Difference between revisions of "Team:ICT-Mumbai/InterLab"

 
(7 intermediate revisions by 3 users not shown)
Line 94: Line 94:
 
</div>
 
</div>
  
−
<a href="#safety" class="w3-bar-item w3-button w3-hide-small"><i class="fa fa-flag" aria-hidden="true"></i>
+
<a href="https://2017.igem.org/Team:ICT-Mumbai/Safety" class="w3-bar-item w3-button w3-hide-small"><i class="fa fa-flag" aria-hidden="true"></i>
 
  Safety</a>
 
  Safety</a>
  
−
<a href="https://2017.igem.org/Team:ICT-Mumbai/HP" class="w3-bar-item w3-button w3-hide-small"><i class="fa fa-handshake-o" aria-hidden="true"></i>
+
<a href="https://2017.igem.org/Team:ICT-Mumbai/HP/Gold_Integrated" class="w3-bar-item w3-button w3-hide-small"><i class="fa fa-handshake-o" aria-hidden="true"></i>
 
Human Practices</a>
 
Human Practices</a>
  
Line 119: Line 119:
 
<div class="bgimg-1 w3-display-container" id="home">
 
<div class="bgimg-1 w3-display-container" id="home">
 
   <div class="w3-display-middle" style="white-space:nowrap;">
 
   <div class="w3-display-middle" style="white-space:nowrap;">
−
     <span class="w3-center w3-opacity-max w3-padding-large w3-white w3-xxxlarge w3-wide w3-animate-fading"> Interlab study<span class="w3-hide-small">
+
     <span class="w3-center w3-opacity-max w3-padding-large w3-white w3-xxxlarge w3-wide w3-animate-fading"> InterLab study<span class="w3-hide-small">
 
   </div>
 
   </div>
 
</div>
 
</div>
Line 184: Line 184:
 
</style>
 
</style>
  
−
<p style="height:70 px;  font-family:'Lato';  font-size:20px; colour:lightgrey;">The <a href="https://2017.igem.org/Competition/InterLab_Study">2017 InterLab study</a> was initiated to answer two questions: (1) How close can the numbers be when fluorescence is measured all around the world? (2) How reliable will BCD RBS devices turn out to be in labs around the world?</p>
+
<p style="height:70 px;  font-family:'Lato';  font-size:20px; colour:lightgrey;">The <a href="https://2017.igem.org/Competition/InterLab_Study"><mark>2017 InterLab study</mark></a> was initiated to answer two questions: (1) How close can the numbers be when fluorescence is measured all around the world? (2) How reliable will BCD RBS devices turn out to be in labs around the world?</p>
  
 
<p style="height:70 px;  font-family:'Lato';  font-size:20px; colour:lightgrey;">Team ICT-Mumbai participated in the InterLab study and contributed data that will help in answering these two questions. While carrying out this study, we also learned a few things, which we wish to highlight below.</p>
 
<p style="height:70 px;  font-family:'Lato';  font-size:20px; colour:lightgrey;">Team ICT-Mumbai participated in the InterLab study and contributed data that will help in answering these two questions. While carrying out this study, we also learned a few things, which we wish to highlight below.</p>
Line 192: Line 192:
 
<p style="height:70 px;  font-family:'Lato';  font-size:20px; colour:lightgrey;">As can be seen from the figure above, the strengths of the promoters tested are as follows: J23101>J23106>J23117.</p>
 
<p style="height:70 px;  font-family:'Lato';  font-size:20px; colour:lightgrey;">As can be seen from the figure above, the strengths of the promoters tested are as follows: J23101>J23106>J23117.</p>
  
−
<p style="height:70 px;  font-family:'Lato';  font-size:20px; colour:lightgrey;">These three promoters are part of a family of constitutive promoters, of which J23100 is the strongest. The sequences of these promoters (obtained from <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_J23117">here</a>) are depicted below. Nucleotides that differ from the those in promoter J23100 are depicted in red.</p>
+
<p style="height:70 px;  font-family:'Lato';  font-size:20px; colour:lightgrey;">These three promoters are part of a family of constitutive promoters, of which J23100 is the strongest. The sequences of these promoters (obtained from <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_J23117"><mark>here</mark></a>) are depicted below. Nucleotides that differ from the those in promoter J23100 are depicted in red.</p>
  
 
<p style="text-align:center;"><img src="https://static.igem.org/mediawiki/2017/8/80/ICT-Mumbai_interlab_promoter_seq_image.png"></p>
 
<p style="text-align:center;"><img src="https://static.igem.org/mediawiki/2017/8/80/ICT-Mumbai_interlab_promoter_seq_image.png"></p>
Line 219: Line 219:
 
<button class="accordion">Protocols</button>
 
<button class="accordion">Protocols</button>
 
<div class="panel">
 
<div class="panel">
−
<p style="height:70 px;  font-family:'Lato';  font-size:20px; colour:lightgrey;">The protocols that we followed are as given in <a href="https://static.igem.org/mediawiki/2017/8/85/InterLab_2017_Plate_Reader_Protocol.pdf">this PDF file</a>.
+
<p style="height:70 px;  font-family:'Lato';  font-size:20px; colour:lightgrey;">The protocols that we followed are as given in <a href="https://static.igem.org/mediawiki/2017/8/85/InterLab_2017_Plate_Reader_Protocol.pdf"><mark>this PDF file</mark></a>.
 
</p>
 
</p>
 
</div>
 
</div>
Line 243: Line 243:
 
<button class="accordion">Complete data submitted</button>
 
<button class="accordion">Complete data submitted</button>
 
<div class="panel">
 
<div class="panel">
−
<p style="height:70 px;  font-family:'Lato';  font-size:20px; colour:lightgrey;"><a href="https://static.igem.org/mediawiki/2017/3/3b/ICT-Mumbai_interlab_excelfile.xls">Download Excel file</a></p>
+
<p style="height:70 px;  font-family:'Lato';  font-size:20px; colour:lightgrey;"><a href="https://static.igem.org/mediawiki/2017/3/3b/ICT-Mumbai_interlab_excelfile.xls"><mark>Download Excel file</mark></a></p>
 
</div>
 
</div>
  

Latest revision as of 02:16, 2 November 2017

ICT-Mumbai 2017

InterLab study
What we learned from the InterLab study

The 2017 InterLab study was initiated to answer two questions: (1) How close can the numbers be when fluorescence is measured all around the world? (2) How reliable will BCD RBS devices turn out to be in labs around the world?

Team ICT-Mumbai participated in the InterLab study and contributed data that will help in answering these two questions. While carrying out this study, we also learned a few things, which we wish to highlight below.

As can be seen from the figure above, the strengths of the promoters tested are as follows: J23101>J23106>J23117.

These three promoters are part of a family of constitutive promoters, of which J23100 is the strongest. The sequences of these promoters (obtained from here) are depicted below. Nucleotides that differ from the those in promoter J23100 are depicted in red.

It is interesting to note that a single base change in J23117 at position 24 (from T to G) leads to a drastic change in promoter strength. The other changes in the sequence of J23117 with respect to J23100 are also found in J23101 and J23106, and as the latter two are quite strong promoters, in the absence of any other information, and taking the liberty of discounting other alternative explanations, it may be presumed that these changes are not responsible for the decreased promoter strength observed in J23117.

The two RBS sequences used here cannot be compared to each other as B0034 is a conventional ‘monocistronic design’ (MCD), while J364100 is a ‘bicistronic design’ (BCD). However, it can be concluded that MCD leads to higher protein synthesis, compared to BCD.

InterLab study measurements


The protocols that we followed are as given in this PDF file.

  • Instrument: PerkinElmer EnSpire multimode plate reader
  • Excitation filter position: Top
  • Excitation wavelength: 485 nm
  • Emission wavelength: 521 nm
  • Measurement height: 9.5 mm
  • Number of flashes: 100
  • Reference AD gain: 2

Download Excel file