Ann's Notebook

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Ann's Notebook

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