<html lang="en"> <head> <title>Evolution of C4 photosynthesis predicted by constraint-based modelling</title> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta http-equiv="X-UA-Compatible" content="ie=edge"> <link href="https://unpkg.com/@stencila/thema@2/dist/themes/elife/styles.css" rel="stylesheet"> <script src="https://unpkg.com/@stencila/thema@2/dist/themes/elife/index.js" type="text/javascript"></script> <script src="https://unpkg.com/@stencila/components@<=1/dist/stencila-components/stencila-components.esm.js" type="module"></script> <script src="https://unpkg.com/@stencila/components@<=1/dist/stencila-components/stencila-components.js" type="text/javascript" nomodule=""></script> </head> <body> <main role="main"> <article itemscope="" itemtype="http://schema.org/Article" data-itemscope="root"> <h1 itemprop="headline">Evolution of C4 photosynthesis predicted by constraint-based modelling</h1> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Evolution%20of%20C4%20photosynthesis%20predicted%20by%20constraint-based%20modelling"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="Mary-Ann Blätke"><span data-itemprop="givenNames"><span itemprop="givenName">Mary-Ann</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Blätke</span></span><span data-itemprop="emails"><a itemprop="email" href="mailto:blaetke@ipk-gatersleben.de">blaetke@ipk-gatersleben.de</a></span><span data-itemprop="affiliations"><a itemprop="affiliation" href="#author-organization-1">1</a></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="Andrea Bräutigam"><span data-itemprop="givenNames"><span itemprop="givenName">Andrea</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Bräutigam</span></span><span data-itemprop="affiliations"><a itemprop="affiliation" href="#author-organization-1">1</a><a itemprop="affiliation" href="#author-organization-2">2</a></span> </li> </ol> <ol data-itemprop="affiliations"> <li itemscope="" itemtype="http://schema.org/Organization" itemid="#author-organization-1" id="author-organization-1"><span itemprop="name">Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)</span><address itemscope="" itemtype="http://schema.org/PostalAddress" itemprop="address"><span itemprop="addressLocality">Tübingen</span><span itemprop="addressCountry">Germany</span></address></li> <li itemscope="" itemtype="http://schema.org/Organization" itemid="#author-organization-2" id="author-organization-2"><span itemprop="name">Computational Biology, Faculty of Biology, Bielefeld University, Universitätsstraße</span><address itemscope="" itemtype="http://schema.org/PostalAddress" itemprop="address"><span itemprop="addressLocality">Bielefeld</span><span itemprop="addressCountry">Germany</span></address></li> </ol><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span><time itemprop="datePublished" datetime="2019-12-04">2019-12-04</time> <ul data-itemprop="genre"> <li itemprop="genre">Research Article</li> </ul> <ul data-itemprop="about"> <li itemscope="" itemtype="http://schema.org/DefinedTerm" itemprop="about"><span itemprop="name">Computational and Systems Biology</span></li> <li itemscope="" itemtype="http://schema.org/DefinedTerm" itemprop="about"><span itemprop="name">Plant Biology</span></li> </ul> <ul data-itemprop="keywords"> <li itemprop="keywords">metabolic networks</li> <li itemprop="keywords">constraint-based model</li> <li itemprop="keywords">C4 photosynthesis</li> <li itemprop="keywords">model evolution</li> <li itemprop="keywords">flux balance analysis</li> <li itemprop="keywords">None</li> </ul> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/publisher-id"><span itemprop="name">publisher-id</span><span itemprop="value" data-itemtype="http://schema.org/Number">49305</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"> <span itemprop="name">doi</span><span itemprop="value">10.7554/eLife.49305</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/elocation-id"><span itemprop="name">elocation-id</span><span itemprop="value">e49305</span> </li> </ul> <section data-itemprop="description"> <h2 data-itemtype="http://schema.stenci.la/Heading">Abstract</h2> <meta itemprop="description" content="Constraint-based modelling (CBM) is a powerful tool for the analysis of evolutionary trajectories. Evolution, especially evolution in the distant past, is not easily accessible to laboratory experimentation. Modelling can provide a window into evolutionary processes by allowing the examination of selective pressures which lead to particular optimal solutions in the model. To study the evolution of C4 photosynthesis from a ground state of C3 photosynthesis, we initially construct a C3 model. After duplication into two cells to reflect typical C4 leaf architecture, we allow the model to predict the optimal metabolic solution under various conditions. The model thus identifies resource limitation in conjunction with high photorespiratory flux as a selective pressure relevant to the evolution of C4. It also predicts that light availability and distribution play a role in guiding the evolutionary choice of possible decarboxylation enzymes. The data shows evolutionary CBM in eukaryotes predicts molecular evolution with precision."> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">Constraint-based modelling (CBM) is a powerful tool for the analysis of evolutionary trajectories. Evolution, especially evolution in the distant past, is not easily accessible to laboratory experimentation. Modelling can provide a window into evolutionary processes by allowing the examination of selective pressures which lead to particular optimal solutions in the model. To study the evolution of C4 photosynthesis from a ground state of C3 photosynthesis, we initially construct a C3 model. After duplication into two cells to reflect typical C4 leaf architecture, we allow the model to predict the optimal metabolic solution under various conditions. The model thus identifies resource limitation in conjunction with high photorespiratory flux as a selective pressure relevant to the evolution of C4. It also predicts that light availability and distribution play a role in guiding the evolutionary choice of possible decarboxylation enzymes. The data shows evolutionary CBM in eukaryotes predicts molecular evolution with precision.</p> </section> <h2 itemscope="" itemtype="http://schema.stenci.la/Heading" id="introduction">Introduction </h2> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">Identifying specific evolutionary trajectories and modelling the outcome of adaptive strategies at the molecular levels is a major challenge in evolutionary systems biology <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib55"><span>55</span><span>Papp et al.</span><span>2011</span></a></cite>. The evolution of novel metabolic pathways from existing parts may be predicted using constraint-based modelling (CBM) <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib52"><span>52</span><span>Orth et al.</span><span>2010</span></a></cite>. In CBM, selective pressures are coded via the objective functions for which the model is optimised. The factors which constrain evolution are integrated into the models via changes in model inputs or outputs and via flux constraints. We hypothesised that the evolution of the agriculturally important trait of C4 photosynthesis is accessible to CBM. </p> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">C4 photosynthesis evolved independently in at least 67 independent origins in the plant kingdom <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib65"><span>65</span><span>Scheben et al.</span><span>2017</span></a></cite> and it allows colonisation of marginal habitats <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib63"><span>63</span><span>Sage et al.</span><span>2012</span></a></cite> and high biomass production in annuals such as crops <span itemscope="" itemtype="http://schema.stenci.la/CiteGroup"><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib62"><span>62</span><span>Sage</span><span>2004</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib23"><span>23</span><span>Edwards et al.</span><span>2010</span></a></cite></span>. The C4 cycle acts as a biochemical pump which enriches the CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> concentration at the site of Rubisco to overcome a major limitation of carbon fixation <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib62"><span>62</span><span>Sage</span><span>2004</span></a></cite>. Enrichment is beneficial because Rubisco, the carbon fixation enzyme, can react productively with CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> and form two molecules of 3-PGA, but it also reacts with O<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> and produces 2-phosphoglycolate which requires detoxification by photorespiration <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib51"><span>51</span><span>Ogren and Bowes</span><span>1971</span></a></cite>. The ratio between both reactions is determined by the enzyme specificity towards CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub>, by the temperature, and the concentrations of both reactants, which in turn is modulated by stresses such as drought and pathogen load. Evolution of Rubisco itself is constrained since any increase in specificity is paid for by a reduction in speed <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib73"><span>73</span><span>Spreitzer and Salvucci</span><span>2002</span></a></cite>. Lower speeds most likely cause maladaptivity since Rubisco is a comparatively slow enzyme and can comprise up to 50% of the total leaf protein <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib24"><span>24</span><span>Ellis</span><span>1979</span></a></cite>. In the C4 cycle, phosphoenolpyruvate carboxylase affixes CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> to a C3 acid, phosphoenolpyruvate (PEP), forming a C4 acid, oxaloacetate (OAA). After stabilisation of the resulting C4 acid by reduction to malate or transamination to aspartate, it is transferred to the site of Rubisco and decarboxylated by one of three possible decarboxylation enzymes, NADP-dependent malic enzyme (NADP-ME), NAD-dependent malic enzyme (NAD-ME), or PEP carboxykinase (PEP-CK) <span itemscope="" itemtype="http://schema.stenci.la/CiteGroup"><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib30"><span>30</span><span>Hatch</span><span>1987</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib67"><span>67</span><span>Schlüter et al.</span><span>2016</span></a></cite></span>. Species such as corn (<em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Zea mays</em>) <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib57"><span>57</span><span>Pick et al.</span><span>2011</span></a></cite> and great millet (<em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Sorghum bicolor</em>) <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib20"><span>20</span><span>Döring et al.</span><span>2016</span></a></cite> use NADP-ME, species like common millet (<em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Panicum miliaceum</em>) <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib30"><span>30</span><span>Hatch</span><span>1987</span></a></cite> and African spinach (<em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Gynandropsis gynandra</em>) <span itemscope="" itemtype="http://schema.stenci.la/CiteGroup"><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib25"><span>25</span><span>Feodorova et al.</span><span>2010</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib82"><span>82</span><span>Voznesenskaya et al.</span><span>2007</span></a></cite></span> use NAD-ME and species such as guinea grass (<em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Panicum maximum</em>) <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib12"><span>12</span><span>Bräutigam et al.</span><span>2014</span></a></cite> use mainly PEP-CK with the evolutionary constraints leading to one or the other enzyme unknown. Mixed forms are only known to occur between a malic enzyme and PEP-CK but not between both malic enzymes <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib83"><span>83</span><span>Wang et al.</span><span>2014</span></a></cite>. After decarboxylation, the C3 acid diffuses back to the site of phosphoenolpyruvate carboxylase (PEPC) and is recycled for another C4 cycle by pyruvate phosphate dikinase (PPDK) <span itemscope="" itemtype="http://schema.stenci.la/CiteGroup"><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib30"><span>30</span><span>Hatch</span><span>1987</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib67"><span>67</span><span>Schlüter et al.</span><span>2016</span></a></cite></span>. All the enzymes involved in the C4 cycle are also present in C3 plants <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib4"><span>4</span><span>Aubry et al.</span><span>2011</span></a></cite>. In its most typical form, this C4 cycle is distributed between different cell types in a leaf in an arrangement called Kranz anatomy <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib29"><span>29</span><span>Haberlandt and Engelmann</span><span>1904</span></a></cite>. Initial carbon fixation by PEPC occurs in the mesophyll cell, the outer layer of photosynthetic tissue. The secondary fixation by Rubisco after decarboxylation occurs in an inner layer of photosynthetic tissue, the bundle sheath which in turn surrounds the veins. Both cells are connected by plasmodesmata which are pores with limited transfer specificity between cells. A model which may test possible carbon fixation pathways at the molecular level thus requires two cell architectures connected by transport processes <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib15"><span>15</span><span>Bräutigam and Weber</span><span>2010</span></a></cite>.</p> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">CBM of genome-scale or close to it are well suited to study evolution (summarised in <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib55"><span>55</span><span>Papp et al.</span><span>2011</span></a></cite>). Evolution of different metabolic modes from a ground state, the metabolism of <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Escherichia coli</em>, such as glycerol usage <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib39"><span>39</span><span>Lewis et al.</span><span>2010</span></a></cite> or endosymbiotic metabolism <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib54"><span>54</span><span>Pál et al.</span><span>2006</span></a></cite> have been successfully predicted. Metabolic maps of eukaryotic metabolism are of higher complexity compared to bacteria since they require information about intracellular compartmentation and intracellular transport <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib21"><span>21</span><span>Duarte</span><span>2004</span></a></cite> and may require multicellular approaches. In plants, aspects of complex metabolic pathways, such as the energetics of CAM photosynthesis <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib17"><span>17</span><span>Cheung et al.</span><span>2014</span></a></cite>, and fluxes in C3 and C4 metabolism <span itemscope="" itemtype="http://schema.stenci.la/CiteGroup"><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib11"><span>11</span><span>Boyle and Morgan</span><span>2009</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib28"><span>28</span><span>Gomes de Oliveira Dal’Molin et al.</span><span>2011</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib19"><span>19</span><span>de Oliveira Dal'Molin et al.</span><span>2010</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib2"><span>2</span><span>Arnold and Nikoloski</span><span>2014</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib64"><span>64</span><span>Saha et al.</span><span>2011</span></a></cite></span> have been elucidated with genome scale models. The C4 cycle is not predicted by these current C4 models unless the C4 cycle is forced by constraints <span itemscope="" itemtype="http://schema.stenci.la/CiteGroup"><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib28"><span>28</span><span>Gomes de Oliveira Dal’Molin et al.</span><span>2011</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib47"><span>47</span><span>Mallmann et al.</span><span>2014</span></a></cite></span>. In the C4GEM model, the fluxes representing the C4 cycle are a priori constrained to the cell types <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib28"><span>28</span><span>Gomes de Oliveira Dal’Molin et al.</span><span>2011</span></a></cite>, and in the Mallmann model, the C4 fluxes are induced by activating flux through PEPC <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib47"><span>47</span><span>Mallmann et al.</span><span>2014</span></a></cite>. Models in which specific a priori constraints activated C4 were successfully used to study metabolism under conditions of photosynthesis, photorespiration, and respiration <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib64"><span>64</span><span>Saha et al.</span><span>2011</span></a></cite> and to study N-assimilation under varying conditions <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib71"><span>71</span><span>Simons et al.</span><span>2013</span></a></cite>. However, they are incapable of testing under which conditions the pathway may evolve.</p> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">Schematic models suggest that the C4 cycle evolves from its ancestral metabolic state C3 photosynthesis along a sequence of stages (summarised in <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib62"><span>62</span><span>Sage</span><span>2004</span></a></cite>; <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib14"><span>14</span><span>Bräutigam and Gowik</span><span>2016</span></a></cite>). In the presence of tight vein spacing and of photosynthetically active bundle sheath cells (i.e. Kranz anatomy), a key intermediate in which the process of photorespiration is divided between cell types is thought to evolve <span itemscope="" itemtype="http://schema.stenci.la/CiteGroup"><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib48"><span>48</span><span>Monson</span><span>1999</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib63"><span>63</span><span>Sage et al.</span><span>2012</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib31"><span>31</span><span>Heckmann et al.</span><span>2013</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib6"><span>6</span><span>Bauwe</span><span>2010</span></a></cite></span>. The metabolic fluxes in this intermediate suggest an immediate path towards C4 photosynthesis <span itemscope="" itemtype="http://schema.stenci.la/CiteGroup"><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib47"><span>47</span><span>Mallmann et al.</span><span>2014</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib14"><span>14</span><span>Bräutigam and Gowik</span><span>2016</span></a></cite></span>. <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib31"><span>31</span><span>Heckmann et al.</span><span>2013</span></a></cite> built a kinetic model in which the complex C4 cycle was represented by a single enzyme, PEPC. Assuming carbon assimilation as a proxy for fitness, the model showed that the evolution from a C3 progenitor species with Kranz-type anatomy towards C4 photosynthesis occurs in modular, individually adaptive steps on a Mount Fuji fitness landscape. It is frequently assumed that evolution of C4 photosynthesis requires water limitation <span itemscope="" itemtype="http://schema.stenci.la/CiteGroup"><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib14"><span>14</span><span>Bräutigam and Gowik</span><span>2016</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib31"><span>31</span><span>Heckmann et al.</span><span>2013</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib47"><span>47</span><span>Mallmann et al.</span><span>2014</span></a></cite></span>. However, ecophysiological research showed that C4 can likely evolve in wet habitats <span itemscope="" itemtype="http://schema.stenci.la/CiteGroup"><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib53"><span>53</span><span>Osborne and Freckleton</span><span>2009</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib44"><span>44</span><span>Lundgren and Christin</span><span>2017</span></a></cite></span>. CBM presents a possible avenue to study the evolution of C4 photosynthesis including its metabolic complexity <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">in silico</em>.</p> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">In this study, we establish a generic two-celled, constraint-based model starting from the <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Arabidopsis</em> core model <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib2"><span>2</span><span>Arnold and Nikoloski</span><span>2014</span></a></cite>. We test under which conditions and constraints C4 photosynthesis is predicted as the optimal solution. Finally, we test which constraints result in the prediction of the particular C4 modes with their different decarboxylation enzymes. In the process, we demonstrate that evolution is predictable at the molecular level in an eukaryotic system and define the selective pressures and limitations guiding the 'choice' of metabolic flux.</p> <h2 itemscope="" itemtype="http://schema.stenci.la/Heading" id="materials-and-methods"> Materials and methods</h2> <h3 itemscope="" itemtype="http://schema.stenci.la/Heading" id="flux-balance-analysis">Flux Balance Analysis</h3> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">Flux balance analysis (FBA) is a CBM approach <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib52"><span>52</span><span>Orth et al.</span><span>2010</span></a></cite> to investigate the steady-state behaviour of a metabolic network defined by its stoichiometric matrix <span itemscope="" itemtype="http://schema.stenci.la/MathFragment"><span class="mjx-chtml"><span class="mjx-math" aria-label="S"><span class="mjx-mrow" aria-hidden="true"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.519em; padding-bottom: 0.298em; padding-right: 0.032em;">S</span></span></span></span></span></span>. By employing linear programming, FBA allows computing an optimised flux distribution that minimises and/or maximises the synthesis and/or consumption rate of one specific metabolite or a combination of various metabolites. Next to the steady-state assumption and stoichiometric matrix <span itemscope="" itemtype="http://schema.stenci.la/MathFragment"><span class="mjx-chtml"><span class="mjx-math" aria-label="S"><span class="mjx-mrow" aria-hidden="true"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.519em; padding-bottom: 0.298em; padding-right: 0.032em;">S</span></span></span></span></span></span>, FBA relies on the definition of the reaction directionality and reversibility, denoted by the lower bound <span itemscope="" itemtype="http://schema.stenci.la/MathFragment"><span class="mjx-chtml"><span class="mjx-math" aria-label="{v}_{min}"><span class="mjx-mrow" aria-hidden="true"><span class="mjx-msubsup"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">v</span></span></span></span></span><span class="mjx-sub" style="font-size: 70.7%; vertical-align: -0.212em; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">m</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">i</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">n</span></span></span></span></span></span></span></span></span></span> and upper bound <span itemscope="" itemtype="http://schema.stenci.la/MathFragment"><span class="mjx-chtml"><span class="mjx-math" aria-label="{v}_{max}"><span class="mjx-mrow" aria-hidden="true"><span class="mjx-msubsup"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">v</span></span></span></span></span><span class="mjx-sub" style="font-size: 70.7%; vertical-align: -0.212em; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">m</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">a</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">x</span></span></span></span></span></span></span></span></span></span> , as well as the definition of an objective function <span itemscope="" itemtype="http://schema.stenci.la/MathFragment"><span class="mjx-chtml"><span class="mjx-math" aria-label="z"><span class="mjx-mrow" aria-hidden="true"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em; padding-right: 0.003em;">z</span></span></span></span></span></span>. The objective function <span itemscope="" itemtype="http://schema.stenci.la/MathFragment"><span class="mjx-chtml"><span class="mjx-math" aria-label="z"><span class="mjx-mrow" aria-hidden="true"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em; padding-right: 0.003em;">z</span></span></span></span></span></span> defines a flux distribution <span itemscope="" itemtype="http://schema.stenci.la/MathFragment"><span class="mjx-chtml"><span class="mjx-math" aria-label="v"><span class="mjx-mrow" aria-hidden="true"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">v</span></span></span></span></span></span>, with respect to an objective <span itemscope="" itemtype="http://schema.stenci.la/MathFragment"><span class="mjx-chtml"><span class="mjx-math" aria-label="c"><span class="mjx-mrow" aria-hidden="true"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">c</span></span></span></span></span></span>. </p><span itemscope="" itemtype="http://schema.stenci.la/MathBlock"><span class="mjx-chtml MJXc-display" style="text-align: center;"><span class="mjx-math" aria-label="{\displaystyle \begin{array}{ll}\text{min/max}& {z}_{{}_{FBA}}={c}^{T}v\\ \text{s.t.}\\ & S\cdot v=0\\ & {v}_{min}\le v\le {v}_{max}\end{array}}"><span class="mjx-mrow" aria-hidden="true"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mstyle"><span class="mjx-mrow"><span class="mjx-mtable" style="vertical-align: -2.455em; padding: 0px 0.167em;"><span class="mjx-table"><span class="mjx-mtr" style="height: 1.411em;"><span class="mjx-mtd" style="padding: 0px 0.5em 0px 0px; text-align: left; width: 4.028em;"><span class="mjx-mrow" style="margin-top: -0.141em;"><span class="mjx-mtext"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.446em; padding-bottom: 0.593em;">min/max</span></span><span class="mjx-strut"></span></span></span><span class="mjx-mtd" style="padding: 0px 0px 0px 0.5em; text-align: left; width: 6.881em;"><span class="mjx-mrow" style="margin-top: -0.141em;"><span class="mjx-msubsup"><span class="mjx-base" style="margin-right: -0.003em;"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em; padding-right: 0.003em;">z</span></span></span></span></span><span class="mjx-sub" style="font-size: 70.7%; vertical-align: -0.212em; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-msubsup"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"></span></span></span><span class="mjx-sub" style="font-size: 83.3%; vertical-align: -0.317em; padding-right: 0.06em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em; padding-right: 0.106em;">F</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">B</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.519em; padding-bottom: 0.298em;">A</span></span></span></span></span></span></span></span></span></span><span class="mjx-mo MJXc-space3"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.077em; padding-bottom: 0.298em;">=</span></span><span class="mjx-msubsup MJXc-space3"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">c</span></span></span></span></span><span class="mjx-sup" style="font-size: 70.7%; vertical-align: 0.513em; padding-left: 0px; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em; padding-right: 0.12em;">T</span></span></span></span></span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">v</span></span><span class="mjx-strut"></span></span></span></span><span class="mjx-mtr" style="height: 1.4em;"><span class="mjx-mtd" style="padding: 0.2em 0.5em 0px 0px; text-align: left;"><span class="mjx-mrow" style="margin-top: -0.2em;"><span class="mjx-mtext"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.298em; padding-bottom: 0.372em;">s.t.</span></span><span class="mjx-strut"></span></span></span><span class="mjx-mtd" style="padding: 0.2em 0px 0px 0.5em; text-align: left;"><span style="margin-top: -0.2em;"></span></span></span><span class="mjx-mtr" style="height: 1.4em;"><span class="mjx-mtd" style="padding: 0.2em 0.5em 0px 0px; text-align: left;"><span class="mjx-mrow" style="margin-top: -0.2em;"><span class="mjx-strut"></span></span></span><span class="mjx-mtd" style="padding: 0.2em 0px 0px 0.5em; text-align: left;"><span class="mjx-mrow" style="margin-top: -0.2em;"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.519em; padding-bottom: 0.298em; padding-right: 0.032em;">S</span></span><span class="mjx-mo MJXc-space2"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.004em; padding-bottom: 0.298em;">⋅</span></span><span class="mjx-mi MJXc-space2"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">v</span></span><span class="mjx-mo MJXc-space3"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.077em; padding-bottom: 0.298em;">=</span></span><span class="mjx-mn MJXc-space3"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.372em; padding-bottom: 0.372em;">0</span></span><span class="mjx-strut"></span></span></span></span><span class="mjx-mtr" style="height: 1.2em;"><span class="mjx-mtd" style="padding: 0.2em 0.5em 0px 0px; text-align: left;"><span class="mjx-mrow" style="margin-top: -0.2em;"><span class="mjx-strut"></span></span></span><span class="mjx-mtd" style="padding: 0.2em 0px 0px 0.5em; text-align: left;"><span class="mjx-mrow" style="margin-top: -0.2em;"><span class="mjx-msubsup"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">v</span></span></span></span></span><span class="mjx-sub" style="font-size: 70.7%; vertical-align: -0.212em; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">m</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">i</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">n</span></span></span></span></span></span><span class="mjx-mo MJXc-space3"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.372em; padding-bottom: 0.446em;">≤</span></span><span class="mjx-mi MJXc-space3"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">v</span></span><span class="mjx-mo MJXc-space3"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.372em; padding-bottom: 0.446em;">≤</span></span><span class="mjx-msubsup MJXc-space3"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">v</span></span></span></span></span><span class="mjx-sub" style="font-size: 70.7%; vertical-align: -0.212em; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">m</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">a</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">x</span></span></span></span></span></span><span class="mjx-strut"></span></span></span></span></span></span></span></span></span></span></span></span></span></span> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">The degeneracy problem, the possible existence of alternate optimal solutions, is one of the major issues of constraint-based optimisation, such as FBA <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib46"><span>46</span><span>Mahadevan and Schilling</span><span>2003</span></a></cite>. To avoid this problem, we use the parsimonious version of FBA (pFBA) <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib39"><span>39</span><span>Lewis et al.</span><span>2010</span></a></cite>. This approach incorporates the flux parsimony as a constraint to find the solution with the minimum absolute flux value among the alternative optima, which is in agreement with the assumption that the cell is evolutionary optimised to allocate a minimum amount of resources to achieve its objective.</p><span itemscope="" itemtype="http://schema.stenci.la/MathBlock"><span class="mjx-chtml MJXc-display" style="text-align: center;"><span class="mjx-math" aria-label="\begin{array}{cc}\text{min/max}\hfill & {z}_{{}_{pFBA}}=\sum \left|{v}_{i}\right|\hfill \\ \text{s.t.}\hfill & \\ & S\cdot v=0\hfill \\ & {v}_{min}\le v\le {v}_{max}\hfill \\ & {c}^{T}v={z}_{{}_{FBA}}\hfill \end{array}"><span class="mjx-mrow" aria-hidden="true"><span class="mjx-mtable" style="vertical-align: -3.288em; padding: 0px 0.167em;"><span class="mjx-table"><span class="mjx-mtr" style="height: 1.466em;"><span class="mjx-mtd" style="padding: 0px 0.5em 0px 0px; text-align: left; width: 4.028em;"><span class="mjx-mrow" style="margin-top: -0.2em;"><span class="mjx-mtext"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.446em; padding-bottom: 0.593em;">min/max</span></span><span class="mjx-strut"></span></span></span><span class="mjx-mtd" style="padding: 0px 0px 0px 0.5em; text-align: left; width: 6.881em;"><span class="mjx-mrow" style="margin-top: -0.2em;"><span class="mjx-msubsup"><span class="mjx-base" style="margin-right: -0.003em;"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em; padding-right: 0.003em;">z</span></span></span></span></span><span class="mjx-sub" style="font-size: 70.7%; vertical-align: -0.212em; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-msubsup"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"></span></span></span><span class="mjx-sub" style="font-size: 83.3%; vertical-align: -0.317em; padding-right: 0.06em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.446em;">p</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em; padding-right: 0.106em;">F</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">B</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.519em; padding-bottom: 0.298em;">A</span></span></span></span></span></span></span></span></span></span><span class="mjx-mo MJXc-space3"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.077em; padding-bottom: 0.298em;">=</span></span><span class="mjx-mo MJXc-space3"><span class="mjx-char MJXc-TeX-size1-R" style="padding-top: 0.519em; padding-bottom: 0.519em;">∑</span></span><span class="mjx-mrow MJXc-space1"><span class="mjx-mo"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.446em; padding-bottom: 0.593em;">|</span></span><span class="mjx-msubsup"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">v</span></span></span></span></span><span class="mjx-sub" style="font-size: 70.7%; vertical-align: -0.212em; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">i</span></span></span></span></span></span><span class="mjx-mo"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.446em; padding-bottom: 0.593em;">|</span></span></span><span class="mjx-strut"></span></span></span></span><span class="mjx-mtr" style="height: 1.4em;"><span class="mjx-mtd" style="padding: 0.2em 0.5em 0px 0px; text-align: left;"><span class="mjx-mrow" style="margin-top: -0.2em;"><span class="mjx-mtext"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.298em; padding-bottom: 0.372em;">s.t.</span></span><span class="mjx-strut"></span></span></span><span class="mjx-mtd" style="padding: 0.2em 0px 0px 0.5em;"><span class="mjx-mrow" style="margin-top: -0.2em;"><span class="mjx-strut"></span></span></span></span><span class="mjx-mtr" style="height: 1.4em;"><span class="mjx-mtd" style="padding: 0.2em 0.5em 0px 0px;"><span class="mjx-mrow" style="margin-top: -0.2em;"><span class="mjx-strut"></span></span></span><span class="mjx-mtd" style="padding: 0.2em 0px 0px 0.5em; text-align: left;"><span class="mjx-mrow" style="margin-top: -0.2em;"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.519em; padding-bottom: 0.298em; padding-right: 0.032em;">S</span></span><span class="mjx-mo MJXc-space2"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.004em; padding-bottom: 0.298em;">⋅</span></span><span class="mjx-mi MJXc-space2"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">v</span></span><span class="mjx-mo MJXc-space3"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.077em; padding-bottom: 0.298em;">=</span></span><span class="mjx-mn MJXc-space3"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.372em; padding-bottom: 0.372em;">0</span></span><span class="mjx-strut"></span></span></span></span><span class="mjx-mtr" style="height: 1.4em;"><span class="mjx-mtd" style="padding: 0.2em 0.5em 0px 0px;"><span class="mjx-mrow" style="margin-top: -0.2em;"><span class="mjx-strut"></span></span></span><span class="mjx-mtd" style="padding: 0.2em 0px 0px 0.5em; text-align: left;"><span class="mjx-mrow" style="margin-top: -0.2em;"><span class="mjx-msubsup"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">v</span></span></span></span></span><span class="mjx-sub" style="font-size: 70.7%; vertical-align: -0.212em; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">m</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">i</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">n</span></span></span></span></span></span><span class="mjx-mo MJXc-space3"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.372em; padding-bottom: 0.446em;">≤</span></span><span class="mjx-mi MJXc-space3"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">v</span></span><span class="mjx-mo MJXc-space3"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.372em; padding-bottom: 0.446em;">≤</span></span><span class="mjx-msubsup MJXc-space3"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">v</span></span></span></span></span><span class="mjx-sub" style="font-size: 70.7%; vertical-align: -0.212em; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">m</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">a</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">x</span></span></span></span></span></span><span class="mjx-strut"></span></span></span></span><span class="mjx-mtr" style="height: 1.411em;"><span class="mjx-mtd" style="padding: 0.2em 0.5em 0px 0px;"><span class="mjx-mrow" style="margin-top: -0.141em;"><span class="mjx-strut"></span></span></span><span class="mjx-mtd" style="padding: 0.2em 0px 0px 0.5em; text-align: left;"><span class="mjx-mrow" style="margin-top: -0.141em;"><span class="mjx-msubsup"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">c</span></span></span></span></span><span class="mjx-sup" style="font-size: 70.7%; vertical-align: 0.513em; padding-left: 0px; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em; padding-right: 0.12em;">T</span></span></span></span></span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">v</span></span><span class="mjx-mo MJXc-space3"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.077em; padding-bottom: 0.298em;">=</span></span><span class="mjx-msubsup MJXc-space3"><span class="mjx-base" style="margin-right: -0.003em;"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em; padding-right: 0.003em;">z</span></span></span></span></span><span class="mjx-sub" style="font-size: 70.7%; vertical-align: -0.212em; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-msubsup"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"></span></span></span><span class="mjx-sub" style="font-size: 83.3%; vertical-align: -0.317em; padding-right: 0.06em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em; padding-right: 0.106em;">F</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">B</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.519em; padding-bottom: 0.298em;">A</span></span></span></span></span></span></span></span></span></span><span class="mjx-strut"></span></span></span></span></span></span></span></span></span></span> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">All FBA experiments in this study employ pFBA and are performed using the cobrapy module in a python 2.7 environment run on a personal computer (macOS Sierra, 4 GHz Intel Core i7, 32 GB 1867 MHz DDR3). All FBA experiments are available as jupyter notebooks in the supplementary material and can also be accessed and executed from the GitHub repository <a href="https://github.com/ma-blaetke/CBM_C3_C4_Metabolism" itemscope="" itemtype="http://schema.stenci.la/Link">https://github.com/ma-blaetke/CBM_C3_C4_Metabolism</a> (<cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib10"><span>10</span><span>Blätke</span><span>2019</span></a></cite>; copy archived at <a href="https://github.com/elifesciences-publications/CBM_C3_C4_Metabolism" itemscope="" itemtype="http://schema.stenci.la/Link">https://github.com/elifesciences-publications/CBM_C3_C4_Metabolism</a>). </p> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="1" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>##### Import Modules ##### ## numpy import numpy as np ## pandas import pandas as pd pd.set_option('display.max_rows', None) pd.set_option('display.max_columns', None) pd.set_option('display.width', None) pd.set_option('display.max_colwidth', None) ## plotly import plotly import plotly.graph_objects as go from plotly.subplots import make_subplots ## cobra import cobra ## escher from escher import Builder ## ipython HTML display from IPython.display import HTML ## goatools from goatools import obo_parser ## tqdm from tqdm.notebook import trange, tqdm ## string import string print(f"Code Cell 1: Import Python Modules")</code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 1: Import Python Modules </code></pre> </figure> </stencila-code-chunk> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="2" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>print(f"Code Cell 2: Set Parameters") ##### Set Parameters ##### inf = float(1e6) </code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 2: Set Parameters </code></pre> </figure> </stencila-code-chunk> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="3" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>print(f"Code Cell 3: Define Functions") ##### Define Functions - SBML Model and FBA ##### ## Load SBML model def load_sbml_model(): ''' Return cobra model Parameters: Returns: cobra_model (cobra.model): cobra model of specified sbm file ''' sbml_file = 'elife-49305.ipython.src/2018-23-05-mb-genC3.sbml' cobra_model = cobra.io.sbml.read_sbml_model(sbml_file) return cobra_model ## Add reactions to model def add_rxn(name, D_mets, model, rev=True): ''' Add new reaction to cobra model Parameters: name (str): short name/id of reaction D_mets (dict): dictionary of metabolites and their stoichimetric coeffcients attending at reaction model (cobra.model): cobra model to add the reaction rev (bool): reversiblity of reaction (default: True) Returns: ''' r_name = name r_obj = cobra.Reaction(rname) r_obj.name = r_name r_obj.id = r_name model.add_reaction(r_obj) r_obj.add_metabolites(D_mets) r_obj.objective_coefficient = 0 r_obj.bounds = (-inf,inf) if rev else (0,inf) ## Set flux of a reaction to a fixed value def set_fixed_flux(r_id, val, model): ''' Set flux of reaction to a fixed value Parameters: r_id (str): reaction id val (float): flux value model (cobra.model): cobra model to add the reaction Returns: ''' r_obj = model.reactions.get_by_id(r_id) r_obj.bounds = (val,val) ## Set lower and upper flux bound of a reaction def set_bounds(r_id, val_tuple, model): ''' Set flux bounds of reaction Parameters: r_id (str): reaction id val_tuple (tuple): (lower_bound, upper_bound) model (cobra.model): cobra model to add the reaction Returns: ''' r_obj = model.reactions.get_by_id(r_id) r_obj.bounds = val_tuple ## Set flux ratio for two reactions def set_fixed_flux_ratio(r_dict, name, model): ''' Set flux ratio of two reactions Parameters: r_dict (dict): rdictionary with two keys (reaction ids) and their proportion in the ratio {r_id1: prop1, r_ids2: prop2} name (str): name of constraint model (cobra.model): cobra model to add the reaction Returns: ''' if len(r_dict) == 2: r_id1 = list(r_dict.keys())[0] r_obj1 = model.reactions.get_by_id(r_id1) r_v1 = list(r_dict.values())[0] r_id2 = list(r_dict.keys())[1] r_obj2 = model.reactions.get_by_id(r_id2) r_v2 = list(r_dict.values())[1] const = model.problem.Constraint( float(r_v1) * r_obj2.flux_expression - float(r_v2) * r_obj1.flux_expression, lb = 0.0, ub = 0.0, name = name) model.add_cons_vars(const) return const</code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 3: Define Functions </code></pre> </figure> </stencila-code-chunk> <h3 itemscope="" itemtype="http://schema.stenci.la/Heading" id="generic-model-for-c3-metabolism">Generic model for C3 metabolism</h3> <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="metabolic-model">Metabolic model</h4> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">The generic model representing the metabolism of a mesophyll cell of a mature photosynthetically active C3 leaf, further on called <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">one-cell</em> model, is based on the <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Arabidopsis</em> core model <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib2"><span>2</span><span>Arnold and Nikoloski</span><span>2014</span></a></cite>. The model is compartmentalised into cytosol (c), chloroplast (h), mitochondria (m), and peroxisome (p). Each reaction in the <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Arabidopsis</em> core model <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib2"><span>2</span><span>Arnold and Nikoloski</span><span>2014</span></a></cite> was compared with the corresponding entry in AraCyc <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib49"><span>49</span><span>Mueller et al.</span><span>2003</span></a></cite>. Based on the given information, we corrected co-factors, gene associations, enzyme commission numbers and reversibility (information from BRENDA <cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib68"><span>68</span><span>Schomburg et al.</span><span>2002</span></a></cite> were included). The gene associations and their GO terms <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib3"><span>3</span><span>Ashburner et al.</span><span>2000</span></a></cite> of the cellular components were used to correct the location of reactions. Major additions to the model are the cyclic electron flow <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib70"><span>70</span><span>Shikanai</span><span>2016</span></a></cite>, alternative oxidases in mitochondria and chloroplast <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib81"><span>81</span><span>Vishwakarma et al.</span><span>2015</span></a></cite>, as well as several transport processes between the compartments and the cytosol <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib42"><span>42</span><span>Linka and Weber</span><span>2010</span></a></cite>. NAD-dependent dehydrogenase to oxidise malate is present in all compartments <span itemscope="" itemtype="http://schema.stenci.la/CiteGroup"><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib27"><span>27</span><span>Gietl</span><span>1992</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib9"><span>9</span><span>Berkemeyer et al.</span><span>1998</span></a></cite></span>, which excludes the interconversion of NAD and NADP by cycles through the nitrate reductase present in the <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Arabidopsis</em> core model. Correctly defining the protonation state of the metabolites in the various cellular compartments is a general drawback of metabolic models due to the lack of knowledge in that area. This issue mainly affects biochemical reactions and transport reactions involving protons. We added a sink/source reaction for protons in the form:</p><span itemscope="" itemtype="http://schema.stenci.la/MathBlock"><span class="mjx-chtml MJXc-display" style="text-align: center;"><span class="mjx-math" aria-label="\begin{array}{cc}\leftrightarrow H\mathrm{\_}\{x\}\hfill & x=c,h,m,p\hfill \end{array}"><span class="mjx-mrow" aria-hidden="true"><span class="mjx-mtable" style="vertical-align: -0.288em; padding: 0px 0.167em;"><span class="mjx-table"><span class="mjx-mtr" style="height: 1.075em;"><span class="mjx-mtd" style="padding: 0px 0.5em 0px 0px; text-align: left; width: 4.238em;"><span class="mjx-mrow" style="margin-top: -0.2em;"><span class="mjx-mo"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.225em; padding-bottom: 0.372em;">↔</span></span><span class="mjx-mi MJXc-space3"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em; padding-right: 0.057em;">H</span></span><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-main-R" style="margin-top: -0.291em; padding-bottom: 0.372em;">_</span></span></span></span><span class="mjx-mo"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.446em; padding-bottom: 0.593em;">{</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">x</span></span><span class="mjx-mo"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.446em; padding-bottom: 0.593em;">}</span></span><span class="mjx-strut"></span></span></span><span class="mjx-mtd" style="padding: 0px 0px 0px 0.5em; text-align: left; width: 5.63em;"><span class="mjx-mrow" style="margin-top: -0.2em;"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">x</span></span><span class="mjx-mo MJXc-space3"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.077em; padding-bottom: 0.298em;">=</span></span><span class="mjx-mi MJXc-space3"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">c</span></span><span class="mjx-mo"><span class="mjx-char MJXc-TeX-main-R" style="margin-top: -0.144em; padding-bottom: 0.519em;">,</span></span><span class="mjx-mi MJXc-space1"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">h</span></span><span class="mjx-mo"><span class="mjx-char MJXc-TeX-main-R" style="margin-top: -0.144em; padding-bottom: 0.519em;">,</span></span><span class="mjx-mi MJXc-space1"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">m</span></span><span class="mjx-mo"><span class="mjx-char MJXc-TeX-main-R" style="margin-top: -0.144em; padding-bottom: 0.519em;">,</span></span><span class="mjx-mi MJXc-space1"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.446em;">p</span></span><span class="mjx-strut"></span></span></span></span></span></span></span></span></span></span> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">to all compartments to prevent futile fluxes of protons and other metabolites coupled through the proton transport. The curated <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">one-cell</em> model is provided in <a href="#fig1sdata1" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 1—source data 1</a>.</p> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="4" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>print(f"Code Cell 4: Load Metabolic Model of C3 Photosynthesis in Arabidposis thaliana") ##### Load model ##### c3_model = load_sbml_model() # Model summary c3_num_mets = len(c3_model.metabolites) c3_num_rxn = len(c3_model.reactions) c3_num_transport_rxn = len(c3_model.reactions.query(lambda rxn: (rxn.id.startswith('Tr_')))) c3_num_export_rxn = len(c3_model.reactions.query(lambda rxn: (rxn.id.startswith('Ex_')))) c3_num_import_rxn = len(c3_model.reactions.query(lambda rxn: (rxn.id.startswith('Im_')))) df_c3_model_summary = pd.DataFrame([c3_num_mets, c3_num_rxn, c3_num_transport_rxn, c3_num_export_rxn, c3_num_import_rxn], index=['total metabolites','total reactions','transport reactions', 'export reactions' ,'import reactions'], columns=['Count']) df_c3_model_summary</code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 4: Load Metabolic Model of C3 Photosynthesis in Arabidposis thaliana </code></pre> <table itemscope="" itemtype="http://schema.org/Table"> <thead> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <th itemscope="" itemtype="http://schema.stenci.la/TableCell"></th> <th itemscope="" itemtype="http://schema.stenci.la/TableCell">Count</th> </tr> </thead> <tbody> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">total metabolites </td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">413</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">total reactions</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">572</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">transport reactions </td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">139</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">export reactions </td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">90</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">import reactions </td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">8</span></td> </tr> </tbody> </table> </figure> </stencila-code-chunk> <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="import">Import</h4> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="5" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>print(f"Code Cell 5: Add Constraints on Metabolite Input") ##### Add constraints on metabolite uptake ##### ## CONSTRAINT: CO2 uptake rate in C3 plants is about 20 μmol/(m2*s) f_c3_CO2 = 20 #[μmol/(m2*s)] set_bounds('Im_CO2', (0, f_c3_CO2), c3_model) ## CONSTRAINT: max. photon consumption 1000 μE f_c3_hnu = 1000 #[μE] set_bounds('Im_hnu', (0, f_c3_hnu), c3_model) ## CONSTRAINT: Fluxes of other import reactions set_bounds('Im_H2O', (-inf, inf), c3_model) set_bounds('Im_H2S', (0.,0.), c3_model) set_bounds('Im_NH4', (0., 0.), c3_model) set_bounds('Im_NO3', (0., inf), c3_model) set_bounds('Im_Pi', (0., inf), c3_model) set_bounds('Im_SO4', (0., inf), c3_model) set_bounds('Ex_O2', (-inf, inf), c3_model) set_bounds('Ex_Suc', (0., inf), c3_model) set_bounds('Ex_starch', (0., inf), c3_model) set_bounds('Ex_AA', (0., inf), c3_model) </code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 5: Add Constraints on Metabolite Input </code></pre> </figure> </stencila-code-chunk> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">As in <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib2"><span>2</span><span>Arnold and Nikoloski</span><span>2014</span></a></cite>, we assume photoautotrophic growth conditions. Only the import of light, water, CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub>, inorganic phosphate (<span itemscope="" itemtype="http://schema.stenci.la/MathFragment"><span class="mjx-chtml"><span class="mjx-math" aria-label="\mathrm{Pi}"><span class="mjx-mrow" aria-hidden="true"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.372em; padding-bottom: 0.372em;">P</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.372em; padding-bottom: 0.372em;">i</span></span></span></span></span></span></span></span>), nitrate/ammonium, and sulphates/hydrogen sulphide is allowed, compare <a href="#table3" itemscope="" itemtype="http://schema.stenci.la/Link">Table 3</a>. More specifically, we do only allow for nitrate uptake, since it is the main source (80%) of nitrogen in leaves <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib45"><span>45</span><span>Macduff and Bakken</span><span>2003</span></a></cite>. The CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> uptake is limited to <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">f_c3_CO2</code><output slot="output"></output></stencila-code-expression> μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s) <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib37"><span>37</span><span>Lacher</span><span>2003</span></a></cite>. Therefore, the carbon input constrains the model.</p> <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="export">Export</h4> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="6" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>print(f"Code Cell 6: Add Constraints on Metabolite Output") ##### Add constraints on metabolite secretion ##### ## CONSTRAINT: Fluxes of other import reactions set_bounds('Ex_O2', (-inf, inf), c3_model) set_bounds('Ex_Suc', (0., inf), c3_model) set_bounds('Ex_starch', (0., inf), c3_model) set_bounds('Ex_AA', (0., inf), c3_model) ## CONSTRAINT: Output of sucrose : total amino acid r_suc_aa = (2.2, 1.0) const_c3_suc_aa = set_fixed_flux_ratio({'Ex_Suc':r_suc_aa[0],'Ex_AA':r_suc_aa[1]}, 'const_c3_suc_aa', c3_model) ## CONSTRAINT: Output of sucrose : starch r_suc_starch = (1.0, 1.0) const_c3_suc_starch = set_fixed_flux_ratio({'Ex_Suc':r_suc_starch[0],'Ex_starch':r_suc_starch[1]}, 'const_c3_suc_starch', c3_model)</code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 6: Add Constraints on Metabolite Output </code></pre> </figure> </stencila-code-chunk> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">In contrast to <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib2"><span>2</span><span>Arnold and Nikoloski</span><span>2014</span></a></cite>, we focus on mature, fully differentiated and photosynthetic active leaves supporting the growth of the plant through the export of nutrients in the phloem sap, mainly sucrose and amino acids. An output reaction for sucrose <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Ex_Suc</em> is already included in the model. An additional export reaction <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Ex_AA</em> represents the relative proportion of 18 amino acids in the phloem sap of <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Arabidopsis</em> as stoichiometric coefficients in accordance to experimentally measured data from <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib85"><span>85</span><span>Wilkinson and Douglas</span><span>2003</span></a></cite>. The ratio of exported sucrose : total amino acid is estimated to be <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">r_suc_aa[0]</code><output slot="output"></output> </stencila-code-expression> : <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">r_suc_aa[1]</code><output slot="output"></output> </stencila-code-expression><span data-itemtype="http://schema.org/Number">0</span><cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib85"><span>85</span><span>Wilkinson and Douglas</span><span>2003</span></a></cite>. This ratio is included as a flux ratio constraint of the reactions <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Ex_Suc</em> and <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Ex_AA</em>. Furthermore, it is known that the export of sucrose and the formation of starch is approximately the same <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib74"><span>74</span><span>Stitt and Zeeman</span><span>2012</span></a></cite>, which is reflected by the flux ratio constraint <span itemscope="" itemtype="http://schema.stenci.la/MathFragment"><span class="mjx-chtml"><span class="mjx-math" aria-label="{v}_{Ex\mathrm{\_}Suc}:{v}_{Ex\mathrm{\_}starch}"><span class="mjx-mrow" aria-hidden="true"><span class="mjx-msubsup"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">v</span></span></span></span></span><span class="mjx-sub" style="font-size: 70.7%; vertical-align: -0.23em; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em; padding-right: 0.026em;">E</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">x</span></span><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-main-R" style="margin-top: -0.291em; padding-bottom: 0.372em;">_</span></span></span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.519em; padding-bottom: 0.298em; padding-right: 0.032em;">S</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">u</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">c</span></span></span></span></span></span><span class="mjx-mo MJXc-space3"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.151em; padding-bottom: 0.372em;">:</span></span><span class="mjx-msubsup MJXc-space3"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">v</span></span></span></span></span><span class="mjx-sub" style="font-size: 70.7%; vertical-align: -0.219em; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em; padding-right: 0.026em;">E</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">x</span></span><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-main-R" style="margin-top: -0.291em; padding-bottom: 0.372em;">_</span></span></span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">s</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.372em; padding-bottom: 0.298em;">t</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">a</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">r</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">c</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">h</span></span></span></span></span></span></span></span></span></span> = <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">r_suc_starch[0]</code><output slot="output"></output> </stencila-code-expression>:<stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">r_suc_starch[1]</code><output slot="output"></output> </stencila-code-expression>. The model allows for the export of water and oxygen. The flux of all other export reactions is set to 0, see <a href="#table3" itemscope="" itemtype="http://schema.stenci.la/Link">Table 3</a> for a summary.</p> <figure itemscope="" itemtype="http://schema.stenci.la/Figure" id="table3" title="Table 3."> <label data-itemprop="label">Table 3.</label> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="7" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>print(f"Code Cell 7: Create Table on Flux Boundary Constraints of Input and Output Reactions") #### Table 3 #### #{ # "caption": "#### Flux boundary constraints of Im-/export reactions", # "id": "table3", # "label": "Table 3.", # "trusted": true #} index = c3_model.reactions.query(lambda rxn: (rxn.id.startswith('Ex_') or rxn.id.startswith('Im_'))).list_attr('id') lower_bounds = c3_model.reactions.query(lambda rxn: (rxn.id.startswith('Ex_') or rxn.id.startswith('Im_'))).list_attr('lower_bound') upper_bounds = c3_model.reactions.query(lambda rxn: (rxn.id.startswith('Ex_') or rxn.id.startswith('Im_'))).list_attr('upper_bound') cols = ['Lower bound [μmol/(m^2^s)]', 'Upper bound [μmol/(m^2^s)]' ] df_ex_im_rxn_bounds = pd.DataFrame(np.array([lower_bounds, upper_bounds]).T,index=index, columns=cols) df_ex_im_rxn_bounds.index.name = 'Reaction ID' df_ex_im_rxn_bounds.style.applymap(lambda val: 'color: red' if val != 0 else 'color: black')</code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 7: Create Table on Flux Boundary Constraints of Input and Output Reactions </code></pre> <table id="T_b217f_" itemscope="" itemtype="http://schema.org/Table"> <thead> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <th itemscope="" itemtype="http://schema.stenci.la/TableCell"></th> <th itemscope="" itemtype="http://schema.stenci.la/TableCell">Lower bound [μmol/(m^2^s)]</th> <th itemscope="" itemtype="http://schema.stenci.la/TableCell">Upper bound [μmol/(m^2^s)]</th> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <th itemscope="" itemtype="http://schema.stenci.la/TableCell">Reaction ID</th> <th itemscope="" itemtype="http://schema.stenci.la/TableCell"></th> <th itemscope="" itemtype="http://schema.stenci.la/TableCell"></th> </tr> </thead> <tbody> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Im_hnu</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">1000</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Im_CO2</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">20</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Im_H2O</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">-1000000</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">1000000</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Im_Pi</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">1000000</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Im_NO3</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">1000000</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Im_NH4</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Im_SO4</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">1000000</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Im_H2S</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_O2</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">-1000000</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">1000000</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Ala_c</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Ala_h</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Ala_m</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Ala_p</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Arg_c</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Arg_h</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Arg_m</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Arg_p</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Asn_c</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Asn_h</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Asn_m</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Asn_p</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Asp_c</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Asp_h</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Asp_m</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Asp_p</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Cys_c</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Cys_h</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Cys_m</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Cys_p</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Gln_c</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Gln_h</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Gln_m</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Gln_p</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Glu_c</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Glu_h</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Glu_m</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Glu_p</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Gly_c</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Gly_h</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Gly_m</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Gly_p</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_His_c</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_His_h</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_His_m</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_His_p</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Ile_c</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Ile_h</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Ile_m</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Ile_p</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Leu_c</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Leu_h</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Leu_m</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Leu_p</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Lys_c</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Lys_h</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Lys_m</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Lys_p</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Met_c</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Met_h</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Met_m</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Met_p</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Phe_c</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Phe_h</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Phe_m</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Phe_p</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Pro_c</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Pro_h</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Pro_m</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Pro_p</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Ser_c</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Ser_h</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Ser_m</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Ser_p</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Thr_c</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Thr_h</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Thr_m</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Thr_p</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Trp_c</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Trp_h</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Trp_m</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Trp_p</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Tyr_c</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Tyr_h</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Tyr_m</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Tyr_p</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Val_c</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Val_h</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Val_m</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Val_p</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_starch</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">1000000</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Glc</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Frc</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Suc</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">1000000</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_cellulose</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Mas</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_MACP</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_Tre</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Ex_AA</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">1000000</span></td> </tr> </tbody> </table> </figure> </stencila-code-chunk> <figcaption> <h5 itemscope="" itemtype="http://schema.stenci.la/Heading" id="flux-boundary-constraints-of-im-export-reactions">Flux boundary constraints of Im-/export reactions</h5> </figcaption> </figure> <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="additional-constraints"> Additional Constraints</h4> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="8" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>print(f"Code Cell 8: Add Constraints on ATP maintenance costs") ## CONSTRAINT: Maintenance cost atp_cost_L3_m = 0.009111187245501572 #Mitochondria-L3-ATP Cost [µmol*s-1*m-2] atp_cost_L3_h = 0.15270708327974447 #Chloroplast-L3-ATP Cost [µmol*s-1*m-2] atp_cost_L3_p = 0.0076669066992201855 #Peroxisome-L3-ATP Cost [µmol*s-1*m-2] atp_cost_L3_c = 0.042683072918274702 #Cytosl/Other-L3-ATP Cost [µmol*s-1*m-2] set_fixed_flux('NGAM_c',atp_cost_L3_c + atp_cost_L3_p, c3_model) set_fixed_flux('NGAM_m',atp_cost_L3_m, c3_model) set_fixed_flux('NGAM_h',atp_cost_L3_h, c3_model)</code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 8: Add Constraints on ATP maintenance costs </code></pre> </figure> </stencila-code-chunk> <figure itemscope="" itemtype="http://schema.stenci.la/Figure" id="table4" title="Table 4."> <label data-itemprop="label">Table 4.</label> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="9" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>#### Table 4 #### #{ # "caption": "#### Maintenance costs by compartment", # "id": "table4", # "label": "Table 4.", # "trusted": true #} df_maintenance = pd.DataFrame([atp_cost_L3_c,atp_cost_L3_h, atp_cost_L3_m, atp_cost_L3_p], index=['cytosol','chloroplast','mitochondria','peroxisome'], columns=['Flux [μmol/(m^2^s)]']) df_maintenance.index.name = 'Compartment' df_maintenance</code></pre> <figure slot="outputs"> <table itemscope="" itemtype="http://schema.org/Table"> <thead> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <th itemscope="" itemtype="http://schema.stenci.la/TableCell"></th> <th itemscope="" itemtype="http://schema.stenci.la/TableCell">Flux [μmol/(m^2^s)]</th> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <th itemscope="" itemtype="http://schema.stenci.la/TableCell">Compartment</th> <th itemscope="" itemtype="http://schema.stenci.la/TableCell"></th> </tr> </thead> <tbody> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">cytosol</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0.042683</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">chloroplast</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0.152707</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">mitochondria</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0.009111</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">peroxisome</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">0.007667</span></td> </tr> </tbody> </table> </figure> </stencila-code-chunk> <figcaption> <h5 itemscope="" itemtype="http://schema.stenci.la/Heading" id="maintenance-costs-by-compartment">Maintenance costs by compartment</h5> </figcaption> </figure> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">We explicitly include the maintenance costs in our model to cover the amounts of ATP that is used to degradation and re-synthesis proteins for each compartment. <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib40"><span>40</span><span>Li et al.</span><span>2017</span></a></cite> specifies the ATP costs for protein degradation and synthesis of each compartment of a mature <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Arabidopsis</em> leaf. Based on the given data, we were able to calculate the flux rates to constrain the maintenance reactions in each compartment (<a href="#table4" itemscope="" itemtype="http://schema.stenci.la/Link">Table 4</a>).</p> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">The <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">one-cell</em> model contains maintenance reactions only for the cytsol (<em itemscope="" itemtype="http://schema.stenci.la/Emphasis">NGAM_c</em>), chloroplast (<em itemscope="" itemtype="http://schema.stenci.la/Emphasis">NGAM_h</em>) and mitochondria (<em itemscope="" itemtype="http://schema.stenci.la/Emphasis">NGAM_m</em>) in the form:</p> <span itemscope="" itemtype="http://schema.stenci.la/MathBlock"><span class="mjx-chtml MJXc-display" style="text-align: center;"><span class="mjx-math" aria-label="\begin{array}{cc}ATP\mathrm{\_}\{x\}+H2O\mathrm{\_}\{x\}\to ADP\mathrm{\_}\{x\}+H\mathrm{\_}\{x\}+Pi\mathrm{\_}\{x\}\hfill & x=c,h,m\hfill \end{array}"><span class="mjx-mrow" aria-hidden="true"><span class="mjx-mtable" style="vertical-align: -0.288em; padding: 0px 0.167em;"><span class="mjx-table"><span class="mjx-mtr" style="height: 1.075em;"><span class="mjx-mtd" style="padding: 0px 0.5em 0px 0px; text-align: left; width: 24.252em;"><span class="mjx-mrow" style="margin-top: -0.2em;"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.519em; padding-bottom: 0.298em;">A</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em; padding-right: 0.12em;">T</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em; padding-right: 0.109em;">P</span></span><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-main-R" style="margin-top: -0.291em; padding-bottom: 0.372em;">_</span></span></span></span><span class="mjx-mo"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.446em; padding-bottom: 0.593em;">{</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">x</span></span><span class="mjx-mo"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.446em; padding-bottom: 0.593em;">}</span></span><span class="mjx-mo MJXc-space2"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.298em; padding-bottom: 0.446em;">+</span></span><span class="mjx-mi MJXc-space2"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em; padding-right: 0.057em;">H</span></span><span class="mjx-mn"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.372em; padding-bottom: 0.372em;">2</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.519em; padding-bottom: 0.298em;">O</span></span><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-main-R" style="margin-top: -0.291em; padding-bottom: 0.372em;">_</span></span></span></span><span class="mjx-mo"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.446em; padding-bottom: 0.593em;">{</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">x</span></span><span class="mjx-mo"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.446em; padding-bottom: 0.593em;">}</span></span><span class="mjx-mo MJXc-space3"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.225em; padding-bottom: 0.372em;">→</span></span><span class="mjx-mi MJXc-space3"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.519em; padding-bottom: 0.298em;">A</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">D</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em; padding-right: 0.109em;">P</span></span><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-main-R" style="margin-top: -0.291em; padding-bottom: 0.372em;">_</span></span></span></span><span class="mjx-mo"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.446em; padding-bottom: 0.593em;">{</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">x</span></span><span class="mjx-mo"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.446em; padding-bottom: 0.593em;">}</span></span><span class="mjx-mo MJXc-space2"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.298em; padding-bottom: 0.446em;">+</span></span><span class="mjx-mi MJXc-space2"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em; padding-right: 0.057em;">H</span></span><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-main-R" style="margin-top: -0.291em; padding-bottom: 0.372em;">_</span></span></span></span><span class="mjx-mo"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.446em; padding-bottom: 0.593em;">{</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">x</span></span><span class="mjx-mo"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.446em; padding-bottom: 0.593em;">}</span></span><span class="mjx-mo MJXc-space2"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.298em; padding-bottom: 0.446em;">+</span></span><span class="mjx-mi MJXc-space2"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em; padding-right: 0.109em;">P</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">i</span></span><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-main-R" style="margin-top: -0.291em; padding-bottom: 0.372em;">_</span></span></span></span><span class="mjx-mo"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.446em; padding-bottom: 0.593em;">{</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">x</span></span><span class="mjx-mo"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.446em; padding-bottom: 0.593em;">}</span></span><span class="mjx-strut"></span></span></span><span class="mjx-mtd" style="padding: 0px 0px 0px 0.5em; text-align: left; width: 4.682em;"><span class="mjx-mrow" style="margin-top: -0.2em;"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">x</span></span><span class="mjx-mo MJXc-space3"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.077em; padding-bottom: 0.298em;">=</span></span><span class="mjx-mi MJXc-space3"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">c</span></span><span class="mjx-mo"><span class="mjx-char MJXc-TeX-main-R" style="margin-top: -0.144em; padding-bottom: 0.519em;">,</span></span><span class="mjx-mi MJXc-space1"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">h</span></span><span class="mjx-mo"><span class="mjx-char MJXc-TeX-main-R" style="margin-top: -0.144em; padding-bottom: 0.519em;">,</span></span><span class="mjx-mi MJXc-space1"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">m</span></span><span class="mjx-strut"></span></span></span></span></span></span></span></span></span></span> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">An equivalent maintenance reaction cannot be formulated for the peroxisome since in the <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">one-cell</em> model ATP/ADP are not included as peroxisomal metabolites. The flux through the maintenance reactions is fixed to the determined maintenance costs given in <a href="#table4" itemscope="" itemtype="http://schema.stenci.la/Link">Table 4</a>. The peroxisomal maintenance costs are added to the cytosolic maintenance costs.</p> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="10" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>print(f"Code Cell 10: Add Constraint on Rubisco Oxygenation : Decarboxylation Ratio") ## CONSTRAINT: oxygenation : decarboxylation = 1 : 10 r_c3_rbc_rbo = (10.0, 1.0) const_c3_rbc_rbo = set_fixed_flux_ratio({'RBC_h':r_c3_rbc_rbo[0],'RBO_h':r_c3_rbc_rbo[1]}, 'const_c3_rbc_rbo', c3_model)</code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 10: Add Constraint on Rubisco Oxygenation : Decarboxylation Ratio </code></pre> </figure> </stencila-code-chunk> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">The CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> and O<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> partial pressures determine the ratio of the oxygenation : carboxylation rate of Rubisco (given by reactions <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">RBO_h</em> and <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">RBC_h</em>) and can be described by the mathematical expression:</p><span itemscope="" itemtype="http://schema.stenci.la/MathBlock"><span class="mjx-chtml MJXc-display" style="text-align: center;"><span class="mjx-math" aria-label="{\displaystyle \frac{{v}_{RBO\mathrm{\_}h}}{{v}_{RBC\mathrm{\_}h}}=\frac{1}{{S}_{R}}\cdot \frac{{p}_{{O}_{2}}}{{p}_{C{O}_{2}}},}"><span class="mjx-mrow" aria-hidden="true"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mstyle"><span class="mjx-mrow"><span class="mjx-mfrac"><span class="mjx-box MJXc-stacked" style="width: 3.094em; padding: 0px 0.12em;"><span class="mjx-numerator" style="width: 3.094em; top: -1.232em;"><span class="mjx-msubsup"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">v</span></span></span></span></span><span class="mjx-sub" style="font-size: 70.7%; vertical-align: -0.229em; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">R</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">B</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.519em; padding-bottom: 0.298em;">O</span></span><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-main-R" style="margin-top: -0.291em; padding-bottom: 0.372em;">_</span></span></span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">h</span></span></span></span></span></span></span><span class="mjx-denominator" style="width: 3.094em; bottom: -0.91em;"><span class="mjx-msubsup"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">v</span></span></span></span></span><span class="mjx-sub" style="font-size: 70.7%; vertical-align: -0.23em; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">R</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">B</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.519em; padding-bottom: 0.298em; padding-right: 0.045em;">C</span></span><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-main-R" style="margin-top: -0.291em; padding-bottom: 0.372em;">_</span></span></span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">h</span></span></span></span></span></span></span><span style="border-bottom: 1.3px solid; top: -0.296em; width: 3.094em;" class="mjx-line"></span></span><span style="height: 2.142em; vertical-align: -0.91em;" class="mjx-vsize"></span></span><span class="mjx-mo MJXc-space3"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.077em; padding-bottom: 0.298em;">=</span></span><span class="mjx-mfrac MJXc-space3"><span class="mjx-box MJXc-stacked" style="width: 1.385em; padding: 0px 0.12em;"><span class="mjx-numerator" style="width: 1.385em; top: -1.368em;"><span class="mjx-mn"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.372em; padding-bottom: 0.372em;">1</span></span></span><span class="mjx-denominator" style="width: 1.385em; bottom: -0.953em;"><span class="mjx-msubsup"><span class="mjx-base" style="margin-right: -0.032em;"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.519em; padding-bottom: 0.298em; padding-right: 0.032em;">S</span></span></span></span></span><span class="mjx-sub" style="font-size: 70.7%; vertical-align: -0.212em; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">R</span></span></span></span></span></span></span><span style="border-bottom: 1.3px solid; top: -0.296em; width: 1.385em;" class="mjx-line"></span></span><span style="height: 2.32em; vertical-align: -0.953em;" class="mjx-vsize"></span></span><span class="mjx-mo MJXc-space2"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.004em; padding-bottom: 0.298em;">⋅</span></span><span class="mjx-mfrac MJXc-space2"><span class="mjx-box MJXc-stacked" style="width: 2.139em; padding: 0px 0.12em;"><span class="mjx-numerator" style="width: 2.139em; top: -1.433em;"><span class="mjx-msubsup"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.446em;">p</span></span></span></span></span><span class="mjx-sub" style="font-size: 70.7%; vertical-align: -0.36em; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-msubsup"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.519em; padding-bottom: 0.298em;">O</span></span></span></span></span><span class="mjx-sub" style="font-size: 83.3%; vertical-align: -0.267em; padding-right: 0.06em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mn"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.372em; padding-bottom: 0.372em;">2</span></span></span></span></span></span></span></span></span></span></span><span class="mjx-denominator" style="width: 2.139em; bottom: -1.112em;"><span class="mjx-msubsup"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.446em;">p</span></span></span></span></span><span class="mjx-sub" style="font-size: 70.7%; vertical-align: -0.36em; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.519em; padding-bottom: 0.298em; padding-right: 0.045em;">C</span></span><span class="mjx-msubsup"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.519em; padding-bottom: 0.298em;">O</span></span></span></span></span><span class="mjx-sub" style="font-size: 83.3%; vertical-align: -0.267em; padding-right: 0.06em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mn"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.372em; padding-bottom: 0.372em;">2</span></span></span></span></span></span></span></span></span></span></span><span style="border-bottom: 1.3px solid; top: -0.296em; width: 2.139em;" class="mjx-line"></span></span><span style="height: 2.546em; vertical-align: -1.112em;" class="mjx-vsize"></span></span><span class="mjx-mo"><span class="mjx-char MJXc-TeX-main-R" style="margin-top: -0.144em; padding-bottom: 0.519em;">,</span></span></span></span></span></span></span></span></span></span> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">where <span itemscope="" itemtype="http://schema.stenci.la/MathFragment"><span class="mjx-chtml"><span class="mjx-math" aria-label="{S}_{R}"><span class="mjx-mrow" aria-hidden="true"><span class="mjx-msubsup"><span class="mjx-base" style="margin-right: -0.032em;"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.519em; padding-bottom: 0.298em; padding-right: 0.032em;">S</span></span></span></span></span><span class="mjx-sub" style="font-size: 70.7%; vertical-align: -0.212em; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">R</span></span></span></span></span></span></span></span></span></span> specifies the ability of Rubisco to bind CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> over O<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub>. In the case of a mature leave and ambient CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> and O<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> partial pressures in temperate regions with adequate water supply, the ratio <span itemscope="" itemtype="http://schema.stenci.la/MathFragment"><span class="mjx-chtml"><span class="mjx-math" aria-label="{v}_{RB{O}_{h}}/{v}_{RB{C}_{h}}"><span class="mjx-mrow" aria-hidden="true"><span class="mjx-msubsup"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">v</span></span></span></span></span><span class="mjx-sub" style="font-size: 70.7%; vertical-align: -0.229em; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">R</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">B</span></span><span class="mjx-msubsup"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.519em; padding-bottom: 0.298em;">O</span></span></span></span></span><span class="mjx-sub" style="font-size: 83.3%; vertical-align: -0.295em; padding-right: 0.06em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">h</span></span></span></span></span></span></span></span></span></span><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mo"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.446em; padding-bottom: 0.593em;">/</span></span></span></span><span class="mjx-msubsup"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">v</span></span></span></span></span><span class="mjx-sub" style="font-size: 70.7%; vertical-align: -0.23em; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">R</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">B</span></span><span class="mjx-msubsup"><span class="mjx-base" style="margin-right: -0.045em;"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.519em; padding-bottom: 0.298em; padding-right: 0.045em;">C</span></span></span></span></span><span class="mjx-sub" style="font-size: 83.3%; vertical-align: -0.295em; padding-right: 0.06em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">h</span></span></span></span></span></span></span></span></span></span></span></span></span></span> is fixed and is predicted to be <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">int(r_c3_rbc_rbo[0])</code><output slot="output"></output> </stencila-code-expression>:<stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">int(r_c3_rbc_rbo[1])</code><output slot="output"></output> </stencila-code-expression>, which is encoded by an additional flux ratio constraint.</p> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="11" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>print(f"Code Cell 11: Add Constraint on NADPH dehydrogenase and plastoquinol oxidase") ## CONSTRAINT: fluxes through the chloroplastic NADPH dehydrogenase and plastoquinol oxidase were set to zero #because the contributions of NADPH dehydrogenase (Yamamoto et al., 2011) and plastoquinol oxidase #(Josse et al., 2000) to photosynthesis are thought to be minor. set_bounds('AOX4_h',(0,0), c3_model) set_bounds('iCitDHNADP_h',(0,0), c3_model)</code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 11: Add Constraint on NADPH dehydrogenase and plastoquinol oxidase </code></pre> </figure> </stencila-code-chunk> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">We assume no flux for the chloroplastic NADPH dehydrogenase (<em itemscope="" itemtype="http://schema.stenci.la/Emphasis">iCitDHNADP_h</em>) and plastoquinol oxidase (<em itemscope="" itemtype="http://schema.stenci.la/Emphasis">AOX4_h</em>) because <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib33"><span>33</span><span>Josse et al.</span><span>2000</span></a></cite> and <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib88"><span>88</span><span>Yamamoto et al.</span><span>2011</span></a></cite> have shown that their effect on the photosynthesis is minor.</p> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="12" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>print(f"Code Cell 12: Add additional Transport Constraints") ## CONSTRAINT: NTT is only active at night set_fixed_flux('Tr_NTT',0, c3_model) ## CONSTRAINT: No uncoupled pyruvate transport set_bounds('Tr_Pyr1',(0,0), c3_model) set_bounds('Tr_Pyr2',(0,0), c3_model) ## CONSTRAINT: set_bounds('G6PDH_h', (0.,0.), c3_model) set_bounds('PPIF6PK_c', (0,0.), c3_model)</code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 12: Add additional Transport Constraints </code></pre> </figure> </stencila-code-chunk> <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="objective">Objective</h4> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="13" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>print(f"Code Cell 13: Add Objective - Optimize Sucrose Output") ## Optimize/Maximize sucrose output r_c3_opt_id = "Ex_Suc" r_c3_opt_obj = c3_model.reactions.get_by_id(r_c3_opt_id) r_c3_opt_obj.objective_coefficient = 1.</code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 13: Add Objective - Optimize Sucrose Output </code></pre> </figure> </stencila-code-chunk> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">In accordance with the assumption of mature, fully differentiated and photosynthetic active leaf, the model’s objective is to maximise the phloem sap output defined by reactions <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">r_c3_opt_id</code><output slot="output"></output> </stencila-code-expression>. Additionally, we assume that the involved plant cells put only a minimal metabolic effort, in the form of energy and resources, into the production of phloem sap as possible. This assumption is in correspondence with minimising the nitrogen investment by reducing the number of enzymes that are active in a metabolic network. Therefore, we perform a parsimonious FBA to minimise the total flux.</p> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">For enhanced compliance with the recent standards of the systems biology community, the <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">one-cell</em> model is encoded in SBML level 3. Meta-information on subsystems, publications, cross-references are provided as evidence code in the form of MIRIAM URI’s. FBA related information, gene association rules, charge and formula of a species element are encoded using the Flux Balance Constraints package developed for SBML level 3. All fluxes in the model are consistently defined as μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s).</p> <h3 itemscope="" itemtype="http://schema.stenci.la/Heading" id="generic-model-for-c4-metabolism">Generic model for C4 metabolism</h3> <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="metabolic-model-1">Metabolic model</h4> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="14" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>print(f"Code Cell 14: Initiate Metabolic Model of C4 Photosynthesis") ## Intitialize C4 model c4_model = cobra.Model('c4_model') ## Define cell types cell_types = ['M', 'B'] ## Duplicate metabolites for m in c3_model.metabolites: for cell in cell_types: m_dt = cobra.Metabolite('['+cell+']_'+m.id, name = m.formula, compartment = m.compartment) c4_model.add_metabolites([m_dt]) ## Duplicate reactions for r_c3_obj in c3_model.reactions: for cell in cell_types: r_c4_obj = cobra.Reaction('['+cell+']_'+r_c3_obj.id) r_c4_obj.name = r_c3_obj.name r_c4_obj.subsystem = r_c3_obj.subsystem r_c4_obj.bounds = r_c3_obj.bounds c4_model.add_reaction(r_c4_obj) r_c4_obj.add_metabolites({'['+cell+']_'+m_c3_obj.id: r_c3_obj.get_coefficient(m_c3_obj) for m_c3_obj in r_c3_obj.metabolites}) ## Model Summary c4_num_mets = len(c4_model.metabolites) c4_num_rxn = len(c4_model.reactions) df_c4_model_summary = pd.DataFrame([c4_num_mets, c4_num_rxn], index=['Number of metabolites','Number of reactions'], columns=['Count']) df_c4_model_summary</code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 14: Initiate Metabolic Model of C4 Photosynthesis </code></pre> <table itemscope="" itemtype="http://schema.org/Table"> <thead> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <th itemscope="" itemtype="http://schema.stenci.la/TableCell"></th> <th itemscope="" itemtype="http://schema.stenci.la/TableCell">Count</th> </tr> </thead> <tbody> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Number of metabolites</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">826</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Number of reactions </td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">1144</span></td> </tr> </tbody> </table> </figure> </stencila-code-chunk> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">The generic model of C4 metabolism, short <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">two-cell</em> model, comprises two copies of the <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">one-cell</em> model to represent one mesophyll and one bundle sheath cell. Reactions and metabolites belonging to the metabolic network of the mesophyll are indicated with the prefix <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">[M]</em>, whereas the prefix for the bundle sheath is <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">[B]</em>. The separate mesophyll and bundle sheath networks are connected via reversible transport reactions of the cytosolic metabolites indicated with the prefix <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">[MB]</em>, <a href="#fig2" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 2</a>. The C4 evolution not only confined Rubisco to the bundle sheath cells, the CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> concentrating mechanism steadily supplies Rubisco with CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> in such a way that the oxygenation rate is negligible. Therefore, the bundle sheath network is equipped with two Rubisco populations. The native Rubisco population binds external CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> and adheres to forced oxygenation : carboxylation ratios, where the optimised evolutionary population binds only internal CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> and the carboxylation occurs independently of the oxygenation. External CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> is defined as _[B]_CO2_ex_<em itemscope="" itemtype="http://schema.stenci.la/Emphasis">{_c,h</em>} supplied by the mesophyll network. Internal CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> given by _[B]_CO2_<em itemscope="" itemtype="http://schema.stenci.la/Emphasis">{_c,h,m</em>} originates from reactions in the bundle sheath network producing CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub>. External CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> in the bundle sheath network is only allowed to move to the chloroplast <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">[B]_Tr_CO2h_Ex</em> and to react with Rubisco <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">[B]_RBC_h_Ex</em>. The differentiation of two Rubisco populations binding either external or internal CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> approximates the concentration-dependent shift of the oxygenation : carboxylation ratio.</p> <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="imports">Imports</h4> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="15" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>print(f"Code Cell 15: Adapt CO2 Input Constraint") ## CONSTRAINT: CO2 uptake rate uin C4 plants is higher, about 40 μmol/(m2*s) f_C4_CO2_M = 40 #[μmol/(m2*s)] set_bounds('[M]_Im_CO2', (0, f_C4_CO2_M), c4_model) ## CONSTRAINT: No CO2 uptake in bundle sheat cells due to suberin layer in cell membranes f_C4_CO2_B = 0 #[μmol/(m2*s)] set_fixed_flux('[B]_Im_CO2', f_C4_CO2_B, c4_model) ## Other constraints on inputs are directly transfered from the c3 model</code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 15: Adapt CO2 Input Constraint </code></pre> </figure> </stencila-code-chunk> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">As for the <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">one-cell</em> model, we assume photoautotrophic growth conditions, see <a href="#table3" itemscope="" itemtype="http://schema.stenci.la/Link">Table 3</a>. During C4 evolution the CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> assimilation became more efficient allowing higher CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> assimilation rates. <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Zea mays</em> achieves up to <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">f_C4_CO2_M</code><output slot="output"></output> </stencila-code-expression> μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s) ([M]_Im_CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub>) <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib60"><span>60</span><span>Rozema</span><span>1993</span></a></cite>. We assume that the CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> uptake from the environment by the bundle sheath has to be bridged by the mesophyll. Therefore, the input flux of [B]_Im_CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> is set to <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">f_C4_CO2_B</code><output slot="output"></output> </stencila-code-expression>.</p> <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="exports">Exports</h4> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="16" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>print(f"Code Cell 16: Adapt Output Constraints") ## CONSTRAINT: Output of sucrose : total amino acid and sucrose : starch r_suc_aa = (2.2, 1.0) const_c4_suc_aa_b = set_fixed_flux_ratio({'[B]_Ex_Suc':r_suc_aa[0],'[B]_Ex_AA':r_suc_aa[1]}, 'const_c4_suc_aa_b', c4_model) const_c4_suc_aa_m = set_fixed_flux_ratio({'[M]_Ex_Suc':r_suc_aa[0],'[M]_Ex_AA':r_suc_aa[1]}, 'const_c4_suc_aa_m', c4_model) r_suc_starch = (1.0, 1.0) const_c4_suc_starch_b = set_fixed_flux_ratio({'[B]_Ex_Suc':r_suc_starch[0],'[B]_Ex_starch':r_suc_starch[1]}, 'const_c4_suc_starch_b', c4_model) const_c4_suc_starch_m = set_fixed_flux_ratio({'[M]_Ex_Suc':r_suc_starch[0],'[M]_Ex_starch':r_suc_starch[1]}, 'const_c4_suc_starch_m', c4_model) ## Other constraints on outputs are directly transfered from the c4 model</code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 16: Adapt Output Constraints </code></pre> </figure> </stencila-code-chunk> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">The outputs of the <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">one-cell</em> model are transferred to the mesophyll and bundle sheath network, as well as the corresponding flux ratios, see <a href="#table3" itemscope="" itemtype="http://schema.stenci.la/Link">Table 3</a>.</p> <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="additional-constraints-1"> Additional Constraints</h4> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="17" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>print(f"Code Cell 17: Add Metabolite Exchange Reactions") ## Metabolites excluded from M/BS exchange no_transport = ['NO3','NO2', 'O2','Na', 'H2S', 'SO4', 'H2O','FBP','F26BP','DPGA','H','ACD','AC','M_DASH_THF', '5M_DASH_THF', 'H_DASH_Cys', 'aH_DASH_Cys', 'ORO', 'DHO', 'GABA','A_DASH_Ser','PRPP','AD','THF','DHF','ADN','Mas','CoA','GluP', 'A_DASH_CoA','cellulose1','cellulose2','cellulose3','starch1', 'starch2','starch3','TRXox','TRXrd','Glu_DASH_SeA','T6P','aMet', 'PPi', 'P5C', 'NH4', 'Pi', 'CO2', 'OAA','HCO3', 'UTP', 'UDP', 'UDPG', 'ATP', 'ADP', 'AMP', 'IMP', 'XMP', 'GTP', 'GDP', 'GMP', 'OMP', 'UMP', 'CTP', 'GDP', 'CDP', 'dADP', 'dCDP', 'dGDP', 'dUDP', 'dUTP', 'dUMP', 'dTMP', 'dTDP', 'GTP', 'dATP', 'dCTP', 'dGTP', 'dTTP', 'NAD', 'NADH', 'NADP', 'NADPH'] ## dd M/BS exchange reactions L_r_transport = [] for m_c3_obj in c3_model.metabolites: if m_c3_obj.id[-1:] == 'c' and m_c3_obj.id[:-2] not in no_transport: r_c4_obj = cobra.Reaction('[MB]_'+m_c3_obj.id) r_c4_obj.name = '[MB]_'+m_c3_obj.id r_c4_obj.subsystem = 'Exchange' r_c4_obj.bounds = (-inf, inf) c4_model.add_reaction(r_c4_obj) r_c4_obj.add_metabolites({'[M]_'+m_c3_obj.id: -1,'[B]_'+m_c3_obj.id: 1 }) L_r_transport.append('[MB]_'+m_c3_obj.id) ## Model Summary c4_num_mets = len(c4_model.metabolites) c4_num_rxn = len(c4_model.reactions) df_c4_model_summary = pd.DataFrame([c4_num_mets, c4_num_rxn], index=['Number of metabolites','Number of reactions'], columns=['Count']) df_c4_model_summary</code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 17: Add Metabolite Exchange Reactions </code></pre> <table itemscope="" itemtype="http://schema.org/Table"> <thead> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <th itemscope="" itemtype="http://schema.stenci.la/TableCell"></th> <th itemscope="" itemtype="http://schema.stenci.la/TableCell">Count</th> </tr> </thead> <tbody> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Number of metabolites</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">826</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Number of reactions </td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">1188</span></td> </tr> </tbody> </table> </figure> </stencila-code-chunk> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">The mesophyll and bundle sheath networks are connected by a range of cytosolic transport metabolites including amino acids, sugars (glucose, fructose, sucrose, trehalose, ribose), single phosphorylated sugar (glucose-6-phosphate, glucose-1-phosphate, fructose-6-phosphate, sucrose-6-phosphate), mono-/di-/tri-carboxylic acids (phosphoenolpyruvate, pyruvate, citrate, cis-aconitate, isocitrate, <span itemscope="" itemtype="http://schema.stenci.la/MathFragment"><span class="mjx-chtml"><span class="mjx-math" aria-label="\alpha"><span class="mjx-mrow" aria-hidden="true"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">α</span></span></span></span></span></span>-ketoglutarate, succinate, fumarate, malate), glyceric acids (2-Phosphoglycerate, 3-Phosphoglycerate), glycolate, glycerate, glyceraldehyde-3-phosphate, di-hydroxyacetone-phosphate and CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub>. Nucleotides, NAD/NADH, NADP/NADPH, pyrophosphate, inorganic phosphate are not considered as transport metabolites. Oxaloacetate has been excluded as transport metabolite since concentrations of oxaloacetate are very low <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">in vivo</em> and it is reasonably unstable in aqueous solutions. Other small molecules that can be imported by the bundle sheath from the environment, as well as protons and HCO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">3</span></sub><sup itemscope="" itemtype="http://schema.stenci.la/Superscript">-</sup>, are not exchanged between the two cell types.</p> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="18" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>print(f"Code Cell 18: Add Constraints for CO2 Uptake in BS Cells and Rubisco Carboxylation : Oxygenation Ratio") ## CONSTRAINT: Add external CO2 species to bundle sheath #(the original CO2 species is treated as internal CO2) m_list_CO_Ex= ['[B]_CO2_ex_c','[B]_CO2_ex_h'] for m_id in m_list_CO_Ex: m_obj = cobra.Metabolite(m_id) c4_model.add_metabolites(m_obj) ## CONSTRAINT: Copy reactions 'Tr_CO2h', 'RBC_h' and replace internal CO2 with external CO2 in the copied reactions r_list_CO_Ex = ['Tr_CO2h', 'RBC_h'] for r_id in r_list_CO_Ex: r_obj = c4_model.reactions.get_by_id('[B]_'+r_id) r_obj_Ex = cobra.Reaction(r_obj.id+'_Ex') r_obj_Ex.name = r_obj.id+'_Ex' r_obj_Ex.subsystem = r_obj.subsystem r_obj_Ex.bounds = r_obj.bounds c4_model.add_reaction(r_obj_Ex) r_obj_Ex.add_metabolites({m_obj.id if not m_obj.id[:-2] == '[B]_CO2' else '[B]_CO2_ex'+m_obj.id[-2:]: r_obj.get_coefficient(m_obj) for m_obj in r_obj.metabolites}) ## CONSTRAINT: CO2 exchange between mesophyll and bundle sheat r_c4_obj = cobra.Reaction('[MB]_CO2_c') r_c4_obj.name = '[MB]_CO2_c' r_c4_obj.subsystem = 'Exchange' r_c4_obj.bounds = (-inf, inf) c4_model.add_reaction(r_c4_obj) r_c4_obj.add_metabolites({'[M]_CO2_c': -1,'[B]_CO2_ex_c': 1 }) L_r_transport.append('[MB]_CO2_c') ## CONSTRAINT: oxygenation : carboxylation = 1 : 3 r_c4_rbc_rbo = (3.0, 1.0) const_c4_rbc_rbo_b = set_fixed_flux_ratio({'[B]_RBC_h_Ex':r_c4_rbc_rbo[0],'[B]_RBO_h':r_c4_rbc_rbo[1]}, 'const_c4_rbc_rbo_b', c4_model) const_c4_rbc_rbo_m = set_fixed_flux_ratio({'[M]_RBC_h':r_c4_rbc_rbo[0],'[M]_RBO_h':r_c4_rbc_rbo[1]}, 'const_c4_rbc_rbo_m', c4_model) #Model Summary c4_num_mets = len(c4_model.metabolites) c4_num_rxn = len(c4_model.reactions) df_c4_model_summary = pd.DataFrame([c4_num_mets, c4_num_rxn], index=['Number of metabolites','Number of reactions'], columns=['Count']) df_c4_model_summary</code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 18: Add Constraints for CO2 Uptake in BS Cells and Rubisco Carboxylation : Oxygenation Ratio </code></pre> <table itemscope="" itemtype="http://schema.org/Table"> <thead> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <th itemscope="" itemtype="http://schema.stenci.la/TableCell"></th> <th itemscope="" itemtype="http://schema.stenci.la/TableCell">Count</th> </tr> </thead> <tbody> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Number of metabolites</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">828</span></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Number of reactions </td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">1191</span></td> </tr> </tbody> </table> </figure> </stencila-code-chunk> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">The ATP costs for cell maintenance in the <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">genC3</em> model are assigned to both cell types in the <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">two-cell</em> model. Due to declining CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> concentrations over evolutionary time and/or adverse conditions which close the stromata, the oxygenation : carboxylation ratio of the native Rubisco population in the bundle sheath and the mesophyll is increased and can be predicted as <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">r_c4_rbc_rbo[0]</code><output slot="output"></output> </stencila-code-expression> : <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">r_c4_rbc_rbo[1]</code><output slot="output"></output> </stencila-code-expression>, the corresponding flux ratios are adapted accordingly.</p> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="19" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>print(f"Code Cell 19: Add Constraint on Photon Uptake") ## Reaction variables for light uptake B_Im_hnu = c4_model.reactions.get_by_id("[B]_Im_hnu") M_Im_hnu = c4_model.reactions.get_by_id("[M]_Im_hnu") ## CONSTRAINT: Total Photon uptake limited to 1000 µE f_c4_hnu_ub = 1000 #[μE] f_c4_hnu_lb = 0 #[μE] const_hnu_sum = c4_model.problem.Constraint( B_Im_hnu.flux_expression + M_Im_hnu.flux_expression, lb = f_c4_hnu_lb, ub = f_c4_hnu_ub, name = 'const_hnu_sum', ) c4_model.add_cons_vars(const_hnu_sum) ## CONSTRAINT: Total Photon uptake by bundle sheath must be less equal than in mesophyll const_hnu_ratio = c4_model.problem.Constraint( M_Im_hnu.flux_expression - B_Im_hnu.flux_expression, lb = f_c4_hnu_lb, ub = f_c4_hnu_ub, name = 'const_hnu_ratio') c4_model.add_cons_vars(const_hnu_ratio)</code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 19: Add Constraint on Photon Uptake </code></pre> </figure> </stencila-code-chunk> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">Furthermore, we assume that the total photon uptake in the mesophyll and bundle sheath is in the range of <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">f_c4_hnu_lb</code><output slot="output"></output> </stencila-code-expression> μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s) to <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">f_c4_hnu_lb</code><output slot="output"></output> </stencila-code-expression> μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s). Since they are more central in the leaf, the photon uptake by the bundle sheath must be equal or less compared to the mesophyll.</p> <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="objective-1">Objective</h4> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="20" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>print(f"Code Cell 20: Add Objective to Optimize Sucrose Output") ## Optimize/Maximize sucrose output r_opt_id = "[B]_Ex_Suc" r_opt_obj = c4_model.reactions.get_by_id(r_opt_id) r_opt_obj.objective_coefficient = 1.</code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 20: Add Objective to Optimize Sucrose Output </code></pre> </figure> </stencila-code-chunk> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">The maximisation of the phloem sap output through the bundle sheath and the minimisation of the metabolic effort are kept as objectives in the <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">two-cell</em> model.</p> <h2 itemscope="" itemtype="http://schema.stenci.la/Heading" id="results">Results</h2> <h3 itemscope="" itemtype="http://schema.stenci.la/Heading" id="the-curated-arabidopsis-core-model-predicts-physiological-results">The curated <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Arabidopsis</em> core model predicts physiological results</h3> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">Flux balance analysis requires five types of information, the metabolic map of the organism, the input, the output, a set of constraints (i.e. limitations on input, directionality of reactions, forced flux through reactions), and optimisation criteria for the algorithm which approximate the selective pressures the metabolism evolved under. In this context, inputs define the resources that need to be taken up by the metabolic network to fulfil a particular metabolic function, which is related to the outputs, for example the synthesis of metabolites part of the biomass or other specific products. In CBM, the objective is most likely related to the in- and/or outputs.</p> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">For reconstruction of the C3 metabolic map we curated the <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Arabidopsis</em> core model <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib2"><span>2</span><span>Arnold and Nikoloski</span><span>2014</span></a></cite> manually (<a href="#table1" itemscope="" itemtype="http://schema.stenci.la/Link">Table 1</a>) to represent the metabolism of a mesophyll cell in a mature photosynthetically active leaf of a C3 plant , further on called <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">one-cell</em> model (provided in <a href="#fig1sdata1" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 1—source data 1</a>). The <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Arabidopsis</em> core model is a bottom-up-assembled, large-scale model relying solely on <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Arabidopsis</em>-specific annotations and the inclusion of only manually curated reactions of the primary metabolism. The <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Arabidopsis</em> core model is accurate with respect to mass and energy conservation, allowing optimal nutrient utilisation and biochemically sound predictions <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib2"><span>2</span><span>Arnold and Nikoloski</span><span>2014</span></a></cite>.</p> <table id="table1" itemscope="" itemtype="http://schema.org/Table"> <caption><label data-itemprop="label">Table 1.</label> <div itemprop="caption"> <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="curation-of-the-arabidopsis-core-model-from-narrative-bib2">Curation of the <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Arabidopsis</em> core model from <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib2"><span>2</span><span>Arnold and Nikoloski</span><span>2014</span></a></cite>.</h4> </div> </caption> <thead> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <th itemscope="" itemtype="http://schema.stenci.la/TableCell"><em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Arabidopsis core model</em></th> <th itemscope="" itemtype="http://schema.stenci.la/TableCell">Observation</th> <th itemscope="" itemtype="http://schema.stenci.la/TableCell"><em itemscope="" itemtype="http://schema.stenci.la/Emphasis">one-cell model</em></th> <th itemscope="" itemtype="http://schema.stenci.la/TableCell">Reference</th> </tr> </thead> <tbody> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">NADP-dependent malate dehydrogenases in all compartments</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">cycles through nitrate reductase to interconvert NAD and NADP</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">NAD-dependent malate dehydrogenases in all compartments, NADP-dependent malate dehydrogenase only in chloroplast</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">(<cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib76"><span>76</span><span>Swarbreck et al.</span><span>2008</span></a></cite>)</td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Cyclic electron flow </td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">absence of cyclic electron flow</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">added</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">(<cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib70"><span>70</span><span>Shikanai</span><span>2016</span></a></cite>) </td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Alternative oxidase</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">missing alternative routes for electrons to pass the electron transport chain to reduce oxygen</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">added alternative oxidase reactions to the chloroplast and mitochondria</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">(<cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib81"><span>81</span><span>Vishwakarma et al.</span><span>2015</span></a></cite>)</td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Alanine transferase</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">No alanine transferase in cytosol Alanine transferase</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">added</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">(<cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib41"><span>41</span><span>Liepman and Olsen</span><span>2003</span></a></cite>)</td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Transport chloroplast </td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">no maltose transporter by MEX1</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">added</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">(<cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib42"><span>42</span><span>Linka and Weber</span><span>2010</span></a></cite>)</td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">no glucose transporter by MEX1 and pGlcT MEX1</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">added</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">no unidirectional transport of ATP, ADP, AMP by BT-like</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">added</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">no Mal/OAA, Mal/Pyr, and Mal/Glu exchange by DiTs</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">added</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">no folate transporter by FBT and FOLT1</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">added</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Transport Mitochondria </td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">no Mal/OAA, Cit/iCit, Mal/KG exchange by DTC</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">added</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">(<cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib42"><span>42</span><span>Linka and Weber</span><span>2010</span></a></cite>)</td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">no H+ importer by UCPs import</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">added</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">no OAA/Pi exchange by DIC1-3</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">added</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">no ATP/Pi exchange by APCs</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">added</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">no NAD/ADP and NAD/AMP exchange by NDT2</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">added</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">no ThPP/ATP exchange by TPCs</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">added</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">no Asp/Glu by AGCs</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">added</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">no uncoupled Ala exchange</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">added</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Transport peroxisome </td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">missing NAD/NADH, NAD/ADP, NAD/AMP exchange by PXN</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">added</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">(<cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib42"><span>42</span><span>Linka and Weber</span><span>2010</span></a></cite>)</td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">no ATP/ADP and ATP/AMP exchange by PNCs</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">added</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">H<sup itemscope="" itemtype="http://schema.stenci.la/Superscript">+</sup> sinks/sources</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">H<sup itemscope="" itemtype="http://schema.stenci.la/Superscript">+</sup> sinks/source reaction for the cytosol and futile transport cycles introduced by H<sup itemscope="" itemtype="http://schema.stenci.la/Superscript">+</sup> -coupled transport reactions</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">H<sup itemscope="" itemtype="http://schema.stenci.la/Superscript">+</sup> sinks/source reaction added for each compartment</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">ATPase stoichiometry </td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">False H<sup itemscope="" itemtype="http://schema.stenci.la/Superscript">+</sup>/ATP ratios for the plastidal and mitochondrial ATP synthase</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">H<sup itemscope="" itemtype="http://schema.stenci.la/Superscript">+</sup>/ATP ratio set to 3 : 1 (chloroplast) and 4:1 (mitochondria)</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">(<cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib56"><span>56</span><span>Petersen et al.</span><span>2012</span></a></cite>; <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib79"><span>79</span><span>Turina et al.</span><span>2016</span></a></cite>)</td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Alanine/aspartate transferase</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">no direct conversion of alanine and aspartate</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">added to cytosol, chloroplast and mitochondria</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">(<cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib69"><span>69</span><span>Schultz and Coruzzi</span><span>1995</span></a></cite>; <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib22"><span>22</span><span>Duff et al.</span><span>2012</span></a></cite>)</td> </tr> </tbody> </table> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">For the inputs, we considered a photoautotrophic growth scenario with a fixed CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> uptake of about <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">f_c3_CO2</code><output slot="output"></output></stencila-code-expression> μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s) <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib37"><span>37</span><span>Lacher</span><span>2003</span></a></cite>. Light, sulphates, and phosphate are freely available. Due to the observation that nitrate is the main source (80%) of nitrogen in leaves in many species <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib45"><span>45</span><span>Macduff and Bakken</span><span>2003</span></a></cite>, we set nitrate as the sole nitrogen source. If both ammonia and nitrate are allowed, the model will inevitably predict the physiologically incorrect sole use of ammonia since fewer reactions and less energy are required to convert it into glutamate, the universal amino group currency in plants. Water and oxygen can be freely exchanged with the environment in both directions.</p> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">To compute the output, we assume a mature fully differentiated and photosynthetically active leaf, which is optimised for the synthesis and export of sucrose and amino acids to the phloem under minimal metabolic effort. Following the examples of models in bacteria, many plant models use a biomass function which assumes that the leaf is required to build itself <span itemscope="" itemtype="http://schema.stenci.la/CiteGroup"><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib19"><span>19</span><span>de Oliveira Dal'Molin et al.</span><span>2010</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib2"><span>2</span><span>Arnold and Nikoloski</span><span>2014</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib64"><span>64</span><span>Saha et al.</span><span>2011</span></a></cite></span> using photoautotrophic that is <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib2"><span>2</span><span>Arnold and Nikoloski</span><span>2014</span></a></cite> or heterotrophic that is <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib17"><span>17</span><span>Cheung et al.</span><span>2014</span></a></cite> energy and molecule supply. In plants, however, leaves transition from a sink phase in which they build themselves from metabolites delivered by the phloem to a source phase in which they produce metabolites for other organs including sink leaves <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib78"><span>78</span><span>Turgeon</span><span>1989</span></a></cite>. The composition of <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Arabidopsis</em> phloem exudate <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib85"><span>85</span><span>Wilkinson and Douglas</span><span>2003</span></a></cite> was used to constrain the relative proportions of the 18 amino acids and the ratio of sucrose : total amino acids (r<em itemscope="" itemtype="http://schema.stenci.la/Emphasis">suc_aa<a href="" itemscope="" itemtype="http://schema.stenci.la/Link"><span data-itemtype="http://schema.org/Number">0</span></a> : r_suc_aa<a href="" itemscope="" itemtype="http://schema.stenci.la/Link"><span data-itemtype="http://schema.org/Number">1</span></a>). To account for daily carbon storage as starch for export during the night, we assume that half of the assimilated carbon is stored in the _one-cell</em> model. We explicitly account for maintenance costs by the use of a generic ATPase and use the measured ATP costs for protein degradation and synthesis of a mature <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Arabidopsis</em> leaf <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib40"><span>40</span><span>Li et al.</span><span>2017</span></a></cite> as a constraint. We initially assume a low photorespiratory flux according to the ambient CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> and O<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> partial pressures considering no heat, drought, salt or osmotic stress which may alter the ratio towards higher flux towards the oxygenation reaction.</p> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">To develop a largely unconstrained model and detect possible errors in the metabolic map, we initially kept the model unconstrained with regard to fixed fluxes, flux ratios, and reaction directions. Different model iterations were run in (re-)design, simulate, validate cycles against known physiology with errors sequentially eliminated and a minimal set of constraints required for a C3 model recapitulating extant plant metabolism determined. After each change, the CBM predicted all fluxes which were output as a table and manually examined (for example see <a href="#fig1sdata2" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 1—source data 2</a>).</p> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">The initial FBA resulted in carbon fixation by enzymes such as the malic enzymes which, in reality, are constrained by the kinetics of the enzymes towards decarboxylation. All decarboxylation reactions were made unidirectional towards decarboxylation to prevent erroneous carbon fixation in the flux distribution. The next iteration of FBA predicted loops through nitrate reductases which ultimately converted NADH to NADPH. We traced this loop to an error in the initial model, in which malate dehydrogenases in the cytosol and mitochondrion were NADP-dependent instead of NAD-dependent. After correction of the co-factor in the <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">one-cell</em> model, the loops through nitrate reductases were no longer observed. Another iteration predicted excessive flux through the mitochondrial membrane where multiple metabolites were exchanged and identified missing transport processes as the likely reason. Based on <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib42"><span>42</span><span>Linka and Weber</span><span>2010</span></a></cite>, we added known fluxes across the mitochondrial and plastidic envelope membranes which remedied the excessive fluxes in the solution. The chloroplastic ADP/ATP carrier protein is constrained to zero flux since its mutant is only affected during the night but not if light is available <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib59"><span>59</span><span>Reiser et al.</span><span>2004</span></a></cite>.</p> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">The obtained flux distribution still contained excessive fluxes through multiple transport proteins across internal membranes which ultimately transferred protons between the organelles and the cytosol. Since for most if not all transport proteins the precise protonation state of metabolites during transport is unknown and hence cannot be correctly integrated into the model, we allowed protons to appear and disappear as needed in all compartments. This provision precludes conclusions about the energetics of membrane transport. ATP generation occurred in a distorted way distributed across different organelles which were traced to the H<sup itemscope="" itemtype="http://schema.stenci.la/Superscript">+</sup> consumption of the ATPases in mitochondria and chloroplasts. The stoichiometry was altered to to 3:1 (chloroplast) and 4:1 (mitochondria) <span itemscope="" itemtype="http://schema.stenci.la/CiteGroup"><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib56"><span>56</span><span>Petersen et al.</span><span>2012</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib79"><span>79</span><span>Turina et al.</span><span>2016</span></a></cite></span>. We assume no flux for the chloroplastic NADPH dehydrogenase and plastoquinol oxidase because <span itemscope="" itemtype="http://schema.stenci.la/CiteGroup"><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib33"><span>33</span><span>Josse et al.</span><span>2000</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib88"><span>88</span><span>Yamamoto et al.</span><span>2011</span></a></cite></span> have shown that their effect on photosynthesis is minor.</p> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">In preparation for modelling the C4 cycle, we ensured that all reactions known to occur in C4 (i.e. malate/pyruvate exchange, likely via DiT2 in maize <cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib84"><span>84</span><span>Weissmann et al.</span><span>2016</span></a></cite>, possibly promiscuous amino transferases <cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib22"><span>22</span><span>Duff et al.</span><span>2012</span></a></cite>) are present in the <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">one-cell</em> model, since <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib4"><span>4</span><span>Aubry et al.</span><span>2011</span></a></cite> showed that all genes encoding enzymes and transporters underlying the C4 metabolism are already present in the genome of C3 plants. We integrated cyclic electron flow <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib70"><span>70</span><span>Shikanai</span><span>2016</span></a></cite> and alternative oxidases in the mitochondria <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib81"><span>81</span><span>Vishwakarma et al.</span><span>2015</span></a></cite>, since both have been hypothesised to be important during the evolution and/or execution of the C4 cycle. Models and analysis workflows provided as jupyter notebooks <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib77"><span>77</span><span>Thomas et al.</span><span>2016</span></a></cite> are available as supplementary material or can be accessed on GitHub <a href="https://github.com/ma-blaetke/CBM_C3_C4_Metabolism" itemscope="" itemtype="http://schema.stenci.la/Link">https://github.com/ma-blaetke/CBM_C3_C4_Metabolism</a> (<cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib10"><span>10</span><span>Blätke</span><span>2019</span></a></cite>; copy archived at <a href="https://github.com/elifesciences-publications/CBM_C3_C4_Metabolism" itemscope="" itemtype="http://schema.stenci.la/Link">https://github.com/elifesciences-publications/CBM_C3_C4_Metabolism</a>). </p> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">The <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">one-cell</em> model comprises in total <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">c3_num_mets</code><output slot="output"></output> </stencila-code-expression> metabolites and <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">c3_num_rxn</code><output slot="output"></output> </stencila-code-expression> reactions, whereof <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">c3_num_transport_rxn</code><output slot="output"></output> </stencila-code-expression> are internal transporters, <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">c3_num_export_rxn</code><output slot="output"></output> </stencila-code-expression> are export and <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">c3_num_import_rxn</code><output slot="output"></output> </stencila-code-expression> import reactions (see also below), which are involved in 59 subsystems. <a href="#fig1" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 1</a> provides an overview of the primary subsystems according to <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib2"><span>2</span><span>Arnold and Nikoloski</span><span>2014</span></a></cite>.</p> <figure itemscope="" itemtype="http://schema.stenci.la/Figure" id="fig1" title="Figure 1."> <label data-itemprop="label">Figure 1.</label><img src="index.html.media/fig1.jpg" alt="" itemscope="" itemtype="http://schema.org/ImageObject"> <figcaption> <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="schematic-representation-of-the-primary-subsystems-in-the-one-cell-model-and-the-used-inputoutput-constraints-adapted-from-narrative-bib2"> Schematic representation of the primary subsystems in the <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">one-cell</em> model and the used input/output constraints; adapted from <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib2"><span>2</span><span>Arnold and Nikoloski</span><span>2014</span></a></cite>.</h4> </figcaption> </figure> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="21" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>###################################################################################################################################### ###################################################################################################################################### ############## EXPERIMENT 1: Effect of CO2 Uptake ############## ###################################################################################################################################### ###################################################################################################################################### print(f"Code Cell 21: Experiment 1 -- Effect of CO2 Uptake") #Create copy of c3 model c3_model_exp1 = c3_model.copy() #Optimize/Maximize sucrose output result_exp1_1_fba = c3_model_exp1.optimize('maximize') #perform FBA #Optimize/Minimize total flux if result_exp1_1_fba.status == 'optimal': result_exp1_1_pfba = cobra.flux_analysis.parsimonious.pfba(c3_model_exp1) #Fetch flux for CO2 uptake v_co2_exp1 = result_exp1_1_pfba.fluxes['Im_CO2'] #Array defining proprtion of CO2 uptake co2_ratios_exp1 = np.linspace(0,1,21) df_result_exp1 = pd.DataFrame() #Iterate over proportions of CO2 uptake for co2_ratio in tqdm(co2_ratios_exp1): #Fix upper flux bound for photon uptake set_bounds('Im_CO2', (0, v_co2_exp1 * co2_ratio), c3_model_exp1) #Optimize/Maximize sucrose output result_exp1_2_fba = c3_model_exp1.optimize('maximize') #perform FBA #Optimize/Minimize total flux if result_exp1_2_fba.status == 'optimal': # check if feasible result_exp1_2_pfba = cobra.flux_analysis.parsimonious.pfba(c3_model_exp1) #perform pFBA if result_exp1_2_pfba.status == 'optimal': df_result_exp1[v_co2_exp1 * co2_ratio] = result_exp1_2_pfba.fluxes</code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 21: Experiment 1 -- Effect of CO2 Uptake </code></pre> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code> 0%| | 0/21 [00:00<?, ?it/s]</code></pre> </figure> </stencila-code-chunk> <figure itemscope="" itemtype="http://schema.stenci.la/Figure" id="fig1s1" title="Figure 1—figure supplement 1"><label data-itemprop="label">Figure 1—figure supplement 1</label> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="22" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>###################################################################### ############## Figure 1—figure supplement 1 ############## ###################################################################### #{ # "caption": "#### Effect of CO~2. Dependence of the phloem output on CO~2~ input flux in the range 0 μmol/(m^2^s)–20 μmol/(m^2^s). Sucrose and starch are produced in the same amounts, each of them consists of 12 C-atoms.", # "id": "fig1s1", # "label": "Figure 1—figure supplement 1", # "trusted": true #} #Define reactions of interest by id r_ids_exp1 = ['Ex_Suc','Ex_AA'] #Create figure fig_exp1 = go.Figure() #Add traces for reactions of interest for r_id in r_ids_exp1: #Create trace trace = go.Scatter( y = df_result_exp1.loc[r_id,:], x = df_result_exp1.columns, name = r_id, mode = 'lines+markers', ) #Add trace fig_exp1.add_trace(trace) #Update xaxes fig_exp1.update_xaxes( title = dict( text = 'CO\u2082 Uptake [µmol/(m\u00B2s)]', font = dict(size=18) ), tickfont = dict(size=16) ) #Update yaxes fig_exp1.update_yaxes( title = dict( text = 'Flux [µmol/(m\u00B2s)]', font = dict(size=18) ), tickfont = dict(size=16) ) #Update layout fig_exp1.update_layout( width=1000, height=500, title = dict( text='<b>Phloem Export</b>', x=0.5, font=dict(size=20) ), legend=dict( font=dict(size=18), ) ) #Show figure fig_exp1.show()</code></pre> <figure slot="outputs"><span data-itemtype="http://schema.stenci.la/Null">null</span> <stencila-image-plotly> <picture> <script type="application/vnd.plotly.v1+json"> {"config":{"plotlyServerURL":"https://plot.ly"},"data":[{"mode":"lines+markers","name":"Ex_Suc","type":"scatter","x":[0,0.9999999999999982,1.9999999999999964,2.999999999999995,3.999999999999993,4.999999999999991,5.99999999999999,6.9999999999999885,7.999999999999986,8.999999999999984,9.999999999999982,10.99999999999998,11.99999999999998,12.999999999999977,13.999999999999977,14.999999999999973,15.999999999999972,16.99999999999997,17.999999999999968,18.999999999999968,19.999999999999964],"y":[1.3980644671705006e-18,0.038358935016476865,0.07671787003295295,0.11507680504943016,0.15343574006590668,0.19179467508238376,0.2301536100988608,0.26851254511533734,0.3068714801318123,0.3452304151482894,0.38358935016476753,0.421948285181243,0.46030722019772063,0.4986661552141951,0.5370250902306747,0.5753840252471492,0.6137429602636246,0.6521018952801053,0.6904608302965819,0.7288197653130595,0.7671787003295351]},{"mode":"lines+markers","name":"Ex_AA","type":"scatter","x":[0,0.9999999999999982,1.9999999999999964,2.999999999999995,3.999999999999993,4.999999999999991,5.99999999999999,6.9999999999999885,7.999999999999986,8.999999999999984,9.999999999999982,10.99999999999998,11.99999999999998,12.999999999999977,13.999999999999977,14.999999999999973,15.999999999999972,16.99999999999997,17.999999999999968,18.999999999999968,19.999999999999964],"y":[6.35483848713864e-19,0.017435879552943987,0.03487175910588771,0.05230763865883189,0.06974351821177577,0.08717939776471989,0.104615277317664,0.12205115687060789,0.13948703642355106,0.15692291597649521,0.17435879552943978,0.1917946750823832,0.20923055463532755,0.22666643418827054,0.24410231374121577,0.2615381932941587,0.27897407284710213,0.2964099524000479,0.31384583195299176,0.3312817115059361,0.34871759105887956]}],"layout":{"height":500,"legend":{"font":{"size":18}},"template":{"data":{"bar":[{"error_x":{"color":"#2a3f5f"},"error_y":{"color":"#2a3f5f"},"marker":{"line":{"color":"#E5ECF6","width":0.5}},"type":"bar"}],"barpolar":[{"marker":{"line":{"color":"#E5ECF6","width":0.5}},"type":"barpolar"}],"carpet":[{"aaxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"baxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"type":"carpet"}],"choropleth":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"choropleth"}],"contour":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"contour"}],"contourcarpet":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"contourcarpet"}],"heatmap":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"heatmap"}],"heatmapgl":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"heatmapgl"}],"histogram":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"histogram"}],"histogram2d":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"histogram2d"}],"histogram2dcontour":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"histogram2dcontour"}],"mesh3d":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"mesh3d"}],"parcoords":[{"line":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"parcoords"}],"pie":[{"automargin":true,"type":"pie"}],"scatter":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatter"}],"scatter3d":[{"line":{"colorbar":{"outlinewidth":0,"ticks":""}},"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatter3d"}],"scattercarpet":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattercarpet"}],"scattergeo":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattergeo"}],"scattergl":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattergl"}],"scattermapbox":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattermapbox"}],"scatterpolar":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterpolar"}],"scatterpolargl":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterpolargl"}],"scatterternary":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterternary"}],"surface":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"surface"}],"table":[{"cells":{"fill":{"color":"#EBF0F8"},"line":{"color":"white"}},"header":{"fill":{"color":"#C8D4E3"},"line":{"color":"white"}},"type":"table"}]},"layout":{"annotationdefaults":{"arrowcolor":"#2a3f5f","arrowhead":0,"arrowwidth":1},"autotypenumbers":"strict","coloraxis":{"colorbar":{"outlinewidth":0,"ticks":""}},"colorscale":{"diverging":[[0,"#8e0152"],[0.1,"#c51b7d"],[0.2,"#de77ae"],[0.3,"#f1b6da"],[0.4,"#fde0ef"],[0.5,"#f7f7f7"],[0.6,"#e6f5d0"],[0.7,"#b8e186"],[0.8,"#7fbc41"],[0.9,"#4d9221"],[1,"#276419"]],"sequential":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"sequentialminus":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]]},"colorway":["#636efa","#EF553B","#00cc96","#ab63fa","#FFA15A","#19d3f3","#FF6692","#B6E880","#FF97FF","#FECB52"],"font":{"color":"#2a3f5f"},"geo":{"bgcolor":"white","lakecolor":"white","landcolor":"#E5ECF6","showlakes":true,"showland":true,"subunitcolor":"white"},"hoverlabel":{"align":"left"},"hovermode":"closest","mapbox":{"style":"light"},"paper_bgcolor":"white","plot_bgcolor":"#E5ECF6","polar":{"angularaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"bgcolor":"#E5ECF6","radialaxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"scene":{"xaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"},"yaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"},"zaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"}},"shapedefaults":{"line":{"color":"#2a3f5f"}},"ternary":{"aaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"baxis":{"gridcolor":"white","linecolor":"white","ticks":""},"bgcolor":"#E5ECF6","caxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"title":{"x":0.05},"xaxis":{"automargin":true,"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","zerolinewidth":2},"yaxis":{"automargin":true,"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","zerolinewidth":2}}},"title":{"font":{"size":20},"text":"<b>Phloem Export</b>","x":0.5},"width":1000,"xaxis":{"tickfont":{"size":16},"title":{"font":{"size":18},"text":"CO₂ Uptake [µmol/(m²s)]"}},"yaxis":{"tickfont":{"size":16},"title":{"font":{"size":18},"text":"Flux [µmol/(m²s)]"}}}} </script><img src="index.html.media/0" alt="" itemscope="" itemtype="http://schema.org/ImageObject"> </picture> </stencila-image-plotly> </figure> </stencila-code-chunk> <figcaption> <h5 itemscope="" itemtype="http://schema.stenci.la/Heading" id="effect-of-co2-dependence-of-the-phloem-output-on-co2-input-flux-in-the-range-0-μmolm2s20-μmolm2s-sucrose-and-starch-are-produced-in-the-same-amounts-each-of-them-consists-of-12-c-atoms"> Effect of CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript">2. Dependence of the phloem output on CO</sub>2~ input flux in the range 0 μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s)–20 μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s). Sucrose and starch are produced in the same amounts, each of them consists of 12 C-atoms.</h5> </figcaption> </figure> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="23" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>###################################################################################################################################### ###################################################################################################################################### ############## EXPERIMENT 2: Effect of PPFD ############## ###################################################################################################################################### ###################################################################################################################################### print(f"Code Cell 23: Experiment 2 -- Effect of PPFD") #Create copy of c3 model c3_model_exp2 = c3_model.copy() #Optimize/Maximize sucrose output result_exp2_1_fba = c3_model_exp2.optimize('maximize') #perform FBA #Optimize/Minimize total flux if result_exp2_1_fba.status == 'optimal': result_exp2_1_pfba = cobra.flux_analysis.parsimonious.pfba(c3_model_exp2) #Fetch flux for photon uptake v_hnu_exp2 = result_exp2_1_pfba.fluxes['Im_hnu'] #Array defining proprtion of photon uptake hnu_ratios_exp2 = np.linspace(0,2,21) df_result_exp2 = pd.DataFrame() #Iterate over proportions of photon uptake for hnu_ratio in tqdm(hnu_ratios_exp2): #Fix upper flux bound for photon uptake set_bounds('Im_hnu', (v_hnu_exp2 * hnu_ratio, v_hnu_exp2 * hnu_ratio), c3_model_exp2) #Optimize/Maximize sucrose output result_exp2_2_fba = c3_model_exp2.optimize('maximize') #perform FBA #Optimize/Minimize total flux if result_exp2_2_fba.status == 'optimal': # check if feasible result_exp2_2_pfba = cobra.flux_analysis.parsimonious.pfba(c3_model_exp2) #perform pFBA if result_exp2_2_pfba.status == 'optimal': df_result_exp2[v_hnu_exp2 * hnu_ratio] = result_exp2_2_pfba.fluxes</code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 23: Experiment 2 -- Effect of PPFD </code></pre> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code> 0%| | 0/21 [00:00<?, ?it/s]</code></pre> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>/Users/blaetke/opt/anaconda3/envs/elife-49305-era/lib/python3.9/site-packages/cobra/util/solver.py:508: UserWarning: Solver status is 'infeasible'. </code></pre> </figure> </stencila-code-chunk> <figure itemscope="" itemtype="http://schema.stenci.la/Figure" id="fig1s2" title="Figure 1—figure supplement 2"><label data-itemprop="label">Figure 1—figure supplement 2</label> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="24" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>###################################################################### ############## Figure 1—figure supplement 2 ############## ###################################################################### #{ # "caption": "#### PPFD variation. Dependence of phloem output on the PPFD in the range 0 μmol/(m^2^s)–400 μmol/(m^2^s). Sucrose and starch are produced in the same amounts, each of them consists of 12 C-atoms.", # "id": "fig1s2, # "label": "Figure 1—figure supplement 2", # "trusted": true #} #Define reactions of interest by id r_ids_exp2 = ['Ex_Suc','Ex_AA'] #Create figure fig_exp2 = go.Figure() #Add traces for reactions of interest for r_id in r_ids_exp2: #Create trace trace = go.Scatter( y = df_result_exp2.loc[r_id,:], x = df_result_exp2.columns, name = r_id, mode = 'lines+markers', ) #Add trace fig_exp2.add_trace(trace) #Update xaxes fig_exp2.update_xaxes( title = dict( text = '<b>PPFD [µE]</b>', font = dict(size=18) ), tickfont = dict(size=16) ) #Update yaxes fig_exp2.update_yaxes( title = dict( text = 'Flux [µmol/(m\u00B2s)]', font = dict(size=18) ), tickfont = dict(size=16) ) #Update layout fig_exp2.update_layout( width=1000, height=500, title = dict( text='Phloem Export', x=0.5, font=dict(size=20) ), legend=dict( font=dict(size=18), ) ) #Show figure fig_exp2.show()</code></pre> <figure slot="outputs"> <stencila-image-plotly> <picture> <script type="application/vnd.plotly.v1+json"> {"config":{"plotlyServerURL":"https://plot.ly"},"data":[{"mode":"lines+markers","name":"Ex_Suc","type":"scatter","x":[19.371121164846407,38.742242329692814,58.11336349453923,77.48448465938563,96.85560582423203,116.22672698907846,135.59784815392484,154.96896931877126,174.34009048361764,193.71121164846406,213.08233281331047,232.45345397815692,251.82457514300327,271.1956963078497,290.5668174726961,309.9379386375425,329.30905980238896,348.6801809672353,368.05130213208173,387.4224232969281],"y":[0.07626410540071105,0.15322582229672554,0.23018753919273882,0.30714925608875343,0.3841109729847692,0.4610726898807833,0.5380344067767904,0.614996123672806,0.6919578405688215,0.7671787003295384,0.7671787003295389,0.767178700329537,0.7671787003295369,0.7671787003295362,0.7671787003295373,0.7671787003295346,0.7671787003295393,0.767178700329536,0.76717870032954,0.767178700329536]},{"mode":"lines+markers","name":"Ex_AA","type":"scatter","x":[19.371121164846407,38.742242329692814,58.11336349453923,77.48448465938563,96.85560582423203,116.22672698907846,135.59784815392484,154.96896931877126,174.34009048361764,193.71121164846406,213.08233281331047,232.45345397815692,251.82457514300327,271.1956963078497,290.5668174726961,309.9379386375425,329.30905980238896,348.6801809672353,368.05130213208173,387.4224232969281],"y":[0.03466550245486863,0.06964810104396617,0.10463069963306311,0.13961329822216065,0.17459589681125873,0.20957849540035606,0.2445610939894502,0.27954369257854816,0.3145262911676461,0.34871759105888106,0.34871759105888134,0.34871759105888045,0.3487175910588804,0.34871759105888006,0.3487175910588806,0.3487175910588794,0.3487175910588815,0.34871759105887995,0.34871759105888184,0.34871759105887995]}],"layout":{"height":500,"legend":{"font":{"size":18}},"template":{"data":{"bar":[{"error_x":{"color":"#2a3f5f"},"error_y":{"color":"#2a3f5f"},"marker":{"line":{"color":"#E5ECF6","width":0.5}},"type":"bar"}],"barpolar":[{"marker":{"line":{"color":"#E5ECF6","width":0.5}},"type":"barpolar"}],"carpet":[{"aaxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"baxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"type":"carpet"}],"choropleth":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"choropleth"}],"contour":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"contour"}],"contourcarpet":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"contourcarpet"}],"heatmap":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"heatmap"}],"heatmapgl":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"heatmapgl"}],"histogram":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"histogram"}],"histogram2d":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"histogram2d"}],"histogram2dcontour":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"histogram2dcontour"}],"mesh3d":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"mesh3d"}],"parcoords":[{"line":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"parcoords"}],"pie":[{"automargin":true,"type":"pie"}],"scatter":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatter"}],"scatter3d":[{"line":{"colorbar":{"outlinewidth":0,"ticks":""}},"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatter3d"}],"scattercarpet":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattercarpet"}],"scattergeo":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattergeo"}],"scattergl":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattergl"}],"scattermapbox":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattermapbox"}],"scatterpolar":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterpolar"}],"scatterpolargl":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterpolargl"}],"scatterternary":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterternary"}],"surface":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"surface"}],"table":[{"cells":{"fill":{"color":"#EBF0F8"},"line":{"color":"white"}},"header":{"fill":{"color":"#C8D4E3"},"line":{"color":"white"}},"type":"table"}]},"layout":{"annotationdefaults":{"arrowcolor":"#2a3f5f","arrowhead":0,"arrowwidth":1},"autotypenumbers":"strict","coloraxis":{"colorbar":{"outlinewidth":0,"ticks":""}},"colorscale":{"diverging":[[0,"#8e0152"],[0.1,"#c51b7d"],[0.2,"#de77ae"],[0.3,"#f1b6da"],[0.4,"#fde0ef"],[0.5,"#f7f7f7"],[0.6,"#e6f5d0"],[0.7,"#b8e186"],[0.8,"#7fbc41"],[0.9,"#4d9221"],[1,"#276419"]],"sequential":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"sequentialminus":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]]},"colorway":["#636efa","#EF553B","#00cc96","#ab63fa","#FFA15A","#19d3f3","#FF6692","#B6E880","#FF97FF","#FECB52"],"font":{"color":"#2a3f5f"},"geo":{"bgcolor":"white","lakecolor":"white","landcolor":"#E5ECF6","showlakes":true,"showland":true,"subunitcolor":"white"},"hoverlabel":{"align":"left"},"hovermode":"closest","mapbox":{"style":"light"},"paper_bgcolor":"white","plot_bgcolor":"#E5ECF6","polar":{"angularaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"bgcolor":"#E5ECF6","radialaxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"scene":{"xaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"},"yaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"},"zaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"}},"shapedefaults":{"line":{"color":"#2a3f5f"}},"ternary":{"aaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"baxis":{"gridcolor":"white","linecolor":"white","ticks":""},"bgcolor":"#E5ECF6","caxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"title":{"x":0.05},"xaxis":{"automargin":true,"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","zerolinewidth":2},"yaxis":{"automargin":true,"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","zerolinewidth":2}}},"title":{"font":{"size":20},"text":"Phloem Export","x":0.5},"width":1000,"xaxis":{"tickfont":{"size":16},"title":{"font":{"size":18},"text":"<b>PPFD [µE]</b>"}},"yaxis":{"tickfont":{"size":16},"title":{"font":{"size":18},"text":"Flux [µmol/(m²s)]"}}}} </script><img src="index.html.media/1" alt="" itemscope="" itemtype="http://schema.org/ImageObject"> </picture> </stencila-image-plotly> </figure> </stencila-code-chunk> <figcaption> <h5 itemscope="" itemtype="http://schema.stenci.la/Heading" id="ppfd-variation-dependence-of-phloem-output-on-the-ppfd-in-the-range-0-μmolm2s400-μmolm2s-sucrose-and-starch-are-produced-in-the-same-amounts-each-of-them-consists-of-12-c-atoms"> PPFD variation. Dependence of phloem output on the PPFD in the range 0 μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s)–400 μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s). Sucrose and starch are produced in the same amounts, each of them consists of 12 C-atoms.</h5> </figcaption> </figure> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="25" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>###################################################################################################################################### ###################################################################################################################################### ############## EXPERIMENT 3: Simulate C3 Fluxes ############## ###################################################################################################################################### ###################################################################################################################################### print(f"Code Cell 25: Experiment 3 -- Simulate C3 Fluxes") #Create copy of c3 model c3_model_exp3 = c3_model.copy() #Optimize/Maximize sucrose output result_exp3_fba = c3_model_exp3.optimize('maximize') #Optimize/Minimize total flux if result_exp3_fba.status == 'optimal': result_exp3_pfba = cobra.flux_analysis.parsimonious.pfba(c3_model_exp3) #Load GO Term Database goDB = obo_parser.GODag('elife-49305.ipython.src/go_basic.obo') def get_go_term(go_ids): if isinstance(go_ids, list): go_terms = [goDB[go_id].name for go_id in go_ids] else: go_terms= [goDB[go_ids].name] return go_terms #Filter all biochemical reactions c3_biochem_rxn = c3_model_exp3.reactions.query(lambda x: ~x.id.startswith('Tr') and ~x.id.startswith('Ex') and ~x.id.startswith('Im')) #Grab annotation provided for the biochemical reactions, keep only GO IDs df_anno = pd.DataFrame( c3_biochem_rxn.list_attr('annotation'), index=c3_biochem_rxn.list_attr('id') ).drop(['doi','ec-code','kegg.reaction','pubmed','isbn'], axis=1) #Get GO Terms of GO IDs df_anno['go term'] = df_anno['go'].apply(lambda go_ids: get_go_term(go_ids)) #Create Dataframe mapping GO IDs to biochemical reactions df_go_term = pd.DataFrame(False,index=df_anno.index, columns=set(df_anno['go term'].sum())) for r_id in df_anno.index: df_go_term.loc[r_id,df_anno.loc[r_id,'go term'][0]] = True #Define metabolites of interest (here energy equivalents) met_classes = ['ATP','NADH', 'NADPH'] #Set up list to store Go terms go_terms = [] #Search for all GO terms related to the reactions the metabolites are involved in for met_class in met_classes: #Find the specific metabolite ids in all compartments met_ids = c3_model_exp3.metabolites.query(lambda x: x.id.startswith(met_class)).list_attr('id') #Find reactions reactions and assigned GO Terms for all the metabolites for met_id in met_ids: #Get reaction ids rxn_ids = [r_obj.id for r_obj in c3_model_exp3.metabolites.get_by_id(met_id).reactions] #Get & collect GO Terms go_terms += df_anno.loc[df_anno.index.intersection(rxn_ids),'go term'].sum() #Create final list of all unique GO Terms go_terms = list(set(go_terms)) go_terms = sorted(go_terms) + ['Others']</code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 25: Experiment 3 -- Simulate C3 Fluxes elife-49305.ipython.src/go_basic.obo: fmt(1.2) rel(2017-10-20) 47,002 GO Terms </code></pre> </figure> </stencila-code-chunk> <figure itemscope="" itemtype="http://schema.stenci.la/Figure" id="fig1s3" title="Figure 1—figure supplement 3"><label data-itemprop="label">Figure 1—figure supplement 3</label> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-scrolled="false" data-execution_count="26" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>############################################################################## ############## Figure 1—figure supplement 3 ############## ############################################################################## #{ # "caption": "### Energy Flux Distribution in the _one-cell_ Model. (**A**) ATP production and consumption, (**B**) NADPH production and consumption, (**C**) NADH production and consumption.", # "id": "fig1s3", # "label": "Figure 1—figure supplement 3", # "trusted": true #} def get_flux_by_go_term(df_rxn_go_term, rxn_fluxes): ''' Return flux sum for go terms Parameters: rxn_fluxes (dict): dictionary of reactions and their flux values df_rxn_go_term (dataframe): dataframe relating reactions and go terms Returns: df_rxn_go_term_flux (dataframe): go term related to prodcution of a specified energy equivalent and flux sum ''' #Convert dictionary of reaction fluxes into series s_rxn_fluxes = pd.Series(rxn_fluxes) #Get flux sum flux_sum = s_rxn_fluxes.sum() #Determine flux sum for go terms s_rxn_fluxes = s_rxn_fluxes[s_rxn_fluxes / flux_sum > 0.01] df_rxn_go_term = df_rxn_go_term.loc[s_rxn_fluxes.index, df_rxn_go_term.loc[s_rxn_fluxes.index,:].sum() > 0] df_rxn_go_term_flux = df_rxn_go_term.mul(s_rxn_fluxes[s_rxn_fluxes.index.intersection(df_rxn_go_term.index)],axis=0).sum() df_rxn_go_term_flux['Others'] = flux_sum - df_rxn_go_term_flux.sum() return df_rxn_go_term_flux def prod_cons_charts(met_id, rxn_fluxes_prod, rxn_fluxes_cons, go_terms, df_rxn_go_term): ''' Creates figure with two pie charts for production and consumption of a specified energy equivalent, and returns two lists of go terms related to the production and consumption Parameters: met_id (int): metabolite id of the energy equivalent rxn_fluxes_prod (dict): dictionary of reactions producing the energy equivalents and their flux values rxn_fluxes_cons (dict): dictionary of reactions consuming the energy equivalents and their flux values go_terms (list): list of all go terms df_rxn_go_term (dataframe): dataframe relating reactions and go terms Returns: trace_prod (plotly trace): pie chart of go term related to prodcution go_term_fluxes_prod (dataframe): go term related to prodcution of a specified energy equivalent and flux sum trace_cons (plotly trace): pie chart of go term related to consumption go_term_fluxes_cons (dataframe): go term related to consumption of a specified energy equivalent and flux sum ''' #Get GO terms for production and consuption of energy equivalent go_term_fluxes_prod = get_flux_by_go_term(df_rxn_go_term, rxn_fluxes_prod) go_term_fluxes_cons = get_flux_by_go_term(df_rxn_go_term, rxn_fluxes_cons) #Create index of GO terms for production and consuption of energy equivalent go_term_index = go_term_fluxes_prod.index.union(go_term_fluxes_cons.index) #Create trace for GO terms of energy equivalent production trace_prod = go.Pie( labels = go_term_fluxes_prod.index, values = go_term_fluxes_prod, marker=dict(line=dict(color='#FFF', width=1)), ) #Create trace for GO terms of energy equivalent consumption trace_cons = go.Pie( labels = go_term_fluxes_cons.index, values = go_term_fluxes_cons, marker=dict(line=dict(color='#FFF', width=1)), ) return trace_prod, go_term_fluxes_prod, trace_cons, go_term_fluxes_cons #Set up Dataframe to store total production and consumption flux per metabolite class df_prod_cons = pd.DataFrame(index=met_classes, columns=['Production', 'Consumption']) df_prod_cons_percentage = pd.DataFrame(index=go_terms) #Create figure with subplots fig_exp31 = make_subplots( rows=3, cols=2, subplot_titles = ['<b>Production</b>','<b>Consumption</b>'] * 3, row_titles = [f'<b>({list(string.ascii_uppercase)[i]}) {met_class}</b>' for i, met_class in enumerate(met_classes)], specs=[[{"type": "pie"}, {"type": "pie"}],[{"type": "pie"}, {"type": "pie"}],[{"type": "pie"}, {"type": "pie"}]], vertical_spacing = 0.0 ) #Create pie charts reflecting the proportions of a metabolite class produced or consumped by Go Terms for i, met_class in enumerate(met_classes): #Find the specific metabolite ids in all compartments met_ids = c3_model_exp3.metabolites.query(lambda x: x.id.startswith(met_class)).list_attr('id') #Set up dictionaries to hold fluxes producing or consuming a certain metabolite fluxes_prod_met_class = {} fluxes_cons_met_class = {} for met_id in met_ids: #Get reactions and fluxes producing or consuming a certain metabolite (excluding transport, import and export reactions) fluxes = {r_obj.id: result_exp3_pfba.fluxes[r_obj.id] * r_obj.get_coefficient(met_id) for r_obj in c3_model_exp3.metabolites.get_by_id(met_id).reactions if not r_obj.id[:3] in ['Tr_', 'Im_', 'Ex_']} #Extract reactions and fluxes producing a certain metabolite fluxes_prod = {r_id: abs(flux) for r_id, flux in fluxes.items() if flux > 0} fluxes_prod_met_class = {**fluxes_prod_met_class, **fluxes_prod} #Extract reactions and fluxes consuming a certain metabolite fluxes_cons = {r_id: abs(flux) for r_id, flux in fluxes.items() if flux < 0} fluxes_cons_met_class = {**fluxes_cons_met_class, **fluxes_cons} #Store total fluxes df_prod_cons.loc[met_class] = [sum(fluxes_prod_met_class.values()), sum(fluxes_cons_met_class.values())] #Plot porportion of fluxes by Go Terms trace_prod, go_term_fluxes_prod, trace_cons, go_term_fluxes_cons = prod_cons_charts(met_class, fluxes_prod_met_class, fluxes_cons_met_class, go_terms, df_go_term) #Add trace to figure #fig_exp31.append_trace(trace_go,i+1,1) #Add trace to figure fig_exp31.append_trace(trace_prod,i+1,1) #Add trace to figure fig_exp31.append_trace(trace_cons,i+1,2) #save flux sum for GO Terms df_prod_cons_percentage[f'{met_class}_prod'] = np.nan df_prod_cons_percentage[f'{met_class}_prod'].loc[go_term_fluxes_prod.index] = go_term_fluxes_prod df_prod_cons_percentage[f'{met_class}_cons'] = np.nan df_prod_cons_percentage[f'{met_class}_cons'].loc[go_term_fluxes_cons.index] = go_term_fluxes_cons df_prod_cons_percentage.dropna(how='all', inplace=True) df_prod_cons_percentage = df_prod_cons_percentage / df_prod_cons_percentage.sum() * 100 df_prod_percentage = df_prod_cons.loc[:,'Production'] / df_prod_cons['Production'].sum() * 100 #Update traces fig_exp31.update_traces( textposition='inside', textinfo='percent' ) #Get all GO terms in figure go_term_labels = list(set([label for trace in fig_exp31['data'] for label in trace['labels']])) #Create list colors according to number of GO terms in figure colors = ['hsl('+str(h)+',50%'+',50%)' for h in np.linspace(0, 360, len(go_term_labels))] #Assign color to GO term go_term_color = pd.Series(index=go_term_labels, data=colors) #Re-color trace in figure for trace in fig_exp31['data']: trace['marker']['colors'] = go_term_color[trace['labels']].values #Update annotations fig_exp31.update_annotations( font=dict(size=18) ) #Re-position subfigure enumeration for anno in fig_exp31['layout']['annotations']: if anno['xanchor'] == 'left': anno['x'] = 0.1 anno['y'] = anno['y'] + 0.15 anno['textangle'] = 0 anno['xanchor'] = 'right' if 'Production' in anno['text'] or 'Consumption' in anno['text']: anno['y'] = anno['y'] - 0.025 #Update layout fig_exp31.update_layout( uniformtext_minsize=12, uniformtext_mode='hide', width=1000, height=2000, legend=dict( font=dict(size=18), orientation = 'h', xanchor = 'center', x = 0.5, y = 0.05 ) ) #Show figure fig_exp31.show()</code></pre> <figure slot="outputs"> <stencila-image-plotly> <picture> <script type="application/vnd.plotly.v1+json"> {"config":{"plotlyServerURL":"https://plot.ly"},"data":[{"domain":{"x":[0,0.44],"y":[0.6666666666666666,1]},"labels":["photosynthesis, light reaction","canonical glycolysis","oxidative phosphorylation","Others"],"marker":{"colors":["hsl(221.53846153846155,50%,50%)","hsl(83.07692307692308,50%,50%)","hsl(110.76923076923077,50%,50%)","hsl(27.692307692307693,50%,50%)"],"line":{"color":"#FFF","width":1}},"textinfo":"percent","textposition":"inside","type":"pie","values":[72.64170436817403,1.121464544442154,0.755266715283052,0.2249228462329853]},{"domain":{"x":[0.54,0.98],"y":[0.6666666666666666,1]},"labels":["reductive pentose-phosphate cycle","photorespiration","starch biosynthetic process","nucleotide metabolic process","Others"],"marker":{"colors":["hsl(332.3076923076923,50%,50%)","hsl(360.0,50%,50%)","hsl(55.38461538461539,50%,50%)","hsl(249.23076923076923,50%,50%)","hsl(27.692307692307693,50%,50%)"],"line":{"color":"#FFF","width":1}},"textinfo":"percent","textposition":"inside","type":"pie","values":[69.30004832889051,1.0244588683012938,1.5343574006590757,0.7671787003295376,1.0540752408132619]},{"domain":{"x":[0,0.44],"y":[0.3333333333333333,0.6666666666666666]},"labels":["gluconeogenesis","photorespiration","canonical glycolysis","pyruvate dehydrogenase activity","Others"],"marker":{"colors":["hsl(166.15384615384616,50%,50%)","hsl(360.0,50%,50%)","hsl(83.07692307692308,50%,50%)","hsl(276.9230769230769,50%,50%)","hsl(27.692307692307693,50%,50%)"],"line":{"color":"#FFF","width":1}},"textinfo":"percent","textposition":"inside","type":"pie","values":[0.6795084822307396,1.0593306274071819,1.121464544442154,0.16110752706920287,0.011158962913884629]},{"domain":{"x":[0.54,0.98],"y":[0.3333333333333333,0.6666666666666666]},"labels":["alternative respiration","glutamate biosynthetic process","photorespiration","nitrate assimilation","glyoxylate cycle","Others"],"marker":{"colors":["hsl(0.0,50%,50%)","hsl(138.46153846153845,50%,50%)","hsl(360.0,50%,50%)","hsl(193.84615384615387,50%,50%)","hsl(304.61538461538464,50%,50%)","hsl(27.692307692307693,50%,50%)"],"line":{"color":"#FFF","width":1}},"textinfo":"percent","textposition":"inside","type":"pie","values":[0.22658001458491558,0.4969290699457337,1.0244588683012938,0.778257746326894,0.49692906994573555,0.00941537495858924]},{"domain":{"x":[0,0.44],"y":[0,0.3333333333333333]},"labels":["photosynthesis, light reaction","Others"],"marker":{"colors":["hsl(221.53846153846155,50%,50%)","hsl(27.692307692307693,50%,50%)"],"line":{"color":"#FFF","width":1}},"textinfo":"percent","textposition":"inside","type":"pie","values":[46.31579482186791,0.41349914607931026]},{"domain":{"x":[0.54,0.98],"y":[0,0.3333333333333333]},"labels":["reductive pentose-phosphate cycle","Others"],"marker":{"colors":["hsl(332.3076923076923,50%,50%)","hsl(27.692307692307693,50%,50%)"],"line":{"color":"#FFF","width":1}},"textinfo":"percent","textposition":"inside","type":"pie","values":[46.035225766495344,0.6940682014518487]}],"layout":{"annotations":[{"font":{"size":18},"showarrow":false,"text":"<b>Production</b>","x":0.22,"xanchor":"center","xref":"paper","y":0.975,"yanchor":"bottom","yref":"paper"},{"font":{"size":18},"showarrow":false,"text":"<b>Consumption</b>","x":0.76,"xanchor":"center","xref":"paper","y":0.975,"yanchor":"bottom","yref":"paper"},{"font":{"size":18},"showarrow":false,"text":"<b>Production</b>","x":0.22,"xanchor":"center","xref":"paper","y":0.6416666666666666,"yanchor":"bottom","yref":"paper"},{"font":{"size":18},"showarrow":false,"text":"<b>Consumption</b>","x":0.76,"xanchor":"center","xref":"paper","y":0.6416666666666666,"yanchor":"bottom","yref":"paper"},{"font":{"size":18},"showarrow":false,"text":"<b>Production</b>","x":0.22,"xanchor":"center","xref":"paper","y":0.3083333333333333,"yanchor":"bottom","yref":"paper"},{"font":{"size":18},"showarrow":false,"text":"<b>Consumption</b>","x":0.76,"xanchor":"center","xref":"paper","y":0.3083333333333333,"yanchor":"bottom","yref":"paper"},{"font":{"size":18},"showarrow":false,"text":"<b>(A) ATP</b>","textangle":0,"x":0.1,"xanchor":"right","xref":"paper","y":0.9833333333333333,"yanchor":"middle","yref":"paper"},{"font":{"size":18},"showarrow":false,"text":"<b>(B) NADH</b>","textangle":0,"x":0.1,"xanchor":"right","xref":"paper","y":0.65,"yanchor":"middle","yref":"paper"},{"font":{"size":18},"showarrow":false,"text":"<b>(C) NADPH</b>","textangle":0,"x":0.1,"xanchor":"right","xref":"paper","y":0.31666666666666665,"yanchor":"middle","yref":"paper"}],"height":2000,"legend":{"font":{"size":18},"orientation":"h","x":0.5,"xanchor":"center","y":0.05},"template":{"data":{"bar":[{"error_x":{"color":"#2a3f5f"},"error_y":{"color":"#2a3f5f"},"marker":{"line":{"color":"#E5ECF6","width":0.5}},"type":"bar"}],"barpolar":[{"marker":{"line":{"color":"#E5ECF6","width":0.5}},"type":"barpolar"}],"carpet":[{"aaxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"baxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"type":"carpet"}],"choropleth":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"choropleth"}],"contour":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"contour"}],"contourcarpet":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"contourcarpet"}],"heatmap":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"heatmap"}],"heatmapgl":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"heatmapgl"}],"histogram":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"histogram"}],"histogram2d":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"histogram2d"}],"histogram2dcontour":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"histogram2dcontour"}],"mesh3d":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"mesh3d"}],"parcoords":[{"line":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"parcoords"}],"pie":[{"automargin":true,"type":"pie"}],"scatter":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatter"}],"scatter3d":[{"line":{"colorbar":{"outlinewidth":0,"ticks":""}},"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatter3d"}],"scattercarpet":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattercarpet"}],"scattergeo":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattergeo"}],"scattergl":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattergl"}],"scattermapbox":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattermapbox"}],"scatterpolar":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterpolar"}],"scatterpolargl":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterpolargl"}],"scatterternary":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterternary"}],"surface":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"surface"}],"table":[{"cells":{"fill":{"color":"#EBF0F8"},"line":{"color":"white"}},"header":{"fill":{"color":"#C8D4E3"},"line":{"color":"white"}},"type":"table"}]},"layout":{"annotationdefaults":{"arrowcolor":"#2a3f5f","arrowhead":0,"arrowwidth":1},"autotypenumbers":"strict","coloraxis":{"colorbar":{"outlinewidth":0,"ticks":""}},"colorscale":{"diverging":[[0,"#8e0152"],[0.1,"#c51b7d"],[0.2,"#de77ae"],[0.3,"#f1b6da"],[0.4,"#fde0ef"],[0.5,"#f7f7f7"],[0.6,"#e6f5d0"],[0.7,"#b8e186"],[0.8,"#7fbc41"],[0.9,"#4d9221"],[1,"#276419"]],"sequential":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"sequentialminus":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]]},"colorway":["#636efa","#EF553B","#00cc96","#ab63fa","#FFA15A","#19d3f3","#FF6692","#B6E880","#FF97FF","#FECB52"],"font":{"color":"#2a3f5f"},"geo":{"bgcolor":"white","lakecolor":"white","landcolor":"#E5ECF6","showlakes":true,"showland":true,"subunitcolor":"white"},"hoverlabel":{"align":"left"},"hovermode":"closest","mapbox":{"style":"light"},"paper_bgcolor":"white","plot_bgcolor":"#E5ECF6","polar":{"angularaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"bgcolor":"#E5ECF6","radialaxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"scene":{"xaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"},"yaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"},"zaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"}},"shapedefaults":{"line":{"color":"#2a3f5f"}},"ternary":{"aaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"baxis":{"gridcolor":"white","linecolor":"white","ticks":""},"bgcolor":"#E5ECF6","caxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"title":{"x":0.05},"xaxis":{"automargin":true,"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","zerolinewidth":2},"yaxis":{"automargin":true,"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","zerolinewidth":2}}},"uniformtext":{"minsize":12,"mode":"hide"},"width":1000}} </script><img src="index.html.media/2" alt="" itemscope="" itemtype="http://schema.org/ImageObject"> </picture> </stencila-image-plotly> </figure> </stencila-code-chunk> <figcaption> <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="energy-flux-distribution-in-the-one-cell-model-a-atp-production-and-consumption-b-nadph-production-and-consumption-c-nadh-production-and-consumption"> Energy Flux Distribution in the <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">one-cell</em> Model. (<strong itemscope="" itemtype="http://schema.stenci.la/Strong">A</strong>) ATP production and consumption, (<strong itemscope="" itemtype="http://schema.stenci.la/Strong">B</strong>) NADPH production and consumption, (<strong itemscope="" itemtype="http://schema.stenci.la/Strong">C</strong>) NADH production and consumption.</h4> </figcaption> </figure> <figure itemscope="" itemtype="http://schema.stenci.la/Figure" id="fig1s4" title="Figure 1—figure supplement 4"><label data-itemprop="label">Figure 1—figure supplement 4</label> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="27" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>######################################################################### ############## Figure 1—figure supplement 4 ############## ######################################################################### #{ # "caption": "### Energy Flux Distribution in the _one-cell_ Model. (**A**) proportion of ATP, NADPH, NADH used as energy equivalent, (**B**) proportion of respiratory ATP used for maintenance.", # "id": "fig1s4", # "label": "Figure 1—figure supplement 4", # "trusted": true #} #Create figure with subplots fig_exp32 = make_subplots( rows=1, cols=2, subplot_titles = ['<b>(A) Proportion of Energy Equivalents</b>', '<b>(B) Proportion of Respiratory ATP</b>'], specs=[[{"type": "pie"}, {"type": "pie"}]]) #Create trace for energy equivalents trace_energy = go.Pie( labels = df_prod_cons.index, values = df_prod_cons['Production'], marker=dict(line=dict(color='#FFF', width=1)), showlegend = False, ) #Add trace to figure fig_exp32.append_trace(trace_energy,1,1) #Create trace for energy maintenace in respect to respiratory ATP rxn_maintenance = ['NGAM_h','NGAM_c','NGAM_m'] rxn_maintenance_flux = [result_exp3_pfba.fluxes[r_id] for r_id in rxn_maintenance] atp_flux = result_exp3_pfba.fluxes['cplx5_m'] * c3_model_exp3.reactions.get_by_id('cplx5_m').get_coefficient('ATP_m') atp_maintenance_percentage = sum(rxn_maintenance_flux) / (atp_flux) * 100 trace_maintenance = go.Pie( labels = rxn_maintenance + ['Others'], values = rxn_maintenance_flux + [atp_flux - sum(rxn_maintenance_flux)], textfont=dict(size=18,family='Arial',), marker=dict(line=dict(color='#FFF', width=1)), showlegend = False, ) #Add trace to figure fig_exp32.append_trace(trace_maintenance,1,2) #Update traces fig_exp32.update_traces( textposition='outside', textinfo='percent+label' ) #Update annotations fig_exp32.update_annotations( font=dict(size=18) ) #Update layout fig_exp32.update_layout( uniformtext_minsize=16, uniformtext_mode='hide', width=1000, height=500) #Show figure fig_exp32.show()</code></pre> <figure slot="outputs"> <stencila-image-plotly> <picture> <script type="application/vnd.plotly.v1+json"> {"config":{"plotlyServerURL":"https://plot.ly"},"data":[{"domain":{"x":[0,0.45],"y":[0,1]},"labels":["ATP","NADH","NADPH"],"marker":{"line":{"color":"#FFF","width":1}},"showlegend":false,"textinfo":"percent+label","textposition":"outside","type":"pie","values":[74.74335847413222,3.0325701440631625,46.72929396794722]},{"domain":{"x":[0.55,1],"y":[0,1]},"labels":["NGAM_h","NGAM_c","NGAM_m","Others"],"marker":{"line":{"color":"#FFF","width":1}},"showlegend":false,"textfont":{"family":"Arial","size":18},"textinfo":"percent+label","textposition":"outside","type":"pie","values":[0.152707083279744,0.0503499796174949,0.00911118724550157,0.5430984651403115]}],"layout":{"annotations":[{"font":{"size":18},"showarrow":false,"text":"<b>(A) Proportion of Energy Equivalents</b>","x":0.225,"xanchor":"center","xref":"paper","y":1,"yanchor":"bottom","yref":"paper"},{"font":{"size":18},"showarrow":false,"text":"<b>(B) Proportion of Respiratory ATP</b>","x":0.775,"xanchor":"center","xref":"paper","y":1,"yanchor":"bottom","yref":"paper"}],"height":500,"template":{"data":{"bar":[{"error_x":{"color":"#2a3f5f"},"error_y":{"color":"#2a3f5f"},"marker":{"line":{"color":"#E5ECF6","width":0.5}},"type":"bar"}],"barpolar":[{"marker":{"line":{"color":"#E5ECF6","width":0.5}},"type":"barpolar"}],"carpet":[{"aaxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"baxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"type":"carpet"}],"choropleth":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"choropleth"}],"contour":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"contour"}],"contourcarpet":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"contourcarpet"}],"heatmap":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"heatmap"}],"heatmapgl":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"heatmapgl"}],"histogram":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"histogram"}],"histogram2d":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"histogram2d"}],"histogram2dcontour":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"histogram2dcontour"}],"mesh3d":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"mesh3d"}],"parcoords":[{"line":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"parcoords"}],"pie":[{"automargin":true,"type":"pie"}],"scatter":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatter"}],"scatter3d":[{"line":{"colorbar":{"outlinewidth":0,"ticks":""}},"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatter3d"}],"scattercarpet":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattercarpet"}],"scattergeo":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattergeo"}],"scattergl":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattergl"}],"scattermapbox":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattermapbox"}],"scatterpolar":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterpolar"}],"scatterpolargl":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterpolargl"}],"scatterternary":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterternary"}],"surface":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"surface"}],"table":[{"cells":{"fill":{"color":"#EBF0F8"},"line":{"color":"white"}},"header":{"fill":{"color":"#C8D4E3"},"line":{"color":"white"}},"type":"table"}]},"layout":{"annotationdefaults":{"arrowcolor":"#2a3f5f","arrowhead":0,"arrowwidth":1},"autotypenumbers":"strict","coloraxis":{"colorbar":{"outlinewidth":0,"ticks":""}},"colorscale":{"diverging":[[0,"#8e0152"],[0.1,"#c51b7d"],[0.2,"#de77ae"],[0.3,"#f1b6da"],[0.4,"#fde0ef"],[0.5,"#f7f7f7"],[0.6,"#e6f5d0"],[0.7,"#b8e186"],[0.8,"#7fbc41"],[0.9,"#4d9221"],[1,"#276419"]],"sequential":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"sequentialminus":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]]},"colorway":["#636efa","#EF553B","#00cc96","#ab63fa","#FFA15A","#19d3f3","#FF6692","#B6E880","#FF97FF","#FECB52"],"font":{"color":"#2a3f5f"},"geo":{"bgcolor":"white","lakecolor":"white","landcolor":"#E5ECF6","showlakes":true,"showland":true,"subunitcolor":"white"},"hoverlabel":{"align":"left"},"hovermode":"closest","mapbox":{"style":"light"},"paper_bgcolor":"white","plot_bgcolor":"#E5ECF6","polar":{"angularaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"bgcolor":"#E5ECF6","radialaxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"scene":{"xaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"},"yaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"},"zaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"}},"shapedefaults":{"line":{"color":"#2a3f5f"}},"ternary":{"aaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"baxis":{"gridcolor":"white","linecolor":"white","ticks":""},"bgcolor":"#E5ECF6","caxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"title":{"x":0.05},"xaxis":{"automargin":true,"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","zerolinewidth":2},"yaxis":{"automargin":true,"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","zerolinewidth":2}}},"uniformtext":{"minsize":16,"mode":"hide"},"width":1000}} </script><img src="index.html.media/3" alt="" itemscope="" itemtype="http://schema.org/ImageObject"> </picture> </stencila-image-plotly> </figure> </stencila-code-chunk> <figcaption> <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="energy-flux-distribution-in-the-one-cell-model-a-proportion-of-atp-nadph-nadh-used-as-energy-equivalent-b-proportion-of-respiratory-atp-used-for-maintenance"> Energy Flux Distribution in the <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">one-cell</em> Model. (<strong itemscope="" itemtype="http://schema.stenci.la/Strong">A</strong>) proportion of ATP, NADPH, NADH used as energy equivalent, (<strong itemscope="" itemtype="http://schema.stenci.la/Strong">B</strong>) proportion of respiratory ATP used for maintenance.</h4> </figcaption> </figure> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">The <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">one-cell</em> model requires a photosynthetic photon flux density (PPFD) of <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(result_exp3_pfba['Im_hnu'],2)</code><output slot="output"></output> </stencila-code-expression> μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s) (<a href="#table2" itemscope="" itemtype="http://schema.stenci.la/Link">Table 2</a>). The <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">one-cell</em> model takes up the maximal amount of CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> to produce the maximum amount of phloem sap, as well as <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(result_exp3_pfba['Im_NO3'],2)</code><output slot="output"></output> </stencila-code-expression> μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s) of NO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">3</span></sub><sup itemscope="" itemtype="http://schema.stenci.la/Superscript">-</sup> and <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(result_exp3_pfba['Im_H2O'],2)</code><output slot="output"></output> </stencila-code-expression> μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s) of H<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub>O. According to the assumed ratio of sucrose and amino acids in the phloem sap, the flux of sucrose predicted by the model is <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(result_exp3_pfba['Ex_Suc'],2)</code><output slot="output"></output> </stencila-code-expression> μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s) and of amino acids <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(result_exp3_pfba['Ex_AA'],2)</code><output slot="output"></output> </stencila-code-expression> μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s). The rate of oxygen supply by the network is <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(result_exp3_pfba['Ex_O2'],2)</code><output slot="output"></output> </stencila-code-expression> μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s). Part of the complete flux table is displayed in <a href="#table2" itemscope="" itemtype="http://schema.stenci.la/Link">Table 2</a>; the full table is available, see <a href="#fig1sdata2" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 1—source data 2</a>. The flux table of all reactions did not display circular fluxes, and the reactions were within expected physiological ranges (<a href="#fig1sdata2" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 1—source data 2</a>).</p> <table id="table2" itemscope="" itemtype="http://schema.org/Table"> <caption><label data-itemprop="label">Table 2.</label> <div itemprop="caption"> <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="inputoutput-fluxes-of-one-cell-model-in-comparison-to-physiological-observations"> Input/output fluxes of <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">one-cell</em> model in comparison to physiological observations.</h4> </div> </caption> <thead> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <th itemscope="" itemtype="http://schema.stenci.la/TableCell">Molecular Species</th> <th itemscope="" itemtype="http://schema.stenci.la/TableCell">Flux [µmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript">2</sup>/s)]</th> <th itemscope="" itemtype="http://schema.stenci.la/TableCell"> Physiological Range [µmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript">2</sup>/s)]</th> <th itemscope="" itemtype="http://schema.stenci.la/TableCell">Reference</th> </tr> </thead> <tbody> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">(i) Inputs</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Photons</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"> <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(result_exp3_pfba['Im_hnu'],2)</code><output slot="output"></output></stencila-code-expression> </td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">100 - 400</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib5"><span>5</span><span>Bailey et al.</span><span>2001</span></a></cite></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">CO2</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"> <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(result_exp3_pfba['Im_CO2'],2)</code><output slot="output"></output></stencila-code-expression> </td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">20</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib37"><span>37</span><span>Lacher</span><span>2003</span></a></cite> </td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">NO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript">3</sub><sup itemscope="" itemtype="http://schema.stenci.la/Superscript">-</sup></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"> <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(result_exp3_pfba['Im_NO3'],2)</code><output slot="output"></output></stencila-code-expression> </td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">0.11 - 0.18</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib35"><span>35</span><span>Kiba et al.</span><span>2012</span></a></cite></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">H<sub itemscope="" itemtype="http://schema.stenci.la/Subscript">2</sub>O</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"> <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(result_exp3_pfba['Im_H2O'],2)</code><output slot="output"></output></stencila-code-expression> </td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">-</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">(ii) Outputs</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">O<sub itemscope="" itemtype="http://schema.stenci.la/Subscript">2</sub></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"> <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(result_exp3_pfba['Ex_O2'],2)</code><output slot="output"></output></stencila-code-expression> </td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><span data-itemtype="http://schema.org/Number">16.5</span></td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"><cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib75"><span>75</span><span>Sun et al.</span><span>1999</span></a></cite> </td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Amino Acids</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"> <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(result_exp3_pfba['Ex_AA'],2)</code><output slot="output"></output></stencila-code-expression> </td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">-</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> </tr> <tr itemscope="" itemtype="http://schema.stenci.la/TableRow"> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">Sucrose/Starch</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"> <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(result_exp3_pfba['Ex_Suc'],2)</code><output slot="output"></output></stencila-code-expression> </td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell">-</td> <td itemscope="" itemtype="http://schema.stenci.la/TableCell"></td> </tr> </tbody> </table> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">The CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> uptake rate and the phloem sap output have a positive linear relationship, see <a href="#fig1s1" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 1—figure supplement 1</a>. The same is true for the correlation of the PPFD and phloem sap output in the range of 100 μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s)–200 μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s), see <a href="#fig1s2" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 1—figure supplement 2)</a>. Above 200 μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s), the CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> uptake rate acts as a limiting factor restricting the increase of phloem sap production. If either the PPFD or the CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> uptake rate is zero, the phloem sap cannot be produced, compare <a href="#fig1s1" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 1—figure supplement 1</a> and <a href="#fig1s2" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 1—figure supplement 2</a>. Most of the metabolic processes use ATP/ADP as main energy equivalent (<stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(df_prod_percentage['ATP'],2)</code><output slot="output"></output> </stencila-code-expression>%), followed by NADP/NADPH (<stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(df_prod_percentage['NADPH'],2)</code><output slot="output"></output> </stencila-code-expression>%) and NAD/NADH (<stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(df_prod_percentage['NADH'],2)</code><output slot="output"></output> </stencila-code-expression>%), see <a href="#fig1s4" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 1—figure supplement 4(A)</a>. Nearly all ATP is produced by the light reactions (<stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(df_prod_cons_percentage.loc['photosynthesis, light reaction','ATP_prod'],2)</code><output slot="output"></output> </stencila-code-expression>%) and consumed by the reductive pentose phosphate cycle ( <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(df_prod_cons_percentage.loc['reductive pentose-phosphate cycle','ATP_cons'],2)</code><output slot="output"></output></stencila-code-expression> %), see <a href="#fig1s3" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 1—figure supplement 3(A)</a>. The oxidative phosphorylation produces only ( <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(df_prod_cons_percentage.loc['oxidative phosphorylation','ATP_prod'],2)</code><output slot="output"></output> </stencila-code-expression>%) of ATP. In proportion, the maintenance cost for protein synthesis and degradation makeup <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(atp_maintenance_percentage,2)</code><output slot="output"></output> </stencila-code-expression>% of the respiratory ATP produced by the oxidative phosphorylation (<a href="#fig1s4" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 1—figure supplement 4(B)</a>). Similarly, nearly all NADPH is produced by the light reaction (<stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(df_prod_cons_percentage.loc['photosynthesis, light reaction','NADPH_prod'],2)</code><output slot="output"></output> </stencila-code-expression>%), which is consumed by the reductive pentose-phosphate cycle (<stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(df_prod_cons_percentage.loc['reductive pentose-phosphate cycle','NADPH_cons'],2)</code><output slot="output"></output> </stencila-code-expression>%) as well (<a href="#fig1s3" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 1—figure supplement 3(C)</a>). The canonical glycolysis and photorespiration produce nearly equal amounts of NADH, <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(df_prod_cons_percentage.loc['canonical glycolysis','NADH_prod'],2)</code><output slot="output"></output> </stencila-code-expression>% and <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(df_prod_cons_percentage.loc['photorespiration','NADH_prod'],2)</code><output slot="output"></output></stencila-code-expression>%), significantly less NADH is produced through gluconeogenesis (<stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(df_prod_cons_percentage.loc['gluconeogenesis','NADH_prod'],2)</code><output slot="output"></output></stencila-code-expression>%) and pyruvate dehydrogenase activity (<stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(df_prod_cons_percentage.loc['pyruvate dehydrogenase activity','NADH_prod'],2)</code><output slot="output"></output> </stencila-code-expression>)%. Photorespiration (<stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(df_prod_cons_percentage.loc['photorespiration','NADH_cons'],2)</code><output slot="output"></output></stencila-code-expression>%), Nitrate assimilation ( <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(df_prod_cons_percentage.loc['nitrate assimilation','NADH_cons'],2)</code><output slot="output"></output> </stencila-code-expression>%), glutamate biosynthesis (<stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(df_prod_cons_percentage.loc['glutamate biosynthetic process','NADH_cons'],2)</code><output slot="output"></output> </stencila-code-expression>%), glyoxylate cycle (<stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(df_prod_cons_percentage.loc['glyoxylate cycle','NADH_cons'],2)</code><output slot="output"></output> </stencila-code-expression>%) and alternative respiration (<stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(df_prod_cons_percentage.loc['alternative respiration','NADH_cons'],2)</code><output slot="output"></output> </stencila-code-expression>%) consume the produced NADH (<a href="#fig1s3" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 1—figure supplement 3(B)</a>).</p> <h3 itemscope="" itemtype="http://schema.stenci.la/Heading" id="a-c4-cycle-is-predicted-under-resource-limitation">A C4 cycle is predicted under resource limitation</h3> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">To rebuild the characteristic physiology of C4 leaves, we duplicated the <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">one-cell</em> model and connected the two network copies by bi-directional transport of cytosolic metabolites including amino acids, sugars, single phosphorylated sugars, mono-/di-/tri-carboxylic acids, glyceric acids, glycolate, glycerate, glyceraldehyde-3-phosphate, di-hydroxyacetone-phosphate and CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub>, see Materials and methods for details. Since CBM is limited to static model analysis, we introduced two Rubisco populations in the bundle sheath network to approximate CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> concentration-dependent changes in the oxygenation : carboxylation ratio of Rubisco (<span itemscope="" itemtype="http://schema.stenci.la/MathFragment"><span class="mjx-chtml"><span class="mjx-math" aria-label="{v}_{RBO}/{v}_{RBC}"><span class="mjx-mrow" aria-hidden="true"><span class="mjx-msubsup"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">v</span></span></span></span></span><span class="mjx-sub" style="font-size: 70.7%; vertical-align: -0.229em; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">R</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">B</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.519em; padding-bottom: 0.298em;">O</span></span></span></span></span></span><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mo"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.446em; padding-bottom: 0.593em;">/</span></span></span></span><span class="mjx-msubsup"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.298em;">v</span></span></span></span></span><span class="mjx-sub" style="font-size: 70.7%; vertical-align: -0.23em; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">R</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">B</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.519em; padding-bottom: 0.298em; padding-right: 0.045em;">C</span></span></span></span></span></span></span></span></span></span>) itself. We kept the native constrained Rubisco population that is forced to undertake oxygenation reactions and added a CCM-dependent Rubisco population which can only carboxylate ribulose 1,5-bisphosphate. The CCM-dependent Rubisco population is only able to use CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> produced by the bundle sheath network but not environmental CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> released by the mesophyll. C4 plants have a higher CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> consumption and thus, an increased CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> uptake of <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">f_C4_CO2_M</code><output slot="output"></output> </stencila-code-expression> μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s) was allowed <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib38"><span>38</span><span>Leakey et al.</span><span>2006</span></a></cite>. All other constraints and the objective of the <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">one-cell</em> model are maintained in the <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">two-cell</em> model, see <a href="#fig2" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 2</a>.</p> <figure itemscope="" itemtype="http://schema.stenci.la/Figure" id="fig2" title="Figure 2."> <label data-itemprop="label">Figure 2.</label><img src="index.html.media/fig2.jpg" alt="" itemscope="" itemtype="http://schema.org/ImageObject"> <figcaption> <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="schematic-representation-of-the-primary-subsystems-in-the-two-cell-model-and-the-used-inputoutput-constraints-adapted-from-narrative-bib2"> Schematic representation of the primary subsystems in the <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">two-cell</em> model and the used input/output constraints; adapted from <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib2"><span>2</span><span>Arnold and Nikoloski</span><span>2014</span></a></cite>.</h4> </figcaption> </figure> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="28" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>###################################################################################################################################### ###################################################################################################################################### ############## EXPERIMENT 4: Effect of Photorespiratory Flux (Decarboxylation-Oxygenation Ratio) ############## ###################################################################################################################################### ###################################################################################################################################### print(f"Code Cell 28: Experiment 4-- Effect of Photorespiratory Flux (Decarboxylation-Oxygenation Ratio)") #Remove original c4_rbc_rbo constraints from c4 model c4_model.remove_cons_vars(const_c4_rbc_rbo_b) c4_model.remove_cons_vars(const_c4_rbc_rbo_m) #Create copy of c4 model c4_model_exp4 = c4_model.copy() #Reaction Variables B_Ex_Suc = c4_model_exp4.reactions.get_by_id("[B]_Ex_Suc") #Proportions of Decarboxylation in the RBC : RBO ratio rbc_proportions = np.arange(1,10.25,0.25) #Initiate dataframe to save results df_result_exp4 = pd.DataFrame(index=c4_model.reactions.list_attr('id'), columns=rbc_proportions) #Iterate over for rbc_value in tqdm(rbc_proportions): #Set c4_rbc_rbo constraints r_c4_rbc_rbo = (float(rbc_value), 1.0) const_c4_rbc_rbo_b_exp4 = set_fixed_flux_ratio({'[B]_RBC_h_Ex':r_c4_rbc_rbo[0],'[B]_RBO_h':r_c4_rbc_rbo[1]}, 'const_c4_rbc_rbo_b_exp4', c4_model_exp4) const_c4_rbc_rbo_m_exp4 = set_fixed_flux_ratio({'[M]_RBC_h':r_c4_rbc_rbo[0],'[M]_RBO_h':r_c4_rbc_rbo[1]}, 'const_c4_rbc_rbo_m_exp4', c4_model_exp4) #Optimize/Maximize sucrose output B_Ex_Suc.objective_coefficient = 1. result_exp4_fba = c4_model_exp4.optimize('maximize') #Optimize/Minimize total flux if result_exp4_fba.status == 'optimal': result_exp4_pfba = cobra.flux_analysis.parsimonious.pfba(c4_model_exp4) df_result_exp4[rbc_value] = result_exp4_pfba.fluxes #Remove c4_rbc_rbo constraint c4_model_exp4.remove_cons_vars(const_c4_rbc_rbo_b_exp4) c4_model_exp4.remove_cons_vars(const_c4_rbc_rbo_m_exp4) #Reset original c4_rbc_rbo constraints in c4 model c4_model.add_cons_vars(const_c4_rbc_rbo_b) c4_model.add_cons_vars(const_c4_rbc_rbo_m)</code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 28: Experiment 4-- Effect of Photorespiratory Flux (Decarboxylation-Oxygenation Ratio) </code></pre> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code> 0%| | 0/37 [00:00<?, ?it/s]</code></pre> </figure> </stencila-code-chunk> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">Initially, we optimised for the classical objective function of minimal total flux through the metabolic network at different levels of photorespiration. These different levels of photorespiration integrate changes to external CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> concentration and stomatal opening status which is governed by plant water status and biotic interactions. From the complete flux distribution, we extracted fluxes of PEPC and PPDK, the decarboxylation enzymes, Rubisco and metabolite transporter between the two cells to ascertain the presence of a C4 cycle, see <a href="#fig3" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 3</a>, <a href="#fig4" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 3</a>, and <a href="#fig3s1" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 3—figure supplement 1</a>. At low photorespiratory levels, flux through PEPC is barely detectable (<a href="#fig3" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 3(A)</a>). If photorespiration increases to moderate levels, flux through PEPC can be predicted and increases to <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">f_C4_CO2_M</code><output slot="output"></output> </stencila-code-expression> μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s), that is all CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> is funnelled through PEPC, for high photorespiratory fluxes. Concomitant with flux through PEPC, the activity of the decarboxylation enzymes changes (<a href="#fig3" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 3(B)</a>). At low to intermediate levels of photorespiratory flux, glycine decarboxylase complex activity is predicted to shuttle CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> to the bundle sheath at up to <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">round(df_result_exp4.loc['[B]_GlyDH_m'].max(),2)</code><output slot="output"></output></stencila-code-expression> μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s). Decarboxylation of C4 acids is initially mostly mediated by PEP-CK and is largely taken over by NADP-ME at high fluxes through photorespiration. Flux through NAD-ME is very low under all photorespiration levels. The decarboxylation enzymes dictate flux through the different Rubiscos in the model (<a href="#fig3" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 3(C)</a>). At low photorespiratory flux, both the Rubiscos in mesophyll and bundle sheath are active. Only very little flux occurs through the CCM-dependent Rubisco, which is a result of the glycine decarboxylase (<a href="#fig3" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 3(B)</a>). With increasing photorespiratory flux, this flux through glycine decarboxylase increases (<a href="#fig3" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 3(B)</a>) and therefore, total Rubisco activity exceeds the carbon intake flux (<a href="#fig3" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 3(C)</a>). Carbon fixation switches to the CCM-dependent Rubisco with increasing flux through PEPC (<a href="#fig3" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 3(A)</a>) and the classic C4 cycle decarboxylation enzymes (<a href="#fig3" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 3(B)</a>). Flux through PPDK mostly reflects flux through PEPC (<a href="#fig3" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 3(D)</a>). The transport fluxes between the cells change with changing photosynthetic mode (<a href="#fig4" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 4</a>).</p> <figure itemscope="" itemtype="http://schema.stenci.la/Figure" id="fig3" title="Figure 3."> <label data-itemprop="label">Figure 3.</label> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="29" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>######################################################## ############## Figure 3. ############## ######################################################## #{ # "caption": "### Effect of oxygenation : carboxylation ratio on the major steps in C4 cycle, including (**A**) activity of phosphoenolpyruvate carboxylase (PEPC), (**B**) activity of Rubisco, (**C**) activity of the decarboxylation enzymes, (**D**) activity of pyruvate phosphate dikinase (PPDK)", # "id": "fig3", # "label": "Figure 3.", # "trusted": true #} #Dictionary of c4 cycle reactions and their subplots D_rxn ={ (1,1): {'rxn':['[M]_PEPC2_c', '[B]_PEPC2_c'], 'title':'PEPC'}, (1,2): {'rxn':['[B]_MalDH4_h', '[B]_MalDH2_m', '[B]_PEPC1_c', '[B]_GlyDH_m' ], 'title': 'Decarboxylation Enzymes'}, (2,1): {'rxn':['[M]_RBC_h', '[B]_RBC_h_Ex', '[B]_RBC_h'], 'title': 'Decarboxylation by Rubisco'}, (2,2): {'rxn':['[M]_PyrPiDK_h','[B]_PyrPiDK_h' ], 'title':'PPDK'} } #Dictionary of legend names for c4 cycle reactions D_rxn_alias = { '[M]_PEPC2_c': ('Mesophyll',0), '[B]_PEPC2_c': ('Bundle Sheath',1), '[B]_MalDH4_h': ('NADP-ME',6), '[B]_MalDH2_m': ('NAD-ME',7), '[B]_PEPC1_c': ('PEPCK',8), '[B]_GlyDH_m': ('Gly DH',9), '[M]_RBC_h': ('Mesophyll, constrained',0), '[B]_RBC_h_Ex': ('Bundle sheath, constrained',1), '[B]_RBC_h': ('Bundle sheath, unconstrained',2), '[M]_PyrPiDK_h': ('Mesophyll',0), '[B]_PyrPiDK_h':('Bundle Sheath',1) } #Create figure with subplots fig_exp41 = make_subplots(rows=2, cols=2, subplot_titles=[f"<b>({list(string.ascii_uppercase)[i]}) {info['title']}</b>" for i, info in enumerate(D_rxn.values())], y_title= 'Flux [µmol/(m\u00B2s)]', x_title= 'Rubisco Carboxylation : Oxygenation Ratio', #horizontal_spacing=0, vertical_spacing=0.1, specs=[[{},{}],[{},{}]] ) #Add traces to the figure for i, item in enumerate(D_rxn.items()): pos_x_y = item[0] info = item[1] #Add empty trace to group legend by title trace = go.Scatter( x = [None], y = [None], name = f"<b>({list(string.ascii_uppercase)[i]}) {info['title']}</b>", legendgroup = info['title'], mode = 'markers', marker = dict(color='black', symbol='triangle-right') ) fig_exp41.add_trace(trace,pos_x_y[0],pos_x_y[1]) for r_id in info['rxn']: #Add trace with an a reaction group trace = go.Bar( x = df_result_exp4.columns, y = abs(df_result_exp4.loc[r_id]), name = D_rxn_alias[r_id][0], legendgroup=info['title'], marker=dict(color = plotly.colors.DEFAULT_PLOTLY_COLORS[D_rxn_alias[r_id][1]]) ) fig_exp41.add_trace(trace,pos_x_y[0],pos_x_y[1]) #Update xaxes fig_exp41.update_xaxes( tickfont=dict(size=16), ticksuffix=' : 1', tickangle=25, title=dict(font=dict(size=18)) ) #Update yaxes fig_exp41.update_yaxes( tickfont=dict(size=16), title=dict(font=dict(size=18)) ) #Update annotations fig_exp41.update_annotations(font=dict(size=18)) #Update layout fig_exp41.update_layout( barmode='stack', width= 1000, height=800, legend=dict( orientation = 'v', tracegroupgap = 10, traceorder='grouped', font=dict(size=18), ) ) #Show figure fig_exp41.show()</code></pre> <figure slot="outputs"> <stencila-image-plotly> <picture> <script type="application/vnd.plotly.v1+json"> {"config":{"plotlyServerURL":"https://plot.ly"},"data":[{"legendgroup":"PEPC","marker":{"color":"black","symbol":"triangle-right"},"mode":"markers","name":"<b>(A) PEPC</b>","type":"scatter","x":[null],"xaxis":"x","y":[null],"yaxis":"y"},{"legendgroup":"PEPC","marker":{"color":"rgb(31, 119, 180)"},"name":"Mesophyll","type":"bar","x":[1,1.25,1.5,1.75,2,2.25,2.5,2.75,3,3.25,3.5,3.75,4,4.25,4.5,4.75,5,5.25,5.5,5.75,6,6.25,6.5,6.75,7,7.25,7.5,7.75,8,8.25,8.5,8.75,9,9.25,9.5,9.75,10],"xaxis":"x","y":[39.98605129634526,39.98605129635822,39.9860512963576,39.14091484122681,35.62044106011301,29.876740971754916,22.129859366576895,17.152139165785396,11.888867152312336,10.991614402236022,10.840198205510568,5.1634592526901,4.650414395495162,4.396371917760623,4.126602606868101,1.931830165435687,1.566400467604104,1.4435600298338471,1.3892048976191373,1.4763471322216106,1.2900586290940885,1.0882175072419993,0.9815758706309268,0.7640311083398601,0.6459847779510611,0.5503593575883734,0.5321430439565199,0.5321430439558235,0.5321430439558523,0.5321430439558518,0.5321430439558733,0.5321430439558443,0.5321430439558265,0.5321430439558719,0.5321430439559226,0.5321430439558539,0.5321430439557263],"yaxis":"y"},{"legendgroup":"PEPC","marker":{"color":"rgb(255, 127, 14)"},"name":"Bundle Sheath","type":"bar","x":[1,1.25,1.5,1.75,2,2.25,2.5,2.75,3,3.25,3.5,3.75,4,4.25,4.5,4.75,5,5.25,5.5,5.75,6,6.25,6.5,6.75,7,7.25,7.5,7.75,8,8.25,8.5,8.75,9,9.25,9.5,9.75,10],"xaxis":"x","y":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"yaxis":"y"},{"legendgroup":"Decarboxylation Enzymes","marker":{"color":"black","symbol":"triangle-right"},"mode":"markers","name":"<b>(B) Decarboxylation Enzymes</b>","type":"scatter","x":[null],"xaxis":"x2","y":[null],"yaxis":"y2"},{"legendgroup":"Decarboxylation Enzymes","marker":{"color":"rgb(227, 119, 194)"},"name":"NADP-ME","type":"bar","x":[1,1.25,1.5,1.75,2,2.25,2.5,2.75,3,3.25,3.5,3.75,4,4.25,4.5,4.75,5,5.25,5.5,5.75,6,6.25,6.5,6.75,7,7.25,7.5,7.75,8,8.25,8.5,8.75,9,9.25,9.5,9.75,10],"xaxis":"x2","y":[37.139549025113396,37.13954902512561,37.13954902512494,36.000101232680876,30.995292696700258,19.501602704177902,3.6107902320193515,1.0301402683826562,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"yaxis":"y2"},{"legendgroup":"Decarboxylation Enzymes","marker":{"color":"rgb(127, 127, 127)"},"name":"NAD-ME","type":"bar","x":[1,1.25,1.5,1.75,2,2.25,2.5,2.75,3,3.25,3.5,3.75,4,4.25,4.5,4.75,5,5.25,5.5,5.75,6,6.25,6.5,6.75,7,7.25,7.5,7.75,8,8.25,8.5,8.75,9,9.25,9.5,9.75,10],"xaxis":"x2","y":[0.3222150541383057,0.3222150541384097,0.32221505413840523,0.32221505413838264,0.32221505413841584,0.3222150541384058,0.3222150541384053,0.32221505413840273,0.32221505413841006,0.3222150541384362,0.32221505413831053,0.3222150541384068,0.322215054138293,0.3222150541384058,0.3222150541384115,0.3222150541384078,0.32221505413840584,0.3222150541383408,0.3222150541384043,0.3222150541384063,0.32221505413839285,0.32221505413840595,0.3222150541384093,0.1855177584433292,0.08810556257493989,0,0,0,0,0,0,0,0,0,0,0,0],"yaxis":"y2"},{"legendgroup":"Decarboxylation Enzymes","marker":{"color":"rgb(188, 189, 34)"},"name":"PEPCK","type":"bar","x":[1,1.25,1.5,1.75,2,2.25,2.5,2.75,3,3.25,3.5,3.75,4,4.25,4.5,4.75,5,5.25,5.5,5.75,6,6.25,6.5,6.75,7,7.25,7.5,7.75,8,8.25,8.5,8.75,9,9.25,9.5,9.75,10],"xaxis":"x2","y":[1.9921441731378609,1.9921441731383331,1.9921441731384015,2.286455510451694,3.770790265318469,9.520780169482757,17.664711036463284,15.267640799308491,11.034509054218075,10.137256304141765,9.985840107416525,4.30910115459584,3.796056297401204,3.542013819666365,3.2722445087738463,1.0774720673414286,0.712042369509846,0.5892019317397634,0.5348467995248833,0.6219890341273518,0.4357005309998661,0.23385940914772363,0.1272177725366577,0.046370305940683955,0.025736171420287175,0.018216313632520797,0,0,0,0,0,0,0,0,0,0,0],"yaxis":"y2"},{"legendgroup":"Decarboxylation Enzymes","marker":{"color":"rgb(23, 190, 207)"},"name":"Gly DH","type":"bar","x":[1,1.25,1.5,1.75,2,2.25,2.5,2.75,3,3.25,3.5,3.75,4,4.25,4.5,4.75,5,5.25,5.5,5.75,6,6.25,6.5,6.75,7,7.25,7.5,7.75,8,8.25,8.5,8.75,9,9.25,9.5,9.75,10],"xaxis":"x2","y":[0.004184611092705274,0.004184611092706615,0.004184611092706557,0.24565216970147785,1.0955871701538942,2.250698016559975,3.5759809451945457,4.156312224056414,4.6870486351002585,4.464867210188357,4.167877909783455,4.647196883581717,4.421139223698763,4.191205714457059,3.9885677988137833,4.009892098558165,3.846149693968053,3.674898065046585,3.5129888291598275,3.3528545384088866,3.228850666697849,3.1160113142219696,3.004528874610197,2.9095194398347632,2.81418936240747,2.723887503421621,2.6344451612560884,2.549598046731541,2.4700538768678175,2.395330565783725,2.3170430081614093,2.234794879766157,2.1640106931456895,2.09783093641956,2.034801867995977,1.9712322050198532,1.916258403268703],"yaxis":"y2"},{"legendgroup":"Decarboxylation by Rubisco","marker":{"color":"black","symbol":"triangle-right"},"mode":"markers","name":"<b>(C) Decarboxylation by Rubisco</b>","type":"scatter","x":[null],"xaxis":"x3","y":[null],"yaxis":"y3"},{"legendgroup":"Decarboxylation by Rubisco","marker":{"color":"rgb(31, 119, 180)"},"name":"Mesophyll, constrained","type":"bar","x":[1,1.25,1.5,1.75,2,2.25,2.5,2.75,3,3.25,3.5,3.75,4,4.25,4.5,4.75,5,5.25,5.5,5.75,6,6.25,6.5,6.75,7,7.25,7.5,7.75,8,8.25,8.5,8.75,9,9.25,9.5,9.75,10],"xaxis":"x3","y":[1.6435782728072022e-14,2.26866472444074e-18,2.7755575615628914e-17,0.8451364551306997,4.36561023624473,10.109310324602674,17.8589816705092,22.8367018713004,28.097184144045308,28.994436894121744,29.14585309083525,33.729013678106945,34.242058535288216,34.496101013036316,34.76587032392894,36.96064276536125,37.31044482745155,37.44891290095533,37.50326803317767,37.412497344791035,35.91370273551233,33.164012201080574,31.078938098456643,30.205970567029418,29.671811341791663,29.236959531748298,28.78866894183963,28.559516855400847,28.358580390070387,28.09925898572238,27.80544306222485,27.528825784641104,27.44061351469908,27.265488955108317,27.191276619736396,26.885434116645943,26.867555250750584],"yaxis":"y3"},{"legendgroup":"Decarboxylation by Rubisco","marker":{"color":"rgb(255, 127, 14)"},"name":"Bundle sheath, constrained","type":"bar","x":[1,1.25,1.5,1.75,2,2.25,2.5,2.75,3,3.25,3.5,3.75,4,4.25,4.5,4.75,5,5.25,5.5,5.75,6,6.25,6.5,6.75,7,7.25,7.5,7.75,8,8.25,8.5,8.75,9,9.25,9.5,9.75,10],"xaxis":"x3","y":[0,0,0,0,0,0,0,0,0,0,0,1.0935783655606337,1.0935783655602591,1.0935783655606794,1.0935783655606806,1.093578365560611,1.1092060013019263,1.0935783655604165,1.0935783655606435,1.0972068193450328,2.7822899317494847,5.733821588035206,7.925537327270723,9.016049620988293,9.668255176615025,10.19873240702102,10.665239310611012,10.8943913970011,11.09532786233138,11.354649266679429,11.656922409067162,11.951797630050919,12.051668959768358,12.2340688138134,12.317711731969913,12.634359543609134,12.66117736814229],"yaxis":"y3"},{"legendgroup":"Decarboxylation by Rubisco","marker":{"color":"rgb(44, 160, 44)"},"name":"Bundle sheath, unconstrained","type":"bar","x":[1,1.25,1.5,1.75,2,2.25,2.5,2.75,3,3.25,3.5,3.75,4,4.25,4.5,4.75,5,5.25,5.5,5.75,6,6.25,6.5,6.75,7,7.25,7.5,7.75,8,8.25,8.5,8.75,9,9.25,9.5,9.75,10],"xaxis":"x3","y":[40.1750562306991,40.17505623071212,40.17505623071152,39.57138733418953,36.90084855352811,32.3122593115761,25.887870894304175,21.490481972374543,16.760736110673818,15.641301935685595,15.192896438555167,9.995476459533025,9.256373942455065,8.772397955478889,8.299990728943095,6.126542587255065,5.597370484833368,5.303278418141605,5.08701405004017,5.014021993891704,4.703729619052981,4.389049144725159,4.17092506850233,3.8583708714358274,3.644994463619769,3.4590671842711966,3.3514085284740336,3.266561413948598,3.1870172440848776,3.1122939330007844,3.034006375378482,2.9504684397158347,2.8767894492700394,2.8106096925439377,2.7454883185740733,2.6819186555978565,2.622760242753828],"yaxis":"y3"},{"legendgroup":"PPDK","marker":{"color":"black","symbol":"triangle-right"},"mode":"markers","name":"<b>(D) PPDK</b>","type":"scatter","x":[null],"xaxis":"x4","y":[null],"yaxis":"y4"},{"legendgroup":"PPDK","marker":{"color":"rgb(31, 119, 180)"},"name":"Mesophyll","type":"bar","x":[1,1.25,1.5,1.75,2,2.25,2.5,2.75,3,3.25,3.5,3.75,4,4.25,4.5,4.75,5,5.25,5.5,5.75,6,6.25,6.5,6.75,7,7.25,7.5,7.75,8,8.25,8.5,8.75,9,9.25,9.5,9.75,10],"xaxis":"x4","y":[39.98884103707367,39.988841037086694,39.9888410370861,38.1226594753349,30.952749150591075,19.468823250618374,9.09883171532253,6.469093517389321,4.154302253966259,2.883904778893799,2.819804541655032,0,0.02650253692046567,0.026502536920474898,0.026502536920467723,0.026502536920474946,0.02650253692047491,0.026502536920466783,0.026502536920474832,0.02650253692047497,0.026502536920472462,0.026502536920474985,0.026502536920474527,0.026502536920467244,0.026502536920475,0.026502536920482548,0.016738444370846976,0.016738444370826337,0.01673844437083267,0.016738444370826278,0.016738444370802304,0.018028251638201636,0.020923055463535956,0.02092305546355019,0.02301536100989549,0.02301536100988664,0.02301536100983926],"yaxis":"y4"},{"legendgroup":"PPDK","marker":{"color":"rgb(255, 127, 14)"},"name":"Bundle Sheath","type":"bar","x":[1,1.25,1.5,1.75,2,2.25,2.5,2.75,3,3.25,3.5,3.75,4,4.25,4.5,4.75,5,5.25,5.5,5.75,6,6.25,6.5,6.75,7,7.25,7.5,7.75,8,8.25,8.5,8.75,9,9.25,9.5,9.75,10],"xaxis":"x4","y":[0.08508709221834057,0.08508709221835369,0.08508709221838687,0.0850870922183825,0.08508709221836705,0.09485118476801874,0.1004306662249556,0.10043066622492941,0.01464613882446864,0.014646138824469655,0.014646138824442325,0.014646138824472996,0.014646138824472885,0.0146461388244635,0.014646138824473012,0.014646138824478861,0.01464613882446909,0.014646138824459438,0.014646138824471001,0.014646138824471903,0.014646138824492866,0.07461062632278202,0.08508709221837385,0.0850870922183568,0.08508709221832456,0.0850870922183499,0.08683772116470537,0.06096158786126307,0.03442280942132766,0.028295435796872728,0.03640594990138121,0.050386219957687155,0.05554526666349489,0.062103364020111226,0.0642784355566179,0.0885742681289507,0.0885742681289348],"yaxis":"y4"}],"layout":{"annotations":[{"font":{"size":18},"showarrow":false,"text":"<b>(A) PEPC</b>","x":0.225,"xanchor":"center","xref":"paper","y":1,"yanchor":"bottom","yref":"paper"},{"font":{"size":18},"showarrow":false,"text":"<b>(B) Decarboxylation Enzymes</b>","x":0.775,"xanchor":"center","xref":"paper","y":1,"yanchor":"bottom","yref":"paper"},{"font":{"size":18},"showarrow":false,"text":"<b>(C) Decarboxylation by Rubisco</b>","x":0.225,"xanchor":"center","xref":"paper","y":0.45,"yanchor":"bottom","yref":"paper"},{"font":{"size":18},"showarrow":false,"text":"<b>(D) PPDK</b>","x":0.775,"xanchor":"center","xref":"paper","y":0.45,"yanchor":"bottom","yref":"paper"},{"font":{"size":18},"showarrow":false,"text":"Rubisco Carboxylation : Oxygenation Ratio","x":0.5,"xanchor":"center","xref":"paper","y":0,"yanchor":"top","yref":"paper","yshift":-30},{"font":{"size":18},"showarrow":false,"text":"Flux [µmol/(m²s)]","textangle":-90,"x":0,"xanchor":"right","xref":"paper","xshift":-40,"y":0.5,"yanchor":"middle","yref":"paper"}],"barmode":"stack","height":800,"legend":{"font":{"size":18},"orientation":"v","tracegroupgap":10,"traceorder":"grouped"},"template":{"data":{"bar":[{"error_x":{"color":"#2a3f5f"},"error_y":{"color":"#2a3f5f"},"marker":{"line":{"color":"#E5ECF6","width":0.5}},"type":"bar"}],"barpolar":[{"marker":{"line":{"color":"#E5ECF6","width":0.5}},"type":"barpolar"}],"carpet":[{"aaxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"baxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"type":"carpet"}],"choropleth":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"choropleth"}],"contour":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"contour"}],"contourcarpet":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"contourcarpet"}],"heatmap":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"heatmap"}],"heatmapgl":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"heatmapgl"}],"histogram":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"histogram"}],"histogram2d":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"histogram2d"}],"histogram2dcontour":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"histogram2dcontour"}],"mesh3d":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"mesh3d"}],"parcoords":[{"line":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"parcoords"}],"pie":[{"automargin":true,"type":"pie"}],"scatter":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatter"}],"scatter3d":[{"line":{"colorbar":{"outlinewidth":0,"ticks":""}},"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatter3d"}],"scattercarpet":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattercarpet"}],"scattergeo":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattergeo"}],"scattergl":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattergl"}],"scattermapbox":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattermapbox"}],"scatterpolar":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterpolar"}],"scatterpolargl":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterpolargl"}],"scatterternary":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterternary"}],"surface":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"surface"}],"table":[{"cells":{"fill":{"color":"#EBF0F8"},"line":{"color":"white"}},"header":{"fill":{"color":"#C8D4E3"},"line":{"color":"white"}},"type":"table"}]},"layout":{"annotationdefaults":{"arrowcolor":"#2a3f5f","arrowhead":0,"arrowwidth":1},"autotypenumbers":"strict","coloraxis":{"colorbar":{"outlinewidth":0,"ticks":""}},"colorscale":{"diverging":[[0,"#8e0152"],[0.1,"#c51b7d"],[0.2,"#de77ae"],[0.3,"#f1b6da"],[0.4,"#fde0ef"],[0.5,"#f7f7f7"],[0.6,"#e6f5d0"],[0.7,"#b8e186"],[0.8,"#7fbc41"],[0.9,"#4d9221"],[1,"#276419"]],"sequential":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"sequentialminus":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]]},"colorway":["#636efa","#EF553B","#00cc96","#ab63fa","#FFA15A","#19d3f3","#FF6692","#B6E880","#FF97FF","#FECB52"],"font":{"color":"#2a3f5f"},"geo":{"bgcolor":"white","lakecolor":"white","landcolor":"#E5ECF6","showlakes":true,"showland":true,"subunitcolor":"white"},"hoverlabel":{"align":"left"},"hovermode":"closest","mapbox":{"style":"light"},"paper_bgcolor":"white","plot_bgcolor":"#E5ECF6","polar":{"angularaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"bgcolor":"#E5ECF6","radialaxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"scene":{"xaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"},"yaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"},"zaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"}},"shapedefaults":{"line":{"color":"#2a3f5f"}},"ternary":{"aaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"baxis":{"gridcolor":"white","linecolor":"white","ticks":""},"bgcolor":"#E5ECF6","caxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"title":{"x":0.05},"xaxis":{"automargin":true,"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","zerolinewidth":2},"yaxis":{"automargin":true,"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","zerolinewidth":2}}},"width":1000,"xaxis":{"anchor":"y","domain":[0,0.45],"tickangle":25,"tickfont":{"size":16},"ticksuffix":" : 1","title":{"font":{"size":18}}},"xaxis2":{"anchor":"y2","domain":[0.55,1],"tickangle":25,"tickfont":{"size":16},"ticksuffix":" : 1","title":{"font":{"size":18}}},"xaxis3":{"anchor":"y3","domain":[0,0.45],"tickangle":25,"tickfont":{"size":16},"ticksuffix":" : 1","title":{"font":{"size":18}}},"xaxis4":{"anchor":"y4","domain":[0.55,1],"tickangle":25,"tickfont":{"size":16},"ticksuffix":" : 1","title":{"font":{"size":18}}},"yaxis":{"anchor":"x","domain":[0.55,1],"tickfont":{"size":16},"title":{"font":{"size":18}}},"yaxis2":{"anchor":"x2","domain":[0.55,1],"tickfont":{"size":16},"title":{"font":{"size":18}}},"yaxis3":{"anchor":"x3","domain":[0,0.45],"tickfont":{"size":16},"title":{"font":{"size":18}}},"yaxis4":{"anchor":"x4","domain":[0,0.45],"tickfont":{"size":16},"title":{"font":{"size":18}}}}} </script><img src="index.html.media/4" alt="" itemscope="" itemtype="http://schema.org/ImageObject"> </picture> </stencila-image-plotly> </figure> </stencila-code-chunk> <figcaption> <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="effect-of-oxygenation--carboxylation-ratio-on-the-major-steps-in-c4-cycle-including-a-activity-of-phosphoenolpyruvate-carboxylase-pepc-b-activity-of-rubisco-c-activity-of-the-decarboxylation-enzymes-d-activity-of-pyruvate-phosphate-dikinase-ppdk"> Effect of oxygenation : carboxylation ratio on the major steps in C4 cycle, including (<strong itemscope="" itemtype="http://schema.stenci.la/Strong">A</strong>) activity of phosphoenolpyruvate carboxylase (PEPC), (<strong itemscope="" itemtype="http://schema.stenci.la/Strong">B</strong>) activity of Rubisco, (<strong itemscope="" itemtype="http://schema.stenci.la/Strong">C</strong>) activity of the decarboxylation enzymes, (<strong itemscope="" itemtype="http://schema.stenci.la/Strong">D</strong>) activity of pyruvate phosphate dikinase (PPDK)</h4> </figcaption> </figure> <figure itemscope="" itemtype="http://schema.stenci.la/Figure" id="fig4" title="Figure 4."> <label data-itemprop="label">Figure 4.</label> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="30" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>######################################################## ############## Figure 4. ############## ######################################################## #(E) and (F) have been integrated into one graph #{ # "caption": "### Effect of oxygenation : carboxylation ratio on the metabolite exchange between mesophyll and bundle sheath cells in the in C4 cycle. Positive fluxes represent the transport of metabolites from the mesophyll to the bundle sheath, negative fluxes indicate the transport of metabolites from the bundle sheath to the meophyll.", # "id": "fig4", # "label": "Figure 4.", # "trusted": true #} #Get exchange reaction between mesophyll and bundle sheath rxn_mb_transport = c4_model.reactions.query(lambda rxn: (rxn.id.startswith('[MB]'))).list_attr('id') #Extract fluxes for exchange reactions df_result_exp4_transport = df_result_exp4.loc[rxn_mb_transport] df_result_exp4_transport = df_result_exp4_transport[(abs(df_result_exp4_transport) > 0.01).sum(axis=1) > 0] df_result_exp4_transport = df_result_exp4_transport.reindex(df_result_exp4_transport.mean(axis=1).sort_values().index) #Create Figure fig_exp42 = go.Figure() #Add trace trace = go.Heatmap( x=df_result_exp4_transport.columns, y=df_result_exp4_transport.index.str.split('_',expand=True).get_level_values(1), z=df_result_exp4_transport, colorscale = 'RdBu_R', colorbar = dict( tickfont=dict(size=16), title = dict( text='<b>Flux [µmol/(m\u00B2s)]</b>', side='right', font=dict(size=18) ) ) ) fig_exp42.add_trace(trace) #Update axes fig_exp42.update_xaxes( tickfont=dict(size=16), ticksuffix=' : 1', tickangle=25, title= dict(text='Rubisco Carboxylation : Oxygenation Ratio',font=dict(size=18)) ) #Update yaxes fig_exp42.update_yaxes( tickfont=dict(size=16) ) #Update layout fig_exp42.update_layout( barmode='stack', width= 1000, height=800, title = dict( text = '<b>(E) + (F) Transport between Mesophyll and Bundle Sheath</b>', font = dict(size=18), x = 0.5 ) ) #Show figure fig_exp42.show()</code></pre> <figure slot="outputs"> <stencila-image-plotly> <picture> <script type="application/vnd.plotly.v1+json"> {"config":{"plotlyServerURL":"https://plot.ly"},"data":[{"colorbar":{"tickfont":{"size":16},"title":{"font":{"size":18},"side":"right","text":"<b>Flux [µmol/(m²s)]</b>"}},"colorscale":[[0,"rgb(5,48,97)"],[0.1,"rgb(33,102,172)"],[0.2,"rgb(67,147,195)"],[0.3,"rgb(146,197,222)"],[0.4,"rgb(209,229,240)"],[0.5,"rgb(247,247,247)"],[0.6,"rgb(253,219,199)"],[0.7,"rgb(244,165,130)"],[0.8,"rgb(214,96,77)"],[0.9,"rgb(178,24,43)"],[1,"rgb(103,0,31)"]],"type":"heatmap","x":[1,1.25,1.5,1.75,2,2.25,2.5,2.75,3,3.25,3.5,3.75,4,4.25,4.5,4.75,5,5.25,5.5,5.75,6,6.25,6.5,6.75,7,7.25,7.5,7.75,8,8.25,8.5,8.75,9,9.25,9.5,9.75,10],"y":["Pyr","PEP","Ala","GCEA","PGA","F6P","G6P","Glu","2PGA","Fum","KG","Arg","Asn","Thr","Gln","S6P","Gly","Suc","Asp","DHAP","GAP","GCA","CO2","Mal"],"z":[[-37.86465639335766,-37.875815356284036,-37.86465639336951,-35.48147244065476,-28.19020839422258,-15.907852642148947,0,0,0,0,0,0.004882046274824326,0.03138458319528828,0.031384583195299236,0.03138458319529205,0.03138458319529927,0.031384583195299236,0.03138458319529012,0.031384583195299125,0.0313845831952993,0.11786654577787566,0.05790205827959344,0.04742559238400412,0.1841228880790901,0.28153508394751225,0.3696406465224311,0.36300797130179163,0.38888410460469186,0.4154228830446416,0.42155025666908347,0.41343974256458366,0.4007492797756412,0.39848503689517045,0.39192693953857066,0.3918441735484594,0.3675483409760672,0.3675483409759757],[0.8996913849315893,0.8996913849319403,0.8996913849318935,0,-3.770790265318469,-9.520780169482753,-12.149469581057508,-9.801487578199211,-6.716309532454133,-7.089454257450284,-7.002138297963895,-4.145203886798166,-3.658661566524053,-3.404619088789165,-3.134849777896641,-0.9400773364642296,-0.5902752743739113,-0.4518072008626004,-0.3974520686476849,-0.4882227570345466,-0.43570053099986683,-0.23385940914772363,-0.005864050848159675,0,0,0,0,0,0,0,0,0,-0.02897204879415418,-0.044713046026669784,0,0,0],[-2.1193025974411865,-2.1081436345278393,-2.11930259744177,-2.636304988405106,-2.757658710093681,-3.5609706084694293,-9.09883171532249,-6.469093517389321,-4.149420207691429,-2.8790227326190325,-2.8149224953801975,-8.251661040942412e-18,0,0,0,0,0,0,0,0,0,0,0,0,-3.520708710802096e-15,0,0,-3.537992542311668e-15,0,0,0,0,0,4.219366248668622e-15,0,0,0],[0,-2.9107476952698656e-34,0,-0.17590865148970172,-1.0258436519421181,-2.180954498348199,-3.5062374269827745,-4.0865687058446385,-4.617305116888484,-4.395123691976582,-4.098134391571691,-4.571361793365704,-4.134051210147431,-3.3585254741879673,-2.5005465778440588,-0.02757891502352393,0,0,0,0,0,-2.0159070652422945e-15,1.2418066800344842e-18,0,-7.838034745635193e-18,0,0,0,1.692212742047244e-15,0,0.008457218889668546,0.024135547755859105,0.030004999880297863,0.03728029433295378,0.04252626602115814,0.053331574575078755,0.058085922129592515],[-5.4446817064113,-6.34158335061661,-6.341583350616533,-5.960698973967668,-2.1210962707522856,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3.710699076871937e-15,0,0,0,0,0,0,0,0,0,0,0,0,0,-0.07070197251749794,-0.06288978536903918,-0.09013139119320486],[0,0,-0.0018598271523138905,-0.8872408753844528,-3.234834780106607,-7.857193889757931,0,-4.520413136069575,-4.4376494834977256e-15,0,0,0.04691623185641795,0,0,0,-2.887207290789635e-14,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2.2156101161318538e-15,-1.2722685009803226e-16,0,0,0,0,0],[-0.0018598271523396317,-0.001859827152314049,0,0,-0.4116630453539973,0,-8.334191446237652,0,0,0,0,0,0.556422263756727,0.4154764872435477,0.1778437982583754,-2.9049917467093834e-14,0.15869103241130234,0.28360945967254436,0.39745206864768007,0.488222757034526,0.4357005309998865,0.2338594091477271,0.005864050848122623,2.824842913307191e-15,4.2463172489772865e-15,-3.7833817965005223e-14,-1.7110771943972212e-15,-1.22555167907024e-14,-1.825387264790405e-14,-1.1407181295981475e-14,3.950776351349637e-14,-4.007659123106754e-14,0.028972048794201222,0.04471304602666417,0.07070197251747888,0.06288978536903635,0.09013139119324794],[-0.30198943385689725,-0.3131483967708771,-0.30198943385699045,-0.3131483967708717,-0.011158962913882924,-0.011158962913879373,-0.02231792582776807,-0.31384583195299093,-0.011158962913883954,-0.01115896291390056,-0.4368620328112532,-0.011158962913884003,-0.011158962913880275,-0.01115896291388417,-0.011158962913884227,-0.01115896291388367,-0.011158962913883906,-0.011158962913885519,-0.011158962913884267,-0.011158962913884187,-0.011158962913883677,0,-0.011158962913891514,-0.01115896291387558,0,-0.011158962913884152,-0.011158962913898096,0,0,0,0,0,0,0,0,0,0],[-0.896901644203155,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],[0.013948703642383785,0.01394870364235539,0.013948703642355195,0.013948703642355238,0.013948703642334716,0.013948703642355221,0.011158962913884195,0.011158962913884084,0,0.013948703642353606,0,0.013948703642355235,0.013948703642350353,0.01394870364235523,0.01394870364234076,0.013948703642355235,0.013948703642355221,0.013948703642352423,0.013948703642355176,0.013948703642355243,0.013948703642354591,0,0.013948703642356623,0.013948703642338732,0,0,0,0.01394870364235528,-7.472161440659179e-19,0,1.9344760797912974e-16,0.01394870364235428,0.013948703642362904,0,2.889371393047727e-15,0,0.0139487036423105],[-0.011158962913880471,0,-0.011158962913883757,0,0,0,0.011158962913880464,0.3034256139509042,0,1.1225387633644864e-18,0.2252715638239641,0,0,0,0,0,0,0,0,0,0,-0.011158962913884449,0,0,-0.011158962913884296,0,0,-0.011158962913883332,-0.01115896291389069,-0.011158962913884359,-0.011158962913885009,-0.011158962913883987,-0.011158962913885141,-0.011158962913885314,-0.011158962913885776,-0.011158962913884275,-0.011158962913880528],[0.01115896291388073,0.01115896291388431,0.011158962913884157,0.01115896291388419,0.011158962913884204,0.011158962913884175,0.011158962913884195,0.011158962913884084,0.011158962913884166,0.011158962913884195,0.01115896291388089,0.011158962913884187,0.011158962913880282,0.011158962913884185,0.011158962913884197,0.011158962913884187,0.011158962913884175,0.011158962913881939,0.011158962913884138,0.011158962913884197,0.011158962913883673,0.011158962913884204,0.011158962913884357,0.011158962913884171,0.011158962913884202,0.011158962913884185,0.011158962913897985,0.011158962913884228,0.011158962913884197,0.011158962913884185,0.01115896291388438,0.011158962913884072,0.011158962913884176,0.011158962913884603,0.011158962913885665,0.011158962913884216,0.011158962913881524],[0,0,0,-6.858276944334915e-15,0,-2.956153855316774e-15,0,0,0.07044095339388946,0.07044095339389399,0.07044095339387313,0.07044095339389393,0.07044095339384895,0.07044095339391267,0.070440953393894,0.07044095339386489,0.07044095339389775,0.07044095339387703,0.07044095339389363,0.07044095339388234,0.07044095339387699,0.010476465895586375,-6.863912291961234e-15,8.811764585246452e-15,-5.070684260592243e-34,2.0628978960905053e-16,0,5.67762522766535e-18,6.402083592927319e-15,0,0,0,0,0,0,0,0],[0.05579481456940365,0.05579481456942155,0.05579481456942078,0.05579481456942094,0.05579481456942102,0.047425592384007745,0.03556919428800525,0.0355691942880291,0.047425592384007696,0.047425592384007835,0.04742559238399378,0.0474255923840096,0.04742559238399119,0.04742559238400595,0.047425592384009584,0.047425592384007786,0.047425592384007745,0.04742559238399824,0.047425592384007585,0.047425592384007835,0.04742559238400561,0.04742559238400786,0.04742559238400848,0.047425592384002145,0.04742559238400785,0.04742559238400778,0.005057163907656425,0,0,0,0,0,-6.831120210915212e-17,3.944217841227233e-15,0.004184611092708359,0.004184611092708919,0.004184611092708561],[0.30198943385689725,0.3019894338569941,0.30198943385698995,0.3019894338569872,0,3.20684680623771e-15,3.906818444147464e-16,0,0,0,0.2017981841602393,0,0,0,0,0,0,0,0,0,0,0,6.863912291961234e-15,-8.81176458524645e-15,0,0,0,8.464773295652838e-16,5.5352991338144635e-15,0,0,0,-1.2119947072076488e-16,-8.467726285674484e-18,0,-1.8711627641200293e-31,0],[0,0,0,0,0,0,0,0,0,0,0.07892815284206661,1.5343574006590766,1.5343574006585594,1.5343574006590568,1.5343574006590834,0.9400773364642321,0.43158424196261824,0.1681977411900217,0,-2.780273687427056e-15,-2.477675080841889e-15,4.811285516490271e-16,1.916937523828277e-16,-5.394669283541862e-16,-1.2075874969009513e-15,0,0,-3.0347865424752e-16,-2.7937461010985233e-16,0,2.539416326755723e-16,1.7096176933146507e-14,-6.71043448654937e-17,1.5178321840496025e-15,0,-4.509167220311649e-16,6.629883408479902e-15],[0.004882046274822819,0.004882046274824377,0.004882046274824318,0.31190851200266523,0.9631579865046275,0,-3.582057531712841e-15,0,0.004882046274824322,0.004882046274824329,0.004882046274822896,0.004882046274824332,0.004882046274822499,0.004882046274824596,0.004882046274824336,0.00758564414102781,0.1540968651549123,0.26775837623272214,0.34400761488193327,0.28170583628221085,0.35420739236192644,0.4242561064513367,0.4996276449391833,0.5201834783059304,0.5001656112166525,0.5019608613860231,0.513931253844124,0.4901532850024994,0.4749882687511106,0.45496454487464444,0.433647026357463,0.41097856246300996,0.3880435625886268,0.36961872084136543,0.3461061390468521,0.3270590077809457,0.3107761628606616],[0,0,0,0,0,0,0,0,0,0,-1.9810487941327558e-14,0,0,0,0,0.5942800641948726,1.1027731586964495,1.3661596594687468,1.5343574006590688,1.5343574006590806,1.5343574006590075,1.534357400659078,1.5343574006590976,1.5343574006590717,1.5343574006590792,1.5343574006590754,1.5343574006609728,1.5343574006590808,1.5343574006590786,1.5343574006590754,1.534357400659103,1.5343574006589982,1.5343574006590743,1.5343574006591343,1.534357400659279,1.5343574006590794,1.534357400658706],[2.7644301408999166,2.7644301409006586,2.764430140900699,2.985565029050067,2.75765871009368,3.849011338684087,9.052103558120596,6.713893266312629,4.32401456919852,3.0176382810575464,2.9697531058102675,0.24357712964125502,0.23531321225883522,0.17963899990268092,0.13390755496661036,0.5883824744452333,0.4426598990963225,0.29699296624554816,0.18966023490705594,0.22935501790334215,0.13390755496662474,0.1262208297995002,0.03804572947437092,0,0,0,0,0,0,0,0,0,0,0,0,0,0],[2.8840295762599273,0,2.8840295762608705,3.4239699246760367,4.769192180765706,10.92590869107608,11.402906247555807,7.589127937387698,3.163587677894098,3.520172230196412,3.4616050725609315,0.6281193474610227,0.07076949097358541,0,0,0,-5.610408978932343e-15,1.0959746643746223e-15,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],[2.5597222165752687,5.4437517928369825,2.559722216576113,3.4239699246761006,4.76919218076568,6.452065368164618,9.080754779739385,6.732772776881065,3.5527218545600285,3.5692820272538026,3.4616050725608862,1.935810906821631,1.4971124111351437,1.4547852008865865,1.4226485789791843,0,-8.532896704189771e-15,2.6720614578310352e-15,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],[0,-1.8149317795525917e-18,-1.652341565881877e-17,0.1759086514897017,1.2245291778925722,4.493026810934522,7.1435926682036825,8.304255225927415,9.365728048015102,8.921365198191305,8.327386597381501,8.994403647495185,8.560514633822054,8.11672965012619,7.725748960873105,7.778484352736165,7.312874146610221,6.870249936890735,6.479650437425195,6.229697487347574,5.636291776498286,4.8868678919963795,4.2866294934058935,3.959657170491779,3.7435466267426953,3.535605258233386,3.3245579384011608,3.1949456640814797,3.0698342800076883,2.951006241273523,2.8206671314191025,2.6843222457352365,2.5925342726541856,2.4950718958865696,2.4185271398154846,2.3112044320108716,2.247253684677105],[0,0,0,0,0,0,0,0,0,0,0,1.0935783655606337,1.0935783655602593,1.0935783655606797,1.0935783655606806,1.093578365560611,1.1092060013019263,1.0935783655604165,1.0935783655606435,1.097206819345033,2.7822899317494847,5.733821588035207,7.925537327270723,9.016049620988294,9.668255176615027,10.198732407021021,10.665239310611012,10.8943913970011,11.095327862331382,11.354649266679429,11.656922409067164,11.951797630050919,12.051668959768358,12.2340688138134,12.317711731969911,12.634359543609134,12.66117736814229],[37.14699559095874,37.14699559097097,37.146995590970306,36.080724247690135,32.788156785532756,25.966355337044497,13.031027651254412,10.391517742270855,7.442103991061097,7.837278825483365,7.747696507647585,4.7831848273537645,4.278403887541321,4.080035622162847,3.8559977562064254,1.2067503952954015,0.9870432728126967,1.009869767893248,1.0628473670170007,1.1102948186231993,1.0194537784324103,0.899212572888079,0.8772737988553736,0.6977747660386862,0.5936771392922291,0.498051718929542,0.5270858800488543,0.5181943403134756,0.5321430439558464,0.5321430439558519,0.5321430439558773,0.51819434031349,0.5181943403134645,0.532143043955872,0.5279584328632116,0.527958432863146,0.5140097292207095]]}],"layout":{"barmode":"stack","height":800,"template":{"data":{"bar":[{"error_x":{"color":"#2a3f5f"},"error_y":{"color":"#2a3f5f"},"marker":{"line":{"color":"#E5ECF6","width":0.5}},"type":"bar"}],"barpolar":[{"marker":{"line":{"color":"#E5ECF6","width":0.5}},"type":"barpolar"}],"carpet":[{"aaxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"baxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"type":"carpet"}],"choropleth":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"choropleth"}],"contour":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"contour"}],"contourcarpet":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"contourcarpet"}],"heatmap":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"heatmap"}],"heatmapgl":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"heatmapgl"}],"histogram":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"histogram"}],"histogram2d":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"histogram2d"}],"histogram2dcontour":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"histogram2dcontour"}],"mesh3d":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"mesh3d"}],"parcoords":[{"line":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"parcoords"}],"pie":[{"automargin":true,"type":"pie"}],"scatter":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatter"}],"scatter3d":[{"line":{"colorbar":{"outlinewidth":0,"ticks":""}},"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatter3d"}],"scattercarpet":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattercarpet"}],"scattergeo":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattergeo"}],"scattergl":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattergl"}],"scattermapbox":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattermapbox"}],"scatterpolar":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterpolar"}],"scatterpolargl":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterpolargl"}],"scatterternary":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterternary"}],"surface":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"surface"}],"table":[{"cells":{"fill":{"color":"#EBF0F8"},"line":{"color":"white"}},"header":{"fill":{"color":"#C8D4E3"},"line":{"color":"white"}},"type":"table"}]},"layout":{"annotationdefaults":{"arrowcolor":"#2a3f5f","arrowhead":0,"arrowwidth":1},"autotypenumbers":"strict","coloraxis":{"colorbar":{"outlinewidth":0,"ticks":""}},"colorscale":{"diverging":[[0,"#8e0152"],[0.1,"#c51b7d"],[0.2,"#de77ae"],[0.3,"#f1b6da"],[0.4,"#fde0ef"],[0.5,"#f7f7f7"],[0.6,"#e6f5d0"],[0.7,"#b8e186"],[0.8,"#7fbc41"],[0.9,"#4d9221"],[1,"#276419"]],"sequential":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"sequentialminus":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]]},"colorway":["#636efa","#EF553B","#00cc96","#ab63fa","#FFA15A","#19d3f3","#FF6692","#B6E880","#FF97FF","#FECB52"],"font":{"color":"#2a3f5f"},"geo":{"bgcolor":"white","lakecolor":"white","landcolor":"#E5ECF6","showlakes":true,"showland":true,"subunitcolor":"white"},"hoverlabel":{"align":"left"},"hovermode":"closest","mapbox":{"style":"light"},"paper_bgcolor":"white","plot_bgcolor":"#E5ECF6","polar":{"angularaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"bgcolor":"#E5ECF6","radialaxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"scene":{"xaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"},"yaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"},"zaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"}},"shapedefaults":{"line":{"color":"#2a3f5f"}},"ternary":{"aaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"baxis":{"gridcolor":"white","linecolor":"white","ticks":""},"bgcolor":"#E5ECF6","caxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"title":{"x":0.05},"xaxis":{"automargin":true,"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","zerolinewidth":2},"yaxis":{"automargin":true,"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","zerolinewidth":2}}},"title":{"font":{"size":18},"text":"<b>(E) + (F) Transport between Mesophyll and Bundle Sheath</b>","x":0.5},"width":1000,"xaxis":{"tickangle":25,"tickfont":{"size":16},"ticksuffix":" : 1","title":{"font":{"size":18},"text":"Rubisco Carboxylation : Oxygenation Ratio"}},"yaxis":{"tickfont":{"size":16}}}} </script><img src="index.html.media/5" alt="" itemscope="" itemtype="http://schema.org/ImageObject"> </picture> </stencila-image-plotly> </figure> </stencila-code-chunk> <figcaption> <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="effect-of-oxygenation--carboxylation-ratio-on-the-metabolite-exchange-between-mesophyll-and-bundle-sheath-cells-in-the-in-c4-cycle-positive-fluxes-represent-the-transport-of-metabolites-from-the-mesophyll-to-the-bundle-sheath-negative-fluxes-indicate-the-transport-of-metabolites-from-the-bundle-sheath-to-the-meophyll"> Effect of oxygenation : carboxylation ratio on the metabolite exchange between mesophyll and bundle sheath cells in the in C4 cycle. Positive fluxes represent the transport of metabolites from the mesophyll to the bundle sheath, negative fluxes indicate the transport of metabolites from the bundle sheath to the meophyll.</h4> </figcaption> </figure> <figure itemscope="" itemtype="http://schema.stenci.la/Figure" id="fig3s1" title="Figure 3—figure supplement 1"><label data-itemprop="label">Figure 3—figure supplement 1</label> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="31" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>############################################################## ############## FIGURE 3 - Supplement 1 ############## ############################################################## #{ # "caption": "### Flux maps illustrating the effect of the oxygenation : carboxylation ratio of Rubisco on the C3-C4 trajectory. Flux maps illustrating the effect of the proportion of photorespiratory flux through Rubisco. (**A**) Low photorespiratory flux; (**B**) Moderate photorespiratory flux; and (**C**) High photorespiratory flux. (Arc width and colour are set relative to flux values in μmol/(m^2^s), grey arcs - no flux).", # "id": "fig3s1", # "label": "Figure 3—figure supplement 1", # "trusted": true #} # Rubisco carboxylation proportion to display on metabolic map show_co2_proportion = {1: 'High Photorespiratory Flux',3: 'Moderate Photorespiratory Flux', 10: 'Low Photorespiratory Flux'} # Build metabolic map and add flux solution for each ratio for i, co2_proportion in enumerate(sorted(show_co2_proportion.keys(), reverse=True)): #Build map b = Builder( map_json = 'elife-49305.ipython.src/2018-06-29-mb-C4-RBO-RBC-Ratio.json', reaction_styles = ['color','size', 'text'], reaction_data = df_result_exp4[co2_proportion], reaction_scale = [ {'type': 'value', 'value': 40, 'color': '#ff0000', 'size': 25}, {'type': 'value', 'value': -40, 'color': '#ff0000', 'size': 25}, {'type': 'value', 'value': 20, 'color': '#209123', 'size': 20}, {'type': 'value', 'value': -20, 'color': '#209123', 'size': 20}, {'type': 'value', 'value': 0.01, 'color': '#9696ff', 'size': 5}, {'type': 'value', 'value': -0.01, 'color': '#9696ff', 'size': 5}, {'type': 'value', 'value': 0, 'color': '#ccc', 'size': 3}], menu = False, height = 1000 ) #Add title print(f"({list(string.ascii_uppercase)[i]}) {show_co2_proportion[co2_proportion]}") #Display display(b)</code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>(A) Low Photorespiratory Flux </code></pre> <pre><output>Builder(height=1000, menu=False, reaction_data={'[M]_PSII_h': 29.0802147928429, '[B]_PSII_h': 18.8652312755852…</output></pre> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>(B) Moderate Photorespiratory Flux </code></pre> <pre><output>Builder(height=1000, menu=False, reaction_data={'[M]_PSII_h': 39.33216931971396, '[B]_PSII_h': 18.001451340808…</output></pre> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>(C) High Photorespiratory Flux </code></pre> <pre><output>Builder(height=1000, menu=False, reaction_data={'[M]_PSII_h': 24.226697390955252, '[B]_PSII_h': 18.17818261340…</output></pre> </figure> </stencila-code-chunk> <figcaption> <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="flux-maps-illustrating-the-effect-of-the-oxygenation--carboxylation-ratio-of-rubisco-on-the-c3-c4-trajectory-flux-maps-illustrating-the-effect-of-the-proportion-of-photorespiratory-flux-through-rubisco-a-low-photorespiratory-flux-b-moderate-photorespiratory-flux-and-c-high-photorespiratory-flux-arc-width-and-colour-are-set-relative-to-flux-values-in-μmolm2s-grey-arcs---no-flux"> Flux maps illustrating the effect of the oxygenation : carboxylation ratio of Rubisco on the C3-C4 trajectory. Flux maps illustrating the effect of the proportion of photorespiratory flux through Rubisco. (<strong itemscope="" itemtype="http://schema.stenci.la/Strong">A</strong>) Low photorespiratory flux; (<strong itemscope="" itemtype="http://schema.stenci.la/Strong">B</strong>) Moderate photorespiratory flux; and (<strong itemscope="" itemtype="http://schema.stenci.la/Strong">C</strong>) High photorespiratory flux. (Arc width and colour are set relative to flux values in μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s), grey arcs - no flux). </h4> </figcaption> </figure> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">At low rates of photorespiration when PEPC is barely active, the only flux towards the bundle sheath is CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> diffusion with no fluxes towards the mesophyll (<a href="#fig4" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 4</a>). In the intermediate phase glycolate and glycerate are predicted to be transported and a low-level C4 cycle dependent on the transport of aspartate, malate, PEP and alanine operates (<a href="#fig4" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 4</a>). In case of high photorespiratory rates, the exchange between mesophyll and bundle sheath is mainly carried by malate and pyruvate (<a href="#fig4" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 4</a>). Flux through PPDK (<a href="#fig3" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 3(D)</a>) is lower than flux through PEPC (<a href="#fig3" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 3(A)</a>) at the intermediate stage. Evolution of C4 photosynthesis with NADP-ME as the major decarboxylation enzyme is predicted if the photorespiratory flux is high and model optimised for minimal total flux, in other words, resource limitation.</p> <h3 itemscope="" itemtype="http://schema.stenci.la/Heading" id="c4-modes-with-different-decarboxylation-enzymes-result-from-different-set-of-constraints"> C4 modes with different decarboxylation enzymes result from different set of constraints </h3> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="32" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>###################################################################################################################################### ###################################################################################################################################### ############## EXPERIMENT 5: Effect of Decarboxylation Enzymes on the c4 mode ############## ###################################################################################################################################### ###################################################################################################################################### print(f"Code Cell 32: Experiment 5 -- Effect of Decarboxylation Enzymes on the c4 mode") #Create copy of c4 model c4_model_exp5 = c4_model.copy() #Reaction variables B_Ex_Suc = c4_model_exp5.reactions.get_by_id("[B]_Ex_Suc") B_RBO = c4_model_exp5.reactions.get_by_id("[B]_RBO_h") M_RBO = c4_model_exp5.reactions.get_by_id("[M]_RBO_h") #Decarboxylation reactions ids and names of enzymes c4_mode_r_id_enzyme = {'[B]_MalDH4_h': 'NADP-ME', '[B]_PEPC1_c': 'PEP-CK', '[B]_MalDH2_m': 'NAD-ME',} #Set flux through decarboxylation enzymes two zero for c4_mode_r_id in c4_mode_r_id_enzyme.keys(): set_fixed_flux(c4_mode_r_id, 0, c4_model_exp5) #Initialise data frames to hold results df_result_exp5_pfba = pd.DataFrame(index=c4_model.reactions.list_attr('id'), columns=c4_mode_r_id_enzyme.keys(), dtype='float64') df_result_exp5_pfva = pd.DataFrame(index=c4_model.reactions.list_attr('id'), columns=c4_mode_r_id_enzyme.keys(), dtype='float64') #Get exchange reaction between mesophyll and bundle sheath rxn_mb_transport = c4_model.reactions.query(lambda rxn: (rxn.id.startswith('[MB]'))).list_attr('id') #Perform FBA experiment for each decarboxylation enzyme for c4_mode_r_id in tqdm(c4_mode_r_id_enzyme.keys()): #Allow non-zero flux for current decarboxylation enzyme set_bounds(c4_mode_r_id, (0,inf), c4_model_exp5) #Optimization - Maximize sucrose output & Minimize Oxygenation by Rubisco B_Ex_Suc.objective_coefficient = 1. B_RBO.objective_coefficient = -1. M_RBO.objective_coefficient = -1. result_exp5_fba = c4_model_exp5.optimize('maximize') #Optimize/Minimize total flux if result_exp5_fba.status == 'optimal': result_exp5_pfba = cobra.flux_analysis.parsimonious.pfba(c4_model_exp5) df_result_exp5_pfba[c4_mode_r_id] = result_exp5_pfba.fluxes pfba_factor = 0.015 result_exp5_pfva = cobra.flux_analysis.flux_variability_analysis(c4_model_exp5,reaction_list=rxn_mb_transport, pfba_factor= 1 + pfba_factor) df_result_exp5_pfva[c4_mode_r_id] = result_exp5_pfva.apply(lambda x: (x[0], x[1]), axis=1) #Reset flux of current decarboxylation enzyme to zero set_fixed_flux(c4_mode_r_id, 0, c4_model_exp5)</code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 32: Experiment 5 -- Effect of Decarboxylation Enzymes on the c4 mode </code></pre> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code> 0%| | 0/3 [00:00<?, ?it/s]</code></pre> </figure> </stencila-code-chunk> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">Among the known independent evolutionary events leading to C4 photosynthesis, 20 are towards NAD-ME while 21 occurred towards NADP-ME <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib62"><span>62</span><span>Sage</span><span>2004</span></a></cite>. PEP-CK is dominant or at least co-dominant only in <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Panicum maximum</em><span data-itemtype="http://schema.org/Number">0</span><cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib12"><span>12</span><span>Bräutigam et al.</span><span>2014</span></a></cite>, <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Alloteropsis semialata semialata</em><span data-itemtype="http://schema.org/Number">0</span><cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib18"><span>18</span><span>Christin et al.</span><span>2012</span></a></cite>, and in the <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Chloridoideae</em><span data-itemtype="http://schema.org/Number">0</span><cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib62"><span>62</span><span>Sage</span><span>2004</span></a></cite>. To analyse whether the predicted evolution of the C4 cycle is independent of a particular decarboxylation enzyme, we performed three separate experiments, where only one decarboxylation enzyme can be active at a time. The other decarboxylation enzymes were de-activated by constraining the reaction flux to zero resulting in three different predictions, one for each decarboxylation enzyme. The flux distributions obtained under the assumption of oxygenation : carboxylation ratio of 1 : 3 and minimisation of photorespiration as an additional objective predicts the emergence of a C4 cycle for each known decarboxylation enzyme. To visualise the possible C4 fluxes, the flux distribution for candidate C4 cycle enzymes was extracted from each of the three predictions and visualised as arc width and color (<a href="#fig4" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 4</a>). While the flux distribution in the mesophyll is identical for three predicted C4 cycles of the decarboxylation enzymes, it is diverse in the bundle sheath due to the different localisation of the decarboxylation and related transport processes, see <a href="#fig4" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 4</a>. The flux distribution does not completely mimic the variation in transfer acids known from laboratory experiments <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib30"><span>30</span><span>Hatch</span><span>1987</span></a></cite> since all of the decarboxylation enzymes use the malate/pyruvate shuttle. In the case of NAD-ME and PEP-CK, the <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">two-cell</em> model also predicts a supplementary flux through the aspartate/alanine shuttle. We tested whether transfer acids other than malate and pyruvate are feasible and explored the near-optimal space. To this end, the model predictions are repeated, allowing deviation from the optimal solution and the changes recorded. Deviations from the optimal solution are visualised as error bars (<a href="#fig5" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 5</a>). Performing a flux variability analysis (FVA) and allowing the minimal total flux to differ by <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">pfba_factor * 100</code><output slot="output"></output> </stencila-code-expression>%, predicts that for most metabolites which are transferred between mesophyll and bundle sheath, the variability is similar for all three decarboxylation types. For the NAD-ME and PEP-CK types, changes in the near-optimal space were observed for the transfer acids malate, aspartate, pyruvate and alanine. Minor differences were present for triose phosphates and phosphoglycerates as well as for PEP. For the NADP-ME type, FVA identifies only minor variation (<a href="#fig5" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 5</a>). In the case of NAD-ME but not in the case of NADP-ME the activity of the malate/pyruvate shuttle can be taken over by the aspartate/alanine shuttle and partly taken over in case of PEP-CK, see <a href="#fig5" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 5</a>. The aspartate/alanine shuttle is thus only a near-optimal solution when the model and by proxy evolutionary constraints are resource efficiency and minimal photorespiration.</p> <figure itemscope="" itemtype="http://schema.stenci.la/Figure" id="fig5" title="Figure 5."> <label data-itemprop="label">Figure 5.</label> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="33" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>######################################################## ############## Figure 5. ############## ######################################################## #{ # "caption": "### Flux maps illustrating the effect of the C4 mode. (**A**) NADP-ME, (**B**) PEP-CK, (**C**) NAD-ME. (Arc width and colour are set relative to flux values in μmol/(m^2^s), grey arcs - no flux).", # "id": "fig5", # "label": "Figure 5.", # "trusted": true #} # Build metabolic map and add flux solution for decarboxylation enzyme for i, c4_mode_r_id in enumerate(c4_mode_r_id_enzyme.keys()): #Build map b = Builder( map_json = 'elife-49305.ipython.src/2018-06-29-mb-C4-Map-Decarb-Enzymes.json', reaction_styles = ['color','size', 'text'], reaction_data = df_result_exp5_pfba[c4_mode_r_id], reaction_scale = [ {'type': 'value', 'value': 40, 'color': '#ff0000', 'size': 25}, {'type': 'value', 'value': -40, 'color': '#ff0000', 'size': 25}, {'type': 'value', 'value': 20, 'color': '#209123', 'size': 20}, {'type': 'value', 'value': -20, 'color': '#209123', 'size': 20}, {'type': 'value', 'value': 0.01, 'color': '#9696ff', 'size': 5}, {'type': 'value', 'value': -0.01, 'color': '#9696ff', 'size': 5}, {'type': 'value', 'value': 0, 'color': '#ccc', 'size': 3}], menu = False, height = 1000 ) #Add title print(f"({list(string.ascii_uppercase)[i]}) {c4_mode_r_id_enzyme[c4_mode_r_id]}") #Display display(b)</code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>(A) NADP-ME </code></pre> <pre><output>Builder(height=1000, menu=False, reaction_data={'[M]_PSII_h': 24.504287664634546, '[B]_PSII_h': 17.85320161911…</output></pre> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>(B) PEP-CK </code></pre> <pre><output>Builder(height=1000, menu=False, reaction_data={'[M]_PSII_h': 24.049836369752107, '[B]_PSII_h': 19.40600140368…</output></pre> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>(C) NAD-ME </code></pre> <pre><output>Builder(height=1000, menu=False, reaction_data={'[M]_PSII_h': 23.350924803251964, '[B]_PSII_h': 19.36547262051…</output></pre> </figure> </stencila-code-chunk> <figcaption> <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="flux-maps-illustrating-the-effect-of-the-c4-mode-a-nadp-me-b-pep-ck-c-nad-me--arc-width-and-colour-are-set-relative-to-flux-values-in-μmolm2s-grey-arcs---no-flux"> Flux maps illustrating the effect of the C4 mode. (<strong itemscope="" itemtype="http://schema.stenci.la/Strong">A</strong>) NADP-ME, (<strong itemscope="" itemtype="http://schema.stenci.la/Strong">B</strong>) PEP-CK, (<strong itemscope="" itemtype="http://schema.stenci.la/Strong">C</strong>) NAD-ME. (Arc width and colour are set relative to flux values in μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s), grey arcs - no flux). </h4> </figcaption> </figure> <figure itemscope="" itemtype="http://schema.stenci.la/Figure" id="fig5" title="Figure 5."> <label data-itemprop="label">Figure 5.</label> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="34" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>######################################################## ############## Figure 6. ############## ######################################################## #{ # "caption": "### Flux variability analysis of metabolite exchange with 1.5% deviation of the total flux minimum. The upper bar defines the maximum exchange flux, while the lower bar defines the minimum exchange flux, points indicate the value of the original flux solution under minimal metabolic effort constraint. Positive flux values correspond to the transport direction from mesophyll to bundle sheath, negative values to the transport direction from bundle sheath to mesophyll.", # "id": "fig6", # "label": "Figure 6.", # "trusted": true #} #Create figure with subplots fig_exp5 = make_subplots( rows = 3, cols = 1, subplot_titles = [f"<b>FVA with {enzyme} (pFBA Factor = 1.5 %)</b>" for enzyme in c4_mode_r_id_enzyme.values()], y_title = 'Flux [µmol/(m\u00B2s)]', x_title = 'Exchange Metabolites', vertical_spacing=0.1 ) #Get exchange reaction between mesophyll and bundle sheath rxn_mb_transport = c4_model.reactions.query(lambda rxn: (rxn.id.startswith('[MB]'))).list_attr('id') #Add subplot for each decarboxylation enzyme for i, c4_mode_r_id in enumerate(c4_mode_r_id_enzyme.keys()): #Create trace trace = go.Scatter( x = df_result_exp5_pfba.loc[rxn_mb_transport,:].index.str.split('_',expand=True).get_level_values(1), y = df_result_exp5_pfba.loc[rxn_mb_transport,c4_mode_r_id], mode = 'markers', name = c4_mode_r_id, error_y = dict( type = 'data', symmetric = False, array = df_result_exp5_pfva.loc[rxn_mb_transport,c4_mode_r_id].apply(lambda x: x[1]) - df_result_exp5_pfba.loc[rxn_mb_transport,c4_mode_r_id], arrayminus = df_result_exp5_pfba.loc[rxn_mb_transport,c4_mode_r_id] - df_result_exp5_pfva.loc[rxn_mb_transport,c4_mode_r_id].apply(lambda x: x[0]), ) ) #Add trace fig_exp5.add_trace(trace,i+1,1) #Add annotation - postive flux: transport from mesophyll to bundle sheath anno_ms2bs = dict( x=-1, y=25, xref=f"x{i+1}", yref=f"y{i+1}", text= u"[M] \u2192 [BS]", textangle= -90, showarrow=False, font=dict( size=6, color='#000000' ), align='center', ) fig_exp5.add_annotation(anno_ms2bs) #Add annotation - negative flux: transport from bundle sheath to mesophyll anno_ms2bs = dict( x=-1, y=-25, xref=f"x{i+1}", yref=f"y{i+1}", text= '[BS] \u2192 [M]', textangle= -90, showarrow=False, font=dict( size=6, color='#000000' ), align='center', ) fig_exp5.add_annotation(anno_ms2bs) #Update xaxes fig_exp5.update_xaxes( tickangle = 35, tickfont=dict(size=16) ) #Update yaxes fig_exp5.update_yaxes( range = [-50, 50], tickfont=dict(size=16) ) #Update layout fig_exp5.update_layout( width = 1000, height = 1000, showlegend = False ) #Update annotations fig_exp5.update_annotations(font=dict(size=18)) #Show figure fig_exp5.show()</code></pre> <figure slot="outputs"> <stencila-image-plotly> <picture> <script type="application/vnd.plotly.v1+json"> {"config":{"plotlyServerURL":"https://plot.ly"},"data":[{"error_y":{"array":[1.4169492588936716,10.411175848863763,10.919658454781743,13.838736679211191,12.212487854619393,10.224035646469941,4.956211838862828,2.761206788425576,3.49356704431469,0,5.114358995594053,12.55139857353857,10.662304872581267,13.235726766140266,12.260058302901712,1.0168384161217965,0.5548277608166704,0.8538678259606853,8.153489348381479,0.5167159019898402,0.524770085036623,0.922304221685984,2.534505216705989,9.911160518039202,10.628537800988989,1.3675266484823048,1.4336311853246042,0,3.899658373995862e-15,0.5451173740451283,3.37403716077489e-16,2.8630201037954577,7.190577855006298e-15,0.42269161762290225,7.348090504476003,0.9223042216861504,0.012553833278119734,1.9168694409543718e-16,0.008369222185413156,0.008369222185413156,0.007671787003295392,0.006276916639059865,0.004184611092706578,0.02510766655623946,2.661065976313582e-14],"arrayminus":[2.1570634723978217,10.921518281936,10.15340966803017,11.267363401771513,12.204310711375946,10.411175848864538,2.7199887781378633,4.742839039370958,4.671440230653213,0,9.911160518034073,9.304561707604384,16.025227227223073,12.450002897044635,7.348860504001799,0.5548277608164748,1.157377264669058,0.7711184944397078,10.46075880009073,0.5548277608166349,0.8050552602212727,0.5450712350908762,2.349930444698598,5.122055521805472,8.153489348380141,1.2515874879134137,2.022153266067877,-2.5890084170251988e-30,0.07253325894024319,0.4868088542738063,0.004882046274824041,1.8293149804525781,2.285358335730291e-15,0.5464477702891659,12.191308621325993,0.39591463120287523,8.310702368948068e-17,0.0027897407284708754,5.540192418402168e-17,5.480217621278784e-17,5.05999957440138e-17,4.155144313801624e-17,2.770234122982689e-17,0.008369222185413272,0],"symmetric":false,"type":"data"},"mode":"markers","name":"[B]_MalDH4_h","type":"scatter","x":["Glc","G6P","G1P","GAP","DHAP","F6P","S6P","Suc","Frc","Tre","Mal","PEP","2PGA","PGA","Pyr","Cit","cACN","iCit","KG","SCA","Rib","Fum","Gln","Asp","Glu","Asn","Ser","Cys","Thr","Gly","Met","Pro","GCA","GCEA","Ala","Arg","Lys","His","Ile","Leu","Phe","Trp","Tyr","Val","CO2"],"xaxis":"x","y":[0,0,0,2.0434617347354,2.051830956920811,-0.0018598271523139023,0,0,0,0,39.05063523949531,0.0027897407284451703,0,-4.096222605232365,-39.779455004808284,-0.3222150541383839,0.3222150541383839,2.312412178066359e-16,-3.843999044314699e-16,-2.1746918411441152e-16,0,0.013948703642353661,0.30198943385696925,0.8607904923730043,-0.3131483967708516,0,-0.009764092549647992,0,0.055794814569417095,0.0048820462748240204,0.004882046274823996,-7.001316090757099e-17,-2.7018657201820476e-16,0,-0.2045039860002362,0.011158962913882808,0,0.002789740728470855,0,-5.997479712338349e-19,-1.8510142467272598e-19,0,0,5.997479712338352e-19,0],"yaxis":"y"},{"error_y":{"array":[1.7507769201496957,12.829738855536762,11.292398346466603,22.534667475546165,15.040641488053339,10.707262854164885,8.51057036359539,2.809513707245175,3.8108707832344577,0,8.112299375720632,12.194851913837073,10.752448301840372,14.976201833098044,21.92852245127788,0.6936677921624679,0.9283389114125473,0.9164129265692881,13.079670554023863,0.5852454295028037,0.5714920872207337,1.0552631417798184,3.0919987828884676,21.710585248896912,10.84419104765738,1.5065474564647623,1.462404954211764,0,-8.187894806610529e-16,0.5940633036400018,0.0004207772064339756,3.729458394797992,-1.2916991643040386e-14,0.4686457370500874,9.827582319397694,1.0557329369101975,0.012553833278119679,-4.119968255444917e-17,0.008369222185413123,0.008369222185413123,0.00767178700329536,0.006276916639059839,0.00418461109270656,0.02510766655623936,-5.3528562212754265e-14],"arrayminus":[3.0907620901592674,11.294258173620552,10.526149559714712,13.281030521248942,16.30235645051272,12.883688579495155,2.7634777127332097,8.51057036360195,8.210805274390472,0,21.701516809942344,21.11741070543761,18.41771452881841,13.963590365736403,9.832491625428652,0.9283389114123947,0.9050825128071662,0.8097016388574402,10.84419104765597,0.6079454056820832,1.2989131279728607,0.6044878324286334,2.5702743249223157,8.099223660575369,13.378946585008935,1.6706693982453062,3.1620538553065574,0,0.072533258940247,0.5333161015677698,0.004461269068390262,2.083912103983056,-1.4951769330854583e-14,0.6198643445786823,21.925455625145887,0.4267203539387394,-1.6758315773824502e-16,0.002789740728466932,-1.117233542665228e-16,-1.117233542665228e-16,-1.0241307474431253e-16,-8.379251569989207e-17,-3.724254450311982e-17,0.008369222185412976,0],"symmetric":false,"type":"data"},"mode":"markers","name":"[B]_PEPC1_c","type":"scatter","x":["Glc","G6P","G1P","GAP","DHAP","F6P","S6P","Suc","Frc","Tre","Mal","PEP","2PGA","PGA","Pyr","Cit","cACN","iCit","KG","SCA","Rib","Fum","Gln","Asp","Glu","Asn","Ser","Cys","Thr","Gly","Met","Pro","GCA","GCEA","Ala","Arg","Lys","His","Ile","Leu","Phe","Trp","Tyr","Val","CO2"],"xaxis":"x2","y":[0,0,0,0,5.777136804374031,-0.001859827152314055,0,0,0,0,36.251609684639895,0,0,-5.775276977221717,-37.28241888380993,-0.012974610484553124,0.012974610484553124,0,0,0,5.7941246819086325e-19,0.013948703642355407,0,3.660236824438096,-0.011158962913856346,0,-0.008922538136780695,0,0.055794814569421626,0.0044612690683903476,0.004461269068390347,0,0,0,-2.701960884208306,0.011158962913884326,0,0.002789740728471081,0,0,0,0,0,0,0],"yaxis":"y2"},{"error_y":{"array":[1.767239282296414,13.551454525995592,12.014113416282113,30.402362734627395,23.80818960612948,11.246934715952928,5.282771457970862,3.345917164758928,3.8104190188626506,0,12.547591676085926,16.36940099279795,16.761723936677335,15.452312524652994,32.04141507164757,0.6532242293698236,0.9616569105416133,0.9599316839086817,13.918033068671466,0.6428074772066223,0.6361407755807857,1.3062222325466994,2.9923486211215007,31.71397667493047,15.157893105932025,1.5870575283666972,1.6484248700970352,2.4868691059021498e-14,3.0531133177191805e-16,0.6568746437544061,-2.6020852139652106e-17,3.2427787656294047,2.454354042383017e-15,0.5193299249994839,14.492589266602607,1.3063934240782729,0.012553833278119682,-2.0773313624822265e-16,0.008369222185413125,0.00836922218541312,0.007671787003295364,0.006276916639059841,0.004184611092706562,0.025107666556239364,9.269314779469923e-15],"arrayminus":[2.2607651626098035,12.01411341628333,11.247864629529893,15.76933399719828,17.386224145741977,13.551454525997459,3.1871799785409696,5.139326012008003,5.062314600721192,0,31.707882577056957,29.56654598926651,31.927112450285257,26.480255488830707,14.493484265840628,0.9708499600168023,0.9666916626085874,0.8517038065922743,15.15376578416186,0.6496556292976634,0.8974648137100628,0.6649137596408838,2.641871016545104,12.537964609285744,13.918033068672317,1.4805894648014573,2.4199379976033866,0,0.07253325894024655,0.5543024955353576,0.004882046274868367,2.399232819302064,1.5926625395691664e-14,0.6458984921342663,31.99505920455909,0.4164082227585517,6.078518561020609e-17,0.002789740728471265,4.052960997763264e-17,4.0529609977632637e-17,3.715214247949658e-17,3.0397207483224474e-17,2.0261728536735366e-17,0.00836922218541323,0],"symmetric":false,"type":"data"},"mode":"markers","name":"[B]_MalDH2_m","type":"scatter","x":["Glc","G6P","G1P","GAP","DHAP","F6P","S6P","Suc","Frc","Tre","Mal","PEP","2PGA","PGA","Pyr","Cit","cACN","iCit","KG","SCA","Rib","Fum","Gln","Asp","Glu","Asn","Ser","Cys","Thr","Gly","Met","Pro","GCA","GCEA","Ala","Arg","Lys","His","Ile","Leu","Phe","Trp","Tyr","Val","CO2"],"xaxis":"x3","y":[0,-0.0018598271522988485,0,3.74629122383562,6.139289429788596,0,4.3131372568881845e-15,-2.2819359028878164e-15,0,0,30.95362155476165,-4.644167575710869,0,-5.239553250760972,-31.36929292330391,-9.22574955654617e-16,0,-1.5531584348509022e-18,-0.3131483967708568,1.553158434850902e-18,0,0.013948703642359032,0.30198943385697175,8.957804177109272,0,1.971148584245132e-14,-0.009764092549648684,0,0.05579481456942106,0.004882046274824341,0.004882046274824342,-1.0714271618977858e-15,0,1.5531584348512479e-18,-8.61466606750725,0.011158962913887795,0,0.002789740728471249,0,0,0,0,0,0,0],"yaxis":"y3"}],"layout":{"annotations":[{"font":{"size":18},"showarrow":false,"text":"<b>FVA with NADP-ME (pFBA Factor = 1.5 %)</b>","x":0.5,"xanchor":"center","xref":"paper","y":1,"yanchor":"bottom","yref":"paper"},{"font":{"size":18},"showarrow":false,"text":"<b>FVA with PEP-CK (pFBA Factor = 1.5 %)</b>","x":0.5,"xanchor":"center","xref":"paper","y":0.6333333333333333,"yanchor":"bottom","yref":"paper"},{"font":{"size":18},"showarrow":false,"text":"<b>FVA with NAD-ME (pFBA Factor = 1.5 %)</b>","x":0.5,"xanchor":"center","xref":"paper","y":0.26666666666666666,"yanchor":"bottom","yref":"paper"},{"font":{"size":18},"showarrow":false,"text":"Exchange Metabolites","x":0.5,"xanchor":"center","xref":"paper","y":0,"yanchor":"top","yref":"paper","yshift":-30},{"font":{"size":18},"showarrow":false,"text":"Flux [µmol/(m²s)]","textangle":-90,"x":0,"xanchor":"right","xref":"paper","xshift":-40,"y":0.5,"yanchor":"middle","yref":"paper"},{"align":"center","font":{"color":"#000000","size":18},"showarrow":false,"text":"[M] → [BS]","textangle":-90,"x":-1,"xref":"x","y":25,"yref":"y"},{"align":"center","font":{"color":"#000000","size":18},"showarrow":false,"text":"[BS] → [M]","textangle":-90,"x":-1,"xref":"x","y":-25,"yref":"y"},{"align":"center","font":{"color":"#000000","size":18},"showarrow":false,"text":"[M] → [BS]","textangle":-90,"x":-1,"xref":"x2","y":25,"yref":"y2"},{"align":"center","font":{"color":"#000000","size":18},"showarrow":false,"text":"[BS] → [M]","textangle":-90,"x":-1,"xref":"x2","y":-25,"yref":"y2"},{"align":"center","font":{"color":"#000000","size":18},"showarrow":false,"text":"[M] → [BS]","textangle":-90,"x":-1,"xref":"x3","y":25,"yref":"y3"},{"align":"center","font":{"color":"#000000","size":18},"showarrow":false,"text":"[BS] → [M]","textangle":-90,"x":-1,"xref":"x3","y":-25,"yref":"y3"}],"height":1000,"showlegend":false,"template":{"data":{"bar":[{"error_x":{"color":"#2a3f5f"},"error_y":{"color":"#2a3f5f"},"marker":{"line":{"color":"#E5ECF6","width":0.5}},"type":"bar"}],"barpolar":[{"marker":{"line":{"color":"#E5ECF6","width":0.5}},"type":"barpolar"}],"carpet":[{"aaxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"baxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"type":"carpet"}],"choropleth":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"choropleth"}],"contour":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"contour"}],"contourcarpet":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"contourcarpet"}],"heatmap":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"heatmap"}],"heatmapgl":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"heatmapgl"}],"histogram":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"histogram"}],"histogram2d":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"histogram2d"}],"histogram2dcontour":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"histogram2dcontour"}],"mesh3d":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"mesh3d"}],"parcoords":[{"line":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"parcoords"}],"pie":[{"automargin":true,"type":"pie"}],"scatter":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatter"}],"scatter3d":[{"line":{"colorbar":{"outlinewidth":0,"ticks":""}},"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatter3d"}],"scattercarpet":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattercarpet"}],"scattergeo":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattergeo"}],"scattergl":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattergl"}],"scattermapbox":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattermapbox"}],"scatterpolar":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterpolar"}],"scatterpolargl":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterpolargl"}],"scatterternary":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterternary"}],"surface":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"surface"}],"table":[{"cells":{"fill":{"color":"#EBF0F8"},"line":{"color":"white"}},"header":{"fill":{"color":"#C8D4E3"},"line":{"color":"white"}},"type":"table"}]},"layout":{"annotationdefaults":{"arrowcolor":"#2a3f5f","arrowhead":0,"arrowwidth":1},"autotypenumbers":"strict","coloraxis":{"colorbar":{"outlinewidth":0,"ticks":""}},"colorscale":{"diverging":[[0,"#8e0152"],[0.1,"#c51b7d"],[0.2,"#de77ae"],[0.3,"#f1b6da"],[0.4,"#fde0ef"],[0.5,"#f7f7f7"],[0.6,"#e6f5d0"],[0.7,"#b8e186"],[0.8,"#7fbc41"],[0.9,"#4d9221"],[1,"#276419"]],"sequential":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"sequentialminus":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]]},"colorway":["#636efa","#EF553B","#00cc96","#ab63fa","#FFA15A","#19d3f3","#FF6692","#B6E880","#FF97FF","#FECB52"],"font":{"color":"#2a3f5f"},"geo":{"bgcolor":"white","lakecolor":"white","landcolor":"#E5ECF6","showlakes":true,"showland":true,"subunitcolor":"white"},"hoverlabel":{"align":"left"},"hovermode":"closest","mapbox":{"style":"light"},"paper_bgcolor":"white","plot_bgcolor":"#E5ECF6","polar":{"angularaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"bgcolor":"#E5ECF6","radialaxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"scene":{"xaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"},"yaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"},"zaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"}},"shapedefaults":{"line":{"color":"#2a3f5f"}},"ternary":{"aaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"baxis":{"gridcolor":"white","linecolor":"white","ticks":""},"bgcolor":"#E5ECF6","caxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"title":{"x":0.05},"xaxis":{"automargin":true,"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","zerolinewidth":2},"yaxis":{"automargin":true,"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","zerolinewidth":2}}},"width":1000,"xaxis":{"anchor":"y","domain":[0,1],"tickangle":35,"tickfont":{"size":16}},"xaxis2":{"anchor":"y2","domain":[0,1],"tickangle":35,"tickfont":{"size":16}},"xaxis3":{"anchor":"y3","domain":[0,1],"tickangle":35,"tickfont":{"size":16}},"yaxis":{"anchor":"x","domain":[0.7333333333333334,1],"range":[-50,50],"tickfont":{"size":16}},"yaxis2":{"anchor":"x2","domain":[0.3666666666666667,0.6333333333333333],"range":[-50,50],"tickfont":{"size":16}},"yaxis3":{"anchor":"x3","domain":[0,0.26666666666666666],"range":[-50,50],"tickfont":{"size":16}}}} </script><img src="index.html.media/6" alt="" itemscope="" itemtype="http://schema.org/ImageObject"> </picture> </stencila-image-plotly> </figure> </stencila-code-chunk> <figcaption> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">Flux variability analysis of metabolite exchange with 1.5% deviation of the total flux minimum. The upper bar defines the maximum exchange flux, while the lower bar defines the minimum exchange flux, points indicate the value of the original flux solution under minimal metabolic effort constraint. Positive flux values correspond to the transport direction from mesophyll to bundle sheath, negative values to the transport direction from bundle sheath to mesophyll.</p> </figcaption> </figure> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-tags="" data-execution_count="35" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>###################################################################################################################################### ###################################################################################################################################### ############## EXPERIMENT 6: Effect of PPFD and Photon Distribution betwenn Mesophyll and Bundle Sheath ############## ###################################################################################################################################### ###################################################################################################################################### print(f"Code Cell 35: Experiment 6 -- Effect of PPFD and Photon Distribution betwenn Mesophyll and Bundle Sheath") #Remove original constraints on PPFD from c4 model c4_model.remove_cons_vars(const_hnu_sum) c4_model.remove_cons_vars(const_hnu_ratio) #Create copy of c4 model c4_model_exp6 = c4_model.copy() #Reaction variables B_Ex_Suc = c4_model_exp6.reactions.get_by_id("[B]_Ex_Suc") M_Im_hnu = c4_model_exp6.reactions.get_by_id("[M]_Im_hnu") B_Im_hnu = c4_model_exp6.reactions.get_by_id("[B]_Im_hnu") B_RBO = c4_model_exp6.reactions.get_by_id("[B]_RBO_h") M_RBO = c4_model_exp6.reactions.get_by_id("[M]_RBO_h") #Decarboxylation reactions ids and names of enzymes c4_mode_r_id_enzyme = {'[B]_MalDH4_h': 'NADP-ME', '[B]_PEPC1_c': 'PEP-CK', '[B]_MalDH2_m': 'NAD-ME', } #Porportions of light hitting the mesophyll #ds_prop_light_m = pd.Series(np.arange(0.5,10.1,0.1)) ds_prop_light_m = pd.Series(np.concatenate((np.arange(0.5,1.,0.1, dtype='float64'),np.arange(1,11,1)),axis = 0)) min_ppfd_bs_m = 1/ds_prop_light_m.max() max_ppfd_bs_m = 1/ds_prop_light_m.min() #Maximum light uptake hnu_max = 1000 #Total PPFD #ds_ppfd = pd.Series(np.arange(0,hnu_max+50,50)) ds_ppfd = pd.Series(sorted(np.concatenate((np.array([0,50,150]),np.arange(100,hnu_max+100,100)), axis=None))) #Initialise dataframes to hold results light_index = pd.MultiIndex.from_product([ds_ppfd.values,ds_prop_light_m.values, ], names=["PPFD", "prop_light_M"]) df_result_exp6 = pd.DataFrame(index=c4_model.reactions.list_attr('id'), columns=light_index, dtype='float64') #Test all combinations of PPFD and photon distribution for light in tqdm(light_index): #Add constraint on PPFD ppfd = light[0] const_hnu1_exp6 = c4_model_exp6.problem.Constraint( 1.0 * M_Im_hnu.flux_expression + 1.0 * B_Im_hnu.flux_expression, lb = float(ppfd), ub = float(ppfd), name = 'const_hnu1_exp6', ) c4_model_exp6.add_cons_vars(const_hnu1_exp6) #Add contraint on light distribution prop = light[1] const_hnu2_exp6 = set_fixed_flux_ratio({'[M]_Im_hnu':prop,'[B]_Im_hnu':1}, 'const_hnu2_exp6', c4_model_exp6) #Optimization - Maximize sucrose output & Minimize Oxygenation by Rubisco B_Ex_Suc.objective_coefficient = 1. B_RBO.objective_coefficient = -1. M_RBO.objective_coefficient = -1. result_exp6_fba = c4_model_exp6.optimize('maximize') #Optimize/Minimize total flux if result_exp6_fba.status == 'optimal': result_exp6_pfba = cobra.flux_analysis.parsimonious.pfba(c4_model_exp6) df_result_exp6[light] = result_exp6_pfba.fluxes #Remove light constraints c4_model_exp6.remove_cons_vars(const_hnu1_exp6) c4_model_exp6.remove_cons_vars(const_hnu2_exp6) #Add original constraints on PPFD back to c4 model c4_model.add_cons_vars(const_hnu_sum) c4_model.add_cons_vars(const_hnu_ratio) #Transpose results df_result_exp6 = df_result_exp6.T</code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 35: Experiment 6 -- Effect of PPFD and Photon Distribution betwenn Mesophyll and Bundle Sheath </code></pre> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code> 0%| | 0/195 [00:00<?, ?it/s]</code></pre> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>/Users/blaetke/opt/anaconda3/envs/elife-49305-era/lib/python3.9/site-packages/cobra/util/solver.py:508: UserWarning: Solver status is 'infeasible'. </code></pre> </figure> </stencila-code-chunk> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">To analyse the effect of other conditions on the particular C4 state, we apply the minimisation of photorespiration as an additional objective to minimal total flux. Since NAD-ME and PEP-CK type plants use amino acids as transfer acids in nature, nitrogen availability has been tagged as a possible evolutionary constraint that selects for decarboxylation by NAD-ME or PEP-CK. When nitrate uptake was limiting, the optimal solution to the model predicted overall reduced flux towards the phloem output (<a href="#fig8s1" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 8—figure supplement 1</a>) but reactions were predicted to occur in the same proportions as predicted for unlimited nitrate uptake. Flux through NADP-ME and supplementary flux through PEP-CK dropped proportionally, since restricting nitrogen limits the export of all metabolites from the system and reduced CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> uptake is observed (<a href="#fig8s1" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 8—figure supplement 1</a>). Similarly, limiting water or CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> uptake into the model resulted in overall reduced flux towards the phloem output, see <a href="#fig8s2" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 8—figure supplement 2</a> and <a href="#fig8s3" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 8—figure supplement 3</a>, but reactions were predicted to occur in the same proportions as predicted for unlimited uptake.</p> <figure itemscope="" itemtype="http://schema.stenci.la/Figure" id="fig7" title="Figure 7."> <label data-itemprop="label">Figure 7.</label> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="36" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>######################################################## ############## FIGURE 7 ############## ######################################################## #{ # "caption": "### Effect of total PPFD on CO~2~ uptake rate in C4 mode.", # "id": "fig7", # "label": "Figure 7.", # "trusted": true #} #Create figure fig_exp61 = go.Figure() #Create trace for co2 flux trace = go.Scatter( y = df_result_exp6.mean(axis=0, level='PPFD')['[M]_Im_CO2'], x = df_result_exp6.index.get_level_values(0).unique(), error_y=dict( array = df_result_exp6.var(axis=0, level='PPFD')['[M]_Im_CO2'] ) ) #Add trace to figure fig_exp61.add_trace(trace) #Update yaxes fig_exp61.update_yaxes( title = dict(text='Flux [µmol/(m\u00B2s)]',font=dict(size=18)), tickfont=dict(size=16) ) #Update xaxes fig_exp61.update_xaxes( title = dict(text='PPFD [µE]',font=dict(size=18)), tickangle = 35, tickfont=dict(size=16), #type='category' ) #Update layout fig_exp61.update_layout( width = 1000, height = 500, title = dict(text='<b>CO\u2082 Uptake</b>', font=dict(size=20), x=0.5) ) #Show figure fig_exp61.show()</code></pre> <figure slot="outputs"> <stencila-image-plotly> <picture> <script type="application/vnd.plotly.v1+json"> {"config":{"plotlyServerURL":"https://plot.ly"},"data":[{"error_y":{"array":[null,1.854409138227542e-26,4.0214776615186805e-26,7.197521821470499e-26,4.8146660322769043e-26,8.290579211963897e-24,9.833260271773663e-24,5.085457188267971e-25,1.7608817893045387e-25,1.6739022924236789e-22,1.0554385522673458e-22,1.528452533434476e-23,1.3865351042522356e-23]},"type":"scatter","x":[0,50,100,150,200,300,400,500,600,700,800,900,1000],"y":[null,4.949304674503245,9.933616667752169,14.91792866100104,19.90224065425007,29.870864640746877,39.83948862724493,40.00000000000018,40.00000000000009,39.99999999999729,39.99999999999832,40.000000000000675,39.99999999999993]}],"layout":{"height":500,"template":{"data":{"bar":[{"error_x":{"color":"#2a3f5f"},"error_y":{"color":"#2a3f5f"},"marker":{"line":{"color":"#E5ECF6","width":0.5}},"type":"bar"}],"barpolar":[{"marker":{"line":{"color":"#E5ECF6","width":0.5}},"type":"barpolar"}],"carpet":[{"aaxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"baxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"type":"carpet"}],"choropleth":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"choropleth"}],"contour":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"contour"}],"contourcarpet":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"contourcarpet"}],"heatmap":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"heatmap"}],"heatmapgl":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"heatmapgl"}],"histogram":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"histogram"}],"histogram2d":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"histogram2d"}],"histogram2dcontour":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"histogram2dcontour"}],"mesh3d":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"mesh3d"}],"parcoords":[{"line":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"parcoords"}],"pie":[{"automargin":true,"type":"pie"}],"scatter":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatter"}],"scatter3d":[{"line":{"colorbar":{"outlinewidth":0,"ticks":""}},"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatter3d"}],"scattercarpet":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattercarpet"}],"scattergeo":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattergeo"}],"scattergl":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattergl"}],"scattermapbox":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattermapbox"}],"scatterpolar":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterpolar"}],"scatterpolargl":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterpolargl"}],"scatterternary":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterternary"}],"surface":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"surface"}],"table":[{"cells":{"fill":{"color":"#EBF0F8"},"line":{"color":"white"}},"header":{"fill":{"color":"#C8D4E3"},"line":{"color":"white"}},"type":"table"}]},"layout":{"annotationdefaults":{"arrowcolor":"#2a3f5f","arrowhead":0,"arrowwidth":1},"autotypenumbers":"strict","coloraxis":{"colorbar":{"outlinewidth":0,"ticks":""}},"colorscale":{"diverging":[[0,"#8e0152"],[0.1,"#c51b7d"],[0.2,"#de77ae"],[0.3,"#f1b6da"],[0.4,"#fde0ef"],[0.5,"#f7f7f7"],[0.6,"#e6f5d0"],[0.7,"#b8e186"],[0.8,"#7fbc41"],[0.9,"#4d9221"],[1,"#276419"]],"sequential":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"sequentialminus":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]]},"colorway":["#636efa","#EF553B","#00cc96","#ab63fa","#FFA15A","#19d3f3","#FF6692","#B6E880","#FF97FF","#FECB52"],"font":{"color":"#2a3f5f"},"geo":{"bgcolor":"white","lakecolor":"white","landcolor":"#E5ECF6","showlakes":true,"showland":true,"subunitcolor":"white"},"hoverlabel":{"align":"left"},"hovermode":"closest","mapbox":{"style":"light"},"paper_bgcolor":"white","plot_bgcolor":"#E5ECF6","polar":{"angularaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"bgcolor":"#E5ECF6","radialaxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"scene":{"xaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"},"yaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"},"zaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"}},"shapedefaults":{"line":{"color":"#2a3f5f"}},"ternary":{"aaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"baxis":{"gridcolor":"white","linecolor":"white","ticks":""},"bgcolor":"#E5ECF6","caxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"title":{"x":0.05},"xaxis":{"automargin":true,"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","zerolinewidth":2},"yaxis":{"automargin":true,"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","zerolinewidth":2}}},"title":{"font":{"size":20},"text":"<b>CO₂ Uptake</b>","x":0.5},"width":1000,"xaxis":{"tickangle":35,"tickfont":{"size":16},"title":{"font":{"size":18},"text":"PPFD [µE]"}},"yaxis":{"tickfont":{"size":16},"title":{"font":{"size":18},"text":"Flux [µmol/(m²s)]"}}}} </script><img src="index.html.media/7" alt="" itemscope="" itemtype="http://schema.org/ImageObject"> </picture> </stencila-image-plotly> </figure> </stencila-code-chunk> <figcaption> <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="effect-of-total-ppfd-on-co2-uptake-rate-in-c4-mode">Effect of total PPFD on CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> uptake rate in C4 mode. </h4> </figcaption> </figure> <figure itemscope="" itemtype="http://schema.stenci.la/Figure" id="fig8" title="Figure 8."> <label data-itemprop="label">Figure 8.</label> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="37" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>######################################################## ############## FIGURE 8 ############## ######################################################## #{ # "caption": "### Effect of light on the C4 mode. Heat-maps illustrating the activity of the decarboxylation enzymes PEP-CK, NADP-ME, and NAD-ME relative to the CO~2~ uptake rate in dependence of the total PPFD and the photon distribution among mesophyll and bundle sheath.", # "id": "fig8", # "label": "Figure 8.", # "trusted": true #} #Create figure with subplot fig_exp62 = make_subplots( rows=3, cols=1, subplot_titles = [f"<b>{enzyme}</b>" for enzyme in c4_mode_r_id_enzyme.values()], y_title= 'PPFD [BS] : PPFD [M]', x_title = 'Total PPFD [µE]', vertical_spacing = 0.1 ) #Get co2 flux for all combinations df_im_co2 = df_result_exp6['[M]_Im_CO2'].reset_index().pivot_table(index='PPFD', columns='prop_light_M', aggfunc='mean') #Get low light threshold low_light_thres = df_im_co2[((df_im_co2.round(1) < df_im_co2.round(1).max().max()).sum(axis=1) != 0)].index.max() #Save heatmap dataframes dfs_r_id_co2 = {} #Add subplot for each decarboxylation enzyme for i, r_id in enumerate(c4_mode_r_id_enzyme.keys()): #Get decarboxylation flux of current enzyme for all combinations df_r_id = df_result_exp6[r_id].reset_index().pivot_table(index='PPFD', columns='prop_light_M', aggfunc='mean') dfs_r_id_co2[r_id] = pd.DataFrame(df_r_id.values/df_im_co2.values, index = df_r_id.index, columns = df_r_id.columns) #Create trace trace = go.Heatmap( z = (df_r_id.values/df_im_co2.values).T, x = df_im_co2.index, y = [round(value,1) for value in df_im_co2.columns.get_level_values(1)], colorbar = dict( title = dict( text = 'Decarboxylation Rate : CO\u2082 Uptake Rate', font = dict(size=18) ), xpad = 20, titleside = 'right' ), zmin = 0, zmax = 1, name= c4_mode_r_id_enzyme[r_id], showscale = True if i == 0 else False, ) #Add trace to figure fig_exp62.append_trace(trace,i+1,1) #Max percentage of decarboylation by NADPME under low light nadpme_max_low_light = dfs_r_id_co2['[B]_MalDH4_h'].loc[:low_light_thres].max().max().round(2) * 100 #Update yaxes fig_exp62.update_yaxes( tickprefix= '1:', tickfont=dict(size=16), type='category' ) #Update xaxes fig_exp62.update_xaxes( tickangle = 35, tickvals=df_im_co2.index, tickfont=dict(size=16), type='category' ) #Update annotations fig_exp62.update_annotations( font=dict(size=20) ) #Update layout fig_exp62.update_layout( width = 600, height = 1000 ) #Show figure fig_exp62.show()</code></pre> <figure slot="outputs"> <stencila-image-plotly> <picture> <script type="application/vnd.plotly.v1+json"> {"config":{"plotlyServerURL":"https://plot.ly"},"data":[{"colorbar":{"title":{"font":{"size":18},"side":"right","text":"Decarboxylation Rate : CO₂ Uptake Rate"},"xpad":20},"name":"NADP-ME","showscale":true,"type":"heatmap","x":[50,100,150,200,300,400,500,600,700,800,900,1000],"xaxis":"x","y":[0.5,0.6,0.7,0.8,0.9,1,2,3,4,5,6,7,8,9,10],"yaxis":"y","z":[[0.22328497441870734,0.22921868031345635,0.2311872993480956,0.2321698775008893,0.2331513041159709,0.23364158622917702,0.6078125865309847,0.16115289011544265,0,0,0,0],[0.23578075762955925,0.21866836988740107,0.2559651890433698,0.25847492908821706,0.2609817278312515,0.2622340258295369,0.7434374137206686,0.083123787452973,0.055226990079038196,0,0,0],[0.2235864151990471,0.23260310558412697,0.23584738322395873,0.23734048098432434,0.2388318289010953,0.23957684762896533,0.833717576447137,0.01316707029997545,0.13564978419667023,0,0,0],[0.21898832462878023,0.22813264874579178,0.23082975288406155,0.23230212067534226,0.233772762917133,0.23450743790454665,0.8743628639013354,0.47242451577226385,0.10276727335995887,0.03352560119014923,0,0],[0.2284372939441597,0.23729626652660624,0.24023539805070016,0.2417023788999555,0.24291482026108796,0.24364680729733856,0.9060729168482897,0.6484543469213202,0.038805285055851624,0.1066250163953983,0,0],[0.23649239243074202,0.24532208685767184,0.24850432505539155,0.2497136374032112,0.25117405645107155,0.25190362433336866,0.9224442873831064,0.7801127567951986,0.07814307265434003,0.15666715800800246,0.013315837676382584,0],[0.15965839119808206,0.16665742400624964,0.16897948537055738,0.17013847384129777,0.17154892428413962,0.17187441051521585,0.9338723038848171,0.707733974973703,0.705972951138854,0.7151061770647219,0.7492439399035885,0.4860046201469575],[0.10704157251472043,0.1220721794294405,0.12470858039273522,0.12589827443180485,0.1270865742023756,0.11958123595080092,0.7987301756906527,0.7270006218797034,0.7077339749736979,0.7077339749736715,0.7074550009008582,0.7074550009008578],[0.07547148130541041,0.08276719940643479,0.08518769172321777,0.08639580910225389,0.08760251062198517,0.08820533121180528,0.7507207653338794,0.7270006218797039,0.7755512886775755,0.8526487915124271,0.7970802513777459,0.7678365145127088],[0.054424753831323405,0.06179464325683715,0.06423974331162911,0.06546014291742061,0.06667911226971812,0.06728806138615927,0.7333596542228326,0.627790687402959,0.7134813516518526,0.7934635152173309,0.8493352322327458,0.9475725366781986],[0.03939137706489482,0.046814246007088584,0.04927692301702286,0.05050609564252172,0.051733827733129685,0.05234715436813504,0.7218919091706905,0.5825894942788615,0.6526612259972646,0.724057324397884,0.7850237003420475,0.9149652154202894],[0.02811634449013705,0.03557894807033697,0.038054807796299626,0.039290560186590745,0.04052486432987599,0.041141474104453735,0.7015248310142106,0.5508975139541007,0.5901612259972795,0.6526612259972822,0.7167129108609922,0.8150605029684861],[0.019346874709526094,0.02684038300760663,0.029326495958823397,0.030567365942764022,0.03180678169533417,0.03242594501042164,0.6201639597847827,0.5289843087007053,0.5415501148861116,0.5969452603497671,0.6525984568308176,0.7081318154158877],[0.012331298885176648,0.019849530957025394,0.02234384648754401,0.023588810548378702,0.024832315565628666,0.02545352173544081,0.5507195153403879,0.5112340524155965,0.5026612259972375,0.5525008159053836,0.6025008159053884,0.6525008159053781],[0.006591282301393165,0.014129742916606689,0.016630769649049137,0.01787908340705147,0.01912593419708627,0.019748811782762745,0.4939013335221901,0.4969330266494302,0.4707802750127039,0.6542737218475158,0.7077339749737003,0.7077339749736964]],"zmax":1,"zmin":0},{"colorbar":{"title":{"font":{"size":18},"side":"right","text":"Decarboxylation Rate : CO₂ Uptake Rate"},"xpad":20},"name":"PEP-CK","showscale":false,"type":"heatmap","x":[50,100,150,200,300,400,500,600,700,800,900,1000],"xaxis":"x2","y":[0.5,0.6,0.7,0.8,0.9,1,2,3,4,5,6,7,8,9,10],"yaxis":"y2","z":[[0.7550770990560894,0.7491433931613394,0.7471747741267001,0.7461921959739065,0.7452107693586937,0.7447204872456159,0.37082846101666256,0.5569211277494159,0.6055105492260888,0.5893302436799169,0.5048243093108477,0.4214909759775208],[0.742581315845235,0.7596937035873949,0.7223968844314275,0.7198871443865795,0.7173803456435456,0.7161280476452601,0.2352036338269768,0.7083295244465478,0.5480105540650396,0.5754710008284848,0.5516993093108364,0.47357430931083644],[0.7547756582757502,0.7457589678906693,0.742514690250837,0.7410215924904722,0.739530244573702,0.7387852258458342,0.14457475350944535,0.870917538124039,0.5077991570062464,0.5754710008284831,0.5954576946603121,0.5195301916637023],[0.7672198946448416,0.7580755705278305,0.7553784663895593,0.753906098598278,0.7524354563564906,0.7517007813690766,0.10402536339279084,0.41281252501026167,0.6125978263431281,0.5588612485094837,0.5754710008284829,0.541447500390824],[0.7577709253294649,0.7489119527470129,0.7459728212229219,0.7445058403736685,0.7432933990125384,0.7425614119762802,0.07237633602427168,0.2367826938612,0.7725027971033824,0.5223115409068566,0.5754710008284833,0.5534979179518703],[0.7497158268428811,0.7408861324159498,0.7377038942182294,0.7364945818704102,0.73503416282255,0.7343045949402527,0.05600496548945513,0.19522707176679094,0.807093968128182,0.5066146083617469,0.5708652318681404,0.5534979179518658],[0.8265498280755854,0.8195507952673703,0.8172287339030632,0.8160697454323116,0.8146592949894826,0.8143338087584066,0.04306438643652628,0.2709070725739411,0.27266809640878975,0.2635232465632193,0.20996041577932187,0.3992324206355687],[0.8791666467590105,0.8562898940447662,0.8536534930822893,0.8524637990431063,0.8512754992725987,0.8666269833227207,0.17991087185699028,0.24831017267332348,0.26953835602903703,0.27090707257397245,0.27118604664678225,0.2711860466467824],[0.9107367379678407,0.903441019867212,0.9010205275503393,0.8998124101714747,0.8986057086517206,0.8980028880620664,0.22792028221376612,0.2483101726733292,0.20136941875417597,0.12419598935894857,0.18156079616989582,0.21090914831224983],[0.931783465442476,0.9244135760167725,0.921968475961727,0.9207480763563202,0.9195291070040837,0.9189201578876879,0.2452813933248129,0.34757241478873835,0.26515969589579075,0.18338126565404625,0.12930581531489946,0.029752101963201417],[0.9468168422087567,0.9393939732665638,0.9369312962568267,0.9357021236312554,0.9344743915402398,0.933861064905467,0.25674913837695357,0.39605155326878155,0.3260844368276978,0.2545837231497583,0.1936173472055988,0.06367583212735474],[0.9580918747833472,0.9506292712029054,0.9481534114776636,0.9469176590870495,0.9456833549437197,0.9450667451690974,0.2772208318107509,0.4278481488708604,0.38858443682768773,0.3260844368276853,0.26192813668665155,0.16358054457915772],[0.9668613445640164,0.9593678362659268,0.9568817233146529,0.9556408533309858,0.9544014375691457,0.9537822742630283,0.35847708776285786,0.44976135412425317,0.4371955479388451,0.3818004024751938,0.3261472059941434,0.2705092321317541],[0.9738769203883642,0.9663586883169578,0.9638643727863937,0.9626194087250092,0.9613759037080378,0.9607546975379451,0.427921532207256,0.46751161040936623,0.4760844368277228,0.4262448469195631,0.3762448469195879,0.32624484691958583],[0.97961693697216,0.9720784763571526,0.9695774496241425,0.9683291358663254,0.9670822850764793,0.9664594074907671,0.48473971402545585,0.48181263617553016,0.507965387812257,0.3244719409774377,0.27101168785125945,0.2710116878512666]],"zmax":1,"zmin":0},{"colorbar":{"title":{"font":{"size":18},"side":"right","text":"Decarboxylation Rate : CO₂ Uptake Rate"},"xpad":20},"name":"NAD-ME","showscale":false,"type":"heatmap","x":[50,100,150,200,300,400,500,600,700,800,900,1000],"xaxis":"x3","y":[0.5,0.6,0.7,0.8,0.9,1,2,3,4,5,6,7,8,9,10],"yaxis":"y3","z":[[0.008055376353460195,0.008055376353460146,0.008055376353460274,0.008055376353460335,0.008055376353602348,0.00805537635346392,0.0080553763534593,0.2686224060362466,0.38090690060223786,0.3812977549021704,0.45994068409257927,0.5432740174259025],[0.008055376353461137,0.008055376353460144,0.008055376353460153,0.008055376353460127,0.008055376353460231,0.008055376353460222,0.008055376353459598,0.19496413792873557,0.3773691183096058,0.4051375989451545,0.4130656840925904,0.49119068409258965],[0.008055376353459985,0.008055376353460144,0.008055376353460294,0.008055376353460245,0.008055376353460162,0.00805537635346018,0.008055376353459189,0.10138963960036217,0.33715772125077065,0.40513759894515255,0.38129775490216916,0.4452348017397217],[0.00020923055463527084,0.00020923055463566967,0.00020923055463536964,0.0002092305546351782,0.00020923055463524073,0.0002092305546350059,0.008055376353459803,0.1001981878309183,0.27007012891035326,0.388219812754054,0.4051375989451517,0.42005329224095295],[0.00020923055463224803,0.00020923055463764948,0.00020923055463546413,0.0002092305546328966,0.00020923055463666263,0.0002092305546352554,0.00805537635346008,0.10019818783092076,0.17412714645420976,0.35167010515142766,0.4051375989451516,0.4049826133491293],[0.0002092305546357606,0.00020923055463517053,0.00020923055463516253,0.00020923055463542206,0.00020923055463520335,0.00020923055463535563,0.0080553763534602,0.010095400051451354,0.10019818783091998,0.32215346224369396,0.3983246945109392,0.4049826133491284],[0.00020923055464716067,0.00020923055463587713,0.0002092305546354212,0.00020923055463539415,0.0002092305546356169,0.00020923055463554306,0.008055376353460297,0.008055376353459976,0.008055376353459709,0.0080553763534602,0.02681788087548229,0.10078519577586648],[0.00020923055465515056,0.00805537635361163,0.008055376353460542,0.008055376353460588,0.008055376353460894,0.00020923055468574853,0.008055376353460028,0.008055376353460793,0.008055376353460432,0.008055376353460533,0.00805537635346102,0.00805537635346026],[0.0002092305548179395,0.00020923055464849456,0.00020923055467113495,0.00020923055458439325,0.00020923055463114028,0.00020923055451099824,0.00805537635346049,0.008055376353460092,0.008055376353460634,0.008055376353459372,0.008055376353459818,0.008055376353460885],[0.0002092305545444696,0.0002092305546323615,0.00020923055481184003,0.00020923055457431694,0.0002092305545446866,0.00020923055452182397,0.008055376353458788,0.008055376353458913,0.008055376353460271,0.008055376353458406,0.008055376353460547,0.008055376353460276],[0.00020923055461993844,0.0002092305546234677,0.00020923055451934087,0.00020923055455777424,0.00020923055476195813,0.00020923055464480052,0.008055376353460266,0.00805537635346103,0.008055376353460255,0.008055376353460422,0.008055376353458217,0.008055376353459211],[0.00020923055470435935,0.00020923055482553738,0.00020923055446417336,0.00020923055462639424,0.0002092305546482933,0.0002092305546706354,0.008055376353460281,0.008055376353459646,0.008055376353459529,0.008055376353462698,0.008055376353460268,0.00805537635345946],[0.0002092305546744455,0.00020923055467788004,0.0002092305547069961,0.00020923055456987578,0.00020923055920954803,0.0002092305549002913,0.00805537635346014,0.00805537635346039,0.008055376353461192,0.008055376353460384,0.00805537635345958,0.008055376353460883],[0.00020923055467693814,0.00020923055445246633,0.00020923055450544037,0.00020923055475223493,0.00020923055461165595,0.00020923055475317328,0.008055376353460174,0.008055376353459954,0.008055376353460651,0.008055376353460934,0.008055376353461428,0.008055376353460628],[0.00020923055467429337,0.000209230554565856,0.00020923055485838466,0.0002092305547579264,0.0002092305546629071,0.00020923055468174978,0.008055376353460153,0.008055376353458803,0.008055376353460987,0.008055376353462778,0.008055376353459901,0.00805537635345949]],"zmax":1,"zmin":0}],"layout":{"annotations":[{"font":{"size":20},"showarrow":false,"text":"<b>NADP-ME</b>","x":0.5,"xanchor":"center","xref":"paper","y":1,"yanchor":"bottom","yref":"paper"},{"font":{"size":20},"showarrow":false,"text":"<b>PEP-CK</b>","x":0.5,"xanchor":"center","xref":"paper","y":0.6333333333333333,"yanchor":"bottom","yref":"paper"},{"font":{"size":20},"showarrow":false,"text":"<b>NAD-ME</b>","x":0.5,"xanchor":"center","xref":"paper","y":0.26666666666666666,"yanchor":"bottom","yref":"paper"},{"font":{"size":20},"showarrow":false,"text":"Total PPFD [µE]","x":0.5,"xanchor":"center","xref":"paper","y":0,"yanchor":"top","yref":"paper","yshift":-30},{"font":{"size":20},"showarrow":false,"text":"PPFD [BS] : PPFD [M]","textangle":-90,"x":0,"xanchor":"right","xref":"paper","xshift":-40,"y":0.5,"yanchor":"middle","yref":"paper"}],"height":1000,"template":{"data":{"bar":[{"error_x":{"color":"#2a3f5f"},"error_y":{"color":"#2a3f5f"},"marker":{"line":{"color":"#E5ECF6","width":0.5}},"type":"bar"}],"barpolar":[{"marker":{"line":{"color":"#E5ECF6","width":0.5}},"type":"barpolar"}],"carpet":[{"aaxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"baxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"type":"carpet"}],"choropleth":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"choropleth"}],"contour":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"contour"}],"contourcarpet":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"contourcarpet"}],"heatmap":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"heatmap"}],"heatmapgl":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"heatmapgl"}],"histogram":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"histogram"}],"histogram2d":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"histogram2d"}],"histogram2dcontour":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"histogram2dcontour"}],"mesh3d":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"mesh3d"}],"parcoords":[{"line":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"parcoords"}],"pie":[{"automargin":true,"type":"pie"}],"scatter":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatter"}],"scatter3d":[{"line":{"colorbar":{"outlinewidth":0,"ticks":""}},"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatter3d"}],"scattercarpet":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattercarpet"}],"scattergeo":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattergeo"}],"scattergl":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattergl"}],"scattermapbox":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattermapbox"}],"scatterpolar":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterpolar"}],"scatterpolargl":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterpolargl"}],"scatterternary":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterternary"}],"surface":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"surface"}],"table":[{"cells":{"fill":{"color":"#EBF0F8"},"line":{"color":"white"}},"header":{"fill":{"color":"#C8D4E3"},"line":{"color":"white"}},"type":"table"}]},"layout":{"annotationdefaults":{"arrowcolor":"#2a3f5f","arrowhead":0,"arrowwidth":1},"autotypenumbers":"strict","coloraxis":{"colorbar":{"outlinewidth":0,"ticks":""}},"colorscale":{"diverging":[[0,"#8e0152"],[0.1,"#c51b7d"],[0.2,"#de77ae"],[0.3,"#f1b6da"],[0.4,"#fde0ef"],[0.5,"#f7f7f7"],[0.6,"#e6f5d0"],[0.7,"#b8e186"],[0.8,"#7fbc41"],[0.9,"#4d9221"],[1,"#276419"]],"sequential":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"sequentialminus":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]]},"colorway":["#636efa","#EF553B","#00cc96","#ab63fa","#FFA15A","#19d3f3","#FF6692","#B6E880","#FF97FF","#FECB52"],"font":{"color":"#2a3f5f"},"geo":{"bgcolor":"white","lakecolor":"white","landcolor":"#E5ECF6","showlakes":true,"showland":true,"subunitcolor":"white"},"hoverlabel":{"align":"left"},"hovermode":"closest","mapbox":{"style":"light"},"paper_bgcolor":"white","plot_bgcolor":"#E5ECF6","polar":{"angularaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"bgcolor":"#E5ECF6","radialaxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"scene":{"xaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"},"yaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"},"zaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"}},"shapedefaults":{"line":{"color":"#2a3f5f"}},"ternary":{"aaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"baxis":{"gridcolor":"white","linecolor":"white","ticks":""},"bgcolor":"#E5ECF6","caxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"title":{"x":0.05},"xaxis":{"automargin":true,"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","zerolinewidth":2},"yaxis":{"automargin":true,"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","zerolinewidth":2}}},"width":600,"xaxis":{"anchor":"y","domain":[0,1],"tickangle":35,"tickfont":{"size":16},"tickvals":[50,100,150,200,300,400,500,600,700,800,900,1000],"type":"category"},"xaxis2":{"anchor":"y2","domain":[0,1],"tickangle":35,"tickfont":{"size":16},"tickvals":[50,100,150,200,300,400,500,600,700,800,900,1000],"type":"category"},"xaxis3":{"anchor":"y3","domain":[0,1],"tickangle":35,"tickfont":{"size":16},"tickvals":[50,100,150,200,300,400,500,600,700,800,900,1000],"type":"category"},"yaxis":{"anchor":"x","domain":[0.7333333333333334,1],"tickfont":{"size":16},"tickprefix":"1:","type":"category"},"yaxis2":{"anchor":"x2","domain":[0.3666666666666667,0.6333333333333333],"tickfont":{"size":16},"tickprefix":"1:","type":"category"},"yaxis3":{"anchor":"x3","domain":[0,0.26666666666666666],"tickfont":{"size":16},"tickprefix":"1:","type":"category"}}} </script><img src="index.html.media/8" alt="" itemscope="" itemtype="http://schema.org/ImageObject"> </picture> </stencila-image-plotly> </figure> </stencila-code-chunk> <figcaption> <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="effect-of-light-on-the-c4-mode-heat-maps-illustrating-the-activity-of-the-decarboxylation-enzymes-pep-ck-nadp-me-and-nad-me-relative-to-the-co2-uptake-rate-in-dependence-of-the-total-ppfd-and-the-photon-distribution-among-mesophyll-and-bundle-sheath"> Effect of light on the C4 mode. Heat-maps illustrating the activity of the decarboxylation enzymes PEP-CK, NADP-ME, and NAD-ME relative to the CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> uptake rate in dependence of the total PPFD and the photon distribution among mesophyll and bundle sheath.</h4> </figcaption> </figure> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">Given that C4 plants sometimes optimise light availability to the bundle sheath <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib8"><span>8</span><span>Bellasio and Lundgren</span><span>2016</span></a></cite> we next explored light availability and light distribution. The model prediction is re-run with changes in the constraints, and the resulting tables of fluxes are queried for CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> uptake and fluxes through the decarboxylation enzymes. In the experiment, we varied the total PPFD between <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">ds_ppfd.min()</code><output slot="output"></output> </stencila-code-expression> μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s) to <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">ds_ppfd.max()</code><output slot="output"></output> </stencila-code-expression> μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s) and photon distribution <span itemscope="" itemtype="http://schema.stenci.la/MathFragment"><span class="mjx-chtml"><span class="mjx-math" aria-label="PPF{D}_{B}"><span class="mjx-mrow" aria-hidden="true"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em; padding-right: 0.109em;">P</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em; padding-right: 0.109em;">P</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em; padding-right: 0.106em;">F</span></span><span class="mjx-msubsup"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">D</span></span></span></span></span><span class="mjx-sub" style="font-size: 70.7%; vertical-align: -0.212em; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">B</span></span></span></span></span></span></span></span></span></span> / <span itemscope="" itemtype="http://schema.stenci.la/MathFragment"><span class="mjx-chtml"><span class="mjx-math" aria-label="PPF{D}_{M}"><span class="mjx-mrow" aria-hidden="true"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em; padding-right: 0.109em;">P</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em; padding-right: 0.109em;">P</span></span><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em; padding-right: 0.106em;">F</span></span><span class="mjx-msubsup"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em;">D</span></span></span></span></span><span class="mjx-sub" style="font-size: 70.7%; vertical-align: -0.212em; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.446em; padding-bottom: 0.298em; padding-right: 0.081em;">M</span></span></span></span></span></span></span></span></span></span> in the range between <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">min_ppfd_bs_m</code><output slot="output"></output> </stencila-code-expression> to <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">max_ppfd_bs_m</code><output slot="output"></output> </stencila-code-expression>, see <a href="#fig7" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 7</a> and <a href="#fig8" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 8</a>. Under light limitation, if the total PPFD is lower than <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">low_light_thres</code><output slot="output"></output> </stencila-code-expression> μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s) , the CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> uptake rate is reduced, leading to a decreased activity of the decarboxylation enzymes (<a href="#fig7" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 7</a>). PEP-CK is used in the optimal solutions active under light-limiting conditions (<a href="#fig8" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 8</a>). Under limiting light conditions, photon distribution with a higher proportion in the bundle sheath shifts decarboxylation towards NADP-ME but only to up to <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">nadpme_max_low_light</code><output slot="output"></output> </stencila-code-expression>%. Under non-limiting conditions, the distribution of light availability determines the optimal decarboxylation enzyme. NADP-ME is the preferred decarboxylation enzyme with supplemental contributions by PEP-CK if light availability is near the threshold of <stencila-code-expression programming-language="py" itemscope="" itemtype="http://schema.stenci.la/CodeExpression"><code class="py" slot="text">low_light_thres</code><output slot="output"></output> </stencila-code-expression> μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s) or if at least twice as many photons are absorbed by the mesophyll. Excess light availability and a higher proportion of photons reaching the bundle sheath leads to optimal solutions which favour PEP-CK as the decarboxylation enzyme. In the case of very high light availability and an abrupt shift towards the bundle sheath, NAD-ME becomes the optimal solution (<a href="#fig8" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 8</a>). NAD-ME is the least favourable enzyme overall, only low activity is predicted under extreme light conditions, where the bundle sheath absorbs equal or more photons than the mesophyll (<a href="#fig8" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 8</a>). PEP-CK complements the activity of NADP-ME and NAD-ME to 100% in many conditions, meaning the <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">two-cell</em> model also predicts the co-existence of PEP-CK/NADP-ME and PEP-CK/NAD-ME mode, while the flux distribution indicates no parallel use of NAD-ME and NADP-ME, compare <a href="#fig8" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 8</a>.</p> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="38" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>###################################################################################################################################### ###################################################################################################################################### ############## EXPERIMENT 7: Effect of N-Limtation on C4 Mode ############## ###################################################################################################################################### ###################################################################################################################################### print(f"Code Cell 38: Experiment 7 -- Effect of N-Limtation on C4 Mode") #Create copy of c4 model c4_model_exp7 = c4_model.copy() #Reaction variables B_Ex_Suc = c4_model_exp7.reactions.get_by_id("[B]_Ex_Suc") M_Im_NO3 = c4_model_exp7.reactions.get_by_id("[M]_Im_NO3") B_Im_NO3 = c4_model_exp7.reactions.get_by_id("[B]_Im_NO3") B_RBO = c4_model_exp7.reactions.get_by_id("[B]_RBO_h") M_RBO = c4_model_exp7.reactions.get_by_id("[M]_RBO_h") #Decarboxylation reactions ids and names of enzymes c4_mode_r_id_enzyme = {'[B]_MalDH2_m': 'NAD-ME', '[B]_PEPC1_c': 'PEP-CK', '[B]_MalDH4_h': 'NADP-ME'} #NO3 flux no3_flux = np.arange(0,2.1,0.2) #Initialise dataframes to hold results df_result_exp7 = pd.DataFrame(index=c4_model.reactions.list_attr('id'), columns=no3_flux, dtype='float64') #Test all no3 values for no3_value in tqdm(df_result_exp7.columns): #Add N-limitation constraint const_NO3_exp7 = c4_model_exp7.problem.Constraint( M_Im_NO3.flux_expression + B_Im_NO3.flux_expression, lb = no3_value, ub = no3_value, name='const_NO3_exp7') c4_model_exp7.add_cons_vars(const_NO3_exp7) #Optimization - Maximize sucrose output & Minimize Oxygenation by Rubisco B_Ex_Suc.objective_coefficient = 1. B_RBO.objective_coefficient = -1. M_RBO.objective_coefficient = -1. result_exp7_fba = c4_model_exp7.optimize('maximize') #Optimize/Minimize total flux if result_exp7_fba.status == 'optimal': result_exp7_pfba = cobra.flux_analysis.parsimonious.pfba(c4_model_exp7) df_result_exp7[no3_value] = result_exp7_pfba.fluxes #Remove N-limitation constraint c4_model_exp7.remove_cons_vars(const_NO3_exp7) </code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 38: Experiment 7 -- Effect of N-Limtation on C4 Mode </code></pre> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code> 0%| | 0/11 [00:00<?, ?it/s]</code></pre> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>/Users/blaetke/opt/anaconda3/envs/elife-49305-era/lib/python3.9/site-packages/cobra/util/solver.py:508: UserWarning: Solver status is 'infeasible'. </code></pre> </figure> </stencila-code-chunk> <figure itemscope="" itemtype="http://schema.stenci.la/Figure" id="fig8s1" title="Figure 8—figure supplement 1"><label data-itemprop="label">Figure 8—figure supplement 1</label> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="39" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>################################################################################## ############## Figure 8—figure supplement 1 ############## ################################################################################## #{ # "caption": "### Effect of NO~3~^-^ limitation on the flux through the different decarboxylation enzymes.", # "id": "fig8s1, # "label": "Figure 8—figure supplement 1", # "trusted": true #} #Create figure fig_exp7 = go.Figure() #Add trace for each decarboxylation enzyme for i, r_id in enumerate(c4_mode_r_id_enzyme.keys()): #Create bar plot trace trace = go.Bar( y = df_result_exp7.loc[r_id], x = df_result_exp7.columns, name = c4_mode_r_id_enzyme[r_id] ) #Add trace to figure fig_exp7.add_trace(trace) #Update xaxes fig_exp7.update_xaxes( title = dict( text = 'NO\u2083 Uptake Rate [µmol/(m\u00B2s)]', font = dict(size=18) ), tickfont = dict(size=16) ) #Update yaxes fig_exp7.update_yaxes( range = [0, 40], title = dict( text = 'Flux [µmol/(m\u00B2s)]', font = dict(size=18) ), tickfont = dict(size=16) ) #Update layout fig_exp7.update_layout( barmode='stack', width= 1000, height=500, legend=dict( font=dict(size=18), ) ) #Show figure fig_exp7.show()</code></pre> <figure slot="outputs"> <stencila-image-plotly> <picture> <script type="application/vnd.plotly.v1+json"> {"config":{"plotlyServerURL":"https://plot.ly"},"data":[{"name":"NAD-ME","type":"bar","x":[0,0.2,0.4,0.6000000000000001,0.8,1,1.2000000000000002,1.4000000000000001,1.6,1.8,2],"y":[0,0.06103038309115161,0.12206076618230244,0.1830911492734241,0.2441215323645955,0.3051519154557477,null,null,null,null,null]},{"name":"PEP-CK","type":"bar","x":[0,0.2,0.4,0.6000000000000001,0.8,1,1.2000000000000002,1.4000000000000001,1.6,1.8,2],"y":[0,0.4589562340471031,0.8172125087724892,1.1754687835409652,1.5337250583102895,1.8919813330790494,null,null,null,null,null]},{"name":"NADP-ME","type":"bar","x":[0,0.2,0.4,0.6000000000000001,0.8,1,1.2000000000000002,1.4000000000000001,1.6,1.8,2],"y":[0,6.952932801596668,14.006565562562411,21.06019832345768,28.113831084357503,35.16746384525628,null,null,null,null,null]}],"layout":{"barmode":"stack","height":500,"legend":{"font":{"size":18}},"template":{"data":{"bar":[{"error_x":{"color":"#2a3f5f"},"error_y":{"color":"#2a3f5f"},"marker":{"line":{"color":"#E5ECF6","width":0.5}},"type":"bar"}],"barpolar":[{"marker":{"line":{"color":"#E5ECF6","width":0.5}},"type":"barpolar"}],"carpet":[{"aaxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"baxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"type":"carpet"}],"choropleth":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"choropleth"}],"contour":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"contour"}],"contourcarpet":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"contourcarpet"}],"heatmap":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"heatmap"}],"heatmapgl":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"heatmapgl"}],"histogram":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"histogram"}],"histogram2d":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"histogram2d"}],"histogram2dcontour":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"histogram2dcontour"}],"mesh3d":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"mesh3d"}],"parcoords":[{"line":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"parcoords"}],"pie":[{"automargin":true,"type":"pie"}],"scatter":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatter"}],"scatter3d":[{"line":{"colorbar":{"outlinewidth":0,"ticks":""}},"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatter3d"}],"scattercarpet":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattercarpet"}],"scattergeo":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattergeo"}],"scattergl":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattergl"}],"scattermapbox":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattermapbox"}],"scatterpolar":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterpolar"}],"scatterpolargl":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterpolargl"}],"scatterternary":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterternary"}],"surface":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"surface"}],"table":[{"cells":{"fill":{"color":"#EBF0F8"},"line":{"color":"white"}},"header":{"fill":{"color":"#C8D4E3"},"line":{"color":"white"}},"type":"table"}]},"layout":{"annotationdefaults":{"arrowcolor":"#2a3f5f","arrowhead":0,"arrowwidth":1},"autotypenumbers":"strict","coloraxis":{"colorbar":{"outlinewidth":0,"ticks":""}},"colorscale":{"diverging":[[0,"#8e0152"],[0.1,"#c51b7d"],[0.2,"#de77ae"],[0.3,"#f1b6da"],[0.4,"#fde0ef"],[0.5,"#f7f7f7"],[0.6,"#e6f5d0"],[0.7,"#b8e186"],[0.8,"#7fbc41"],[0.9,"#4d9221"],[1,"#276419"]],"sequential":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"sequentialminus":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]]},"colorway":["#636efa","#EF553B","#00cc96","#ab63fa","#FFA15A","#19d3f3","#FF6692","#B6E880","#FF97FF","#FECB52"],"font":{"color":"#2a3f5f"},"geo":{"bgcolor":"white","lakecolor":"white","landcolor":"#E5ECF6","showlakes":true,"showland":true,"subunitcolor":"white"},"hoverlabel":{"align":"left"},"hovermode":"closest","mapbox":{"style":"light"},"paper_bgcolor":"white","plot_bgcolor":"#E5ECF6","polar":{"angularaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"bgcolor":"#E5ECF6","radialaxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"scene":{"xaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"},"yaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"},"zaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"}},"shapedefaults":{"line":{"color":"#2a3f5f"}},"ternary":{"aaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"baxis":{"gridcolor":"white","linecolor":"white","ticks":""},"bgcolor":"#E5ECF6","caxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"title":{"x":0.05},"xaxis":{"automargin":true,"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","zerolinewidth":2},"yaxis":{"automargin":true,"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","zerolinewidth":2}}},"width":1000,"xaxis":{"tickfont":{"size":16},"title":{"font":{"size":18},"text":"NO₃ Uptake Rate [µmol/(m²s)]"}},"yaxis":{"range":[0,40],"tickfont":{"size":16},"title":{"font":{"size":18},"text":"Flux [µmol/(m²s)]"}}}} </script><img src="index.html.media/9" alt="" itemscope="" itemtype="http://schema.org/ImageObject"> </picture> </stencila-image-plotly> </figure> </stencila-code-chunk> <figcaption> <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="effect-of-no3--limitation-on-the-flux-through-the-different-decarboxylation-enzymes"> Effect of NO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">3</span></sub><sup itemscope="" itemtype="http://schema.stenci.la/Superscript">-</sup> limitation on the flux through the different decarboxylation enzymes.</h4> </figcaption> </figure> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="40" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>###################################################################################################################################### ###################################################################################################################################### ############## EXPERIMENT 8: Effect of H2O-Limtation on C4 Mode ############## ###################################################################################################################################### ###################################################################################################################################### print(f"Code Cell 40: Experiment 8 -- Effect of H2O-Limtation on C4 Mode") #Create copy of c4 model c4_model_exp8 = c4_model.copy() #Reaction variables B_Ex_Suc = c4_model_exp8.reactions.get_by_id("[B]_Ex_Suc") M_Im_H2O = c4_model_exp8.reactions.get_by_id("[M]_Im_H2O") B_Im_H2O = c4_model_exp8.reactions.get_by_id("[B]_Im_H2O") B_RBO = c4_model_exp8.reactions.get_by_id("[B]_RBO_h") M_RBO = c4_model_exp8.reactions.get_by_id("[M]_RBO_h") #Decarboxylation reactions ids and names of enzymes c4_mode_r_id_enzyme = {'[B]_MalDH2_m': 'NAD-ME', '[B]_PEPC1_c': 'PEP-CK', '[B]_MalDH4_h': 'NADP-ME'} #H2O flux h2O_flux = np.arange(0,45,5) #Initialise dataframes to hold results df_result_exp8 = pd.DataFrame(index=c4_model.reactions.list_attr('id'), columns=h2O_flux, dtype='float64') #Test all H2O values for h2o_value in tqdm(df_result_exp8.columns): #Add max H2O-uptake constraint const_h2o_exp8 = c4_model_exp8.problem.Constraint( M_Im_H2O.flux_expression + B_Im_H2O.flux_expression, lb = 0, ub = h2o_value, name='const_h2o_exp8') c4_model_exp8.add_cons_vars(const_h2o_exp8) #Optimize/Maximize sucrose output B_Ex_Suc.objective_coefficient = 1. B_RBO.objective_coefficient = -1. M_RBO.objective_coefficient = -1. result_exp8_fba = c4_model_exp8.optimize('maximize') #Optimize/Minimize total flux if result_exp8_fba.status == 'optimal': result_exp8_pfba = cobra.flux_analysis.parsimonious.pfba(c4_model_exp8) df_result_exp8[h2o_value] = result_exp8_pfba.fluxes #Remove max H2O-uptake constraint c4_model_exp8.remove_cons_vars(const_h2o_exp8) </code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 40: Experiment 8 -- Effect of H2O-Limtation on C4 Mode </code></pre> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code> 0%| | 0/9 [00:00<?, ?it/s]</code></pre> </figure> </stencila-code-chunk> <figure itemscope="" itemtype="http://schema.stenci.la/Figure" id="fig8s2" title="Figure 8—figure supplement 2"><label data-itemprop="label">Figure 8—figure supplement 2</label> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="41" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>################################################################################## ############## Figure 8—figure supplement 2 ############## ################################################################################## #{ # "caption": "### Effect of H~2~O imitation on the flux through the different decarboxylation enzymes.", # "id": "fig8s2", # "label": "Figure 8—figure supplement 2", # "trusted": true #} #Create figure fig_exp8 = go.Figure() #Add trace for each decarboxylation enzyme for i, r_id in enumerate(c4_mode_r_id_enzyme.keys()): #Create bar plot trace trace = go.Bar( y = df_result_exp8.loc[r_id], x = df_result_exp8.columns, name = c4_mode_r_id_enzyme[r_id] ) #Add trace to figure fig_exp8.add_trace(trace) #Update xaxes fig_exp8.update_xaxes( title = dict( text = 'Max H\u2082O Uptake Rate [µmol/(m\u00B2s)]', font = dict(size=18) ), tickfont = dict(size=16) ) #Update yaxes fig_exp8.update_yaxes( range = [0, 40], title = dict( text = 'Flux [µmol/(m\u00B2s)]', font = dict(size=18) ), tickfont = dict(size=16) ) #Update layout fig_exp8.update_layout( barmode='stack', width= 1000, height=500, legend=dict( font=dict(size=18), ) ) #Show figure fig_exp8.show()</code></pre> <figure slot="outputs"> <stencila-image-plotly> <picture> <script type="application/vnd.plotly.v1+json"> {"config":{"plotlyServerURL":"https://plot.ly"},"data":[{"name":"NAD-ME","type":"bar","x":[0,5,10,15,20,25,30,35,40],"y":[-3.966547616032975e-18,0.04430082368847517,0.08860164737695075,0.1329024710654283,0.17720329475390112,0.22150411844237636,0.26580494213085154,0.3101057658193266,0.32221505413840695]},{"name":"PEP-CK","type":"bar","x":[0,5,10,15,20,25,30,35,40],"y":[0,0.35252208289754244,0.6208031360451295,0.8808547244502359,1.1409063128553074,1.4009579012603686,1.6610094896654566,1.9210610780705455,1.992144173138372]},{"name":"NADP-ME","type":"bar","x":[0,5,10,15,20,25,30,35,40],"y":[0,5.027630764533123,10.139502558816211,15.259603817841771,20.379705076867328,25.49980633589293,30.61990759491848,35.74000885394403,37.139549025125085]}],"layout":{"barmode":"stack","height":500,"legend":{"font":{"size":18}},"template":{"data":{"bar":[{"error_x":{"color":"#2a3f5f"},"error_y":{"color":"#2a3f5f"},"marker":{"line":{"color":"#E5ECF6","width":0.5}},"type":"bar"}],"barpolar":[{"marker":{"line":{"color":"#E5ECF6","width":0.5}},"type":"barpolar"}],"carpet":[{"aaxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"baxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"type":"carpet"}],"choropleth":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"choropleth"}],"contour":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"contour"}],"contourcarpet":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"contourcarpet"}],"heatmap":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"heatmap"}],"heatmapgl":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"heatmapgl"}],"histogram":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"histogram"}],"histogram2d":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"histogram2d"}],"histogram2dcontour":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"histogram2dcontour"}],"mesh3d":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"mesh3d"}],"parcoords":[{"line":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"parcoords"}],"pie":[{"automargin":true,"type":"pie"}],"scatter":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatter"}],"scatter3d":[{"line":{"colorbar":{"outlinewidth":0,"ticks":""}},"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatter3d"}],"scattercarpet":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattercarpet"}],"scattergeo":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattergeo"}],"scattergl":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattergl"}],"scattermapbox":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattermapbox"}],"scatterpolar":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterpolar"}],"scatterpolargl":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterpolargl"}],"scatterternary":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterternary"}],"surface":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"surface"}],"table":[{"cells":{"fill":{"color":"#EBF0F8"},"line":{"color":"white"}},"header":{"fill":{"color":"#C8D4E3"},"line":{"color":"white"}},"type":"table"}]},"layout":{"annotationdefaults":{"arrowcolor":"#2a3f5f","arrowhead":0,"arrowwidth":1},"autotypenumbers":"strict","coloraxis":{"colorbar":{"outlinewidth":0,"ticks":""}},"colorscale":{"diverging":[[0,"#8e0152"],[0.1,"#c51b7d"],[0.2,"#de77ae"],[0.3,"#f1b6da"],[0.4,"#fde0ef"],[0.5,"#f7f7f7"],[0.6,"#e6f5d0"],[0.7,"#b8e186"],[0.8,"#7fbc41"],[0.9,"#4d9221"],[1,"#276419"]],"sequential":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"sequentialminus":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]]},"colorway":["#636efa","#EF553B","#00cc96","#ab63fa","#FFA15A","#19d3f3","#FF6692","#B6E880","#FF97FF","#FECB52"],"font":{"color":"#2a3f5f"},"geo":{"bgcolor":"white","lakecolor":"white","landcolor":"#E5ECF6","showlakes":true,"showland":true,"subunitcolor":"white"},"hoverlabel":{"align":"left"},"hovermode":"closest","mapbox":{"style":"light"},"paper_bgcolor":"white","plot_bgcolor":"#E5ECF6","polar":{"angularaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"bgcolor":"#E5ECF6","radialaxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"scene":{"xaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"},"yaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"},"zaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"}},"shapedefaults":{"line":{"color":"#2a3f5f"}},"ternary":{"aaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"baxis":{"gridcolor":"white","linecolor":"white","ticks":""},"bgcolor":"#E5ECF6","caxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"title":{"x":0.05},"xaxis":{"automargin":true,"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","zerolinewidth":2},"yaxis":{"automargin":true,"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","zerolinewidth":2}}},"width":1000,"xaxis":{"tickfont":{"size":16},"title":{"font":{"size":18},"text":"Max H₂O Uptake Rate [µmol/(m²s)]"}},"yaxis":{"range":[0,40],"tickfont":{"size":16},"title":{"font":{"size":18},"text":"Flux [µmol/(m²s)]"}}}} </script><img src="index.html.media/10" alt="" itemscope="" itemtype="http://schema.org/ImageObject"> </picture> </stencila-image-plotly> </figure> </stencila-code-chunk> <figcaption> <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="effect-of-h2o-imitation-on-the-flux-through-the-different-decarboxylation-enzymes"> Effect of H<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub>O imitation on the flux through the different decarboxylation enzymes.</h4> </figcaption> </figure> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="42" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>###################################################################################################################################### ###################################################################################################################################### ############## EXPERIMENT 9: Effect of CO2-Limtation on C4 Mode ############## ###################################################################################################################################### ###################################################################################################################################### print(f"Code Cell 42: Experiment 9 -- Effect of CO2-Limtation on C4 Mode") #Create copy of c4 model c4_model_exp9 = c4_model.copy() #Reaction variables B_Ex_Suc = c4_model_exp9.reactions.get_by_id("[B]_Ex_Suc") M_Im_CO2 = c4_model_exp9.reactions.get_by_id("[M]_Im_CO2") B_Im_CO2 = c4_model_exp9.reactions.get_by_id("[B]_Im_CO2") B_RBO = c4_model_exp9.reactions.get_by_id("[B]_RBO_h") M_RBO = c4_model_exp9.reactions.get_by_id("[M]_RBO_h") #Decarboxylation reactions ids and names of enzymes c4_mode_r_id_enzyme = {'[B]_MalDH2_m': 'NAD-ME', '[B]_PEPC1_c': 'PEP-CK', '[B]_MalDH4_h': 'NADP-ME'} #H2O flux co2_flux = np.arange(0,45,5) #Initialise dataframes to hold results df_result_exp9 = pd.DataFrame(index=c4_model.reactions.list_attr('id'), columns=co2_flux, dtype='float64') #Test all CO2 values for co2_value in tqdm(df_result_exp9.columns): #Add max CO2-uptake constraint const_co2_exp9 = c4_model_exp9.problem.Constraint( M_Im_CO2.flux_expression + B_Im_CO2.flux_expression, lb = 0, ub = co2_value, name='const_co2_exp9') c4_model_exp9.add_cons_vars(const_co2_exp9) #Optimize/Maximize sucrose output B_Ex_Suc.objective_coefficient = 1. B_RBO.objective_coefficient = -1. M_RBO.objective_coefficient = -1. result_exp9_fba = c4_model_exp9.optimize('maximize') #Optimize/Minimize total flux if result_exp9_fba.status == 'optimal': result_exp9_pfba = cobra.flux_analysis.parsimonious.pfba(c4_model_exp9) df_result_exp9[co2_value] = result_exp9_pfba.fluxes #Remove max CO2-uptake constraint c4_model_exp9.remove_cons_vars(const_co2_exp9) </code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 42: Experiment 9 -- Effect of CO2-Limtation on C4 Mode </code></pre> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code> 0%| | 0/9 [00:00<?, ?it/s]</code></pre> </figure> </stencila-code-chunk> <figure itemscope="" itemtype="http://schema.stenci.la/Figure" id="fig8s3" title="Figure 8—figure supplement 3"><label data-itemprop="label">Figure 8—figure supplement 3</label> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="43" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>################################################################################## ############## Figure 8—figure supplement 3 ############## ################################################################################## #{ # "caption": "### Effect of CO~2~ limitation on the flux through the different decarboxylation enzymes.", # "id": "fig8s3", # "label": "Figure 8—figure supplement 3", # "trusted": true #} #Create figure fig_exp9 = go.Figure() #Add trace for each decarboxylation enzyme for i, r_id in enumerate(c4_mode_r_id_enzyme.keys()): #Create bar plot trace trace = go.Bar( y = df_result_exp9.loc[r_id], x = df_result_exp9.columns, name = c4_mode_r_id_enzyme[r_id] ) #Add trace to figure fig_exp9.add_trace(trace) #Update xaxes fig_exp9.update_xaxes( title = dict( text = 'Max CO\u2082 Uptake Rate [µmol/(m\u00B2s)]', font = dict(size=18) ), tickfont = dict(size=16) ) #Update yaxes fig_exp9.update_yaxes( range = [0, 40], title = dict( text = 'Flux [µmol/(m\u00B2s)]', font = dict(size=18) ), tickfont = dict(size=16) ) #Update layout fig_exp9.update_layout( barmode='stack', width= 1000, height=500, legend=dict( font=dict(size=18), ) ) #Show figure fig_exp9.show()</code></pre> <figure slot="outputs"> <stencila-image-plotly> <picture> <script type="application/vnd.plotly.v1+json"> {"config":{"plotlyServerURL":"https://plot.ly"},"data":[{"name":"NAD-ME","type":"bar","x":[0,5,10,15,20,25,30,35,40],"y":[0,0.04027688176730067,0.08055376353460161,0.12083064530190185,0.16110752706920273,0.20138440883650333,0.24166129060380367,0.2819381723711062,0.32221505413840157]},{"name":"PEP-CK","type":"bar","x":[0,5,10,15,20,25,30,35,40],"y":[0,0.32239206774951923,0.5735610127108305,0.8099915394487696,1.0464220661866734,1.2828525929245913,1.5192831196624816,1.7557136464003993,1.9921441731383704]},{"name":"NADP-ME","type":"bar","x":[0,5,10,15,20,25,30,35,40],"y":[0,4.569069582033393,9.209362286854986,13.864393409899991,18.519424532945006,23.17445565598999,27.829486779035076,32.484517902080064,37.139549025124985]}],"layout":{"barmode":"stack","height":500,"legend":{"font":{"size":18}},"template":{"data":{"bar":[{"error_x":{"color":"#2a3f5f"},"error_y":{"color":"#2a3f5f"},"marker":{"line":{"color":"#E5ECF6","width":0.5}},"type":"bar"}],"barpolar":[{"marker":{"line":{"color":"#E5ECF6","width":0.5}},"type":"barpolar"}],"carpet":[{"aaxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"baxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"type":"carpet"}],"choropleth":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"choropleth"}],"contour":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"contour"}],"contourcarpet":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"contourcarpet"}],"heatmap":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"heatmap"}],"heatmapgl":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"heatmapgl"}],"histogram":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"histogram"}],"histogram2d":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"histogram2d"}],"histogram2dcontour":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"histogram2dcontour"}],"mesh3d":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"mesh3d"}],"parcoords":[{"line":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"parcoords"}],"pie":[{"automargin":true,"type":"pie"}],"scatter":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatter"}],"scatter3d":[{"line":{"colorbar":{"outlinewidth":0,"ticks":""}},"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatter3d"}],"scattercarpet":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattercarpet"}],"scattergeo":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattergeo"}],"scattergl":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattergl"}],"scattermapbox":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattermapbox"}],"scatterpolar":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterpolar"}],"scatterpolargl":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterpolargl"}],"scatterternary":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterternary"}],"surface":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"surface"}],"table":[{"cells":{"fill":{"color":"#EBF0F8"},"line":{"color":"white"}},"header":{"fill":{"color":"#C8D4E3"},"line":{"color":"white"}},"type":"table"}]},"layout":{"annotationdefaults":{"arrowcolor":"#2a3f5f","arrowhead":0,"arrowwidth":1},"autotypenumbers":"strict","coloraxis":{"colorbar":{"outlinewidth":0,"ticks":""}},"colorscale":{"diverging":[[0,"#8e0152"],[0.1,"#c51b7d"],[0.2,"#de77ae"],[0.3,"#f1b6da"],[0.4,"#fde0ef"],[0.5,"#f7f7f7"],[0.6,"#e6f5d0"],[0.7,"#b8e186"],[0.8,"#7fbc41"],[0.9,"#4d9221"],[1,"#276419"]],"sequential":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"sequentialminus":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]]},"colorway":["#636efa","#EF553B","#00cc96","#ab63fa","#FFA15A","#19d3f3","#FF6692","#B6E880","#FF97FF","#FECB52"],"font":{"color":"#2a3f5f"},"geo":{"bgcolor":"white","lakecolor":"white","landcolor":"#E5ECF6","showlakes":true,"showland":true,"subunitcolor":"white"},"hoverlabel":{"align":"left"},"hovermode":"closest","mapbox":{"style":"light"},"paper_bgcolor":"white","plot_bgcolor":"#E5ECF6","polar":{"angularaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"bgcolor":"#E5ECF6","radialaxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"scene":{"xaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"},"yaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"},"zaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"}},"shapedefaults":{"line":{"color":"#2a3f5f"}},"ternary":{"aaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"baxis":{"gridcolor":"white","linecolor":"white","ticks":""},"bgcolor":"#E5ECF6","caxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"title":{"x":0.05},"xaxis":{"automargin":true,"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","zerolinewidth":2},"yaxis":{"automargin":true,"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","zerolinewidth":2}}},"width":1000,"xaxis":{"tickfont":{"size":16},"title":{"font":{"size":18},"text":"Max CO₂ Uptake Rate [µmol/(m²s)]"}},"yaxis":{"range":[0,40],"tickfont":{"size":16},"title":{"font":{"size":18},"text":"Flux [µmol/(m²s)]"}}}} </script><img src="index.html.media/11" alt="" itemscope="" itemtype="http://schema.org/ImageObject"> </picture> </stencila-image-plotly> </figure> </stencila-code-chunk> <figcaption> <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="effect-of-co2-limitation-on-the-flux-through-the-different-decarboxylation-enzymes"> Effect of CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> limitation on the flux through the different decarboxylation enzymes.</h4> </figcaption> </figure> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="44" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>###################################################################################################################################### ###################################################################################################################################### ############## EXPERIMENT 10: Effect of Malate/Aspartate-Exchange Ratio on C4 Mode ############## ###################################################################################################################################### ###################################################################################################################################### print(f"Code Cell 46: Experiment 10 -- Effect of Malate/Aspartate-Exchange Ratio on C4 Mode") #Create copy of c4 model c4_model_exp10 = c4_model.copy() #Reaction variables B_Ex_Suc = c4_model_exp10.reactions.get_by_id("[B]_Ex_Suc") B_RBO = c4_model_exp10.reactions.get_by_id("[B]_RBO_h") M_RBO = c4_model_exp10.reactions.get_by_id("[M]_RBO_h") #Decarboxylation reactions ids and names of enzymes c4_mode_r_id_enzyme = {'[B]_MalDH2_m': 'NAD-ME', '[B]_PEPC1_c': 'PEP-CK', '[B]_MalDH4_h': 'NADP-ME'} #Max exchange flux ex_flux = 40 #Malate flux mal_flux = np.arange(0,45,5) #Initialise dataframes to hold results df_result_exp10 = pd.DataFrame(index=c4_model.reactions.list_attr('id'), columns=mal_flux, dtype='float64') #Test all mal/asp exchange values for mal_value in tqdm(df_result_exp10.columns): #Add Mal/Asp transport constraint set_fixed_flux('[MB]_Mal_c',mal_value, c4_model_exp10) set_fixed_flux('[MB]_Asp_c',ex_flux - mal_value, c4_model_exp10) #Optimize/Maximize sucrose output B_Ex_Suc.objective_coefficient = 1. B_RBO.objective_coefficient = -1. M_RBO.objective_coefficient = -1. result_exp10_fba = c4_model_exp10.optimize('maximize') #Optimize/Minimize total flux if result_exp10_fba.status == 'optimal': result_exp10_pfba = cobra.flux_analysis.parsimonious.pfba(c4_model_exp10) df_result_exp10[mal_value] = result_exp10_pfba.fluxes </code></pre> <figure slot="outputs"> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>Code Cell 46: Experiment 10 -- Effect of Malate/Aspartate-Exchange Ratio on C4 Mode </code></pre> <pre class="language-text" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code> 0%| | 0/9 [00:00<?, ?it/s]</code></pre> </figure> </stencila-code-chunk> <figure itemscope="" itemtype="http://schema.stenci.la/Figure" id="fig8s4" title="Figure 8—figure supplement 4"><label data-itemprop="label">Figure 8—figure supplement 4</label> <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk" data-execution_count="45" data-programminglanguage="python"> <pre class="language-python" itemscope="" itemtype="http://schema.stenci.la/CodeBlock" slot="text"><code>################################################################################## ############## Figure 8—figure supplement 4 ############## ################################################################################## #{ # "caption": "### Effect of malate:aspartate transport ratio on the flux through the different decarboxylation enzymes.", # "id": "fig8s4", # "label": "Figure 8—figure supplement 4", # "trusted": true #} #Create Figure fig_exp10 = go.Figure() #Add Trace for each decarboxylation enzyme for i, r_id in enumerate(c4_mode_r_id_enzyme.keys()): #Create bar plot trace trace = go.Bar( y = df_result_exp10.loc[r_id], x = df_result_exp10.columns, name = c4_mode_r_id_enzyme[r_id] ) #Add trace to figure fig_exp10.add_trace(trace) #Update xaxes fig_exp10.update_xaxes( tickvals = df_result_exp10.columns, ticktext = [f'{mal_value} : {ex_flux - mal_value}' for mal_value in df_result_exp10.columns], title = dict( text = 'Mal : Asp Exchange', font = dict(size=18) ), tickfont = dict(size=16) ) #Update yaxes fig_exp10.update_yaxes( range = [0, 40], title = dict( text = 'Flux [µmol/(m\u00B2s)]', font = dict(size=18) ), tickfont = dict(size=16) ) #Update layout fig_exp10.update_layout( barmode='stack', width= 1000, height=500, legend=dict( font=dict(size=18), ) ) #Show figure fig_exp10.show()</code></pre> <figure slot="outputs"> <stencila-image-plotly> <picture> <script type="application/vnd.plotly.v1+json"> {"config":{"plotlyServerURL":"https://plot.ly"},"data":[{"name":"NAD-ME","type":"bar","x":[0,5,10,15,20,25,30,35,40],"y":[0.3222150541384147,0.32221505413840423,0.3222150541382019,0.32221505413840756,0.32221505413843743,0.3222150541384076,0.3222150541383681,0.039161655269898975,0.28804073020721815]},{"name":"PEP-CK","type":"bar","x":[0,5,10,15,20,25,30,35,40],"y":[39.138667550084676,34.39214622068937,29.39214622067046,24.39214622068955,19.392146220692524,14.392146220689847,9.25929835256164,4.460882604222239,0]},{"name":"NADP-ME","type":"bar","x":[0,5,10,15,20,25,30,35,40],"y":[0,4.746521329395081,9.746521329402078,14.746521329395057,19.746521329393936,24.74652132939491,29.879369197520674,34.96083834473009,39.17702648510854]}],"layout":{"barmode":"stack","height":500,"legend":{"font":{"size":18}},"template":{"data":{"bar":[{"error_x":{"color":"#2a3f5f"},"error_y":{"color":"#2a3f5f"},"marker":{"line":{"color":"#E5ECF6","width":0.5}},"type":"bar"}],"barpolar":[{"marker":{"line":{"color":"#E5ECF6","width":0.5}},"type":"barpolar"}],"carpet":[{"aaxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"baxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"type":"carpet"}],"choropleth":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"choropleth"}],"contour":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"contour"}],"contourcarpet":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"contourcarpet"}],"heatmap":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"heatmap"}],"heatmapgl":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"heatmapgl"}],"histogram":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"histogram"}],"histogram2d":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"histogram2d"}],"histogram2dcontour":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"histogram2dcontour"}],"mesh3d":[{"colorbar":{"outlinewidth":0,"ticks":""},"type":"mesh3d"}],"parcoords":[{"line":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"parcoords"}],"pie":[{"automargin":true,"type":"pie"}],"scatter":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatter"}],"scatter3d":[{"line":{"colorbar":{"outlinewidth":0,"ticks":""}},"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatter3d"}],"scattercarpet":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattercarpet"}],"scattergeo":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattergeo"}],"scattergl":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattergl"}],"scattermapbox":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scattermapbox"}],"scatterpolar":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterpolar"}],"scatterpolargl":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterpolargl"}],"scatterternary":[{"marker":{"colorbar":{"outlinewidth":0,"ticks":""}},"type":"scatterternary"}],"surface":[{"colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"type":"surface"}],"table":[{"cells":{"fill":{"color":"#EBF0F8"},"line":{"color":"white"}},"header":{"fill":{"color":"#C8D4E3"},"line":{"color":"white"}},"type":"table"}]},"layout":{"annotationdefaults":{"arrowcolor":"#2a3f5f","arrowhead":0,"arrowwidth":1},"autotypenumbers":"strict","coloraxis":{"colorbar":{"outlinewidth":0,"ticks":""}},"colorscale":{"diverging":[[0,"#8e0152"],[0.1,"#c51b7d"],[0.2,"#de77ae"],[0.3,"#f1b6da"],[0.4,"#fde0ef"],[0.5,"#f7f7f7"],[0.6,"#e6f5d0"],[0.7,"#b8e186"],[0.8,"#7fbc41"],[0.9,"#4d9221"],[1,"#276419"]],"sequential":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]],"sequentialminus":[[0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1,"#f0f921"]]},"colorway":["#636efa","#EF553B","#00cc96","#ab63fa","#FFA15A","#19d3f3","#FF6692","#B6E880","#FF97FF","#FECB52"],"font":{"color":"#2a3f5f"},"geo":{"bgcolor":"white","lakecolor":"white","landcolor":"#E5ECF6","showlakes":true,"showland":true,"subunitcolor":"white"},"hoverlabel":{"align":"left"},"hovermode":"closest","mapbox":{"style":"light"},"paper_bgcolor":"white","plot_bgcolor":"#E5ECF6","polar":{"angularaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"bgcolor":"#E5ECF6","radialaxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"scene":{"xaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"},"yaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"},"zaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","gridwidth":2,"linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white"}},"shapedefaults":{"line":{"color":"#2a3f5f"}},"ternary":{"aaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"baxis":{"gridcolor":"white","linecolor":"white","ticks":""},"bgcolor":"#E5ECF6","caxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"title":{"x":0.05},"xaxis":{"automargin":true,"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","zerolinewidth":2},"yaxis":{"automargin":true,"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","zerolinewidth":2}}},"width":1000,"xaxis":{"tickfont":{"size":16},"ticktext":["0 : 40","5 : 35","10 : 30","15 : 25","20 : 20","25 : 15","30 : 10","35 : 5","40 : 0"],"tickvals":[0,5,10,15,20,25,30,35,40],"title":{"font":{"size":18},"text":"Mal : Asp Exchange"}},"yaxis":{"range":[0,40],"tickfont":{"size":16},"title":{"font":{"size":18},"text":"Flux [µmol/(m²s)]"}}}} </script><img src="index.html.media/12" alt="" itemscope="" itemtype="http://schema.org/ImageObject"> </picture> </stencila-image-plotly> </figure> </stencila-code-chunk> <figcaption> <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="effect-of-malateaspartate-transport-ratio-on-the-flux-through-the-different-decarboxylation-enzymes"> Effect of malate:aspartate transport ratio on the flux through the different decarboxylation enzymes.</h4> </figcaption> </figure> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">Finally, we assumed that intercellular transport capacity for charged metabolites might be different between species. Assuming a fixed transport ratio between aspartate and malate (<a href="#fig8s4" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 8—figure supplement 4</a>) introduces a shift in the C4 state. Higher proportions of malate exchange foster the use of NADP-ME (<a href="#fig8s4" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 8—figure supplement 4</a>). In contrast, higher portions of aspartate exchange foster the use of PEP-CK (<a href="#fig8s4" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 8—figure supplement 4</a>).</p> <h2 itemscope="" itemtype="http://schema.stenci.la/Heading" id="discussion">Discussion</h2> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">Evolutionary CBM can suggest the molecular outcomes of past evolutionary events if models are parametrised with objective functions representing possible selective pressures. In the case of C4 photosynthesis, more than sixty independent evolutionary origins represent metabolic types characterised by their decarboxylation enzyme. The selective pressure which drives evolution towards one or the other flux are unknown and were tested using CBM.</p> <h3 itemscope="" itemtype="http://schema.stenci.la/Heading" id="one-cell-model-reflects-c3-plant-physiology"><em itemscope="" itemtype="http://schema.stenci.la/Emphasis">One-cell</em> model reflects C3 plant physiology</h3> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">To analyse evolution towards C4 photosynthesis based on C3 metabolism, a CBM of C3 metabolism is required (<a href="#fig1" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 1</a>). Design, simulation, validation cycles used current knowledge about plant biochemistry <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib32"><span>32</span><span>Heldt</span><span>2015</span></a></cite> to identify possible errors in the metabolic map required for modelling. Even after error correction (<a href="#table1" itemscope="" itemtype="http://schema.stenci.la/Link">Table 1</a>), a significant problem remained, namely excessive fluxes to balance protons in all compartments. This observation leads to the realisation that the biochemical knowledge about transport reactions does not extend to the protonation state of the substrates, which affects all eukaryotic CBM efforts. In plants, predominantly export and vacuolar transport reactions are directly or indirectly coupled with proton gradients to energise transport <span itemscope="" itemtype="http://schema.stenci.la/CiteGroup"><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib16"><span>16</span><span>Bush</span><span>1993</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib50"><span>50</span><span>Neuhaus</span><span>2007</span></a></cite></span>. For chloroplasts and mitochondria, proton-coupled transport reactions have been described but may couple different metabolite transporters together rather than energising them <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib26"><span>26</span><span>Furumoto et al.</span><span>2011</span></a></cite>. Introducing proton sinks in all compartments solves the immediate modelling problem. However, intracellular transport reactions and their energetic costs are no longer correctly assessed by the model. Despite this band-aid fix which will be required for all eukaryotic constraint-based models which include proton-coupled transport reactions, the curated <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">one-cell</em> model correctly predicts energy usage and its distribution (<a href="#fig1s3" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 1—figure supplement 3</a>, <a href="#fig1s4" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 1—figure supplement 4</a> and <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib40"><span>40</span><span>Li et al.</span><span>2017</span></a></cite>). This indicates that in models which exclude vacuolar transport and energised export reactions, energy calculations remain likely within the correct order of magnitude. Overall, our <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">one-cell</em> model operates within parameters expected for a C3 plant: The predicted PPFD lies within the range of light intensities used for normal growth condition of <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Arabidopsis thaliana</em>, which varies between 100 μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s)–200 μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s), see <a href="#table2" itemscope="" itemtype="http://schema.stenci.la/Link">Table 2</a>. The gross rate of O<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> evolution for a PPFD of 200 μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s) is estimated to be 16.5 μmol/(m<sup itemscope="" itemtype="http://schema.stenci.la/Superscript"><span data-itemtype="http://schema.org/Number">2</span></sup>s) in the literature <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib75"><span>75</span><span>Sun et al.</span><span>1999</span></a></cite>, which is in close proximity to the predicted flux of the <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">one-cell</em> model, see <a href="#table2" itemscope="" itemtype="http://schema.stenci.la/Link">Table 2</a>. For the amount of respiratory ATP that is used for maintenance, <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib40"><span>40</span><span>Li et al.</span><span>2017</span></a></cite> predicted an even lower proportion of energy 16%, see <a href="#fig1s4" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 1—figure supplement 4(B)</a>. The model’s flux map is in accordance with known C3 plant physiology <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib32"><span>32</span><span>Heldt</span><span>2015</span></a></cite>, and its input and output parameters match expected values (<a href="#fig2" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 2(B)</a>). The current model excludes specialised metabolism since the output function focuses solely on substances exported through the phloem in a mature leaf. If the model were to be used to study biotic interactions in the future, the addition of specialised metabolism in the metabolic map and a new output function would be required.</p> <h3 itemscope="" itemtype="http://schema.stenci.la/Heading" id="the-two-cell-model-predicts-a-c4-cycle-if-photorespiration-is-present">The two-cell model predicts a C4 cycle if photorespiration is present</h3> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">Most evolutionary concepts about C4 photosynthesis assume that selective pressure drives pathway evolution due to photorespiration and carbon limitation <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib31"><span>31</span><span>Heckmann et al.</span><span>2013</span></a></cite>. Most extant C4 species occupy dry and arid niches <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib23"><span>23</span><span>Edwards et al.</span><span>2010</span></a></cite>, even more, the period of C4 plant evolution was accompanied with an increased oxygen concentration in the atmosphere <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib62"><span>62</span><span>Sage</span><span>2004</span></a></cite>. Therefore, it is frequently assumed that carbon limitation by excessive photorespiration drives the evolution of C4 photosynthesis. Yet, in most habitats plants are limited by nutrients other than carbon <span itemscope="" itemtype="http://schema.stenci.la/CiteGroup"><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib1"><span>1</span><span>Agren et al.</span><span>2012</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib36"><span>36</span><span>Körner</span><span>2015</span></a></cite></span>. Ecophysiological analyses also show that C4 can evolve in non-arid habitats <span itemscope="" itemtype="http://schema.stenci.la/CiteGroup"><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib43"><span>43</span><span>Liu and Osborne</span><span>2015</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib44"><span>44</span><span>Lundgren and Christin</span><span>2017</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib53"><span>53</span><span>Osborne and Freckleton</span><span>2009</span></a></cite></span>. To resolve this apparent contradiction, we tested whether resource limitation may also lead to the evolution of a C4 cycle. We optimised the model approximating resource limitation via an objective function for total minimal flux at different photorespiratory levels. Indeed, with increasing photorespiration, the optimisation for resource efficiency leads to the emergence of the C4 cycle as the optimal solution. Balancing the resource cost of photorespiration against the resource cost of the C4 cycle, the model predicts that N limitation may have facilitated C4 evolution given high levels of photorespiration. Other possible selective pressures such as biotic interactions can currently not be tested using the model since specialised metabolism is not included in the metabolic map or the output function. Extant C4 species have higher C : N ratios reflecting the N-savings the operational C4 cycle enables <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib61"><span>61</span><span>Sage et al.</span><span>1987</span></a></cite>. The photorespiratory pump using glycine decarboxylase based CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> enrichment also emerges from the model, showing that C2 photosynthesis is also predicted under simple resource limitation. Indeed N-savings have been reported from C2 plants compared with their C3 sister lineages <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib66"><span>66</span><span>Schlüter et al.</span><span>2016</span></a></cite>. Simply minimising photorespiration as the objective function also yields C4 photosynthesis as the optimal solution. Hence, two alternatively or parallelly acting selective pressures towards C4 photosynthesis, limitation in C and/or N, are identified by the model. In both cases, the model correctly predicts the C4 cycle of carboxylation and decarboxylation and the C2 photorespiratory pump as observed in extant plants. The evolution of C4 photosynthesis in response to multiple selective pressures underscores its adaptive value and potential for agriculture. Intermediacy also evolves indicating that it, too, is likely an added value trait which could be pursued by breeding and engineering efforts.</p> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">The optimal solutions for the metabolic flux patterns predict an intermediate stage in which CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> transport via photorespiratory intermediates glycolate and glycerate (<a href="#fig4" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 4</a>) and decarboxylation by glycine decarboxylase complex (<a href="#fig3" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 3(B)</a>) is essential. All of the models of C4 evolution <span itemscope="" itemtype="http://schema.stenci.la/CiteGroup"><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib48"><span>48</span><span>Monson</span><span>1999</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib6"><span>6</span><span>Bauwe</span><span>2010</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib63"><span>63</span><span>Sage et al.</span><span>2012</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib31"><span>31</span><span>Heckmann et al.</span><span>2013</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib86"><span>86</span><span>Williams et al.</span><span>2013</span></a></cite></span> predict that the establishment of a photorespiratory CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> pump is an essential intermediate step towards the C4 cycle. The photorespiratory CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> pump, also known as C2 photosynthesis, relocates the photorespiratory CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> release to the bundle sheath cells. Plants using the photorespiratory CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> pump are often termed C3-C4 intermediates owing to their physiological properties <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib63"><span>63</span><span>Sage et al.</span><span>2012</span></a></cite>. Displaying the flux solution in <a href="#fig3" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 3 (A) -(D)</a> and <a href="#fig4" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 4</a> on a metabolic map in <a href="#fig3s1" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 3—figure supplement 1</a> clearly illustrates that increasing photorespiratory flux through Rubisco drives the two-cell metabolic model from C3 to C4 metabolism by passing the C3-C4 intermediate state. On the C3-C4 trajectory, the activity of Rubisco is shifted from the mesophyll to the bundle sheath, as well as from the constrained to the CCM-dependent Rubisco population as a consequence of the increased costs of photorespiration under increased <span itemscope="" itemtype="http://schema.stenci.la/MathFragment"><span class="mjx-chtml"><span class="mjx-math" aria-label="{p}_{{O}_{2}}:{p}_{C{O}_{2}}"><span class="mjx-mrow" aria-hidden="true"><span class="mjx-msubsup"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.446em;">p</span></span></span></span></span><span class="mjx-sub" style="font-size: 70.7%; vertical-align: -0.36em; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-msubsup"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.519em; padding-bottom: 0.298em;">O</span></span></span></span></span><span class="mjx-sub" style="font-size: 83.3%; vertical-align: -0.267em; padding-right: 0.06em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mn"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.372em; padding-bottom: 0.372em;">2</span></span></span></span></span></span></span></span></span></span><span class="mjx-mo MJXc-space3"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.151em; padding-bottom: 0.372em;">:</span></span><span class="mjx-msubsup MJXc-space3"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.225em; padding-bottom: 0.446em;">p</span></span></span></span></span><span class="mjx-sub" style="font-size: 70.7%; vertical-align: -0.36em; padding-right: 0.071em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.519em; padding-bottom: 0.298em; padding-right: 0.045em;">C</span></span><span class="mjx-msubsup"><span class="mjx-base"><span class="mjx-texatom"><span class="mjx-mrow"><span class="mjx-mi"><span class="mjx-char MJXc-TeX-math-I" style="padding-top: 0.519em; padding-bottom: 0.298em;">O</span></span></span></span></span><span class="mjx-sub" style="font-size: 83.3%; vertical-align: -0.267em; padding-right: 0.06em;"><span class="mjx-texatom" style=""><span class="mjx-mrow"><span class="mjx-mn"><span class="mjx-char MJXc-TeX-main-R" style="padding-top: 0.372em; padding-bottom: 0.372em;">2</span></span></span></span></span></span></span></span></span></span></span></span></span></span> ratio, see <a href="#equ5" itemscope="" itemtype="http://schema.stenci.la/Link">Equation 5</a>. The increase of the oxygenation rate in the photorespiration constraint drives the reprogramming of the metabolism to avoid oxygenation by establishing the C4 cycle. Therefore, our analysis recovers the evolutionary C3-C4 trajectory and confirms the emergence of a photorespiratory CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> pump as an essential step during the C4 evolution also under optimisation for resources <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib31"><span>31</span><span>Heckmann et al.</span><span>2013</span></a></cite>. The model may also provide a reason for why some plant species have halted their evolution in this intermediary phase <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib65"><span>65</span><span>Scheben et al.</span><span>2017</span></a></cite>. Under the conditions of resource limitations and intermediate photorespiration, the model predicts intermediacy as the optimal solution. In a very narrow corridor of conditions, no further changes are required to reach optimality and the model thus predicts that a small number of species may remain intermediate.</p> <h3 itemscope="" itemtype="http://schema.stenci.la/Heading" id="two-cell-model-realises-different-c4-states"><em itemscope="" itemtype="http://schema.stenci.la/Emphasis">Two-cell</em> model realises different C4 states</h3> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">Since the model predicts C4 metabolism without specific constraints, different input and reaction constraints can be tested for their influence on the molecular nature of the C4 cycle. This approach may identify the selective pressure and boundaries limiting evolution. Initial optimisation without additional constraints or input limitations predict a C4 cycle based on decarboxylation by NADP-ME (<a href="#fig3" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 3</a> and <a href="#fig3s1" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 3—figure supplement 1(A)</a>). This prediction recapitulates intuition; the NADP-ME based C4 cycle is considered the 'most straight forward' incarnation of C4 photosynthesis, it is always explained first in textbooks and is a major focus of research. The NADP-ME based cycle thus represents the stoichiometrically optimal solution when resource limitation or photorespiration are considered. Once NADP-ME is no longer available via constraint, PEP-CK and NAD-ME become optimal solutions albeit with a prediction of malate and pyruvate as the transfer acids (<a href="#fig8" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 8</a>). The FVA identified aspartate and alanine as slightly less optimal solutions (<a href="#fig6" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 6</a>). Since <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">in vivo</em> this slightly less optimal solution has evolved in all NAD-ME origins tested to date, kinetic rather than stoichiometric reasons suggest themselves for the use of aspartate and alanine <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib13"><span>13</span><span>Bräutigam et al.</span><span>2018</span></a></cite>.</p> <h3 itemscope="" itemtype="http://schema.stenci.la/Heading" id="light-is-a-potential-evolutionary-driver-for-the-different-c4-states">Light is a potential evolutionary driver for the different C4 states</h3> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">Since all extant C3 species and therefore also the ancestors of all C4 species contain all decarboxylation enzymes <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib4"><span>4</span><span>Aubry et al.</span><span>2011</span></a></cite>, it is unlikely that unavailability of an enzyme is the reason for the evolution of different decarboxylation enzymes in different origins <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib62"><span>62</span><span>Sage</span><span>2004</span></a></cite>. Stochastic processes during evolution, that is up-regulation of particular enzyme concentrations via changes in expression and therefore elements <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">cis</em> to the gene <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib14"><span>14</span><span>Bräutigam and Gowik</span><span>2016</span></a></cite>, may have played a role in determining which C4 cycle evolved. Alternatively, environmental determinants may have contributed to the evolution of different C4 cycles. Physiological experiments have pointed to a connection between nitrogen use efficiency and type of decarboxylation enzyme <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib58"><span>58</span><span>Pinto et al.</span><span>2016</span></a></cite>. Hence the variation in nitrogen input to the model was tested for their influence on optimal solutions with regard to decarboxylation enzymes. Input limitation of nitrogen, water as a metabolite, and CO<sub itemscope="" itemtype="http://schema.stenci.la/Subscript"><span data-itemtype="http://schema.org/Number">2</span></sub> limited the output of the system but did not change the optimal solution concerning decarboxylation, see <a href="#fig8s1" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 8—figure supplement 1</a>, <a href="#fig8s2" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 8—figure supplement 2</a>, and <a href="#fig8s3" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 8—figure supplement 3</a>, making it an unlikely candidate as the cause. Differences in nitrogen use is possibly a consequence of decarboxylation type.</p> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">In some grasses, light penetrable cells overlay the vascular bundle leading to different light availability (summarised in <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib8"><span>8</span><span>Bellasio and Lundgren</span><span>2016</span></a></cite> and <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib34"><span>34</span><span>Karabourniotis et al.</span><span>2000</span></a></cite>) and hence light availability and distribution were tested (<a href="#fig8" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 8</a>). Changes in light input and distribution of light input between mesophyll and bundle sheath indeed altered the optimal solutions (<a href="#fig8" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 8</a>). The changes in the solution can be traced to the energy status of the plant cells. For very high light intensities, the alternative oxidases in the mitochondria are used to dissipate the energy and hence a path towards NAD-ME is paved. Under light limitation, the C4 cycle requires high efficiency and hence PEP-CK which, at least in part allows energy conservation by using PEP rather than pyruvate as the returning C4 acid, is favoured. Interestingly, the sensitivity of different species towards environmental changes in light is influenced by the decarboxylation enzyme present <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib72"><span>72</span><span>Sonawane et al.</span><span>2018</span></a></cite>. NADP-ME species are less compromised compared to NAD-ME species by shade possibly reflecting an evolutionary remnant as NAD-ME is predicted to emerge only in high light conditions. PEP-CK is more energy efficient compared to malic enzyme based decarboxylation which requires PEP recycling by PPDK at the cost of two molecules of ATP (<a href="#fig3" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 3(D)</a>). Notably, two C4 plants known to rely on PEP-CK <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">P. maximum</em> and <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">A. semialata</em> (African accessions) are shade plants which grow in the understory <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib44"><span>44</span><span>Lundgren and Christin</span><span>2017</span></a></cite>. PEP-CK can be co-active with NADP-ME and NAD-ME (<a href="#fig8" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 8</a>). This co-use of PEP-CK with a malic enzyme has been shown in C4 plants <span itemscope="" itemtype="http://schema.stenci.la/CiteGroup"><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib57"><span>57</span><span>Pick et al.</span><span>2011</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib87"><span>87</span><span>Wingler et al.</span><span>1999</span></a></cite></span> and explained as an adaptation to different energy availability and changes in light conditions <span itemscope="" itemtype="http://schema.stenci.la/CiteGroup"><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib57"><span>57</span><span>Pick et al.</span><span>2011</span></a></cite><cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib7"><span>7</span><span>Bellasio and Griffiths</span><span>2014</span></a></cite></span>. Dominant use of PEP-CK in the absence of malic enzyme activity as suggested (<a href="#fig3" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 3(B)</a>, <a href="#fig3s1" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 3—figure supplement 1</a> and <a href="#fig5" itemscope="" itemtype="http://schema.stenci.la/Link">Figure 5</a>) is rare <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">in vivo</em><span data-itemtype="http://schema.org/Number">0</span><cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib80"><span>80</span><span>Ueno and Sentoku</span><span>2006</span></a></cite> but observed in <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">P. maximum</em> and in <em itemscope="" itemtype="http://schema.stenci.la/Emphasis">A. semialata</em>. While the model predictions are in line with ecological observations, we cannot exclude that kinetic constraints (i.e. <cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a href="#bib13"><span>13</span><span>Bräutigam et al.</span><span>2018</span></a></cite>) may also explain why a stoichiometrically optimal solution such as the NADP-ME cycle is not favoured in nature where NADP-ME and NAD-ME species evolve in nearly equal proportions <cite itemscope="" itemtype="http://schema.stenci.la/Cite" data-citationmode="Narrative"><a href="#bib62"><span>62</span><span>Sage</span><span>2004</span></a></cite>.</p> <h3 itemscope="" itemtype="http://schema.stenci.la/Heading" id="conclusion">Conclusion</h3> <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">CBM of photosynthetically active plant cells revealed a major knowledge gap impeding CBM, namely the unknown protonation state of most transport substrates during intracellular transport processes. When photoautotrophic metabolism was optimised in a single cell for minimal metabolic flux and therefore, optimal resource use, C3 photosynthetic metabolism was predicted as the optimal solution. Under low photorespiratory conditions, a two-celled model which contains a CCM-dependent Rubisco optimised for resource use, still predicts C3 photosynthesis. However, under medium to high photorespiratory conditions, a molecularly correct C4 cycle emerged as the optimal solution under resource limitation and photorespiration reduction as objective functions which points to resource limitation as an additional driver of C4 evolution. Light and light distribution was the environmental variable governing the choice of decarboxylation enzymes. Modelling compartmented eukaryotic cells correctly predicts the evolutionary trajectories leading to extant C4 photosynthetic plant species. </p> <section data-itemprop="references"> <h2 data-itemtype="http://schema.stenci.la/Heading">References</h2> <ol> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib1"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="GI Agren"><span data-itemprop="givenNames"><span itemprop="givenName">GI</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Agren</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="JÅ Wetterstedt"><span data-itemprop="givenNames"><span itemprop="givenName">JÅ</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Wetterstedt</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="MF Billberger"><span data-itemprop="givenNames"><span itemprop="givenName">MF</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Billberger</span></span> </li> </ol><time itemprop="datePublished" datetime="2012">2012</time><span itemprop="headline">Nutrient limitation on terrestrial plant growth--modeling the interaction between nitrogen and phosphorus</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">194</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">New Phytologist</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">953</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">960</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Nutrient%20limitation%20on%20terrestrial%20plant%20growth--modeling%20the%20interaction%20between%20nitrogen%20and%20phosphorus"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1111/j.1469-8137.2012.04116.x</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">22458659</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib2"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="A Arnold"><span data-itemprop="givenNames"><span itemprop="givenName">A</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Arnold</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="Z Nikoloski"><span data-itemprop="givenNames"><span itemprop="givenName">Z</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Nikoloski</span></span> </li> </ol><time itemprop="datePublished" datetime="2014">2014</time><span itemprop="headline" content="Bottom-up metabolic reconstruction of Arabidopsis and its application to determining the metabolic costs of e…">Bottom-up metabolic reconstruction of Arabidopsis and its application to determining the metabolic costs of enzyme production</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">165</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Plant Physiology</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">1380</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">1391</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Bottom-up%20metabolic%20reconstruction%20of%20Arabidopsis%20and%20its%20application%20to%20determining%20the%20metabolic%20costs%20of%20e%E2%80%A6"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1104/pp.114.235358</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">24808102</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib3"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="M Ashburner"><span data-itemprop="givenNames"><span itemprop="givenName">M</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Ashburner</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="CA Ball"><span data-itemprop="givenNames"><span itemprop="givenName">CA</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Ball</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="JA Blake"><span data-itemprop="givenNames"><span itemprop="givenName">JA</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Blake</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="D Botstein"><span data-itemprop="givenNames"><span itemprop="givenName">D</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Botstein</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="H Butler"><span data-itemprop="givenNames"><span itemprop="givenName">H</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Butler</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="JM Cherry"><span data-itemprop="givenNames"><span itemprop="givenName">JM</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Cherry</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="AP Davis"><span data-itemprop="givenNames"><span itemprop="givenName">AP</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Davis</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="K Dolinski"><span data-itemprop="givenNames"><span itemprop="givenName">K</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Dolinski</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="SS Dwight"><span data-itemprop="givenNames"><span itemprop="givenName">SS</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Dwight</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="JT Eppig"><span data-itemprop="givenNames"><span itemprop="givenName">JT</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Eppig</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="MA Harris"><span data-itemprop="givenNames"><span itemprop="givenName">MA</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Harris</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="DP Hill"><span data-itemprop="givenNames"><span itemprop="givenName">DP</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Hill</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="L Issel-Tarver"><span data-itemprop="givenNames"><span itemprop="givenName">L</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Issel-Tarver</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="A Kasarskis"><span data-itemprop="givenNames"><span itemprop="givenName">A</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Kasarskis</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="S Lewis"><span data-itemprop="givenNames"><span itemprop="givenName">S</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Lewis</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="JC Matese"><span data-itemprop="givenNames"><span itemprop="givenName">JC</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Matese</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="JE Richardson"><span data-itemprop="givenNames"><span itemprop="givenName">JE</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Richardson</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="M Ringwald"><span data-itemprop="givenNames"><span itemprop="givenName">M</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Ringwald</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="GM Rubin"><span data-itemprop="givenNames"><span itemprop="givenName">GM</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Rubin</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="G Sherlock"><span data-itemprop="givenNames"><span itemprop="givenName">G</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Sherlock</span></span> </li> </ol><time itemprop="datePublished" datetime="2000">2000</time><span itemprop="headline">Gene ontology: tool for the unification of biology</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">25</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Nature Genetics</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">25</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">29</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Gene%20ontology:%20tool%20for%20the%20unification%20of%20biology"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1038/75556</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib4"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="S Aubry"><span data-itemprop="givenNames"><span itemprop="givenName">S</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Aubry</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="NJ Brown"><span data-itemprop="givenNames"><span itemprop="givenName">NJ</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Brown</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="JM Hibberd"><span data-itemprop="givenNames"><span itemprop="givenName">JM</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Hibberd</span></span> </li> </ol><time itemprop="datePublished" datetime="2011">2011</time><span itemprop="headline">The role of proteins in C(3) plants prior to their recruitment into the C(4) pathway</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">62</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Journal of Experimental Botany</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">3049</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">3059</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=The%20role%20of%20proteins%20in%20C(3)%20plants%20prior%20to%20their%20recruitment%20into%20the%20C(4)%20pathway"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1093/jxb/err012</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">21321052</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib5"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="S Bailey"><span data-itemprop="givenNames"><span itemprop="givenName">S</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Bailey</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="RG Walters"><span data-itemprop="givenNames"><span itemprop="givenName">RG</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Walters</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="S Jansson"><span data-itemprop="givenNames"><span itemprop="givenName">S</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Jansson</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="P Horton"><span data-itemprop="givenNames"><span itemprop="givenName">P</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Horton</span></span> </li> </ol><time itemprop="datePublished" datetime="2001">2001</time><span itemprop="headline" content="Acclimation of Arabidopsis thaliana to the light environment: the existence of separate low light and high li…">Acclimation of Arabidopsis thaliana to the light environment: the existence of separate low light and high light responses</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">213</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Planta</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">794</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">801</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Acclimation%20of%20Arabidopsis%20thaliana%20to%20the%20light%20environment:%20the%20existence%20of%20separate%20low%20light%20and%20high%20li%E2%80%A6"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1007/s004250100556</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">11678285</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib6"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="H Bauwe"><span data-itemprop="givenNames"><span itemprop="givenName">H</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Bauwe</span></span> </li> </ol><time itemprop="datePublished" datetime="2010">2010</time><span itemprop="headline">Photorespiration: The bridge to C4 photosynthesis</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"><span itemprop="name">Springer</span><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Springer"> </span></span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Photorespiration:%20The%20bridge%20to%20C4%20photosynthesis"> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib7"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="C Bellasio"><span data-itemprop="givenNames"><span itemprop="givenName">C</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Bellasio</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="H Griffiths"><span data-itemprop="givenNames"><span itemprop="givenName">H</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Griffiths</span></span> </li> </ol><time itemprop="datePublished" datetime="2014">2014</time><span itemprop="headline" content="The operation of two decarboxylases, Transamination, and partitioning of C4 metabolic processes between mesop…">The operation of two decarboxylases, Transamination, and partitioning of C4 metabolic processes between mesophyll and bundle sheath cells allows light capture to be balanced for the maize C4 pathway</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">164</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Plant Physiology</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">466</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">480</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=The%20operation%20of%20two%20decarboxylases,%20Transamination,%20and%20partitioning%20of%20C4%20metabolic%20processes%20between%20mesop%E2%80%A6"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1104/pp.113.228221</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">24254314</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib8"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="C Bellasio"><span data-itemprop="givenNames"><span itemprop="givenName">C</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Bellasio</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="MR Lundgren"><span data-itemprop="givenNames"><span itemprop="givenName">MR</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Lundgren</span></span> </li> </ol><time itemprop="datePublished" datetime="2016">2016</time><span itemprop="headline">Anatomical constraints to C4 evolution: light harvesting capacity in the bundle sheath</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">212</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">The New Phytologist</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">485</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">496</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Anatomical%20constraints%20to%20C4%20evolution:%20light%20harvesting%20capacity%20in%20the%20bundle%20sheath"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1111/nph.14063</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">27375085</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib9"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="M Berkemeyer"><span data-itemprop="givenNames"><span itemprop="givenName">M</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Berkemeyer</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="R Scheibe"><span data-itemprop="givenNames"><span itemprop="givenName">R</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Scheibe</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="O Ocheretina"><span data-itemprop="givenNames"><span itemprop="givenName">O</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Ocheretina</span></span> </li> </ol><time itemprop="datePublished" datetime="1998">1998</time><span itemprop="headline">A novel, non-redox-regulated NAD-dependent malate dehydrogenase from chloroplasts of Arabidopsis thaliana L</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">273</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Journal of Biological Chemistry</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">27927</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">27933</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=A%20novel,%20non-redox-regulated%20NAD-dependent%20malate%20dehydrogenase%20from%20chloroplasts%20of%20Arabidopsis%20thaliana%20L"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1074/jbc.273.43.27927</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">9774405</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib10"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="MA Blätke"><span data-itemprop="givenNames"><span itemprop="givenName">MA</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Blätke</span></span> </li> </ol><time itemprop="datePublished" datetime="2019">2019</time><a itemprop="url" href="https://github.com/ma-blaetke/CBM_C3_C4_Metabolism"><span itemprop="headline">Evolution of C4 photosynthesis predicted by constraint-based modelling</span></a><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Evolution%20of%20C4%20photosynthesis%20predicted%20by%20constraint-based%20modelling"> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib11"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="NR Boyle"><span data-itemprop="givenNames"><span itemprop="givenName">NR</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Boyle</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="JA Morgan"><span data-itemprop="givenNames"><span itemprop="givenName">JA</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Morgan</span></span> </li> </ol><time itemprop="datePublished" datetime="2009">2009</time><span itemprop="headline">Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">3</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">BMC Systems Biology</span></span></span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Flux%20balance%20analysis%20of%20primary%20metabolism%20in%20Chlamydomonas%20reinhardtii"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1186/1752-0509-3-4</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">19128495</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib12"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="A Bräutigam"><span data-itemprop="givenNames"><span itemprop="givenName">A</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Bräutigam</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="S Schliesky"><span data-itemprop="givenNames"><span itemprop="givenName">S</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Schliesky</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="C Külahoglu"><span data-itemprop="givenNames"><span itemprop="givenName">C</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Külahoglu</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="CP Osborne"><span data-itemprop="givenNames"><span itemprop="givenName">CP</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Osborne</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="AP Weber"><span data-itemprop="givenNames"><span itemprop="givenName">AP</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Weber</span></span> </li> </ol><time itemprop="datePublished" datetime="2014">2014</time><span itemprop="headline" content="Towards an integrative model of C4 photosynthetic subtypes: insights from comparative transcriptome analysis …">Towards an integrative model of C4 photosynthetic subtypes: insights from comparative transcriptome analysis of NAD-ME, NADP-ME, and PEP-CK C4 species</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">65</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Journal of Experimental Botany</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">3579</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">3593</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Towards%20an%20integrative%20model%20of%20C4%20photosynthetic%20subtypes:%20insights%20from%20comparative%20transcriptome%20analysis%20%E2%80%A6"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1093/jxb/eru100</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">24642845</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib13"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="A Bräutigam"><span data-itemprop="givenNames"><span itemprop="givenName">A</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Bräutigam</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="U Schlüter"><span data-itemprop="givenNames"><span itemprop="givenName">U</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Schlüter</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="MR Lundgren"><span data-itemprop="givenNames"><span itemprop="givenName">MR</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Lundgren</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="S Flachbart"><span data-itemprop="givenNames"><span itemprop="givenName">S</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Flachbart</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="O Ebenhöh"><span data-itemprop="givenNames"><span itemprop="givenName">O</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Ebenhöh</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="G Schönknecht"><span data-itemprop="givenNames"><span itemprop="givenName">G</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Schönknecht</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="P-A Christin"><span data-itemprop="givenNames"><span itemprop="givenName">P-A</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Christin</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="S Bleuler"><span data-itemprop="givenNames"><span itemprop="givenName">S</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Bleuler</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="J-M Droz"><span data-itemprop="givenNames"><span itemprop="givenName">J-M</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Droz</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="C Osborne"><span data-itemprop="givenNames"><span itemprop="givenName">C</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Osborne</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="A Weber"><span data-itemprop="givenNames"><span itemprop="givenName">A</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Weber</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="U Gowik"><span data-itemprop="givenNames"><span itemprop="givenName">U</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Gowik</span></span> </li> </ol><time itemprop="datePublished" datetime="2018">2018</time><span itemprop="headline">Biochemical mechanisms driving rapid fluxes in C4 photosynthesis</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">bioRxiv</span></span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Biochemical%20mechanisms%20driving%20rapid%20fluxes%20in%20C4%20photosynthesis"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1101/387431</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib14"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="A Bräutigam"><span data-itemprop="givenNames"><span itemprop="givenName">A</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Bräutigam</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="U Gowik"><span data-itemprop="givenNames"><span itemprop="givenName">U</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Gowik</span></span> </li> </ol><time itemprop="datePublished" datetime="2016">2016</time><span itemprop="headline">Photorespiration connects C3 and C4 photosynthesis</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">67</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Journal of Experimental Botany</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">2953</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">2962</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Photorespiration%20connects%20C3%20and%20C4%20photosynthesis"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1093/jxb/erw056</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">26912798</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib15"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="A Bräutigam"><span data-itemprop="givenNames"><span itemprop="givenName">A</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Bräutigam</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="APM Weber"><span data-itemprop="givenNames"><span itemprop="givenName">APM</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Weber</span></span> </li> </ol><time itemprop="datePublished" datetime="2010">2010</time><span itemprop="headline">Transport processes: Connecting the reactions of C4 photosynthesis</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"><span itemprop="name">Springer</span><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Springer"> </span></span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Transport%20processes:%20Connecting%20the%20reactions%20of%20C4%20photosynthesis"> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib16"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="DR Bush"><span data-itemprop="givenNames"><span itemprop="givenName">DR</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Bush</span></span> </li> </ol><time itemprop="datePublished" datetime="1993">1993</time><span itemprop="headline">Proton-Coupled sugar and amino acid transporters in plants</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">44</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Annual Review of Plant Physiology and Plant Molecular Biology</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">513</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">542</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Proton-Coupled%20sugar%20and%20amino%20acid%20transporters%20in%20plants"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1146/annurev.pp.44.060193.002501</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib17"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="CY Cheung"><span data-itemprop="givenNames"><span itemprop="givenName">CY</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Cheung</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="MG Poolman"><span data-itemprop="givenNames"><span itemprop="givenName">MG</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Poolman</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="DA Fell"><span data-itemprop="givenNames"><span itemprop="givenName">DA</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Fell</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="RG Ratcliffe"><span data-itemprop="givenNames"><span itemprop="givenName">RG</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Ratcliffe</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="LJ Sweetlove"><span data-itemprop="givenNames"><span itemprop="givenName">LJ</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Sweetlove</span></span> </li> </ol><time itemprop="datePublished" datetime="2014">2014</time><span itemprop="headline" content="A diel flux balance model captures interactions between light and dark metabolism during Day-Night cycles in …">A diel flux balance model captures interactions between light and dark metabolism during Day-Night cycles in C3 and crassulacean acid metabolism leaves</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">165</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Plant Physiology</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">917</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">929</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=A%20diel%20flux%20balance%20model%20captures%20interactions%20between%20light%20and%20dark%20metabolism%20during%20Day-Night%20cycles%20in%20%E2%80%A6"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1104/pp.113.234468</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">24596328</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib18"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="PA Christin"><span data-itemprop="givenNames"><span itemprop="givenName">PA</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Christin</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="EJ Edwards"><span data-itemprop="givenNames"><span itemprop="givenName">EJ</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Edwards</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="G Besnard"><span data-itemprop="givenNames"><span itemprop="givenName">G</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Besnard</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="SF Boxall"><span data-itemprop="givenNames"><span itemprop="givenName">SF</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Boxall</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="R Gregory"><span data-itemprop="givenNames"><span itemprop="givenName">R</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Gregory</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="EA Kellogg"><span data-itemprop="givenNames"><span itemprop="givenName">EA</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Kellogg</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="J Hartwell"><span data-itemprop="givenNames"><span itemprop="givenName">J</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Hartwell</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="CP Osborne"><span data-itemprop="givenNames"><span itemprop="givenName">CP</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Osborne</span></span> </li> </ol><time itemprop="datePublished" datetime="2012">2012</time><span itemprop="headline">Adaptive evolution of C(4) photosynthesis through recurrent lateral gene transfer</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">22</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Current Biology</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">445</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">449</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Adaptive%20evolution%20of%20C(4)%20photosynthesis%20through%20recurrent%20lateral%20gene%20transfer"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1016/j.cub.2012.01.054</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">22342748</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib19"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="CG de Oliveira Dal'Molin"><span data-itemprop="givenNames"><span itemprop="givenName">CG</span></span><span data-itemprop="familyNames"><span itemprop="familyName">de</span><span itemprop="familyName">Oliveira</span><span itemprop="familyName">Dal'Molin</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="LE Quek"><span data-itemprop="givenNames"><span itemprop="givenName">LE</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Quek</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="RW Palfreyman"><span data-itemprop="givenNames"><span itemprop="givenName">RW</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Palfreyman</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="SM Brumbley"><span data-itemprop="givenNames"><span itemprop="givenName">SM</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Brumbley</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="LK Nielsen"><span data-itemprop="givenNames"><span itemprop="givenName">LK</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Nielsen</span></span> </li> </ol><time itemprop="datePublished" datetime="2010">2010</time><span itemprop="headline">AraGEM, a genome-scale reconstruction of the primary metabolic network in Arabidopsis</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">152</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Plant Physiology</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">579</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">589</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=AraGEM,%20a%20genome-scale%20reconstruction%20of%20the%20primary%20metabolic%20network%20in%20Arabidopsis"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1104/pp.109.148817</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">20044452</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib20"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="F Döring"><span data-itemprop="givenNames"><span itemprop="givenName">F</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Döring</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="M Streubel"><span data-itemprop="givenNames"><span itemprop="givenName">M</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Streubel</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="A Bräutigam"><span data-itemprop="givenNames"><span itemprop="givenName">A</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Bräutigam</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="U Gowik"><span data-itemprop="givenNames"><span itemprop="givenName">U</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Gowik</span></span> </li> </ol><time itemprop="datePublished" datetime="2016">2016</time><span itemprop="headline" content="Most photorespiratory genes are preferentially expressed in the bundle sheath cells of the C4 grass Sorghum b…">Most photorespiratory genes are preferentially expressed in the bundle sheath cells of the C4 grass Sorghum bicolor</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">67</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Journal of Experimental Botany</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">3053</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">3064</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Most%20photorespiratory%20genes%20are%20preferentially%20expressed%20in%20the%20bundle%20sheath%20cells%20of%20the%20C4%20grass%20Sorghum%20b%E2%80%A6"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1093/jxb/erw041</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">26976818</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib21"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="NC Duarte"><span data-itemprop="givenNames"><span itemprop="givenName">NC</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Duarte</span></span> </li> </ol><time itemprop="datePublished" datetime="2004">2004</time><span itemprop="headline" content="Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale meta…">Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">14</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Genome Research</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">1298</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">1309</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Reconstruction%20and%20validation%20of%20Saccharomyces%20cerevisiae%20iND750,%20a%20fully%20compartmentalized%20genome-scale%20meta%E2%80%A6"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1101/gr.2250904</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib22"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="SM Duff"><span data-itemprop="givenNames"><span itemprop="givenName">SM</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Duff</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="TJ Rydel"><span data-itemprop="givenNames"><span itemprop="givenName">TJ</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Rydel</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="AL McClerren"><span data-itemprop="givenNames"><span itemprop="givenName">AL</span></span><span data-itemprop="familyNames"><span itemprop="familyName">McClerren</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="W Zhang"><span data-itemprop="givenNames"><span itemprop="givenName">W</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Zhang</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="JY Li"><span data-itemprop="givenNames"><span itemprop="givenName">JY</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Li</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="EJ Sturman"><span data-itemprop="givenNames"><span itemprop="givenName">EJ</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Sturman</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="C Halls"><span data-itemprop="givenNames"><span itemprop="givenName">C</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Halls</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="S Chen"><span data-itemprop="givenNames"><span itemprop="givenName">S</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Chen</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="J Zeng"><span data-itemprop="givenNames"><span itemprop="givenName">J</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Zeng</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="J Peng"><span data-itemprop="givenNames"><span itemprop="givenName">J</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Peng</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="CN Kretzler"><span data-itemprop="givenNames"><span itemprop="givenName">CN</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Kretzler</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="A Evdokimov"><span data-itemprop="givenNames"><span itemprop="givenName">A</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Evdokimov</span></span> </li> </ol><time itemprop="datePublished" datetime="2012">2012</time><span itemprop="headline" content="The enzymology of alanine aminotransferase (AlaAT) isoforms from Hordeum vulgare and other organisms, and the…">The enzymology of alanine aminotransferase (AlaAT) isoforms from Hordeum vulgare and other organisms, and the HvAlaAT crystal structure</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">528</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Archives of Biochemistry and Biophysics</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">90</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">101</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=The%20enzymology%20of%20alanine%20aminotransferase%20(AlaAT)%20isoforms%20from%20Hordeum%20vulgare%20and%20other%20organisms,%20and%20the%E2%80%A6"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1016/j.abb.2012.06.006</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">22750542</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib23"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="EJ Edwards"><span data-itemprop="givenNames"><span itemprop="givenName">EJ</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Edwards</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="CP Osborne"><span data-itemprop="givenNames"><span itemprop="givenName">CP</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Osborne</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="CA Strömberg"><span data-itemprop="givenNames"><span itemprop="givenName">CA</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Strömberg</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="SA Smith"><span data-itemprop="givenNames"><span itemprop="givenName">SA</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Smith</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="WJ Bond"><span data-itemprop="givenNames"><span itemprop="givenName">WJ</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Bond</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="PA Christin"><span data-itemprop="givenNames"><span itemprop="givenName">PA</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Christin</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="AB Cousins"><span data-itemprop="givenNames"><span itemprop="givenName">AB</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Cousins</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="MR Duvall"><span data-itemprop="givenNames"><span itemprop="givenName">MR</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Duvall</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="DL Fox"><span data-itemprop="givenNames"><span itemprop="givenName">DL</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Fox</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="RP Freckleton"><span data-itemprop="givenNames"><span itemprop="givenName">RP</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Freckleton</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="O Ghannoum"><span data-itemprop="givenNames"><span itemprop="givenName">O</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Ghannoum</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="J Hartwell"><span data-itemprop="givenNames"><span itemprop="givenName">J</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Hartwell</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="Y Huang"><span data-itemprop="givenNames"><span itemprop="givenName">Y</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Huang</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="CM Janis"><span data-itemprop="givenNames"><span itemprop="givenName">CM</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Janis</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="JE Keeley"><span data-itemprop="givenNames"><span itemprop="givenName">JE</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Keeley</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="EA Kellogg"><span data-itemprop="givenNames"><span itemprop="givenName">EA</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Kellogg</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="AK Knapp"><span data-itemprop="givenNames"><span itemprop="givenName">AK</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Knapp</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="AD Leakey"><span data-itemprop="givenNames"><span itemprop="givenName">AD</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Leakey</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="DM Nelson"><span data-itemprop="givenNames"><span itemprop="givenName">DM</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Nelson</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="JM Saarela"><span data-itemprop="givenNames"><span itemprop="givenName">JM</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Saarela</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="RF Sage"><span data-itemprop="givenNames"><span itemprop="givenName">RF</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Sage</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="OE Sala"><span data-itemprop="givenNames"><span itemprop="givenName">OE</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Sala</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="N Salamin"><span data-itemprop="givenNames"><span itemprop="givenName">N</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Salamin</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="CJ Still"><span data-itemprop="givenNames"><span itemprop="givenName">CJ</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Still</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="B Tipple"><span data-itemprop="givenNames"><span itemprop="givenName">B</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Tipple</span></span> </li> <li itemscope="" itemtype="http://schema.org/Organization" itemprop="author"><span itemprop="name">C4 Grasses Consortium</span></li> </ol><time itemprop="datePublished" datetime="2010">2010</time><span itemprop="headline">The origins of C4 grasslands: integrating evolutionary and ecosystem science</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">328</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Science</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">587</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">591</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=The%20origins%20of%20C4%20grasslands:%20integrating%20evolutionary%20and%20ecosystem%20science"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1126/science.1177216</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">20431008</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib24"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="RJ Ellis"><span data-itemprop="givenNames"><span itemprop="givenName">RJ</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Ellis</span></span> </li> </ol><time itemprop="datePublished" datetime="1979">1979</time><span itemprop="headline">The most abundant protein in the world</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">4</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Trends in Biochemical Sciences</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">241</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">244</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=The%20most%20abundant%20protein%20in%20the%20world"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1016/0968-0004(79)90212-3</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib25"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="TA Feodorova"><span data-itemprop="givenNames"><span itemprop="givenName">TA</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Feodorova</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="EV Voznesenskaya"><span data-itemprop="givenNames"><span itemprop="givenName">EV</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Voznesenskaya</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="GE Edwards"><span data-itemprop="givenNames"><span itemprop="givenName">GE</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Edwards</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="EH Roalson"><span data-itemprop="givenNames"><span itemprop="givenName">EH</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Roalson</span></span> </li> </ol><time itemprop="datePublished" datetime="2010">2010</time><span itemprop="headline">Biogeographic patterns of diversification and the origins of C4 in Cleome (cleomaceae)</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">35</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Systematic Botany</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">811</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">826</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Biogeographic%20patterns%20of%20diversification%20and%20the%20origins%20of%20C4%20in%20Cleome%20(cleomaceae)"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1600/036364410X539880</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib26"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="T Furumoto"><span data-itemprop="givenNames"><span itemprop="givenName">T</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Furumoto</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="T Yamaguchi"><span data-itemprop="givenNames"><span itemprop="givenName">T</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Yamaguchi</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="Y Ohshima-Ichie"><span data-itemprop="givenNames"><span itemprop="givenName">Y</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Ohshima-Ichie</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="M Nakamura"><span data-itemprop="givenNames"><span itemprop="givenName">M</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Nakamura</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="Y Tsuchida-Iwata"><span data-itemprop="givenNames"><span itemprop="givenName">Y</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Tsuchida-Iwata</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="M Shimamura"><span data-itemprop="givenNames"><span itemprop="givenName">M</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Shimamura</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="J Ohnishi"><span data-itemprop="givenNames"><span itemprop="givenName">J</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Ohnishi</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="S Hata"><span data-itemprop="givenNames"><span itemprop="givenName">S</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Hata</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="U Gowik"><span data-itemprop="givenNames"><span itemprop="givenName">U</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Gowik</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="P Westhoff"><span data-itemprop="givenNames"><span itemprop="givenName">P</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Westhoff</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="A Bräutigam"><span data-itemprop="givenNames"><span itemprop="givenName">A</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Bräutigam</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="AP Weber"><span data-itemprop="givenNames"><span itemprop="givenName">AP</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Weber</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="K Izui"><span data-itemprop="givenNames"><span itemprop="givenName">K</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Izui</span></span> </li> </ol><time itemprop="datePublished" datetime="2011">2011</time><span itemprop="headline">A plastidial sodium-dependent pyruvate transporter</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">476</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Nature</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">472</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">475</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=A%20plastidial%20sodium-dependent%20pyruvate%20transporter"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1038/nature10250</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">21866161</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib27"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="C Gietl"><span data-itemprop="givenNames"><span itemprop="givenName">C</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Gietl</span></span> </li> </ol><time itemprop="datePublished" datetime="1992">1992</time><span itemprop="headline" content="Malate dehydrogenase isoenzymes: cellular locations and role in the flow of metabolites between the cytoplasm…">Malate dehydrogenase isoenzymes: cellular locations and role in the flow of metabolites between the cytoplasm and cell organelles</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">1100</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Biochimica Et Biophysica Acta (BBA) - Bioenergetics</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">217</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">234</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Malate%20dehydrogenase%20isoenzymes:%20cellular%20locations%20and%20role%20in%20the%20flow%20of%20metabolites%20between%20the%20cytoplasm%E2%80%A6"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1016/0167-4838(92)90476-T</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib28"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="C Gomes de Oliveira Dal’Molin"><span data-itemprop="givenNames"><span itemprop="givenName">C</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Gomes</span><span itemprop="familyName">de</span><span itemprop="familyName">Oliveira</span><span itemprop="familyName">Dal’Molin</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="L-E Quek"><span data-itemprop="givenNames"><span itemprop="givenName">L-E</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Quek</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="RW Palfreyman"><span data-itemprop="givenNames"><span itemprop="givenName">RW</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Palfreyman</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="LK Nielsen"><span data-itemprop="givenNames"><span itemprop="givenName">LK</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Nielsen</span></span> </li> </ol><time itemprop="datePublished" datetime="2011">2011</time><span itemprop="headline">AlgaGEM – a genome-scale metabolic reconstruction of algae based on the Chlamydomonas reinhardtii genome</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">12</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">BMC Genomics</span></span></span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=AlgaGEM%20%E2%80%93%20a%20genome-scale%20metabolic%20reconstruction%20of%20algae%20based%20on%20the%20Chlamydomonas%20reinhardtii%20genome"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1186/1471-2164-12-S4-S5</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib29"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="GFJ Haberlandt"><span data-itemprop="givenNames"><span itemprop="givenName">GFJ</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Haberlandt</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="V. erlagvonW Engelmann"><span data-itemprop="givenNames"><span itemprop="givenName">V.</span><span itemprop="givenName">erlagvonW</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Engelmann</span></span> </li> </ol><time itemprop="datePublished" datetime="1904">1904</time><span itemprop="headline">Physiologische Pflanzenanatomie</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"><span itemprop="name">Macmillan and Company</span><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Macmillan%20and%20Company"> </span></span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Physiologische%20Pflanzenanatomie"> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib30"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="MD Hatch"><span data-itemprop="givenNames"><span itemprop="givenName">MD</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Hatch</span></span> </li> </ol><time itemprop="datePublished" datetime="1987">1987</time><span itemprop="headline">C4 photosynthesis: a unique elend of modified biochemistry, anatomy and ultrastructure</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">895</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Biochimica Et Biophysica Acta (BBA) - Reviews on Bioenergetics</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">81</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">106</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=C4%20photosynthesis:%20a%20unique%20elend%20of%20modified%20biochemistry,%20anatomy%20and%20ultrastructure"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1016/S0304-4173(87)80009-5</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib31"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="D Heckmann"><span data-itemprop="givenNames"><span itemprop="givenName">D</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Heckmann</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="S Schulze"><span data-itemprop="givenNames"><span itemprop="givenName">S</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Schulze</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="A Denton"><span data-itemprop="givenNames"><span itemprop="givenName">A</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Denton</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="U Gowik"><span data-itemprop="givenNames"><span itemprop="givenName">U</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Gowik</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="P Westhoff"><span data-itemprop="givenNames"><span itemprop="givenName">P</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Westhoff</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="AP Weber"><span data-itemprop="givenNames"><span itemprop="givenName">AP</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Weber</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="MJ Lercher"><span data-itemprop="givenNames"><span itemprop="givenName">MJ</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Lercher</span></span> </li> </ol><time itemprop="datePublished" datetime="2013">2013</time><span itemprop="headline">Predicting C4 photosynthesis evolution: modular, individually adaptive steps on a mount fuji fitness landscape</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">153</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Cell</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">1579</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">1588</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Predicting%20C4%20photosynthesis%20evolution:%20modular,%20individually%20adaptive%20steps%20on%20a%20mount%20fuji%20fitness%20landscape"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1016/j.cell.2013.04.058</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">23791184</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib32"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="HW Heldt"><span data-itemprop="givenNames"><span itemprop="givenName">HW</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Heldt</span></span> </li> </ol><time itemprop="datePublished" datetime="2015">2015</time><span itemprop="headline">Piechulla B. Pflanzenbiochemie</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"><span itemprop="name">Springer</span><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Springer"> </span></span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Piechulla%20B.%20Pflanzenbiochemie"> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib33"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="EM Josse"><span data-itemprop="givenNames"><span itemprop="givenName">EM</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Josse</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="AJ Simkin"><span data-itemprop="givenNames"><span itemprop="givenName">AJ</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Simkin</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="J Gaffé"><span data-itemprop="givenNames"><span itemprop="givenName">J</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Gaffé</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="AM Labouré"><span data-itemprop="givenNames"><span itemprop="givenName">AM</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Labouré</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="M Kuntz"><span data-itemprop="givenNames"><span itemprop="givenName">M</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Kuntz</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="P Carol"><span data-itemprop="givenNames"><span itemprop="givenName">P</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Carol</span></span> </li> </ol><time itemprop="datePublished" datetime="2000">2000</time><span itemprop="headline">A plastid terminal oxidase associated with carotenoid desaturation during chromoplast differentiation</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">123</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Plant Physiology</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">1427</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">1436</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=A%20plastid%20terminal%20oxidase%20associated%20with%20carotenoid%20desaturation%20during%20chromoplast%20differentiation"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1104/pp.123.4.1427</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">10938359</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib34"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="G Karabourniotis"><span data-itemprop="givenNames"><span itemprop="givenName">G</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Karabourniotis</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="JF Bornman"><span data-itemprop="givenNames"><span itemprop="givenName">JF</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Bornman</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="D Nikolopoulos"><span data-itemprop="givenNames"><span itemprop="givenName">D</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Nikolopoulos</span></span> </li> </ol><time itemprop="datePublished" datetime="2000">2000</time><span itemprop="headline" content="A possible optical role of the bundle sheath extensions of the heterobaric leaves of Vitis vinifera and Querc…">A possible optical role of the bundle sheath extensions of the heterobaric leaves of Vitis vinifera and Quercus coccifera</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">23</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Plant, Cell & Environment</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">423</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">430</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=A%20possible%20optical%20role%20of%20the%20bundle%20sheath%20extensions%20of%20the%20heterobaric%20leaves%20of%20Vitis%20vinifera%20and%20Querc%E2%80%A6"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1046/j.1365-3040.2000.00558.x</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib35"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="T Kiba"><span data-itemprop="givenNames"><span itemprop="givenName">T</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Kiba</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="AB Feria-Bourrellier"><span data-itemprop="givenNames"><span itemprop="givenName">AB</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Feria-Bourrellier</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="F Lafouge"><span data-itemprop="givenNames"><span itemprop="givenName">F</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Lafouge</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="L Lezhneva"><span data-itemprop="givenNames"><span itemprop="givenName">L</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Lezhneva</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="S Boutet-Mercey"><span data-itemprop="givenNames"><span itemprop="givenName">S</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Boutet-Mercey</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="M Orsel"><span data-itemprop="givenNames"><span itemprop="givenName">M</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Orsel</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="V Bréhaut"><span data-itemprop="givenNames"><span itemprop="givenName">V</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Bréhaut</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="A Miller"><span data-itemprop="givenNames"><span itemprop="givenName">A</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Miller</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="F Daniel-Vedele"><span data-itemprop="givenNames"><span itemprop="givenName">F</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Daniel-Vedele</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="H Sakakibara"><span data-itemprop="givenNames"><span itemprop="givenName">H</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Sakakibara</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="A Krapp"><span data-itemprop="givenNames"><span itemprop="givenName">A</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Krapp</span></span> </li> </ol><time itemprop="datePublished" datetime="2012">2012</time><span itemprop="headline">The Arabidopsis nitrate transporter NRT2.4 plays a double role in roots and shoots of nitrogen-starved plants</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">24</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">The Plant Cell</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">245</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">258</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=The%20Arabidopsis%20nitrate%20transporter%20NRT2.4%20plays%20a%20double%20role%20in%20roots%20and%20shoots%20of%20nitrogen-starved%20plants"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1105/tpc.111.092221</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">22227893</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib36"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="C Körner"><span data-itemprop="givenNames"><span itemprop="givenName">C</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Körner</span></span> </li> </ol><time itemprop="datePublished" datetime="2015">2015</time><span itemprop="headline">Paradigm shift in plant growth control</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">25</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Current Opinion in Plant Biology</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">107</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">114</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Paradigm%20shift%20in%20plant%20growth%20control"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1016/j.pbi.2015.05.003</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">26037389</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib37"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="W Lacher"><span data-itemprop="givenNames"><span itemprop="givenName">W</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Lacher</span></span> </li> </ol><time itemprop="datePublished" datetime="2003">2003</time><span itemprop="headline">Physiological Plant Ecology: Ecophysiology and Stress Physiology of Functional Groups</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"><span itemprop="name">Springer</span><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Springer"> </span></span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Physiological%20Plant%20Ecology:%20Ecophysiology%20and%20Stress%20Physiology%20of%20Functional%20Groups"> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib38"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="AD Leakey"><span data-itemprop="givenNames"><span itemprop="givenName">AD</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Leakey</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="M Uribelarrea"><span data-itemprop="givenNames"><span itemprop="givenName">M</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Uribelarrea</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="EA Ainsworth"><span data-itemprop="givenNames"><span itemprop="givenName">EA</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Ainsworth</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="SL Naidu"><span data-itemprop="givenNames"><span itemprop="givenName">SL</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Naidu</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="A Rogers"><span data-itemprop="givenNames"><span itemprop="givenName">A</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Rogers</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="DR Ort"><span data-itemprop="givenNames"><span itemprop="givenName">DR</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Ort</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="SP Long"><span data-itemprop="givenNames"><span itemprop="givenName">SP</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Long</span></span> </li> </ol><time itemprop="datePublished" datetime="2006">2006</time><span itemprop="headline" content="Photosynthesis, productivity, and yield of maize are not affected by open-air elevation of CO2 concentration …">Photosynthesis, productivity, and yield of maize are not affected by open-air elevation of CO2 concentration in the absence of drought</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">140</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Plant Physiology</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">779</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">790</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Photosynthesis,%20productivity,%20and%20yield%20of%20maize%20are%20not%20affected%20by%20open-air%20elevation%20of%20CO2%20concentration%20%E2%80%A6"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1104/pp.105.073957</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">16407441</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib39"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="NE Lewis"><span data-itemprop="givenNames"><span itemprop="givenName">NE</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Lewis</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="KK Hixson"><span data-itemprop="givenNames"><span itemprop="givenName">KK</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Hixson</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="TM Conrad"><span data-itemprop="givenNames"><span itemprop="givenName">TM</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Conrad</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="JA Lerman"><span data-itemprop="givenNames"><span itemprop="givenName">JA</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Lerman</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="P Charusanti"><span data-itemprop="givenNames"><span itemprop="givenName">P</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Charusanti</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="AD Polpitiya"><span data-itemprop="givenNames"><span itemprop="givenName">AD</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Polpitiya</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="JN Adkins"><span data-itemprop="givenNames"><span itemprop="givenName">JN</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Adkins</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="G Schramm"><span data-itemprop="givenNames"><span itemprop="givenName">G</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Schramm</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="SO Purvine"><span data-itemprop="givenNames"><span itemprop="givenName">SO</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Purvine</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="D Lopez-Ferrer"><span data-itemprop="givenNames"><span itemprop="givenName">D</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Lopez-Ferrer</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="KK Weitz"><span data-itemprop="givenNames"><span itemprop="givenName">KK</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Weitz</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="R Eils"><span data-itemprop="givenNames"><span itemprop="givenName">R</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Eils</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="R König"><span data-itemprop="givenNames"><span itemprop="givenName">R</span></span><span data-itemprop="familyNames"><span itemprop="familyName">König</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="RD Smith"><span data-itemprop="givenNames"><span itemprop="givenName">RD</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Smith</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="BØ Palsson"><span data-itemprop="givenNames"><span itemprop="givenName">BØ</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Palsson</span></span> </li> </ol><time itemprop="datePublished" datetime="2010">2010</time><span itemprop="headline">Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">6</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Molecular Systems Biology</span></span></span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Omic%20data%20from%20evolved%20E.%20coli%20are%20consistent%20with%20computed%20optimal%20growth%20from%20genome-scale%20models"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1038/msb.2010.47</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">20664636</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib40"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="L Li"><span data-itemprop="givenNames"><span itemprop="givenName">L</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Li</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="CJ Nelson"><span data-itemprop="givenNames"><span itemprop="givenName">CJ</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Nelson</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="J Trösch"><span data-itemprop="givenNames"><span itemprop="givenName">J</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Trösch</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="I Castleden"><span data-itemprop="givenNames"><span itemprop="givenName">I</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Castleden</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="S Huang"><span data-itemprop="givenNames"><span itemprop="givenName">S</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Huang</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="AH Millar"><span data-itemprop="givenNames"><span itemprop="givenName">AH</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Millar</span></span> </li> </ol><time itemprop="datePublished" datetime="2017">2017</time><span itemprop="headline">Protein degradation rate in Arabidopsis thaliana Leaf Growth and Development</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">29</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">The Plant Cell</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">207</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">228</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Protein%20degradation%20rate%20in%20Arabidopsis%20thaliana%20Leaf%20Growth%20and%20Development"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1105/tpc.16.00768</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">28138016</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib41"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="AH Liepman"><span data-itemprop="givenNames"><span itemprop="givenName">AH</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Liepman</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="LJ Olsen"><span data-itemprop="givenNames"><span itemprop="givenName">LJ</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Olsen</span></span> </li> </ol><time itemprop="datePublished" datetime="2003">2003</time><span itemprop="headline" content="Alanine aminotransferase homologs catalyze the glutamate:glyoxylate aminotransferase reaction in peroxisomes …">Alanine aminotransferase homologs catalyze the glutamate:glyoxylate aminotransferase reaction in peroxisomes of Arabidopsis</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">131</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Plant Physiology</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">215</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">227</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Alanine%20aminotransferase%20homologs%20catalyze%20the%20glutamate:glyoxylate%20aminotransferase%20reaction%20in%20peroxisomes%20%E2%80%A6"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1104/pp.011460</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">12529529</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib42"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="N Linka"><span data-itemprop="givenNames"><span itemprop="givenName">N</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Linka</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="AP Weber"><span data-itemprop="givenNames"><span itemprop="givenName">AP</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Weber</span></span> </li> </ol><time itemprop="datePublished" datetime="2010">2010</time><span itemprop="headline">Intracellular metabolite transporters in plants</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">3</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Molecular Plant</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">21</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">53</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Intracellular%20metabolite%20transporters%20in%20plants"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1093/mp/ssp108</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">20038549</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib43"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="H Liu"><span data-itemprop="givenNames"><span itemprop="givenName">H</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Liu</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="CP Osborne"><span data-itemprop="givenNames"><span itemprop="givenName">CP</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Osborne</span></span> </li> </ol><time itemprop="datePublished" datetime="2015">2015</time><span itemprop="headline" content="Water relations traits of C4 grasses depend on phylogenetic lineage, photosynthetic pathway, and habitat wate…">Water relations traits of C4 grasses depend on phylogenetic lineage, photosynthetic pathway, and habitat water availability</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">66</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Journal of Experimental Botany</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">761</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">773</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Water%20relations%20traits%20of%20C4%20grasses%20depend%20on%20phylogenetic%20lineage,%20photosynthetic%20pathway,%20and%20habitat%20wate%E2%80%A6"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1093/jxb/eru430</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">25504656</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib44"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="MR Lundgren"><span data-itemprop="givenNames"><span itemprop="givenName">MR</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Lundgren</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="PA Christin"><span data-itemprop="givenNames"><span itemprop="givenName">PA</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Christin</span></span> </li> </ol><time itemprop="datePublished" datetime="2017">2017</time><span itemprop="headline">Despite phylogenetic effects, C3-C4 lineages bridge the ecological gap to C4 photosynthesis</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">68</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Journal of Experimental Botany</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">241</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">254</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Despite%20phylogenetic%20effects,%20C3-C4%20lineages%20bridge%20the%20ecological%20gap%20to%20C4%20photosynthesis"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1093/jxb/erw451</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">28025316</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib45"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="JH Macduff"><span data-itemprop="givenNames"><span itemprop="givenName">JH</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Macduff</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="AK Bakken"><span data-itemprop="givenNames"><span itemprop="givenName">AK</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Bakken</span></span> </li> </ol><time itemprop="datePublished" datetime="2003">2003</time><span itemprop="headline" content="Diurnal variation in uptake and xylem contents of inorganic and assimilated N under continuous and interrupte…">Diurnal variation in uptake and xylem contents of inorganic and assimilated N under continuous and interrupted N supply to Phleum pratense and Festuca pratensis</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">54</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Journal of Experimental Botany</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">431</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">444</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Diurnal%20variation%20in%20uptake%20and%20xylem%20contents%20of%20inorganic%20and%20assimilated%20N%20under%20continuous%20and%20interrupte%E2%80%A6"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1093/jxb/erg058</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">12493871</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib46"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="R Mahadevan"><span data-itemprop="givenNames"><span itemprop="givenName">R</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Mahadevan</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="CH Schilling"><span data-itemprop="givenNames"><span itemprop="givenName">CH</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Schilling</span></span> </li> </ol><time itemprop="datePublished" datetime="2003">2003</time><span itemprop="headline">The effects of alternate optimal solutions in constraint-based genome-scale metabolic models</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">5</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Metabolic Engineering</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">264</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">276</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=The%20effects%20of%20alternate%20optimal%20solutions%20in%20constraint-based%20genome-scale%20metabolic%20models"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1016/j.ymben.2003.09.002</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">14642354</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib47"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="J Mallmann"><span data-itemprop="givenNames"><span itemprop="givenName">J</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Mallmann</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="D Heckmann"><span data-itemprop="givenNames"><span itemprop="givenName">D</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Heckmann</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="A Bräutigam"><span data-itemprop="givenNames"><span itemprop="givenName">A</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Bräutigam</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="MJ Lercher"><span data-itemprop="givenNames"><span itemprop="givenName">MJ</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Lercher</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="AP Weber"><span data-itemprop="givenNames"><span itemprop="givenName">AP</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Weber</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="P Westhoff"><span data-itemprop="givenNames"><span itemprop="givenName">P</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Westhoff</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="U Gowik"><span data-itemprop="givenNames"><span itemprop="givenName">U</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Gowik</span></span> </li> </ol><time itemprop="datePublished" datetime="2014">2014</time><span itemprop="headline">The role of photorespiration during the evolution of C4 photosynthesis in the genus Flaveria</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">3</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">eLife</span></span></span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=The%20role%20of%20photorespiration%20during%20the%20evolution%20of%20C4%20photosynthesis%20in%20the%20genus%20Flaveria"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.7554/eLife.02478</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">24935935</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib48"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="RK Monson"><span data-itemprop="givenNames"><span itemprop="givenName">RK</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Monson</span></span> </li> </ol><time itemprop="datePublished" datetime="1999">1999</time><span itemprop="headline">The Origins of C4 Genes and Evolutionary Pattern in the C4 Metabolic Phenotype</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"><span itemprop="name">Elsevier</span><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Elsevier"> </span></span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=The%20Origins%20of%20C4%20Genes%20and%20Evolutionary%20Pattern%20in%20the%20C4%20Metabolic%20Phenotype"> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib49"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="LA Mueller"><span data-itemprop="givenNames"><span itemprop="givenName">LA</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Mueller</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="P Zhang"><span data-itemprop="givenNames"><span itemprop="givenName">P</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Zhang</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="SY Rhee"><span data-itemprop="givenNames"><span itemprop="givenName">SY</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Rhee</span></span> </li> </ol><time itemprop="datePublished" datetime="2003">2003</time><span itemprop="headline">AraCyc: a biochemical pathway database for Arabidopsis</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">132</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Plant Physiology</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">453</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">460</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=AraCyc:%20a%20biochemical%20pathway%20database%20for%20Arabidopsis"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1104/pp.102.017236</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">12805578</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib50"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="HE Neuhaus"><span data-itemprop="givenNames"><span itemprop="givenName">HE</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Neuhaus</span></span> </li> </ol><time itemprop="datePublished" datetime="2007">2007</time><span itemprop="headline">Transport of primary metabolites across the plant vacuolar membrane</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">581</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">FEBS Letters</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">2223</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">2226</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Transport%20of%20primary%20metabolites%20across%20the%20plant%20vacuolar%20membrane"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1016/j.febslet.2007.02.003</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">17307167</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib51"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="WL Ogren"><span data-itemprop="givenNames"><span itemprop="givenName">WL</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Ogren</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="G Bowes"><span data-itemprop="givenNames"><span itemprop="givenName">G</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Bowes</span></span> </li> </ol><time itemprop="datePublished" datetime="1971">1971</time><span itemprop="headline">Ribulose diphosphate carboxylase regulates soybean photorespiration</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">230</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Nature New Biology</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">159</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">160</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Ribulose%20diphosphate%20carboxylase%20regulates%20soybean%20photorespiration"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1038/newbio230159a0</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">5279476</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib52"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="JD Orth"><span data-itemprop="givenNames"><span itemprop="givenName">JD</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Orth</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="I Thiele"><span data-itemprop="givenNames"><span itemprop="givenName">I</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Thiele</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="BØ Palsson"><span data-itemprop="givenNames"><span itemprop="givenName">BØ</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Palsson</span></span> </li> </ol><time itemprop="datePublished" datetime="2010">2010</time><span itemprop="headline">What is flux balance analysis?</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">28</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Nature Biotechnology</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">245</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">248</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=What%20is%20flux%20balance%20analysis?"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1038/nbt.1614</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">20212490</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib53"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="CP Osborne"><span data-itemprop="givenNames"><span itemprop="givenName">CP</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Osborne</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="RP Freckleton"><span data-itemprop="givenNames"><span itemprop="givenName">RP</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Freckleton</span></span> </li> </ol><time itemprop="datePublished" datetime="2009">2009</time><span itemprop="headline">Ecological selection pressures for C4 photosynthesis in the grasses</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">276</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Proceedings of the Royal Society B: Biological Sciences</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">1753</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">1760</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Ecological%20selection%20pressures%20for%20C4%20photosynthesis%20in%20the%20grasses"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1098/rspb.2008.1762</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib54"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="C Pál"><span data-itemprop="givenNames"><span itemprop="givenName">C</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Pál</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="B Papp"><span data-itemprop="givenNames"><span itemprop="givenName">B</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Papp</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="MJ Lercher"><span data-itemprop="givenNames"><span itemprop="givenName">MJ</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Lercher</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="P Csermely"><span data-itemprop="givenNames"><span itemprop="givenName">P</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Csermely</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="SG Oliver"><span data-itemprop="givenNames"><span itemprop="givenName">SG</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Oliver</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="LD Hurst"><span data-itemprop="givenNames"><span itemprop="givenName">LD</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Hurst</span></span> </li> </ol><time itemprop="datePublished" datetime="2006">2006</time><span itemprop="headline">Chance and necessity in the evolution of minimal metabolic networks</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">440</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Nature</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">667</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">670</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Chance%20and%20necessity%20in%20the%20evolution%20of%20minimal%20metabolic%20networks"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1038/nature04568</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">16572170</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib55"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="B Papp"><span data-itemprop="givenNames"><span itemprop="givenName">B</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Papp</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="B Szappanos"><span data-itemprop="givenNames"><span itemprop="givenName">B</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Szappanos</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="RA Notebaart"><span data-itemprop="givenNames"><span itemprop="givenName">RA</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Notebaart</span></span> </li> </ol><time itemprop="datePublished" datetime="2011">2011</time><span itemprop="headline">Use of genome-scale metabolic models in evolutionary systems biology</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"><span itemprop="name">Humana Press</span><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Humana%20Press"> </span></span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Use%20of%20genome-scale%20metabolic%20models%20in%20evolutionary%20systems%20biology"> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib56"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="J Petersen"><span data-itemprop="givenNames"><span itemprop="givenName">J</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Petersen</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="K Förster"><span data-itemprop="givenNames"><span itemprop="givenName">K</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Förster</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="P Turina"><span data-itemprop="givenNames"><span itemprop="givenName">P</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Turina</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="P Gräber"><span data-itemprop="givenNames"><span itemprop="givenName">P</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Gräber</span></span> </li> </ol><time itemprop="datePublished" datetime="2012">2012</time><span itemprop="headline">Comparison of the H+/ATP ratios of the H+-ATP synthases from yeast and from chloroplast</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">109</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">PNAS</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">11150</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">11155</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Comparison%20of%20the%20H+/ATP%20ratios%20of%20the%20H+-ATP%20synthases%20from%20yeast%20and%20from%20chloroplast"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1073/pnas.1202799109</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">22733773</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib57"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="TR Pick"><span data-itemprop="givenNames"><span itemprop="givenName">TR</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Pick</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="A Bräutigam"><span data-itemprop="givenNames"><span itemprop="givenName">A</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Bräutigam</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="U Schlüter"><span data-itemprop="givenNames"><span itemprop="givenName">U</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Schlüter</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="AK Denton"><span data-itemprop="givenNames"><span itemprop="givenName">AK</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Denton</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="C Colmsee"><span data-itemprop="givenNames"><span itemprop="givenName">C</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Colmsee</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="U Scholz"><span data-itemprop="givenNames"><span itemprop="givenName">U</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Scholz</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="H Fahnenstich"><span data-itemprop="givenNames"><span itemprop="givenName">H</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Fahnenstich</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="R Pieruschka"><span data-itemprop="givenNames"><span itemprop="givenName">R</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Pieruschka</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="U Rascher"><span data-itemprop="givenNames"><span itemprop="givenName">U</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Rascher</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="U Sonnewald"><span data-itemprop="givenNames"><span itemprop="givenName">U</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Sonnewald</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="AP Weber"><span data-itemprop="givenNames"><span itemprop="givenName">AP</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Weber</span></span> </li> </ol><time itemprop="datePublished" datetime="2011">2011</time><span itemprop="headline" content="Systems analysis of a maize leaf developmental gradient redefines the current C4 model and provides candidate…">Systems analysis of a maize leaf developmental gradient redefines the current C4 model and provides candidates for regulation</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">23</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">The Plant Cell</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">4208</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">4220</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Systems%20analysis%20of%20a%20maize%20leaf%20developmental%20gradient%20redefines%20the%20current%20C4%20model%20and%20provides%20candidate%E2%80%A6"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1105/tpc.111.090324</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">22186372</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib58"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="H Pinto"><span data-itemprop="givenNames"><span itemprop="givenName">H</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Pinto</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="JR Powell"><span data-itemprop="givenNames"><span itemprop="givenName">JR</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Powell</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="RE Sharwood"><span data-itemprop="givenNames"><span itemprop="givenName">RE</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Sharwood</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="DT Tissue"><span data-itemprop="givenNames"><span itemprop="givenName">DT</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Tissue</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="O Ghannoum"><span data-itemprop="givenNames"><span itemprop="givenName">O</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Ghannoum</span></span> </li> </ol><time itemprop="datePublished" datetime="2016">2016</time><span itemprop="headline" content="Variations in nitrogen use efficiency reflect the biochemical subtype while variations in water use efficienc…">Variations in nitrogen use efficiency reflect the biochemical subtype while variations in water use efficiency reflect the evolutionary lineage of C4 grasses at inter-glacial CO2</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">39</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Plant, Cell & Environment</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">514</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">526</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Variations%20in%20nitrogen%20use%20efficiency%20reflect%20the%20biochemical%20subtype%20while%20variations%20in%20water%20use%20efficienc%E2%80%A6"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1111/pce.12636</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">26381794</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib59"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="J Reiser"><span data-itemprop="givenNames"><span itemprop="givenName">J</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Reiser</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="N Linka"><span data-itemprop="givenNames"><span itemprop="givenName">N</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Linka</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="L Lemke"><span data-itemprop="givenNames"><span itemprop="givenName">L</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Lemke</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="W Jeblick"><span data-itemprop="givenNames"><span itemprop="givenName">W</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Jeblick</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="HE Neuhaus"><span data-itemprop="givenNames"><span itemprop="givenName">HE</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Neuhaus</span></span> </li> </ol><time itemprop="datePublished" datetime="2004">2004</time><span itemprop="headline">Molecular physiological analysis of the two plastidic ATP/ADP transporters from Arabidopsis</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">136</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Plant Physiology</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">3524</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">3536</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Molecular%20physiological%20analysis%20of%20the%20two%20plastidic%20ATP/ADP%20transporters%20from%20Arabidopsis"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1104/pp.104.049502</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">15516503</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib60"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="J Rozema"><span data-itemprop="givenNames"><span itemprop="givenName">J</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Rozema</span></span> </li> </ol><time itemprop="datePublished" datetime="1993">1993</time><span itemprop="headline" content="Plant responses to atmospheric carbon dioxide enrichment: interactions with some soil and atmospheric conditi…">Plant responses to atmospheric carbon dioxide enrichment: interactions with some soil and atmospheric conditions</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">105</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Vegetatio</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">173</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">190</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Plant%20responses%20to%20atmospheric%20carbon%20dioxide%20enrichment:%20interactions%20with%20some%20soil%20and%20atmospheric%20conditi%E2%80%A6"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.2134/asaspecpub61.c1</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib61"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="RF Sage"><span data-itemprop="givenNames"><span itemprop="givenName">RF</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Sage</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="RW Pearcy"><span data-itemprop="givenNames"><span itemprop="givenName">RW</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Pearcy</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="JR Seemann"><span data-itemprop="givenNames"><span itemprop="givenName">JR</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Seemann</span></span> </li> </ol><time itemprop="datePublished" datetime="1987">1987</time><span itemprop="headline" content="The nitrogen use efficiency of C(3) and C(4) Plants : iii. leaf nitrogen effects on the activity of carboxyla…">The nitrogen use efficiency of C(3) and C(4) Plants : iii. leaf nitrogen effects on the activity of carboxylating enzymes in Chenopodium album (L.) and Amaranthus retroflexus (L.)</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">85</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Plant Physiology</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">355</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">359</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=The%20nitrogen%20use%20efficiency%20of%20C(3)%20and%20C(4)%20Plants%20:%20iii.%20leaf%20nitrogen%20effects%20on%20the%20activity%20of%20carboxyla%E2%80%A6"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1104/pp.85.2.355</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">16665701</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib62"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="RF Sage"><span data-itemprop="givenNames"><span itemprop="givenName">RF</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Sage</span></span> </li> </ol><time itemprop="datePublished" datetime="2004">2004</time><span itemprop="headline">The evolution of C4 photosynthesis</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">161</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">New Phytologist</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">341</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">370</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=The%20evolution%20of%20C4%20photosynthesis"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1111/j.1469-8137.2004.00974.x</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib63"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="RF Sage"><span data-itemprop="givenNames"><span itemprop="givenName">RF</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Sage</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="TL Sage"><span data-itemprop="givenNames"><span itemprop="givenName">TL</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Sage</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="F Kocacinar"><span data-itemprop="givenNames"><span itemprop="givenName">F</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Kocacinar</span></span> </li> </ol><time itemprop="datePublished" datetime="2012">2012</time><span itemprop="headline">Photorespiration and the evolution of C4 photosynthesis</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">63</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Annual Review of Plant Biology</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">19</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">47</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Photorespiration%20and%20the%20evolution%20of%20C4%20photosynthesis"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1146/annurev-arplant-042811-105511</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">22404472</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib64"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="R Saha"><span data-itemprop="givenNames"><span itemprop="givenName">R</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Saha</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="PF Suthers"><span data-itemprop="givenNames"><span itemprop="givenName">PF</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Suthers</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="CD Maranas"><span data-itemprop="givenNames"><span itemprop="givenName">CD</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Maranas</span></span> </li> </ol><time itemprop="datePublished" datetime="2011">2011</time><span itemprop="headline">Zea mays iRS1563: a comprehensive genome-scale metabolic reconstruction of maize metabolism</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">6</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">PLOS ONE</span></span></span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Zea%20mays%20iRS1563:%20a%20comprehensive%20genome-scale%20metabolic%20reconstruction%20of%20maize%20metabolism"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1371/journal.pone.0021784</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">21755001</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib65"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="A Scheben"><span data-itemprop="givenNames"><span itemprop="givenName">A</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Scheben</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="F Wolter"><span data-itemprop="givenNames"><span itemprop="givenName">F</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Wolter</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="J Batley"><span data-itemprop="givenNames"><span itemprop="givenName">J</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Batley</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="H Puchta"><span data-itemprop="givenNames"><span itemprop="givenName">H</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Puchta</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="D Edwards"><span data-itemprop="givenNames"><span itemprop="givenName">D</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Edwards</span></span> </li> </ol><time itemprop="datePublished" datetime="2017">2017</time><span itemprop="headline">Towards CRISPR/Cas crops - bringing together genomics and genome editing</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">216</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">New Phytologist</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">682</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">698</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Towards%20CRISPR/Cas%20crops%20-%20bringing%20together%20genomics%20and%20genome%20editing"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1111/nph.14702</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">28762506</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib66"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="U Schlüter"><span data-itemprop="givenNames"><span itemprop="givenName">U</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Schlüter</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="A Bräutigam"><span data-itemprop="givenNames"><span itemprop="givenName">A</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Bräutigam</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="U Gowik"><span data-itemprop="givenNames"><span itemprop="givenName">U</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Gowik</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="M Melzer"><span data-itemprop="givenNames"><span itemprop="givenName">M</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Melzer</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="PA Christin"><span data-itemprop="givenNames"><span itemprop="givenName">PA</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Christin</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="S Kurz"><span data-itemprop="givenNames"><span itemprop="givenName">S</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Kurz</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="T Mettler-Altmann"><span data-itemprop="givenNames"><span itemprop="givenName">T</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Mettler-Altmann</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="AP Weber"><span data-itemprop="givenNames"><span itemprop="givenName">AP</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Weber</span></span> </li> </ol><time itemprop="datePublished" datetime="2016">2016</time><span itemprop="headline">Photosynthesis in C3-C4 intermediate Moricandia species</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">68</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Journal of Experimental Botany</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">191</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">206</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Photosynthesis%20in%20C3-C4%20intermediate%20Moricandia%20species"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1093/jxb/erw391</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">28110276</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib67"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="U Schlüter"><span data-itemprop="givenNames"><span itemprop="givenName">U</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Schlüter</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="AK Denton"><span data-itemprop="givenNames"><span itemprop="givenName">AK</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Denton</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="A Bräutigam"><span data-itemprop="givenNames"><span itemprop="givenName">A</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Bräutigam</span></span> </li> </ol><time itemprop="datePublished" datetime="2016">2016</time><span itemprop="headline">Understanding metabolite transport and metabolism in C4 plants through RNA-seq</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">31</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Current Opinion in Plant Biology</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">83</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">90</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Understanding%20metabolite%20transport%20and%20metabolism%20in%20C4%20plants%20through%20RNA-seq"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1016/j.pbi.2016.03.007</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">27082280</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib68"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="I Schomburg"><span data-itemprop="givenNames"><span itemprop="givenName">I</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Schomburg</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="A Chang"><span data-itemprop="givenNames"><span itemprop="givenName">A</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Chang</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="O Hofmann"><span data-itemprop="givenNames"><span itemprop="givenName">O</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Hofmann</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="C Ebeling"><span data-itemprop="givenNames"><span itemprop="givenName">C</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Ebeling</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="F Ehrentreich"><span data-itemprop="givenNames"><span itemprop="givenName">F</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Ehrentreich</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="D Schomburg"><span data-itemprop="givenNames"><span itemprop="givenName">D</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Schomburg</span></span> </li> </ol><time itemprop="datePublished" datetime="2002">2002</time><span itemprop="headline">BRENDA: a resource for enzyme data and metabolic information</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">27</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Trends in Biochemical Sciences</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">54</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">56</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=BRENDA:%20a%20resource%20for%20enzyme%20data%20and%20metabolic%20information"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1016/S0968-0004(01)02027-8</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">11796225</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib69"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="CJ Schultz"><span data-itemprop="givenNames"><span itemprop="givenName">CJ</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Schultz</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="GM Coruzzi"><span data-itemprop="givenNames"><span itemprop="givenName">GM</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Coruzzi</span></span> </li> </ol><time itemprop="datePublished" datetime="1995">1995</time><span itemprop="headline" content="The aspartate aminotransferase gene family of Arabidopsis encodes isoenzymes localized to three distinct subc…">The aspartate aminotransferase gene family of Arabidopsis encodes isoenzymes localized to three distinct subcellular compartments</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">7</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">The Plant Journal</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">61</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">75</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=The%20aspartate%20aminotransferase%20gene%20family%20of%20Arabidopsis%20encodes%20isoenzymes%20localized%20to%20three%20distinct%20subc%E2%80%A6"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1046/j.1365-313X.1995.07010061.x</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">7894512</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib70"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="T Shikanai"><span data-itemprop="givenNames"><span itemprop="givenName">T</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Shikanai</span></span> </li> </ol><time itemprop="datePublished" datetime="2016">2016</time><span itemprop="headline">Regulatory network of proton motive force: contribution of cyclic electron transport around photosystem I</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">129</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Photosynthesis Research</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">253</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">260</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Regulatory%20network%20of%20proton%20motive%20force:%20contribution%20of%20cyclic%20electron%20transport%20around%20photosystem%20I"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1007/s11120-016-0227-0</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">26858094</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib71"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="M Simons"><span data-itemprop="givenNames"><span itemprop="givenName">M</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Simons</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="A Misra"><span data-itemprop="givenNames"><span itemprop="givenName">A</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Misra</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="G Sriram"><span data-itemprop="givenNames"><span itemprop="givenName">G</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Sriram</span></span> </li> </ol><time itemprop="datePublished" datetime="2013">2013</time><span itemprop="headline">Genome-scale models of plant metabolism</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"><span itemprop="name">Humana Press</span><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Humana%20Press"> </span></span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Genome-scale%20models%20of%20plant%20metabolism"> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib72"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="BV Sonawane"><span data-itemprop="givenNames"><span itemprop="givenName">BV</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Sonawane</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="RE Sharwood"><span data-itemprop="givenNames"><span itemprop="givenName">RE</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Sharwood</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="S Whitney"><span data-itemprop="givenNames"><span itemprop="givenName">S</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Whitney</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="O Ghannoum"><span data-itemprop="givenNames"><span itemprop="givenName">O</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Ghannoum</span></span> </li> </ol><time itemprop="datePublished" datetime="2018">2018</time><span itemprop="headline">Shade compromises the photosynthetic efficiency of NADP-ME less than that of PEP-CK and NAD-ME C4 grasses</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">69</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Journal of Experimental Botany</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">3053</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">3068</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Shade%20compromises%20the%20photosynthetic%20efficiency%20of%20NADP-ME%20less%20than%20that%20of%20PEP-CK%20and%20NAD-ME%20C4%20grasses"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1093/jxb/ery129</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">29659931</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib73"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="RJ Spreitzer"><span data-itemprop="givenNames"><span itemprop="givenName">RJ</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Spreitzer</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="ME Salvucci"><span data-itemprop="givenNames"><span itemprop="givenName">ME</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Salvucci</span></span> </li> </ol><time itemprop="datePublished" datetime="2002">2002</time><span itemprop="headline">Rubisco: structure, regulatory interactions, and possibilities for a better enzyme</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">53</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Annual Review of Plant Biology</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">449</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">475</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Rubisco:%20structure,%20regulatory%20interactions,%20and%20possibilities%20for%20a%20better%20enzyme"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1146/annurev.arplant.53.100301.135233</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">12221984</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib74"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="M Stitt"><span data-itemprop="givenNames"><span itemprop="givenName">M</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Stitt</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="SC Zeeman"><span data-itemprop="givenNames"><span itemprop="givenName">SC</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Zeeman</span></span> </li> </ol><time itemprop="datePublished" datetime="2012">2012</time><span itemprop="headline">Starch turnover: pathways, regulation and role in growth</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">15</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Current Opinion in Plant Biology</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">282</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">292</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Starch%20turnover:%20pathways,%20regulation%20and%20role%20in%20growth"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1016/j.pbi.2012.03.016</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">22541711</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib75"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="J Sun"><span data-itemprop="givenNames"><span itemprop="givenName">J</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Sun</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="TW Okita"><span data-itemprop="givenNames"><span itemprop="givenName">TW</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Okita</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="GE Edwards"><span data-itemprop="givenNames"><span itemprop="givenName">GE</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Edwards</span></span> </li> </ol><time itemprop="datePublished" datetime="1999">1999</time><span itemprop="headline" content="Modification of Carbon Partitioning, Photosynthetic Capacity, and O2 Sensitivity in Arabidopsis Plants with L…">Modification of Carbon Partitioning, Photosynthetic Capacity, and O2 Sensitivity in Arabidopsis Plants with Low ADP-Glucose Pyrophosphorylase Activity</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">119</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Plant Physiology</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">267</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">276</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Modification%20of%20Carbon%20Partitioning,%20Photosynthetic%20Capacity,%20and%20O2%20Sensitivity%20in%20Arabidopsis%20Plants%20with%20L%E2%80%A6"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1104/pp.119.1.267</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib76"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="D Swarbreck"><span data-itemprop="givenNames"><span itemprop="givenName">D</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Swarbreck</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="C Wilks"><span data-itemprop="givenNames"><span itemprop="givenName">C</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Wilks</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="P Lamesch"><span data-itemprop="givenNames"><span itemprop="givenName">P</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Lamesch</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="TZ Berardini"><span data-itemprop="givenNames"><span itemprop="givenName">TZ</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Berardini</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="M Garcia-Hernandez"><span data-itemprop="givenNames"><span itemprop="givenName">M</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Garcia-Hernandez</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="H Foerster"><span data-itemprop="givenNames"><span itemprop="givenName">H</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Foerster</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="D Li"><span data-itemprop="givenNames"><span itemprop="givenName">D</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Li</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="T Meyer"><span data-itemprop="givenNames"><span itemprop="givenName">T</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Meyer</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="R Muller"><span data-itemprop="givenNames"><span itemprop="givenName">R</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Muller</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="L Ploetz"><span data-itemprop="givenNames"><span itemprop="givenName">L</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Ploetz</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="A Radenbaugh"><span data-itemprop="givenNames"><span itemprop="givenName">A</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Radenbaugh</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="S Singh"><span data-itemprop="givenNames"><span itemprop="givenName">S</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Singh</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="V Swing"><span data-itemprop="givenNames"><span itemprop="givenName">V</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Swing</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="C Tissier"><span data-itemprop="givenNames"><span itemprop="givenName">C</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Tissier</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="P Zhang"><span data-itemprop="givenNames"><span itemprop="givenName">P</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Zhang</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="E Huala"><span data-itemprop="givenNames"><span itemprop="givenName">E</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Huala</span></span> </li> </ol><time itemprop="datePublished" datetime="2008">2008</time><span itemprop="headline">The Arabidopsis information resource (TAIR): gene structure and function annotation</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">36</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Nucleic Acids Research</span></span></span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=The%20Arabidopsis%20information%20resource%20(TAIR):%20gene%20structure%20and%20function%20annotation"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1093/nar/gkm965</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">17986450</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib77"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="K Thomas"><span data-itemprop="givenNames"><span itemprop="givenName">K</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Thomas</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="R-K Benjamin"><span data-itemprop="givenNames"><span itemprop="givenName">R-K</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Benjamin</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="P Fernando"><span data-itemprop="givenNames"><span itemprop="givenName">P</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Fernando</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="G Brian"><span data-itemprop="givenNames"><span itemprop="givenName">G</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Brian</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="B Matthias"><span data-itemprop="givenNames"><span itemprop="givenName">B</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Matthias</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="F Jonathan"><span data-itemprop="givenNames"><span itemprop="givenName">F</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Jonathan</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="K Kyle"><span data-itemprop="givenNames"><span itemprop="givenName">K</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Kyle</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="H Jessica"><span data-itemprop="givenNames"><span itemprop="givenName">H</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Jessica</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="G Jason"><span data-itemprop="givenNames"><span itemprop="givenName">G</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Jason</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="C Sylvain"><span data-itemprop="givenNames"><span itemprop="givenName">C</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Sylvain</span></span> </li> </ol><time itemprop="datePublished" datetime="2016">2016</time><span itemprop="headline">Jupyter notebooks: a publishing format for reproducible computational workflows</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Jupyter%20notebooks:%20a%20publishing%20format%20for%20reproducible%20computational%20workflows"> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib78"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="R Turgeon"><span data-itemprop="givenNames"><span itemprop="givenName">R</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Turgeon</span></span> </li> </ol><time itemprop="datePublished" datetime="1989">1989</time><span itemprop="headline">The Sink-Source transition in leaves</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">40</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Annual Review of Plant Physiology and Plant Molecular Biology</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">119</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">138</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=The%20Sink-Source%20transition%20in%20leaves"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1146/annurev.pp.40.060189.001003</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib79"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="P Turina"><span data-itemprop="givenNames"><span itemprop="givenName">P</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Turina</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="J Petersen"><span data-itemprop="givenNames"><span itemprop="givenName">J</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Petersen</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="P Gräber"><span data-itemprop="givenNames"><span itemprop="givenName">P</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Gräber</span></span> </li> </ol><time itemprop="datePublished" datetime="2016">2016</time><span itemprop="headline">Thermodynamics of proton transport coupled ATP synthesis</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">1857</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Biochimica Et Biophysica Acta (BBA) - Bioenergetics</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">653</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">664</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Thermodynamics%20of%20proton%20transport%20coupled%20ATP%20synthesis"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1016/j.bbabio.2016.02.019</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib80"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="O Ueno"><span data-itemprop="givenNames"><span itemprop="givenName">O</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Ueno</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="N Sentoku"><span data-itemprop="givenNames"><span itemprop="givenName">N</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Sentoku</span></span> </li> </ol><time itemprop="datePublished" datetime="2006">2006</time><span itemprop="headline">Comparison of leaf structure and photosynthetic characteristics of C3 and C4 Alloteropsis semialata subspecies</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">29</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Plant, Cell and Environment</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">257</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">268</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Comparison%20of%20leaf%20structure%20and%20photosynthetic%20characteristics%20of%20C3%20and%20C4%C2%A0Alloteropsis%20semialata%20subspecies"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1111/j.1365-3040.2005.01418.x</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib81"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="A Vishwakarma"><span data-itemprop="givenNames"><span itemprop="givenName">A</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Vishwakarma</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="SD Tetali"><span data-itemprop="givenNames"><span itemprop="givenName">SD</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Tetali</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="J Selinski"><span data-itemprop="givenNames"><span itemprop="givenName">J</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Selinski</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="R Scheibe"><span data-itemprop="givenNames"><span itemprop="givenName">R</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Scheibe</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="K Padmasree"><span data-itemprop="givenNames"><span itemprop="givenName">K</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Padmasree</span></span> </li> </ol><time itemprop="datePublished" datetime="2015">2015</time><span itemprop="headline" content="Importance of the alternative oxidase (AOX) pathway in regulating cellular redox and ROS homeostasis to optim…">Importance of the alternative oxidase (AOX) pathway in regulating cellular redox and ROS homeostasis to optimize photosynthesis during restriction of the cytochrome oxidase pathway in Arabidopsis thaliana</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">116</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Annals of Botany</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">555</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">569</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Importance%20of%20the%20alternative%20oxidase%20(AOX)%20pathway%20in%20regulating%20cellular%20redox%20and%20ROS%20homeostasis%20to%20optim%E2%80%A6"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1093/aob/mcv122</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">26292995</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib82"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="EV Voznesenskaya"><span data-itemprop="givenNames"><span itemprop="givenName">EV</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Voznesenskaya</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="NK Koteyeva"><span data-itemprop="givenNames"><span itemprop="givenName">NK</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Koteyeva</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="SDX Chuong"><span data-itemprop="givenNames"><span itemprop="givenName">SDX</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Chuong</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="AN Ivanova"><span data-itemprop="givenNames"><span itemprop="givenName">AN</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Ivanova</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="J Barroca"><span data-itemprop="givenNames"><span itemprop="givenName">J</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Barroca</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="LA Craven"><span data-itemprop="givenNames"><span itemprop="givenName">LA</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Craven</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="GE Edwards"><span data-itemprop="givenNames"><span itemprop="givenName">GE</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Edwards</span></span> </li> </ol><time itemprop="datePublished" datetime="2007">2007</time><span itemprop="headline" content="Physiological, anatomical and biochemical characterisation of photosynthetic types in genus Cleome (Cleomacea…">Physiological, anatomical and biochemical characterisation of photosynthetic types in genus Cleome (Cleomaceae)</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">34</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Functional Plant Biology</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">247</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">267</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Physiological,%20anatomical%20and%20biochemical%20characterisation%20of%20photosynthetic%20types%20in%20genus%20Cleome%20(Cleomacea%E2%80%A6"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1071/FP06287</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib83"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="Y Wang"><span data-itemprop="givenNames"><span itemprop="givenName">Y</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Wang</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="A Bräutigam"><span data-itemprop="givenNames"><span itemprop="givenName">A</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Bräutigam</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="AP Weber"><span data-itemprop="givenNames"><span itemprop="givenName">AP</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Weber</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="XG Zhu"><span data-itemprop="givenNames"><span itemprop="givenName">XG</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Zhu</span></span> </li> </ol><time itemprop="datePublished" datetime="2014">2014</time><span itemprop="headline">Three distinct biochemical subtypes of C4 photosynthesis? A modelling analysis</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">65</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Journal of Experimental Botany</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">3567</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">3578</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Three%20distinct%20biochemical%20subtypes%20of%20C4%20photosynthesis?%20A%20modelling%20analysis"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1093/jxb/eru058</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">24609651</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib84"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="S Weissmann"><span data-itemprop="givenNames"><span itemprop="givenName">S</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Weissmann</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="F Ma"><span data-itemprop="givenNames"><span itemprop="givenName">F</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Ma</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="K Furuyama"><span data-itemprop="givenNames"><span itemprop="givenName">K</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Furuyama</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="J Gierse"><span data-itemprop="givenNames"><span itemprop="givenName">J</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Gierse</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="H Berg"><span data-itemprop="givenNames"><span itemprop="givenName">H</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Berg</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="Y Shao"><span data-itemprop="givenNames"><span itemprop="givenName">Y</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Shao</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="M Taniguchi"><span data-itemprop="givenNames"><span itemprop="givenName">M</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Taniguchi</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="DK Allen"><span data-itemprop="givenNames"><span itemprop="givenName">DK</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Allen</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="TP Brutnell"><span data-itemprop="givenNames"><span itemprop="givenName">TP</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Brutnell</span></span> </li> </ol><time itemprop="datePublished" datetime="2016">2016</time><span itemprop="headline" content="Interactions of C4 subtype metabolic activities and transport in maize are revealed through the characterizat…">Interactions of C4 subtype metabolic activities and transport in maize are revealed through the characterization of DCT2 mutants</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">28</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">The Plant Cell</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">466</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">484</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Interactions%20of%20C4%20subtype%20metabolic%20activities%20and%20transport%20in%20maize%20are%20revealed%20through%20the%20characterizat%E2%80%A6"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1105/tpc.15.00497</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">26813621</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib85"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="TL Wilkinson"><span data-itemprop="givenNames"><span itemprop="givenName">TL</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Wilkinson</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="AE Douglas"><span data-itemprop="givenNames"><span itemprop="givenName">AE</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Douglas</span></span> </li> </ol><time itemprop="datePublished" datetime="2003">2003</time><span itemprop="headline">Phloem amino acids and the host plant range of the polyphagous aphid, aphis fabae</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">106</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Entomologia Experimentalis Et Applicata</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">103</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">113</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Phloem%20amino%20acids%20and%20the%20host%20plant%20range%20of%20the%20polyphagous%20aphid,%20aphis%20fabae"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1046/j.1570-7458.2003.00014.x</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib86"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="BP Williams"><span data-itemprop="givenNames"><span itemprop="givenName">BP</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Williams</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="IG Johnston"><span data-itemprop="givenNames"><span itemprop="givenName">IG</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Johnston</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="S Covshoff"><span data-itemprop="givenNames"><span itemprop="givenName">S</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Covshoff</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="JM Hibberd"><span data-itemprop="givenNames"><span itemprop="givenName">JM</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Hibberd</span></span> </li> </ol><time itemprop="datePublished" datetime="2013">2013</time><span itemprop="headline">Phenotypic landscape inference reveals multiple evolutionary paths to C4 photosynthesis</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">2</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">eLife</span></span></span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Phenotypic%20landscape%20inference%20reveals%20multiple%20evolutionary%20paths%20to%20C4%20photosynthesis"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.7554/eLife.00961</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">24082995</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib87"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="A Wingler"><span data-itemprop="givenNames"><span itemprop="givenName">A</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Wingler</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="RP Walker"><span data-itemprop="givenNames"><span itemprop="givenName">RP</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Walker</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="ZH Chen"><span data-itemprop="givenNames"><span itemprop="givenName">ZH</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Chen</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="RC Leegood"><span data-itemprop="givenNames"><span itemprop="givenName">RC</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Leegood</span></span> </li> </ol><time itemprop="datePublished" datetime="1999">1999</time><span itemprop="headline" content="Phosphoenolpyruvate carboxykinase is involved in the decarboxylation of aspartate in the bundle sheath of mai…">Phosphoenolpyruvate carboxykinase is involved in the decarboxylation of aspartate in the bundle sheath of maize</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">120</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">Plant Physiology</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">539</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">546</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=Phosphoenolpyruvate%20carboxykinase%20is%20involved%20in%20the%20decarboxylation%20of%20aspartate%20in%20the%20bundle%20sheath%20of%20mai%E2%80%A6"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1104/pp.120.2.539</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">10364405</span> </li> </ul> </li> <li itemscope="" itemtype="http://schema.org/Article" itemprop="citation" id="bib88"> <ol data-itemprop="authors"> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="H Yamamoto"><span data-itemprop="givenNames"><span itemprop="givenName">H</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Yamamoto</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="L Peng"><span data-itemprop="givenNames"><span itemprop="givenName">L</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Peng</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="Y Fukao"><span data-itemprop="givenNames"><span itemprop="givenName">Y</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Fukao</span></span> </li> <li itemscope="" itemtype="http://schema.org/Person" itemprop="author"> <meta itemprop="name" content="T Shikanai"><span data-itemprop="givenNames"><span itemprop="givenName">T</span></span><span data-itemprop="familyNames"><span itemprop="familyName">Shikanai</span></span> </li> </ol><time itemprop="datePublished" datetime="2011">2011</time><span itemprop="headline" content="An src homology 3 domain-like fold protein forms a ferredoxin binding site for the chloroplast NADH dehydroge…">An src homology 3 domain-like fold protein forms a ferredoxin binding site for the chloroplast NADH dehydrogenase-like complex in Arabidopsis</span><span itemscope="" itemtype="http://schema.org/PublicationVolume" itemprop="isPartOf"><span itemprop="volumeNumber" data-itemtype="http://schema.org/Number">23</span><span itemscope="" itemtype="http://schema.org/Periodical" itemprop="isPartOf"><span itemprop="name">The Plant Cell</span></span></span><span itemprop="pageStart" data-itemtype="http://schema.org/Number">1480</span><span itemprop="pageEnd" data-itemtype="http://schema.org/Number">1493</span><span itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher"> <meta itemprop="name" content="Unknown"><span itemscope="" itemtype="http://schema.org/ImageObject" itemprop="logo"> <meta itemprop="url" content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown"> </span> </span> <meta itemprop="image" content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=An%20src%20homology%203%20domain-like%20fold%20protein%20forms%20a%20ferredoxin%20binding%20site%20for%20the%20chloroplast%20NADH%20dehydroge%E2%80%A6"> <ul data-itemprop="identifiers"> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/doi"><span itemprop="name">doi</span><span itemprop="value">10.1105/tpc.110.080291</span> </li> <li itemscope="" itemtype="http://schema.org/PropertyValue" itemprop="identifier"> <meta itemprop="propertyID" content="https://registry.identifiers.org/registry/pmid"><span itemprop="name">pmid</span><span itemprop="value" data-itemtype="http://schema.org/Number">21505067</span> </li> </ul> </li> </ol> </section> </article> </main> </body> </html>