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Sp'23: Week 16 (5/8/23 - 5/12/23): Wrapping Up the Semester

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This week was the final chance to hope that transformation occurred, but unfortunately, there was contamination again (whose common occurrence among my projects was finally likely discovered as I had somehow formed the habit of using non-sterile microcentrifuge tubes for plasmid extractions). Three out of six of my transformation plates (which included the -Cm plate "3.24C3" and two of my +Cm plates "4.5B1" and "4.5B2") showed visible signs of contamination: Deinococcus aquaticus should show up as a plate streaked with pink, but there were white colonies of an unknown organism growing on them instead (which Dr. Tuohy assumed might be Staphylococcus-- a common bacteria found on our skin!). Because of this, I decided to conduct a full investigation via gram stain analysis to attempt to find the source of the culprit (this was before we realized that I was using non-sterile microcentrifuge tubes). I first did gram stains of the six pl...
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Sp'23: Week 15 (5/1/23 - 5/5/23): Strong Yields

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This week, I started out by using the nanodrop to first check the growth of E. coli with pRad1 in tubes "4.27A" and "4.27B," both of which had been used for multiple extractions last week, and both of which had also been placed back into the 37 degree Celsius incubator for the weekend (which was done to see how the E. coli would grow). Overall, the nanodrop showed slightly lower OD600 readings, which means that the E. coli were out of their exponential growth phase and had growth that had likely come to its plateau (last week's final OD600 readings were at 1.04 and 1.08 for tubes "4.27A" and "4.27B" respectively ). The OD600 readings for the same tubes are shown in their respective orders:  Since the growth had not changed much, I decided that it was safe to move forward with a single plasmid extraction per tube (as I theorized that doing less extractions per tube would result in a higher pRad1 plasmid yield). I once again used th...
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Sp'23: Week 14 (4/24/23 - 4/28/23): The Week of Kit Comparisons

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Quite a bit was accomplished this week in preparation for another soon-to-be-attempted transformation of Deinococcus aquaticus  using the plasmid pRad1 extracted from E. coli. To begin, nanodrop readings were done on both tubes (tube "4.21C" and "4.21D") that had been inoculated last week with E. coli + the pRad1 plasmid into LB + Ampicillin [mic concentration of 50 ug/mL]. Now, usually E. coli when placed into the shaking incubator at a lower growth temperature of 32 degrees Celsius will grow over the weekend and can be measured a few days later to show growth. However, the OD600 readings showed negative readings, which indicated no growth, and verified that E. coli likely never grew in last week's LB tubes (tubes "4.14A" and "4.14B") either. The respective readings of tubes "4.21C" and "4.21D" were as such:  These negative readings, indicating no growth, unfortunately meant that I would need to re-inoculate E...
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