- Department of Biology, University of York, York, United Kingdom
| | - Ali Ferjani
- Department of Biology, Tokyo Gakugei University, Tokyo, Japan
| | - Christian Fleck
- Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Breisgau, Germany
| | - Olivier Hamant
- Laboratoire de Reproduction et Développement des Plantes, École normale supérieure (ENS) de Lyon, Université Claude Bernard Lyon (UCBL), Lyon, France
- Institut national de recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), CNRS, Université de Lyon, Lyon, France
- Author for correspondence: O. Hamant and A. P. Mahönen, E-mail: ,
| | | | - Yuling Jiao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Dorota Kwiatkowska
- Institute of Biology, Biotechnology and Environment Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Boon L. Lim
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
| | - Ari Pekka Mahönen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Richard J. Morris
- Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
| | - Bela M. Mulder
- Department of Living Matter, Institute AMOLF, Amsterdam, The Netherlands
| | - Naomi Nakayama
- Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Ross Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North CarolinaUSA
| | - Lucia C. Strader
- Department of Biology, Duke University, Durham, North Carolina, USA
- NSF Science and Technology Center for Engineering Mechanobiology, Department of Biology, Washington University in St. Louis, St. Louis, MissouriUSA
| | - Kirsten ten Tusscher
- Theoretical Biology, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Minako Ueda
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Sebastian Wolf
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
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6
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Azpeitia E, Balanzario EP, Wagner A. Signaling pathways have an inherent need for noise to acquire information. BMC Bioinformatics 2020; 21:462. [PMID: 33066727 PMCID: PMC7568421 DOI: 10.1186/s12859-020-03778-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 09/23/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND All living systems acquire information about their environment. At the cellular level, they do so through signaling pathways. Such pathways rely on reversible binding interactions between molecules that detect and transmit the presence of an extracellular cue or signal to the cell's interior. These interactions are inherently stochastic and thus noisy. On the one hand, noise can cause a signaling pathway to produce the same response for different stimuli, which reduces the amount of information a pathway acquires. On the other hand, in processes such as stochastic resonance, noise can improve the detection of weak stimuli and thus the acquisition of information. It is not clear whether the kinetic parameters that determine a pathway's operation cause noise to reduce or increase the acquisition of information. RESULTS We analyze how the kinetic properties of the reversible binding interactions used by signaling pathways affect the relationship between noise, the response to a signal, and information acquisition. Our results show that, under a wide range of biologically sensible parameter values, a noisy dynamic of reversible binding interactions is necessary to produce distinct responses to different stimuli. As a consequence, noise is indispensable for the acquisition of information in signaling pathways. CONCLUSIONS Our observations go beyond previous work by showing that noise plays a positive role in signaling pathways, demonstrating that noise is essential when such pathways acquire information.
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Affiliation(s)
- Eugenio Azpeitia
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Centro de Ciencias Matemáticas, Universidad Nacional Autónoma de México, Morelia, Mexico
| | - Eugenio P Balanzario
- Centro de Ciencias Matemáticas, Universidad Nacional Autónoma de México, Morelia, Mexico
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zurich, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- The Santa Fe Institute, Santa Fe, NM, USA.
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7
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Martí Ruiz MC, Jung HJ, Webb AAR. Circadian gating of dark-induced increases in chloroplast- and cytosolic-free calcium in Arabidopsis. THE NEW PHYTOLOGIST 2020; 225:1993-2005. [PMID: 31644821 PMCID: PMC7028143 DOI: 10.1111/nph.16280] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/11/2019] [Indexed: 05/22/2023]
Abstract
Changes in the spatiotemporal concentration of free Ca2+ ([Ca2+ ]) in different organelles of the cell contribute to responses of plants to physiological and environmental stimuli. One example are [Ca2+ ] increases in the stroma of chloroplasts during light-to-dark transitions; however, the function and mechanisms responsible are unknown, in part because there is a disagreement in the literature concerning whether corresponding dark-induced changes in cytosolic [Ca2+ ] ([Ca2+ ]cyt ) can be detected. We have measured changes in [Ca2+ ]cyt upon darkness in addition to the already known dark-induced increases in [Ca2+ ]stroma in the aerial part of the Arabidopsis thaliana plant. These [Ca2+ ]cyt transients depend on the photoperiod and time of day, peaking at anticipated dusk, and are superimposed on daily 24 h oscillations in [Ca2+ ]cyt . We also find that the magnitude of the dark-induced increases in Ca2+ in both the cytosol and chloroplasts are gated by the nuclear circadian oscillator. The modulation of the magnitude of dark-induced increases in [Ca2+ ]stroma and [Ca2+ ]cyt by transcriptional regulators in the nucleus that are part of the circadian oscillator demonstrates a new role for the circadian system in subcellular Ca2+ signalling, in addition to its role in driving circadian oscillations of [Ca2+ ] in the cytosol and chloroplasts.
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Affiliation(s)
- María Carmen Martí Ruiz
- Department of Stress Biology and Plant PathologyCEBAS‐CSICCampus Universitario de EspinardoMurcia30100Spain
- Department of Plant SciencesUniversity of CambridgeDowning StreetCambridge,CB2 3EAUK
| | - Hyun Ju Jung
- Department of Plant SciencesUniversity of CambridgeDowning StreetCambridge,CB2 3EAUK
| | - Alex A. R. Webb
- Department of Plant SciencesUniversity of CambridgeDowning StreetCambridge,CB2 3EAUK
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8
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Jia C, Grima R. Small protein number effects in stochastic models of autoregulated bursty gene expression. J Chem Phys 2020; 152:084115. [DOI: 10.1063/1.5144578] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Chen Jia
- Division of Applied and Computational Mathematics, Beijing Computational Science Research Center, Beijing 100193, China
| | - Ramon Grima
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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9
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Grzegorczyk M, Aderhold A, Husmeier D. Overview and Evaluation of Recent Methods for Statistical Inference of Gene Regulatory Networks from Time Series Data. Methods Mol Biol 2019; 1883:49-94. [PMID: 30547396 DOI: 10.1007/978-1-4939-8882-2_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
A challenging problem in systems biology is the reconstruction of gene regulatory networks from postgenomic data. A variety of reverse engineering methods from machine learning and computational statistics have been proposed in the literature. However, deciding on the best method to adopt for a particular application or data set might be a confusing task. The present chapter provides a broad overview of state-of-the-art methods with an emphasis on conceptual understanding rather than a deluge of mathematical details, and the pros and cons of the various approaches are discussed. Guidance on practical applications with pointers to publicly available software implementations are included. The chapter concludes with a comprehensive comparative benchmark study on simulated data and a real-work application taken from the current plant systems biology.
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Affiliation(s)
- Marco Grzegorczyk
- Johann Bernoulli Institute, University of Groningen, Groningen, The Netherlands
| | - Andrej Aderhold
- Center for Computer Science, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Dirk Husmeier
- School of Mathematics and Statistics, University of Glasgow, Glasgow, UK.
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10
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Millar AJ, Urquiza U, Freeman PL, Hume A, Plotkin GD, Sorokina O, Zardilis A, Zielinski T. Practical steps to digital organism models, from laboratory model species to 'Crops in silico. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2403-2418. [PMID: 30615184 DOI: 10.1093/jxb/ery435] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/28/2018] [Indexed: 05/20/2023]
Abstract
A recent initiative named 'Crops in silico' proposes that multi-scale models 'have the potential to fill in missing mechanistic details and generate new hypotheses to prioritize directed engineering efforts' in plant science, particularly directed to crop species. To that end, the group called for 'a paradigm shift in plant modelling, from largely isolated efforts to a connected community'. 'Wet' (experimental) research has been especially productive in plant science, since the adoption of Arabidopsis thaliana as a laboratory model species allowed the emergence of an Arabidopsis research community. Parts of this community invested in 'dry' (theoretical) research, under the rubric of Systems Biology. Our past research combined concepts from Systems Biology and crop modelling. Here we outline the approaches that seem most relevant to connected, 'digital organism' initiatives. We illustrate the scale of experimental research required, by collecting the kinetic parameter values that are required for a quantitative, dynamic model of a gene regulatory network. By comparison with the Systems Biology Markup Language (SBML) community, we note computational resources and community structures that will help to realize the potential for plant Systems Biology to connect with a broader crop science community.
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Affiliation(s)
- Andrew J Millar
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Uriel Urquiza
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Alastair Hume
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- EPCC, Bayes Centre, University of Edinburgh, Edinburgh, UK
| | - Gordon D Plotkin
- Laboratory for the Foundations of Computer Science, School of Informatics, University of Edinburgh, Edinburgh, UK
| | - Oxana Sorokina
- Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh, Edinburgh, UK
| | - Argyris Zardilis
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Tomasz Zielinski
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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11
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Jones MA, Morohashi K, Grotewold E, Harmer SL. Arabidopsis JMJD5/JMJ30 Acts Independently of LUX ARRHYTHMO Within the Plant Circadian Clock to Enable Temperature Compensation. FRONTIERS IN PLANT SCIENCE 2019; 10:57. [PMID: 30774641 PMCID: PMC6367231 DOI: 10.3389/fpls.2019.00057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/16/2019] [Indexed: 05/08/2023]
Abstract
The circadian system ensures that plants respond appropriately to environmental change by predicting regular transitions that occur during diel cycles. In order to be most useful, the circadian system needs to be compensated against daily and seasonal changes in temperature that would otherwise alter the pace of this biological oscillator. We demonstrate that an evening-phased protein, the putative histone demethylase JMJD5, contributes to temperature compensation. JMJD5 is co-expressed with components of the Evening Complex, an agglomeration of proteins including EARLY FLOWERING3 (ELF3), ELF4, and LUX ARRHYTHYMO (LUX), which also integrates temperature changes into the molecular clockwork. One role of the Evening Complex is to regulate expression of PSEUDORESPONSE REGULATOR9 (PRR9) and PRR7, important components of the temperature compensation mechanism. Surprisingly we find that LUX, but not other Evening Complex components, is dispensable for clock function at low temperatures. Further genetic analysis suggests JMJD5 acts in a parallel pathway to LUX within the circadian system. Although an intact JMJD5 catalytic domain is required for its function within the clock, our findings suggest JMJD5 does not directly regulate H3K36 methylation at circadian loci. Such data refine our understanding of how JMDJ5 acts within the Arabidopsis circadian system.
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Affiliation(s)
- Matthew A. Jones
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
- Department of Plant Biology, University of California, Davis, Davis, CA, United States
| | - Kengo Morohashi
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Stacey L. Harmer
- Department of Plant Biology, University of California, Davis, Davis, CA, United States
- *Correspondence: Stacey L. Harmer,
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12
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Mombaerts L, Carignano A, Robertson FC, Hearn TJ, Junyang J, Hayden D, Rutterford Z, Hotta CT, Hubbard KE, Maria MRC, Yuan Y, Hannah MA, Goncalves J, Webb AAR. Dynamical differential expression (DyDE) reveals the period control mechanisms of the Arabidopsis circadian oscillator. PLoS Comput Biol 2019; 15:e1006674. [PMID: 30703082 PMCID: PMC6377142 DOI: 10.1371/journal.pcbi.1006674] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 02/15/2019] [Accepted: 11/26/2018] [Indexed: 12/12/2022] Open
Abstract
The circadian oscillator, an internal time-keeping device found in most organisms, enables timely regulation of daily biological activities by maintaining synchrony with the external environment. The mechanistic basis underlying the adjustment of circadian rhythms to changing external conditions, however, has yet to be clearly elucidated. We explored the mechanism of action of nicotinamide in Arabidopsis thaliana, a metabolite that lengthens the period of circadian rhythms, to understand the regulation of circadian period. To identify the key mechanisms involved in the circadian response to nicotinamide, we developed a systematic and practical modeling framework based on the identification and comparison of gene regulatory dynamics. Our mathematical predictions, confirmed by experimentation, identified key transcriptional regulatory mechanisms of circadian period and uncovered the role of blue light in the response of the circadian oscillator to nicotinamide. We suggest that our methodology could be adapted to predict mechanisms of drug action in complex biological systems.
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Affiliation(s)
- Laurent Mombaerts
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Alberto Carignano
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Fiona C. Robertson
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Timothy J. Hearn
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Jin Junyang
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - David Hayden
- Department of Engineering, University of Cambridge, Cambridge, United Kingdom
| | - Zoe Rutterford
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Carlos T. Hotta
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Katherine E. Hubbard
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Marti Ruiz C. Maria
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Ye Yuan
- Department of Engineering, University of Cambridge, Cambridge, United Kingdom
| | | | - Jorge Goncalves
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
- Department of Engineering, University of Cambridge, Cambridge, United Kingdom
| | - Alex A. R. Webb
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
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13
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Gould PD, Domijan M, Greenwood M, Tokuda IT, Rees H, Kozma-Bognar L, Hall AJ, Locke JC. Coordination of robust single cell rhythms in the Arabidopsis circadian clock via spatial waves of gene expression. eLife 2018; 7:31700. [PMID: 29697372 PMCID: PMC5988422 DOI: 10.7554/elife.31700] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 04/25/2018] [Indexed: 11/13/2022] Open
Abstract
The Arabidopsis circadian clock orchestrates gene regulation across the day/night cycle. Although a multiple feedback loop circuit has been shown to generate the 24-hr rhythm, it remains unclear how robust the clock is in individual cells, or how clock timing is coordinated across the plant. Here we examine clock activity at the single cell level across Arabidopsis seedlings over several days under constant environmental conditions. Our data reveal robust single cell oscillations, albeit desynchronised. In particular, we observe two waves of clock activity; one going down, and one up the root. We also find evidence of cell-to-cell coupling of the clock, especially in the root tip. A simple model shows that cell-to-cell coupling and our measured period differences between cells can generate the observed waves. Our results reveal the spatial structure of the plant clock and suggest that unlike the centralised mammalian clock, the Arabidopsis clock has multiple coordination points.
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Affiliation(s)
- Peter D Gould
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Mirela Domijan
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom.,Department of Mathematical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Mark Greenwood
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.,Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom.,Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Isao T Tokuda
- Department of Mechanical Engineering, Ritsumeikan University, Kusatsu, Japan
| | - Hannah Rees
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Laszlo Kozma-Bognar
- Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary.,Department of Genetics, University of Szeged, Szeged, Hungary
| | - Anthony Jw Hall
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.,Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - James Cw Locke
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom.,Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.,Microsoft Research, Cambridge, United Kingdom
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14
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Guadagno CR, Ewers BE, Weinig C. Circadian Rhythms and Redox State in Plants: Till Stress Do Us Part. FRONTIERS IN PLANT SCIENCE 2018; 9:247. [PMID: 29556244 PMCID: PMC5844964 DOI: 10.3389/fpls.2018.00247] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 02/12/2018] [Indexed: 05/22/2023]
Abstract
A growing body of evidence demonstrates a significant relationship between cellular redox state and circadian rhythms. Each day these two vital components of plant biology influence one another, dictating the pace for metabolism and physiology. Diverse environmental stressors can disrupt this condition and, although plant scientists have made significant progress in re-constructing functional networks of plant stress responses, stress impacts on the clock-redox crosstalk is poorly understood. Inter-connected phenomena such as redox state and metabolism, internal and external environments, cellular homeostasis and rhythms can impede predictive understanding of coordinated regulation of plant stress response. The integration of circadian clock effects into predictive network models is likely to increase final yield and better predict plant responses to stress. To achieve such integrated understanding, it is necessary to consider the internal clock not only as a gatekeeper of environmental responses but also as a target of stress syndromes. Using chlorophyll fluorescence as a reliable and high-throughput probe of stress coupled to functional genomics and metabolomics will provide insights on the crosstalk across a wide range of stress severity and duration, including potential insights into oxidative stress response and signaling. We suggest the efficiency of photosystem II in light conditions (Fv'/Fm') to be the most dynamic of the fluorescence variables and therefore the most reliable parameter to follow the stress response from early sensing to mortality.
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Affiliation(s)
| | - Brent E. Ewers
- Department of Botany, University of Wyoming, Laramie, WY, United States
- Program in Ecology, University of Wyoming, Laramie, WY, United States
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, WY, United States
- Program in Ecology, University of Wyoming, Laramie, WY, United States
- Department of Molecular and Cellular Life Sciences, University of Wyoming, Laramie, WY, United States
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15
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Oakenfull RJ, Davis SJ. Shining a light on the Arabidopsis circadian clock. PLANT, CELL & ENVIRONMENT 2017; 40:2571-2585. [PMID: 28732105 DOI: 10.1111/pce.13033] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 07/10/2017] [Accepted: 07/11/2017] [Indexed: 05/23/2023]
Abstract
The circadian clock provides essential timing information to ensure optimal growth to prevailing external environmental conditions. A major time-setting mechanism (zeitgeber) in clock synchronization is light. Differing light wavelengths, intensities, and photoperiodic duration are processed for the clock-setting mechanism. Many studies on light-input pathways to the clock have focused on Arabidopsis thaliana. Photoreceptors are specific chromic proteins that detect light signals and transmit this information to the central circadian oscillator through a number of different signalling mechanisms. The most well-characterized clock-mediating photoreceptors are cryptochromes and phytochromes, detecting blue, red, and far-red wavelengths of light. Ultraviolet and shaded light are also processed signals to the oscillator. Notably, the clock reciprocally generates rhythms of photoreceptor action leading to so-called gating of light responses. Intermediate proteins, such as Phytochrome interacting factors (PIFs), constitutive photomorphogenic 1 (COP1) and EARLY FLOWERING 3 (ELF3), have been established in signalling pathways downstream of photoreceptor activation. However, the precise details for these signalling mechanisms are not fully established. This review highlights both historical and recent efforts made to understand overall light input to the oscillator, first looking at how each wavelength of light is detected, this is then related to known input mechanisms and their interactions.
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Affiliation(s)
| | - Seth J Davis
- Department of Biology, University of York, York, YO10 5DD, UK
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16
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17
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Grzegorczyk M, Aderhold A, Husmeier D. Targeting Bayes factors with direct-path non-equilibrium thermodynamic integration. Comput Stat 2017; 32:717-761. [PMID: 32103862 PMCID: PMC7010372 DOI: 10.1007/s00180-017-0721-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 02/27/2017] [Indexed: 11/21/2022]
Abstract
Thermodynamic integration (TI) for computing marginal likelihoods is based on an inverse annealing path from the prior to the posterior distribution. In many cases, the resulting estimator suffers from high variability, which particularly stems from the prior regime. When comparing complex models with differences in a comparatively small number of parameters, intrinsic errors from sampling fluctuations may outweigh the differences in the log marginal likelihood estimates. In the present article, we propose a TI scheme that directly targets the log Bayes factor. The method is based on a modified annealing path between the posterior distributions of the two models compared, which systematically avoids the high variance prior regime. We combine this scheme with the concept of non-equilibrium TI to minimise discretisation errors from numerical integration. Results obtained on Bayesian regression models applied to standard benchmark data, and a complex hierarchical model applied to biopathway inference, demonstrate a significant reduction in estimator variance over state-of-the-art TI methods.
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Affiliation(s)
- Marco Grzegorczyk
- Johann Bernoulli Institute (JBI), Groningen University, Groningen, The Netherlands
| | - Andrej Aderhold
- School of Mathematics and Statistics, Glasgow University, Glasgow, UK
| | - Dirk Husmeier
- School of Mathematics and Statistics, Glasgow University, Glasgow, UK
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18
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Aderhold A, Husmeier D, Grzegorczyk M. Approximate Bayesian inference in semi-mechanistic models. STATISTICS AND COMPUTING 2016; 27:1003-1040. [PMID: 32226236 PMCID: PMC7089672 DOI: 10.1007/s11222-016-9668-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 05/05/2016] [Indexed: 06/10/2023]
Abstract
Inference of interaction networks represented by systems of differential equations is a challenging problem in many scientific disciplines. In the present article, we follow a semi-mechanistic modelling approach based on gradient matching. We investigate the extent to which key factors, including the kinetic model, statistical formulation and numerical methods, impact upon performance at network reconstruction. We emphasize general lessons for computational statisticians when faced with the challenge of model selection, and we assess the accuracy of various alternative paradigms, including recent widely applicable information criteria and different numerical procedures for approximating Bayes factors. We conduct the comparative evaluation with a novel inferential pipeline that systematically disambiguates confounding factors via an ANOVA scheme.
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Affiliation(s)
- Andrej Aderhold
- School of Mathematics and Statistics, Glasgow University, Glasgow, UK
| | - Dirk Husmeier
- School of Mathematics and Statistics, Glasgow University, Glasgow, UK
| | - Marco Grzegorczyk
- Johann Bernoulli Institute (JBI), Groningen University, Groningen, The Netherlands
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19
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Voliotis M, Thomas P, Grima R, Bowsher CG. Stochastic Simulation of Biomolecular Networks in Dynamic Environments. PLoS Comput Biol 2016; 12:e1004923. [PMID: 27248512 PMCID: PMC4889045 DOI: 10.1371/journal.pcbi.1004923] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 04/17/2016] [Indexed: 01/26/2023] Open
Abstract
Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach for stochastic simulation of networks embedded in the dynamic environment of the cell and its surroundings. We thus sample trajectories of the stochastic process described by the chemical master equation with time-varying propensities. A comparative analysis shows that existing approaches can either fail dramatically, or else can impose impractical computational burdens due to numerical integration of reaction propensities, especially when cell ensembles are studied. Here we introduce the Extrande method which, given a simulated time course of dynamic network inputs, provides a conditionally exact and several orders-of-magnitude faster simulation solution. The new approach makes it feasible to demonstrate—using decision-making by a large population of quorum sensing bacteria—that robustness to fluctuations from upstream signaling places strong constraints on the design of networks determining cell fate. Our approach has the potential to significantly advance both understanding of molecular systems biology and design of synthetic circuits. Simulation algorithms have become indispensable tools in modern quantitative biology, providing deep insight into many biochemical systems, including gene regulatory networks. However, current stochastic simulation approaches handle the effects of fluctuating extracellular signals and upstream processes poorly, either failing to give qualitatively reliable predictions or being very inefficient computationally. Here we introduce the Extrande method, a novel approach for simulation of biomolecular networks embedded in the dynamic environment of the cell and its surroundings. The method is accurate and computationally efficient, and hence fills an important gap in the field of stochastic simulation. In particular, we employ it to study a bacterial decision-making network and demonstrate that robustness to fluctuations from upstream signaling places strong constraints on the design of networks determining cell fate.
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Affiliation(s)
| | - Philipp Thomas
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Ramon Grima
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (RG); (CGB)
| | - Clive G. Bowsher
- School of Mathematics, University of Bristol, Bristol, United Kingdom
- * E-mail: (RG); (CGB)
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20
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De Caluwé J, Xiao Q, Hermans C, Verbruggen N, Leloup JC, Gonze D. A Compact Model for the Complex Plant Circadian Clock. FRONTIERS IN PLANT SCIENCE 2016; 7:74. [PMID: 26904049 PMCID: PMC4742534 DOI: 10.3389/fpls.2016.00074] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Accepted: 01/16/2016] [Indexed: 05/23/2023]
Abstract
The circadian clock is an endogenous timekeeper that allows organisms to anticipate and adapt to the daily variations of their environment. The plant clock is an intricate network of interlocked feedback loops, in which transcription factors regulate each other to generate oscillations with expression peaks at specific times of the day. Over the last decade, mathematical modeling approaches have been used to understand the inner workings of the clock in the model plant Arabidopsis thaliana. Those efforts have produced a number of models of ever increasing complexity. Here, we present an alternative model that combines a low number of equations and parameters, similar to the very earliest models, with the complex network structure found in more recent ones. This simple model describes the temporal evolution of the abundance of eight clock gene mRNA/protein and captures key features of the clock on a qualitative level, namely the entrained and free-running behaviors of the wild type clock, as well as the defects found in knockout mutants (such as altered free-running periods, lack of entrainment, or changes in the expression of other clock genes). Additionally, our model produces complex responses to various light cues, such as extreme photoperiods and non-24 h environmental cycles, and can describe the control of hypocotyl growth by the clock. Our model constitutes a useful tool to probe dynamical properties of the core clock as well as clock-dependent processes.
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Affiliation(s)
- Joëlle De Caluwé
- Unité de Chronobiologie Théorique, Faculté des Sciences, Université Libre de BruxellesBrussels, Belgium
| | - Qiying Xiao
- Laboratory of Plant Physiology and Molecular Genetics, Faculté des Sciences, Université Libre de BruxellesBrussels, Belgium
| | - Christian Hermans
- Laboratory of Plant Physiology and Molecular Genetics, Faculté des Sciences, Université Libre de BruxellesBrussels, Belgium
| | - Nathalie Verbruggen
- Laboratory of Plant Physiology and Molecular Genetics, Faculté des Sciences, Université Libre de BruxellesBrussels, Belgium
| | - Jean-Christophe Leloup
- Unité de Chronobiologie Théorique, Faculté des Sciences, Université Libre de BruxellesBrussels, Belgium
| | - Didier Gonze
- Unité de Chronobiologie Théorique, Faculté des Sciences, Université Libre de BruxellesBrussels, Belgium
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Abstract
As the amount of biological data in the public domain grows, so does the range of modeling and analysis techniques employed in systems biology. In recent years, a number of theoretical computer science developments have enabled modeling methodology to keep pace. The growing interest in systems biology in executable models and their analysis has necessitated the borrowing of terms and methods from computer science, such as formal analysis, model checking, static analysis, and runtime verification. Here, we discuss the most important and exciting computational methods and tools currently available to systems biologists. We believe that a deeper understanding of the concepts and theory highlighted in this review will produce better software practice, improved investigation of complex biological processes, and even new ideas and better feedback into computer science.
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Affiliation(s)
- Ezio Bartocci
- Faculty of Informatics, Technische Universität Wien, Vienna, Austria
| | - Pietro Lió
- Computer Laboratory, University of Cambridge, Cambridge, United Kingdom
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22
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Jing B, Yuan J, Yin Z, Lv C, Lu S, Xiong H, Tang H, Ye G, Shi F. Dynamic properties of the segmentation clock mediated by microRNA. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:196-206. [PMID: 25755706 PMCID: PMC4348866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 12/22/2014] [Indexed: 06/04/2023]
Abstract
Somites are embryonic precursors that give rise to the axial skeleton and skeletal muscles and form the segmental vertebrate body plan. Somitogenesis is controlled by the "segmentation clock", which contains multiple oscillator genes that must be tightly regulated at both the transcriptional and post-transcriptional levels for proper clock function. However, how the segmentation clock governs the formation of the somites at post-transcriptional level, remains unclear. In this work, we develop an integrated model with three modules for the segmentation clock and explore the mechanism for somite segmentation based on the dynamics of the network. By numerical simulations, we find that the amplitude and period of the somite segmentation clock are sensitive to Notch activity, which is fine-tuned by Lunatic fringe (Lfng) and microRNA (miRNA), and Lfng and miRNA are essential for forming the proper segmentation during somitogenesis. Moreover, miRNA is found to have a crucial role in minimizing the fluctuation period and amplitude to maintain coherent oscillation. Introduction of stochasticity in the model enables us to explain the available experimental data with dampening of oscillations. These findings uncover a fresh mechanism for regulation of the segmentation clock at a post-transcriptional level and provide important insights into how the relatively subtle effects of miRNAs on target genes can have broad effects in developmental situations that have critical requirements for tight posttranscriptional regulation.
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Affiliation(s)
- Bo Jing
- College of Veterinary Medicine, Sichuan Agricultural UniversityYa’an 625014, Sichuan, China
| | - Julin Yuan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for AgricultureYangling 712100, Shanxi, China
- Department of Germplasm and Environmental Sciences, Zhejiang Institute of Freshwater FisheriesHuzhou 313001, Zhejiang, China
| | - Zhongqiong Yin
- College of Veterinary Medicine, Sichuan Agricultural UniversityYa’an 625014, Sichuan, China
| | - Cheng Lv
- College of Veterinary Medicine, Sichuan Agricultural UniversityYa’an 625014, Sichuan, China
| | - Shengming Lu
- Chengdu Shengming Pharmaceutical technology Co., LTDChengdu, Sichuan, China
| | - Haoshan Xiong
- Sichuan Institute of Veterinary Drugs ControlChengdu 610041, Sichuan, China
| | - Huaqiao Tang
- Chengdu Qiankun Veterinary Pharmaceutcal Co., LTDSichuan, China
| | - Gang Ye
- College of Veterinary Medicine, Sichuan Agricultural UniversityYa’an 625014, Sichuan, China
| | - Fei Shi
- College of Veterinary Medicine, Sichuan Agricultural UniversityYa’an 625014, Sichuan, China
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23
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Bravi B, Longo G. The Unconventionality of Nature: Biology, from Noise to Functional Randomness. UNCONVENTIONAL COMPUTATION AND NATURAL COMPUTATION 2015. [DOI: 10.1007/978-3-319-21819-9_1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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24
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Guerriero ML, Akman OE, van Ooijen G. Stochastic models of cellular circadian rhythms in plants help to understand the impact of noise on robustness and clock structure. FRONTIERS IN PLANT SCIENCE 2014; 5:564. [PMID: 25374576 PMCID: PMC4204444 DOI: 10.3389/fpls.2014.00564] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 09/30/2014] [Indexed: 05/25/2023]
Abstract
Rhythmic behavior is essential for plants; for example, daily (circadian) rhythms control photosynthesis and seasonal rhythms regulate their life cycle. The core of the circadian clock is a genetic network that coordinates the expression of specific clock genes in a circadian rhythm reflecting the 24-h day/night cycle. Circadian clocks exhibit stochastic noise due to the low copy numbers of clock genes and the consequent cell-to-cell variation: this intrinsic noise plays a major role in circadian clocks by inducing more robust oscillatory behavior. Another source of noise is the environment, which causes variation in temperature and light intensity: this extrinsic noise is part of the requirement for the structural complexity of clock networks. Advances in experimental techniques now permit single-cell measurements and the development of single-cell models. Here we present some modeling studies showing the importance of considering both types of noise in understanding how plants adapt to regular and irregular light variations. Stochastic models have proven useful for understanding the effect of regular variations. By contrast, the impact of irregular variations and the interaction of different noise sources are less well studied.
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Affiliation(s)
| | - Ozgur E. Akman
- Centre for Systems, Dynamics and Control, College of Engineering, Mathematics and Physical Sciences, University of ExeterExeter, UK
| | - Gerben van Ooijen
- Institute of Molecular Plant Sciences, University of EdinburghEdinburgh, UK
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25
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Fu J, Yang L, Dai S. Conservation of Arabidopsis thaliana circadian clock genes in Chrysanthemum lavandulifolium. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 80:337-347. [PMID: 24844451 DOI: 10.1016/j.plaphy.2014.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 04/05/2014] [Indexed: 06/03/2023]
Abstract
In Arabidopsis, circadian clock genes play important roles in photoperiod pathway by regulating the daytime expression of CONSTANS (CO), but related reports for chrysanthemum are notably limited. In this study, we isolated eleven circadian clock genes, which lie in the three interconnected negative and positive feedback loops in a wild diploid chrysanthemum, Chrysanthemum lavandulifolium. With the exception of ClELF3, ClPRR1 and ClPRR73, most of the circadian clock genes are expressed more highly in leaves than in other tested tissues. The diurnal rhythms of these circadian clock genes are similar to those of their homologs in Arabidopsis. ClELF3 and ClZTL are constitutively expressed at all time points in both assessed photoperiods. The expression succession from morning to night of the PSEUDO RESPONSE REGULATOR (PRR) gene family occurs in the order ClPRR73/ClPRR37, ClPRR5, and then ClPRR1. ClLHY is expressed during the dawn period, and ClGIs is expressed during the dusk period. The peak expression levels of ClFKF1 and ClGIs are synchronous in the inductive photoperiod. However, in the non-inductive night break (NB) condition or non-24 h photoperiod, the peak expression level of ClFKF1 is significantly changed, indicating that ClFKF1 itself or the synchronous expression of ClFKF1 and ClGIs might be essential to initiate the flowering of C. lavandulifolium. This study provides the first extensive evaluation of circadian clock genes, and it presents a useful foundation for dissecting the functions of circadian clock genes in C. lavandulifolium.
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Affiliation(s)
- Jianxin Fu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture and College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Liwen Yang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture and College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Silan Dai
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture and College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China.
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26
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Fox SE, Geniza M, Hanumappa M, Naithani S, Sullivan C, Preece J, Tiwari VK, Elser J, Leonard JM, Sage A, Gresham C, Kerhornou A, Bolser D, McCarthy F, Kersey P, Lazo GR, Jaiswal P. De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum. PLoS One 2014; 9:e96855. [PMID: 24821410 PMCID: PMC4018402 DOI: 10.1371/journal.pone.0096855] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 04/12/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid wheat, and is therefore a useful model for the study of components regulating photomorphogenesis in diploid wheat. In order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes of two Triticum monococcum subspecies, the wild winter wheat T. monococcum ssp. aegilopoides (accession G3116) and the domesticated spring wheat T. monococcum ssp. monococcum (accession DV92) by generating de novo assemblies of RNA-Seq data derived from both etiolated and green seedlings. PRINCIPAL FINDINGS The de novo transcriptome assemblies of DV92 and G3116 represent 120,911 and 117,969 transcripts, respectively. We successfully mapped ∼90% of these transcripts from each accession to barley and ∼95% of the transcripts to T. urartu genomes. However, only ∼77% transcripts mapped to the annotated barley genes and ∼85% transcripts mapped to the annotated T. urartu genes. Differential gene expression analyses revealed 22% more light up-regulated and 35% more light down-regulated transcripts in the G3116 transcriptome compared to DV92. The DV92 and G3116 mRNA sequence reads aligned against the reference barley genome led to the identification of ∼500,000 single nucleotide polymorphism (SNP) and ∼22,000 simple sequence repeat (SSR) sites. CONCLUSIONS De novo transcriptome assemblies of two accessions of the diploid wheat T. monococcum provide new empirical transcriptome references for improving Triticeae genome annotations, and insights into transcriptional programming during photomorphogenesis. The SNP and SSR sites identified in our analysis provide additional resources for the development of molecular markers.
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Affiliation(s)
- Samuel E. Fox
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Matthew Geniza
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Molecular and Cellular Biology Graduate Program, Oregon State University, Corvallis, Oregon, United States of America
| | - Mamatha Hanumappa
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Chris Sullivan
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Vijay K. Tiwari
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Jeffrey M. Leonard
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America
| | - Abigail Sage
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Cathy Gresham
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Arnaud Kerhornou
- European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
| | - Dan Bolser
- European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
| | - Fiona McCarthy
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Paul Kersey
- European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
| | - Gerard R. Lazo
- USDA-ARS, Western Regional Research Center, Albany, California, United States of America
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America
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27
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Gyllenstrand N, Karlgren A, Clapham D, Holm K, Hall A, Gould PD, Källman T, Lagercrantz U. No time for spruce: rapid dampening of circadian rhythms in Picea abies (L. Karst). PLANT & CELL PHYSIOLOGY 2014; 55:535-50. [PMID: 24363286 DOI: 10.1093/pcp/pct199] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The identification and cloning of full-length homologs of circadian clock genes from Picea abies represent a first step to study the function and evolution of the circadian clock in gymnosperms. Phylogenetic analyses suggest that the sequences of key circadian clock genes are conserved between angiosperms and gymnosperms. though fewer homologous copies were found for most gene families in P. abies. We detected diurnal cycling of circadian clock genes in P. abies using quantitative real-time PCR; however, cycling appeared to be rapidly dampened under free-running conditions. Given the unexpected absence of transcriptional cycling during constant conditions, we employed a complementary method to assay circadian rhythmic outputs and measured delayed fluorescence in seedlings of Norway spruce. Neither of the two approaches to study circadian rhythms in Norway spruce could detect robust ∼24 h cycling behavior under constant conditions. These data suggest gene conservation but fundamental differences in clock function between gymnosperms and other plant taxa.
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Affiliation(s)
- Niclas Gyllenstrand
- Department of Plant Biology and Forest Genetics, Uppsala Biocenter, Swedish University for Agricultural Sciences, Uppsala, PO Box 7080, SE-750 07 Uppsala, Sweden
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28
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Chew YH, Smith RW, Jones HJ, Seaton DD, Grima R, Halliday KJ. Mathematical models light up plant signaling. THE PLANT CELL 2014; 26:5-20. [PMID: 24481073 PMCID: PMC3963593 DOI: 10.1105/tpc.113.120006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 12/13/2014] [Accepted: 01/13/2014] [Indexed: 05/08/2023]
Abstract
Plants respond to changes in the environment by triggering a suite of regulatory networks that control and synchronize molecular signaling in different tissues, organs, and the whole plant. Molecular studies through genetic and environmental perturbations, particularly in the model plant Arabidopsis thaliana, have revealed many of the mechanisms by which these responses are actuated. In recent years, mathematical modeling has become a complementary tool to the experimental approach that has furthered our understanding of biological mechanisms. In this review, we present modeling examples encompassing a range of different biological processes, in particular those regulated by light. Current issues and future directions in the modeling of plant systems are discussed.
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Affiliation(s)
- Yin Hoon Chew
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JH, United Kingdom
- SynthSys, Edinburgh EH9 3JD, United Kingdom
| | - Robert W. Smith
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JH, United Kingdom
| | - Harriet J. Jones
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JH, United Kingdom
- SynthSys, Edinburgh EH9 3JD, United Kingdom
| | - Daniel D. Seaton
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JH, United Kingdom
- SynthSys, Edinburgh EH9 3JD, United Kingdom
| | - Ramon Grima
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JH, United Kingdom
- SynthSys, Edinburgh EH9 3JD, United Kingdom
| | - Karen J. Halliday
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JH, United Kingdom
- SynthSys, Edinburgh EH9 3JD, United Kingdom
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Schmal C, Leloup JC, Gonze D. Modeling and simulating the Arabidopsis thaliana circadian clock using XPP-AUTO. Methods Mol Biol 2014; 1158:337-58. [PMID: 24792063 DOI: 10.1007/978-1-4939-0700-7_23] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Circadian clocks are endogenous timekeepers that produce oscillations with a period of about one day. Their rhythmicity originates from complex gene regulatory networks at the cellular level. In the last decades, computational models have been proven to be a powerful tool in order to understand the dynamics and design principles of the complex regulatory circuitries underlying the circadian clocks of different organisms. We present the process of model development using a small and simplified two-gene regulatory network of the Arabidopsis circadian clock. Subsequently, we discuss important numerical techniques to analyze such a mathematical model using XPP-AUTO. We show how to solve deterministic and stochastic ordinary differential equations and how to compute bifurcation diagrams or simulate phase-shift experiments. We finally discuss the contributions of modeling to the understanding and dissection of the Arabidopsis circadian system.
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Affiliation(s)
- Christoph Schmal
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany,
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Aderhold A, Husmeier D, Grzegorczyk M. Statistical inference of regulatory networks for circadian regulation. Stat Appl Genet Mol Biol 2014; 13:227-73. [DOI: 10.1515/sagmb-2013-0051] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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An S, Harang R, Meeker K, Granados-Fuentes D, Tsai CA, Mazuski C, Kim J, Doyle FJ, Petzold LR, Herzog ED. A neuropeptide speeds circadian entrainment by reducing intercellular synchrony. Proc Natl Acad Sci U S A 2013; 110:E4355-61. [PMID: 24167276 PMCID: PMC3832006 DOI: 10.1073/pnas.1307088110] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Shift work or transmeridian travel can desynchronize the body's circadian rhythms from local light-dark cycles. The mammalian suprachiasmatic nucleus (SCN) generates and entrains daily rhythms in physiology and behavior. Paradoxically, we found that vasoactive intestinal polypeptide (VIP), a neuropeptide implicated in synchrony among SCN cells, can also desynchronize them. The degree and duration of desynchronization among SCN neurons depended on both the phase and the dose of VIP. A model of the SCN consisting of coupled stochastic cells predicted both the phase- and the dose-dependent response to VIP and that the transient phase desynchronization, or "phase tumbling", could arise from intrinsic, stochastic noise in small populations of key molecules (notably, Period mRNA near its daily minimum). The model also predicted that phase tumbling following brief VIP treatment would accelerate entrainment to shifted environmental cycles. We tested this using a prepulse of VIP during the day before a shift in either a light cycle in vivo or a temperature cycle in vitro. Although VIP during the day does not shift circadian rhythms, the VIP pretreatment approximately halved the time required for mice to reentrain to an 8-h shifted light schedule and for SCN cultures to reentrain to a 10-h shifted temperature cycle. We conclude that VIP below 100 nM synchronizes SCN cells and above 100 nM reduces synchrony in the SCN. We show that exploiting these mechanisms that transiently reduce cellular synchrony before a large shift in the schedule of daily environmental cues has the potential to reduce jet lag.
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Affiliation(s)
- Sungwon An
- Department of Biology, Washington University in St. Louis, Saint Louis, MO 63130
| | - Rich Harang
- Department of Computer Science, University of California, Santa Barbara, CA 93106-3110; and
| | - Kirsten Meeker
- Department of Computer Science, University of California, Santa Barbara, CA 93106-3110; and
| | | | - Connie A. Tsai
- Department of Biology, Washington University in St. Louis, Saint Louis, MO 63130
| | - Cristina Mazuski
- Department of Biology, Washington University in St. Louis, Saint Louis, MO 63130
| | - Jihee Kim
- Department of Biology, Washington University in St. Louis, Saint Louis, MO 63130
| | - Francis J. Doyle
- Department of Chemical Engineering, University of California, Santa Barbara CA 93106-5080
| | - Linda R. Petzold
- Department of Computer Science, University of California, Santa Barbara, CA 93106-3110; and
| | - Erik D. Herzog
- Department of Biology, Washington University in St. Louis, Saint Louis, MO 63130
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Bujdoso N, Davis SJ. Mathematical modeling of an oscillating gene circuit to unravel the circadian clock network of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2013; 4:3. [PMID: 23355842 PMCID: PMC3555133 DOI: 10.3389/fpls.2013.00003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Accepted: 01/03/2013] [Indexed: 05/04/2023]
Abstract
The Arabidopsis thaliana circadian clock is an interconnected network highly tractable to systems approaches. Most elements in the transcriptional-translational oscillator were identified by genetic means and the expression of clock genes in various mutants led to the founding hypothesis of a positive-negative feedback loop being the core clock. The identification of additional clock genes beyond those defined in the core led to the use of systems approaches to decipher this angiosperm oscillator circuit. Kinetic modeling was first used to explain periodicity effects of various circadian mutants. This conformed in a flexible way to experimental details. Such observations allowed a recursive use of hypothesis generating from modeling, followed by experimental corroboration. More recently, the biochemical finding of new description of a DNA-binding activity for one class of clock components directed improvements in feature generation, one of which revealed that the core of the oscillator is a negative-negative feedback loop. The recursive use of modeling and experimental validation has thus revealed many essential transcriptional components that drive negative arms in the circadian oscillator. What awaits is to more fully describe the positive arms and an understanding of how additional pathways converge on the clock.
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Affiliation(s)
| | - Seth J. Davis
- *Correspondence: Seth J. Davis, Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany. e-mail:
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Middleton AM, Farcot E, Owen MR, Vernoux T. Modeling regulatory networks to understand plant development: small is beautiful. THE PLANT CELL 2012; 24:3876-91. [PMID: 23110896 PMCID: PMC3517225 DOI: 10.1105/tpc.112.101840] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We now have unprecedented capability to generate large data sets on the myriad genes and molecular players that regulate plant development. Networks of interactions between systems components can be derived from that data in various ways and can be used to develop mathematical models of various degrees of sophistication. Here, we discuss why, in many cases, it is productive to focus on small networks. We provide a brief and accessible introduction to relevant mathematical and computational approaches to model regulatory networks and discuss examples of small network models that have helped generate new insights into plant biology (where small is beautiful), such as in circadian rhythms, hormone signaling, and tissue patterning. We conclude by outlining some of the key technical and modeling challenges for the future.
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Affiliation(s)
- Alistair M. Middleton
- Center for Modeling and Simulation in the Biosciences and Interdisciplinary Center for Scientific Computing, University of Heidelberg, 69120 Heidelberg, Germany
| | - Etienne Farcot
- Virtual Plants Inria Team, Université Montpellier 2, 34095 Montpellier cedex 5, France
| | - Markus R. Owen
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
- Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom
| | - Teva Vernoux
- Laboratoire de Reproduction et Développement des Plantes, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Ecole Normale Supérieure de Lyon, Université Lyon I, Université de Lyon, 69364 Lyon cedex 07, France
- Address correspondence to
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Spontaneous spatiotemporal waves of gene expression from biological clocks in the leaf. Proc Natl Acad Sci U S A 2012; 109:6757-62. [PMID: 22496591 DOI: 10.1073/pnas.1118814109] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The circadian clocks that drive daily rhythms in animals are tightly coupled among the cells of some tissues. The coupling profoundly affects cellular rhythmicity and is central to contemporary understanding of circadian physiology and behavior. In contrast, studies of the clock in plant cells have largely ignored intercellular coupling, which is reported to be very weak or absent. We used luciferase reporter gene imaging to monitor circadian rhythms in leaves of Arabidopsis thaliana plants, achieving resolution close to the cellular level. Leaves grown without environmental cycles for up to 3 wk reproducibly showed spatiotemporal waves of gene expression consistent with intercellular coupling, using several reporter genes. Within individual leaves, different regions differed in phase by up to 17 h. A broad range of patterns was observed among leaves, rather than a common spatial distribution of circadian properties. Leaves exposed to light-dark cycles always had fully synchronized rhythms, which could desynchronize rapidly. After 4 d in constant light, some leaves were as desynchronized as leaves grown without any rhythmic input. Applying light-dark cycles to such a leaf resulted in full synchronization within 2-4 d. Thus, the rhythms of all cells were coupled to external light-dark cycles far more strongly than the cellular clocks were coupled to each other. Spontaneous desynchronization under constant conditions was limited, consistent with weak intercellular coupling among heterogeneous clocks. Both the weakness of coupling and the heterogeneity among cells are relevant to interpret molecular studies and to understand the physiological functions of the plant circadian clock.
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Thomas P, Straube AV, Grima R. Communication: limitations of the stochastic quasi-steady-state approximation in open biochemical reaction networks. J Chem Phys 2012; 135:181103. [PMID: 22088045 DOI: 10.1063/1.3661156] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
It is commonly believed that, whenever timescale separation holds, the predictions of reduced chemical master equations obtained using the stochastic quasi-steady-state approximation are in very good agreement with the predictions of the full master equations. We use the linear noise approximation to obtain a simple formula for the relative error between the predictions of the two master equations for the Michaelis-Menten reaction with substrate input. The reduced approach is predicted to overestimate the variance of the substrate concentration fluctuations by as much as 30%. The theoretical results are validated by stochastic simulations using experimental parameter values for enzymes involved in proteolysis, gluconeogenesis, and fermentation.
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Affiliation(s)
- Philipp Thomas
- Department of Physics, Humboldt University of Berlin, Newtonstr. 15, D-12489 Berlin, Germany
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