Difference between revisions of "Team:UC San Diego/Notebook"
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Revision as of 08:10, 18 September 2015
TIMELINE
September 24-28
Giant Jamboree!
Giant Jamboree!
Computational
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WEEK 14Wet Lab
+Final preparations before the wiki freeze.
WEEK 14Section 13
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WEEK 13Wet Lab
+ Mapped out errors in the parts that we assembled
+ Mutagenesis to fix recurring errors in C sequence
Section 13
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WEEK 12Wet Lab
+ Attempted Gibson Assembly with CDE with AB
+ Designed sequence primers
+ Miniprepped full size clones
Section 13
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WEEK 11Wet Lab
+ Attempted full gibson assembly of AB fragment
+ Miniprepped CDE fragments
Section 13
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WEEK 10Wet Lab
+ Selected error free clones for CDE fragments from sequencing data
+ Designed primers for PacBio Sequencing
+ Transformed error free clones of CDE
week 9
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WEEK 9Wet Lab
+ Assembled using Gibson Assembly and sequenced CDE fragments
+ PCR and transformed fragments
Section 13
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WEEK 8Wet Lab
+ Received our DNA fragments from SGI.
+ Attempted to PCR and transform our fragments.
Section 13
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WEEK 7Wet Lab
+ Assembled Interlab Devices. Resuspended and measured them successfully.
+ Prepared YPD plates.
Section 13
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WEEK 6Wet Lab
+ Continued interlab study with miniprep, restriction digests, ligation, gel electrophoresis and gel purification.
WEEK 6Section 13
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WEEK 5Wet Lab
+ Started interlab study with transformation.
WEEK 5Section 13
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WEEK 4Wet Lab
+ Sent our genes to SGI and ordered lab supplies. Almost ready to go!
WEEK 4Section 13
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WEEK 3Wet Lab
+ Added frp gene sequence from Vibrio Harveyi to our plasmid to stabilize the production of luciferase.
+ Optimized our plasmid sequences.
Computational
Read papers on drive
Read about metabolic control analysis
Compiled notes on bioluminescent system
Literature research:understanding bioluminescent mechanism
> aldehyde synthesis
> FMNH2 production
> light production
Familiarized with COBRA module
Primer to Genome-Scale Modeled and COBRA Tutorial (Jahir)
Continued literature search for key mechanisms regarding our auto-induced bioluminescent reaction in a yeast model
>auto-induced therefore no coupling between cells (removed LuxI and LuxR genes)
Wet Lab
+ Created a preliminary design for the plasmids using ApE.
+ Improved them over the week by adding tags, removed illegal restriction sites, and changing repetitive sequences.
Computational
Developed Primer to MATLAB Programming
> lecture material from MIT course and UCSD course
> reading material from UCSD course
> study and practice material MIT course and UCSD course
Wet Lab
+ Found genes coding for fatty acid reductase complex that have been validated in an in vitro synthesis paper.
+ Planned how to assemble our plasmids and determined nucleotide sequences for lux A-E of Photobacterium Phosphoreum.
+ Compared the amino acid sequences to those of other organisms on BLAST to check for significant discrepancies in our sequence.