6/19/09 and 6/25/09

• M9 salts
• Liquid LB
• Antibiotic stock solutions
• LB plates

7/22/09 and 7/23/09

• Media preparation for transformation
• Comp. cell protocol
• Protocol for getting parts from the biobricks
• Transformation protocol
• Transformation of RBS for Pu promoter, Bacteriophage lysis cassette, lambda lysis device, T4 lysis device

7/24/09

• Protocol for miniprep
• Miniprep of RBS for Pu promoter, Bacteriophage lysis cassette, lambda lysis device, T4 lysis device

7/25/09

• Protocol for using the nanodrop
• Protocol for a digestion
• Nanodrop concentrations of the RBS for Pu promoter, Bacteriophage lysis cassette, lambda lysis device, T4 lysis device
• Digestion of the RBS for Pu promoter and the Bacteriophage lysis cassette

7/27/09

• Plated overnight cultures for Pu colony PCR
• Protocol for running a gel
• Ran gel of the RBS for Pu promoter and Bacteriophage lysis cassette
• Plated Pu-luciferase part sent from the registry

7/28/09

• Overnight culture for frozen stock of Pu-luciferase biobrick
• Digest of lambda and T4 killer genes to check part length with EcoRI, PstI, BglII and EcoRI/BglII

7/29/09

• Frozen stock of Pu-luciferase biobrick
• Gel of lambda and T4 killer genes digested with EcoRI, PstI, BglII and EcoRI/BglII
• Digest of lambda and T4 killer genes with EcoRI/PstI, EcoRI/XhoI, XhoI

7/30/09

• Gel of lambda and T4 killer genes digested with EcoRI/PstI, EcoRI/XhoI, XhoI
• Gel of Pu promoter colony PCR

8/3/09

• Analysis of Pu promoter colony PCR
  • Primer sequence
  • PCR conditions

8/4/09

• Protocol for colony PCR
• Colony PCR for Pu Promoter
• Gel of Colony PCR for Pu promoter with samples at different annealing temperatures
• Meeting with Pablo about HPLC

8/5/09

• Protocol for DNA purification
• DNA purification of Pu promoter colony PCR
• Optimization of Pu promoter colony PCR
• Nanodrop of Pu promoter

8/6/09

• Protocol for DNA precipitation
• DNA concentration of Pu promoter
• Nanodrop results for concentrated Pu promoter

8/8/09

• Comp. cell preparation and transformation of a GFP generator

8/9/09

• Pu promoter colony PCR round 2
• Gel of Pu promoter colony PCR round 2
• DNA purification of colony PCR round 2
• Nanodrop of colony PCR round 2 and leu landing pad
• Miniprep of GFP generator
• Nanodrop of GFP generator
• Digest for Pu-RBS-GFP

8/10/09

• Gel of digest for Pu-RBS-GFP

8/11/09

• Digest of GFP generator
• Gel of GFP generator
• Pu promoter colony PCR round 3
• Gel of Pu promoter colony PCR round 3
• DNA purification of Pu promoter colony PCR round 3
• Nanodrop of Pu promoter colony PCR round 3

8/12/09

• Pu promoter round 3 digestion
• DNA purification of digest for Pu-RBS-GFP
• Nanodrop of digest for Pu-RBS-GFP

8/13/09

• Gel of purified DNA for digest round 1
• Digest of DNA for Pu-RBS-GFP ligation round 2
• Trouble shooting DNA purification process
• Gel of digested Pu, GFP, leu LP round 2
• DNA purification of digested Pu, GFP, leu LP round 2
• Nanodrop of digested Pu, GFP, leu LP round 2

GRE/VACATION

9/8/09

• ligation protocol
• Pu-GFP-leu landing pad ligation

9/9/09

• ATCC sodium benzoate plate and liquid media recipes
• Media prep for transformation of Pu GFP leu landing pad

9/10/09 and 9/11/09

• Comp. cell preparation and transformation of Pu GFP leu landing pad ligation into E. coli and P. putida mt-2 (with TOL plasmid)

9/12/09

• Pu GFP leu landing pad transformation results
• Start overnight cultures for Pu GFP leu landing pad miniprep

9/13/09

• Pu GFP leu landing pad transformation results
• Start overnight cultures for Pu GFP leu landing pad miniprep

9/14/09

• Nanodrop of Pu GFP leu landing pad miniprep
• Digest of Pu GFP leu landing pad with EcoRI to determine the plasmids with the insert

9/15/09

• Gel of Pu GFP leu landing pad ligation miniprepped products digested with EcoRI

9/16/09

• Gel of Pu GFP leu landing pad ligation miniprepped products digested with EcoRI round 2

9/18/09

• Primer design for sequencing of Pu GFP leu landing pad

9/22/09

• Weekly team meeting: project modifications

10/2/09

• Protocol for primer design
• Primer design for PrXylR

10/5/09

• Colony PCR PrXylR

10/6/09

• Gel of Colony PCR PrXylR

10/9/09

• Protocol for gel extraction
• Gel extraction of PrXylR colony PCR
• Nanodrop of PrXylR gel extraction
• Gel of PrXylR gel extraction

10/10/09

• PrXylR PCR amplification from gel extraction
• Revised Pu promoter colony PCR
• Gel of PrXylR and Revised Pu promoter PCR

10/11/09

• Purification of revised Pu promoter
• Nanodrop of revised Pu promoter
• Digest of revised Pu promoter and GFP generator

10/13/09 abd 10/14/09

• Miniprep of leu landing pad
• Nanodrop of leu landing pad miniprep
• Digest of leu landing pad and PrXylR
• Gel of Digested Revised Pu, GFP generator, PrXylR, LeuLP and uncut Leu LP for ligation
• Ligation of Pu/GFP and PrXylR/LeuLP

10/15/09 abd 10/16/09

• Comp. cell prep and transformation of PrXylR/LeuLP and Pu/GFP

10/18/09

• Miniprep of Pu/GFP and 1 PrXylR transformation colony

10/19/09

• Nanodrop of miniprepped Pu/GFP and PrXylR/LeuLP ligation products
• Digestion of miniprepped Pu/GFP and PrXylR/LeuLP ligation products
• Gel of digested Pu/GFP and PrXylR/LeuLP
• Submitting Parts to the Registry