Team:BU Wellesley Software/Notebook/MargauxNotebook

From 2011.igem.org

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6/1/11-6/6/11
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==6/1/11-6/6/11:BU-WELLESLEY TEAM BOOT CAMP ==
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BU-WELLESLEY TEAM BOOT CAMP
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  The boot camp gave me an opportunity to meet the Wellesley students and learn more about the computational/software side of the team.
 
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  Biology:
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The boot camp gave me an opportunity to meet the Wellesley students and learn more about the computational/software side of the team.
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-Reviewed a lot of terms and concepts that I had not seen in two years
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Biology:
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-Reviewed a lot of terms and concepts that I had not seen in two years
       -How to use restriction enzymes to cut and place different parts of the biobrick
       -How to use restriction enzymes to cut and place different parts of the biobrick
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-Saw the lab and practiced using a pipette, running a gel, etc.
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-Saw the lab and practiced using a pipette, running a gel, etc.
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-Watched an interesting background talk on tuberculosis and how we will assist in the efforts to understanding it
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-Watched an interesting background talk on tuberculosis and how we will assist in the efforts to understanding it
       -TB transitions from an active to a latent state
       -TB transitions from an active to a latent state
       -Hard to treat because the bacteria deceives the body's own immune system by covering itself in lipids
       -Hard to treat because the bacteria deceives the body's own immune system by covering itself in lipids
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Computational:
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Computational:
-Difficulties in setting up the logic behind using inverstases  
-Difficulties in setting up the logic behind using inverstases  
-Built a "hello world" application on Clotho as an introduction as to how create new applications  
-Built a "hello world" application on Clotho as an introduction as to how create new applications  
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6/7/11
 
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We set up plasmid preps.
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We set up plasmid preps.
In the lab meeting, we began looking at the parts and the part registry page to build up some new plasmids with different parts. I worked with Shannon to find three RBS from the Anderson Collection. We chose the following based on their antibiotic resistance and strength:
In the lab meeting, we began looking at the parts and the part registry page to build up some new plasmids with different parts. I worked with Shannon to find three RBS from the Anderson Collection. We chose the following based on their antibiotic resistance and strength:
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   -6.5% (strength)
   -6.5% (strength)
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3.Bba_J61110  
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3.Bba_J61100  
   -On both 2010/2011 plates (2010 Distribution Plate 1-Well 5J)
   -On both 2010/2011 plates (2010 Distribution Plate 1-Well 5J)
   -Resistance A
   -Resistance A
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We then plated them and set them aside to grow.  
We then plated them and set them aside to grow.  
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6/8/11
 
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We had the weekly lab meeting and discussed the work flow to build constructs.  
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We also noted that our bacteria with the three different RBS had grown with two different colored colonies. We   
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We had the weekly lab meeting and discussed the work flow to build constructs.  
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removed a piece of each colony in each sample (3 samples, 2 colonies each, 6 tubes) and did a prep for a plasmid  
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We also noted that our bacteria with the three different RBS had grown with two different colored colonies. We   
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prep.
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removed a piece of each colony in each sample (3 samples, 2 colonies each, 6 tubes) and did a prep for a plasmid  
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prep.
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6/9/11
 
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  Performed a plasmid prep on all six samples. The bacteria that grew during the prep for the plasmid prep showed
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Performed a plasmid prep on all six samples. The bacteria that grew during the prep for the plasmid prep showed
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  stringy lifeforms and bacteria in forms that we were not expecting. DNA quantification was low, and the gel  
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stringy lifeforms and bacteria in forms that we were not expecting. DNA quantification was low, and the gel  
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  electrophoresis showed nothing notable. We then checked the bacteria samples under a light microscope with a gram
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electrophoresis showed nothing notable. We then checked the bacteria samples under a light microscope with a gram
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  stain and saw that while the Ecoli we intended to be there was there, there were also other types of bacteria that  
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stain and saw that while the Ecoli we intended to be there was there, there were also other types of bacteria that  
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  were contaminating the sample.  
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were contaminating the sample.  
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6/10/11
 
      
      
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Autoclaved all our tips to make sure that they were not the source of contamination. Researched about how to build  
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Autoclaved all our tips to make sure that they were not the source of contamination. Researched about how to build  
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the constructs we are hoping to make.
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the constructs we are hoping to make.

Revision as of 17:34, 17 June 2011

6/1/11-6/6/11:BU-WELLESLEY TEAM BOOT CAMP

The boot camp gave me an opportunity to meet the Wellesley students and learn more about the computational/software side of the team.

Biology: -Reviewed a lot of terms and concepts that I had not seen in two years 

     -How to use restriction enzymes to cut and place different parts of the biobrick

-Saw the lab and practiced using a pipette, running a gel, etc. -Watched an interesting background talk on tuberculosis and how we will assist in the efforts to understanding it 

     -TB transitions from an active to a latent state
     -Hard to treat because the bacteria deceives the body's own immune system by covering itself in lipids

Computational: -Difficulties in setting up the logic behind using inverstases -Built a "hello world" application on Clotho as an introduction as to how create new applications -Explored Clotho and its pros and cons


We set up plasmid preps.

In the lab meeting, we began looking at the parts and the part registry page to build up some new plasmids with different parts. I worked with Shannon to find three RBS from the Anderson Collection. We chose the following based on their antibiotic resistance and strength:

1.Bba_J61101 

 -On both 2010/2011 plates  (2010 Distribution Plate 1-Well 5L) 
 -Resistance A
 -11.9% (strength)

2.Bba_J61127 

 -On both 2010/2011 plates (2010 Distribution Plate 1-Well 11N)
 -Resistance A
 -6.5% (strength)

3.Bba_J61100 

 -On both 2010/2011 plates (2010 Distribution Plate 1-Well 5J)
 -Resistance A
 -4.75% (strength)

We then plated them and set them aside to grow.


We had the weekly lab meeting and discussed the work flow to build constructs. We also noted that our bacteria with the three different RBS had grown with two different colored colonies. We removed a piece of each colony in each sample (3 samples, 2 colonies each, 6 tubes) and did a prep for a plasmid prep.


Performed a plasmid prep on all six samples. The bacteria that grew during the prep for the plasmid prep showed stringy lifeforms and bacteria in forms that we were not expecting. DNA quantification was low, and the gel electrophoresis showed nothing notable. We then checked the bacteria samples under a light microscope with a gram stain and saw that while the Ecoli we intended to be there was there, there were also other types of bacteria that were contaminating the sample.


Autoclaved all our tips to make sure that they were not the source of contamination. Researched about how to build the constructs we are hoping to make.

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