Difference between revisions of "Team:SHSBNU China/Experiments"

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<p style="font-family: Serif;font-size: 3.5vw; font-weight: bold;text-align: center;margin: 0.5vw 0vw 0.5vw 0vw">Experiment</p>
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<div class="second_classfication">
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<a class="snd_class" href="https://2018.igem.org/Team:SHSBNU_China/Experiments#Outline">Outline</a>
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<a class="snd_class" href="https://2018.igem.org/Team:SHSBNU_China/Experiments#P1">Period #1</a>
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<a class="snd_class" href="https://2018.igem.org/Team:SHSBNU_China/Experiments#P2">Period #2</a>
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<div class="second_classfication">
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<a class="snd_class" href="https://2018.igem.org/Team:SHSBNU_China/Experiments#P3">Period #3</a>
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</div>
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<a class="snd_class" href="https://2018.igem.org/Team:SHSBNU_China/Protocal">Protocal</a>
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<a class="snd_class" href="https://2018.igem.org/Team:SHSBNU_China/InterLab">InterLab</a>
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<h1>Experiment</h1>
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</div>
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<div id="sec_content">
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<div>
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<h2 id="Outline">I. Outline</h2>
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</div>
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<div class="content">
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<p class="text">
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Our system includes two main components as mentioned previously. So our experiments were mainly divided in three periods, verifying both parts individually and verifying Biofilm x Laccase system as a whole.
 +
</p>
 +
<p class="text">
 +
The first period was to construct our biofilm + Spytag, which would be used for combination later on. This period included creating part BBA_K2684006, <i>csgA – SpyTag</i> and BBA_K2684004, <i>sfGFP – SpyCatcher</i>. As well as improving a previously part, BBa_K1583000, <i>csgA</i>. The biofilm + <i>SpyTag</i> ’s ability of combining protein domains + <i>SpyCatcher</i> was measured and our biofilm with <i>SpyTag</i> system tend to be successful.
 +
</p>
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<p class="text">
 +
The second period is focused to construct and measure the laccase activity of our parts: BBA_K2684000, <i>CotA</i>, BBA_K2684001, <i>Pelb - cotA</i>, BBA_K2684002, <i>PhoA - cotA</i>, BBA_K2684003, <i>OmpA - cotA</i>, BBA_K2684005, <i>cotA - SpyCatcher</i>. The laccase activity of the 5 parts were measured.
 +
</p>
 +
<p class="text">
 +
The final period is mainly focused on combination of period 1 and 2 which means constructing our Biofilm x Laccase system. Experiments were conducted to measure the laccase activity of the total Biofilm x Laccase system. A significant difference was confirmed between the experiment group and the control group. Thus, our system is successful. 
 +
</p>
 +
</div>
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<div>
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<h2 id="P1">II. Period 1 - <i>CsgA - SpyTag</i></h2>
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</div>
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<div class="content">
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<div class="content">
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<div style="width:35.9vw" class="content_pic_right">
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<img class="pictures" id = "21000" src="https://static.igem.org/mediawiki/2018/b/b9/T--SHSBNU_China--21000.png"/>
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<p class="pic_text"></p>
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</div>
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<p class="text">
 +
Gene <i>csgA</i> found in the genome of MG1655 wild type is capable of forming biofilm. Using CRISPR, we knocked out gene <i>csgA</i> on MG1655’s genome creating ΔMG1655 strain. The cell ΔMG1655 would then be used as chassis cell. Gene <i>csgA</i> was fused into plasmid pET28a. A <i>Spytag</i> sequence was then fused after <i>csgA</i> gene, creating <i>csgA-spycatcher</i> (BBa_K2684006).
 +
</p>
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<div style="width:14vw" class="content_pic_left">
 +
<img class="pictures" id = "21001" src="https://static.igem.org/mediawiki/2018/8/87/T--SHSBNU_China--21001.jpg"/>
 +
<p class="pic_text">Reaction stock leftover in experiment</p>
 +
</div>
 +
<p class="text">
 +
Using sfGFP – spycatcher protein, the combing function of Spytag and spycatcher system on the biofilm was tested. Gene <i>csgA</i> on the plasmid of pET28a was transferred in to ΔMG1655 as control group. Gene <i>csgA – Spytag</i> on the plasmid of pET28a was transferred in to ΔMG1655 as experiment. To verify the function of Spytag on <i>csgA</i>, the experiment was design to compare the combing rate of sf-GFP – spycatcher protein with cells that have csgA – SpyTag (Experiment) or csgA (Control).
 +
</p>
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<div style="width:20vw" class="content_pic_right">
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<img class="pictures" id = "21002" src="https://static.igem.org/mediawiki/2018/5/57/T--SHSBNU_China--21002.jpg"/>
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<p class="pic_text"></p>
 +
</div>
 +
<p class="text">
 +
Link: Protocol for <a href="https://2018.igem.org/Team:SHSBNU_China/Protocal#SSS">SpyTag-SpyCatcher</a> system verification
 +
</p>
 +
<p class="text">
 +
As can be seen from the result,
 +
</p>
 +
<p class="text">
 +
Thus we can confirm our <i>csgA – SpyTag</i> system is functional.
 +
</p>
 +
</div>
 +
</div>
 +
 
 +
<div>
 +
<h2 id="P2">III. Period 2 - <i>CotA - SpyCatcher</i></h2>
 +
</div>
 +
<div class="content">
 +
<p class="text">
 +
Gene <i>cotA</i> from B. substiles could translate as laccase protein (BBa_K2684000). The sequence was fused on to pET28a plasmid.
 +
</p>
 +
<div style="width:24vw" class="content_pic_left">
 +
<img class="pictures" id = "22000" src="https://static.igem.org/mediawiki/2018/b/b9/T--SHSBNU_China--22000.png"/>
 +
<p class="pic_text"></p>
 +
</div>
 +
<p class="text">
 +
We then added the <i>SpyCatcher</i> sequence after <i>cotA</i> gene so that we can produce laccase protein with spycatcher (BBa_K2684005).
 +
</p>
 +
<div style="width:24vw" class="content_pic_left">
 +
<img class="pictures" id = "22001" src="https://static.igem.org/mediawiki/2018/7/72/T--SHSBNU_China--10002.png"/>
 +
<p class="pic_text"></p>
 +
</div>
 +
<p class="text">
 +
We also figured a way to secret our CotA protein out of the host cell. Signal peptides are small parts of protein and their function is to lead whatever behind it out of the cell. A signal peptide sequence was also added ahead of <i>cotA</i> sequence. Three signal peptides was tested: Pelb, PhoA, OmpA (BBa_K2684001, BBa_K2684002, BBa_K2684003).
 +
</p>
 +
<div style="width:24vw" class="content_pic_left">
 +
<img class="pictures" id = "22002" src="https://static.igem.org/mediawiki/2018/8/80/T--SHSBNU_China--10003.png"/>
 +
<p class="pic_text"></p>
 +
</div>
 +
<p class="text">
 +
ABTS is a substance that is wildly used in commercial laccase activity assay kits. ABTS is in a clear solution and when it reacts with laccase, it would turn to a bullish-green color that has an absorbance peak at 420nm. We used laccase activity assay kit from Solarbio, type BC1635 which functions based on the previous mentioned method. We set a negative control group by transferring pET28a plasmid in to BL21 – DE3 strain. We set 4 experiment groups by transferring <i>cotA, OmpA - cotA, PhoA - cotA, PelB – cotA</i> gene into BL21 – DE3. We measured the laccase activity of all 5 groups mentioned above to check if our laccase is functional.
 +
</p>
 +
<p class="text">
 +
Link Protocol for <a href="https://2018.igem.org/Team:SHSBNU_China/Protocal#LAA">laccase activity assay, scale of protein</a>
 +
</p>
 +
<p class="text">
 +
Link Protocol for <a href="https://2018.igem.org/Team:SHSBNU_China/Protocal#LAM">Laccase activity measuring kit</a>
 +
</p>
 +
</div>
 +
 
 +
<div>
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<h2 id="P3">IV. Period 3 - <i>Biofilm x Laccase</i></h2>
 +
</div>
 +
<div class="content">
 +
<p class="text">
 +
The final period is to assay the laccase activity of Biofilm x Laccase system as a whole. Four group of experiments was conducted.
 +
</p>
 +
<table bgcolor="#f0f0f0" cellspacing="1px">
 +
 
 +
<tr bgcolor="#f0f0f0">
 +
<td>Group name (in protocol, step 13)</td>
 +
<td>Biofilm + SypTag</td>
 +
<td>Enzyme</td>
 +
</tr>
 +
 
 +
<tr bgcolor="#f0f0f0">
 +
<td>1</td>
 +
<td>No</td>
 +
<td>CotA</td>
 +
</tr>
 +
 
 +
<tr bgcolor="#f0f0f0">
 +
<td>2</td>
 +
<td>No</td>
 +
<td>CotA - SpyCatcher</td>
 +
</tr>
 +
 
 +
<tr bgcolor="#f0f0f0">
 +
<td>3</td>
 +
<td>Yes</td>
 +
<td>CotA</td>
 +
</tr>
 +
 
 +
<tr bgcolor="#f0f0f0">
 +
<td>4</td>
 +
<td>Yes</td>
 +
<td>CotA - SpyCatcher</td>
 +
</tr>
 +
 
 +
</table>
 +
<p class="text">
 +
The method of centrifuging and removing the supernatant was to remove uncombined enzyme after the reaction of SpyTag and SpyCatcher (Step 14).
 +
</p>
 +
<p class="text">
 +
Link Protocol for <a href="https://2018.igem.org/Team:SHSBNU_China/Protocal#BXL">Biofilm x laccase</a>
 +
</p>
 +
<p class="text">
 +
Link Protocol for <a href="https://2018.igem.org/Team:SHSBNU_China/Protocal#LAM">Laccase activity measuring kit</a>
 +
</p>
 +
<div style="width:32vw" class="content_pic_left">
 +
<img class="pictures" id = "23000" src="https://static.igem.org/mediawiki/2018/4/4a/T--SHSBNU_China--23000.jpg"/>
 +
<p class="pic_text"></p>
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</div>
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Revision as of 06:15, 17 October 2018

Section Sample

Experiment

I. Outline

Our system includes two main components as mentioned previously. So our experiments were mainly divided in three periods, verifying both parts individually and verifying Biofilm x Laccase system as a whole.

The first period was to construct our biofilm + Spytag, which would be used for combination later on. This period included creating part BBA_K2684006, csgA – SpyTag and BBA_K2684004, sfGFP – SpyCatcher. As well as improving a previously part, BBa_K1583000, csgA. The biofilm + SpyTag ’s ability of combining protein domains + SpyCatcher was measured and our biofilm with SpyTag system tend to be successful.

The second period is focused to construct and measure the laccase activity of our parts: BBA_K2684000, CotA, BBA_K2684001, Pelb - cotA, BBA_K2684002, PhoA - cotA, BBA_K2684003, OmpA - cotA, BBA_K2684005, cotA - SpyCatcher. The laccase activity of the 5 parts were measured.

The final period is mainly focused on combination of period 1 and 2 which means constructing our Biofilm x Laccase system. Experiments were conducted to measure the laccase activity of the total Biofilm x Laccase system. A significant difference was confirmed between the experiment group and the control group. Thus, our system is successful. 

II. Period 1 - CsgA - SpyTag

Gene csgA found in the genome of MG1655 wild type is capable of forming biofilm. Using CRISPR, we knocked out gene csgA on MG1655’s genome creating ΔMG1655 strain. The cell ΔMG1655 would then be used as chassis cell. Gene csgA was fused into plasmid pET28a. A Spytag sequence was then fused after csgA gene, creating csgA-spycatcher (BBa_K2684006).

Reaction stock leftover in experiment

Using sfGFP – spycatcher protein, the combing function of Spytag and spycatcher system on the biofilm was tested. Gene csgA on the plasmid of pET28a was transferred in to ΔMG1655 as control group. Gene csgA – Spytag on the plasmid of pET28a was transferred in to ΔMG1655 as experiment. To verify the function of Spytag on csgA, the experiment was design to compare the combing rate of sf-GFP – spycatcher protein with cells that have csgA – SpyTag (Experiment) or csgA (Control).

Link: Protocol for SpyTag-SpyCatcher system verification

As can be seen from the result,

Thus we can confirm our csgA – SpyTag system is functional.

III. Period 2 - CotA - SpyCatcher

Gene cotA from B. substiles could translate as laccase protein (BBa_K2684000). The sequence was fused on to pET28a plasmid.

We then added the SpyCatcher sequence after cotA gene so that we can produce laccase protein with spycatcher (BBa_K2684005).

We also figured a way to secret our CotA protein out of the host cell. Signal peptides are small parts of protein and their function is to lead whatever behind it out of the cell. A signal peptide sequence was also added ahead of cotA sequence. Three signal peptides was tested: Pelb, PhoA, OmpA (BBa_K2684001, BBa_K2684002, BBa_K2684003).

ABTS is a substance that is wildly used in commercial laccase activity assay kits. ABTS is in a clear solution and when it reacts with laccase, it would turn to a bullish-green color that has an absorbance peak at 420nm. We used laccase activity assay kit from Solarbio, type BC1635 which functions based on the previous mentioned method. We set a negative control group by transferring pET28a plasmid in to BL21 – DE3 strain. We set 4 experiment groups by transferring cotA, OmpA - cotA, PhoA - cotA, PelB – cotA gene into BL21 – DE3. We measured the laccase activity of all 5 groups mentioned above to check if our laccase is functional.

Link Protocol for laccase activity assay, scale of protein

Link Protocol for Laccase activity measuring kit

IV. Period 3 - Biofilm x Laccase

The final period is to assay the laccase activity of Biofilm x Laccase system as a whole. Four group of experiments was conducted.

Group name (in protocol, step 13) Biofilm + SypTag Enzyme
1 No CotA
2 No CotA - SpyCatcher
3 Yes CotA
4 Yes CotA - SpyCatcher

The method of centrifuging and removing the supernatant was to remove uncombined enzyme after the reaction of SpyTag and SpyCatcher (Step 14).

Link Protocol for Biofilm x laccase

Link Protocol for Laccase activity measuring kit