Difference between revisions of "Team:SDU-Denmark/Proof"

 
(21 intermediate revisions by 4 users not shown)
Line 13: Line 13:
 
     <div class="row">
 
     <div class="row">
 
     <div class="col-sm-11 col-sm-push-1" >
 
     <div class="col-sm-11 col-sm-push-1" >
 +
 +
<style>
 +
.image{
 +
    -webkit-box-shadow: 4px 4px 5px 0px rgba(150,150,150,1);
 +
    -moz-box-shadow: 4px 4px 5px 0px rgba(150,150,150,1);
 +
    box-shadow: 4px 4px 5px 0px rgba(150,150,150,1);
 +
    margin-bottom:10px;
 +
}
 +
</style>
 
<!----------CONTENT--------------------------------->
 
<!----------CONTENT--------------------------------->
  
<h3>Bacteriocins - They work!</h3>
+
<h3><img src="https://static.igem.org/mediawiki/2016/e/e9/T--SDU-Denmark--minibacto.png" height="16px" style="display:inline-block;margin-right:5px;vertical-align:middle;">Bacteriocins - They work!</h3>
<p>During the project we designed BioBricks, which contain the genes encoding a single bacteriocin or a hybrid bacteriocin. We <a href="https://2016.igem.org/Team:SDU-Denmark/Demonstrate#purify" target="_blank">purified</a> the bacteriocins using the IMPACT method and determined the respective concentrations using a <a href="https://2016.igem.org/Team:SDU-Denmark/Demonstrate#determine" target="_blank">Bradford Standard Protein Assay</a> with Bovine Serum Albumin (BSA). The first key criteria in order to purify the bacteriocins were to <a href="https://2016.igem.org/Team:SDU-Denmark/Demonstrate#purify" target="_blank">correctly incorporate</a> the bacteriocin into the IMPACT vector pTXB1. We identified successful ligation between our bacteriocins and the pTXB1 with colony PCR, thus the first key criteria were achieved. Let the purification begin! </p>
+
<p>We designed BioBricks, which contain the genes encoding a single or a hybrid bacteriocin. We <a href="https://2016.igem.org/Team:SDU-Denmark/Demonstrate#purify" target="_blank">purified</a> the bacteriocins using the IMPACT method and determined the respective concentrations using a <a href="https://2016.igem.org/Team:SDU-Denmark/Demonstrate#determine" target="_blank">Bradford Standard Protein Assay</a> with Bovine Serum Albumin. In order to purify the bacteriocins we <a href="https://2016.igem.org/Team:SDU-Denmark/Demonstrate#purify" target="_blank">correctly incorporate</a> the bacteriocin into the IMPACT vector pTXB1.</p>
<h5>Purified bacteriocins inhibit the growth of <i>MRSA</i> and <i>P. aeruginosa</i></h5>
+
<br>
<p> Our MIC test shows <a href="https://2016.igem.org/Team:SDU-Denmark/Demonstrate#MIC" target="_blank">growth inhibition</a> of the strains MRSA:USA300, MRSA:CC398, hetero-VISA and <i>P. aeruginosa</i>:PAO1. The bacteriocins LacticinQ and the hybrid Laterosporulin-ThuricinS did not elicit their activity towards <em>P. aeruginosa.</em> However, the absence of inhibition could be due to a higher MIC value, i.e. the need of a higher concentration to inhibit growth than used in the MIC test, which still leaves the hybrid as a potential inhibitor of <i>P. aeruginosa.</i></p>
+
<h5>Purified bacteriocins inhibit the growth of MRSA and <i>P. aeruginosa</i></h5>
 +
<p> Our MIC-tests showed <a href="https://2016.igem.org/Team:SDU-Denmark/Demonstrate#MIC" target="_blank">growth inhibition</a> of the strains MRSA:USA300, MRSA:CC398, hetero-VISA and <i>P. aeruginosa</i>:PAO1. The bacteriocins LacticinQ and the hybrid Laterosporulin-ThuricinS did not inhibit the growth of <em>P. aeruginosa.</em> However, the absence of inhibition could be due too low concentration used in the MIC test.</p>
  
 +
<br>
 
<h5>Synergistic effect of bacteriocins</h5>
 
<h5>Synergistic effect of bacteriocins</h5>
 
<div>
 
<div>
Line 31: Line 42:
 
       <a href="#closepop" title="Closepop" class="closepop">X</a>
 
       <a href="#closepop" title="Closepop" class="closepop">X</a>
 
       <img src="https://static.igem.org/mediawiki/2016/e/eb/T--SDU-Denmark--MICvisualdatacorrect.png" alt="" width="100%">
 
       <img src="https://static.igem.org/mediawiki/2016/e/eb/T--SDU-Denmark--MICvisualdatacorrect.png" alt="" width="100%">
       <p>Figure 1 visualizes MIC values for each bacteriocin towards each tested strain. The respective strains are listed in the x-axis and the MIC values are plotted logarithmic(2) on the y-axis. The lowest bar indicates the bacteriocin eliciting the strongest effect.</p>
+
       <p>Figure 1: visualizes MIC values for each bacteriocin towards each tested strain. The respective strains are listed on the x-axis and the MIC values are plotted logarithmic(2) on the y-axis. The lowest bar indicates the bacteriocin eliciting the strongest effect.</p>
 
     </div>
 
     </div>
 
</div>
 
</div>
  
<p  class="figuretext"><em>Figure 1 visualizes MIC values for each bacteriocin towards each tested strain. The respective strains are listed in the x-axis and the MIC values are plotted logarithmic(2) on the y-axis. The lowest bar indicates the bacteriocin eliciting the strongest effect.</em></p></div>
+
<p  class="figuretext"><em>Figure 1: visualizes MIC values for each bacteriocin towards each tested strain. The respective strains are listed on the x-axis and the MIC values are plotted logarithmic(2) on the y-axis. The lowest bar indicates the bacteriocin eliciting the strongest effect.</em></p></div>
  
<p>Compared to traditional antibiotics, our results show that the bacteriocins has <a href="https://2016.igem.org/Team:SDU-Denmark/Demonstrate#synergy" target="_blank">similar or better effect</a>. The bacteriocins show inhibition of growth towards MRSA strains and <em>P. aeruginosa</em> at concentrations were the traditional antibiotics does not elicit an effect. The bacteriocins therefore show promising results to support the idea of bacteriocins being a supplement for traditional antibiotics, of which multiresistant bacterias has become less sensitive towards.</p>
+
<p>Our results showed that the bacteriocins have a <a href="https://2016.igem.org/Team:SDU-Denmark/Demonstrate#synergy" target="_blank">similar or better effect</a> compared to traditional antibiotics. The bacteriocins therefore show promising results to support the idea of bacteriocins being a supplement for traditional antibiotics.</p>
<p>The bacteriocins not only inhibited the growth of the tested strains BUT the bacteriocins also showed <a href="https://2016.igem.org/Team:SDU-Denmark/Demonstrate#synergy" target="_blank">synergestic effect</a>. The synergistic effect is shown by a decrease in MIC when the bacteriocin Laterosporulin and ThuricinS are combined as a hybrid compared to their MIC value as single proteins. The hybrid LacticinQ-LacticinZ also shows a decreased MIC compared to LacticinQ as a single acting bacteriocin. The absence of inhibition towards<i> P. aeruginosa </i> by Laterosporulin-ThuricinS when in a hybrid, compared to their single protein effect, could be stated as a loss of effect. However, the MIC values overall decrease towards the<i> S. aureus</i> strains, thus indicating a stronger effect. The observation leaves the possibility of a gain of effect towards strains not tested in the MIC test. The gain of effect could possible prove another characteristic of the designed hybrid bacteriocins. This leaves the opportunity to design an antimicrobial compound as needed.</p></div><br>
+
<p>The bacteriocins did not only inhibit the growth of the tested strains but also showed <a href="https://2016.igem.org/Team:SDU-Denmark/Demonstrate#synergy" target="_blank">synergestic effect</a>. This is indicated by the decrease in MIC when Laterosporulin and ThuricinS are combined as a hybrid compared to each respective MIC value. The hybrid LacticinQ-LacticinZ also showed a decreased MIC compared to the value of LacticinQ. The absence of inhibition towards<i> P. aeruginosa </i> by the hybrid Laterosporulin-ThuricinS compared to their single protein effect, could be due to a loss of function. However, the hybrid MIC values decreased towards the<i> S. aureus</i> strains, indicating a synergistic effect. The tendency for increased inhibition when bacteriocins are in a hybrid construct leaves the possibility of other strains similarly being inhibited, when exposed to a hybrid bacteriocin. Thus proving an important characteristic of the designed hybrid bacteriocin leaving the opportunity to design a synergistic antimicrobial compound.</p></div><br>
  
 
+
<br>
<h5>Synthetic biology are loading its hyperdrive!</h5>
+
<h3><img src="https://static.igem.org/mediawiki/2016/8/87/T--SDU-Denmark--miniPHB.png" height="16px" style="display:inline-block;margin-right:5px;vertical-align:middle;">A functional Plastic Secretion System</h3>
 
<div>
 
<div>
<div style="float:right;width:60%;padding-left:15px;">
+
<div style="float:right;width:40%;padding-left:15px;">
  
 
<!--SELVE BILLEDET-->
 
<!--SELVE BILLEDET-->
<a href="#proof1"><img src=" https://static.igem.org/mediawiki/2016/e/ed/T--SDU-Denmark--plast_production.jpg" alt="" width="100%"></a>
+
<a href="#proof1"><img class="image" src=" https://static.igem.org/mediawiki/2016/e/ed/T--SDU-Denmark--plast_production.jpg" alt="" width="100%"></a>
 
<!--SELVE BILLEDET SLUT-->
 
<!--SELVE BILLEDET SLUT-->
 
   
 
   
Line 53: Line 64:
 
   <a href="#closepop" title="Closepop" class="closepop">X</a>
 
   <a href="#closepop" title="Closepop" class="closepop">X</a>
 
   <img src=" https://static.igem.org/mediawiki/2016/e/ed/T--SDU-Denmark--plast_production.jpg" alt="" width="100%">
 
   <img src=" https://static.igem.org/mediawiki/2016/e/ed/T--SDU-Denmark--plast_production.jpg" alt="" width="100%">
   <p> Top10/pSB1C3-PanK-Sec secretes visible aggregates of PHB.</p>
+
   <p> <em>Figure 2: Top10/pSB1C3-PanK-Sec secretes visible aggregates of PHB.</em></p>
 
</div>
 
</div>
 
</div>
 
</div>
  
<p class="figuretext"> Top10/pSB1C3-PanK-Sec secretes visible aggregates of PHB.</p></div>
+
<p class="figuretext"><em> Figure 2: Top10/pSB1C3-PanK-Sec secretes visible aggregates of PHB.</em></p></div>
  
<p>We assembled the BioBrick <a target="_blank" href="http://parts.igem.org/Part:BBa_K2018050">K2018050</a>, which consists of a hemolysin based secretion system and pantothenate kinase II. The BioBrick was ligated into pSB1C3 with 3A assembly, prior to testing. The effect of the BioBrick has been confirmed qualitatively through culture growth.</p><br>
+
<p>We designed the BioBrick <a target="_blank" href="http://parts.igem.org/Part:BBa_K2018050">K2018050</a>, consisting of a hemolysin based secretion system and pantothenate kinase II. The BioBrick was fused into the iGEM standard plasmid pSB1C3 via 3A assembly. The functionality of this construct has been qualitatively indicated through culture growth, see figure 2.</p><br>
 +
<p>Since our bacterial strains can secrete plastic, PHB extraction and production can be performed in entirely new and innovative ways. Secretion of PHB allows us to retrieve plastic without using toxic and expensive chemicals and thus allowing us the utilization of a <i>Flow Bio Reactor</i> for continuous PHB extraction.</p><br>
 +
<p>At this point we can not confirm whether the BioBrick can produce more plastic than non-secreting PHB producing strains, as we have not received consistent results from parallel extraction experiments with non- and secreting PHB producing strains. We have however, extracted substantial amounts of PHB from top10/pSB1C3-PanK-sec in order to  assess the possibility of its use in 3D printing.</p>
 
</div>
 
</div>
 
+
<br>
<div>
+
<h5 style="clear:right;">From Culture flask to 3D printing </h5>
<div style="float:right;width:60%;padding-left:15px;">
+
<!--SELVE BILLEDET-->
+
<a href="#proof2"><img src="https://static.igem.org/mediawiki/2016/1/14/T--SDU-Denmark--plast.png" alt="" width="100%"></a>
+
<!--SELVE BILLEDET SLUT-->
+
+
<div id="proof2" class="modalDialog" style="overflow: auto;max-height: 100vh;">
+
  <div>
+
  <a href="#closepop" title="Closepop" class="closepop">X</a>
+
  <img src="https://static.igem.org/mediawiki/2016/1/14/T--SDU-Denmark--plast.png" alt="" width="100%">
+
  <p> Plastic aggregates at CaCl_2 concentration of 0.01M.</p>
+
</div>
+
</div>
+
 
+
<p class="figuretext"> Plastic aggregates at CaCl_2 concentration of 0.01M.</p></div>
+
 
+
<p>Since our bacterial strains can secrete plastic, PHB extraction and production can be performed in entirely new ways. Secretion of PHB allows us to retrieve plastic without using toxic and expensive chemicals and possibly even to utilize a <i>Flow Bio Reactor</i> for continuous PHB production.</p><br>
+
+
<p>At this point we cannot confirm whether the BioBrick can produce more plastic than non-secreting PHB producing strains, as we have not received consistent results from parallel extraction experiments with secreting and non-secreting PHB producing strains. We have however, extracted large enough amounts of PHB from top10/pSB1C3-PanK-sec to 3D print.</p>
+
</div>
+
 
+
<h5 style="clear:right;">3D print of an implantat</h5>
+
 
<div>
 
<div>
<div style="float:right;width:40%;padding:15px 0px 15px 15px;">
+
<p>The designed BioBricks: (<a target="_blank" href="http://parts.igem.org/Part:BBa_K2018022">K2018022</a>,  
<img class="image" src="https://static.igem.org/mediawiki/2016/c/c0/T--SDU-Denmark--Jaw.jpg" alt="" width="100%">
+
</div>
+
<p>The designed biobricks, (<a target="_blank" href="http://parts.igem.org/Part:BBa_K2018022">K2018022</a>,  
+
 
<a target="_blank" href="http://parts.igem.org/Part:BBa_K2018023">K2018023</a>,  
 
<a target="_blank" href="http://parts.igem.org/Part:BBa_K2018023">K2018023</a>,  
 
<a target="_blank" href="http://parts.igem.org/Part:BBa_K2018026">K2018026</a>,  
 
<a target="_blank" href="http://parts.igem.org/Part:BBa_K2018026">K2018026</a>,  
Line 96: Line 85:
 
<a target="_blank" href="http://parts.igem.org/Part:BBa_K2018049">K2018049</a> and  
 
<a target="_blank" href="http://parts.igem.org/Part:BBa_K2018049">K2018049</a> and  
 
<a target="_blank" href="http://parts.igem.org/Part:BBa_K2018050">K2018050</a>)  
 
<a target="_blank" href="http://parts.igem.org/Part:BBa_K2018050">K2018050</a>)  
which contains the genes of accumulating PHB inside the cell and the genes of secreting PHB. The PHB was purified using the hypochlorite recovery. After the PHB had dried overnight the PHB was ready to be filamented. Subsequent the purified PHB will be processed into filaments which can be used under real world conditions through 3D printing.</p>
+
containes the genes for accumulation of PHB inside the cell and the genes of the secretion system. The PHB was recovered by the hypochlorite extraction method. Where we allowed PHB to dry overnight. The purified PHB was processed into filaments and used under real life conditions in 3D printing, as shown below. </p>
 
</div>
 
</div>
  
  
<img class="image" src="https://static.igem.org/mediawiki/2016/4/44/T--SDU-Denmark--3dprint.gif" alt="" width="80%">
+
<img class="image" src="https://static.igem.org/mediawiki/2016/4/44/T--SDU-Denmark--3dprint.gif" alt="" width="80%" style="margin-left:10%;margin-top:25px;">
  
  

Latest revision as of 02:09, 20 October 2016

Proof of Concept


Bacteriocins - They work!

We designed BioBricks, which contain the genes encoding a single or a hybrid bacteriocin. We purified the bacteriocins using the IMPACT method and determined the respective concentrations using a Bradford Standard Protein Assay with Bovine Serum Albumin. In order to purify the bacteriocins we correctly incorporate the bacteriocin into the IMPACT vector pTXB1.


Purified bacteriocins inhibit the growth of MRSA and P. aeruginosa

Our MIC-tests showed growth inhibition of the strains MRSA:USA300, MRSA:CC398, hetero-VISA and P. aeruginosa:PAO1. The bacteriocins LacticinQ and the hybrid Laterosporulin-ThuricinS did not inhibit the growth of P. aeruginosa. However, the absence of inhibition could be due too low concentration used in the MIC test.


Synergistic effect of bacteriocins
X

Figure 1: visualizes MIC values for each bacteriocin towards each tested strain. The respective strains are listed on the x-axis and the MIC values are plotted logarithmic(2) on the y-axis. The lowest bar indicates the bacteriocin eliciting the strongest effect.

Figure 1: visualizes MIC values for each bacteriocin towards each tested strain. The respective strains are listed on the x-axis and the MIC values are plotted logarithmic(2) on the y-axis. The lowest bar indicates the bacteriocin eliciting the strongest effect.

Our results showed that the bacteriocins have a similar or better effect compared to traditional antibiotics. The bacteriocins therefore show promising results to support the idea of bacteriocins being a supplement for traditional antibiotics.

The bacteriocins did not only inhibit the growth of the tested strains but also showed synergestic effect. This is indicated by the decrease in MIC when Laterosporulin and ThuricinS are combined as a hybrid compared to each respective MIC value. The hybrid LacticinQ-LacticinZ also showed a decreased MIC compared to the value of LacticinQ. The absence of inhibition towards P. aeruginosa by the hybrid Laterosporulin-ThuricinS compared to their single protein effect, could be due to a loss of function. However, the hybrid MIC values decreased towards the S. aureus strains, indicating a synergistic effect. The tendency for increased inhibition when bacteriocins are in a hybrid construct leaves the possibility of other strains similarly being inhibited, when exposed to a hybrid bacteriocin. Thus proving an important characteristic of the designed hybrid bacteriocin leaving the opportunity to design a synergistic antimicrobial compound.



A functional Plastic Secretion System

X

Figure 2: Top10/pSB1C3-PanK-Sec secretes visible aggregates of PHB.

Figure 2: Top10/pSB1C3-PanK-Sec secretes visible aggregates of PHB.

We designed the BioBrick K2018050, consisting of a hemolysin based secretion system and pantothenate kinase II. The BioBrick was fused into the iGEM standard plasmid pSB1C3 via 3A assembly. The functionality of this construct has been qualitatively indicated through culture growth, see figure 2.


Since our bacterial strains can secrete plastic, PHB extraction and production can be performed in entirely new and innovative ways. Secretion of PHB allows us to retrieve plastic without using toxic and expensive chemicals and thus allowing us the utilization of a Flow Bio Reactor for continuous PHB extraction.


At this point we can not confirm whether the BioBrick can produce more plastic than non-secreting PHB producing strains, as we have not received consistent results from parallel extraction experiments with non- and secreting PHB producing strains. We have however, extracted substantial amounts of PHB from top10/pSB1C3-PanK-sec in order to assess the possibility of its use in 3D printing.


From Culture flask to 3D printing

The designed BioBricks: (K2018022, K2018023, K2018026, K2018027, K2018028, K2018029, K2018049 and K2018050) containes the genes for accumulation of PHB inside the cell and the genes of the secretion system. The PHB was recovered by the hypochlorite extraction method. Where we allowed PHB to dry overnight. The purified PHB was processed into filaments and used under real life conditions in 3D printing, as shown below.