Team:UC San Diego/Notebook
TIMELINE
September 24-28
Giant Jamboree!
Giant Jamboree!
Modeling
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WEEK 14Wet Lab
+Final preparations before the wiki freeze.
WEEK 14Modeling
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WEEK 13Wet Lab
+ Mapped out errors in the parts that we assembled
+ Mutagenesis to fix recurring errors in C sequence
Modeling
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WEEK 12Wet Lab
+ Attempted Gibson Assembly with CDE with AB
+ Designed sequence primers
+ Miniprepped full size clones
Modeling
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WEEK 11Wet Lab
+ Attempted full gibson assembly of AB fragment
+ Miniprepped CDE fragments
Modeling
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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
Modeling
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WEEK 9Wet Lab
+ Assembled using Gibson Assembly and sequenced CDE fragments
+ PCR and transformed fragments
Modeling
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WEEK 8Wet Lab
+ Received our DNA fragments from SGI thanks to the BioXP!
+ Attempted to PCR and transform our fragments.
Modeling
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WEEK 7Wet Lab
+ Assembled Interlab Devices. Resuspended and measured them successfully.
+ Prepared YPD plates.
Modeling
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WEEK 6Wet Lab
+ Continued interlab study with miniprep, restriction digests, ligation, gel electrophoresis and gel purification.
WEEK 6Modeling
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WEEK 5Wet Lab
+ Started interlab study with transformation.
WEEK 5Modeling
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WEEK 4Wet Lab
+ Sent our genes to SGI and ordered lab supplies. Almost ready to go!
WEEK 4Modeling
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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.
Modeling
Familiarized myself with genome-scale modeling and metabolic control analysis
Literature research: Understanding the different components of the bioluminescent system
>aldehyde synthesis
>light production
Researched Literature on COBRA analysis and methods
>used e.coli as a toy model
>ran stimulations of FBA, robustness analysis, and phenotype phase plane
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.
Modeling
Developed and finalized Primer to MATLAB Programming
Researched potential modeling avenues
>genome scale analysis of synthetic construct
>analysis of the tradeoffs between different genetic circuit designs and gene dynamics
>analysis of metabolic activity in an isolated network via Metabolic Control Analysis
Browsed recent literature for lux system
>identified its advantages and disadvantages as a reporter system
>differences in luciferase systems of beetles and bacteria
Familiarized ourselves with basics of enzyme kinetics
>Michaelis-Menten equations
Downloaded COBRA Toolbox plugin for Matlab
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.