Difference between revisions of "Team:H14Z1 Hangzhou/Model"

 
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         <div class="content">
 
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             <img src="https://static.igem.org/mediawiki/2018/d/d0/T--H14Z1_Hangzhou--head_demonstrate.png" alt="" class="head_div_img" />
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             <img src="https://static.igem.org/mediawiki/2018/a/aa/T--H14Z1_Hangzhou--head_Model.png" alt="" class="head_div_img" />
 
             <div class="content_box">
 
             <div class="content_box">
 
                 <h1 class="content_title">Model</h1>
 
                 <h1 class="content_title">Model</h1>
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                     <p class="content_context" style="line-height: 24px; text-indent: 2em; text-align: justify">
 
                     <p class="content_context" style="line-height: 24px; text-indent: 2em; text-align: justify">
 
                         GSH and SAM are becoming more and more popular health care product, and our project focus on
 
                         GSH and SAM are becoming more and more popular health care product, and our project focus on
                         producing and accumulating GSH and SAM in L. lactis and improving its adhesivity, and, finally,
+
                         producing and accumulating GSH and SAM in <i>L. lactis</i> and improving its adhesivity, and, finally,
 
                         getting “Smart yoghourt” by using the engineered strain. During our experiments, we have
 
                         getting “Smart yoghourt” by using the engineered strain. During our experiments, we have
 
                         collected some data about cell growth and GSH and SAM production, and then modelled according
 
                         collected some data about cell growth and GSH and SAM production, and then modelled according
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                     <h6 class="content_sub_subtitle">Genes and GSH and SAM production</h6>
 
                     <h6 class="content_sub_subtitle">Genes and GSH and SAM production</h6>
 
                     <p class="content_context" style="line-height:24px; text-indent: 2em; text-align: justify">
 
                     <p class="content_context" style="line-height:24px; text-indent: 2em; text-align: justify">
                         We have transferred plasmid pNZ-GMcA to L. lactis, containing gene gshF, metK and cwaA,
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                         We have transferred plasmid pNZ-GMcA to <i>L. lactis</i>, containing gene gshF, metK and cwaA,
 
                         resulting in improvement of producing GSH and SAM and adhesivity of the strain while using for
 
                         resulting in improvement of producing GSH and SAM and adhesivity of the strain while using for
 
                         producing “Smart yoghourt”. As GSH and SAM were the main characteristic of this strain, to get
 
                         producing “Smart yoghourt”. As GSH and SAM were the main characteristic of this strain, to get
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                         models to guide fermentation process in producing “Smart yoghourt”.
 
                         models to guide fermentation process in producing “Smart yoghourt”.
 
                     </p>
 
                     </p>
                     <p><img src="https://static.igem.org/mediawiki/2018/8/8d/T--H14Z1_Hangzhou--project_model_fig1.png"></p>
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                     <p><img style="width: 50%" src="https://static.igem.org/mediawiki/2018/8/8d/T--H14Z1_Hangzhou--project_model_fig1.png"></p>
                     <p class="content_context" style="text-align:center; font-size:8px">
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                     <p class="content_context" style="text-align:center; font-size:18px">
                         Figure. 1 The schematic diagram of biosynthesis synthesis of GSH and SAM in L. lactis/pNZ-GMcA.
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                         Figure. 1 The schematic diagram of biosynthesis synthesis of GSH and SAM in <i>L. lactis</i>/pNZ-GMcA.
 
                     </p>
 
                     </p>
 
                     <h6 class="content_sub_subtitle">Experimental data collection</h6>
 
                     <h6 class="content_sub_subtitle">Experimental data collection</h6>
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                     </p>
 
                     </p>
 
                     <p class="content_context">
 
                     <p class="content_context">
                         4ml L. lactis glycerol stock from -80oC were inoculated to 50 ml GM17 medium and grown
+
                         4ml <i>L. lactis</i> glycerol stock from -80oC were inoculated to 50 ml GM17 medium and grown
 
                         overnight at 30oC without aeration. Then, the pre-culture were inoculated to 50 ml of GM17
 
                         overnight at 30oC without aeration. Then, the pre-culture were inoculated to 50 ml of GM17
 
                         medium with a dilution of 1:100 and grown at 30oC without aeration. OD600 was measured every 2
 
                         medium with a dilution of 1:100 and grown at 30oC without aeration. OD600 was measured every 2
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                     <h3 class="content_subtitle">Modeling</h3>
 
                     <h3 class="content_subtitle">Modeling</h3>
 
                     <p class="content_context">
 
                     <p class="content_context">
                         Eq. 1 and Eq. 2 were fitted to experimental data using the solver of MATLAB 2016, the source
+
                         The cell growth (X) model, GSH Formation (P1) model and SAM Formation (P2) model should be
                         program was shown in Figure 2. Equation parameters were calculated by fitting the experimental
+
                        integrated into a complete mathematical model:
                        data with corresponding models for least squares deviation. The solver of Origin 9.0 was used
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                    </p>
                         for the calculations. The values of those parameters are listed in Table 1.
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                    <p><img style="width: 40%" src="https://static.igem.org/mediawiki/2018/c/c9/T--H14Z1_Hangzhou--project_model_fig10.png"></p>
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                    <p class="content_context">
 +
                        The Levenberg-Marquardt nonlinear regression algorithm was used to seek the best values of the
 +
                         equation parameters in Eq. 3 that minimize the sum of the squared deviations between the
 +
                         calculated values and the experimental data. The values of those parameters is listed in Table
 +
                        1. Then the time courses of cell growth (X), GSH Formation (P1) and SAM Formation (P2) were
 +
                        obtained by integration of Eq. 3 using the ode45 solver in MATLAB 2016 as illustrated in Figure
 +
                        2, and the results were shown in Figures 3, 4 and 5.
 
                     </p>
 
                     </p>
 
                     <p><img src="https://static.igem.org/mediawiki/2018/c/c0/T--H14Z1_Hangzhou--project_model_fig4.png"></p>
 
                     <p><img src="https://static.igem.org/mediawiki/2018/c/c0/T--H14Z1_Hangzhou--project_model_fig4.png"></p>
                     <p class="content_context" style="text-align:center; font-size:8px">
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                     <p class="content_context" style="text-align:center; font-size:18px">
 
                         Figure. 2 The source program of MATLAB for fitting Eqs. 1 and 2.
 
                         Figure. 2 The source program of MATLAB for fitting Eqs. 1 and 2.
 
                     </p>
 
                     </p>
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                     <h6 class="content_sub_subtitle">Kinetics of growth of L.lactis/pNZ-GMcA</h6>
 
                     <h6 class="content_sub_subtitle">Kinetics of growth of L.lactis/pNZ-GMcA</h6>
 
                     <p class="content_context">
 
                     <p class="content_context">
                         Figure 3 shows the time courses of cell growth of L. lactis. The experiment was conducted at
+
                         Figure 3 shows the time courses of cell growth of <i>L. lactis</i>. The experiment was conducted at
 
                         30oC. The initial glucose concentration was 10 g/L. As shown in Figure 2, cell growth under
 
                         30oC. The initial glucose concentration was 10 g/L. As shown in Figure 2, cell growth under
 
                         those conditions is described using the modified logistic cell growth model with a K value of
 
                         those conditions is described using the modified logistic cell growth model with a K value of
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                         inhibition of metabolites such as lactate or low concentration of nutriment.
 
                         inhibition of metabolites such as lactate or low concentration of nutriment.
 
                     </p>
 
                     </p>
                     <p><img src="https://static.igem.org/mediawiki/2018/3/39/T--H14Z1_Hangzhou--project_model_fig6.png"></p>
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                     <p><img style="width: 50%" src="https://static.igem.org/mediawiki/2018/3/39/T--H14Z1_Hangzhou--project_model_fig6.png"></p>
                     <p class="content_context" style="text-align:center; font-size:8px">
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                     <p class="content_context" style="text-align:center; font-size:18px">
                         Figure. 3 Cell growth of L. lactis. Solid lines are best-fit curves of experimental data using
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                         Figure. 3 Cell growth of <i>L. lactis</i>. Solid lines are best-fit curves of experimental data using
 
                         corresponding models using Eq. 1. The scatters were samples at different time.
 
                         corresponding models using Eq. 1. The scatters were samples at different time.
 
                     </p>
 
                     </p>
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                         with a α value of -6.97 and β value of 2.64 GSH per DCW per time (g/g/h). This observation may
 
                         with a α value of -6.97 and β value of 2.64 GSH per DCW per time (g/g/h). This observation may
 
                         be attributed to the fact that gene gshF for GSH production was induced by nisin at 7 h, while
 
                         be attributed to the fact that gene gshF for GSH production was induced by nisin at 7 h, while
                         wild-type L. lactis cannot synthesize GSH. Thus, we supposed GSH formation in L. lactis shows a
+
                         wild-type <i>L. lactis</i> cannot synthesize GSH. Thus, we supposed GSH formation in <i>L. lactis</i> shows a
 
                         mixed with induction associated and non-growth–associated product.
 
                         mixed with induction associated and non-growth–associated product.
 
                     </p>
 
                     </p>
                     <p><img src="https://static.igem.org/mediawiki/2018/a/a6/T--H14Z1_Hangzhou--project_model_fig7.png"></p>
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                     <p><img style="width: 50%" src="https://static.igem.org/mediawiki/2018/a/a6/T--H14Z1_Hangzhou--project_model_fig7.png"></p>
                     <p class="content_context" style="text-align:center; font-size:8px">
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                     <p class="content_context" style="text-align:center; font-size:18px">
                         Figure. 4 GSH production of L. lactis/pNZ-GMcA. Solid lines are best-fit curves of experimental
+
                         Figure. 4 GSH production of <i>L. lactis</i>/pNZ-GMcA. Solid lines are best-fit curves of experimental
 
                         data using corresponding models using Eq. 2. The scatters were samples at different time.
 
                         data using corresponding models using Eq. 2. The scatters were samples at different time.
 
                     </p>
 
                     </p>
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                         value of 1.07 and β value of 0.493 SAM per DCW per time (g/g/h). It is worth noting that the
 
                         value of 1.07 and β value of 0.493 SAM per DCW per time (g/g/h). It is worth noting that the
 
                         Eq. 2 is good for fitting the SAM production data from 0 to 7 h. While after 7 h, the
 
                         Eq. 2 is good for fitting the SAM production data from 0 to 7 h. While after 7 h, the
                         experimental data were slightly deflected from the fitted curve. We supposed that L. lactis can
+
                         experimental data were slightly deflected from the fitted curve. We supposed that <i>L. lactis</i> can
 
                         synthesize little SAM by itself and this might be typical mixed-growth-associated kinetics.
 
                         synthesize little SAM by itself and this might be typical mixed-growth-associated kinetics.
 
                         Expression of gene metK was induced by nisin at 7 h, and then more SAM were formed, resulting
 
                         Expression of gene metK was induced by nisin at 7 h, and then more SAM were formed, resulting
 
                         in deflected from the fitted curve.
 
                         in deflected from the fitted curve.
 
                     </p>
 
                     </p>
                     <p><img src="https://static.igem.org/mediawiki/2018/a/a6/T--H14Z1_Hangzhou--project_model_fig7.png"></p>
+
                     <p><img style="width: 50%" src="https://static.igem.org/mediawiki/2018/5/5c/T--H14Z1_Hangzhou--project_model_fig8.png"></p>
                     <p class="content_context" style="text-align:center; font-size:8px">
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                     <p class="content_context" style="text-align:center; font-size:18px">
                         Figure. 5 SAM production of L. lactis/pNZ-GMcA. Solid lines are best-fit curves of experimental
+
                         Figure. 5 SAM production of <i>L. lactis</i>/pNZ-GMcA. Solid lines are best-fit curves of experimental
 
                         data using corresponding models using Eq. 2. The scatters were samples at different time.
 
                         data using corresponding models using Eq. 2. The scatters were samples at different time.
 
                     </p>
 
                     </p>
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                     <h6 class="content_sub_subtitle">Reference</h6>
 
                     <h6 class="content_sub_subtitle">Reference</h6>
 
                     <p>
 
                     <p>
                         <ol style="margin:0px 50px; text-align: justify; font-style: italic; padding: 1em;">
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                         <ol style="margin:0px 50px; text-align: justify; font-size:16px; padding: 1em;">
 
                             <li>
 
                             <li>
 
                                 Messens W, Verluyten J, Leroy F, et al. 2003. Modelling growth and bacteriocin
 
                                 Messens W, Verluyten J, Leroy F, et al. 2003. Modelling growth and bacteriocin
                                 production by Lactobacillus curvatus LTH 1174 in response to temperature and pH values
+
                                 production by <i>Lactobacillus curvatus</i> LTH 1174 in response to temperature and pH values
 
                                 used for European sausage fermentation processes. Int J Food Microbiol. 81(1):41-52.
 
                                 used for European sausage fermentation processes. Int J Food Microbiol. 81(1):41-52.
 
                             </li>
 
                             </li>
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                             </li>
 
                             </li>
 
                             <li>
 
                             <li>
                                 Lan C Q, Oddone G, Mills D A, et al. 2010. Kinetics of Lactococcus lactis growth and
+
                                 Lan C Q, Oddone G, Mills D A, et al. 2010. Kinetics of <i>Lactococcus lactis</i> growth and
 
                                 metabolite formation under aerobic and anaerobic conditions in the presence or absence
 
                                 metabolite formation under aerobic and anaerobic conditions in the presence or absence
 
                                 of hemin. Biotechnol Bioeng. 95(6):1070-1080.
 
                                 of hemin. Biotechnol Bioeng. 95(6):1070-1080.

Latest revision as of 01:21, 18 October 2018

<!DOCTYPE html>

Model

GSH and SAM are becoming more and more popular health care product, and our project focus on producing and accumulating GSH and SAM in L. lactis and improving its adhesivity, and, finally, getting “Smart yoghourt” by using the engineered strain. During our experiments, we have collected some data about cell growth and GSH and SAM production, and then modelled according to the theory kinetics equations. Through these analyses, we wonder a better optimizing strategy to increase both of the production of GSH and SAM in fermentation.

Genes and GSH and SAM production

We have transferred plasmid pNZ-GMcA to L. lactis, containing gene gshF, metK and cwaA, resulting in improvement of producing GSH and SAM and adhesivity of the strain while using for producing “Smart yoghourt”. As GSH and SAM were the main characteristic of this strain, to get more production of GSH and SAM was important in Smart yoghourt fermentation (Figure 1). Thus, we collected experimental data about cell growth and GSH and SAM production and constructed models to guide fermentation process in producing “Smart yoghourt”.

Figure. 1 The schematic diagram of biosynthesis synthesis of GSH and SAM in L. lactis/pNZ-GMcA.

Experimental data collection

The experimental data were collected as followed:

4ml L. lactis glycerol stock from -80oC were inoculated to 50 ml GM17 medium and grown overnight at 30oC without aeration. Then, the pre-culture were inoculated to 50 ml of GM17 medium with a dilution of 1:100 and grown at 30oC without aeration. OD600 was measured every 2 hours. While OD600 reached 0.4, 50ng/ml nisin were added to the culture to induce the expression of proteins in the plasmid. OD600, GSH and SAM titer were measured every 2 hours.

Theory

Kinetics of Cell Growth

Growth kinetic can be described by a modified logistic model[1-3,5]:

where X is biomass concentration, t time, K empirical equation constant depending on maximum specific growth rate, Xm maximum biomass concentration achievable under the specified conditions, and n inhibition exponent. Xm in Eq. 1 represents the maximum carrying capacity of the system (medium and conditions) for a particular strain and (1-X/Xm) represents the fraction of remaining carrying capacity. The empirical inhibition exponent n is a lumped indicator corresponding to the inhibitive effects of biomass and product accumulation to cell growth. The larger the n value, the more significant the inhibition effects.

Kinetics of Cell Growth

In fermentation processes, product formation associates either with cell growth or with cell maintenance. Formation of products can thus be portrayed by the classic Luedeking–Piret Equation [4,5]:

where X is biomass concentration, t time, α and β are equation coefficients that correspond to growth-associated and non-growth-associated product formation, respectively. Growth-associated product, as indicated by its name, is synthesized in association with cell growth. On the other hand, non-growth-associated product is formed in association with cell maintenance. Accordingly, products accumulated in a fermentation process can be classified into three categories according to the values of α and β as follows:

α > 0 and β = 0, growth-associated product, accumulated as a result of cell growth only;

α = 0 and β > 0, non-growth-associated product, accumulated as a result of cell maintenance only; and

α > 0 and β > 0, mixed-growth-associated product, accumulated as results of both cell growth and cell maintenance.

Modeling

The cell growth (X) model, GSH Formation (P1) model and SAM Formation (P2) model should be integrated into a complete mathematical model:

The Levenberg-Marquardt nonlinear regression algorithm was used to seek the best values of the equation parameters in Eq. 3 that minimize the sum of the squared deviations between the calculated values and the experimental data. The values of those parameters is listed in Table 1. Then the time courses of cell growth (X), GSH Formation (P1) and SAM Formation (P2) were obtained by integration of Eq. 3 using the ode45 solver in MATLAB 2016 as illustrated in Figure 2, and the results were shown in Figures 3, 4 and 5.

Figure. 2 The source program of MATLAB for fitting Eqs. 1 and 2.

Results and discussion

Kinetics of growth of L.lactis/pNZ-GMcA

Figure 3 shows the time courses of cell growth of L. lactis. The experiment was conducted at 30oC. The initial glucose concentration was 10 g/L. As shown in Figure 2, cell growth under those conditions is described using the modified logistic cell growth model with a K value of 0.605/h, maximum biomass concentration of 0.511 g/L, and a power index (n) of 1.29. The exponential phase started after inoculation with about 5 hour’ lag phase and lasted for about 6 h, followed by the deceleration phase. The end of exponential phase might be caused by the inhibition of metabolites such as lactate or low concentration of nutriment.

Figure. 3 Cell growth of L. lactis. Solid lines are best-fit curves of experimental data using corresponding models using Eq. 1. The scatters were samples at different time.

Kinetics of GSH Formation

As shown in Table 1 and Figure 4, GSH formation shows different with all the three categories with a α value of -6.97 and β value of 2.64 GSH per DCW per time (g/g/h). This observation may be attributed to the fact that gene gshF for GSH production was induced by nisin at 7 h, while wild-type L. lactis cannot synthesize GSH. Thus, we supposed GSH formation in L. lactis shows a mixed with induction associated and non-growth–associated product.

Figure. 4 GSH production of L. lactis/pNZ-GMcA. Solid lines are best-fit curves of experimental data using corresponding models using Eq. 2. The scatters were samples at different time.

Kinetics of SAM Formation

As shown in Table 1 and Figure 5, SAM formation shows mixed-growth-associated kinetics with a α value of 1.07 and β value of 0.493 SAM per DCW per time (g/g/h). It is worth noting that the Eq. 2 is good for fitting the SAM production data from 0 to 7 h. While after 7 h, the experimental data were slightly deflected from the fitted curve. We supposed that L. lactis can synthesize little SAM by itself and this might be typical mixed-growth-associated kinetics. Expression of gene metK was induced by nisin at 7 h, and then more SAM were formed, resulting in deflected from the fitted curve.

Figure. 5 SAM production of L. lactis/pNZ-GMcA. Solid lines are best-fit curves of experimental data using corresponding models using Eq. 2. The scatters were samples at different time.

Reference

  1. Messens W, Verluyten J, Leroy F, et al. 2003. Modelling growth and bacteriocin production by Lactobacillus curvatus LTH 1174 in response to temperature and pH values used for European sausage fermentation processes. Int J Food Microbiol. 81(1):41-52.
  2. Pirt SJ. 1965. The maintenance energy of bacteria in growing cultures. Proc R Soc Lond B 163:224–231.
  3. Shuler ML, Kargi F. 2001. Bioprocess engineering: basic concepts, 2nd edn. Manufactured: Prentice Hall.
  4. Luedeking R, Piret EL. 1959. A kinetic study of the lactic acid fermentation. Batch process at controlled pH. J Biochem Microbiol Technol Eng. 1:393–421.
  5. Lan C Q, Oddone G, Mills D A, et al. 2010. Kinetics of Lactococcus lactis growth and metabolite formation under aerobic and anaerobic conditions in the presence or absence of hemin. Biotechnol Bioeng. 95(6):1070-1080.