Month: February 2021

Adèle Mennerat and Ben C. Seheldon, in their paper entitles “How to Deal with PCR Contamination in Molecular Microbial Ecology,” assert that enzymatic treatment of PCR reagents help reduce contamination. The authors provide evidence that two enzymes, DNase 1 and SauAI both reduce contamination but DNase also shows substantial reduction in bacterial richness while SauAI does not affect richness and simultaneously reduces contamination. The purpose of this paper is to encourage use of decontaminating reagents in order to start setting this as standard procedure. The authors establishes a scholarly relationship with academic in microbial ecology as well as other biological sciences.

Mennerat, A., Sheldon, B.C. How to Deal with PCR Contamination in Molecular Microbial Ecology. Microb Ecol 68, 834–841 (2014).

To be perfectly honest, the chimera exercise was extremely difficult for me. I had a really hard time understanding the directions just because this is not something that I had ever done before. The commands were difficult to understand, and trying to remember the different commands that we had used throughout the previous exercise was also something that was difficult. Something that would have helped me was having a video of one of the instructors going through the commands and explaining it so that I could have another way of learning and understanding – since with online classes its a little more difficult to ask questions. However, while it was not an easy feat, I think that I did end up understanding everything by the end of it. In fact, I developed really great appreciation for the Usearch program. I had used BLAST in the past, however, I truly understood the benefits of the Usearch program. I think that with a little bit of practice with the commands, I can definitely use this in the near future. Additionally, I think the chimera exercise also brought my awareness to what chimeras are and why they are important. I did not even think about this concept before this class so I am really happy to have learned about chimeras and how to identify them in nucleotide sequences.

During the most recent panel review I saw a lot of really fantastic proposals. Most of the proposals were really thought out and clear and obviously had a lot of work put into it. One thing I realized was that the panel review process is very meticulous. My group and I reviewed every sentence of every proposal. We wanted to make sure that it met all of the criteria and constantly discussed how it would impact the respective fields. I think this influenced me the most because while we were pretty tough in analyzing everyone’s paper, the process of reading about all of these different topics was so fun! I think that doing research can be extremely draining but seeing the amount of effort and care that students put into their proposal was really inspiring. It makes me want to work much harder. I was also amazed by the amount of detail that some students put into their paper. While my paper was detailed, I think I may have missed a few key aspects of my proposal that would have definitely made it better. My experimentation process was solid but I did not have enough information in my intro about the potential health impacts of my topic. In the past, I have also noticed that my intro for proposals are somewhat lacking so I will definitely take this common mistake and try to remedy it in the future. When it comes to experimental design, I am pretty confident in my abilities. Quantifying microbes and sampling are some of my strengths and I am equipped to make experimental designs around these aspects of research. I think that something I could always improve upon is making sure that I cover all confounding variables that could possibly occur in the experimenting process.