Learning more about the DNA damage repair response means that we can find new targets for therapies regarding diseases that arise from environmental or endogenous mutations (such as cancer).
BLAST is a website that allows you to pick certain primers to compare sequences. The goal is for the primers that you pick to only match the sequence of your gene and not any other gene in the Tetrahymena genome. NCBI was used to find the primers that you want to pick to put through BLAST. NCBI is where certain parameters were inputted and shows results based on those parameters. The parameters were given by the professor. After the results are loaded, you then compare different primers to see which best fits the criteria, which was also given by the professor (such as low HP and 3′ Stab values, low Any and End values, small Tm difference, and Guanine or Cytosine on the 3′ end of the primer)
Do you think that if you were to redo this experiment at a later time then you would be able to get different results or do you think that it is going to be the same?
I think the results would be the same because we did end up with good results for the gene expression experiment and we didn’t see any contamination (on the gels). However, it’s always good to run an experiment more than once so given the opportunity I would run it again. I don’t believe the primer we designed was a good primer considering that it couldn’t be validated in either of the two experiments.
You mentioned there weren’t any bands in figure 2 but it looks like there’s a clear band in the 4th lane. Why wasn’t this used for determining the primers.
The 4th lane is water, so there was no band but the 5th lane is where Rpp0 was used instead of the primers that we designed. Rpp0 was used as a control so it made sense that a band appeared.
I think western blotting would be a good first step because that will allow us to know where the protein functions exactly and then we can determine what other DNA repair proteins also function in that area.
What is the broad impact of this kind of research and why do you think it is so important to scientists today?
Learning more about the DNA damage repair response means that we can find new targets for therapies regarding diseases that arise from environmental or endogenous mutations (such as cancer).
Great video and poster. How exactly did you use BLAST to choose primers that fit your criteria?
BLAST is a website that allows you to pick certain primers to compare sequences. The goal is for the primers that you pick to only match the sequence of your gene and not any other gene in the Tetrahymena genome. NCBI was used to find the primers that you want to pick to put through BLAST. NCBI is where certain parameters were inputted and shows results based on those parameters. The parameters were given by the professor. After the results are loaded, you then compare different primers to see which best fits the criteria, which was also given by the professor (such as low HP and 3′ Stab values, low Any and End values, small Tm difference, and Guanine or Cytosine on the 3′ end of the primer)
Do you think that if you were to redo this experiment at a later time then you would be able to get different results or do you think that it is going to be the same?
I think the results would be the same because we did end up with good results for the gene expression experiment and we didn’t see any contamination (on the gels). However, it’s always good to run an experiment more than once so given the opportunity I would run it again. I don’t believe the primer we designed was a good primer considering that it couldn’t be validated in either of the two experiments.
Hello, great poster and video! I know you spoke of this a little but how exactly do the silver nanoparticles kill the bacteria at the molecular level?
I don’t know if this was meant for my presentation but we didn’t use silver nanoparticles or kill bacteria.
You mentioned there weren’t any bands in figure 2 but it looks like there’s a clear band in the 4th lane. Why wasn’t this used for determining the primers.
The 4th lane is water, so there was no band but the 5th lane is where Rpp0 was used instead of the primers that we designed. Rpp0 was used as a control so it made sense that a band appeared.
Great job! What kind of future experiments would you do to determine Rrm2’s relationship with other DNA repair proteins?
I think western blotting would be a good first step because that will allow us to know where the protein functions exactly and then we can determine what other DNA repair proteins also function in that area.