(1) Drs. Adèle Mennerat and Ben C. Sheldon in their article entitled “How to Deal with PCR Contamination in Molecular Microbial Ecology” (2014) asserts that pre-treating PCR mixes with restriction enzymes DNase 1 and Sau3AI, as well as the reducing agent DTT, reduces contamination levels from unwanted microbial DNA. (2) Mennerat and Sheldon provide evidence that enzymatic treatment reduced contamination because for both enzymes, fewer OTUs were identified after treatment when compared to the negative controls. (3) The purpose of this article is to describe possible methods of reducing contamination in PCR experiments in microbial ecology, as PCR contamination can significantly impact results. (4) Mennerat and Sheldon establish a scholarly relationship with other microbial ecology researchers, as well as other scientists who are experiencing problems with PCR contamination from unwanted microbial DNA.

Mennerat, A, Sheldon, BC. 2014. How to Deal with PCR Contamination in Molecular Microbial Ecology. Microb Ecol 68:834-841.

This is my first exposure to doing anything on the command line, and it’s been quite an experience thus far. I will say that it is extremely satisfying when everything works like it’s supposed to, and it’s relatively easy once I understand what is going on. I would say that I generally understand everything that is happening, though things get a little fuzzy with the statistical analysis stuff because I just haven’t done a lot with that in the past. The whole mothur thing is still weird and confusing to me. I don’t know what it’s actually doing, but I know how to run it at least :). I really liked doing the chimera exercise because it all definitely made sense. I would honestly classify that whole exercise as a eureka moment because it sort of brought things together a bit and seemed more cohesive.

I didn’t really gather much about my writing from reading other people’s research proposals, but it was most certainly inspiring from a project idea point of view. It’s always amazing to see what different things people come up with given the same assignment. I went a little bit more medical with my idea, whereas one that I read focused on analyzing waste water. It definitely reminds me to keep an open mind about things and learn to ask other people for their input and ideas more because they will definitely think about something that I never would have. Hence, the value of peer reviewing! Someone always comes up with something that you missed.

(1) C. Lee Ventola, M.S., in her article entitled “The antibiotic resistance crisis: part 1: causes and threats” (2015) states that bacterial infections have again become a serious threat due to increasing resistance to antibiotics because of abuse of drugs and lack of new drug development. (2) Ventola describes increasing resistance in a number of pathogenic bacterial species and also examines the clinical and economic burden of antibiotic resistance. (3) The purpose of this article is to provide a clear-cut statement of the problem of antibiotic resistance and where it’s coming from in order to encourage change in the prescribing of treatments and the amelioration of other factors that contribute to resistance. (4) Ventola reaches an audience that is integral in creating change in the problem because they are working in the hospitals that are on the front line.

Ventola, C.L. 2015. The Antibiotic Resistance Crisis. P T 40(4):277-283.

The process of peer review starts with someone doing research and writing a paper about what they have done/found. They then submit that paper to a publication (typically a journal) that publishes papers pertaining to the topic they have done their work on. The following process varies from publication to publication, but generally, the submitted paper then goes to an editor. If the editor decides that the paper presents good enough science or is pertinent to the publication or if it’s just generally good enough to be published, the editor will pass it on to other reviewers. (The editor could also just outright reject the paper.) The reviewers (funnily enough) will review the paper and write feedback on it. The editor then takes the feedback from the reviewers and passes it and any feedback they themselves might have back to the author. The author then edits their paper based on the feedback they received and resubmit it. If the editor and the reviewers are satisfied, the paper can then be published in the publication.

A definite pro of this system is that it’s a little bit harder to get bogus science into a respected publication because it has to be screened before it can be published. It also means that papers will probably be a little better written/explained. A con is that the reviewers could potentially have their own biases about the subject or the author or any variety of factors. It’s an extremely subjective process, and considering its whole focus is good science, subjectivity isn’t ideal.

It was definitely interesting to review someone else’s writing. I have obviously done it before in other classes, and I’ve always found that it was ultimately beneficial for my own writing. For example, I wasn’t exactly sure what kind of things that I could include in the background section of my proposal, but after seeing two other proposals, I was able to identify what I would have liked to see in their writing, and I can apply that to my own. One of them lacked (in my personal opinion) an adequate amount of scientific explanation as to why their proposed treatment would be feasible, and when I looked back at my own proposal, I found the same issue with it. I found one of the proposals particularly well done because of the amount of explanation they included, so I’m definitely going to try to do the same thing.

Microbial populations are microbes that are all the same species living in a given area. In an attempt to connect this to the high-throughput sequencing stuff we are going over, I suppose that all the microbes in a given population will have the same 16S sequences (and therefore the same V4 hyper-variable region). Microbial populations differ from microbial communities in that communities are whatever microbes, no matter the species, that live in a given area. The community is impacted by how the microbes all interact with each other. In a microbial community, if you sequenced the 16S genes (like we plan to in lab), then you would get all sorts of different sequences (I think).

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