Team:Davidson-MissouriW/Notebook

From 2010.igem.org

(Difference between revisions)
(Notebook)
(Notebook)
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<li>Ligated pLac-RBS-RFP + RBS-TetA.
<li>Ligated pLac-RBS-RFP + RBS-TetA.
<li>IPTG experiment started on pLacI-RBS-RFP </li>
<li>IPTG experiment started on pLacI-RBS-RFP </li>
 +
<li>Worked on the color schemes for the new Oligator
 +
<li>Created a new construct that might be helpful for the biologists
</ul>
</ul>
<br>
<br>
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<li>EcoRI/PstI diagnostic digest performed on pLac-RBS-RFP in pSB1A7 vector.
<li>EcoRI/PstI diagnostic digest performed on pLac-RBS-RFP in pSB1A7 vector.
<li>IPTG experiment started on plates with pLac and pLacI constructs. </li>
<li>IPTG experiment started on plates with pLac and pLacI constructs. </li>
 +
<li>Began working on a Java code that will run simulations for all the constructs
 +
<li>Researched on NP-Complete problems
</ul>
</ul>
<br>
<br>
Line 104: Line 108:
<li>Flourimeter data collected from IPTG experiment.
<li>Flourimeter data collected from IPTG experiment.
<li>Ligated pLacI-RBS-RFP + RBS-TetA. </li>
<li>Ligated pLacI-RBS-RFP + RBS-TetA. </li>
 +
<li>Worked on graphics of the Java program
 +
<li>Studied specific NP-Complete problems and brainstormed ways to incorporate them in our project
</ul>
</ul>
<br>
<br>
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<li>Picked 4 colonies from pLacI-RBS-RFP-RBS-TetA plates.  
<li>Picked 4 colonies from pLacI-RBS-RFP-RBS-TetA plates.  
<li>IPTG experiment started using newly created IPTG.  </li>
<li>IPTG experiment started using newly created IPTG.  </li>
 +
<li>Debugged the Java program
 +
<li>Created a new page for the GCAT server
</ul>
</ul>
<br>
<br>
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<li>Digested TetA with EcoRI/NheI.
<li>Digested TetA with EcoRI/NheI.
<li>Annealed oligos for optimized and deoptimized TetA segment 1.  </li>
<li>Annealed oligos for optimized and deoptimized TetA segment 1.  </li>
 +
<li>Improved the Java program
 +
<li>Began categorizing the knapsack problem into subparts
</ul>
</ul>
<br>
<br>
Line 125: Line 135:
<li>Ligated annealed TetA oligos into digested TetA.
<li>Ligated annealed TetA oligos into digested TetA.
<li>Inducer curve experiment started on pLac and pLacI constructs.  </li>
<li>Inducer curve experiment started on pLac and pLacI constructs.  </li>
 +
<li>Added buttons to the java program
 +
<li>Brainstormed biological implications in different NP-Complete problems
</ul>
</ul>
<br>
<br>
Line 132: Line 144:
<li>Preparative NheI/BamHI digest performed on TetA.
<li>Preparative NheI/BamHI digest performed on TetA.
<li>Preparative EcoRI/NheI digest performed on TetA. </li>
<li>Preparative EcoRI/NheI digest performed on TetA. </li>
 +
<li>Restructuring and reorganizing the Java program
 +
<li>Reviewed numerical algorithms and its relation to NP-Complete problems
</ul>
</ul>
<br>
<br>
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<hr>
<hr>
<ul>
<ul>
-
<li> Annealed optimized and deoptimized segment 1 TetA ligated into vector.  
+
<li>Annealed optimized and deoptimized segment 1 TetA ligated into vector.  
<li>Annealed optimized and deoptimized segment 2 TetA ligatied into vector.</li>
<li>Annealed optimized and deoptimized segment 2 TetA ligatied into vector.</li>
 +
<li>Added weight characteristic to the fluorescent proteins in the Java code
 +
<li>Continued exploration of NP-Complete problems
</ul>
</ul>
<br>
<br>
Line 145: Line 161:
<ul>
<ul>
<li>Inducer curve experiment started on pLac and pLacI constructs.  
<li>Inducer curve experiment started on pLac and pLacI constructs.  
 +
<li>Picked colonies from TetA segment 1 & 2 optimized & deoptimized plates. </li>
 +
<li>Added histograms to the Java Code
 +
<li>Researched and analyzed the effectiveness of Cre
 +
</ul>
 +
<br>
 +
'''June 28, 2010'''
 +
<hr>
 +
<ul>Added the option for the user to input the weights of the various modules and began work on custom construct builder
<li>Picked colonies from TetA segment 1 & 2 optimized & deoptimized plates. </li>
<li>Picked colonies from TetA segment 1 & 2 optimized & deoptimized plates. </li>
</ul>
</ul>
Line 153: Line 177:
<li>Screened segment 1 optimized and deoptimized candidate clones using RFLP
<li>Screened segment 1 optimized and deoptimized candidate clones using RFLP
<li>Screened segment 2 optimized and deoptimized candidate clones using RFLP </li>
<li>Screened segment 2 optimized and deoptimized candidate clones using RFLP </li>
 +
<li>Finished the simulation program and exported it
 +
<li>Explored the set covering problem
 +
<li>Researched applications of the knapsack problem in cryptography
 +
<li>
</ul>
</ul>
<br>
<br>
Line 160: Line 188:
<li>Tet titration experiment performed on pLac and pLacI +RBS-RFP-RBS-TetA.
<li>Tet titration experiment performed on pLac and pLacI +RBS-RFP-RBS-TetA.
<li>Ligated TetA onto pLac and pLacI +RBS-RFP-RBS-TetA with no terminator.  </li>
<li>Ligated TetA onto pLac and pLacI +RBS-RFP-RBS-TetA with no terminator.  </li>
 +
<li>Some final work on the simulation program
 +
<li>Discussed new ideas such as integer programming
</ul>
</ul>
<br>
<br>

Revision as of 15:22, 27 July 2010

Notebook

June 1, 2010


  • Tested to find lethal concentration of Tet in plated and liquid mediums
  • Verified RCBS with our sequences and researched codon optimization methods
  • Analyzed probabilities for constructs A and B


June 2, 2010


  • Mini prepped, diagnostic RP digest, preparative digest, ligation, pBAD+RBS-RFP
  • Researched different ways to optimize a gene
  • Began simulation for Constructs A and B


June 3, 2010


  • Mini prepped, diagnostic RP digest, preparative digest, ligation, pBAD+RBS-RFP
  • Researched restriction sites and created proposal for gene optimization
  • Continued work on simulation in Java and Matlab


June 4, 2010


  • Mini prepped RBS-TetA-TT
  • RX Fragment digestion for RBS-TetA-TT
  • Analyzed the optimization of tetA sequence and researched properties of Lox sites
  • Debugged Simulations


June 7, 2010


  • Ligate and plasmid check for pSB1A2 or pSB1AK3
  • Began working to improve the Lancelator and created histograms for simulations


June 8, 2010


  • Double digest on pBAD-RBS-RFP to make an RS fragment insert.
  • Worked on a Perl program that check for Bio Brick Restriction Sites


June 9, 2010


  • EcoRI and PstI digest on pLac and pBad colonies.
  • Arabinose and IPTG concentration experiments started.
  • Continued work on the Lancelator program and began working on a different simulation for Construct C and D


June 10, 2010


  • Picked 14 colonies from pLac-RBS-RFP and pLac-RBS-RFP-RBS plates.
  • Started inducer curve experiments.
  • Linked Lancelator code to the website and continued simulations


June 11, 2010


  • Ligated S03736 into pSB1A7 vector.
  • EcoRI/PstI digest on pLac-RBS-RFP-RBS colonies.
  • Added new features to the Lancelator and worked on numerically representing Construct C for the Matlab simulation


June 14, 2010


  • EcoRI/PstI diagnostic digest performed on pBad-RBS-RFP colonies.
  • Inducer curve experiment started on pBad and pLac constructs.
  • Debugged Lancelator and finished numerical representation for the simulation


June 15, 2010


  • Ligated pLac-RBS-RFP + RBS-TetA.
  • IPTG experiment started on pLacI-RBS-RFP
  • Worked on the color schemes for the new Oligator
  • Created a new construct that might be helpful for the biologists


June 16, 2010


  • EcoRI/PstI diagnostic digest performed on pLac-RBS-RFP in pSB1A7 vector.
  • IPTG experiment started on plates with pLac and pLacI constructs.
  • Began working on a Java code that will run simulations for all the constructs
  • Researched on NP-Complete problems


June 17, 2010


  • Flourimeter data collected from IPTG experiment.
  • Ligated pLacI-RBS-RFP + RBS-TetA.
  • Worked on graphics of the Java program
  • Studied specific NP-Complete problems and brainstormed ways to incorporate them in our project


June 18, 2010


  • Picked 4 colonies from pLacI-RBS-RFP-RBS-TetA plates.
  • IPTG experiment started using newly created IPTG.
  • Debugged the Java program
  • Created a new page for the GCAT server


June 21, 2010


  • Digested TetA with EcoRI/NheI.
  • Annealed oligos for optimized and deoptimized TetA segment 1.
  • Improved the Java program
  • Began categorizing the knapsack problem into subparts


June 22, 2010


  • Ligated annealed TetA oligos into digested TetA.
  • Inducer curve experiment started on pLac and pLacI constructs.
  • Added buttons to the java program
  • Brainstormed biological implications in different NP-Complete problems


June 23, 2010


  • Preparative NheI/BamHI digest performed on TetA.
  • Preparative EcoRI/NheI digest performed on TetA.
  • Restructuring and reorganizing the Java program
  • Reviewed numerical algorithms and its relation to NP-Complete problems


June 24, 2010


  • Annealed optimized and deoptimized segment 1 TetA ligated into vector.
  • Annealed optimized and deoptimized segment 2 TetA ligatied into vector.
  • Added weight characteristic to the fluorescent proteins in the Java code
  • Continued exploration of NP-Complete problems


June 27, 2010


  • Inducer curve experiment started on pLac and pLacI constructs.
  • Picked colonies from TetA segment 1 & 2 optimized & deoptimized plates.
  • Added histograms to the Java Code
  • Researched and analyzed the effectiveness of Cre


June 28, 2010


    Added the option for the user to input the weights of the various modules and began work on custom construct builder
  • Picked colonies from TetA segment 1 & 2 optimized & deoptimized plates.


June 29, 2010


  • Screened segment 1 optimized and deoptimized candidate clones using RFLP
  • Screened segment 2 optimized and deoptimized candidate clones using RFLP
  • Finished the simulation program and exported it
  • Explored the set covering problem
  • Researched applications of the knapsack problem in cryptography


June 30, 2010


  • Tet titration experiment performed on pLac and pLacI +RBS-RFP-RBS-TetA.
  • Ligated TetA onto pLac and pLacI +RBS-RFP-RBS-TetA with no terminator.
  • Some final work on the simulation program
  • Discussed new ideas such as integer programming


July 1, 2010


  • Preparative BamHI/NheI digest performed on TetA.
  • New experiment protocol developed for reduced vector background noise.


July 2, 2010


  • Mini prepped, diagnostic RP digest, preparative digest, ligation, pBAD+RBS-RFP


July 6, 2010


  • Ligated S04446 and S04447 to J31007.
  • Tet titration experiment performed on pLac and pLacI +RBS-RFP-RBS-TetA.


July 7, 2010


  • Ligated S04448 to RBS-TetA.
  • Ligated S04449 to RBS-TetA.


July 8, 2010


  • IPTG experiment started using pre-induced method.
  • IPTG experiment started using varying levels of tetracycline.


July 9, 2010


  • Picked optimized and deoptimized TetA colonies.
  • Flourimeter data collected from IPTG experiment.


July 10, 2010


  • Used RFLP to screen for candidate TetA clones.
  • Transformed various pLac and pLacI constructs into MG1655 cells.


July 13, 2010


  • Used RFLP to screen for candidate TetA clones.
  • EcoRI/PstI diagnostic digest performed on K199150.


July 14, 2010


  • Ligated segment 2 optimized and deoptimzed TetA behind segment 1.
  • IPTG experiment started on I715039-1 and I715039-2.


July 15, 2010


  • Cell count data collected from IPTG experiments.
  • Flourimeter data collected from IPTG experiments.


July 16, 2010


  • Tet titration experiment started using pSB3T5 vector.
  • Tet titration experiment started using optimized and deoptimized TetA.


July 19, 2010


  • Cell count data collected from Tet titrations.
  • Tet titration experiment started using optimized and deoptimized TetA.


June 3, 2010


  • Mini prepped, diagnostic RP digest, preparative digest, ligation, pBAD+RBS-RFP


July 20, 2010


  • Flourimeter data collected on IPTG experiment.


July 21, 2010


  • IPTG experiment started on optimized and deoptmized TetA constructs.
  • Passage I715039-1 and I715039-2 experiments started.


July 22, 2010


  • IPTG experiment started using varying tetracycline concentrations.
  • Cell count data collected on IPTG TetA experiment.



July 23, 2010


  • Cell count data collected from IPTG experiment..
  • Flourimeter data collected from IPTG experiment.



July 26, 2010


  • Presented Missouri Western data to Davidson colleagues.
  • Presented Davidson data to Missouri Western colleagues.



July 27, 2010


  • Worked on team wiki.



July 28, 2010


  • n/a
  • n/a



July 30, 2010


  • n/a
  • n/a