Team:TP CC-SanDiego/Results.html

From 2014hs.igem.org

(Difference between revisions)
 
(42 intermediate revisions not shown)
Line 124: Line 124:
         </nav>
         </nav>
         </div>
         </div>
 +
 +
<div id="inside-wrapper-second">
 +
    <div id="secondnav">
 +
          <a href="#header-holder">Data And Analysis</a>
 +
          <a href="#linkheaderone">Conclusion and Future Directions</a>
 +
       
 +
        </div>
 +
    </div>
</div>
</div>
      
      
Line 131: Line 139:
<div id="header-text">
<div id="header-text">
         PCR Amplification <br />
         PCR Amplification <br />
-
    <span style="font-family: 'Lato'; font-size: 18px;">Amplifying vectors and synthesized genes to have desirable tails.</span>
+
    <span style="font-family: 'Lato'; font-size: 20px;">Amplifying vectors and synthesized genes to have desirable tails.</span>
     </div>
     </div>
</div>
</div>
-
<div id="phase-wrapper" style="background:url(https://static.igem.org/mediawiki/2014hs/6/6b/Victory.png); background-size:100%;">
+
<div id="phase-wrapper" style="background:url(https://static.igem.org/mediawiki/2014hs/d/df/B8_new.jpg); background-size:100%;">
   <div id="third-phase">
   <div id="third-phase">
  <center>  <img src="https://static.igem.org/mediawiki/2014hs/1/1f/PCR_Amplification_Results.png" width="720" height="490"/></center> <br>
  <center>  <img src="https://static.igem.org/mediawiki/2014hs/1/1f/PCR_Amplification_Results.png" width="720" height="490"/></center> <br>
     <span style="font-family: Lato; font-size: 18px; color: white;">
     <span style="font-family: Lato; font-size: 18px; color: white;">
-
<p align="left">
+
<p align="left">
By adjusting PCR settings, we were able to amplify the vector and inserts successfully.  
By adjusting PCR settings, we were able to amplify the vector and inserts successfully.  
Successfully amplified inserts and vectors with the desired ends were used for Seamless Cloning. </p></span>   
Successfully amplified inserts and vectors with the desired ends were used for Seamless Cloning. </p></span>   
Line 149: Line 157:
<div id="header-text">
<div id="header-text">
         Transformation<br />
         Transformation<br />
-
    <span style="font-family: Lato; font-size: 18px;">After seamless cloning; E. Coli uptake of assembled plasmid</span>
+
    <span style="font-family: Lato; font-size: 20px;">After seamless cloning; E. Coli uptake of assembled plasmid</span>
     </div>
     </div>
</div>
</div>
      
      
-
<div id="phase-wrapper" style="background:url(https://static.igem.org/mediawiki/2014hs/6/6b/Victory.png); background-size:100%;">
+
<div id="phase-wrapper" style="background:url(https://static.igem.org/mediawiki/2014hs/d/df/B8_new.jpg); background-size:100%;">
   <div id="third-phase">
   <div id="third-phase">
     <img src="https://static.igem.org/mediawiki/2014hs/e/ed/Transofmration_Results.png" width="400" height="400"/>
     <img src="https://static.igem.org/mediawiki/2014hs/e/ed/Transofmration_Results.png" width="400" height="400"/>
         <span style="font-family: Lato; font-size: 18px; color: white;">
         <span style="font-family: Lato; font-size: 18px; color: white;">
-
  <br> <p align="justify"> For AA, AZ, BA, and BZ, at least 10 colonies were grown for each LB+Amp agar plate that cultured the four different types of transformations. </p>
+
  <br> <br><br><br><br> <p align="justify"> For AA, AZ, BA, and BZ, at least 10 colonies were grown for each LB+Amp agar plate that cultured the four different types of transformations. </p>
-
<br>
+
  <p align="justify"> (Note: AA refers to alpha-amylase-ADTZ, AZ refers to alpha-amylase-ZHD101, BA refers to beta-lactamase-ADTZ, and BZ refers to beta-lactamase-ZHD101.) </p>
  <p align="justify"> (Note: AA refers to alpha-amylase-ADTZ, AZ refers to alpha-amylase-ZHD101, BA refers to beta-lactamase-ADTZ, and BZ refers to beta-lactamase-ZHD101.) </p>
Line 168: Line 175:
<div id="header-holder">
<div id="header-holder">
-
<div id="linkheadertwo"></div>
 
<div id="header-text">
<div id="header-text">
         Colony PCR<br />
         Colony PCR<br />
-
    <span style="font-family: 'Lato'; font-size: 18px;">PCR of colonies as template DNA</span>
+
    <span style="font-family: 'Lato'; font-size: 20px;">PCR of colonies as template DNA</span>
     </div>
     </div>
</div>
</div>
-
<div id="phase-wrapper" style="background:url(https://static.igem.org/mediawiki/2014hs/6/6b/Victory.png); background-size:100%;">
+
<div id="phase-wrapper" style="background:url(https://static.igem.org/mediawiki/2014hs/d/df/B8_new.jpg); background-size:100%;">
   <div id="third-phase">
   <div id="third-phase">
     <img src="https://static.igem.org/mediawiki/2014hs/b/bd/Colony_PCR_Results.png" width="800" height="400"/>  
     <img src="https://static.igem.org/mediawiki/2014hs/b/bd/Colony_PCR_Results.png" width="800" height="400"/>  
         <span style="font-family: Lato; font-size: 18px; color: white;">
         <span style="font-family: Lato; font-size: 18px; color: white;">
-
<br><p align="left"> After transformation in an LB+Amp agar plate, numerous colonies were selected individually for Colony PCR. The columns with the bands superficially signify that the desired plasmids are constructed. The colonies that are reported positive are plated separately and re-verified. </p><br>
+
<br><br><br><br><br><p align="left"> After the transformation in an LB+Amp agar plate, numerous colonies were selected individually for Colony PCR. The columns with the bands superficially signifies that the desired plasmids were constructed. The colonies that were reported positive were plated separately and re-verified. <br>
-
 
+
-
 
+
<center>
<center>
 +
AA: 2, 6, 13, 14, 19 ||
-
AA: 2, 6, 13, 14, 19 <br>
+
AZ: 1, 2, 4, 5, 6, 7 ||
-
AZ: 1, 2, 4, 5, 6, 7 <br>
+
BA: 6, 7, 8 ||
-
BA: 6, 7, 8 <br>
+
BZ: 2, 3, 5, 6, 7</center>
-
 
+
-
BZ: 2, 3, 5, 6, 7 </center>
+
</p>
</p>
</span>   
</span>   
Line 202: Line 205:
<div id="header-holder">
<div id="header-holder">
-
<div id="linkheadertwo"></div>
 
<div id="header-text">
<div id="header-text">
         Sequence Verification<br />
         Sequence Verification<br />
-
    <span style="font-family: 'Lato'; font-size: 18px;">Sequenced colonies vs. Theoretical plasmid</span>
+
    <span style="font-family: 'Lato'; font-size: 20px;">Sequenced colonies vs. Theoretical plasmid</span>
     </div>
     </div>
</div>
</div>
-
<div id="phase-wrapper" style="background:url(https://static.igem.org/mediawiki/2014hs/6/6b/Victory.png); background-size:100%;">
+
<div id="phase-wrapper" style="background:url(https://static.igem.org/mediawiki/2014hs/d/df/B8_new.jpg); background-size:100%;">
   <div id="third-phase">
   <div id="third-phase">
-
     <img src="https://static.igem.org/mediawiki/2014hs/archive/0/04/20140621011554%21Sequence_Verification_Analysis.png" width="600" height="400"/>
+
     <img src="https://static.igem.org/mediawiki/2014hs/0/04/Sequence_Verification_Analysis.png" width="600" height="400"/>
         <span style="font-family: Lato; font-size: 18px; color: white;">
         <span style="font-family: Lato; font-size: 18px; color: white;">
</br>  
</br>  
-
  <p align="justify">Using NCBI's Align BLAST, the sequencing data is compared with the theoretical plasmid data. If there is an 100% match, we declared these colonies to be successful. All the mutations that occurred in our set of colonies were deletion or addition mutations. AA13, AA14, AA19, AZ1, AZ5, AZ6, and AZ7 were 100% congruent. AA2 was determined to be a very likely because the error occurred in the region where the sequencing data had various "N"'s and the ab1 peaks were fluctuant.  </p>
+
  <p align="justify">Using NCBI's Align BLAST, the sequencing data was compared with the theoretical plasmid data. If there was a 100% match, we declared these colonies to be successful. All the mutations that occurred in our set of colonies were deletion or addition mutations. AA13, AA14, AA19, AZ1, AZ5, AZ6, and AZ7 were 100% congruent. AA2 was determined to be a very likely because the error occurred in the region where the sequencing data had various "N"'s and the ab1 peaks were fluctuant.  </p>
<p align="left">
<p align="left">
-
None of the beta-lactamse-attached colonies seemed to have the correct plasmids, due to point mutations in the ORF.  
+
None of the beta-lactamase-attached colonies seemed to have the correct plasmids due to point mutations in the ORF.  
<br>
<br>
-
AA: 2 (possible candidate),  6, 13 (100%), 14 (100%), 19 (100%)
+
AA: 2 (possible candidate),  6, 13 (100%), 14 (100%), 19 (100%)
-
AZ: 1 (100%), 2, 4, 5 (100%), 6 (100%), 7 (100%)
+
|| AZ: 1 (100%), 2, 4, 5 (100%), 6 (100%), 7 (100%)
-
BA: 6, 7, 8   
+
|| BA: 6, 7, 8   
-
BZ: 2, 3, 5, 6, 7 </p> </span></div>   
+
|| BZ: 2, 3, 5, 6, 7 </p> </span></div>   
</div>
</div>
<div id="header-holder">
<div id="header-holder">
-
<div id="linkheadertwo"></div>
 
<div id="header-text">
<div id="header-text">
         SDS-PAGE gel 1<br />
         SDS-PAGE gel 1<br />
-
    <span style="font-family: 'Lato'; font-size: 18px;">Visualization of presence and size of protein of interest.</span>
+
    <span style="font-family: 'Lato'; font-size: 20px;">Visualization of presence and size of protein of interest</span>
     </div>
     </div>
</div>
</div>
-
<div id="phase-wrapper" style="background:url(https://static.igem.org/mediawiki/2014hs/6/6b/Victory.png); background-size:100%;">
+
 
 +
 
 +
<div id="phase-wrapper" style="background:url(https://static.igem.org/mediawiki/2014hs/d/df/B8_new.jpg); background-size:100%;">
   <div id="third-phase">
   <div id="third-phase">
     <img src="https://static.igem.org/mediawiki/2014hs/4/49/SDS-PAGE1.png" width="750" height="350"/>
     <img src="https://static.igem.org/mediawiki/2014hs/4/49/SDS-PAGE1.png" width="750" height="350"/>
-
   
 
         <span style="font-family: Lato; font-size: 18px; color: white;">
         <span style="font-family: Lato; font-size: 18px; color: white;">
-
<br> <p align="left">We tested four parameters : pellet, supernatant, IPTG-induced, and non-induced. For both pellets and supernatants, IPTG-induced and IPTG-noninduced is hypothesized to have a stronger band for IPTG-induced, with visible difference in both the pellet and the supernatant. The first gel does show sharp difference between pellet and supernatant, but does not show a clear difference between IPTG-induced and non-induced. It implies that the plasmid is neither expressed nor secreted.</p> </span>   
+
<br><br><br><br><br> <p align="left">We tested four parameters : pellet, supernatant, IPTG-induced, and non-induced. For both pellets and supbernatants, IPTG-induced was hypothesized to have a stronger band for SDS-PAGE, with visible difference in both the pellet and the supernatant. The first gel did show sharp difference between pellet and supernatant, but did not show a clear difference between IPTG-induced and non-induced. It implies that the plasmid was neither expressed nor secreted.</p></span>   
</div>  
</div>  
</div>
</div>
 +
<div id="header-holder">
<div id="header-holder">
-
<div id="linkheadertwo"></div>
 
<div id="header-text">
<div id="header-text">
         Western Blot<br />
         Western Blot<br />
-
    <span style="font-family: 'Lato'; font-size: 18px;">Visualization of presence and size of protein of interest.</span>
+
    <span style="font-family: 'Lato'; font-size: 20px;">Visualization of presence and size of protein of interest</span>
     </div>
     </div>
</div>
</div>
-
<div id="phase-wrapper" style="background:url(https://static.igem.org/mediawiki/2014hs/6/6b/Victory.png); background-size:100%;">
+
<div id="phase-wrapper" style="background:url(https://static.igem.org/mediawiki/2014hs/d/df/B8_new.jpg); background-size:100%;">
   <div id="third-phase">
   <div id="third-phase">
     <img src="https://static.igem.org/mediawiki/2014hs/9/97/Western_results.png" width="640" height="380"/>
     <img src="https://static.igem.org/mediawiki/2014hs/9/97/Western_results.png" width="640" height="380"/>
             <span style="font-family: Lato; font-size: 18px; color: white;">
             <span style="font-family: Lato; font-size: 18px; color: white;">
-
<br> <p align="left">The Western Blot of two AZ colonies and two AA colonies were studied, both IPTG-induced and non-induced. The bands show that the plasmid was expressed at the very least, in the presence of IPTG, and in contrast to non-induced, but only in the pellet. It shows poor secretion. Possible explanations for this results include: </p>
+
<br> <br><br><p align="left">The Western Blot of two AZ colonies and two AA colonies were studied, both IPTG-induced and non-induced. The bands show that the plasmid was expressed at the very least, since it showed a stronger band in the presence of IPTG in the pellet. However, for the supernatant no bands were visible for neither IPTG-induced, nor non-induced, which shows poor secretion. Possible explanations for this results include:
-
 
+
<br> 1. The construct and the attached signal peptides are not functional and do not secrete.  
-
<br> 1. The construct and the attached signal peptides are not functional and do not secrete.  
+
<br> 2. E. Coli's secretion system is generally less effective.
<br> 2. E. Coli's secretion system is generally less effective.
<br> 3. The proteins are stored in the periplasm and not excreted to the extracellular space.  
<br> 3. The proteins are stored in the periplasm and not excreted to the extracellular space.  
-
<br> 4. The protein's structure (size or chemical properties) somehow interfered with the ability of it to be transported out. </span>   
+
<br> 4. The protein's structure (size or chemical properties) somehow interfered with the ability of it to be transported out. </p></span>   
</div>  
</div>  
</div>
</div>
Line 270: Line 271:
<div id="header-holder">
<div id="header-holder">
-
<div id="linkheadertwo"></div>
 
<div id="header-text">
<div id="header-text">
         SDS-PAGE gel 2<br />
         SDS-PAGE gel 2<br />
-
    <span style="font-family: 'Lato'; font-size: 18px;">Visualization of presence and size of protein of interest.</span>
+
    <span style="font-family: 'Lato'; font-size: 20px;">Visualization of presence and size of protein of interest</span>
     </div>
     </div>
</div>
</div>
-
<div id="phase-wrapper" style="background:url(https://static.igem.org/mediawiki/2014hs/6/6b/Victory.png); background-size:100%;">
+
<div id="phase-wrapper" style="background:url(https://static.igem.org/mediawiki/2014hs/d/df/B8_new.jpg); background-size:100%;">
   <div id="third-phase">
   <div id="third-phase">
-
     <img src="https://static.igem.org/mediawiki/2014hs/6/69/SDS_2_results.png" width="600" height="500"/>
+
     <img src="https://static.igem.org/mediawiki/2014hs/archive/6/69/20140621013037%21SDS_2_results.png" width="480" height="400"/>
         <span style="font-family: Lato; font-size: 18px; color: white;">
         <span style="font-family: Lato; font-size: 18px; color: white;">
-
<br> <p align="justify">The SDS-PAGE is tried again. This time, only IPTG-induced supernatant is taken into account to compare amongst colonies and narrow down the list of colonies needing to be tested. Some colonies show expression of proteins of the approximately accurate size in the supernatant, while the previous gel showed none. The ones that do are selected, and of those, a western blot of both IPTG-induced and non-induced is suggested. </p></span>   
+
<br> <br><br><br> <p align="justify">The SDS-PAGE was tried again. This time, only IPTG-induced supernatant was taken into account to compare amongst colonies and narrow down the list of colonies needing to be tested. Some colonies showed expression of proteins of the approximately accurate size in the supernatant, while the previous gel showed none. The ones that did were selected, and of those, a western blot of both IPTG-induced and non-induced was suggested. </p></span>   
</div>  
</div>  
</div>
</div>
 +
 +
 +
 +
<div id="header-holder">
<div id="header-holder">
-
<div id="linkheadertwo"></div>
+
<div id="linkheaderone"></div>
<div id="header-text">
<div id="header-text">
-
         Future Directions<br />
+
         Conclusion And Future Directions<br />
-
    <span style="font-family: 'Lato'; font-size: 18px;">The fight will continue.</span>
+
    <span style="font-family: 'Lato'; font-size: 20px;">The fight will continue.</span>
     </div>
     </div>
</div>
</div>
-
<div id="phase-wrapper" style="background:url(https://static.igem.org/mediawiki/2014hs/6/6b/Victory.png); background-size:100%;">
+
<div id="phase-wrapper" style="background:url(https://static.igem.org/mediawiki/2014hs/d/df/B8_new.jpg); background-size:100%;">
   <div id="third-phase">
   <div id="third-phase">
-
     <img src="" width="900" height="300"/>
+
     <img src="https://static.igem.org/mediawiki/2014/2/23/NEW_LOGO.png" width="200" height="200"/>
         <span style="font-family: Lato; font-size: 18px; color: white;">
         <span style="font-family: Lato; font-size: 18px; color: white;">
<br>  
<br>  
 +
<p align="justify">
 +
Two of the four final constructs, AA and AZ, were sequence verified 100%. The SDS-PAGE analysis initially showed inconclusive levels of expression and extracellular secretion of the alpha-amylase attached proteins. The Western Blot, however, confirmed that expression is present, but did not show any signs of secretion. A secondary SDS-PAGE was done for more induced colonies, and there were signs of secreted protein that are to be explored. Future directions include:
 +
 +
</p>
<p align="left">
<p align="left">
-
1. The colonies selected from SDS-PAGE Gel 2 need to be tested further with Western blotting and compared amongst pellet, supernatant, IPTG-induced, and non-induced. .Just one western blotting of two random colonies does not allow for conclusive results. <br>
+
1. Successful colonies from SDS-PAGE Gel 2 need to be tested further with Western blotting and compared amongst pellet, supernatant, induced, and non-induced. <br>
-
2. Try to succeed in the construction of beta-lactamase signal peptide containing recombinant plasmids, since we were not able to for now. Then compare alpha-amylase signal peptide and beta-lactamse signal peptide levels of secretion. <br>  
+
2. Try to succeed in the construction of beta-lactamase signal peptide containing recombinant plasmids, since we were not able to for now. Then compare alpha-amylase signal peptide and beta-lactamase signal peptide levels of secretion. <br> <br>
3. Do protein functionality assay of secreted ADTZ and ZHD with HPLC. <br>  
3. Do protein functionality assay of secreted ADTZ and ZHD with HPLC. <br>  
4. Try other signal peptides, such as the TAT-dependent pathways or SRP-dependent pathways. <br>
4. Try other signal peptides, such as the TAT-dependent pathways or SRP-dependent pathways. <br>
-
5. Genetically modify plants directly instead of modifying E. Coli. </p><br></span>   
+
5. Genetically modify plants directly instead of modifying E. Coli. <br>
 +
6. Try organisms with more pronounced secretion systems such as yeasts and fungi. </p> </span>   
</div>  
</div>  
</div>
</div>

Latest revision as of 01:53, 1 July 2014

iGEM San Diego

PCR Amplification
Amplifying vectors and synthesized genes to have desirable tails.

By adjusting PCR settings, we were able to amplify the vector and inserts successfully. Successfully amplified inserts and vectors with the desired ends were used for Seamless Cloning.

Transformation
After seamless cloning; E. Coli uptake of assembled plasmid





For AA, AZ, BA, and BZ, at least 10 colonies were grown for each LB+Amp agar plate that cultured the four different types of transformations.

(Note: AA refers to alpha-amylase-ADTZ, AZ refers to alpha-amylase-ZHD101, BA refers to beta-lactamase-ADTZ, and BZ refers to beta-lactamase-ZHD101.)

Colony PCR
PCR of colonies as template DNA





After the transformation in an LB+Amp agar plate, numerous colonies were selected individually for Colony PCR. The columns with the bands superficially signifies that the desired plasmids were constructed. The colonies that were reported positive were plated separately and re-verified.

AA: 2, 6, 13, 14, 19 || AZ: 1, 2, 4, 5, 6, 7 || BA: 6, 7, 8 || BZ: 2, 3, 5, 6, 7

Sequence Verification
Sequenced colonies vs. Theoretical plasmid

Using NCBI's Align BLAST, the sequencing data was compared with the theoretical plasmid data. If there was a 100% match, we declared these colonies to be successful. All the mutations that occurred in our set of colonies were deletion or addition mutations. AA13, AA14, AA19, AZ1, AZ5, AZ6, and AZ7 were 100% congruent. AA2 was determined to be a very likely because the error occurred in the region where the sequencing data had various "N"'s and the ab1 peaks were fluctuant.

None of the beta-lactamase-attached colonies seemed to have the correct plasmids due to point mutations in the ORF.
AA: 2 (possible candidate), 6, 13 (100%), 14 (100%), 19 (100%) || AZ: 1 (100%), 2, 4, 5 (100%), 6 (100%), 7 (100%) || BA: 6, 7, 8 || BZ: 2, 3, 5, 6, 7

SDS-PAGE gel 1
Visualization of presence and size of protein of interest





We tested four parameters : pellet, supernatant, IPTG-induced, and non-induced. For both pellets and supbernatants, IPTG-induced was hypothesized to have a stronger band for SDS-PAGE, with visible difference in both the pellet and the supernatant. The first gel did show sharp difference between pellet and supernatant, but did not show a clear difference between IPTG-induced and non-induced. It implies that the plasmid was neither expressed nor secreted.

Western Blot
Visualization of presence and size of protein of interest



The Western Blot of two AZ colonies and two AA colonies were studied, both IPTG-induced and non-induced. The bands show that the plasmid was expressed at the very least, since it showed a stronger band in the presence of IPTG in the pellet. However, for the supernatant no bands were visible for neither IPTG-induced, nor non-induced, which shows poor secretion. Possible explanations for this results include:
1. The construct and the attached signal peptides are not functional and do not secrete.
2. E. Coli's secretion system is generally less effective.
3. The proteins are stored in the periplasm and not excreted to the extracellular space.
4. The protein's structure (size or chemical properties) somehow interfered with the ability of it to be transported out.

SDS-PAGE gel 2
Visualization of presence and size of protein of interest




The SDS-PAGE was tried again. This time, only IPTG-induced supernatant was taken into account to compare amongst colonies and narrow down the list of colonies needing to be tested. Some colonies showed expression of proteins of the approximately accurate size in the supernatant, while the previous gel showed none. The ones that did were selected, and of those, a western blot of both IPTG-induced and non-induced was suggested.

Conclusion And Future Directions
The fight will continue.

Two of the four final constructs, AA and AZ, were sequence verified 100%. The SDS-PAGE analysis initially showed inconclusive levels of expression and extracellular secretion of the alpha-amylase attached proteins. The Western Blot, however, confirmed that expression is present, but did not show any signs of secretion. A secondary SDS-PAGE was done for more induced colonies, and there were signs of secreted protein that are to be explored. Future directions include:

1. Successful colonies from SDS-PAGE Gel 2 need to be tested further with Western blotting and compared amongst pellet, supernatant, induced, and non-induced.
2. Try to succeed in the construction of beta-lactamase signal peptide containing recombinant plasmids, since we were not able to for now. Then compare alpha-amylase signal peptide and beta-lactamase signal peptide levels of secretion.

3. Do protein functionality assay of secreted ADTZ and ZHD with HPLC.
4. Try other signal peptides, such as the TAT-dependent pathways or SRP-dependent pathways.
5. Genetically modify plants directly instead of modifying E. Coli.
6. Try organisms with more pronounced secretion systems such as yeasts and fungi.