Penn State iGEM 2014 Notebook Page
Here you will find weekly summaries of our wet laboratory progress, team updates, and accomplishments outside the laboratory. Below [link this] is our detailed, day-to-day progress laboratory notebook.
Weekly Summaries
will create links to each week, but will just list down the page Week 1, Week 2, etc etc
Laboratory Notebook
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Biodetoxification |
Codon Optimization |
| Wednesday, May 21, 2014 |
Emily's first experience with cloning! Ashlee led Emily through several practice experiments from designs made earlier in the year: making a gel, loading samples, gel purifying DNA. |
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| Thursday, May 22, 2014 |
Ashlee and Emily performed a transformation. |
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| Friday, May 23, 2014 |
We picked several colonies for overnight growth to do more cloning tomorrow. |
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| Saturday, May 24, 2014 |
Memorial Day Weekend? How about lab cloning weekend! Ashlee conducted plasmid preparation and digestion. |
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| Monday, May 26, 2014 |
Due to a string of failed clonings with the broadhost vector pSEVA251 and the large inserts, new designs are evaluated! Instead of creating a plasmid with the HMF pathway (7.5 kb) and dCas9 system (5.5 kb), we shall add the HMF pathway and dCas9 to the P. putida genome using homologous recombination. |
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| Tuesday, May 27, 2014 |
Inoculated LB broth with ampicillin and dCas9 plasmid from cryogenic storage; inoculated Lb broth with chloramphenicol and FTV vector from Ashlee's past experiment; streaked the HMF vector on a kanamycin plate. |
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| Wednesday, May 28, 2014 |
Emily and Ashlee made cryogenic storage of the dCas9 plasmid; plasmid prepared the FTV and dCas9 vectors; digested FTV vector; inoculated LB broth with a colony from the HMF plate for overnight growth and plasmid preparation tomorrow. |
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| Thursday, May 29, 2014 |
Prepared plasmid containing the HMF pathway; inoculated LB broth with Lambda Red Recombinase plasmid from cryogenic storage. Ashlee, Emily, and graduate student Iman Farasat ordered primers for three plasmids that will be constructed via Gibson Chew-Back and Annealing Assembly, two of which will be inserted into the genome by homologous recombination. |
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| Friday, May 30, 2014 |
Ashlee and Emily made cryogenic storage of the Lambda Red Recombinase plasmid. |
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| Monday, June 2, 2014 |
Constructed dCas9 gene cassette and plasmid backbone with replication origin ColE1 via PCR Rescue. Gel purified dCas9 and ColE1 cassettes. |
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| Tuesday, June 3, 2014 |
Conducted Colony PCR using P. putida KT2440 strain as DNA template to construct two ~1 kb genome overlaps. Plasmid prepared the Lambda Red Recombinase plasmid, DH10B-PKD46, FTV-ptac-LacI-CmR plasmid, and NoHP_15A_Plmra_CmR plasmid containing RFP with a strong, unique promoter. Stock of NoHP_15A_Pkmra_CmR and FTV_ptac_LacI_CmR for cryogenic storage was also made. Lambda Red Recombinase cassette was amplified using PCR Rescue and gel purified. |
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| Wednesday, June 4, 2014 |
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| Thursday, June 5, 2014 |
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| Friday, June 6, 2014 |
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| Saturday, June 7, 2014 |
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| Sunday, June 8, 2014 |
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| Monday, June 9, 2014 |
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| Tuesday, June 10, 2014 |
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| Wednesday, June 11, 2014 |
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| Thursday, June 12, 2014 |
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| Friday, June 13, 2014 |
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| Saturday, June 14, 2014 |
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| Sunday June 15, 2014 |
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| Monday, June 16, 2014 |
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| Tuesday, June 17, 2014 |
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| Wednesday, June 18, 2014 |
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| Thursday, June 19, 2014 |
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| Friday, June 20, 2014 |
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| Saturday, June 21, 2014 |
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| Sunday, June 22, 2014 |
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| Monday, June 23, 2014 |
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| Tuesday, June 24, 2014 |
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| Wednesday, June 25, 2014 |
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| Thursday, June 26, 2014 |
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| Friday, June 27, 2014 |
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| Saturday, June 28, 2014 |
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| Sunday, June 29, 2014 |
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| Monday, June 30, 2014 |
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| Tuesday, July 1, 2014 |
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| Wednesday, July 2, 2014 |
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| Thursday, July 3, 2014 |
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| Friday, July 4, 2014 |
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| Saturday, July 5, 2014 |
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| Sunday, July 6, 2014 |
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| Monday, July 7, 2014 |
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| Tuesday, July 8, 2014 |
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| Wednesday, July 9, 2014 |
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| Thursday, July 10, 2014 |
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| Friday, July 11, 2014 |
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| Saturday, July 12, 2014 |
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| Sunday, July 13, 2014 |
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| Monday, July 14, 2014 |
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| Tuesday, July 15, 2014 |
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| Wednesday, July 16, 2014 |
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| Thursday, July 17, 2014 |
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| Friday, July 18, 2014 |
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| Saturday, July 19, 2014 |
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| Sunday, July 20, 2014 |
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| Monday, July 21, 2014 |
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| Tuesday, July 22, 2014 |
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| Wednesday, July 23, 2014 |
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| Thursday, July 24, 2014 |
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| Friday, July 25, 2014 |
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| Saturday, July 26, 2014 |
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| Sunday, July 27, 2014 |
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| Monday, July 28, 2014 |
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| Tuesday, July 29, 2014 |
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| Wednesday, July 30, 2014 |
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| Thursday, July 31, 2014 |
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