Team:Groningen/parts fail

From 2012.igem.org

(Difference between revisions)
 
(51 intermediate revisions not shown)
Line 1: Line 1:
{{HeaderGroningen2012}}
{{HeaderGroningen2012}}
 +
 +
 +
<html>
<html>
-
<head>
+
<head>
-
<style type="text/css">
+
<style>
-
p
+
z1 {
-
{
+
font-size:18pt;
-
margin-left:150px;
+
line-height:21pt;
-
font-size:12pt;  
+
color:white;
-
line-height:14pt;  
+
}
-
margin-right:150px;
+
z2 {
-
color:white;
+
font-size:14pt;
-
}
+
font-weight: bold;
-
</style>
+
color: rgb(255,103,0);
-
</head>
+
}
-
<body>
+
                        z3 {
-
<p>Failed BioBricks<br>
+
font-size:14pt;
-
<br>
+
line-height:16pt;
-
<b>BBa_K090403</b><br>
+
color: #FF6700;
-
<b>Name</b> Gram-positive Shuttle Vector for Chromosomal Integration<br>
+
font-weight: bold;
-
<b>Intended Purpose</b> Plasmid backbone for cloning in <i>Bacillus subtilis</i><br>
+
}
-
<b>Testing Protocol<b> Restriction analysis (single cut)<br>
+
                        div.ctd {
-
<b>Results</b> The restriction pattern showed that this biobrick is not as described in the parts registry. The cut plasmid is shorter than the expected size.<br>
+
width: 250px;
-
<br>
+
text-align: center;
-
<b>BBa_I742123</b><br>
+
background: #000;
-
<b>Name</b> multi-host vector pTG262 converted to BioBrick vector<br>
+
background-color: rgba(0,0,0,0.3);
-
<b>Intended Purpose</b> plasmid backbone for cloning in <i>Bacilus subtilis</i><br>
+
padding: 5px ;
-
<b>Testing Protocol</b> restriction analysis (single cut) and restriction analysis (dual cut)<br>
+
margin: 30px auto; 
-
<b>Results</b> the restriction enzymes cut at illegal site(s)<br>
+
color: #FFF;
 +
}
 +
div.cte {
 +
width: 280px;
 +
text-align: center;
 +
background: #000;
 +
padding-right:10px;
 +
padding-left:10px;
 +
background-color: rgba(0,0,0,0.3);
 +
margin: 0px auto;
 +
color: #FFF;
 +
}
 +
p {
 +
font-size:12pt;
 +
line-height:14pt;
 +
margin-right:150px;
 +
margin-left:150px;
 +
color: white;
 +
}
 +
table.margintable{
 +
background-color: transparent;
 +
margin-top: 0;
 +
margin-bottom: 0;
 +
margin-left: 150px;
 +
margin-right: 150px;
 +
}
 +
td.textcell90{
 +
vertical-align: top;
 +
font-size:12pt;  
 +
line-height:14pt;  
 +
min-width: 150px;
 +
color:white;
 +
}
 +
a.z2link {
 +
font-size:12pt;
 +
color: rgb(255,103,0);
 +
                              }
 +
p.caption {
 +
margin-left:150px;
 +
margin-right:150px;
 +
font-size:10pt;
 +
line-height:14pt;
 +
color:white;
 +
                              }
 +
</style>
 +
</head>
 +
<body>
 +
<div class="cte">
 +
<div class="ctd">
 +
<z1>Pigment Improvement</z1>
 +
</div>
 +
</div>
 +
 +
<p>
 +
<table class="margintable">
 +
<tr>
 +
<td><z3>BBa_K592010</z3></td>
 +
</tr>
 +
<tr><td class="textcell90">
 +
This BioBrick was intended to be expressed inside <i>E. coli</i> as described by <a class="z2link" href="http://partsregistry.org/Part:BBa_K592010">iGEM Uppsala-Sweden 2011</a>. In our project, we successfully expressed it inside <i>Bacillus subtilis</i> under regulation of sboA promoter. SboA-AmilGFP was shown to be very weakly expressed in <i>Bacillus subtilis</i> on LB plate without rotten meat induction (faint color formation after 2 days). This is probably due to the leakiness of the promoter. We tested the expression of SboA-AmilGFP in <i>B. subtilis</i> subjected to volatiles from spoiled meat using the same setup as we used for the microarray experiment (see our <a class="z2link" href="https://2012.igem.org/Team:Groningen/Sensor">sensor page</a>).<br><br>
 +
</td>
 +
</tr>
 +
<tr><td>
 +
<img src="https://static.igem.org/mediawiki/2012/4/4c/Groningen2012_AP20120924_sboAamilGFPsetup_small.png" width="325"></img>   <img src="http://partsregistry.org/wiki/images/a/ae/Groningen2012_AP20120926_sboAamilGFPsetuppellets.jpg" width="385"></img>
 +
</td>
 +
</tr>
 +
</table>
</p>
</p>
-
</body>
+
<p class=caption><i>
 +
Left: from left to right: Wildtype grown without meat, <i>B. subtilis</i>(SboA-AmilGFP) grown without meat, Wildtype grown with spoiled meat, B.s.(SboA-AmilGFP) grown with spoiled meat.<br>
 +
Right: Pelleted cells after 16 hour growth with/without spoiled meat.</i></p>
 +
 
 +
</p>
 +
<br><br><br>
 +
 
 +
 
 +
<div class="cte">
 +
<div class="ctd">
 +
<z1>Incorrect Biobricks</z1>
 +
</div>
 +
</div>
 +
<br>
 +
<p>
 +
This is the list of incorrect BioBricks that we used from 2012 distribution kit.<br>
 +
<br>
 +
<br>
 +
<z3>BBa_K090403</z3>
 +
<br>
 +
</p>
 +
<table class="margintable">
 +
<tr>
 +
<td class="textcell90">
 +
Name:
 +
</td>
 +
<td class="textcell90">
 +
Gram-positive Shuttle Vector for Chromosomal Integration
 +
</td>
 +
</tr>
 +
<tr>
 +
<td class="textcell90">
 +
Intended Purpose:
 +
</td>
 +
<td class="textcell90">
 +
Plasmid backbone for cloning in <i>Bacillus subtilis</i>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td class="textcell90">
 +
Testing Protocol:
 +
</td>
 +
<td class="textcell90">
 +
Restriction analysis (dual cut with EcoRI and PstI)
 +
</td>
 +
</tr>
 +
<tr>
 +
<td class="textcell90">
 +
Results:
 +
</td>
 +
<td class="textcell90">
 +
The restriction pattern showed that this biobrick is not as described in the parts registry. The cut plasmid is not a single band and shorter than the expected size.
 +
</td>
 +
</tr>
 +
                        <tr>
 +
                                <td class="textcell90">
 +
                                        Gel Pic
 +
                                </td>
 +
                                <td class="textcell90">
 +
                                <img src="https://static.igem.org/mediawiki/2012/b/b1/Groningen2012_EJ_20120926_BBa_K090403test.jpg" width="500"></img>
 +
                                </td>
 +
                        </tr>
 +
</table>
 +
<p>
 +
<br>
 +
<br>
 +
<z3>BBa_I742123</z3>
 +
<br>
 +
</p>
 +
<table class="margintable">
 +
<tr>
 +
<td class="textcell90">
 +
Name:
 +
</td>
 +
<td class="textcell90">
 +
Multi-host vector pTG262 converted to BioBrick vector
 +
</td>
 +
</tr>
 +
<tr>
 +
<td class="textcell90">
 +
Intended Purpose:
 +
</td>
 +
<td class="textcell90">
 +
Plasmid backbone for cloning in <i>Bacillus subtilis</i>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td class="textcell90">
 +
Testing Protocol:
 +
</td>
 +
<td class="textcell90">
 +
Restriction analysis (single cut) and restriction analysis (dual cut)
 +
</td>
 +
</tr>
 +
<tr>
 +
<td class="textcell90">
 +
Results:
 +
</td>
 +
<td class="textcell90">
 +
The restriction enzymes cut at illegal site(s)
 +
</td>
 +
</tr>
 +
<tr>
 +
                                <td class="textcell90">
 +
                                        Gel Pic
 +
                                </td>
 +
                                <td class="textcell90">
 +
                                <img src="https://static.igem.org/mediawiki/2012/3/3a/Groningen2012_EJ_20120926_BBa_I742123test.jpg" width="500"></img>
 +
                                </td>
 +
                        </tr>
 +
</table>
 +
<br><br><br>
 +
<table class="margintable">
 +
<tr>
 +
<td><z3>Remarks</z3></td>
 +
</tr>
 +
<tr><td class="textcell90">After discovering that we did not receive these BioBrick as described in the registry, we took initiative to make our own <i>Bacillus subtilis</i> backbone to accommodate our project's needs. These unexpected BioBricks cost us some time to reconstruct our backbone plan, but in the end we were able to come up with a new backbone plan, the BBa_K818000.
 +
</td>
 +
</tr>
 +
</table>
 +
<br>
 +
<br>
 +
<br>
 +
 
 +
</body>
</html>
</html>
 +
{{Template:SponsorsGroningen2012}}
{{Template:SponsorsGroningen2012}}

Latest revision as of 22:33, 26 September 2012





Pigment Improvement

BBa_K592010
This BioBrick was intended to be expressed inside E. coli as described by iGEM Uppsala-Sweden 2011. In our project, we successfully expressed it inside Bacillus subtilis under regulation of sboA promoter. SboA-AmilGFP was shown to be very weakly expressed in Bacillus subtilis on LB plate without rotten meat induction (faint color formation after 2 days). This is probably due to the leakiness of the promoter. We tested the expression of SboA-AmilGFP in B. subtilis subjected to volatiles from spoiled meat using the same setup as we used for the microarray experiment (see our sensor page).

Left: from left to right: Wildtype grown without meat, B. subtilis(SboA-AmilGFP) grown without meat, Wildtype grown with spoiled meat, B.s.(SboA-AmilGFP) grown with spoiled meat.
Right: Pelleted cells after 16 hour growth with/without spoiled meat.




Incorrect Biobricks

This is the list of incorrect BioBricks that we used from 2012 distribution kit.


BBa_K090403

Name: Gram-positive Shuttle Vector for Chromosomal Integration
Intended Purpose: Plasmid backbone for cloning in Bacillus subtilis
Testing Protocol: Restriction analysis (dual cut with EcoRI and PstI)
Results: The restriction pattern showed that this biobrick is not as described in the parts registry. The cut plasmid is not a single band and shorter than the expected size.
Gel Pic



BBa_I742123

Name: Multi-host vector pTG262 converted to BioBrick vector
Intended Purpose: Plasmid backbone for cloning in Bacillus subtilis
Testing Protocol: Restriction analysis (single cut) and restriction analysis (dual cut)
Results: The restriction enzymes cut at illegal site(s)
Gel Pic



Remarks
After discovering that we did not receive these BioBrick as described in the registry, we took initiative to make our own Bacillus subtilis backbone to accommodate our project's needs. These unexpected BioBricks cost us some time to reconstruct our backbone plan, but in the end we were able to come up with a new backbone plan, the BBa_K818000.



Our sponsors:

Retrieved from "http://2012.igem.org/Team:Groningen/parts_fail"