(1) Adele Mennerat and Ben Sheldon in their review on PCR preparation effectiveness titled “How to Deal with PCR Contamination in Molecular Microbial Ecology.” (2014) explain the influence of Contaminants present within PCR primer reagents, influences of such contaminants and decontamination approaches to lessen the impact and improve data quality. (2) Mennerat and Sheldon provide evidence that enzymatic treatment does reduce contamination levels, but has the potential for adverse influence on microbial richness. (3) The purpose of this study is to provide analysis on potential decontamination methods for the Priming process, and test their influence on two enzymes (DNase 1 and Sau3AI) to determine if the ability to replicate and interpret the data collected from DNA amplification is improved or lessened. (4) Mennerat and Sheldon have developed an academic background in Biological laboratory practices, as well as other areas of study such as Zoology.
Writing Exercise #6 MB 311
Prompt – Following our recent in-class tutorials where you worked your way through learning DNA sequence analysis and chimera detection through your use of the command line, reflect on this learning experience. For some of you, this is a practice you’ve done before – did you learn anything new to add to your knowledge base? Did you think of any work-around that you use that could be helpful to other students just learning this? If this is your first exposure to this, reflect on the process – what was the most intuitive (if anything) part of this process? What was the most difficult to understand? Did you have any “eureka” moments? In the end, does this make sense to you?
This was essentially my first experience with coding. Last term, I did a very small amount of data analysis using R studio in my stats course. However compared to the information and work we have done in the last few weeks in this class, that was nothing.
I found that initially, nothing was intuitive. I don’t have much computer experience, and until the pandemic hit, was not very literate in the abilities of my computer other than basic programs like google docs and some excel work. From the first assignment on, I struggled to understand what was happening. After only being able to complete the first assignment with the help of others at my lab bench, I decided I needed to sit down and just get practice using the interface. I pulled up our two tutorials we had at the time, a google doc and just tried to figure it out. I gained experience using basic commands, navigating between directories, reading actual sequences, etc. I felt I better understood the content and felt relatively confident in my ability to complete the next assignment.
I worked on Assignment #3 with a few people from my lab bench, and was able to contribute and somewhat understand the purpose/ application of the work. I wasn’t able to keep up on the graph creation we did in class, but plan on going back through the lecture and following along soon.
Overall, I think I get the “main points” but am worried about how specific we should be in our report. I understand the overarching themes and why we did the work that we did, but don’t feel I could accurately articulate the finer details of the process.
Writing Exercise #5
The ability to review others ideas and methods in writing on the same prompt was extremely valuable and allowed me to gain new insight into my own writing’s format. In all of my experience peer reviewing, I have found it is easier to see errors in someone else’s work over your own. Perhaps this is because you’re invested in your own work, and know the thoughts behind each statement, rather than reading it at “face value.” However, after reading through and editing other’s work, it is always far easier to then notice errors or inconsistencies in my own. After peer reviewing papers a few weeks ago, I went back and read through my own paper. I noticed several errors and a conceptual miscommunication that I had not picked up on after several readings. I believe exercising this helped me get a higher score and review my own work with a fresh perspective.
Additionally, I feel reading others ideas helps me to become inspired in working on my own. Each paper I have read had fresh, unique ideas which I was, one way or another, able to apply to my own writing. Even if not directly, it allowed me to read my own writing with another “voice” in mind. I think that perspective shift is extremely valuable in exercises like this regardless, but especially during COVID when it is difficult to interact and get others perspectives.