Difference between revisions of "Team:Vilnius-Lithuania/InterLab"

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                     <h1>Trumpas title, per dvi eilutes</h1>
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                     <h1>InterLab Study</h1>
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                    <div class="category">Students</div>
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                     <p>The aim of this year’s InterLab study was to establish a GFP measurement protocol based on engineering principles that anyone with a plate reader could use in their lab.</p>
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                     <p>This is even more likely to occur when the plasmid copy number is low. When the cell divides, lower
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                        copy plasmids tend to be lost in next generations.</p>
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                    <h1>Trumpas title, per dvi eilutes</h1>
 
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                    <div class="category">Students</div>
 
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                    <p>This is even more likely to occur when the plasmid copy number is low. When the cell divides, lower
 
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                        copy plasmids tend to be lost in next generations.</p>
 
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                    <div class="readmore" data-modal="2">read more</div>
 
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                    <h1>Trumpas title, per dvi eilutes</h1>
 
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                    <div class="category">Students</div>
 
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                    <p>This is even more likely to occur when the plasmid copy number is low. When the cell divides, lower
 
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                        copy plasmids tend to be lost in next generations.</p>
 
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                    <div class="category">Students</div>
 
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                    <p>This is even more likely to occur when the plasmid copy number is low. When the cell divides, lower
 
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                        copy plasmids tend to be lost in next generations.</p>
 
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                    <div class="readmore" data-modal="4">read more</div>
 
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                    <h1>Trumpas title, per dvi eilutes</h1>
 
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                    <div class="category">Students</div>
 
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                    <p>This is even more likely to occur when the plasmid copy number is low. When the cell divides, lower
 
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                        copy plasmids tend to be lost in next generations.</p>
 
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                    <div class="readmore" data-modal="5">read more</div>
 
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                    <h1>Trumpas title, per dvi eilutes</h1>
 
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                    <div class="category">Students</div>
 
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                    <p>This is even more likely to occur when the plasmid copy number is low. When the cell divides, lower
 
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                        copy plasmids tend to be lost in next generations.</p>
 
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                    <div class="readmore" data-modal="6">read more</div>
 
 
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         <h1>Trumpas title, per dvi eilutes</h1>
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         <h1>InterLab Study</h1>
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         <h5>Izangos teksto stilius. Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor
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         <h5>The aim of this year’s InterLab study was to establish a GFP measurement protocol based on engineering principles that anyone with a plate reader could use in their lab.</h5>
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<p>
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This study was an interesting and valuable experience that prompted the team to use new equipment which would not have been used in establishing our personal project alone.
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</p>
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<p>
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In the beginning, the preparation of competent cells and their transformation according to the protocol seemed to go well but after the required incubation time, no colonies were grown, which lead to another attempt. With greater precision and care, the transformations succeeded. After the transformations we followed the plate reader protocol supplied by the iGEM HQ using LB broth as the growth medium. Afterwards, we generated a FITC standard curve to calibrate the plate reader and then measured both the fluorescence and absorbance of our samples in 2-hour intervals over a 6-hour period.
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</p>
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<h2>Results and observations</h2>
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        <h2>H2 title</h2>
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         <div class="img-cont">
 
         <div class="img-cont">
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             <img src="http://placehold.it/800x450" alt="img">
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             <img src="https://static.igem.org/mediawiki/2017/c/c1/T--Vilnius-Lithuania--InterlabChar1.png" alt="img">
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             <div class="img-label">Foto aprasymas it anim id est laborum. Sed ut perspiciatis unde omnis iste natus error
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             <div class="img-label"><h6>Figure 1. A standard curve generated by measuring the flourescence of serial dilution of FITC stock (uM). There is a somewhat polynomial trenf for the increase of flourescence as [FITC] increase.</h6>
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             </div>
 
             </div>
 
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        <h2>H2 title</h2>
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<div class="img-cont">
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             pellentesque erat. Curabitur fringilla ipsum id sapien imperdiet sagittis. Nulla vestibulum arcu neque, et
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             <img src="https://static.igem.org/mediawiki/2017/f/fc/T--Vilnius-Lithuania--InterlabChar2.png" alt="img">
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             iaculis lorem vulputate interdum. Nunc accumsan velit ligula, ac euismod felis sagittis quis. Aenean varius
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             <div class="img-label"><h6>Figure 2. A standard curve generated by measuring the flourescence of serial dilutions of FITC stock (uM) displayed in a log scale to demonstrate a linear relationship.</h6>
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             </div>
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         <ul>
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         </div>
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            <li>List item</li>
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            <li>List item</li>
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<ul>
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            <li>List item</li>
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<li><p>The <i>standard</i> curve slopes showed a somewhat polynomial shape (Figure 1), although they were supposed to have a 1:1 slope. This could have been due to a consistent pipetting error. The straight-line log graph without a 1:1 slope could justify this hypothesis (Figure 2). Furthermore, the detector could have been oversaturated, because low concentrations were linear, but at high concentrations it either saturated or fell.</p></li>
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            <li>List item</li>
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<li><p>Based on the part description data from the official iGEM wiki InterLab and part sections: the first three test devices labelled (TD1; TD2; TD3) accordingly differ in their promoter strength with the first one being the strongest, as do the 4th 5th and 6th devices, following the same pattern with the same promoter variability. However, the final three differ in their RBS strength. The first three devices have the B0034 RBS, while the final three have the J364100 RBS. Lastly, the positive control (PC) also contains another version of the RBS labelled B0032.</p></li>
−
        </ul>
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<li><p>The positive and negative controls did not vary in any significant manner (Figure 3), indicating a methodical error, because the positive control should have shown the largest level of fluorescence due to the strongest RBS and a relatively strong promoter, based on the iGEM wiki data.</p></li>
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        <div class="plotly">
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trace521 = {
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  y: ['TD 6 Col 1 Rep 1', '0.019', '0.127', '0.653', '0.874'],
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  mode: 'lines',
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trace531 = {
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  xsrc: 'KarolisP:4:4ce7e5',
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  ysrc: 'KarolisP:4:132cde'
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trace551 = {
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  x: ['', '0', '2', '4', '6'],
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  y: ['TD 6 Col 1 Rep 4', '0.019', '0.128', '0.652', '0.874'],
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trace561 = {
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  x: ['', '0', '2', '4', '6'],
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  y: ['TD 6 Col 2 Rep 1', '0.018', '0.212', '0.653', '0.894'],
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  mode: 'lines',
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  uid: '84b6e3',
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  xsrc: 'KarolisP:4:4ce7e5',
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  ysrc: 'KarolisP:4:416158'
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};
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trace571 = {
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  x: ['', '0', '2', '4', '6'],
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  y: ['TD 6 Col 2 Rep 2', '0.018', '0.214', '0.651', '0.895'],
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  uid: 'ed4a84',
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  xsrc: 'KarolisP:4:4ce7e5',
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  ysrc: 'KarolisP:4:64fa38'
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};
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trace581 = {
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  x: ['', '0', '2', '4', '6'],
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  y: ['TD 6 Col 2 Rep 3', '0.019', '0.212', '0.655', '0.894'],
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  mode: 'lines',
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  name: 'TD 6 Col 2 Rep 3',
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  type: 'scatter',
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  uid: '03ae17',
 +
  xsrc: 'KarolisP:4:4ce7e5',
 +
  ysrc: 'KarolisP:4:b27681'
 +
};
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trace591 = {
 +
  x: ['', '0', '2', '4', '6'],
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  y: ['TD 6 Col 2 Rep 4', '0.018', '0.213', '0.653', '0.894'],
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  mode: 'lines',
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  uid: 'f889c0',
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  xsrc: 'KarolisP:4:4ce7e5',
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  ysrc: 'KarolisP:4:4b2b68'
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};
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data2 = [trace011, trace021, trace031, trace041, trace051, trace061, trace071, trace81, trace91, trace101, trace111, trace121, trace131, trace141, trace151, trace161, trace171, trace181, trace191, trace201, trace211, trace221, trace231, trace241, trace251, trace261, trace271, trace281, trace291, trace301, trace311, trace321, trace331, trace341, trace351, trace361, trace371, trace381, trace391, trace401, trace411, trace421, trace431, trace441, trace451, trace461, trace471, trace481, trace491, trace501, trace511, trace521, trace531, trace541, trace551, trace561, trace571, trace581, trace591];
 +
layout2 = {
 +
  autosize: true,
 +
  hovermode: 'closest',
 +
  showlegend: true,  
 
   xaxis: {
 
   xaxis: {
 
     autorange: true,  
 
     autorange: true,  
−
     range: [-0.5, 4.5],  
+
     range: [0, 6],  
−
     showspikes: true,  
+
     showspikes: false,  
−
     title: '',  
+
     title: 'Time (h)',  
−
     type: 'category'
+
     type: 'linear'
 
   },  
 
   },  
 
   yaxis: {
 
   yaxis: {
 
     autorange: true,  
 
     autorange: true,  
−
     range: [0, 188.042105263],  
+
     range: [-0.0374444444444, 1.05144444444],  
−
     showspikes: true,  
+
     showspikes: false,  
−
     title: 'Plasmid copy number (PCN)',  
+
     title: 'Abs600 (Au)',  
 
     type: 'linear'
 
     type: 'linear'
 
   }
 
   }
 
};
 
};
 
window.onload = function(e){
 
window.onload = function(e){
−
laurynaskarpus = document.getElementById('laurynaskarpus');
+
plot1 = document.getElementById('plot1');
−
Plotly.plot(laurynaskarpus, {
+
plot2 = document.getElementById('plot2');
 +
Plotly.plot(plot1, {
 
   data: data,
 
   data: data,
 
   layout: layout
 
   layout: layout
 +
});
 +
Plotly.newPlot(plot2, {
 +
  data: data2,
 +
  layout: layout2
 
});
 
});
 
}
 
}
 
</script>
 
</script>
 
  </div>
 
  </div>
−
            <div id="laurynaskarpus" style="width:100%;height:auto;"></div>
+
−
     
+
<div id="plot1" style="width:100%;height:auto;">
−
        <p>Phasellus et maximus purus, sit amet mollis neque. Maecenas finibus nec magna sit amet auctor. Ut sed sapien
+
<div class="img-label"><h6>Figure 3. The flourescence of the six test devices both positive and negative controls over 2 colonies were transformed into E. Coli and inoculated in LB broth was measured every second hour for a 6-hour period. There is a sharp increase of flourescence after 4th hour indicating cell maturity for most of the samples</h6>
−
            quis quam auctor dictum. In sit amet eros fermentum, scelerisque lorem sit amet, aliquet est. Integer vitae
+
             </div>.
−
            eros quis velit hendrerit tempor. Aliquam odio nibh, vulputate id gravida vitae, pulvinar commodo urna.
+
</div>
−
            Suspendisse potenti. Duis tristique molestie elementum. Donec risus mi, condimentum nec justo id, tempus
+
−
            pretium sem. Donec quis sodales mauris. Maecenas sit amet felis sit amet quam commodo semper sed vel libero.
+
<ul>
−
            Phasellus euismod faucibus sapien nec tempus. Aenean pulvinar sagittis turpis, non rutrum nibh vulputate
+
<li><p>The first three test devices follow the predicted trend (Figure 3). Since the RBS does not differ and the variability is in the promoter regions, the strongest promoter was given to TD 1, which showed the overall strongest fluorescence over the course of 6 hours. The 2nd and 3rd test devices followed a decreasing trend in fluorescence. Furthermore, when comparing the values of TD1 and TD4, which both have the same promoter strength, but differ in RBS sequence, we showed that the B0034 RBS was significantly stronger than the J364100, indicated by the 6th hour values for TD1 ranging from 3900 to 5020 (Au) between both colonies and the values for TD4 ranging only from 1105 to 1397 (Au).</p></li>
−
            cursus. Phasellus suscipit enim at tincidunt vehicula. Nam imperdiet, magna id fringilla elementum, sem ex
+
</ul>
−
            finibus sapien, at mollis eros ante id massa.</p>
+
−
        <div class="accordeon">
+
<div id="plot2">
−
            <div class="acc-line">
+
<div class="img-label"><h6>Figure 4. The absorbance of the six test devices and both positive and negative controls for 2 colonies inoculated in LB broth was measured every 2 hours for a 6-hour period. the overall trend of an increase over time persists in all samples for both colonies.</h6>
−
                <div class="acc-head">Lorem ipsum dolor sit amet, consectetur</div>
+
</div>
−
                <div class="acc-body">
+
</div>
−
                    <h2>H2 title</h2>
+
−
                    <p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Curabitur non urna pharetra, rutrum nibh vitae,
+
<ul>
−
                        pellentesque erat. Curabitur fringilla ipsum id sapien imperdiet sagittis. Nulla vestibulum arcu neque, et
+
<li><p>By analyzing the Abs600 absorbance values (Figure 4) we should expect a somewhat opposite trend. The negative control shows the highest values of absorbance since there are no genes coding for the GFP protein and the metabolic load is the smallest, when comparing to all the other devices, hence the highest overall absorbance. The devices containing the strongest RBS and promoter sequences should display the lowest levels of absorbance as the cells commit a vast amount of resources to the synthesis of the GFP protein, hence an overall smaller population size and rate of growth. This is displayed in our data as the test devices such as TD6 and TD5 show some of the highest values for absorbance, and the test devices with the strongest RBS and promoter sequences such as TD4 and TD1 present the smallest values. However, the results seem to slightly disagree with this prediction as the TD4 shows the lowest absorption values and the TD1 appears slightly above. A possible explanation for this could be that during the preparation of the samples and the growth phases, environmental effects could have played a role in the differentiation of the data after hour 2 during the exponential phase.</p></li>
−
                        iaculis lorem vulputate interdum. Nunc accumsan velit ligula, ac euismod felis sagittis quis. Aenean varius
+
</ul>
−
                        mollis aliquet. Nam sodales malesuada porttitor. In sed magna sed neque hendrerit ultrices.</p>
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                    <ol>
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                        <li>Ordered list item</li>
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                        <li>Ordered list item</li>
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                        <li>Ordered list item</li>
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                        <li>Ordered list item</li>
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            <div class="acc-line">
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                <div class="acc-head">Lorem ipsum dolor sit amet, consectetur</div>
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                <div class="acc-body">
+
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                    <h2>H2 title</h2>
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                    <p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Curabitur non urna pharetra, rutrum nibh vitae,
+
−
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                        mollis aliquet. Nam sodales malesuada porttitor. In sed magna sed neque hendrerit ultrices.</p>
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                    <ol>
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                        <li>Ordered list item</li>
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                        <li>Ordered list item</li>
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                        <li>Ordered list item</li>
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                        <li>Ordered list item</li>
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            <div class="acc-line">
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                <div class="acc-head">Lorem ipsum dolor sit amet, consectetur</div>
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                <div class="acc-body">
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                    <h2>H2 title</h2>
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                    <p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Curabitur non urna pharetra, rutrum nibh vitae,
+
−
                        pellentesque erat. Curabitur fringilla ipsum id sapien imperdiet sagittis. Nulla vestibulum arcu neque, et
+
−
                        iaculis lorem vulputate interdum. Nunc accumsan velit ligula, ac euismod felis sagittis quis. Aenean varius
+
−
                        mollis aliquet. Nam sodales malesuada porttitor. In sed magna sed neque hendrerit ultrices.</p>
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                    <ol>
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                        <li>Ordered list item</li>
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            <div class="acc-line">
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                <div class="acc-head">Lorem ipsum dolor sit amet, consectetur</div>
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                <div class="acc-body">
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                    <h2>H2 title</h2>
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                    <p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Curabitur non urna pharetra, rutrum nibh vitae,
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−
                        pellentesque erat. Curabitur fringilla ipsum id sapien imperdiet sagittis. Nulla vestibulum arcu neque, et
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                        iaculis lorem vulputate interdum. Nunc accumsan velit ligula, ac euismod felis sagittis quis. Aenean varius
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                        mollis aliquet. Nam sodales malesuada porttitor. In sed magna sed neque hendrerit ultrices.</p>
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                    <ol>
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                        <li>Ordered list item</li>
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+
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            eros quis velit hendrerit tempor. Aliquam odio nibh, vulputate id gravida vitae, pulvinar commodo urna.
+
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            Suspendisse potenti. Duis tristique molestie elementum. Donec risus mi, condimentum nec justo id, tempus
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            pretium sem. Donec quis sodales mauris. Maecenas sit amet felis sit amet quam commodo semper sed vel libero.
+
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            Phasellus euismod faucibus sapien nec tempus. Aenean pulvinar sagittis turpis, non rutrum nibh vulputate
+
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            cursus. Phasellus suscipit enim at tincidunt vehicula. Nam imperdiet, magna id fringilla elementum, sem ex
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            finibus sapien, at mollis eros ante id massa.</p>
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            ultrices. Aenean metus mi, fringilla at ex id, vehicula pulvinar diam. Etiam commodo ex nec vulputate
+
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            facilisis. Nam efficitur sapien ac augue tincidunt dapibus. Vestibulum vitae sagittis lacus, sed sagittis
+
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            nibh. Duis fringilla diam vel gravida hendrerit. Ut eu nunc placerat, venenatis arcu vel, rhoncus justo.</p>
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        <table style="width:100%">
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            <thead>
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                <td>HEAD 1</td>
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                <td>HEAD 2</td>
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                <td>HEAD 3</td>
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                <td>HEAD 4</td>
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                    <td>BODY 11</td>
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                    <td>BODY 12</td>
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                    <td>BODY 21</td>
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                    <td>BODY 22</td>
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                    <td>BODY 23</td>
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                    <td>BODY 24</td>
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                    <td>BODY 31</td>
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                    <td>BODY 32</td>
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                    <td>BODY 33</td>
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                    <td>BODY 34</td>
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+
−
            </tbody>
+
−
            <tfoot>
+
−
                <td>FOOTER 1</td>
+
−
                <td>FOOTER 2</td>
+
−
                <td>FOOTER 3</td>
+
−
                <td>FOOTER 4</td>
+
−
            </tfoot>
+
−
        </table>
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−
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−
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+
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            sed posuere dolor. Vivamus malesuada mollis velit ac hendrerit. Suspendisse nec sem eu mauris tristique
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            luctus.</p>
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+
−
            porta, sagittis tortor accumsan, pellentesque odio. Ut dolor sapien, porttitor vel ex vitae, condimentum
+
−
            tristique leo.</p>
+
−
    </div>
+
−
</div>
+
−
<div class="modal modal-2">
+
−
    <div class="modal-close"></div>
+
−
    <div class="modal-content">
+
−
        <h1>Trumpas title, per dvi eilutes</h1>
+
−
        <h5>Izangos teksto stilius. Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor
+
−
            incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco
+
−
            laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit
+
−
            esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident.</h5>
+
−
        <p>Phasellus et maximus purus, sit amet mollis neque. Maecenas finibus nec magna sit amet auctor. Ut sed sapien
+
−
            quis quam auctor dictum. In sit amet eros fermentum, scelerisque lorem sit amet, aliquet est. Integer vitae
+
−
            eros quis velit hendrerit tempor. Aliquam odio nibh, vulputate id gravida vitae, pulvinar commodo urna.
+
−
            Suspendisse potenti. Duis tristique molestie elementum. Donec risus mi, condimentum nec justo id, tempus
+
−
            pretium sem. Donec quis sodales mauris. Maecenas sit amet felis sit amet quam commodo semper sed vel libero.
+
−
            Phasellus euismod faucibus sapien nec tempus. Aenean pulvinar sagittis turpis, non rutrum nibh vulputate
+
−
            cursus. Phasellus suscipit enim at tincidunt vehicula. Nam imperdiet, magna id fringilla elementum, sem ex
+
−
            finibus sapien, at mollis eros ante id massa.</p>
+
−
        <h2>H2 title</h2>
+
−
        <p>Praesent pulvinar enim consequat dolor efficitur viverra. Curabitur tempus auctor tellus at fermentum.
+
−
            Integer ut sem mollis, scelerisque dolor vehicula, posuere massa. Praesent vitae metus ut sem finibus
+
−
            ultrices. Aenean metus mi, fringilla at ex id, vehicula pulvinar diam. Etiam commodo ex nec vulputate
+
−
            facilisis. Nam efficitur sapien ac augue tincidunt dapibus. Vestibulum vitae sagittis lacus, sed sagittis
+
−
            nibh. Duis fringilla diam vel gravida hendrerit. Ut eu nunc placerat, venenatis arcu vel, rhoncus justo.</p>
+
−
        <p>In consectetur, nibh at laoreet lobortis, ipsum odio gravida velit, a bibendum nibh urna vel lorem. Aliquam
+
−
            luctus porttitor commodo. Nam efficitur rutrum erat id pharetra. Suspendisse interdum commodo egestas. Nulla
+
−
            sed posuere dolor. Vivamus malesuada mollis velit ac hendrerit. Suspendisse nec sem eu mauris tristique
+
−
            luctus.</p>
+
−
        <div class="img-cont">
+
−
             <img src="http://placehold.it/800x450" alt="img">
+
−
            <div class="img-label">Foto aprasymas it anim id est laborum. Sed ut perspiciatis unde omnis iste natus error
+
−
                sit voluptatem.
+
−
            </div>
+
−
        </div>
+
−
        <h2>H2 title</h2>
+
−
        <p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Curabitur non urna pharetra, rutrum nibh vitae,
+
−
            pellentesque erat. Curabitur fringilla ipsum id sapien imperdiet sagittis. Nulla vestibulum arcu neque, et
+
−
            iaculis lorem vulputate interdum. Nunc accumsan velit ligula, ac euismod felis sagittis quis. Aenean varius
+
−
            mollis aliquet. Nam sodales malesuada porttitor. In sed magna sed neque hendrerit ultrices.</p>
+
−
        <p>Phasellus et maximus purus, sit amet mollis neque. Maecenas finibus nec magna sit amet auctor. Ut sed sapien
+
−
            quis quam auctor dictum. In sit amet eros fermentum, scelerisque lorem sit amet, aliquet est. Integer vitae
+
−
            eros quis velit hendrerit tempor. Aliquam odio nibh, vulputate id gravida vitae, pulvinar commodo urna.
+
−
            Suspendisse potenti. Duis tristique molestie elementum. Donec risus mi, condimentum nec justo id, tempus
+
−
            pretium sem. Donec quis sodales mauris. Maecenas sit amet felis sit amet quam commodo semper sed vel libero.
+
−
            Phasellus euismod faucibus sapien nec tempus. Aenean pulvinar sagittis turpis, non rutrum nibh vulputate
+
−
            cursus. Phasellus suscipit enim at tincidunt vehicula. Nam imperdiet, magna id fringilla elementum, sem ex
+
−
            finibus sapien, at mollis eros ante id massa.</p>
+
−
        <p>Praesent pulvinar enim consequat dolor efficitur viverra. Curabitur tempus auctor tellus at fermentum.
+
−
            Integer ut sem mollis, scelerisque dolor vehicula, posuere massa. Praesent vitae metus ut sem finibus
+
−
            ultrices. Aenean metus mi, fringilla at ex id, vehicula pulvinar diam. Etiam commodo ex nec vulputate
+
−
            facilisis. Nam efficitur sapien ac augue tincidunt dapibus. Vestibulum vitae sagittis lacus, sed sagittis
+
−
            nibh. Duis fringilla diam vel gravida hendrerit. Ut eu nunc placerat, venenatis arcu vel, rhoncus justo.</p>
+
−
        <p>In consectetur, nibh at laoreet lobortis, ipsum odio gravida velit, a bibendum nibh urna vel lorem. Aliquam
+
−
            luctus porttitor commodo. Nam efficitur rutrum erat id pharetra. Suspendisse interdum commodo egestas. Nulla
+
−
            sed posuere dolor. Vivamus malesuada mollis velit ac hendrerit. Suspendisse nec sem eu mauris tristique
+
−
            luctus.</p>
+
−
        <p>Pellentesque gravida ipsum quam, eu vulputate elit egestas eu. Ut eros elit, ullamcorper sit amet accumsan
+
−
            eget, mollis pretium libero. Etiam laoreet scelerisque risus, in bibendum velit dapibus at. Sed tempor dolor
+
−
            semper elit aliquet, et fermentum metus tristique. Nulla vel iaculis elit. Vivamus et turpis finibus,
+
−
            rhoncus dui mattis, blandit sem. Maecenas in risus vestibulum, luctus felis ut, malesuada dui. Aenean vitae
+
−
            nunc ex. Nunc vulputate orci nec erat iaculis auctor a nec lacus. Pellentesque non ligula laoreet,
+
−
            sollicitudin diam sit amet, dignissim mi. Duis dictum risus nulla, eu interdum nisl laoreet ut. Integer eu
+
−
            leo iaculis, finibus ante eget, consequat orci. Donec semper leo et posuere vulputate. Aliquam ut nisl
+
−
            porta, sagittis tortor accumsan, pellentesque odio. Ut dolor sapien, porttitor vel ex vitae, condimentum
+
−
            tristique leo.</p>
+
−
    </div>
+
−
</div>
+
−
<div class="modal modal-3">
+
−
    <div class="modal-close"></div>
+
−
    <div class="modal-content">
+
−
        <h1>Trumpas title, per dvi eilutes</h1>
+
−
        <h5>Izangos teksto stilius. Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor
+
−
            incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco
+
−
            laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit
+
−
            esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident.</h5>
+
−
        <p>Phasellus et maximus purus, sit amet mollis neque. Maecenas finibus nec magna sit amet auctor. Ut sed sapien
+
−
            quis quam auctor dictum. In sit amet eros fermentum, scelerisque lorem sit amet, aliquet est. Integer vitae
+
−
            eros quis velit hendrerit tempor. Aliquam odio nibh, vulputate id gravida vitae, pulvinar commodo urna.
+
−
            Suspendisse potenti. Duis tristique molestie elementum. Donec risus mi, condimentum nec justo id, tempus
+
−
            pretium sem. Donec quis sodales mauris. Maecenas sit amet felis sit amet quam commodo semper sed vel libero.
+
−
            Phasellus euismod faucibus sapien nec tempus. Aenean pulvinar sagittis turpis, non rutrum nibh vulputate
+
−
            cursus. Phasellus suscipit enim at tincidunt vehicula. Nam imperdiet, magna id fringilla elementum, sem ex
+
−
            finibus sapien, at mollis eros ante id massa.</p>
+
−
        <h2>H2 title</h2>
+
−
        <p>Praesent pulvinar enim consequat dolor efficitur viverra. Curabitur tempus auctor tellus at fermentum.
+
−
            Integer ut sem mollis, scelerisque dolor vehicula, posuere massa. Praesent vitae metus ut sem finibus
+
−
            ultrices. Aenean metus mi, fringilla at ex id, vehicula pulvinar diam. Etiam commodo ex nec vulputate
+
−
            facilisis. Nam efficitur sapien ac augue tincidunt dapibus. Vestibulum vitae sagittis lacus, sed sagittis
+
−
            nibh. Duis fringilla diam vel gravida hendrerit. Ut eu nunc placerat, venenatis arcu vel, rhoncus justo.</p>
+
−
        <p>In consectetur, nibh at laoreet lobortis, ipsum odio gravida velit, a bibendum nibh urna vel lorem. Aliquam
+
−
            luctus porttitor commodo. Nam efficitur rutrum erat id pharetra. Suspendisse interdum commodo egestas. Nulla
+
−
            sed posuere dolor. Vivamus malesuada mollis velit ac hendrerit. Suspendisse nec sem eu mauris tristique
+
−
            luctus.</p>
+
−
        <div class="img-cont">
+
−
            <img src="http://placehold.it/800x450" alt="img">
+
−
            <div class="img-label">Foto aprasymas it anim id est laborum. Sed ut perspiciatis unde omnis iste natus error
+
−
                sit voluptatem.
+
−
            </div>
+
−
        </div>
+
−
        <h2>H2 title</h2>
+
−
        <p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Curabitur non urna pharetra, rutrum nibh vitae,
+
−
            pellentesque erat. Curabitur fringilla ipsum id sapien imperdiet sagittis. Nulla vestibulum arcu neque, et
+
−
            iaculis lorem vulputate interdum. Nunc accumsan velit ligula, ac euismod felis sagittis quis. Aenean varius
+
−
            mollis aliquet. Nam sodales malesuada porttitor. In sed magna sed neque hendrerit ultrices.</p>
+
−
        <p>Phasellus et maximus purus, sit amet mollis neque. Maecenas finibus nec magna sit amet auctor. Ut sed sapien
+
−
            quis quam auctor dictum. In sit amet eros fermentum, scelerisque lorem sit amet, aliquet est. Integer vitae
+
−
            eros quis velit hendrerit tempor. Aliquam odio nibh, vulputate id gravida vitae, pulvinar commodo urna.
+
−
            Suspendisse potenti. Duis tristique molestie elementum. Donec risus mi, condimentum nec justo id, tempus
+
−
            pretium sem. Donec quis sodales mauris. Maecenas sit amet felis sit amet quam commodo semper sed vel libero.
+
−
            Phasellus euismod faucibus sapien nec tempus. Aenean pulvinar sagittis turpis, non rutrum nibh vulputate
+
−
            cursus. Phasellus suscipit enim at tincidunt vehicula. Nam imperdiet, magna id fringilla elementum, sem ex
+
−
            finibus sapien, at mollis eros ante id massa.</p>
+
−
        <p>Praesent pulvinar enim consequat dolor efficitur viverra. Curabitur tempus auctor tellus at fermentum.
+
−
            Integer ut sem mollis, scelerisque dolor vehicula, posuere massa. Praesent vitae metus ut sem finibus
+
−
            ultrices. Aenean metus mi, fringilla at ex id, vehicula pulvinar diam. Etiam commodo ex nec vulputate
+
−
            facilisis. Nam efficitur sapien ac augue tincidunt dapibus. Vestibulum vitae sagittis lacus, sed sagittis
+
−
            nibh. Duis fringilla diam vel gravida hendrerit. Ut eu nunc placerat, venenatis arcu vel, rhoncus justo.</p>
+
−
        <p>In consectetur, nibh at laoreet lobortis, ipsum odio gravida velit, a bibendum nibh urna vel lorem. Aliquam
+
−
            luctus porttitor commodo. Nam efficitur rutrum erat id pharetra. Suspendisse interdum commodo egestas. Nulla
+
−
            sed posuere dolor. Vivamus malesuada mollis velit ac hendrerit. Suspendisse nec sem eu mauris tristique
+
−
            luctus.</p>
+
−
        <p>Pellentesque gravida ipsum quam, eu vulputate elit egestas eu. Ut eros elit, ullamcorper sit amet accumsan
+
−
            eget, mollis pretium libero. Etiam laoreet scelerisque risus, in bibendum velit dapibus at. Sed tempor dolor
+
−
            semper elit aliquet, et fermentum metus tristique. Nulla vel iaculis elit. Vivamus et turpis finibus,
+
−
            rhoncus dui mattis, blandit sem. Maecenas in risus vestibulum, luctus felis ut, malesuada dui. Aenean vitae
+
−
            nunc ex. Nunc vulputate orci nec erat iaculis auctor a nec lacus. Pellentesque non ligula laoreet,
+
−
            sollicitudin diam sit amet, dignissim mi. Duis dictum risus nulla, eu interdum nisl laoreet ut. Integer eu
+
−
            leo iaculis, finibus ante eget, consequat orci. Donec semper leo et posuere vulputate. Aliquam ut nisl
+
−
            porta, sagittis tortor accumsan, pellentesque odio. Ut dolor sapien, porttitor vel ex vitae, condimentum
+
−
            tristique leo.</p>
+
−
    </div>
+
−
</div>
+
−
<div class="modal modal-4">
+
−
    <div class="modal-close"></div>
+
−
    <div class="modal-content">
+
−
        <h1>Trumpas title, per dvi eilutes</h1>
+
−
        <h5>Izangos teksto stilius. Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor
+
−
            incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco
+
−
            laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit
+
−
            esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident.</h5>
+
−
        <p>Phasellus et maximus purus, sit amet mollis neque. Maecenas finibus nec magna sit amet auctor. Ut sed sapien
+
−
            quis quam auctor dictum. In sit amet eros fermentum, scelerisque lorem sit amet, aliquet est. Integer vitae
+
−
            eros quis velit hendrerit tempor. Aliquam odio nibh, vulputate id gravida vitae, pulvinar commodo urna.
+
−
            Suspendisse potenti. Duis tristique molestie elementum. Donec risus mi, condimentum nec justo id, tempus
+
−
            pretium sem. Donec quis sodales mauris. Maecenas sit amet felis sit amet quam commodo semper sed vel libero.
+
−
            Phasellus euismod faucibus sapien nec tempus. Aenean pulvinar sagittis turpis, non rutrum nibh vulputate
+
−
            cursus. Phasellus suscipit enim at tincidunt vehicula. Nam imperdiet, magna id fringilla elementum, sem ex
+
−
            finibus sapien, at mollis eros ante id massa.</p>
+
−
        <h2>H2 title</h2>
+
−
        <p>Praesent pulvinar enim consequat dolor efficitur viverra. Curabitur tempus auctor tellus at fermentum.
+
−
            Integer ut sem mollis, scelerisque dolor vehicula, posuere massa. Praesent vitae metus ut sem finibus
+
−
            ultrices. Aenean metus mi, fringilla at ex id, vehicula pulvinar diam. Etiam commodo ex nec vulputate
+
−
            facilisis. Nam efficitur sapien ac augue tincidunt dapibus. Vestibulum vitae sagittis lacus, sed sagittis
+
−
            nibh. Duis fringilla diam vel gravida hendrerit. Ut eu nunc placerat, venenatis arcu vel, rhoncus justo.</p>
+
−
        <p>In consectetur, nibh at laoreet lobortis, ipsum odio gravida velit, a bibendum nibh urna vel lorem. Aliquam
+
−
            luctus porttitor commodo. Nam efficitur rutrum erat id pharetra. Suspendisse interdum commodo egestas. Nulla
+
−
            sed posuere dolor. Vivamus malesuada mollis velit ac hendrerit. Suspendisse nec sem eu mauris tristique
+
−
            luctus.</p>
+
−
        <div class="img-cont">
+
−
            <img src="http://placehold.it/800x450" alt="img">
+
−
            <div class="img-label">Foto aprasymas it anim id est laborum. Sed ut perspiciatis unde omnis iste natus error
+
−
                sit voluptatem.
+
−
            </div>
+
−
        </div>
+
−
        <h2>H2 title</h2>
+
−
        <p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Curabitur non urna pharetra, rutrum nibh vitae,
+
−
            pellentesque erat. Curabitur fringilla ipsum id sapien imperdiet sagittis. Nulla vestibulum arcu neque, et
+
−
            iaculis lorem vulputate interdum. Nunc accumsan velit ligula, ac euismod felis sagittis quis. Aenean varius
+
−
            mollis aliquet. Nam sodales malesuada porttitor. In sed magna sed neque hendrerit ultrices.</p>
+
−
        <p>Phasellus et maximus purus, sit amet mollis neque. Maecenas finibus nec magna sit amet auctor. Ut sed sapien
+
−
            quis quam auctor dictum. In sit amet eros fermentum, scelerisque lorem sit amet, aliquet est. Integer vitae
+
−
            eros quis velit hendrerit tempor. Aliquam odio nibh, vulputate id gravida vitae, pulvinar commodo urna.
+
−
            Suspendisse potenti. Duis tristique molestie elementum. Donec risus mi, condimentum nec justo id, tempus
+
−
            pretium sem. Donec quis sodales mauris. Maecenas sit amet felis sit amet quam commodo semper sed vel libero.
+
−
            Phasellus euismod faucibus sapien nec tempus. Aenean pulvinar sagittis turpis, non rutrum nibh vulputate
+
−
            cursus. Phasellus suscipit enim at tincidunt vehicula. Nam imperdiet, magna id fringilla elementum, sem ex
+
−
            finibus sapien, at mollis eros ante id massa.</p>
+
−
        <p>Praesent pulvinar enim consequat dolor efficitur viverra. Curabitur tempus auctor tellus at fermentum.
+
−
            Integer ut sem mollis, scelerisque dolor vehicula, posuere massa. Praesent vitae metus ut sem finibus
+
−
            ultrices. Aenean metus mi, fringilla at ex id, vehicula pulvinar diam. Etiam commodo ex nec vulputate
+
−
            facilisis. Nam efficitur sapien ac augue tincidunt dapibus. Vestibulum vitae sagittis lacus, sed sagittis
+
−
            nibh. Duis fringilla diam vel gravida hendrerit. Ut eu nunc placerat, venenatis arcu vel, rhoncus justo.</p>
+
−
        <p>In consectetur, nibh at laoreet lobortis, ipsum odio gravida velit, a bibendum nibh urna vel lorem. Aliquam
+
−
            luctus porttitor commodo. Nam efficitur rutrum erat id pharetra. Suspendisse interdum commodo egestas. Nulla
+
−
            sed posuere dolor. Vivamus malesuada mollis velit ac hendrerit. Suspendisse nec sem eu mauris tristique
+
−
            luctus.</p>
+
−
        <p>Pellentesque gravida ipsum quam, eu vulputate elit egestas eu. Ut eros elit, ullamcorper sit amet accumsan
+
−
            eget, mollis pretium libero. Etiam laoreet scelerisque risus, in bibendum velit dapibus at. Sed tempor dolor
+
−
            semper elit aliquet, et fermentum metus tristique. Nulla vel iaculis elit. Vivamus et turpis finibus,
+
−
            rhoncus dui mattis, blandit sem. Maecenas in risus vestibulum, luctus felis ut, malesuada dui. Aenean vitae
+
−
            nunc ex. Nunc vulputate orci nec erat iaculis auctor a nec lacus. Pellentesque non ligula laoreet,
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Revision as of 21:33, 1 November 2017

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InterLab Study

The aim of this year’s InterLab study was to establish a GFP measurement protocol based on engineering principles that anyone with a plate reader could use in their lab.

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InterLab Study

The aim of this year’s InterLab study was to establish a GFP measurement protocol based on engineering principles that anyone with a plate reader could use in their lab.

This study was an interesting and valuable experience that prompted the team to use new equipment which would not have been used in establishing our personal project alone.

In the beginning, the preparation of competent cells and their transformation according to the protocol seemed to go well but after the required incubation time, no colonies were grown, which lead to another attempt. With greater precision and care, the transformations succeeded. After the transformations we followed the plate reader protocol supplied by the iGEM HQ using LB broth as the growth medium. Afterwards, we generated a FITC standard curve to calibrate the plate reader and then measured both the fluorescence and absorbance of our samples in 2-hour intervals over a 6-hour period.

Results and observations

img
Figure 1. A standard curve generated by measuring the flourescence of serial dilution of FITC stock (uM). There is a somewhat polynomial trenf for the increase of flourescence as [FITC] increase.
img
Figure 2. A standard curve generated by measuring the flourescence of serial dilutions of FITC stock (uM) displayed in a log scale to demonstrate a linear relationship.

  • The standard curve slopes showed a somewhat polynomial shape (Figure 1), although they were supposed to have a 1:1 slope. This could have been due to a consistent pipetting error. The straight-line log graph without a 1:1 slope could justify this hypothesis (Figure 2). Furthermore, the detector could have been oversaturated, because low concentrations were linear, but at high concentrations it either saturated or fell.

  • Based on the part description data from the official iGEM wiki InterLab and part sections: the first three test devices labelled (TD1; TD2; TD3) accordingly differ in their promoter strength with the first one being the strongest, as do the 4th 5th and 6th devices, following the same pattern with the same promoter variability. However, the final three differ in their RBS strength. The first three devices have the B0034 RBS, while the final three have the J364100 RBS. Lastly, the positive control (PC) also contains another version of the RBS labelled B0032.

  • The positive and negative controls did not vary in any significant manner (Figure 3), indicating a methodical error, because the positive control should have shown the largest level of fluorescence due to the strongest RBS and a relatively strong promoter, based on the iGEM wiki data.

Figure 3. The flourescence of the six test devices both positive and negative controls over 2 colonies were transformed into E. Coli and inoculated in LB broth was measured every second hour for a 6-hour period. There is a sharp increase of flourescence after 4th hour indicating cell maturity for most of the samples
.

  • The first three test devices follow the predicted trend (Figure 3). Since the RBS does not differ and the variability is in the promoter regions, the strongest promoter was given to TD 1, which showed the overall strongest fluorescence over the course of 6 hours. The 2nd and 3rd test devices followed a decreasing trend in fluorescence. Furthermore, when comparing the values of TD1 and TD4, which both have the same promoter strength, but differ in RBS sequence, we showed that the B0034 RBS was significantly stronger than the J364100, indicated by the 6th hour values for TD1 ranging from 3900 to 5020 (Au) between both colonies and the values for TD4 ranging only from 1105 to 1397 (Au).

Figure 4. The absorbance of the six test devices and both positive and negative controls for 2 colonies inoculated in LB broth was measured every 2 hours for a 6-hour period. the overall trend of an increase over time persists in all samples for both colonies.

  • By analyzing the Abs600 absorbance values (Figure 4) we should expect a somewhat opposite trend. The negative control shows the highest values of absorbance since there are no genes coding for the GFP protein and the metabolic load is the smallest, when comparing to all the other devices, hence the highest overall absorbance. The devices containing the strongest RBS and promoter sequences should display the lowest levels of absorbance as the cells commit a vast amount of resources to the synthesis of the GFP protein, hence an overall smaller population size and rate of growth. This is displayed in our data as the test devices such as TD6 and TD5 show some of the highest values for absorbance, and the test devices with the strongest RBS and promoter sequences such as TD4 and TD1 present the smallest values. However, the results seem to slightly disagree with this prediction as the TD4 shows the lowest absorption values and the TD1 appears slightly above. A possible explanation for this could be that during the preparation of the samples and the growth phases, environmental effects could have played a role in the differentiation of the data after hour 2 during the exponential phase.