Difference between revisions of "Team:Hong Kong-CUHK/InterLab"

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<h3> <font size="6">Background</font></h3><br>
 
<h3> <font size="6">Background</font></h3><br>
 +
 
<font size="3">Reliable and repeatable measurement is the golden rule of engineering, and so do synthetic biology. However, most of the fluorescent measurement data generated nowadays can not be compared, because  fluorescence data are usually reported in relative unit, but not in absolute unit. In addition, different groups may perform measurement with different protocol, which makes it hard to reproduce. Therefore, iGEM develop a green fluorescent protein (GFP) measurement protocol in order to produce a more reliable, repeatable measurement of GFP. GFP is one of the most commonly used reporter for measurement and easily to be measured in most of laboratories. In the protocol,the unit for fluorescence data is unified so that the results can be compared. The InterLab protocol also unifies the measurement procedure and prevents different data processing for the measurement. </font>
 
<font size="3">Reliable and repeatable measurement is the golden rule of engineering, and so do synthetic biology. However, most of the fluorescent measurement data generated nowadays can not be compared, because  fluorescence data are usually reported in relative unit, but not in absolute unit. In addition, different groups may perform measurement with different protocol, which makes it hard to reproduce. Therefore, iGEM develop a green fluorescent protein (GFP) measurement protocol in order to produce a more reliable, repeatable measurement of GFP. GFP is one of the most commonly used reporter for measurement and easily to be measured in most of laboratories. In the protocol,the unit for fluorescence data is unified so that the results can be compared. The InterLab protocol also unifies the measurement procedure and prevents different data processing for the measurement. </font>
  
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<h3>The Fourth InterLab</h3>
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<h3><font size="6">The Fourth InterLab</font></h3>
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This year, iGEM invited all teams among the world to join the fourth InterLab Study. The aim of the study is to find out how close can the numbers be when fluorescence is measured all around the world using the same InterLab protocol. We registered for the interlab study and measured all the interlab parts using the InterLab plate reader protocol.
+
 
 +
<font size="3>This year, iGEM invited all teams among the world to join the fourth InterLab Study. The aim of the study is to find out how close can the numbers be when fluorescence is measured all around the world using the same InterLab protocol. We registered for the interlab study and measured all the interlab parts using the InterLab plate reader protocol.</font>
 +
 
 +
<h3><font size="6">Experiment</font></h3>
  
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<h3>Experiment</h3>
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<font size="3>iGEM provided 8 plasmids for the InterLab Study. Devices 1-6 and positive control have the same reporter gene (GFP), terminator (B0015) and backbone (pSB1C3). However, devices 1-3 share the same RBS (B0034), while devices 4-6 share another modified RBS called bicistronic device (BCD2). Different promoters are also used in different plasmid. According to the strength of promoter described by iGEM2006_Berkeley team, device 1 should have the strongest fluorescence and device 3 should have the weakest among devices 1-3, while Device 4 should have the strongest fluorescence and device 6 should have the weakest among devices 4-6.</font>
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iGEM provided 8 plasmids for the InterLab Study. Devices 1-6 and positive control have the same reporter gene (GFP), terminator (B0015) and backbone (pSB1C3). However, devices 1-3 share the same RBS (B0034), while devices 4-6 share another modified RBS called bicistronic device (BCD2). Different promoters are also used in different plasmid. According to the strength of promoter described by iGEM2006_Berkeley team, device 1 should have the strongest fluorescence and device 3 should have the weakest among devices 1-3, while Device 4 should have the strongest fluorescence and device 6 should have the weakest among devices 4-6.
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<table width="80%">
 
<table width="80%">
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<h3>What is Bicistronic Device (BCD)?</h3>
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<h3><font size="6">What is Bicistronic Device (BCD)?</font></h3>
  
 
<p><img src="https://static.igem.org/mediawiki/2017/0/08/CuhkBCDinstruction.PNG"  style="width:594px;height:216px;"></p>
 
<p><img src="https://static.igem.org/mediawiki/2017/0/08/CuhkBCDinstruction.PNG"  style="width:594px;height:216px;"></p>
  
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Bicistronic device (BCD) is a modified ribosome binding site (RBS) with another cistron. The device consists of another cistron (cistron 1) with another RBS (SD2)
+
<font size="3">Bicistronic device (BCD) is a modified ribosome binding site (RBS) with another cistron. The device consists of another cistron (cistron 1) with another RBS (SD2)
−
between RBS (SD1) and gene of interest (cistron 2). Also, the stop codon of cistron 1 overlaps the start codon of cistron 2. Ribosome binding efficiency and translation rate will be affected after the secondary structure near the RBS has changed due to the change of gene of interest. This device can maintain the ribosome binding efficiency and translation rate even though the gene of interest has changed. Therefore, it is used to control the amount of fluorescence in this study. BCD is expected to generate a more reliable and precise gene expression.
+
between RBS (SD1) and gene of interest (cistron 2). Also, the stop codon of cistron 1 overlaps the start codon of cistron 2. Ribosome binding efficiency and translation rate will be affected after the secondary structure near the RBS has changed due to the change of gene of interest. This device can maintain the ribosome binding efficiency and translation rate even though the gene of interest has changed. Therefore, it is used to control the amount of fluorescence in this study. BCD is expected to generate a more reliable and precise gene expression.</font>
  
  
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<h3>Method</h3>
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<h3><font size="6">Method</font></h3>
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We follow exactly the interlab protocol provided by iGEM(link) with the below plate reader setting:
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<table width="80%">
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<br>
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<thead>
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Microplate used: Corning® clear flat bottom black 96 well plates<br>
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<tr>
−
Instrument used: BMG LABTECH’s CLARIOstar®
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<th colspan="2"><u>We follow exactly the interlab protocol provided by iGEM(link) with the below plate reader setting: </u></th>
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<br>
+
</tr>
−
<br>
+
</thead>
−
<b>Instrument Settings for measuring OD600 of LUDOX and Cells:</b>
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−
<br>
+
<tr>
−
<br>
+
<th colspan="2">Microplate used: Corning® clear flat bottom black 96 well plates</th>
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<b>-  Endpoint settings</b>
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</tr>
−
<br>
+
 
−
No. of flashes per well: 10
+
<tr>
−
<br>
+
<th colspan="2">Instrument used: BMG LABTECH’s CLARIOstar®</th>
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Scan mode: orbital averaging
+
</tr>
−
<br>
+
 
−
Scan diameter [mm]: 3
+
<tr>
−
<br>
+
<th colspan="2">Instrument Settings for measuring OD600 of LUDOX and Cells:</th>
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<br>
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</tr>
−
<b>-  Optic settings</b>
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−
<br>
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<tr>
−
Excitation: 600
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<th colspan="2">Endpoint settings</th>
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<br>
+
</tr>
−
<br>
+
 
−
<b>-  General settings</b>
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<tr>
−
<br>
+
<th>No. of flashes per well</th>
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Top optic used<br>
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<th>10</th>
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Settling time [s]: 0.1<br>
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</tr>
−
Reading direction: bidirectional, horizontal left to right, top to bottom
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−
<br>
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<tr>
−
Target temperature [°C]: 25
+
<th>Scan mode</th>
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<br>
+
<th>orbital averaging</th>
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<br>
+
</tr>
−
<b>Instrument Settings for measuring fluorecence of Fluorescein and GFP:</b>
+
 
−
<br>
+
<tr>
−
<br>
+
<th>Scan diameter [mm]</th>
−
<b>-  Endpoint settings</b>
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<th>3</th>
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<br>
+
</tr>
−
No. of flashes per well: 8
+
 
−
<br>
+
<tr>
−
Scan mode: orbital averaging
+
<th colspan="2">Optic settings</th>
−
<br>
+
<tr>
−
Scan diameter [mm]: 3
+
 
−
<br>
+
<tr>
−
<br>
+
<th>Excitation</th>
−
<b>-  Optic settings</b>
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<th>600</th>
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<br>
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</tr>
−
Excitation: 470-15
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−
<br>
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<tr>
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Emission: 515-20
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<th colspan="2">General settings</th>
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<br>
+
</tr>
−
Gain: 500
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−
<br>
+
<tr>
−
Focal height [mm]: 9
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<th colspan="2">Top optic used</th>
−
<br>
+
</tr>
−
<br>
+
 
−
<b>-  General settings
+
<tr>
−
</b>
+
<th>Settling time [s]</th>
−
<br>
+
<th>0.1</th>
−
Top optic used
+
</tr>
−
<br>
+
 
−
Reading direction: bidirectional, horizontal left to right, top to bottom
+
<tr>
−
<br>
+
<th>Reading direction</th>
−
Target temperature [°C]: 25
+
<th>bidirectional, horizontal left to right, top to bottom</th>
−
<br>
+
</tr>
−
</p>
+
 
−
<br>
+
<tr>
−
<br>
+
<th>Target temperature [°C]</th>
 +
<th>25</th>
 +
</tr>
 +
 
 +
<tr>
 +
<th  colspan="2">Instrument Settings for measuring fluorecence of Fluorescein and GFP:</th>
 +
</tr>
 +
 
 +
<tr>
 +
<th colspan="2">Endpoint settings</th>
 +
</tr>
 +
 
 +
<tr>
 +
<th>No. of flashes per well</th>
 +
<th>8</th>
 +
</tr>
 +
 
 +
<tr>
 +
<th>Scan mode</th>
 +
<th>orbital averaging</th>
 +
</tr>
 +
 
 +
<tr>
 +
<th>Scan diameter [mm]</th>
 +
<th>3</th>
 +
</tr>
 +
 
 +
<tr>
 +
<th colspan="2">Optic settings</th>
 +
</tr>
 +
 
 +
<tr>
 +
<th>Excitation:</th>
 +
<th>470-15</th>
 +
</tr>
 +
 
 +
<tr>
 +
<th>Emission</th>
 +
<th>515-20</th>
 +
</tr>
 +
 
 +
<tr>
 +
<th>Gain</th>
 +
<th>500</th>
 +
</tr>
 +
 
 +
<tr>
 +
<th>Focal height [mm]</th>
 +
<th>9</th>
 +
</tr>
 +
 
 +
<tr>
 +
<th colspan="2">General settings</th>
 +
</tr>
 +
 
 +
<tr>
 +
<th colspan="2">Top optic used</th>
 +
</tr>
 +
 
 +
<tr>
 +
<th>Reading direction</th>
 +
<th>bidirectional, horizontal left to right, top to bottom</th>
 +
</tr>
 +
 
 +
<tr>
 +
<th>Target temperature [°C]</th>
 +
<th>25
 +
</th>
 +
</tr>
  
 
<h3>Experiment</h3>
 
<h3>Experiment</h3>

Revision as of 11:42, 29 September 2017





Background


Reliable and repeatable measurement is the golden rule of engineering, and so do synthetic biology. However, most of the fluorescent measurement data generated nowadays can not be compared, because fluorescence data are usually reported in relative unit, but not in absolute unit. In addition, different groups may perform measurement with different protocol, which makes it hard to reproduce. Therefore, iGEM develop a green fluorescent protein (GFP) measurement protocol in order to produce a more reliable, repeatable measurement of GFP. GFP is one of the most commonly used reporter for measurement and easily to be measured in most of laboratories. In the protocol,the unit for fluorescence data is unified so that the results can be compared. The InterLab protocol also unifies the measurement procedure and prevents different data processing for the measurement.

The Fourth InterLab

Experiment Summary of parts measured Promoter (strength) RBS Coding Sequence Terminator Backbone Device 1 (J364000) J23101(1791) B0034 GFP B0015 pSB1C3 Device 2 (J364001) J23106(1185) Device 3 (J364002) J23117(162) Device 4 (J364003) J23101(1791) BCD2 Device 5 (J364004) J23106(1185) Device 6 (J364005) J23117(162) Positive control (I20270) J23151(N/A) B0032 Negative control (R0040) R0040 (N/A) N/A

What is Bicistronic Device (BCD)?

Bicistronic device (BCD) is a modified ribosome binding site (RBS) with another cistron. The device consists of another cistron (cistron 1) with another RBS (SD2) between RBS (SD1) and gene of interest (cistron 2). Also, the stop codon of cistron 1 overlaps the start codon of cistron 2. Ribosome binding efficiency and translation rate will be affected after the secondary structure near the RBS has changed due to the change of gene of interest. This device can maintain the ribosome binding efficiency and translation rate even though the gene of interest has changed. Therefore, it is used to control the amount of fluorescence in this study. BCD is expected to generate a more reliable and precise gene expression.

Method

Experiment




The colonies was observed from blue light box. The controls show that the plasmid containing GFP gene will give fluorescence.

The strength of promoter is correlated to the strength of promoter. The higher the strength, the higher the expression of GFP. Among the colonies from devices 4-6, the colonies from device 4 show the highest fluorescence while those from device 6 show the lowest. Among the colonies from devices 1-3, the colonies from device 3 show the lowest fluorescence but no significant difference in fluorescence between the colonies from devices 1 and 2.

Fig.1 shows an increasing trend of the cell growth under OD600 absorbance



Fig.2 shows an increasing trend of the fluorescence.



Fig.3 shows the trend of fluorescence per cell.



Among devices 4-6, the data match with the fluorescence of their colonies and the strength of their promoters. Device 4 has the highest fluorescence per cell and device 6 has the lowest. Among devices 1-3, the data also match with the fluorescence of their colonies and the strength of their promoters. Device 1 has the highest fluorescence per cell and device 3 has the lowest.

Interestingly, the fluorescence per cell of device 6 and negative control are very close. The fluorescence per cell of device 6 is even lower than the negative control at some time points. This shows that device 6 produces very little amount of GFP and the result may also be affected by the measurement error in plate reader.

Another interesting point is the fluorescence per cell of all devices peaked at (t=2hours). One of the possible reasons is the cells spend more energy on cell division but not on producing GFP.








Reference
1. Mutalik VK, Guimaraes JC, Cambray G, Lam C, Christoffersen MJ, Mai QA, Tran AB, Paull M, Keasling JD, Arkin AP, Endy D. Precise and reliable gene expression via standard transcription and translation initiation elements. Nat Methods. 2013 Apr;10(4):354-60.

     

Email: igemcuhk1617@gmail.com

We follow exactly the interlab protocol provided by iGEM(link) with the below plate reader setting:
Microplate used: Corning® clear flat bottom black 96 well plates
Instrument used: BMG LABTECH’s CLARIOstar®
Instrument Settings for measuring OD600 of LUDOX and Cells:
Endpoint settings
No. of flashes per well 10
Scan mode orbital averaging
Scan diameter [mm] 3
Optic settings
Excitation 600
General settings
Top optic used
Settling time [s] 0.1
Reading direction bidirectional, horizontal left to right, top to bottom
Target temperature [°C] 25
Instrument Settings for measuring fluorecence of Fluorescein and GFP:
Endpoint settings
No. of flashes per well 8
Scan mode orbital averaging
Scan diameter [mm] 3
Optic settings
Excitation: 470-15
Emission 515-20
Gain 500
Focal height [mm] 9
General settings
Top optic used
Reading direction bidirectional, horizontal left to right, top to bottom
Target temperature [°C] 25