Team:Davidson-MissouriW/Notebook

From 2010.igem.org

(Difference between revisions)
(Notebook)
(Notebook)
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<ul>
<ul>
<li>Ligate and plasmid check for pSB1A2 or pSB1AK3
<li>Ligate and plasmid check for pSB1A2 or pSB1AK3
 +
<li>Began working to improve the Lancelator and created histograms for simulations
  </li>
  </li>
</ul>
</ul>
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<ul>
<ul>
<li>Double digest on pBAD-RBS-RFP to make an RS fragment insert. </li>
<li>Double digest on pBAD-RBS-RFP to make an RS fragment insert. </li>
 +
<li>Worked on a Perl program that check for Bio Brick Restriction Sites
</ul>
</ul>
<br>
<br>
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<li>EcoRI and PstI digest on pLac and pBad colonies.  
<li>EcoRI and PstI digest on pLac and pBad colonies.  
<li>Arabinose and IPTG concentration experiments started. </li>
<li>Arabinose and IPTG concentration experiments started. </li>
 +
<li>Continued work on the Lancelator program and began working on a different simulation for Construct C and D
</ul>
</ul>
<br>
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<li>Picked 14 colonies from pLac-RBS-RFP and pLac-RBS-RFP-RBS plates.
<li>Picked 14 colonies from pLac-RBS-RFP and pLac-RBS-RFP-RBS plates.
<li> Started inducer curve experiments.</li>
<li> Started inducer curve experiments.</li>
 +
<li>Linked Lancelator code to the website and continued simulations
</ul>
</ul>
<br>
<br>
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<ul>
<ul>
<li>Ligated S03736 into pSB1A7 vector.
<li>Ligated S03736 into pSB1A7 vector.
-
<li> EcoRI/PstI digest on pLac-RBS-RFP-RBS colonies.</li>
+
<li>EcoRI/PstI digest on pLac-RBS-RFP-RBS colonies.</li>
 +
<li>Added new features to the Lancelator and worked on numerically representing Construct C for the Matlab simulation
</ul>
</ul>
<br>
<br>
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<li>EcoRI/PstI diagnostic digest performed on pBad-RBS-RFP colonies.   
<li>EcoRI/PstI diagnostic digest performed on pBad-RBS-RFP colonies.   
<li>Inducer curve experiment started on pBad and pLac constructs. </li>
<li>Inducer curve experiment started on pBad and pLac constructs. </li>
 +
<li>Debugged Lancelator and finished numerical representation for the simulation
</ul>
</ul>
<br>
<br>

Revision as of 15:14, 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


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.


June 17, 2010


  • Flourimeter data collected from IPTG experiment.
  • Ligated pLacI-RBS-RFP + RBS-TetA.


June 18, 2010


  • Picked 4 colonies from pLacI-RBS-RFP-RBS-TetA plates.
  • IPTG experiment started using newly created IPTG.


June 21, 2010


  • Digested TetA with EcoRI/NheI.
  • Annealed oligos for optimized and deoptimized TetA segment 1.


June 22, 2010


  • Ligated annealed TetA oligos into digested TetA.
  • Inducer curve experiment started on pLac and pLacI constructs.


June 23, 2010


  • Preparative NheI/BamHI digest performed on TetA.
  • Preparative EcoRI/NheI digest performed on TetA.


June 24, 2010


  • Annealed optimized and deoptimized segment 1 TetA ligated into vector.
  • Annealed optimized and deoptimized segment 2 TetA ligatied into vector.


June 27, 2010


  • Inducer curve experiment started on pLac and pLacI constructs.
  • 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


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.


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