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Park J, Dies M, Lin Y, Hormoz S, Smith-Unna SE, Quinodoz S, Hernández-Jiménez MJ, Garcia-Ojalvo J, Locke JCW, Elowitz MB. Molecular Time Sharing through Dynamic Pulsing in Single Cells. Cell Syst 2018; 6:216-229.e15. [PMID: 29454936 PMCID: PMC6070344 DOI: 10.1016/j.cels.2018.01.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 09/04/2017] [Accepted: 01/10/2018] [Indexed: 11/19/2022]
Abstract
In cells, specific regulators often compete for limited amounts of a core enzymatic resource. It is typically assumed that competition leads to partitioning of core enzyme molecules among regulators at constant levels. Alternatively, however, different regulatory species could time share, or take turns utilizing, the core resource. Using quantitative time-lapse microscopy, we analyzed sigma factor activity dynamics, and their competition for RNA polymerase, in individual Bacillus subtilis cells under energy stress. Multiple alternative sigma factors were activated in ~1-hr pulses in stochastic and repetitive fashion. Pairwise analysis revealed that two sigma factors rarely pulse simultaneously and that some pairs are anti-correlated, indicating that RNAP utilization alternates among different sigma factors. Mathematical modeling revealed how stochastic time-sharing dynamics can emerge from pulse-generating sigma factor regulatory circuits actively competing for RNAP. Time sharing provides a mechanism for cells to dynamically control the distribution of cell states within a population. Since core molecular components are limiting in many other systems, time sharing may represent a general mode of regulation.
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Affiliation(s)
- Jin Park
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Marta Dies
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, 08003 Barcelona, Spain; Department of Physics and Nuclear Engineering, Universitat Politecnica de Catalunya, 08222 Terrassa, Spain; Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Yihan Lin
- Center for Quantitative Biology, and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Sahand Hormoz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Sofia Quinodoz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Jordi Garcia-Ojalvo
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, 08003 Barcelona, Spain.
| | - James C W Locke
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, UK; Microsoft Research, Cambridge, UK.
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.
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Erguler K, Smith-Unna SE, Waldock J, Proestos Y, Christophides GK, Lelieveld J, Parham PE. Large-Scale Modelling of the Environmentally-Driven Population Dynamics of Temperate Aedes albopictus (Skuse). PLoS One 2016; 11:e0149282. [PMID: 26871447 PMCID: PMC4752251 DOI: 10.1371/journal.pone.0149282] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 01/03/2016] [Indexed: 01/04/2023] Open
Abstract
The Asian tiger mosquito, Aedes albopictus, is a highly invasive vector species. It is a proven vector of dengue and chikungunya viruses, with the potential to host a further 24 arboviruses. It has recently expanded its geographical range, threatening many countries in the Middle East, Mediterranean, Europe and North America. Here, we investigate the theoretical limitations of its range expansion by developing an environmentally-driven mathematical model of its population dynamics. We focus on the temperate strain of Ae. albopictus and compile a comprehensive literature-based database of physiological parameters. As a novel approach, we link its population dynamics to globally-available environmental datasets by performing inference on all parameters. We adopt a Bayesian approach using experimental data as prior knowledge and the surveillance dataset of Emilia-Romagna, Italy, as evidence. The model accounts for temperature, precipitation, human population density and photoperiod as the main environmental drivers, and, in addition, incorporates the mechanism of diapause and a simple breeding site model. The model demonstrates high predictive skill over the reference region and beyond, confirming most of the current reports of vector presence in Europe. One of the main hypotheses derived from the model is the survival of Ae. albopictus populations through harsh winter conditions. The model, constrained by the environmental datasets, requires that either diapausing eggs or adult vectors have increased cold resistance. The model also suggests that temperature and photoperiod control diapause initiation and termination differentially. We demonstrate that it is possible to account for unobserved properties and constraints, such as differences between laboratory and field conditions, to derive reliable inferences on the environmental dependence of Ae. albopictus populations.
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Affiliation(s)
- Kamil Erguler
- Energy, Environment and Water Research Center, The Cyprus Institute, 2121 Aglantzia, Nicosia, Cyprus
- * E-mail: (KE); (PEP)
| | - Stephanie E. Smith-Unna
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR, United Kingdom
| | - Joanna Waldock
- Energy, Environment and Water Research Center, The Cyprus Institute, 2121 Aglantzia, Nicosia, Cyprus
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Yiannis Proestos
- Computation-based Science and Technology Research Center, The Cyprus Institute, 2121 Aglantzia, Nicosia, Cyprus
| | - George K. Christophides
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
- Computation-based Science and Technology Research Center, The Cyprus Institute, 2121 Aglantzia, Nicosia, Cyprus
| | - Jos Lelieveld
- Energy, Environment and Water Research Center, The Cyprus Institute, 2121 Aglantzia, Nicosia, Cyprus
- Department of Atmospheric Chemistry, Max Planck Institute for Chemistry, D-55128 Mainz, Germany
| | - Paul E. Parham
- Department of Public Health and Policy, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 3GL, United Kingdom
- Grantham Institute for Climate Change, Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, St. Mary’s campus, Imperial College London, London W2 1PG, United Kingdom
- * E-mail: (KE); (PEP)
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Retkute R, Smith-Unna SE, Smith RW, Burgess AJ, Jensen OE, Johnson GN, Preston SP, Murchie EH. Exploiting heterogeneous environments: does photosynthetic acclimation optimize carbon gain in fluctuating light? J Exp Bot 2015; 66:2437-47. [PMID: 25788730 PMCID: PMC4629418 DOI: 10.1093/jxb/erv055] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plants have evolved complex mechanisms to balance the efficient use of absorbed light energy in photosynthesis with the capacity to use that energy in assimilation, so avoiding potential damage from excess light. This is particularly important under natural light, which can vary according to weather, solar movement and canopy movement. Photosynthetic acclimation is the means by which plants alter their leaf composition and structure over time to enhance photosynthetic efficiency and productivity. However there is no empirical or theoretical basis for understanding how leaves track historic light levels to determine acclimation status, or whether they do this accurately. We hypothesized that in fluctuating light (varying in both intensity and frequency), the light-response characteristics of a leaf should adjust (dynamically acclimate) to maximize daily carbon gain. Using a framework of mathematical modelling based on light-response curves, we have analysed carbon-gain dynamics under various light patterns. The objective was to develop new tools to quantify the precision with which photosynthesis acclimates according to the environment in which plants exist and to test this tool on existing data. We found an inverse relationship between the optimal maximum photosynthetic capacity and the frequency of low to high light transitions. Using experimental data from the literature we were able to show that the observed patterns for acclimation were consistent with a strategy towards maximizing daily carbon gain. Refinement of the model will further determine the precision of acclimation.
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Affiliation(s)
- Renata Retkute
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK School of Mathematical Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Stephanie E Smith-Unna
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Robert W Smith
- Systems and Synthetic Biology, Wageningen UR, Building 316, Dreijenplein 10, 6703HB Wageningen, Netherlands
| | - Alexandra J Burgess
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK
| | - Oliver E Jensen
- School of Mathematics, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Giles N Johnson
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Simon P Preston
- School of Mathematical Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Erik H Murchie
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK
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