Difference between revisions of "Team:BroadRun-NorthernVA/Notebook"

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<h2 align="left" class="pageheading"<font size="4.3"><b>June</b></h2>
 
<h2 align="left" class="pageheading"<font size="4.3"><b>June</b></h2>
  
−
<h align="left" class="subheading"<font size="3.8"><b>Week 1</b></h2>
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<h align="left" class="pageheading"<font size="3.8"><b>Week 1</b></font></h2>
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<li>
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<font size="3.3"><li>
 
       After hearing about the industrial waste water purification issue our corporate sponsor was dealing with, we began to brainstorm ideas for solutions. Our first few solutions were to break down butyric acid into butanol, prevent the pyruvate to butyric acid pathway by secreting a compound that would inhibit the enzymatic activity of acetyl-CoA-acetyl transferase, introducing water bears (tardigrades) to the water system that would feed on the microbes in the water, and eliminating the starch in the water so as to prevent the microbial growth.  
 
       After hearing about the industrial waste water purification issue our corporate sponsor was dealing with, we began to brainstorm ideas for solutions. Our first few solutions were to break down butyric acid into butanol, prevent the pyruvate to butyric acid pathway by secreting a compound that would inhibit the enzymatic activity of acetyl-CoA-acetyl transferase, introducing water bears (tardigrades) to the water system that would feed on the microbes in the water, and eliminating the starch in the water so as to prevent the microbial growth.  
 
Decided on the latter approach: it was more sustainable, efficient, and cost effective than the others.  
 
Decided on the latter approach: it was more sustainable, efficient, and cost effective than the others.  
  
 
     </li>  
 
     </li>  
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</font>
  
−
 
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<h align="left"class="pageheading" <font size="3.8"><b>Week 2-4</b></font></h2>
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<h align="left" class="subheading"<font size="3.8"><b>Week 2-4</b></h2>
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<font size="3.3"><li>Researched the best way to go about this solution.</li>
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<li>Researched the best way to go about this solution.</li>
+
 
<li>Saccharomyces was decided as our organism, because of it ability to thrive in a variety of conditions, both aerobic and anaerobic.  
 
<li>Saccharomyces was decided as our organism, because of it ability to thrive in a variety of conditions, both aerobic and anaerobic.  
 
</li>
 
</li>
  
 
<li>We decided on amylase, specifically alpha amylase, because of its ability to break down a variety of different starches. Alpha amylase can break down starches faster than other forms, because it can act in any substrate</li>
 
<li>We decided on amylase, specifically alpha amylase, because of its ability to break down a variety of different starches. Alpha amylase can break down starches faster than other forms, because it can act in any substrate</li>
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+
</font>
  
  
 
<h2 align="left" class="pageheading"<font size="4.3"><b>July</b></h2>
 
<h2 align="left" class="pageheading"<font size="4.3"><b>July</b></h2>
  
−
<li>More literature research and worked on developing protocols.  
+
<font size="3.3"><li>More literature research and worked on developing protocols.  
 
Ordered materials for the project, enzymes, reagents, buffers, kits, agar plates, LB broth, etc.  
 
Ordered materials for the project, enzymes, reagents, buffers, kits, agar plates, LB broth, etc.  
  
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<li>Ordered materials for the project, enzymes, reagents, buffers, kits, agar plates, LB broth, etc. </li>
 
<li>Ordered materials for the project, enzymes, reagents, buffers, kits, agar plates, LB broth, etc. </li>
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</font>
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 +
<h2 align="left" class="pageheading"<font size="4.3"><b>August</b></h2>
  
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<b><h align="left" class="pageheading"<font size="3.8">Week 1</b></h2></font>
  
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<h2 align="left" class="subheading">August 8</h2>
 
 
<ul class="listitems"><font color="black">
 
<ul class="listitems"><font color="black">
 
<font size="3.3"><li><span>Designed 3 amylase gene constructs to be synthesized through IDT’s offer. The amylase gene used for all three constructs was the alpha amylase coding sequence from Bacillus amyloliquefaciens. The Genbank accession number is J01542.1. First parts used were pCyc (medium) promoter (Part BBa_I766555), Kozak sequence (Part BBa_K165002), Alpha amylase coding sequence (Genbank Accession #J01542.1), and ADH1 Terminator (Part BBa_K801012).The alpha amylase coding sequence contained an EcoR1 restriction site, so GeneDesign was used to eliminate the site and optimize the construct for S.cerevisiae.  
 
<font size="3.3"><li><span>Designed 3 amylase gene constructs to be synthesized through IDT’s offer. The amylase gene used for all three constructs was the alpha amylase coding sequence from Bacillus amyloliquefaciens. The Genbank accession number is J01542.1. First parts used were pCyc (medium) promoter (Part BBa_I766555), Kozak sequence (Part BBa_K165002), Alpha amylase coding sequence (Genbank Accession #J01542.1), and ADH1 Terminator (Part BBa_K801012).The alpha amylase coding sequence contained an EcoR1 restriction site, so GeneDesign was used to eliminate the site and optimize the construct for S.cerevisiae.  

Revision as of 21:38, 7 September 2015

{{BroadRun-NorthernVA}}



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Lab Notebook

Welcome to our Lab Notebook! Here, we have documented the work done in our project so we can see and keep track of how our project is progressing.

June

Week 1
  • After hearing about the industrial waste water purification issue our corporate sponsor was dealing with, we began to brainstorm ideas for solutions. Our first few solutions were to break down butyric acid into butanol, prevent the pyruvate to butyric acid pathway by secreting a compound that would inhibit the enzymatic activity of acetyl-CoA-acetyl transferase, introducing water bears (tardigrades) to the water system that would feed on the microbes in the water, and eliminating the starch in the water so as to prevent the microbial growth. Decided on the latter approach: it was more sustainable, efficient, and cost effective than the others.
    • Week 2-4
  • Researched the best way to go about this solution.
  • Saccharomyces was decided as our organism, because of it ability to thrive in a variety of conditions, both aerobic and anaerobic.
  • We decided on amylase, specifically alpha amylase, because of its ability to break down a variety of different starches. Alpha amylase can break down starches faster than other forms, because it can act in any substrate
    •

    July

  • More literature research and worked on developing protocols. Ordered materials for the project, enzymes, reagents, buffers, kits, agar plates, LB broth, etc.
  • Experiment details were solidified and planned out in more detail.
  • Ordered materials for the project, enzymes, reagents, buffers, kits, agar plates, LB broth, etc.

    • August

    Week 1
    • Designed 3 amylase gene constructs to be synthesized through IDT’s offer. The amylase gene used for all three constructs was the alpha amylase coding sequence from Bacillus amyloliquefaciens. The Genbank accession number is J01542.1. First parts used were pCyc (medium) promoter (Part BBa_I766555), Kozak sequence (Part BBa_K165002), Alpha amylase coding sequence (Genbank Accession #J01542.1), and ADH1 Terminator (Part BBa_K801012).The alpha amylase coding sequence contained an EcoR1 restriction site, so GeneDesign was used to eliminate the site and optimize the construct for S.cerevisiae. However with this combination, IDT would not accept our design, due to repeats and sections with a low GC count. The constructs were redesigned, keeping the same coding sequence and Kozak sequence, but using the minimal cyc promoter (Part ) and minimal adh1 terminator (Part ). In order to test several variants on the expression of amylase, two promoters, and two secretion sequences were used. Plasma DNA was used to map restriction sites, and Gene design used to remove restriction sites. The final makeup of the gene constructs are listed below.

      Construct 1

    • Biobrick prefix
    • Promoterless
    • Kozak sequence (Part BBa_K165002)
    • Native secretion sequence, from Bacillus amyloliquefaciens
    • Alpha amylase coding sequence from Bacillus amyloliquefaciens
    • ADH1 Terminator (Part BBa_K392003)
    • Biobrick Suffix

      • Construct 2

    • Biobrick prefix
    • Minimal cyc promoter (Part BBa_K105027)
    • Kozak sequence (Part BBa_K165002)
    • Native secretion sequence, from Bacillus amyloliquefaciens
    • Alpha amylase coding sequence from Bacillus amyloliquefaciens
    • ADH1 Terminator (Part BBa_K392003)
    • Biobrick Suffix

      • Construct 3

    • Biobrick prefix
    • Minimal cyc promoter (Part BBa_K105027)
    • Kozak sequence (Part BBa_K165002)
    • Native secretion sequence, from Bacillus amyloliquefaciens
    • Alpha amylase coding sequence from Bacillus amyloliquefaciens
    • ADH1 Terminator (Part BBa_K392003)
    • Biobrick Suffix

    Week 2