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alt='Growth curve of Chlorella vulgaris' | alt='Growth curve of Chlorella vulgaris' | ||
style='width:65%'> | style='width:65%'> | ||
− | <p style='font-size:20px'>fig.1 Growth curve of <i>Chlorella vulgaris</i></p> | + | <p style='font-size:20px'>fig.1-1 Growth curve of <i>Chlorella vulgaris</i></p> |
</center> | </center> | ||
<p></p> | <p></p> | ||
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alt='Growth rate of Chlorella vulgaris' | alt='Growth rate of Chlorella vulgaris' | ||
style='width:65%'> | style='width:65%'> | ||
− | <p style='font-size:20px'>fig.2 Growth rate of <i>Chlorella vulgaris</i></p> | + | <p style='font-size:20px'>fig.1-2 Growth rate of <i>Chlorella vulgaris</i></p> |
</center> | </center> | ||
<p></p> | <p></p> | ||
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<h6 style='color:#bc0101; font-family:"Roboto Mono", monospace;'> | <h6 style='color:#bc0101; font-family:"Roboto Mono", monospace;'> | ||
− | + | dP/dt=*dX/dt+*X; | |
<br> | <br> | ||
<br>dN/dt=-V*X; | <br>dN/dt=-V*X; | ||
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<blockquote> | <blockquote> | ||
<p style='color:#702828;font-size:16px; font-family:"Roboto Mono", monospace;'> | <p style='color:#702828;font-size:16px; font-family:"Roboto Mono", monospace;'> | ||
− | + | P: lipid | |
<br>N: nitrogen | <br>N: nitrogen | ||
<br>X: biomass | <br>X: biomass | ||
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alt='Oil accumulation and nirogen source consumption at normal situation' | alt='Oil accumulation and nirogen source consumption at normal situation' | ||
style='width:90%'> | style='width:90%'> | ||
− | <p style='font-size:20px'>fig. | + | <p style='font-size:20px'>fig.2 Oil accumulation and nirogen source consumption at normal situation</p> |
</center> | </center> | ||
<p></p> | <p></p> | ||
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<h6 style='color:#bc0101; font-family:"Roboto Mono", monospace;'> | <h6 style='color:#bc0101; font-family:"Roboto Mono", monospace;'> | ||
− | + | n2=exp((A+C*exp(-exp(-B(t-M))))*(t2-t1))*n1; | |
<br> | <br> | ||
<br>x2=x1+(n2-n1)*((k(ln(b(ns+a))^-1))-e); | <br>x2=x1+(n2-n1)*((k(ln(b(ns+a))^-1))-e); | ||
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<blockquote> | <blockquote> | ||
<p style='color:#702828;font-size:16px; font-family:"Roboto Mono", monospace;'> | <p style='color:#702828;font-size:16px; font-family:"Roboto Mono", monospace;'> | ||
− | + | n1: biomass at frist state | |
<br>n2: biomass at secind state | <br>n2: biomass at secind state | ||
<br>x: biomass concentration(g/l) | <br>x: biomass concentration(g/l) | ||
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<p></p> | <p></p> | ||
<center> | <center> | ||
− | <img src='' | + | <img src='https://static.igem.org/mediawiki/2017/e/e1/T--NYMU-Taipei--model_biomass.gif' |
alt='Biomass in different nitrogen concentration' | alt='Biomass in different nitrogen concentration' | ||
style='width:90%'> | style='width:90%'> | ||
− | <p style='font-size:20px'>fig. | + | <p style='font-size:20px'>fig.3 Biomass in different nitrogen concentration</p> |
</center> | </center> | ||
<p></p> | <p></p> | ||
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<blockquote> | <blockquote> | ||
<p style='color:#702828;font-size:16px; font-family:"Roboto Mono", monospace;'> | <p style='color:#702828;font-size:16px; font-family:"Roboto Mono", monospace;'> | ||
− | + | n: nitrogen concentration | |
<br>Yxn: nitrate coefficient g/g 0.21016 | <br>Yxn: nitrate coefficient g/g 0.21016 | ||
<br>m: maintenance parameter hr^-1 0.0014393 | <br>m: maintenance parameter hr^-1 0.0014393 | ||
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<p></p> | <p></p> | ||
<center> | <center> | ||
− | <img src='' | + | <img src='https://static.igem.org/mediawiki/2017/5/5b/T--NYMU-Taipei--model_ns_nitrogen.gif' |
alt='Nitrogen source in nitrogen starvation' | alt='Nitrogen source in nitrogen starvation' | ||
style='width:90%'> | style='width:90%'> | ||
− | <p style='font-size:20px'>fig. | + | <p style='font-size:20px'>fig.4 Nitrogen source in nitrogen starvation</p> |
</center> | </center> | ||
<p></p> | <p></p> | ||
− | <!-- | + | <!-- Oil accumulation in nitrogen starvation --> |
<h3></h3> | <h3></h3> | ||
− | <h3> | + | <h3>Oil accumulation in nitrogen starvation</h3> |
− | <p> | + | <p>We predict total lipid increase under nitrogen starvation. The model provide theoretical information of top yield. This graph show that if we use symbiotic microbe isolating nitrogen source temporarily and successfully, the productivity will be enhanced. |
</p> | </p> | ||
<h6 style='color:#bc0101; font-family:"Roboto Mono", monospace;'> | <h6 style='color:#bc0101; font-family:"Roboto Mono", monospace;'> | ||
− | + | dp/dt=k1(dx/dt)^2+k2(dx/dt)(x)+e | |
− | + | ||
− | + | ||
</h6> | </h6> | ||
<blockquote> | <blockquote> | ||
<p style='color:#702828;font-size:16px; font-family:"Roboto Mono", monospace;'> | <p style='color:#702828;font-size:16px; font-family:"Roboto Mono", monospace;'> | ||
− | + | p: lipid concentrtion | |
− | + | <br>K1: growth correlation coefficient g^2/g^2 //122.40085 | |
− | + | <br>K2: non-growth correlation coefficient g^-1 //0.28736 | |
− | + | <br>e: a perturbation g/l*hr //-0.078 | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | <br> | + | |
− | <br> | + | |
− | <br> | + | |
</p> | </p> | ||
</blockquote> | </blockquote> | ||
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<p></p> | <p></p> | ||
<center> | <center> | ||
− | <img src='' | + | <img src='https://static.igem.org/mediawiki/2017/e/e8/T--NYMU-Taipei--model_ns_oil.gif' |
− | alt='' | + | alt='Oil accumulation in nitrogen starvation' |
style='width:90%'> | style='width:90%'> | ||
− | <p style='font-size:20px'>fig.5 </p> | + | <p style='font-size:20px'>fig.5 Oil accumulation in nitrogen starvation</p> |
</center> | </center> | ||
<p></p> | <p></p> | ||
− | <!-- | + | <!-- Population of co-cultured Chlorella and modified E.coli --> |
<h3></h3> | <h3></h3> | ||
− | <h3> | + | <h3>Population of co-cultured Chlorella and modified E.coli</h3> |
− | <p> | + | <p>According to our reference experiment data, we find that e.coli can build a relationship with chlorella like symbiosis. So we build a model and use 3 kinds of situations’ value to simulate their change when they are co-cultured. According to it,we get the proper experimental proportion of them at each need. |
</p> | </p> | ||
<h6 style='color:#bc0101; font-family:"Roboto Mono", monospace;'> | <h6 style='color:#bc0101; font-family:"Roboto Mono", monospace;'> | ||
+ | x2=(ax-x^2/(1+b*x*z))/Rx+x/Yx | ||
<br> | <br> | ||
− | <br> | + | <br>z2=(cz-z^2/(1+g*z*x))/Rz+z/Yz |
− | + | ||
</h6> | </h6> | ||
<blockquote> | <blockquote> | ||
<p style='color:#702828;font-size:16px; font-family:"Roboto Mono", monospace;'> | <p style='color:#702828;font-size:16px; font-family:"Roboto Mono", monospace;'> | ||
− | + | X: chlorella vugaris | |
− | + | <br>Z: e.coil | |
− | + | <br>Rx: symbiosis coefficient g/hr //1.0000023 | |
− | + | <br>Rz: symbiosis coefficient g/hr //1.178 | |
− | + | <br>Yx: correlation coefficient//12.576 | |
− | <br> | + | <br>Yz: correlation coefficient//2.276 |
− | <br> | + | <br>a: population constant //0.80467 |
− | <br> | + | <br>c: population constant//0.61198 |
− | <br> | + | <br>b: relative parameter //0.00027 |
− | <br> | + | <br>g: relative parameter //0.0013 |
− | <br> | + | |
− | <br> | + | |
− | <br> | + | |
− | <br> | + | |
</p> | </p> | ||
</blockquote> | </blockquote> | ||
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<p></p> | <p></p> | ||
<center> | <center> | ||
− | <img src='' | + | <img src='https://static.igem.org/mediawiki/2017/a/a5/T--NYMU-Taipei--model_population1.gif' |
− | alt='' | + | alt='Population of co-cultured Chlorella and modified E.coli' |
style='width:90%'> | style='width:90%'> | ||
− | <p style='font-size:20px'>fig.5 </p> | + | <p style='font-size:20px'>fig.5-1 Population of co-cultured Chlorella and modified E.coli</p> |
+ | </center> | ||
+ | <p></p> | ||
+ | |||
+ | <center> | ||
+ | <img src='https://static.igem.org/mediawiki/2017/e/eb/T--NYMU-Taipei--model_population2.gif' | ||
+ | alt='Population of co-cultured Chlorella and modified E.coli' | ||
+ | style='width:90%'> | ||
+ | <p style='font-size:20px'>fig.5-2 Population of co-cultured Chlorella and modified E.coli</p> | ||
+ | </center> | ||
+ | <p></p> | ||
+ | |||
+ | <center> | ||
+ | <img src='https://static.igem.org/mediawiki/2017/b/b0/T--NYMU-Taipei--model_populaiton3.gif' | ||
+ | alt='Population of co-cultured Chlorella and modified E.coli' | ||
+ | style='width:90%'> | ||
+ | <p style='font-size:20px'>fig.5-3 Population of co-cultured Chlorella and modified E.coli</p> | ||
</center> | </center> | ||
<p></p> | <p></p> | ||
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<blockquote> | <blockquote> | ||
<p style='color:#702828;font-size:16px; font-family:"Roboto Mono", monospace;'> | <p style='color:#702828;font-size:16px; font-family:"Roboto Mono", monospace;'> | ||
− | + | ||
<br> | <br> | ||
<br> | <br> | ||
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<blockquote> | <blockquote> | ||
<p style='color:#702828;font-size:16px; font-family:"Roboto Mono", monospace;'> | <p style='color:#702828;font-size:16px; font-family:"Roboto Mono", monospace;'> | ||
− | + | ||
<br> | <br> | ||
<br> | <br> |
Revision as of 12:43, 25 September 2017
Modeling
Growth curve of Chlorella vulgaris
The timing of adding engineering E.coli or purified protein to Chlorella vulgaris culture is critical for our project. Through the initial, final biomass concentration data, the instantaneous rate of a reference time and other lab environment datas, we simulate the change in biomass concentration throughout the culture cycle. The status information in the culture medium at each point is then obtained through the other calculus to obtain the best timing point and the corresponding state.
ln(Xt/X0)/t=A+Bexp(-C(t-M))=μ(specific growth rate)
X: biomass concentration(g/l)
t: time(hr)
A: the asymptotic of ln Xt/Xo as t decrese indefinitely
B: the asymptotic of ln Xt/Xo as t increase indefinitely
C: the relative growth rate at time M
fig.1-1 Growth curve of Chlorella vulgaris
fig.1-2 Growth rate of Chlorella vulgaris
Oil accumulation & Nirogen source consumption
Simulating common system of oil accumulation and nitrogen source consumption, not only get the reference of state before the improvement as well as the stage information, but also as a basic equation after some parameters or organisms join into the system.
dP/dt=*dX/dt+*X;
dN/dt=-V*X;
V=((qM-Q)/(qM-q))*((Vm*N)/(N+Vh));
Q=(X0*Q0+N0-N)/X;
P: lipid
N: nitrogen
X: biomass
α: the instantaneous yield coefficient of product formation due to cell growth
β: the specific formation rate of product
q: Minimum N quota
qM: Maximum N quota
Q: N quota
Vm: Maximum uptake rate of nitrogen
Vh: Half-saturation coefficient
fig.2 Oil accumulation and nirogen source consumption at normal situation
Biomass in different nitrogen concentration
To find the optimal amount of nitrogen removal, we model biomass decrease in different nitrogen concentration environments, and then we can find the best productivity.
n2=exp((A+C*exp(-exp(-B(t-M))))*(t2-t1))*n1;
x2=x1+(n2-n1)*((k(ln(b(ns+a))^-1))-e);
n1: biomass at frist state
n2: biomass at secind state
x: biomass concentration(g/l)
t: time(hr)
A: the asymptotic of ln Xt/Xo as t decrese indefinitely //-39.9532
B: the asymptotic of ln Xt/Xo as t increase indefinitely //-0.0222
C: the relative growth rate at time M hr //45.6931
k: constant //8.15229
b:yield coefficient//1207.569
ns:initial nitrogen concentration
a:regression constant//0.01
e:a perturbation//0.50678
fig.3 Biomass in different nitrogen concentration
Nitrogen concentration in nitrogen starvation
Put normal and modified nitrogen source system together,see their demonstration, like speed and occasion.by constructing this model,we can find out the declining rate of each state,then adjust experiment.
dn/dt=Yxn*dx/dt+m*x
n: nitrogen concentration
Yxn: nitrate coefficient g/g 0.21016
m: maintenance parameter hr^-1 0.0014393
x: biomass concentration
fig.4 Nitrogen source in nitrogen starvation
Oil accumulation in nitrogen starvation
We predict total lipid increase under nitrogen starvation. The model provide theoretical information of top yield. This graph show that if we use symbiotic microbe isolating nitrogen source temporarily and successfully, the productivity will be enhanced.
dp/dt=k1(dx/dt)^2+k2(dx/dt)(x)+e
p: lipid concentrtion
K1: growth correlation coefficient g^2/g^2 //122.40085
K2: non-growth correlation coefficient g^-1 //0.28736
e: a perturbation g/l*hr //-0.078
fig.5 Oil accumulation in nitrogen starvation
Population of co-cultured Chlorella and modified E.coli
According to our reference experiment data, we find that e.coli can build a relationship with chlorella like symbiosis. So we build a model and use 3 kinds of situations’ value to simulate their change when they are co-cultured. According to it,we get the proper experimental proportion of them at each need.
x2=(ax-x^2/(1+b*x*z))/Rx+x/Yx
z2=(cz-z^2/(1+g*z*x))/Rz+z/Yz
X: chlorella vugaris
Z: e.coil
Rx: symbiosis coefficient g/hr //1.0000023
Rz: symbiosis coefficient g/hr //1.178
Yx: correlation coefficient//12.576
Yz: correlation coefficient//2.276
a: population constant //0.80467
c: population constant//0.61198
b: relative parameter //0.00027
g: relative parameter //0.0013
fig.5-1 Population of co-cultured Chlorella and modified E.coli
fig.5-2 Population of co-cultured Chlorella and modified E.coli
fig.5-3 Population of co-cultured Chlorella and modified E.coli
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fig.5
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fig.5