Using a reaction‐diffusion model to estimate day respiration and reassimilation of (photo)respiredCO2in leaves

peer-reviewedMethods using gas exchange measurements to estimate respiration in the light (day respiration Rd) make implicit assumptions about reassimilation of (photo)respired CO2; however, this reassimilation depends on the positions of mitochondria. We used a reaction-diffusion model without making these assumptions to analyse datasets on gas exchange, chlorophyll fluorescence and anatomy for tomato leaves. We investigated how Rd values obtained by the Kok and the Yin methods are affected by these assumptions and how those by the Laisk method are affected by the positions of mitochondria. The Kok method always underestimated Rd. Estimates of Rd by the Yin method and by the reaction-diffusion model agreed only for nonphotorespiratory conditions. Both the Yin and Kok methods ignore reassimilation of (photo)respired CO2, and thus underestimated Rd for photorespiratory conditions, but this was less so in the Yin than in the Kok method. Estimates by the Laisk method were affected by assumed positions of mitochondria. It did not work if mitochondria were in the cytosol between the plasmamembrane and the chloroplast envelope. However, mitochondria were found to be most likely between the tonoplast and chloroplasts. Our reaction-diffusion model effectively estimates Rd, enlightens the dependence of Rd estimates on reassimilation and clarifies (dis)advantages of existing methods.KU Leuve

The role of chloroplast movement in C4 photosynthesis: a theoretical analysis using a three-dimensional reaction-diffusion model for maize

18 Pág.Chloroplasts movement within mesophyll cells in C4 plants is hypothesized to enhance the CO2 concentrating mechanism, but this is difficult to verify experimentally. A three-dimensional (3D) leaf model can help analyse how chloroplast movement influences the operation of the CO2 concentrating mechanism. The first volumetric reaction-diffusion model of C4 photosynthesis that incorporates detailed 3D leaf anatomy, light propagation, ATP and NADPH production, and CO2, O2 and bicarbonate concentration driven by diffusional and assimilation/emission processes was developed. It was implemented for maize leaves to simulate various chloroplast movement scenarios within mesophyll cells: the movement of all mesophyll chloroplasts towards bundle sheath cells (aggregative movement) and movement of only those of interveinal mesophyll cells towards bundle sheath cells (avoidance movement). Light absorbed by bundle sheath chloroplasts relative to mesophyll chloroplasts increased in both cases. Avoidance movement decreased light absorption by mesophyll chloroplasts considerably. Consequently, total ATP and NADPH production and net photosynthetic rate increased for aggregative movement and decreased for avoidance movement compared with the default case of no chloroplast movement at high light intensities. Leakiness increased in both chloroplast movement scenarios due to the imbalance in energy production and demand in mesophyll and bundle sheath cells. These results suggest the need to design strategies for coordinated increases in electron transport and Rubisco activities for an efficient CO2 concentrating mechanism at very high light intensities.The work is supported by the Research Council of KU Leuven (project C1/16/002) and the Research Fund Flanders (project G.0645.13). Wageningen based authors have contributed to this work within the program BioSolar Cells. FJC was funded through the Spanish fellowship Ramon y Cajal (RYC2021-035064-I).Peer reviewe

Microscale modeling of gas exchange during C4 photosythesis

Improving the efficiency of photosynthesis could contribute to better food security under an unprecedented rise in global population and climate-change. The photosynthesis pathway in C4 plants, such as maize (Zea mays L.), Miscanthus (Miscanthus x giganteus), and sugarcane (Saccharum officinarum L.), results in higher productivity and photosynthetic nitrogen and water-use efficiencies than in C3 plants. The mechanism of photosynthesis in C4 crops depends on the archetypal Kranz anatomy, which determines the leaf internal environment, for it influences gas diffusion and light distribution. The low permeability of bundle sheath cell walls to CO2 (gbs) and the high CO2 conductance of mesophyll cells (gm) are crucial for a high C4 photosynthetic efficiency. So far, the relationship between leaf anatomical properties and CO2 conductances such as gbs and gm in C4 plants received less attention than in C3 plants. In addition, these conductances lump a number of anatomical features; mechanistic understanding of the role of each microstructure element in the efficiency of photosynthesis is, therefore, limited. Furthermore, there are only few studies addressing the potential limitations of C4 leaf anatomy on light propagation and efficiency of photosynthesis. To investigate the role of leaf anatomy, as altered by leaf nitrogen content and age on the efficiency of C4 photosynthesis, maize (Zea mays L.) plants were grown under three contrasting nitrogen levels. Combined gas exchange and chlorophyll fluorescence measurements were carried out on fully grown leaves at two leaf ages: young and old. The measured data were combined with a biochemical model of C4 photosynthesis to estimate gbs. The leaf microstructure and ultrastructure were quantified using images obtained from micro-computed tomography and microscopy. Increased nitrogen supply resulted in higher leaf nitrogen content and rate of photosynthesis, whereas leaf aging decreased them. There was a strong positive correlation between gbs and leaf nitrogen content (LNC) while old leaves had lower gbs than young leaves. gm also increased with LNC and decreased with leaf aging. The increase of gbs with LNC was little explained by a change in leaf anatomy. By contrast, the combined effects of LNC and leaf age on anatomical features were responsible for differences in gbs between young leaves and old leaves. It is recommended that changes in the leaf ultrastructure at levels of membranes and plasmodesmata should be investigated to unravel the relationship between anatomy and CO2 conductances further. Furthermore, since gbs thus estimated, lumps a number of microstructural features, the contribution of each individual leaf microstructural feature could not be determined. Therefore, a microscale modeling approach that accounts for each leaf microstructural and ultrastructural features is recommended. A two-dimensional microscale model of gas diffusion and photosynthesis in C4 leaves that incorporates the physical obstructions of leaf anatomy and ultrastructure on gas transport was developed. The leaf anatomical geometry was developed from light microscopy images of the same leaf that was also used in gas exchange measurements. Features such as cell walls, biological membranes, plasmodesmata and suberin layers around bundle sheath cell walls were modeled as resistances. Reaction-diffusion equations for CO2 and bicarbonate in liquid phase media were developed and discretized over the two-dimensional leaf geometry. The model predicted the responses of photosynthesis to irradiance and intercellular CO2 in agreement with that obtained from measurement. The impact of components of the CO2 diffusion pathway on photosynthesis was evaluated quantitatively. The CO2 permeability of the mesophyll-bundle sheath and air space-mesophyll interfaces strongly affected the rate of photosynthesis and gbs. Carbonic anhydrase influenced the rate of photosynthesis, especially at low intercellular CO2 levels. In addition, the suberin layer at the exposed surface of the bundle sheath cells was found beneficial in reducing the retro-diffusion of CO2. One or two-dimensional gas transport models, when applied to analyze the gas diffusion in leaves understate the three-dimensional nature of gas exchange. Therefore, a 3-D microscale model incorporating the actual leaf microstructure was developed. The distribution of light through the leaf tissue was modeled using an adapted Monte Carlo photon transport method. Diffusion of CO2 and O2 was coupled with C4 photosynthesis kinetics and a model of light penetration inside the leaf tissue. The temperature dependency of biochemical and biophysical parameters was incorporated. The typical Kranz-anatomy of the leaf tissue caused large gradients of light intensity and concentration of gases. Maximum photosynthesis at low leakiness was obtained when chlorophyll contents of mesophyll and bundle sheath cells were equal. At elevated CO2, photosynthesis in bundle sheath cells of juvenile leaves could potentially be supported by direct diffusion. Simulations also suggest that the effect of temperature on biophysical processes, in contrast to that on biochemical processes, has little influence on the temperature response of C4 photosynthesis and leakiness. In addition, a systematic analysis showed that cytosolic CO2 release due to decarboxylation of C4 acids would reduce the efficiency of photosynthesis only moderately. The model may serve as a tool to further investigate improving C4 photosynthesis in relation to gas exchange and light propagation

Microscale modeling of gas exchange during C4 photosynthetis

Improving the efficiency of photosynthesis could contribute to better food security under an unprecedented rise in global population and climate-change. The photosynthesis pathway in C4 plants, such as maize (Zea mays L.), Miscanthus (Miscanthus x giganteus), and sugarcane (Saccharum officinarum L.), results in higher productivity and photosynthetic nitrogen and water-use efficiencies than in C3 plants. The mechanism of photosynthesis in C4 crops depends on the archetypal Kranz anatomy, which determines the leaf internal environment, for it influences gas diffusion and light distribution. The low permeability of bundle sheath cell walls to CO2 (gbs) and the high CO2 conductance of mesophyll cells (gm) are crucial for a high C4 photosynthetic efficiency. So far, the relationship between leaf anatomical properties and CO2 conductances such as gbs and gm in C4 plants received less attention than in C3 plants. In addition, these conductances lump a number of anatomical features; mechanistic understanding of the role of each microstructure element in the efficiency of photosynthesis is, therefore, limited. Furthermore, there are only few studies addressing the potential limitations of C4 leaf anatomy on light propagation and efficiency of photosynthesis. To investigate the role of leaf anatomy, as altered by leaf nitrogen content and age on the efficiency of C4 photosynthesis, maize (Zea mays L.) plants were grown under three contrasting nitrogen levels. Combined gas exchange and chlorophyll fluorescence measurements were carried out on fully grown leaves at two leaf ages: young and old. The measured data were combined with a biochemical model of C4 photosynthesis to estimate gbs. The leaf microstructure and ultrastructure were quantified using images obtained from micro-computed tomography and microscopy. Increased nitrogen supply resulted in higher leaf nitrogen content and rate of photosynthesis, whereas leaf aging decreased them. There was a strong positive correlation between gbs and leaf nitrogen content (LNC) while old leaves had lower gbs than young leaves. gm also increased with LNC and decreased with leaf aging. The increase of gbs with LNC was little explained by a change in leaf anatomy. By contrast, the combined effects of LNC and leaf age on anatomical features were responsible for differences in gbs between young leaves and old leaves. It is recommended that changes in the leaf ultrastructure at levels of membranes and plasmodesmata should be investigated to unravel the relationship between anatomy and CO2 conductances further. Furthermore, since gbs thus estimated, lumps a number of microstructural features, the contribution of each individual leaf microstructural feature could not be determined. Therefore, a microscale modeling approach that accounts for each leaf microstructural and ultrastructural features is recommended. A two-dimensional microscale model of gas diffusion and photosynthesis in C4 leaves that incorporates the physical obstructions of leaf anatomy and ultrastructure on gas transport was developed. The leaf anatomical geometry was developed from light microscopy images of the same leaf that was also used in gas exchange measurements. Features such as cell walls, biological membranes, plasmodesmata and suberin layers around bundle sheath cell walls were modeled as resistances. Reaction-diffusion equations for CO2 and bicarbonate in liquid phase media were developed and discretized over the two-dimensional leaf geometry. The model predicted the responses of photosynthesis to irradiance and intercellular CO2 in agreement with that obtained from measurement. The impact of components of the CO2 diffusion pathway on photosynthesis was evaluated quantitatively. The CO2 permeability of the mesophyll-bundle sheath and air space-mesophyll interfaces strongly affected the rate of photosynthesis and gbs. Carbonic anhydrase influenced the rate of photosynthesis, especially at low intercellular CO2 levels. In addition, the suberin layer at the exposed surface of the bundle sheath cells was found beneficial in reducing the retro-diffusion of CO2. One or two-dimensional gas transport models, when applied to analyze the gas diffusion in leaves understate the three-dimensional nature of gas exchange. Therefore, a 3-D microscale model incorporating the actual leaf microstructure was developed. The distribution of light through the leaf tissue was modeled using an adapted Monte Carlo photon transport method. Diffusion of CO2 and O2 was coupled with C4 photosynthesis kinetics and a model of light penetration inside the leaf tissue. The temperature dependency of biochemical and biophysical parameters was incorporated. The typical Kranz-anatomy of the leaf tissue caused large gradients of light intensity and concentration of gases. Maximum photosynthesis at low leakiness was obtained when chlorophyll contents of mesophyll and bundle sheath cells were equal. At elevated CO2, photosynthesis in bundle sheath cells of juvenile leaves could potentially be supported by direct diffusion. Simulations also suggest that the effect of temperature on biophysical processes, in contrast to that on biochemical processes, has little influence on the temperature response of C4 photosynthesis and leakiness. In addition, a systematic analysis showed that cytosolic CO2 release due to decarboxylation of C4 acids would reduce the efficiency of photosynthesis only moderately. The model may serve as a tool to further investigate improving C4 photosynthesis in relation to gas exchange and light propagation.status: publishe

In silico study of the role of cell growth factors in photosynthesis using a virtual leaf tissue generator coupled to a microscale photosynthesis gas exchange model

Computational tools that allow in silico analysis of the role of cell growth and division on photosynthesis are scarce. We present a freely available tool that combines a virtual leaf tissue generator and a two-dimensional microscale model of gas transport during C3 photosynthesis. A total of 270 mesophyll geometries were generated with varying degrees of growth anisotropy, growth extent, and extent of schizogenous airspace formation in the palisade mesophyll. The anatomical properties of the virtual leaf tissue and microscopic cross-sections of actual leaf tissue of tomato (Solanum lycopersicum L.) were statistically compared. Model equations for transport of CO2 in the liquid phase of the leaf tissue were discretized over the geometries. The virtual leaf tissue generator produced a leaf anatomy of tomato that was statistically similar to real tomato leaf tissue. The response of photosynthesis to intercellular CO2 predicted by a model that used the virtual leaf tissue geometry compared well with measured values. The results indicate that the light-saturated rate of photosynthesis was influenced by interactive effects of extent and directionality of cell growth and degree of airspace formation through the exposed surface of mesophyll per leaf area. The tool could be used further in investigations of improving photosynthesis and gas exchange in relation to cell growth and leaf anatomy.status: Published onlin

A two-dimensional microscale model of gas exchange during photosynthesis in maize (Zea mays L.) leaves

CO2 exchange in leaves of maize (Zea mays L.) was examined using a microscale model of combined gas diffusion and C4 photosynthesis kinetics at the leaf tissue level. Based on a generalized scheme of photosynthesis in NADP-malic enzyme type C4 plants, the model accounted for CO2 diffusion in a leaf tissue, CO2 hydration and assimilation in mesophyll cells, CO2 release from decarboxylation of C4 acids, CO2 fixation in bundle sheath cells and CO2 retro-diffusion from bundle sheath cells. The transport equations were solved over a realistic 2-D geometry of the Kranz anatomy obtained from light microscopy images. The predicted responses of photosynthesis rate to changes in ambient CO2 and irradiance compared well with those obtained from gas exchange measurements. A sensitivity analysis showed that the CO2 permeability of the mesophyll-bundle sheath and airspace–mesophyll interfaces strongly affected the rate of photosynthesis and bundle sheath conductance. Carbonic anhydrase influenced the rate of photosynthesis, especially at low intercellular CO2 levels. In addition, the suberin layer at the exposed surface of the bundle sheath cells was found beneficial in reducing the retro-diffusion. The model may serve as a tool to investigate CO2 diffusion further in relation to the Kranz anatomy in C4 plants.publisher: Elsevier articletitle: A two-dimensional microscale model of gas exchange during photosynthesis in maize (Zea mays L.) leaves journaltitle: Plant Science articlelink: http://dx.doi.org/10.1016/j.plantsci.2016.02.003 content_type: article copyright: Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.status: publishe

Virtual Microstructural Leaf Tissue Generation Based on Cell Growth Modeling

A cell growth algorithm for virtual leaf tissue generation is presented based on the biomechanics of plant cells in tissues. The algorithm can account for typical differences in epidermal layers, palisade mesophyll layer and spongy mesophyll layer which have characteristic differences in the shape of cells, arrangement of cells and void fractions present in each layer. The cell is considered as a closed thin walled structure, maintained in tension by turgor pressure. The cell walls are modelled as linear elastic elements which obey Hooke's law. A Voronoi tessellation was used to generate the initial topology of the cells in the spongy mesophyll layer. Then two layers of brick structured cells are added to the top of it to represent the palisade mesophyll and upper epidermis and a single layer is added at bottom of the Voronoi tessellation to represent the lower epidermal layer. Intercellular air spaces are generated by separating the Voronoi cells along the edges starting from where three Voronoi cells are in contact (schizogenous origin) and/or by deleting some of the Voronoi cells (lysigenous origin). Cell expansion then results from turgor pressure acting on the yielding cell wall material. To find the sequence of positions of each vertex and thus the shape of the tissue with time, a system of differential equations for the positions and velocities of each vertex is established and solved using the ordinary differential equation solver in MatLab. Statistical comparison of the cellular characteristics with 2D cross-sectional slices of real leaf tissue of tomato is excellent. The virtual tissues can be used to systematically study effects of leaf structure on water and gas exchange.status: publishe

A two-dimensional microscale model of gas exchange during photosynthesis in maize (Zea mays L.) leaves

CO2 exchange in leaves of maize (Zea mays L.) was examined using a microscale model of combined gas diffusion and C4 photosynthesis kinetics at the leaf tissue level. Based on a generalized scheme of photosynthesis in NADP-malic enzyme type C4 plants, the model accounted for CO2 diffusion in a leaf tissue, CO2 hydration and assimilation in mesophyll cells, CO2 release from decarboxylation of C4 acids, CO2 fixation in bundle sheath cells and CO2 retro-diffusion from bundle sheath cells. The transport equations were solved over a realistic 2-D geometry of the Kranz anatomy obtained from light microscopy images. The predicted responses of photosynthesis rate to changes in ambient CO2 and irradiance compared well with those obtained from gas exchange measurements. A sensitivity analysis showed that the CO2 permeability of the mesophyll-bundle sheath and airspace-mesophyll interfaces strongly affected the rate of photosynthesis and bundle sheath conductance. Carbonic anhydrase influenced the rate of photosynthesis, especially at low intercellular CO2 levels. In addition, the suberin layer at the exposed surface of the bundle sheath cells was found beneficial in reducing the retro-diffusion. The model may serve as a tool to investigate CO2 diffusion further in relation to the Kranz anatomy in C4 plants

Using a reaction-diffusion model to estimate day respiration and reassimilation of (photo)respired CO2 in leaves

Methods using gas exchange measurements to estimate respiration in the light (day respiration R d ) make implicit assumptions about reassimilation of (photo)respired CO2 ; however, this reassimilation depends on the positions of mitochondria. We used a reaction-diffusion model without making these assumptions to analyse datasets on gas exchange, chlorophyll fluorescence and anatomy for tomato leaves. We investigated how R d values obtained by the Kok and the Yin methods are affected by these assumptions and how those by the Laisk method are affected by the positions of mitochondria. The Kok method always underestimated R d . Estimates of R d by the Yin method and by the reaction-diffusion model agreed only for nonphotorespiratory conditions. Both the Yin and Kok methods ignore reassimilation of (photo)respired CO2 , and thus underestimated R d for photorespiratory conditions, but this was less so in the Yin than in the Kok method. Estimates by the Laisk method were affected by assumed positions of mitochondria. It did not work if mitochondria were in the cytosol between the plasmamembrane and the chloroplast envelope. However, mitochondria were found to be most likely between the tonoplast and chloroplasts. Our reaction-diffusion model effectively estimates R d , enlightens the dependence of R d estimates on reassimilation and clarifies (dis)advantages of existing methods.status: publishe

11. De la ville de terre à la ville durable, itinéraire et point de vue d’un pionnier

Parlez-nous de votre parcours… et de votre implication dans la restauration des maisons de la médina de Marrakech. Je suis arrivé à Marrakech en 1982 pour quatre mois en tant que coopérant. Je suis revenu en 1984, mais c’est en 1986 que je m’y suis installé. Je travaillais pour différents cabinets d’architecture et décidais de m’installer dans la médina, par choix et par intérêt. Les choses se sont passées très progressivement parce que l’intérêt pour le patrimoine, c’était chez moi presque ..