Team:NTU Taiwan/index.html

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             <legend><b>Neither Hsp nor constitutive promoter suits our purpose under this circuit structure.</b></legend>
             <legend><b>Neither Hsp nor constitutive promoter suits our purpose under this circuit structure.</b></legend>
             <p>
             <p>
-
                 為了實際了解Hsp或cons在circuit中扮演的功能，我們利用求解穩定態的方式來分析GFP在被Hsp 或cons驅動的repressor調控下，會 與單純由Csp所驅動表現會有什麼差異，進而借此了解是否能透過迴圈設計來達到一個形同改變csp靈敏度的效應。在結果分析上，我們選用GFP maximal conc和T 1/2 GFP max作為評估CSP靈敏度的指標，由於GFP max越大，表示csp在低溫時的訊號越能被我們所觀察到；另一方面，T 1/2 GFP max越低時，代表csp對溫度敏感的範圍變得更小更靈敏。結果顯示，在cons的model中，兩個指標不僅沒有改善的狀況，反而在aR變小時，大幅壓制Csp的活性。另外在Hsp model中，由於Hsp所能表現的溫度範圍和Csp無法重疊，因此如我們上一節所推測的，Hsp完全無法壓低GFP的表現。
+
                 To better understand the role of Hsp and constitutive promoter in our circuit, we analyze the expression pattern difference between repressor-regulated-Csp and Csp alone. By an steady state approach, we may validate if our genetic circuit is in effect changing the sensitivity of Csp. In order to define "markers" that help us discriminate between "bad" results and "good" results, "GFP maximal concentration" (abbreviated as <b>GFP<sub>max</sub></b>) and "temperature corresponding to half of the maximal concentration of GFP" (abbreviated as T1/2) as taken into consideration (Fig. 4). As the value of GFPmax goes up, we are more able to observe the signal under low temperatures; as T1/2 goes down, the temperature-responsive range of Csp narrows down which implies more <b>sensitive</b>. However, in our constitutive promoter model, the two markers do not become "better". The repressor suppresses the activity of Csp significantly when αR becomes small (Fig. 5). Likewise, the markers of Hsp model are "bad" too. Since the active ranges of Csp and Hsp are not overlapping, expression of GFP cannot be suppressed at all as predicted in the last paragraph (Fig. 6). We are going to solve this problem using another genetic circuit!
             </p>
             </p>
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             <img class="tipReveal" src="images/modeling/modelresult1.jpg">
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            <img class="img-responsive" src="images/modeling/modeling3.jpg">
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             <img class="tipReveal img-responsive" src="images/modeling/modelresult1.jpg">
             <div class="tip"> Fig. 4: Expression pattern of GFP under various αA and αR－ a constitutive promoter integrated model. The X, Y axis are values of αA and αR scanned. The Z axis is the maximal GFP concentration. The color bar represents the temperature corresponding to half of the maximal GFP concentration</div>
             <div class="tip"> Fig. 4: Expression pattern of GFP under various αA and αR－ a constitutive promoter integrated model. The X, Y axis are values of αA and αR scanned. The Z axis is the maximal GFP concentration. The color bar represents the temperature corresponding to half of the maximal GFP concentration</div>
 +
            <img class="tipReveal img-responsive" src="images/modeling/modelresult2.jpg">
 +
            <div class="tip"> Fig. 5: Expression pattern of GFP under various αA and αR－ an Hsp integrated model. The X, Y axis are values of αA and αR scanned. The Z axis is the maximal GFP concentration. The color bar represents the temperature corresponding to half of the maximal GFP concentration</div>
 +
        </div> 
 +
 +
        <section class="brown-background">
 +
            <h1 class="header">Code</h1>
 +
        </section>
 +
        <div class="container essay divide">
 +
            <legend><b>consModel</b></legend>
 +
            <pre>slopeHsp = 1.75;
 +
slopeCsp = 1.25;
 +
n = 2;
 +
gamma_A = 1e-2;
 +
gamma_GFP = 8.2e-3;
 +
gamma_R = 1e-2;
 +
ten = 10;
 +
beta_A = 200*1e-6;
 +
 +
[lnalpha_A, lnalpha_R, temperature] = meshgrid((-12:0.2:-3), (-12:0.2:-3), (0:0.01:40));
 +
beta_Csp = 1e-6 ./ (1.0+exp(slopeCsp*(temperature-15)));
 +
beta_Cons = 1e-6;
 +
Ass = beta_Csp./gamma_A;
 +
Rss = beta_Cons./gamma_R;
 +
GFP = (beta_Csp.*(1 + beta_A*(Ass.^n./(Ass.^n+(ten.^lnalpha_A).^n)))) .* ((ten.^lnalpha_R).^n./((ten.^lnalpha_R).^n+Rss.^n)) ./ gamma_GFP;
 +
maxGFP = max(GFP, [], 3);
 +
lnGFP_MAX = log10(maxGFP);
 +
GFP_half_temp = zeros(46, 46);
 +
for i = 1:46
 +
    for j = 1:46
 +
        value = 0;
 +
        temp = 0;
 +
        for t = 2:4000
 +
            if (GFP(i, j, t)-GFP(i, j, t-1)) < value
 +
                value = GFP(i, j, t)-GFP(i, j, t-1);
 +
                temp = t-1;
 +
            end
 +
        end
 +
        GFP_half_temp(i,j) = temp;
 +
    end
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end
 +
GFP_half_temp = GFP_half_temp./100;
 +
[x, y] = meshgrid([-12:0.2:-3]);
 +
surf(x,y,lnGFP_MAX,GFP_half_temp);
 +
h = colorbar;
 +
ylabel(h, 'degree Celsius');
 +
xlabel('alphaA (power of 10)');
 +
ylabel('alphaR (power of 10)');
 +
zlabel('GFP [] (power of 10)');
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axis([-Inf Inf -Inf Inf -20 -2 10 20]);
 +
saveas(h, 'cons', 'jpg');</pre>
 +
            <legend><b>hspModel</b></legend>
 +
            <pre>
 +
slopeHsp = 1.75;
 +
slopeCsp = 1.25;
 +
n = 2;
 +
gamma_A = 1e-2;
 +
gamma_GFP = 8.2e-3;
 +
gamma_R = 1e-2;
 +
ten = 10;
 +
beta_A = 200*1e-6;
 +
 +
[lnalpha_A, lnalpha_R, temperature] = meshgrid((-12:0.2:-3), (-12:0.2:-3), (0:0.01:40));
 +
beta_Csp = 1e-6 ./ (1.0+exp(slopeCsp*(temperature-15)));
 +
beta_Hsp = 1e-6 ./ (1.0+exp(-slopeHsp*(temperature-33.5)));
 +
Ass = beta_Csp./gamma_A;
 +
Rss = beta_Hsp./gamma_R;
 +
GFP = (beta_Csp.*(1 + beta_A*(Ass.^n./(Ass.^n+(ten.^lnalpha_A).^n)))) .* ((ten.^lnalpha_R).^n./((ten.^lnalpha_R).^n+Rss.^n)) ./ gamma_GFP;
 +
maxGFP = max(GFP, [], 3);
 +
lnGFP_MAX = log10(maxGFP);
 +
GFP_half_temp = zeros(46, 46);
 +
for i = 1:46
 +
    for j = 1:46
 +
        value = 0;
 +
        temp = 0;
 +
        for t = 2:4000
 +
            if (GFP(i, j, t)-GFP(i, j, t-1)) < value
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                value = GFP(i, j, t)-GFP(i, j, t-1);
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                temp = t-1;
 +
            end
 +
        end
 +
        GFP_half_temp(i,j) = temp;
 +
    end
 +
end
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GFP_half_temp = GFP_half_temp./100;
 +
[x, y] = meshgrid([-12:0.2:-3]);
 +
surf(x,y,lnGFP_MAX,GFP_half_temp);
 +
h = colorbar;
 +
ylabel(h, 'degree Celsius');
 +
xlabel('alphaA (power of 10)');
 +
ylabel('alphaR (power of 10)');
 +
zlabel('GFP [] (power of 10)');
 +
axis([-Inf Inf -Inf Inf -20 -2 10 20]);
 +
saveas(h, 'latest', 'jpg');</pre>
         </div>   
         </div>   
     </script>
     </script>

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