use light intensity as a constraint to predict the maximum growth

math248 commented 5 years ago

Helle everybody, I work on a linux Ubuntu 18.04 with the icZ843 model of Chlorella Vulgaris. And I use Cobrapy to analyse the model prediction accuracy. And I was wondering if it was possible to predict the max growth at all light intensity. I mean a graph with the OD and the growth rate. Because when I look at the SBML model I see that there are not lower/upper bound for the light intensity and I don't understand how the light is sued in the prediction. Thanks in advance, Regards.

matthiaskoenig commented 5 years ago

@math248 I can't find the icZ843 model in the Bigg data base. Can you provide a link to the SBML then I could have a look how light intensity is used in the model. Best Matthias

math248 commented 5 years ago

You can find the model in the supplementary Data in this link : http://www.plantphysiol.org/content/172/1/589/tab-figures-data You have the Heterotrophy/mixotrophy and photoautotrophy model Thanks matthias :-)

matthiaskoenig commented 5 years ago

Hi @math248, the following happens in the model (as to my knowledge) which is quit clever.

photons of different wavelenght are treated as different species
a handful of light source reaction exists with specific spectra (set of photons of given wavelength which are produced by the light source) and a certain intensity (this is basically the upper and lower bound of the reaction (setting how many photons are created per time unit, which is your light intensity)
some (biological) reactions consume the photons of certain wavelength, e.g. photosystem I to capture electrons (electron chains in photosystems).

See for instance the light source solar_litho which is earth light spectra.

<reaction id="R_PRISM_solar_litho" name="spectral decomposition of solar light measured from Earth&apos;s surface" reversible="false">
        <notes>
          <body xmlns="http://www.w3.org/1999/xhtml">
            <p>GENE_ASSOCIATION: </p>
            <p>SUBSYSTEM: </p>
            <p>EC Number: </p>
            <p>Confidence Level: </p>
            <p>AUTHORS: </p>
            <p/>
          </body>
        </notes>
        <listOfReactants>
          <speciesReference species="M_photonVis_e" stoichiometry="1"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="M_photon298_c" stoichiometry="4.26984325300204e-005"/>
          <speciesReference species="M_photon437_u" stoichiometry="0.088253056987783"/>
          <speciesReference species="M_photon438_u" stoichiometry="0.187390761056649"/>
          <speciesReference species="M_photon450_h" stoichiometry="0.114958292879089"/>
          <speciesReference species="M_photon646_h" stoichiometry="0.18566429641716"/>
          <speciesReference species="M_photon673_u" stoichiometry="0.08361649412414"/>
          <speciesReference species="M_photon680_u" stoichiometry="0.094404940130699"/>
          <speciesReference species="M_photon490_h" stoichiometry="0.19581"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <ci> FLUX_VALUE </ci>
          </math>
          <listOfParameters>
            <parameter id="LOWER_BOUND" value="646.06656" units="mmol_per_gDW_per_hr" constant="false"/>
            <parameter id="UPPER_BOUND" value="646.06656" units="mmol_per_gDW_per_hr" constant="false"/>
            <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr" constant="false"/>
            <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr" constant="false"/>
          </listOfParameters>
        </kineticLaw>
      </reaction>

Other light sources are in there but the flux bounds are set to zero, e.g.

R_PRISM_incandescent_60W
R_PRISM_fluorescent_warm_18W

A photon consumption reaction is for instance

<reaction id="R_PSIblue" name="photosystem I (blue light-activated)" reversible="false">
        <notes>
          <body xmlns="http://www.w3.org/1999/xhtml">
            <p>GENE_ASSOCIATION: (snap_masked_Scaffold_1102-abinit-gene-0.10 and maker_Scaffold_1102-snap-gene-0.11 and maker_Scaffold_1280-augustus-gene-0.117 and maker_Scaffold_1363-augustus-gene-0.48 and augustus_masked_Scaffold_115-abinit-gene-0.2 and genemark_Scaffold_1061-abinit-gene-0.20 and GL433837.1.286 and snap_masked_Scaffold_291-abinit-gene-0.25 and genemark_Scaffold_2058-abinit-gene-0.4 and genemark_Scaffold_1611-abinit-gene-0.13 and maker_Scaffold_615-augustus-gene-0.55)</p>
            <p>SUBSYSTEM: </p>
            <p>EC Number: </p>
            <p>Confidence Level: </p>
            <p>AUTHORS: </p>
            <p/>
          </body>
        </notes>
        <listOfReactants>
          <speciesReference species="M_fdxox_u" stoichiometry="2"/>
          <speciesReference species="M_pccu1p_u" stoichiometry="2"/>
          <speciesReference species="M_photon437_u" stoichiometry="2"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="M_fdxrd_u" stoichiometry="2"/>
          <speciesReference species="M_pccu2p_u" stoichiometry="2"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <ci> FLUX_VALUE </ci>
          </math>
          <listOfParameters>
            <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr" constant="false"/>
            <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr" constant="false"/>
            <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr" constant="false"/>
            <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr" constant="false"/>
          </listOfParameters>
        </kineticLaw>
      </reaction>

So to answer your question:

set the bounds to varying values in the light reaction, with increasing values you increase the intensity. To select the light source (spectra) set the bounds on the respective light source. To define your own light source define a new light source reaction and provide the spectra (via stoichiometric coefficients of photons of given wavelength).

Disclaimer: I looked a few minutes at the model, no in depth analysis or simulation in any way. There could be much more to it. Spectra are discretized in the model (probably this corresponds to the peaks of the spectra). This discretization looks hand-tuned by the modeller so that light sources and consuming reactions work together.

SBRG / bigg_models

use light intensity as a constraint to predict the maximum growth #336