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| - | {{:Team:Cornell/Navbar}}
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| - | {{:Team:Cornell/TOC|right}}
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| - | =June=
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| - | ==June 10th-16th==
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| - | ===June 13th, Wednesday===
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| - | *Set up [[Team:Cornell/Notebook/Phusion_PCR|PCR]] for four fragments of the nah operon as well as the pBMT-1 backbone, using primers designed to mutate cut-sites concurrently with Gibson Assembly. Also set up a PCR for the entire nah operon. Due to length of the fragments, a longer extension time was chosen.
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| - | *If Gibson Assembly fails, but we are able to PCR the entire 10kb nah operon, an alternate method of mutation using three sequential site-directed mutageneses will be pursued.
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| - | **''Work done by: Caleb, Claire, Dylan, Spencer, Steven, and Swati''
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| - | ===June 14th, Thursday===
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| - | *PCR only amplified nah1, nah3, and nah4 - longer fragments (nah2, the full nah operon, and pBMT-1) were not identified on the PCR product gel. Set up another [[Team:Cornell/Notebook/Phusion_PCR|PCR]] with shorter extension time.
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| - | ===June 15th, Friday===
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| - | *PCR of four out of five products visible on gel. Set up PCR of pBMT-1, final fragment required for Gibson Assembly of the nah operon.
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| - | ==June 17th-23rd==
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| - | ===June 17th, Sunday===
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| - | *Successful PCR of pBMT-1 [[Team:Cornell/Notebook/Gel_purification| gel purified]].
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| - | ===June 19th, Tuesday===
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| - | *Ran [[Team:Cornell/Notebook/Gibson_assembly|Gibson Assembly]] of nah operon fragments into pBMT-1 backbone and [[Team:Cornell/Notebook/Transformation_ecoli | transformed]] into DH5a electrocompotent ''E. coli'' cells.
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| - | *Set up [[Team:Cornell/Notebook/Phusion_PCR|PCR]] to amplify the Gibson Assembly products.
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| - | **''Work done by: Dylan and Swati''
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| - | ===June 20th, Wednesday===
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| - | *Set up a [[Team:Cornell/Notebook/Digestion|digestion]] of the PCR of Gibson Assembly products and ran the digested products on a gel to see if Gibson worked.
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| - | *Three colonies on plates of DH5a transformed with Gibson Assembly product. Made liquid cultures to miniprep and sequence.
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| - | **''Work done by: Dylan and Swati''
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| - | ===June 22nd, Friday===
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| - | *[[Team:Cornell/Notebook/Miniprep | Miniprepped]] directly transformed Gibson Assembly product for sequencing using the the Gibson nah1F and nah4R primers (each w/ 20 bp overhangs).
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| - | *Ran undigested miniprep with [[Team:Cornell/Notebook/Gel_electrophoresis|gel electrophoresis]], looking for large bands corresponding to supercoiled DNA. The gel shows distinct bands for all three lanes. We interpreted this to mean that we got product. Submitted for [[Team:Cornell/Notebook/Sequencing|sequencing]]
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| - | ::[[File:Cornell2012_0621_Gibson-entire-plasmid.jpg|600px]]
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| - | ==June 24th-30th==
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| - | ===June 27th, Wednesday===
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| - | [[Image:2012_627_RafDylanGelMaking.jpg|thumb|right|Rafael and Dylan making an agarose gel.]]
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| - | *Ran digest of gibson-assembled nah operon with [[Team:Cornell/Notebook/Gel_electrophoresis|gel electrophoresis]]
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| - | ===June 28th, Thursday===
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| - | [[Image:2012_6_28_StevenArchieGelLoading.jpg|thumb|right|Stephen and Archie Gel purifying our arsR construct]]
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| - | *Gel purified arsR construct
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| - | =July=
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| - | =August=
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