Difference between revisions of "Team:Yale/notebook"

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       <p>For Cyanobacteria, Dan inoculated both Synechocystis sp. 6803 and UTEX 2973 in BG-11.  Along with this, Danny read literature and determined the best proteins to use for increasing the efficiency of MAGE in cyanobacteria.  Colin searched for protocols that could be used for transformation, growth, and various other important processes.</p>
 
       <p>For Cyanobacteria, Dan inoculated both Synechocystis sp. 6803 and UTEX 2973 in BG-11.  Along with this, Danny read literature and determined the best proteins to use for increasing the efficiency of MAGE in cyanobacteria.  Colin searched for protocols that could be used for transformation, growth, and various other important processes.</p>
 
       <p>For the lab overall, we attempted to electroporate various plasmids into E. Coli to improve our technique.  However, these efforts were met with limited success.  </p>
 
       <p>For the lab overall, we attempted to electroporate various plasmids into E. Coli to improve our technique.  However, these efforts were met with limited success.  </p>
      <p class="text-center"><img src="http://client.cameronyick.us/igem/assets/img/journal/pigeon.jpg"></p>
 
 
       <p class="text-center"><a href="dropbox.com/#week3" class="file__link">Go to the Lab Notebook</a></p>
 
       <p class="text-center"><a href="dropbox.com/#week3" class="file__link">Go to the Lab Notebook</a></p>
 
       <h4 class="week_log">Entry for week<a href="#" data-reveal-id="week1">-1</a><a href="#" data-reveal-id="week2">1</a><a href="#" data-reveal-id="week3">2</a><a href="#" data-reveal-id="week4">3</a><a href="#" data-reveal-id="week5">4</a><a href="#" data-reveal-id="week6">5</a><a href="#" data-reveal-id="week7">6</a><a href="#" data-reveal-id="week8">7</a><a href="#" data-reveal-id="week9">8</a><a href="#" data-reveal-id="week10">9</a><a href="#" data-reveal-id="week11">10</a><a href="#" data-reveal-id="week12">10+</a>
 
       <h4 class="week_log">Entry for week<a href="#" data-reveal-id="week1">-1</a><a href="#" data-reveal-id="week2">1</a><a href="#" data-reveal-id="week3">2</a><a href="#" data-reveal-id="week4">3</a><a href="#" data-reveal-id="week5">4</a><a href="#" data-reveal-id="week6">5</a><a href="#" data-reveal-id="week7">6</a><a href="#" data-reveal-id="week8">7</a><a href="#" data-reveal-id="week9">8</a><a href="#" data-reveal-id="week10">9</a><a href="#" data-reveal-id="week11">10</a><a href="#" data-reveal-id="week12">10+</a>
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       <p>This week, we focused on obtaining and using new plasmids, pKT230  and pZE21G, because our prior plasmid, BBa_K125000 was causing various problems, from being improperly annotated online to stubbornly refusing to be isolated using a maxi prep. However, very little actual lab work was done this week. In regards to non-lab work, we researched and described a way to knock out the mutS gene in both Cyanobacteria and Rhizobia and explored the possibility of also porting a CRISPR/Cas9 system into Cyanobacteria or Rhizobia.</p>
 
       <p>This week, we focused on obtaining and using new plasmids, pKT230  and pZE21G, because our prior plasmid, BBa_K125000 was causing various problems, from being improperly annotated online to stubbornly refusing to be isolated using a maxi prep. However, very little actual lab work was done this week. In regards to non-lab work, we researched and described a way to knock out the mutS gene in both Cyanobacteria and Rhizobia and explored the possibility of also porting a CRISPR/Cas9 system into Cyanobacteria or Rhizobia.</p>
 
       <p>For lab work: we successfully miniprepped pKT230 and pZE21G out of E. Coli once the OD was 0.611. The Jacobs-Wagner lab at Yale also graciously gave us S. Meliloti cultures to use: #1021, #WM249, and #MB501. S. meliloti WM249 and MB501 are derivatives of Rm1021 with transposon insertions permitting the efficient electroporation of E. coli plasmid DNA. WM249 contains a Tn5-233 element encoding gentamicin resistance, whereas MB501 (obtained from M. Barnett, Stanford University) contains the same Tn5-233 swapped for trimethoprim resistance. We were also able to isolate the isiAB promoter from Cyanobacteria Synechococcus PCC 6803 using the PCR procedure outlined in the procedural notes. However, the ends of the promoter were custom-made to be gibson-assembly-ed into the BBa_K125000 plasmid, so if we end up switching plasmids we’d need to re-isolate the promoter. </p>
 
       <p>For lab work: we successfully miniprepped pKT230 and pZE21G out of E. Coli once the OD was 0.611. The Jacobs-Wagner lab at Yale also graciously gave us S. Meliloti cultures to use: #1021, #WM249, and #MB501. S. meliloti WM249 and MB501 are derivatives of Rm1021 with transposon insertions permitting the efficient electroporation of E. coli plasmid DNA. WM249 contains a Tn5-233 element encoding gentamicin resistance, whereas MB501 (obtained from M. Barnett, Stanford University) contains the same Tn5-233 swapped for trimethoprim resistance. We were also able to isolate the isiAB promoter from Cyanobacteria Synechococcus PCC 6803 using the PCR procedure outlined in the procedural notes. However, the ends of the promoter were custom-made to be gibson-assembly-ed into the BBa_K125000 plasmid, so if we end up switching plasmids we’d need to re-isolate the promoter. </p>
       <p>Let me explain CRISPR. CRISPR (clustered regularly interspaced short palindromic repeats) is a recently discovered system from certain bacterial adaptive immunity systems  that uses guide RNA and the Cas9 proteins to create gene knockouts and gene replacements. Guide RNA locates a specific homologous sequence in the DNA following a PAM sequence. The Cas9 protein then causes a double stranded break. Currently, we have found in literature that Synechococcus does not have a fully functional CRISPR-Cas system. This means that imported systems will work more effectively due to lack of cross talk. We also found that cyanobacteria are capable of non-homologous end joining (NHEJ). This means that cyanobacteria are prime targets for the porting of CRISPR- Cas systems. In order to test the ability of the imported CRISPR-Cas systems, we will target the UreC gene, a gene which confers sensitivity to solutions of urea and nickel sulfate. Already, we have designed the plasmids for the guide RNA and the Cas9 protein. Cas9 will be placed on a low copy number plasmid (Bba_125000) with an inducible promoter such as isiAB or nirA. gRNA will be placed on high copy number plasmid (KT230) with
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       <p>Let me explain CRISPR. CRISPR (clustered regularly interspaced short palindromic repeats) is a recently discovered system from certain bacterial adaptive immunity systems  that uses guide RNA and the Cas9 proteins to create gene knockouts and gene replacements. Guide RNA locates a specific homologous sequence in the DNA following a PAM sequence. The Cas9 protein then causes a double stranded break in the DNA (see the graphic below put together by the Wuhan University iGEM team in China). Currently, we have found in literature that Synechococcus does not have a fully functional CRISPR-Cas system. This means that imported systems will work more effectively due to lack of cross talk. We also found that cyanobacteria are capable of non-homologous end joining (NHEJ). This means that cyanobacteria are prime targets for the porting of CRISPR- Cas systems. In order to test the ability of the imported CRISPR-Cas systems, we will target the UreC gene, a gene which confers sensitivity to solutions of urea and nickel sulfate. Already, we have designed the plasmids for the guide RNA and the Cas9 protein. Cas9 will be placed on a low copy number plasmid (Bba_125000) with an inducible promoter such as isiAB or nirA. gRNA will be placed on high copy number plasmid (KT230) with
 
a constitutive promoter such as psaA. If necessary, the cas9 protein can be placed next to a tetR promoter, a promoter found in E. Coli but not natively in cyanobacteria. In addition, recently it has been found that CRISPR works in Arabidopsis and several strains of rhizobium. However, no CRISPR has been found in the strains of Rhizobia we intend to use. It has also been shown that Rhizobia exhibits NHEJ. Whether or not pursuing CRISPR would be useful is an idea that needs to be discussed.</p>
 
a constitutive promoter such as psaA. If necessary, the cas9 protein can be placed next to a tetR promoter, a promoter found in E. Coli but not natively in cyanobacteria. In addition, recently it has been found that CRISPR works in Arabidopsis and several strains of rhizobium. However, no CRISPR has been found in the strains of Rhizobia we intend to use. It has also been shown that Rhizobia exhibits NHEJ. Whether or not pursuing CRISPR would be useful is an idea that needs to be discussed.</p>
       <p class="text-center"><img src="http://client.cameronyick.us/igem/assets/img/journal/pigeon.jpg"></p>
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       <p class="text-center"><img src="https://static.igem.org/mediawiki/2015/2/2e/WHU_Cas9_Schematic.png"></p>
 
       <p>In order to port MAGE into Cyanobacteria and Sinorhizobia, the mutS gene must be knocked out. Why? MutS functions in the DNA mismatch repair pathway, which is a highly conserved system from prokaryotes to higher eukaryotes. The mutS protein recognizes a DNA mismatch, but since DNA mismatch is absolutely needed for the MAGE mechanism, a mutS knockout (KO) is essential for high mutagenesis efficiency. We decided that the best way to do this would be with a Flp-FRT Recombination. Here is the strategy for mutS Knockout in Synechococcus sp. PCC 7002:</p>
 
       <p>In order to port MAGE into Cyanobacteria and Sinorhizobia, the mutS gene must be knocked out. Why? MutS functions in the DNA mismatch repair pathway, which is a highly conserved system from prokaryotes to higher eukaryotes. The mutS protein recognizes a DNA mismatch, but since DNA mismatch is absolutely needed for the MAGE mechanism, a mutS knockout (KO) is essential for high mutagenesis efficiency. We decided that the best way to do this would be with a Flp-FRT Recombination. Here is the strategy for mutS Knockout in Synechococcus sp. PCC 7002:</p>
 
       <p>1) Amplify and assemble KO construct: 1 kb Homology Arm (UpF) → FRT → kanR → FRT → 1 kb Homology Arm (DownF)</p>
 
       <p>1) Amplify and assemble KO construct: 1 kb Homology Arm (UpF) → FRT → kanR → FRT → 1 kb Homology Arm (DownF)</p>

Revision as of 12:34, 16 September 2015


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Lab Notebook