Week 2 May 9 - 15 2011
Week 3 May 16 - 22 2011
Ryan vacationing in Whitefish. Having an awesome time.
Week 4 May 23 - 29 2011
First week Ryan begins working full time in the lab. Successfully used PCR to alter prefix and suffix regions to to the Silver standard for the genes xylE and mms6. That way we can fuse signal sequences. On an agarose gel the DNA strands are of expected size for both xylE and mms6 with the fusion standard. After attempting to cut PCR products of xylE and mms6 and cloning into psb1c3 using red/white screening, no white colonies test positive for the product when the plasmids are restricted and resolved on a gel. Miscellaneous plasmids are taken out of the glycerol stock and grown in LB cultures.
Week 5 May 30 - June 5 2011
The problem with the ligation of PCR products into psb1c3 is diagnosed as a result of prefix and suffix restriction sites being too close to the ends of the PCR products. Instead of using red/white colony screening and psb1c3 the polymerase used in the PCR produces blunt ends and therefore blunt end ligation is used for cloning with puc19. Different conditions are used in the blunt end ligation. Since puc19 has to be cut bluntly half the samples have the blunt end restriction enzyme heat killed. Blue/white colony screening has to be used in for puc19 cloning which requires X-Gal and IPTG. Solutions of these are made for the plates. Attempts to assemble miscellaneous parts from synthesis vectors to psb1c3 results in positive testing white colonies on an agarose gel for k331025, an enhanced cyan fluorescent protein with a ribosomal binding site and a c-terminally fused arginine residue tail. One colony for the blunt end ligation cloning of an xylE PCR product produces a band at the expected size when the plasmid is restricted and run on a gel. Attempts to move the remaining miscellaneous parts into psb1c3 produce no positive testing white colonies.
Week 6 June 6 - 12
A glycerol stock of the one colony of xylE and k331025 were made after they were re-transformed and grown in liquid LB culture. After another attempt the mms6 PCR product still refuses to be cloned via blunt end ligation. The same can be said for the another assembly of the miscellaneous parts to psb1c3.
Week 7 June 13 - 19
While these other aspects continue to elude success a plasmid preparation of SO4261, the ten residue arginine tag with a double transcriptional terminator, is transformed and a glycerol stock of it is made is made.
Week 8 June 20 - 26
The xylE from puc19 is assembled with the arginine tag. The miscellaneous parts are also re-assembled into psb1c3. Both through PCR and restriction the gels do not show a positive result for the xylE-arg tag assembly. A blunt end ligation of mms6 into puc19 shows some white colonies.
Week 9 June 27 - July 3
The miscellaneous parts are restricted and run on a gel along with mini-preps of the mms6 colonies that were grown in liquid LB media and while all the remaining miscellaneous parts are consistent with expected results, the mms6 is blank on the gel. A PCR of the mms6 in puc19 also gives the same result on an agarose gel. The xylE and re-assembled, plated, possible colonies are picked and grown in liquid LB media and cultures are mini-prepped.
Week 10 July 4 - 10
After restricting and running on a gel all the xylE-arg tag assemblies came back negative. Sequencing data from samples sent to genewiz come back showing k331025 is the correct sequence and what was thought to be xylE in puc19 is not, in fact, xylE. Time to start from scratch. PCR products of both xylE and mms6 with the fusion standard are gel extracted using a Qiagen gel extraction kit. These gel extractions have DNA presence confirmed on a gel and are then used in a blunt end ligation with puc19.
Week 11 July 11 - 17
Week 12 July 18 - 24
Week 13 July 25 - 31
Week 14 August 1 - 7
Week 15 August 8 - 14
Week 16 August 15 - 21
Week 17 August 22 - 28
Week 18 August 29 - September 4
Week 19 September 5 - 11
Week 20 September 12 - 18
Week 21 September 19 - 25
Final Half Week September 26 - 28
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