Conjugating nah into Shewy: The mysterious failure of past week's ligation lead to a redigestion (in case we run out of DNA) and religation of last week's digestions. Nah to oriT was ligated in ratios of 3:1 and 6:1 - when run on a gel, bands once more failed to appear... But wait! Epiphany! The team realized that we forgot to dephosphorylate the oriT backbone! After that silly mistake, 1:1, 3:1, and 6:1 ratios of nah:oriT were set up in a ligation mixture and electroporated into WM3064. Once again, slow growth and tiny colonies were observed - perhaps due to the strain of putting such a massive operon in a cell. 13 colonies were deemed large enough to try colony PCR, and 3 of them definitely showed bands that corresponded to the length of our construct. We set up liquid cultures for Miniprepping and once again observed slow growth. We tried subculturing - but still, general opaqueness. Miniprepping proceeded anyway, as we are a fairly optimistic bunch (and the cultures were by then over 24 hours old).
Site-directed mutagenesis: After several more unsuccessful attempts, lengthy discussion among teammates, and consultation with several graduate advisors, the team decided to put this subproject on hold for the time being. Swati finished up with one last attempt, then joined Claire for fluorescence testing. That's all, folks!
Daily Details:
September 1
Conjugating nah into Shewy:
Due to the mysterious failings of our attempts to ligate the nah operon, Tina tried to start fresh by re-digesting the nah operon-containing plasmid and the oriT-containing backbone.
Synthetic River Media:
Mark and Chie created synthetic river media based on information on the mineral content of the Athabasca River, and started overnight cultures of numerous strains to test how sodium lactate supplemented river water would grow the cells.
Site-directed mutagenesis: Swati transformed both her mutagenic PCR and her DpnI digest into DH5a after desalting on a membrane. She also ran both of the aforementioned samples on a gel without purifying, in order to check if either the digestion or purification steps were problematic. The gel was yet again blank, suggesting that the PCR itself was the problem.
September 2nd
Conjugating nah into Shewy:
Tina tried ligating an older digestion of the nah operon into the oriT backbone using a molar ratio or 3:1 and 6:1 for nah:backbone. She then de-salted and transformed the ligations into conjugation strain WM3064. Tina then ran a gel of the digested nah operon-containing plasmid and the oriT-containing backbone and extracted the nah operon and oriT backbone bands.
Synthetic River Media:
Mark set up a 96-well plate to test growth of the engineered strains in sodium lactate at varying concentrations, in synthetic river media.
Site-directed mutagenesis:The third transformation attempt yielded no colonies on the plate of DpnI-digested DNA, but three colonies on the PCR only plate, suggesting that these were just excess template. Nonetheless, Swati set up cultures to miniprep the following day. She also realized that she had been using a template that was 10x more concentrated than it was supposed to be. She proceeded to set up a fourth attempt at a mutagenic PCR, this time with the correct template concentration, primers for mutating a different cutsite than she had previously been attempting, and a higher annealing temperature.
September 3rd
Conjugating nah into Shewy:
Tina extracted the nah operon digest and the oriT backbone from yesterday's gel. Tina and Dylan had an epiphany - we forgot to dephosphorylate the backbone! No wonder we kept seeing self-ligations! With a renewed spirit, Tina dephosphorylated the digested oriT backbone then started a sixteen hour 16 degrees Celsius ligation of the extracted digests. Tina tried nah to backbone ratios of 1:1, 3:1, and 6:1.
Synthetic River Media:
Mark returned to the lab to discover that the growth assay went wrong. Numerous issues were identified with the original protocol to explain the failed result, and the protocol was changed.
Site-directed mutagenesis: Swati miniprepped the three suspicious PCR only colonies from the previous day, and digested with PstI to check for successful mutagenesis. She also did a DpnI digest and transformation of the PCR from the previous day. She ran the new PCR & DpnI digest, along with the PstI-digested minipreps of the three earlier colonies, on a gel, but to no avail. The new things showed nothing (again), and the digested minipreps produced completely incorrect bands.
September 4th
Conjugating nah into Shewy:
Tina desalted yesterday's ligations then transformed them into our conjugation strain WM3064. WM3064 is E. coli that is auxotrophic for DAP (diaminopimelic acid epimerase).
Site-directed mutagenesis: The latest transformation did not work. Thus concludes this subproject!
September 5th
Conjugating nah into Shewy:
Caleb and Tina checked the transformation plates - some colonies were visible on all three ligation ratio pltaes, but the colonies were so tiny we decided to wait another day before trying colony PCRs or starting liquid cultures.
September 6th
Conjugating nah into Shewy:
Caleb decided the transformation colonies were large enough to colony PCR and start liquid cultures from. 13 total colony PCRs were performed on colonies from all three ligation mixtures and one positive control was run in parallel to be sure the PCR conditions were correct. Tina ran a gel of the the colony PCRs and the positive control. As can be seen in the gel pictures, colonies 3, 4, and 8 definitely had the nah operon and many other colonies had matching middle bands. These matching middle bands likely indicate some sort of mispriming. Colony 5 was clearly the product of an oriT backbone self-ligation. Caleb and Tina started 15 mL liquid cultures of apparently nah containing colonies 3, 4, and 8 and non-nah-containing colony 5 to Miniprep from tomorrow.
Fluorescence tests: This week started late as Claire was getting over a massive cold. However, with new vim and vigor and her trusty labmate Swati, they set forth to decide the details of how they will run fluorescence tests. To get ready for this, they set up cultures of JG700 and E. coli constitutively producing mRFP under the control of Anderson series promoters.
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