Alia Alshamsi – MB311 Writing Blog

I really liked the panel review exercise we did in class, because it helped me start to think about approaching proposals in different ways through the various roles we had to participate in (primary, secondary, or tertiary reviewer). I also really liked being able to look at other people’s ideas for what research is important, not only to themselves but to the community/population. I think all three of the proposals we reviewed in my group had good relevance and their importance was backed up sufficiently. I also thought the procedures for all three proposals was well done and well researched, and it inspires me to put more work into the procedure sections of any future proposals I might write. Overall, I think the justification part of a proposal is the most crucial part to getting a proposal accepted, and from a personal standpoint, it is also the most enjoyable part to write/research. I think this has definitely shown through in the other proposals I read as well.

The first thing I noticed about Kary Mullis’s article about the discovery of PCR was his great storytelling. I think the intersection between science and the arts is important, especially for communicating science to the general public, and his portrayal of how he came up with the discovery was engaging to read. This also puts into perspective how accessible molecular biology, along with other scientific fields, can be. Scientists truly are real people, and those real people can also come up with amazing inventions and techniques that change the world. While he may not have been completely sober when devising a plan for PCR, Mullis was able to create this innovative technique while doing something as mundane as driving down a highway. It also shows that you can come up with amazing things as long as you have the right knowledge, and you may not need any fancy tools or machines to help you with the idea creation aspect. It also puts into perspective how science can be very humanistic, in the sense that it can bring people together because although science often seems very concrete, we are still all just humans trying to interpret our surroundings and understand why things are the way they are.

Lauren Bakaletz, a researcher for the Center for Microbial Pathogenesis at Ohio State College of Medicine, presents evidence for the hypothesis that viruses and bacteria have effects on pathogenesis during coinfection in her review article titled “Viral-bacterial co-infections in the respiratory tract” (2017). Bakaletz uses information from previously published scientific studies to demonstrate that a primary viral infection can increase the ability for bacteria to establish a more serious secondary infection, using mechanisms such as damage to epithelial cells, immune system suppression, and alteration of the microbiome. The purpose of this review is to consolidate all the currently known information on how coinfection works, in order to kickstart further research into this topic and development of treatments or prevention strategies. Bakaletz addresses any researchers with a baseline knowledge of microbiology who wish to know more about bacterial and viral pathogenesis, presenting them with information to further their knowledge in a specific subtopic such as coinfection.

Bakaletz LO. Viral-bacterial co-infections in the respiratory tract. Curr Opin Microbiol.
2017;35:30-35. doi:10.1016/j.mib.2016.11.003

The process of peer review is crucial in the development of a scientific paper and its publication. The scientists that conducted the research first select a journal to submit to based on a number of factors, such as the topic of the journal and any personal connections a researcher may have to it. Once the first draft is complete, it is sent to the journal’s editor. The editor decides whether the paper and research are at a reasonable enough level to warrant sending it to peer reviewers; the reviewers can be selected randomly (within reason, as the reviewers have to have at least some knowledge of the topic the research is investigating), or reviewers can be suggested by the scientists submitting the work. The peer review process can be open, single-blind (the reviewers know the scientists who did the research, but the scientists do not know the reviewers), or double-blind (neither the reviewers nor the scientists know who the other is). The reviewers analyze the paper and may provide suggestions on how to make the paper better, or the overall research that was conducted. After review, the paper may be sent back to the scientists for revision; if the paper is sufficient enough as deemed by the reviewers, it is sent back to the journal for final approval, where it can then be published. Peer review is important because it provides the opportunity to examine data/findings and make sure they are credible before being released to the public, and also allows people from many different backgrounds to examine the research and find ways to make it more accessible to the public, or just the scientific community. However, peer review can be difficult or cumbersome to get through if the reviewers are biased towards the researchers for whatever reason, and the reviewer may also be a competitor for the scientists submitting the paper.

CRISPR/Cas9 is a new biological mechanism used to edit the genetic information of an organism. This can be done by insertion of a new gene into the genome, deletion of a gene, or performing what is called a base pair substitution, which involves switching out a nucleotide (A, T, C, or G) within the DNA with another nucleotide. Cas9 is the enzyme that mediates this editing, by cutting both strands of DNA in a specific place on the genome. Cas9 is directed to the correct site on the genome using a strand of RNA called sgRNA, or single-guide RNA. This piece of RNA is complementary to the DNA at a very specific location on the genome and guides the Cas9 enzyme to cut in that location, where the insertion, deletion, or editing of a gene can occur. This genetic modification technique is a hot topic within the scientific community because of its potential applications. The high specificity and efficiency of this mechanism is favorable and has been proposed as a treatment for various genetic diseases and conditions, like cancer. By using CRISPR/Cas9, oncogenic genes can be edited or deleted, having suppressive effects on cancerous cells/tumors. It can also insert genes that may be absent in other genetic conditions, or may treat a condition when the products of the gene are expressed. Furthermore, there have been some concerns about using this technology on humans to give someone more “advantageous” traits, later down the line when the technology is further developed.

Hazafa A, Mumtaz M, Farooq MF, et al. CRISPR/Cas9: A powerful genome editing technique for the treatment of cancer cells with present challenges and future directions. Life Sci. 2020;263:118525. doi:10.1016/j.lfs.2020.118525

I have not had much personal experience in genetics throughout my educational career, but from what I understand, cloning involves the generation/production of genetically identical organisms. Bacterial vectors are especially useful for this because of their relatively easy to manipulate genomes and their fast reproduction rate. In the field of bacterial genetics, cloning is often used to study the effects of certain mutations on the function of an organism. This can be done by introducing mutations at certain sites in the genome (like what we are doing for our CRISPR experiment) to produce a certain phenotype or examine that mutation to see what functions it affects in comparison to the wild-type species. In the research lab I am currently working in, I conducted a transformation using Streptococcus pneumoniae, doing a gene knockout to replace a gene encoding a protease with an antibiotic resistance gene. After proceeding with the transformation, I isolated the new bacterial mutant and made stocks of it, which I am using for the current experiments I am running to see how the mutant adheres to epithelial cells in the absence of that protease. Previous to this experiment, I have had very little exposure to genetics, and MB310/311 is the first time I am really being introduced to genetics in the context of bacterial molecular genetics.