Ann's Notebook



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[[media:6_19_09_Media_recipes.pdf| 6/19/09 and 6/25/09]]
 * M9 salts
 * Liquid LB
 * Antibiotic stock solutions
 * LB plates

[[media:7_22_09_and_7_23_09_Transformation_of_RBS_for_Pu_and_Killer_genes.pdf| 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

[[media:7_24_09_Miniprep_and_Digest_of_Pu_promoter_and_killer_genes.pdf| 7/24/09]]
 * Protocol for miniprep
 * Miniprep of RBS for Pu promoter, Bacteriophage lysis cassette, lambda lysis device, T4 lysis device

[[media:7_25_09_Nano_Drop_of_RBS_and_Killer_genes_and_Digest_with_EcoRI_and_XbaI_of_RBS_and_Bactreriophage_lysis_cassette.pdf| 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

[[media:7_27_09_Gel_of_RBS_and_Bacteriophage_lysis_cassette_digest_Plates_for_Pu_promoter_colony_PCR_Streaking_out_Pu_luciferase_part_from_the_registry.pdf| 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

[[media:7_28_09_Frozen_stock_Pu_luciferase_and_digest_of_lambda_T4_killer_genes.pdf| 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

[[media:7_29_09_Frozen_stock_Pu_luciferase_gel_of_lambda_and_T4_digest_of_lambda_and_T4.pdf| 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

[[media:7_30_09_gel_of_lambda_and_T4_killer_gene_and_gel_of_pu_colony_pcr.pdf| 7/30/09]]
 * Gel of lambda and T4 killer genes digested with EcoRI/PstI, EcoRI/XhoI, XhoI
 * Gel of Pu promoter colony PCR

[[media:8_3_09_Analysis_of_Pu_promoter_colony_PCR.pdf| 8/3/09]]
 * Analysis of Pu promoter colony PCR
 * Primer sequence
 * PCR conditions

[[media:8_4_09_Pu_Promoter_colony_PCR_and_HPLC_investigation.pdf| 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

[[media:8_5_09_Pu_promoter_colony_PCR_optimization,_Pu_promoter_purification_and_nanodrop.pdf| 8/5/09]]
 * Protocol for DNA purification
 * DNA purification of Pu promoter colony PCR
 * Optimization of Pu promoter colony PCR
 * Nanodrop of Pu promoter

[[media:8_6_09_Pu_Promoter_DNA_concentration_and_nanodrop.pdf| 8/6/09]]
 * Protocol for DNA precipitation
 * DNA concentration of Pu promoter
 * Nanodrop results for concentrated Pu promoter

[[media:8_8_09_Transformation_of_GFP_generator.pdf| 8/8/09]]
 * Comp. cell preparation and transformation of a GFP generator

[[media:8_9_09_Miniprep_and_nanodrop_GFP_generator_colony_PCR_pu_promoter_round_2_nanodrop_digest_for_pu_gfp_with_leu_landing_pad.pdf| 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

[[media:8_10_09_Gel_of_digested_Pu_GFP_Leu_LP.pdf| 8/10/09]]
 * Gel of digest for Pu-RBS-GFP

[[media:8_11_09_Digest_and_gel_of_GFP_gen_Pu_prom_round_3_PCR_gel_and_nanodrop.pdf| 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

[[media:8_12_09_Digest_Pu_round_3_DNA_purification_and_nanodrop_of_Pu_GFP_digests.pdf| 8/12/09]]
 * Pu promoter round 3 digestion
 * DNA purification of digest for Pu-RBS-GFP
 * Nanodrop of digest for Pu-RBS-GFP

[[media:8_13_09_Pu_GFP_leu_LP_preparations_for_ligation.pdf| 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

[[media:9_8_09_Pu_GFP_leu_landing_pad_ligation.pdf| 9/8/09]]
 * ligation protocol
 * Pu-GFP-leu landing pad ligation

[[media:9_9_09_ATCC_sodium_benzoate_plate_and_liquid_media.pdf| 9/9/09]]
 * ATCC sodium benzoate plate and liquid media recipes
 * Media prep for transformation of Pu GFP leu landing pad

[[media:9_10_09_and_9_11_09_Transformation_of_Pu_GFP_leu_ligation.pdf| 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)

[[media:9_12_09_Pu_GFP_leu_transformation_results.pdf| 9/12/09]]
 * Pu GFP leu landing pad transformation results
 * Start overnight cultures for Pu GFP leu landing pad miniprep

[[media:9_22_09_Team_Meeting_Project_modifications.pdf| 9/13/09]]
 * Pu GFP leu landing pad transformation results
 * Start overnight cultures for Pu GFP leu landing pad miniprep

[[media:9_14_09_Nanodrop_and_digest_of_miniprepped_Pu_GFP_leu_ligations.pdf| 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

[[media:9_15_09_Gel_of_Pu_GFP_leu_ligation_digestion_with_EcoRI_product.pdf| 9/15/09]]
 * Gel of Pu GFP leu landing pad ligation miniprepped products digested with EcoRI

[[media:9_16_2009_digest_of_ligated_Pu_GFP_leu_with_EcoRI_round_2.pdf| 9/16/09]]
 * Gel of Pu GFP leu landing pad ligation miniprepped products digested with EcoRI round 2

[[media:9_18_09_Primer_Design_for_Sequencing_of_Pu_GFP_leu.pdf| 9/18/09]]
 * Primer design for sequencing of Pu GFP leu landing pad

[[media:9_22_09_Team_Meeting_Project_modifications.pdf| 9/22/09]]
 * Weekly team meeting: project modifications

[[media:10_2_09_Pr_XylR_Primers.pdf| 10/2/09]]
 * Protocol for primer design
 * Primer design for PrXylR

[[media:10_5_09_Colony_PCR_PrXylR.pdf| 10/5/09]]
 * Colony PCR PrXylR

[[media:10_6_09_gel_of_colony_PCR_PrXylR.pdf| 10/6/09]]
 * Gel of Colony PCR PrXylR

[[media:10_9_09_Protocol_for_gel_extraction,_gel_extraction_of_PrXylR.pdf| 10/9/09]]
 * Protocol for gel extraction
 * Gel extraction of PrXylR colony PCR
 * Nanodrop of PrXylR gel extraction
 * Gel of PrXylR gel extraction

[[media:10_10_09_PCR_amplification_of_gel_purification_Colony_PCR_of_Pu.pdf| 10/10/09]]
 * PrXylR PCR amplification from gel extraction
 * Revised Pu promoter colony PCR
 * Gel of PrXylR and Revised Pu promoter PCR

[[media:10_11_09_Purification_of_revised_pu_promoter_and_digest_for_ligation.pdf| 10/11/09]]
 * Purification of revised Pu promoter
 * Nanodrop of revised Pu promoter
 * Digest of revised Pu promoter and GFP generator

[[media:10_13_09_and_10_14_09_miniprep_of_leu_LP_digest_of_leu_LP_and_PrXylR.pdf| 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

[[media:10_15_09_10_16_09_Transformation_of_PrXylR_and_Pu_GFP_ligation.pdf| 10/15/09 abd 10/16/09]]
 * Comp. cell prep and transformation of PrXylR/LeuLP and Pu/GFP

[[media:10_18_09_Miniprep_of_Pu_GFP_ligation_round_2_and_PrXylR_ligation.pdf| 10/18/09]]
 * Miniprep of Pu/GFP and 1 PrXylR transformation colony

[[media:10_19_09_Digest_and_gel_of_miniprepped_PuGFP_PrLeuLP_and_prep_for_submission_into_biobricks2.pdf| 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