Month: February 2021

(1) Microbiologist, Adele Mennerat, in her research article entitled “How to Deal with PCR Contamination in Molecular Microbial Ecology” (2014) asserts that enzyme Sau3AI when used to decontaminate PCR reagents can cause higher accuracy in PCR reads when compared to using enzyme DNase 1. (2) Mennerat provides evidence that Sau3AI is the more effective enzyme by comparing similarity in community composition, and finding that Sau3AI was more similar to the original structure. (3) The purpose of this research is to demonstrate that an enzyme is needed to clean up PCR reagents in order for the results to have less decomtanition. (4) Mennerat establishes an instructive and scholarly relationship with microbiologist and any professional that wants to use PCR.  

Mennerat A, Sheldon BC. How to deal with PCR contamination in molecular microbial ecology. Microb Ecol. 2014 Nov;68(4):834-41. doi: 10.1007/s00248-014-0453-y. Epub 2014 Jul 9. PMID: 25004997.

This was my first time using my own terminal to analyze output from high through put sequencing of the 16s rRNA. It was an experience that was both frustrating but also very awarding. Being able to manipulate so much data using just your lab top that quickly is a valuable skill I am sure I will have to use in future research. It was a process that required problem solving skills, for example when the code wasn’t given and you had to look it up, and also team work skills, as I learned how helpful it was to have peers (and especially professors) to bounce ideas off of and help me solve problems. This year has been hard as we haven’t been able to work in person, on a lab bench, to visually learn, so I appreciated having a challenge that brought me closer to a lab bench like experience. I am not saying I am going to switch majors and go into computer science or that I would rather be coding than doing wet lab research but I do have a greater respect for data analysis now.

If I had something to say to the next class it would be; you can get through this, it’s going to be frustrating, you are going to get errors, but when you make the errors you learn because you are forced to confront the mistakes you made. Also that genome analysis is extremely important for microbiology and it is amazing the amount of conclusion you can draw with a few key strokes on your own laptop.

The panel review process of a paper, as I have discussed before, is not only time to improve the authors writing and proposal skills but for the panel to consider their own. In molecular microbiology lab we were able to review in small groups three papers (the larger groups experienced technical difficulties so we were unable to participate) and therefore were able to explore more ideas quicker and contrast experiments easier. Through the process of discussing I discovered concise writing with a plausible but interesting research design drew the groups vote. It made me realized that while I found my own project design interesting I was not writing enough for an audience. It is so valuable to be both the reviewer and the paper being reviewed because feed back comes from both other people and your own experience.

(1)University of Illinois microbiologist Carl Woese in his proposal “Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya” (1990) argues for that phylogenetic system at the time should be updated by expanding from kingdom to a new taxon “domain”. (2) Carl Woese provides background on how the phylogenetic tree was first created, and different branches formed, then cites his own work with microbes to explain how the three newly proposed domains are evolutionarily separate due to molecular level differences. (3) The purpose of this proposal is to present eukarya, bacteria and archaea as the overarching categories for the evolution of life now, demonstrating that on a molecular level archaea is separate from bacteria and actually closer related to eukarya. (4) Woese establishes a solid argument and therefore respect from the other scientists he is proposing this new system too.