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Huang T, Liu H, Tao JP, Zhang JQ, Zhao TM, Hou XL, Xiong AS, You X. Low light intensity elongates period and defers peak time of photosynthesis: a computational approach to circadian-clock-controlled photosynthesis in tomato. HORTICULTURE RESEARCH 2023; 10:uhad077. [PMID: 37323229 PMCID: PMC10261901 DOI: 10.1093/hr/uhad077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 04/09/2023] [Indexed: 06/17/2023]
Abstract
Photosynthesis is involved in the essential process of transforming light energy into chemical energy. Although the interaction between photosynthesis and the circadian clock has been confirmed, the mechanism of how light intensity affects photosynthesis through the circadian clock remains unclear. Here, we propose a first computational model for circadian-clock-controlled photosynthesis, which consists of the light-sensitive protein P, the core oscillator, photosynthetic genes, and parameters involved in the process of photosynthesis. The model parameters were determined by minimizing the cost function ( [Formula: see text]), which is defined by the errors of expression levels, periods, and phases of the clock genes (CCA1, PRR9, TOC1, ELF4, GI, and RVE8). The model recapitulates the expression pattern of the core oscillator under moderate light intensity (100 μmol m -2 s-1). Further simulation validated the dynamic behaviors of the circadian clock and photosynthetic outputs under low (62.5 μmol m-2 s-1) and normal (187.5 μmol m-2 s-1) intensities. When exposed to low light intensity, the peak times of clock and photosynthetic genes were shifted backward by 1-2 hours, the period was elongated by approximately the same length, and the photosynthetic parameters attained low values and showed delayed peak times, which confirmed our model predictions. Our study reveals a potential mechanism underlying the circadian regulation of photosynthesis by the clock under different light intensities in tomato.
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Affiliation(s)
| | | | | | - Jia-Qi Zhang
- College of Horticulture, Nanjing Agricultural University/State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Horticultural Crop Biology and Germplasm Creation in East China of Ministry of Agriculture and Rural Affairs Nanjing 210095, Jiangsu, China
| | - Tong-Min Zhao
- Laboratory for Genetic Improvement of High Efficiency Horticultural Crops in Jiangsu Province, Institute of Vegetable Crop, Jiangsu Province Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
| | - Xi-Lin Hou
- College of Horticulture, Nanjing Agricultural University/State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Horticultural Crop Biology and Germplasm Creation in East China of Ministry of Agriculture and Rural Affairs Nanjing 210095, Jiangsu, China
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Diotto D, Barbera E, Borella L, Trivellin N, Sforza E. Modeling Approach to Capture the Effect of High Frequency Flashing Light in Steady-State Microalgae Cultures. Ind Eng Chem Res 2022. [DOI: 10.1021/acs.iecr.2c03258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Daniele Diotto
- Interdepartmental Centre Giorgio Levi Cases, Via Marzolo 9, Padova35131, Italy
| | - Elena Barbera
- Department of Industrial Engineering DII, University of Padova, Via Marzolo 9, Padova35131, Italy
| | - Lisa Borella
- Department of Industrial Engineering DII, University of Padova, Via Marzolo 9, Padova35131, Italy
| | - Nicola Trivellin
- Department of Industrial Engineering DII, University of Padova, Via Marzolo 9, Padova35131, Italy
| | - Eleonora Sforza
- Department of Industrial Engineering DII, University of Padova, Via Marzolo 9, Padova35131, Italy
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Model-Based Prediction of Perceived Light Flashing in Recirculated Inclined Wavy-Bottomed Photobioreactors. Processes (Basel) 2021. [DOI: 10.3390/pr9071158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Microalgae biomass production rate in short light-path photobioreactors potentially can be improved by mixing-induced flashing light regimes. A cascade photobioreactor features a thin liquid layer flowing down a sloping, wavy-bottomed surface where liquid flow exhibits peculiar local recirculation hydrodynamics, potentially conducive to an ordered flashing light regime. This article presents a model-based analysis of the frequency distribution of perceived irradiance in said wavy-bottomed photobioreactor. The model combines a Lagrangian description of the motion of individual cells, in turn derived from the hydrodynamic parameters of the photobioreactor extracted from an experimentally validated Computational Fluid Dynamic model, with a simplified description of the irradiance field across the culture thickness, down to the spectral analysis of perceived irradiance. The main finding of the work is that the wavy bottomed photobioreactor provides a ‘robust’ spectral excitation to the circulating microalgae up to 3 Hz frequency, while in flat panels and bubble columns excitation decays evenly at a 24 db/octave rate. This analysis paves the way to improving the light flashing performance of the wavy-bottomed photobioreactor with respect to geometry (cavity size and installation inclination) and operation (flow rate).
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Battaglino B, Arduino A, Pagliano C, Sforza E, Bertucco A. Optimization of Light and Nutrients Supply to Stabilize Long-Term Industrial Cultivation of Metabolically Engineered Cyanobacteria: A Model-Based Analysis. Ind Eng Chem Res 2021. [DOI: 10.1021/acs.iecr.0c04887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Beatrice Battaglino
- BioSolar Lab, Applied Science and Technology Department, Politecnico di Torino, Environment Park, Via Livorno 60, 10144 Torino, Italy
| | - Alessandro Arduino
- Istituto Nazionale di Ricerca Metrologica (INRIM), Strada delle Cacce 91, 10135 Torino, Italy
| | - Cristina Pagliano
- BioSolar Lab, Applied Science and Technology Department, Politecnico di Torino, Environment Park, Via Livorno 60, 10144 Torino, Italy
| | - Eleonora Sforza
- Department of Industrial Engineering, Università di Padova, Via Marzolo 9, 35131 Padova, Italy
| | - Alberto Bertucco
- Department of Industrial Engineering, Università di Padova, Via Marzolo 9, 35131 Padova, Italy
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Schediwy K, Trautmann A, Steinweg C, Posten C. Microalgal kinetics - a guideline for photobioreactor design and process development. Eng Life Sci 2019; 19:830-843. [PMID: 32624976 PMCID: PMC6999068 DOI: 10.1002/elsc.201900107] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/13/2019] [Accepted: 09/23/2019] [Indexed: 12/17/2022] Open
Abstract
Kinetics generally describes bio‐(chemical) reaction rates in dependence on substrate concentrations. Kinetics for microalgae is often adapted from heterotrophs and lacks mechanistic foundation, e.g. for light harvesting. Using and understanding kinetic equations as the representation of intracellular mechanisms is essential for reasonable comparisons and simulations of growth behavior. Summarizing growth kinetics in one equation does not yield reliable models. Piecewise linear or rational functions may mimic photosynthesis irradiance response curves, but fail to represent the mechanisms. Our modeling approach for photoautotrophic growth comprises physical and kinetic modules with mechanistic foundation extracted from the literature. Splitting the light submodel into the modules for light distribution, light absorption, and photosynthetic sugar production with independent parameters allows the transfer of kinetics between different reactor designs. The consecutive anabolism depends among others on nutrient concentrations. The nutrient uptake kinetics largely impacts carbon partitioning in the reviewed stoichiometry range of cellular constituents. Consecutive metabolic steps mask each other and demand a maximum value understandable as the minimum principle of growth. These fundamental modules need to be clearly distinguished, but may be modified or extended based on process conditions and progress in research. First, discussion of kinetics helps to understand the physiological situation, for which ranges of parameter values are given. Second, kinetics should be used for photobioreactor design, but also for gassing and nutrient optimization. Numerous examples are given for both aspects. Finally, measuring kinetics more comprehensively and precisely will help in improved process development.
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Affiliation(s)
- Kira Schediwy
- Institute of Process Engineering in Life Sciences, Section III: Bioprocess Engineering Karlsruhe Institute of Technology (KIT) Karlsruhe Germany
| | | | - Christian Steinweg
- Institute of Process Engineering in Life Sciences, Section III: Bioprocess Engineering Karlsruhe Institute of Technology (KIT) Karlsruhe Germany
| | - Clemens Posten
- Institute of Process Engineering in Life Sciences, Section III: Bioprocess Engineering Karlsruhe Institute of Technology (KIT) Karlsruhe Germany
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Gernigon V, Chekroun MA, Cockx A, Guiraud P, Morchain J. How Mixing and Light Heterogeneity Impact the Overall Growth Rate in Photobioreactors. Chem Eng Technol 2019. [DOI: 10.1002/ceat.201900102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Vincent Gernigon
- University of Toulouse, CNRS, INRA, INSALISBP 135 avenue de Rangueil 31077 Toulouse France
| | - Mohammed A. Chekroun
- University of Toulouse, CNRS, INRA, INSALISBP 135 avenue de Rangueil 31077 Toulouse France
| | - Arnaud Cockx
- University of Toulouse, CNRS, INRA, INSALISBP 135 avenue de Rangueil 31077 Toulouse France
| | - Pascal Guiraud
- University of Toulouse, CNRS, INRA, INSALISBP 135 avenue de Rangueil 31077 Toulouse France
| | - Jérôme Morchain
- University of Toulouse, CNRS, INRA, INSALISBP 135 avenue de Rangueil 31077 Toulouse France
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Perin G, Bellan A, Bernardi A, Bezzo F, Morosinotto T. The potential of quantitative models to improve microalgae photosynthetic efficiency. PHYSIOLOGIA PLANTARUM 2019; 166:380-391. [PMID: 30578540 DOI: 10.1111/ppl.12915] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 12/14/2018] [Accepted: 12/18/2018] [Indexed: 06/09/2023]
Abstract
The massive increase in carbon dioxide concentration in the atmosphere driven by human activities is causing huge negative consequences and new sustainable sources of energy, food and materials are highly needed. Algae are unicellular photosynthetic microorganisms that can provide a highly strategic contribution to this challenge as alternative source of biomass to complement crops cultivation. Algae industrial cultures are commonly limited by light availability, and biomass accumulation is strongly dependent on their photon-to-biomass conversion efficiency. Investigation of algae photosynthetic metabolism is thus strategic for the generation of more efficient strains with higher productivity. Algae are cultivated at industrial scale in conditions highly different from the natural niches they adapted to and strains development efforts must fully consider the seminal influence on productivity of regulatory mechanism of photosynthesis as well as of cultivation parameters like cells concentration, light distribution in the culture, mixing, nutrients and carbon dioxide availability. In this review we will focus in particular on how mathematical models can account for the complex influence of all environmental parameters and can be exploited for development of improved algae strains.
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Affiliation(s)
- Giorgio Perin
- Department of Biology, University of Padova, Via Ugo Bassi 58/B 35131, Padova, Italy
| | - Alessandra Bellan
- Department of Biology, University of Padova, Via Ugo Bassi 58/B 35131, Padova, Italy
| | - Andrea Bernardi
- Department of Industrial Engineering, University of Padova, Via Marzolo 9 35131, Padova, Italy
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, SW7 2AZ, London, UK
| | - Fabrizio Bezzo
- Department of Industrial Engineering, University of Padova, Via Marzolo 9 35131, Padova, Italy
| | - Tomas Morosinotto
- Department of Biology, University of Padova, Via Ugo Bassi 58/B 35131, Padova, Italy
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Albarello A, Simionato D, Morosinotto T, Bezzo F. Model-Based Optimization of Microalgae Growth in a Batch Plant. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.9b00270] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A. Albarello
- CAPE-Lab (Computer-Aided Process Engineering Laboratory) and PAR-Lab (Padova Algae Research Laboratory), Department of Industrial Engineering, University of Padova, via Marzolo 9, 35131 Padova, Italy
| | - D. Simionato
- TMCI Padovan SpA, via Caduti del Lavoro 7, 31029 Vittorio Veneto, Italy
| | - T. Morosinotto
- PAR-Lab (Padova Algae Research Laboratory), Department of Biology, University of Padova, via U. Bassi 58/B, 35131 Padova, Italy
| | - F. Bezzo
- CAPE-Lab (Computer-Aided Process Engineering Laboratory) and PAR-Lab (Padova Algae Research Laboratory), Department of Industrial Engineering, University of Padova, via Marzolo 9, 35131 Padova, Italy
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Papacek S, Jablonsky J, Petera K. Advanced integration of fluid dynamics and photosynthetic reaction kinetics for microalgae culture systems. BMC SYSTEMS BIOLOGY 2018; 12:93. [PMID: 30458763 PMCID: PMC6245592 DOI: 10.1186/s12918-018-0611-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Background Photosynthetic microalgae have been in the spotlight of biotechnological production (biofuels, lipids, etc), however, current barriers in mass cultivation of microalgae are limiting its successful industrialization. Therefore, a mathematical model integrating both the biological and hydrodynamical parts of the cultivation process may improve our understanding of relevant phenomena, leading to further optimization of the microalgae cultivation. Results We introduce a unified multidisciplinary simulation tool for microalgae culture systems, particularly the photobioreactors. Our approach describes changes of cell growth determined by dynamics of heterogeneous environmental conditions such as irradiation and mixing of the culture. Presented framework consists of (i) a simplified model of microalgae growth in a culture system (the advection-diffusion-reaction system within a phenomenological model of photosynthesis and photoinhibition), (ii) the fluid dynamics (Navier-Stokes equations), and (iii) the irradiance field description (Beer-Lambert law). To validate the method, a simple case study leading to hydrodynamically induced fluctuating light conditions was chosen. The integration of computational fluid dynamics (ANSYS Fluent) revealed the inner property of the system, the flashing light enhancement phenomenon, known from experiments. Conclusion Our physically accurate model of microalgae culture naturally exhibits features of real system, can be applied to any geometry of microalgae mass cultivation and thus is suitable for biotechnological applications.
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Affiliation(s)
- Stepan Papacek
- Institute of Complex Systems, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, Zámek 136, 373 33 Nové Hrady, Czech Republic
| | - Jiri Jablonsky
- Institute of Complex Systems, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, Zámek 136, 373 33 Nové Hrady, Czech Republic.
| | - Karel Petera
- Czech Technical University in Prague, Faculty of Mechanical Engineering, Technická 4, Prague, 160 00, Czech Republic
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Gao X, Kong B, Vigil RD. Simulation of algal photobioreactors: recent developments and challenges. Biotechnol Lett 2018; 40:1311-1327. [DOI: 10.1007/s10529-018-2595-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 07/23/2018] [Indexed: 11/24/2022]
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11
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Graham PJ, Nguyen B, Burdyny T, Sinton D. A penalty on photosynthetic growth in fluctuating light. Sci Rep 2017; 7:12513. [PMID: 28970553 PMCID: PMC5624943 DOI: 10.1038/s41598-017-12923-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/20/2017] [Indexed: 12/21/2022] Open
Abstract
Fluctuating light is the norm for photosynthetic organisms, with a wide range of frequencies (0.00001 to 10 Hz) owing to diurnal cycles, cloud cover, canopy shifting and mixing; with broad implications for climate change, agriculture and bioproduct production. Photosynthetic growth in fluctuating light is generally considered to improve with increasing fluctuation frequency. Here we demonstrate that the regulation of photosynthesis imposes a penalty on growth in fluctuating light for frequencies in the range of 0.01 to 0.1 Hz (organisms studied: Synechococcus elongatus and Chlamydomonas reinhardtii). We provide a comprehensive sweep of frequencies and duty cycles. In addition, we develop a 2nd order model that identifies the source of the penalty to be the regulation of the Calvin cycle – present at all frequencies but compensated at high frequencies by slow kinetics of RuBisCO.
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Affiliation(s)
- Percival J Graham
- University of Toronto Mechanical and Industrial Engineering, Toronto, Canada
| | - Brian Nguyen
- University of Toronto Mechanical and Industrial Engineering, Toronto, Canada
| | - Thomas Burdyny
- University of Toronto Mechanical and Industrial Engineering, Toronto, Canada
| | - David Sinton
- University of Toronto Mechanical and Industrial Engineering, Toronto, Canada.
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12
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Rudnicki P, Gao X, Kong B, Vigil RD. A comparative study of photosynthetic unit models for algal growth rate and fluorescence prediction under light/dark cycles. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.03.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Bernardi A, Nikolaou A, Meneghesso A, Morosinotto T, Chachuat B, Bezzo F. High-Fidelity Modelling Methodology of Light-Limited Photosynthetic Production in Microalgae. PLoS One 2016; 11:e0152387. [PMID: 27055271 PMCID: PMC4824504 DOI: 10.1371/journal.pone.0152387] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/14/2016] [Indexed: 01/08/2023] Open
Abstract
Reliable quantitative description of light-limited growth in microalgae is key to improving the design and operation of industrial production systems. This article shows how the capability to predict photosynthetic processes can benefit from a synergy between mathematical modelling and lab-scale experiments using systematic design of experiment techniques. A model of chlorophyll fluorescence developed by the authors [Nikolaou et al., J Biotechnol 194:91-99, 2015] is used as starting point, whereby the representation of non-photochemical-quenching (NPQ) process is refined for biological consistency. This model spans multiple time scales ranging from milliseconds to hours, thus calling for a combination of various experimental techniques in order to arrive at a sufficiently rich data set and determine statistically meaningful estimates for the model parameters. The methodology is demonstrated for the microalga Nannochloropsis gaditana by combining pulse amplitude modulation (PAM) fluorescence, photosynthesis rate and antenna size measurements. The results show that the calibrated model is capable of accurate quantitative predictions under a wide range of transient light conditions. Moreover, this work provides an experimental validation of the link between fluorescence and photosynthesis-irradiance (PI) curves which had been theoricized.
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Affiliation(s)
- Andrea Bernardi
- CAPE-Lab (Computer-Aided Process Engineering Laboratory) and PAR-Lab (Padova Algae Research Laboratory), Department of Industrial Engineering, University of Padova, Padova, Italy
| | - Andreas Nikolaou
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London, United Kingdom
| | - Andrea Meneghesso
- PAR-Lab (Padova Algae Research Laboratory), Department of Biology, University of Padova, Padova, Italy
| | - Tomas Morosinotto
- PAR-Lab (Padova Algae Research Laboratory), Department of Biology, University of Padova, Padova, Italy
| | - Benoît Chachuat
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London, United Kingdom
| | - Fabrizio Bezzo
- CAPE-Lab (Computer-Aided Process Engineering Laboratory) and PAR-Lab (Padova Algae Research Laboratory), Department of Industrial Engineering, University of Padova, Padova, Italy
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Gargano I, Olivieri G, Spasiano D, Andreozzi R, Pollio A, Marotta R, D’Ambrosio N, Marzocchella A. Kinetic characterization of the photosynthetic reaction centres in microalgae by means of fluorescence methodology. J Biotechnol 2015. [DOI: 10.1016/j.jbiotec.2015.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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