Difference between revisions of "Team:Tacoma RAINmakers/Notebook"

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    <body>
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        <div id="topbox">
 +
            <h1>Tacoma RAINmakers Lab Notebook</h1>
 +
        </div>
  
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          <h1>Week One </h1> <h2> Digestion and Isolation of pSB1C3 Backbone.</h2>
−
  padding: 35px;
+
          <p> The purpose of digesting the pSB1C3/PArsRGFP construct was to separate the backbone from the former GFP insert. Tacoma RAINmakers sought to isolate the pSB1C3 backbone employed in their 2017 construct, as the GFP reporter complex was no longer desired. Apparent disadvantages of GFP indication in biosensors are ultraviolet readings. The RAINmakers prefered a chromoprotein that produces color in the visible spectrum. Enzymes XbaI and SpeI were used to cleave the terminator sites of the vector, freeing the pSB1C3 backbone. NEB resources confirmed that the Cutsmart Buffer 2.1 is the most compatible with these particular enzymes, providing an optimized environment for digestion. Combining the reagents listed in Table 1.0, the reaction was set at 37ºC in a water bath for 1 hour and 45 minutes. This reaction was completed in duplicate to increase statistical probability of desired backbone DNA.
−
}
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<!--  
 +
<a href="https://2018.igem.org/Team:Rice/Software/Step1"> Details</a></p>  <IMG class="displayed" img src="https://static.igem.org/mediawiki/2018/5/50/T--Rice--softwareimg3.png" alt="Step 1"vertical-align="middle"> <h3> Figure S1. Randomization of six base in the anti Shine-Dalgarno sequence. </h3>
 +
<hr style="border: 1px solid black;" />
 +
-->
  
 +
          <h1>Step 2 </h1> <h2> Use RNADuplex<sup>[2]</sup> to calculate binding energies for all 4096 pairs of SD/ASD sequences.</h2>
 +
<p>We then use RNAduplex from the ViennaRNA package to calculate binding energies for all 4096 pairs of SD/ ASD sequences.<a href="https://2018.igem.org/Team:Rice/Software/Step2"> Details</a></p> <hr style="border: 1px solid black;" />
  
−
/********************************* RESPONSIVE STYLING ********************************/
+
          <h1>Step 3</h1> <h2> Narrow library by eliminating mutant pairs with binding energy more than 0.5 kcal/mol away from wild-type value.</h2>
 +
<p>Again, we use RNAduplex to calculate binding energies, but this time between the candidate ASD sequences with the wild-type SD sequences.<a href="https://2018.igem.org/Team:Rice/Software/Step3"> Details</a></p>
 +
<IMG class="displayed" img src="https://static.igem.org/mediawiki/2018/8/81/T--Rice--softwareimg4.png" alt="Step 2-3"style="width:800px;height:500px" > <h3> Figure S2. Narrowing down based on wild-type ASD/wild-type SD binding energy. </h3>
 +
<hr style="border: 1px solid black;" />
  
  
−
/* IF THE SCREEN IS LESS THAN 1000PX */
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          <h1>Step 4</h1><h2> Use RNADuplex to calculate binding energies between all remaining mutant ASDs with wildtype SD.</h2>
 +
<p>The library is narrowed down again by discarding those candidates with a binding energy less than -1 kcal/mol with the wild type SD sequences. This prevents the orthogonal ribosomes developed from the candidate ASDs from binding with wild type SD sequences over orthogonal mRNA, which ensures orthogonality of the engineered ribosomes.<a href="https://2018.igem.org/Team:Rice/Software/Step4"> Details</a></p><hr style="border: 1px solid black;" />
  
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          <h1>Step 5</h1><h2> Narrow library by eliminating mutant ASD/Wildtype SD pairs with binding energy <-1.0 kcal/mol.</h2>
−
  #content {
+
<p>The library is narrowed down again by discarding those candidates with a binding energy less than -1 kcal/mol with the wild type SD sequences. This prevents the orthogonal ribosomes developed from the candidate ASDs from binding with wild type SD sequences over orthogonal mRNA, which ensures orthogonality of the engineered ribosomes.<a href="https://2018.igem.org/Team:Rice/Software/Step5"> Details</a></p>
−
    width: 100%;
+
<IMG class="displayed" img src="https://static.igem.org/mediawiki/2018/5/5d/T--Rice--softwareimg5.png" alt="Step 4-5"style="width:800px;height:500px"><h3> Figure S3. Ensure orthogonality of chosen sequences. </h3>
−
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−
/* IF THE SCREEN IS LESS THAN 680PX */
+
          <h1>Step 6</h1><h2> Use RNAFold to estimate secondary structure formation of 16s rRNAs containing mutant ASD sequences.</h2>
 +
<p>We use RNAfold from the ViennaRNA package to calculate the secondary structure for the full 16s rRNA. <a href="https://2018.igem.org/Team:Rice/Software/Step6"> Details</a></p><hr style="border: 1px solid black;" />
  
−
@media only screen and (max-width: 680px) {
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          <h1>Step 7</h1><h2> Narrow library by eliminating sequences that lead to 16s rRNA having secondary structure formed at the ASD region.</h2>
−
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<p>Those candidates with secondary structure in the ASD regions are discarded, as this would impair their ability to carry out translation. <a href="https://2018.igem.org/Team:Rice/Software/Step7"> Details</a></p>
−
    display: block;
+
<IMG class="displayed" img src="https://static.igem.org/mediawiki/2018/d/d0/T--Rice--softwareimg6.png" alt="Step 6-7"style="width:800px;height:500px">
−
  }
+
<h3> Figure S4. Elimination of sequences that lead to secondary structure complications. </h3>
−
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+
          <h1>Step 8</h1><h2> Obtain all translation initiation regions (TIRs) from the chosen bacteria's genome.</h2><p>Next, we obtain all the translation initiation regions (TIRs) from the genome.  <a href="https://2018.igem.org/Team:Rice/Software/Step8"> Details</a></p>
 +
<IMG class="displayed" img src="https://static.igem.org/mediawiki/2018/9/97/T--Rice--softwareimg7.png" alt="Step 8-10"style="width:800px;height:500px"><h3> Figure S5. Overview: Obtaining all translation initiation regions from the Coding Region. </h3><IMG class="displayed" img src="https://static.igem.org/mediawiki/2018/4/49/T--Rice--softwareimg8.png" alt="Step 8-10"style="width:1000px;height:650px"><h3> Figure S6. Extracting the TIRs in different situations. </h3>
 +
<hr style="border: 1px solid black;" />
  
−
<script>
+
          <h1>Step 9</h1><h2> Use RNADuplex<sup>[3]</sup> to calculate binding energy of each remaining mutant ASD with those TIRs.</h2>
 +
<p>We use these TIRs in conjunction with RNAduplex once again to calculate the binding energies of the remaining candidate ASDs with those TIRs.<a href="https://2018.igem.org/Team:Rice/Software/Step9"> Details</a></p><hr style="border: 1px solid black;" />
  
−
// This is the jquery part of your template. Try not modify any of this code since it makes your menu work.
+
          <h1>Step 10</h1><h2> Rank candidate mutant ASDs based on number of strong interactions between the ASD sequence and the TIRs from the bacteria genome.</h2>
 +
<p>Candidates are then ranked based on their binding energies with the host TIRs. Candidates with higher binding energies (which are less likely to bind with host TIRs) are given preference, since they are more likely to remain orthogonal to the host processes.<a href="https://2018.igem.org/Team:Rice/Software/Step10"> Details</a></p><hr style="border: 1px solid black;" />
  
−
  $(document).ready(function() {
+
<h1>Reference</h1>
 +
<p>
 +
        [1] Darlington, A.P.S., Kim, J., Jiménez, J.I., &amp; Bates, D.G. (2018). Dynamic allocation of orthogonal ribosomes facilitates uncoupling of co-expressed genes. Nature Communications, 9, 695.
 +
    </p>
 +
<p>
 +
        [2] Ding, Y., Chan, C. Y., &amp; Lawrence, C. E. (2005). RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA, 11(8), 1157–1166. http://doi.org/10.1261/rna.2500605
  
−
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+
     <p>[3]“TBI - RNAduplex - Manpage.” Accessed September 12, 2018. https://www.tbi.univie.ac.at/RNA/RNAduplex.1.html.
−
   
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              Notebook
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  <br><br><br>
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  <p>We have built the team since March 29 this year, one of Team-ECUST Teams. There are initial seven people only, which then gradually expanded to 13 people, during 7 month. <br>
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  We knew nothing at the beginning of the IGEM, through step-by-step understanding and pondering, in the efforts of the team members and with the help of teachers and seniors, we accomplished the whole project finally. </p>
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  <p>Here are our team memorabilia from our team building to the wiki freeze. </p>
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<section class="timeline" style="font-family: 'Spinnaker', sans-serif;background: -webkit-linear-gradient(right, #BE93C5 , #7BC6CC);background: linear-gradient(to left, #BE93C5 , #7BC6CC);">
 
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        <h2 class="timeline__item__content__date">May 13, 2017</h2>
 
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        <p class="timeline__item__content__description">1、Team-ECUST was established, initially 12 students were divided into two teams, our team initial members included Weijie Chen, Yunpeng Dai, Ye Li, Yuyao Jin, Yuanyuan Li, Binjie zhang and Zhenzhou Jiang.
 
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        <br>2、We made researches about previous iGEM teams, wondering who did what.
 
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        </p>
 
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      </div>
 
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        <h2 class="timeline__item__content__date">2017.4.5-2017.4.12</h2>
 
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        <p class="timeline__item__content__description">After the teachers' review, we determined that the primary direction was the photosynthesis of microorganisms.</p>
 
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        <h2 class="timeline__item__content__date">2017.4.12-2017.4.19</h2>
 
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        <p class="timeline__item__content__description">1、We have looked for kinds of ways to enhance the efficiency of photosynthesis and ultimately determined to broaden the absorption spectrum.
 
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        <br>2、Under the recommendation of teachers, we selected Rhodobacter sphaeroides as a chassis biology.
 
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        </p>
 
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        <h2 class="timeline__item__content__date">2017.4.19-2017.4.26</h2>
 
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        <p class="timeline__item__content__description">1、Thanks to Dr. Haoqian Zhang from Beijing who shared his experience about iGEM and proposed improvements to our project.
 
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        <br>2、So far we have determined to broaden the absorption spectra by means of fluorescence resonance energy transformation and studied its application.
 
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        </p>
 
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        <h2 class="timeline__item__content__date">2017.4.26-2017.5.3</h2>
 
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        <p class="timeline__item__content__description">1、In-depth study of light complexes of Rhodobacter sphaeroide and preparation of preliminary modelling.
 
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        <br>2、plan and prepare the Human practice.
 
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        <br>3、Jianchang Huang joined our team .
 
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        </p>
 
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        <h2 class="timeline__item__content__date">2017.5.3-2017.5.10</h2>
 
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        <p class="timeline__item__content__description">1、The design of the initial experimental protocol after survey lots of literature.
 
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        <br>2、With the help of Teacher Lu, the protocol of the photo-reactor was designed preliminarily.
 
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        </p>
 
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      </div>
 
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        <h2 class="timeline__item__content__date">2017.5.10-2017.5.17</h2>
 
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        <p class="timeline__item__content__description">1、In this regular discussion, we and the teachers approved of the feasibility of our protocol.
 
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        <br>2、Continued to deepen our project from all angles.
 
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        <br>3、Light-harvester team was established, and had our own logo.
 
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        </p>
 
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      </div>
 
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        <h2 class="timeline__item__content__date">2017.5.17-2017.5.24</h2>
 
−
        <p class="timeline__item__content__description">Kaiyu Yin, from the Hoa Bioengineering Institute, introduced us to the Gibson Assembly and gene knockout/typing method.</p>
 
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      </div>
 
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    <div class="timeline__item timeline__item--8">
 
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        <h2 class="timeline__item__content__date">2017.5.24-2017.5.31</h2>
 
−
        <p class="timeline__item__content__description">Prof. Gaoyi Tan explained some of the characteristics of Rhodobacter sphaeroide, and Xian Liu teached us how to cultivate Rhodobacter sphaeroide.</p>
 
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        <h2 class="timeline__item__content__date">2017.5.31-2017.6.7</h2>
 
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        <p class="timeline__item__content__description">1、We have studied the primer design and designed the primers for the our project.
 
−
        <br>2、We studied the characteristics of Rhodobacter sphaeroide, and found that they can degrade organic matter and produce hydrogen through photosynthesis.
 
−
        <br>3、Mengqing Zhou，Lu Lu joined our team.
 
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        </p>
 
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      </div>
 
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    <div class="timeline__item timeline__item--10">
 
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        <h2 class="timeline__item__content__date">2017.6.7-2017.6.14</h2>
 
−
        <p class="timeline__item__content__description">1、We have studied the specific mechanism of hydrogen production about Rhodobacter sphaeroide. 
 
−
        <br>2、Investigated the requirements of iGEM medals and improved our project according to the standards.
 
−
        <br>3、We begun to cultivate Rhodobacter sphaeroide.
 
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        </p>
 
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      </div>
 
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    <div class="timeline__item timeline__item--11">
 
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        <h2 class="timeline__item__content__date">2017.6.14-2017.6.21</h2>
 
−
        <p class="timeline__item__content__description">1、Reserving the reagents required for the experiment.
 
−
        <br>2、We designed postcards and mailed it to the University from German.
 
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        </p>
 
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      </div>
 
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    <div class="timeline__item timeline__item--12">
 
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        <h2 class="timeline__item__content__date">2017.6.21-2017.6.28</h2>
 
−
        <p class="timeline__item__content__description">1、Completed a series of tasks according to the requirements of the iGEM official calendar.
 
−
        <br>2、Zhi Yi joined our team.
 
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        </p>
 
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      </div>
 
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    <div class="timeline__item timeline__item--13">
 
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        <h2 class="timeline__item__content__date">2017.6.28-2017.7.5</h2>
 
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        <p class="timeline__item__content__description">1、Jianan Shi，Fengting Lijoined our team.
 
−
        <br>2、We made the final preparations for the summer experiment.
 
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        </p>
 
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      </div>
 
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    <div class="timeline__item timeline__item--14">
 
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        <h2 class="timeline__item__content__date">2017.7.5-2017.7.12</h2>
 
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        <p class="timeline__item__content__description">We did the wet lab work and successfully constructed the Konck out plasmids.</p>
 
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      </div>
 
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    <div class="timeline__item timeline__item--15">
 
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        <h2 class="timeline__item__content__date">2017.7.12-2017.7.19</h2>
 
−
        <p class="timeline__item__content__description">1、We successfully constructed the Knock in plasmid.
 
−
        <br>2、We tried to reconstruct the pIND4 inducible plasmid, but the effect is poor.
 
−
        <br>3,、We produced a brochure about our team.
 
−
        </p>
 
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      </div>
 
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        <h2 class="timeline__item__content__date">2017.7.19-2017.7.26</h2>
 
−
        <p class="timeline__item__content__description">1、We conducted joint transformation experiments of Rhodobacter sphaeroide and did not achieve the predicted effect.
 
−
        <br>2、Tried to build pIND4 with Gibson assembly.
 
−
        <br>3、We completed all the experiments on Interlab.
 
−
        <br>4、We finally determined the scheme of the luminous stirring paddle, and discussed the details.
 
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        </p>
 
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        <h2 class="timeline__item__content__date">2017.7.26-2017.8.2</h2>
 
−
        <p class="timeline__item__content__description">1、We conducted joint transformation experiments of Rhodobacter sphaeroide and did not achieve the predicted effect.
 
−
        <br>2、We successsfully assembled and constructed pIND4 plasmids by Gibson.
 
−
        <br>3、Cooperated with the iGEM team from SJTU.
 
−
        <br>4、We use CAD software to plot the paddle.
 
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        </p>
 
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      </div>
 
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    </div>
 
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        <h2 class="timeline__item__content__date">2017.8.2-2017.8.9</h2>
 
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        <p class="timeline__item__content__description">
 
−
        1、We transform Rhodobacter sphaeroide by electric shock, but  the effect is not good.
 
−
        <br>2、We successfully constructed PIND4-SYFP2 (optimized) plasmids.
 
−
        <br>3、Measured the growth curve of Rhodobacter sphaeroides.
 
−
        <br>4、Thanks to the Synthetic Biology Gene Company as our sponsor, we made team jackets, brochure and postcard.
 
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        </p>
 
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      </div>
 
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        <h2 class="timeline__item__content__date">2017.8.9-2017.8.16</h2>
 
−
        <p class="timeline__item__content__description">
 
−
        1、We transform Rhodobacter sphaeroide by electric shock again, but  the effect is not good.
 
−
        <br>2、We successfully constructed PIND4-SYFP2(unoptimized) plasmids.
 
−
        <br>3、Apply for ECUST-iGEM club
 
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        <br>4、Cooperation with SUIS high school team
 
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        </p>
 
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      </div>
 
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        <h2 class="timeline__item__content__date">2017.8.16-2017.8.23</h2>
 
−
        <p class="timeline__item__content__description">
 
−
        1、We transform Rhodobacter sphaeroide by electric shock, but  the effect is not good.
 
−
        <br>2、Finished our first poster.
 
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        <br>3、Cooperation with Tongji University.
 
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        </p>
 
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        <h2 class="timeline__item__content__date">2017.8.23-2017.8.30</h2>
 
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        <p class="timeline__item__content__description">
 
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        Some of our team members participated in the CCiC meeting.
 
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        </p>
 
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        <h2 class="timeline__item__content__date">2017.8.30-2017.9.6</h2>
 
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        <p class="timeline__item__content__description">
 
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        The SYFP2 expression strain was successfully obtained by electroporation.
 
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        </p>
 
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      </div>
 
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        <h2 class="timeline__item__content__date">2017.9.6-2017.9.13</h2>
 
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        <p class="timeline__item__content__description">
 
−
        We transform Rhodobacter sphaeroide by electric shock, but  the effect is not good.
 
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        </p>
 
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      </div>
 
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        <h2 class="timeline__item__content__date">2017.9.13-2017.9.20</h2>
 
−
        <p class="timeline__item__content__description">
 
−
        We interviewed Prof. Qingli Xu to understand the current energy crisis.
 
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        </p>
 
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      </div>
 
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        <h2 class="timeline__item__content__date">2017.9.20-2017.9.27</h2>
 
−
        <p class="timeline__item__content__description">
 
−
        Completed the requirement for Part-submission and submitted 4 parts.
 
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        </p>
 
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        <h2 class="timeline__item__content__date">2017.9.27-2017.10.4</h2>
 
−
        <p class="timeline__item__content__description">
 
−
        1、We made the PPT and rehearsed it.
 
−
        <br>2、Perfected our modeling.
 
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        </p>
 
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        <h2 class="timeline__item__content__date">2017.10.4-2017.10.11</h2>
 
−
        <p class="timeline__item__content__description">
 
−
        1、Characterization of SYFP2 in cytoplasmic expression.
 
−
        <br>2、Editing Wiki pages.
 
−
        <br>3、Spectral scanning and fluorescence microscopy.
 
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        </p>
 
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        <h2 class="timeline__item__content__date">2017.10.11-2017.10.18</h2>
 
−
        <p class="timeline__item__content__description">
 
−
        1、Perform the final fermentation hydrogen production experiment
 
−
        <br>2、Continue to Edit Wiki pages.
 
−
        <br>3、Assembling a luminous stirring oar and simulating the flow field.
 
−
        <br>4、Interviewed with Guangming Group.
 
−
        <br>5、Hold Fret-me Games.
 
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        <h2 class="timeline__item__content__date">2017.10.18-2017.10.25</h2>
 
−
        <p class="timeline__item__content__description">
 
−
        1、Writing each copy of the wiki page.
 
−
        <br>2、Measuring photosynthetic growth curve.
 
−
        <br>3、Making new uniforms.
 
−
        <br>4、Editing Wiki
 
−
 
−
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−
        <h2 class="timeline__item__content__date">2017.10.25-2017.11.1</h2>
 
−
        <p class="timeline__item__content__description">
 
−
        Optimized the final wiki page and the Registry page
 
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Team:Rice/Software

Tacoma RAINmakers Lab Notebook

Week One

Digestion and Isolation of pSB1C3 Backbone.

The purpose of digesting the pSB1C3/PArsRGFP construct was to separate the backbone from the former GFP insert. Tacoma RAINmakers sought to isolate the pSB1C3 backbone employed in their 2017 construct, as the GFP reporter complex was no longer desired. Apparent disadvantages of GFP indication in biosensors are ultraviolet readings. The RAINmakers prefered a chromoprotein that produces color in the visible spectrum. Enzymes XbaI and SpeI were used to cleave the terminator sites of the vector, freeing the pSB1C3 backbone. NEB resources confirmed that the Cutsmart Buffer 2.1 is the most compatible with these particular enzymes, providing an optimized environment for digestion. Combining the reagents listed in Table 1.0, the reaction was set at 37ºC in a water bath for 1 hour and 45 minutes. This reaction was completed in duplicate to increase statistical probability of desired backbone DNA.

Step 2

Use RNADuplex[2] to calculate binding energies for all 4096 pairs of SD/ASD sequences.

We then use RNAduplex from the ViennaRNA package to calculate binding energies for all 4096 pairs of SD/ ASD sequences. Details

Step 3

Narrow library by eliminating mutant pairs with binding energy more than 0.5 kcal/mol away from wild-type value.

Again, we use RNAduplex to calculate binding energies, but this time between the candidate ASD sequences with the wild-type SD sequences. Details

Step 2-3

Figure S2. Narrowing down based on wild-type ASD/wild-type SD binding energy.

Step 4

Use RNADuplex to calculate binding energies between all remaining mutant ASDs with wildtype SD.

The library is narrowed down again by discarding those candidates with a binding energy less than -1 kcal/mol with the wild type SD sequences. This prevents the orthogonal ribosomes developed from the candidate ASDs from binding with wild type SD sequences over orthogonal mRNA, which ensures orthogonality of the engineered ribosomes. Details

Step 5

Narrow library by eliminating mutant ASD/Wildtype SD pairs with binding energy <-1.0 kcal/mol.

The library is narrowed down again by discarding those candidates with a binding energy less than -1 kcal/mol with the wild type SD sequences. This prevents the orthogonal ribosomes developed from the candidate ASDs from binding with wild type SD sequences over orthogonal mRNA, which ensures orthogonality of the engineered ribosomes. Details

Step 4-5

Figure S3. Ensure orthogonality of chosen sequences.

Step 6

Use RNAFold to estimate secondary structure formation of 16s rRNAs containing mutant ASD sequences.

We use RNAfold from the ViennaRNA package to calculate the secondary structure for the full 16s rRNA. Details

Step 7

Narrow library by eliminating sequences that lead to 16s rRNA having secondary structure formed at the ASD region.

Those candidates with secondary structure in the ASD regions are discarded, as this would impair their ability to carry out translation. Details

Step 6-7

Figure S4. Elimination of sequences that lead to secondary structure complications.

Step 8

Obtain all translation initiation regions (TIRs) from the chosen bacteria's genome.

Next, we obtain all the translation initiation regions (TIRs) from the genome. Details

Step 8-10

Figure S5. Overview: Obtaining all translation initiation regions from the Coding Region.

Step 8-10

Figure S6. Extracting the TIRs in different situations.

Step 9

Use RNADuplex[3] to calculate binding energy of each remaining mutant ASD with those TIRs.

We use these TIRs in conjunction with RNAduplex once again to calculate the binding energies of the remaining candidate ASDs with those TIRs. Details

Step 10

Rank candidate mutant ASDs based on number of strong interactions between the ASD sequence and the TIRs from the bacteria genome.

Candidates are then ranked based on their binding energies with the host TIRs. Candidates with higher binding energies (which are less likely to bind with host TIRs) are given preference, since they are more likely to remain orthogonal to the host processes. Details

Reference

[1] Darlington, A.P.S., Kim, J., Jiménez, J.I., & Bates, D.G. (2018). Dynamic allocation of orthogonal ribosomes facilitates uncoupling of co-expressed genes. Nature Communications, 9, 695.

[2] Ding, Y., Chan, C. Y., & Lawrence, C. E. (2005). RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA, 11(8), 1157–1166. http://doi.org/10.1261/rna.2500605

[3]“TBI - RNAduplex - Manpage.” Accessed September 12, 2018. https://www.tbi.univie.ac.at/RNA/RNAduplex.1.html.