S-STEM Scholar Marisa Ostos Blog

 This week was focused on preparing our bacteria so that we can have our bacteria undergo transformation once more -- hopefully this time with results! One thing that is interesting about doing research in a classroom setting, especially one where materials are shared by larger amounts of people, is that every once in a while, I will need to improvise, whether with scheduling or procedures that are still accurate and get the job done.  One instance of this happened this past week. We had used a freezeback of E. coli that held the smaller plasmid that we will be using for transformation (this one, pRad1, is approximately 6,000 base pairs larger rather than the larger plasmids that are closer to 10,000 that we've been using) to incubate and have our own plates of the same bacteria. By inoculating (and hopefully having growth), we would use these plates to have E. coli (with the pRad1 plasmid) for future use.  Now, when we inoculated the bacteria last week, we knew that we w...

This week was about solidifying my understanding of why certain protocols were in place for different processes we worked on (and as always, lots of learning opportunities). This week, our focus was to be on extracting plasmid, running a gel, and beginning transformation, but alas, the data we obtained did not allow for us to move forward with this task quite yet.  After running three different plasmid extractions from E. coli (one per each of the plasmids we have been focusing on: pRad1, pRadZ1, and pRadZ2), wherein all steps were meticulously followed, we noticed that the data obtained from the nano drop (as in the dsDNA reading that provided a concentration of plasmid) was extremely low:  Because at least 1 microgram (equivalent to 1000 nanograms) is needed to run the experiment, you'd use the calculation of dividing 1000 by the concentration (since the concentration, as seen above on the nanodrop reading, is measured in ng/uL) to figure out the volume of plasmi...

This week served as more of a checks and balances than anything, of which I am glad there are certain protocols in place (and reasons for there being so) that Ensure we are running our experiments in the best manner possible. Since we have not had success in running transformation three different times on plasmids that are almost 10, 000 base pairs in size, we are now focused on making sure that we can transform with a plasma that is just under 2/3 of the size of the ones we had been working with. This plasmid is called pRad1, and what's interesting about this plasmid is that the other two plasmids we had been working with which are larger are, in a sense, derivatives of this grandfather plasmid. They all have the marker which allows for resistance to ampicillin and chlorophenical, and this one can be thought of as being more of the bare bones plasmid of our other two, the "grandfather plasmid" in a way. Now, since last week we had run three sets of inoculations to help g...

First, I will start by saying science is not actually a game, per say (but it can be fun like a game!). However, it is filled with interesting turns, challenges, and acts of waiting that ultimately help to reach a final product. This week, we decided to go a different route than I had planned. The original plan was to run three sets of transformations at once to use as a type of comparative device and as a way to make sure we were running our protocols correctly. With these transformations, we would use a smaller plasmid (that had been verifiably transformed by another classmate in the past) and two larger ones that were around the same size. In this instance, if the smaller plasmid was transformed and the two larger ones weren't, then maybe we'd need to change something within the transformation protocol itself.  Now, one interesting thing about science is that you are dealing with real-world factors, and that includes finances and availability of materials. One fo...