Riely Medau – MB311 Lab Writing Blog

At the panel review, I realized how creative some minds can be. I assume that the most creative people are the most passionate about what they’re learning. It’s too easy to get caught up in doing something for a grade, rather than treating it as something to challenge yourself with. If grades or time didn’t matter, I would imagine that I’d be more creative too. It was also easier to tell what students spent ample amount of time on their papers and who turned them in last minute. Giving yourself enough time to think, write and edit your papers results in a higher quality product. One thing that I’ll take away from this experience is to be more creative. When comparing my proposal idea to other student’s, I could have come up with a better idea. There must be balance between creativity and relevance to others. An idea might sound really obscure to a panel review because your own personal interests are too niche, but on the other hand, you want to think of an idea that no one else has. When thinking about experimental design, more detail and the simpler the better. You have to assume you are presenting an idea to a group of people who have no idea what you are talking about, which I fail to do sometimes.

Another thing I enjoyed about the panel reviews is discussing other papers with the group that I was assigned. Anonymity helped us provide better quality constructive criticism. Being in a group relieved a bit of bias because we were able to hear other people’s opinions and gauge how reasonable our feedback was. It was difficult to rank people’s proposals because we all had different ideas of what was a “good” paper. I was rating proposals based on creativity and relevance, while one of my group members was rating proposals based on how reasonable an author’s procedure was. Mixing all these views on what was “good” helped us pick the most well-rounded proposal. I’m interested to see who the winners are for the proposals since other panels most likely judged differently than my panel.

When thinking of scientists, I picture people who are doctors that have an insurmountable amount of knowledge ahead of me. It’s hard to believe that scientists who make giant discoveries are normal people, but as I have gotten into more upper-division courses, I can see more of professors’ personalities. In lower division courses, the lectures were huge, and it was hard to feel a personal connection with professors at all unless you really went out of your way to go to their office hours or ask questions after class. As I moved through schooling, I could recognize some familiar qualities amongst scientists. Professors who teach a subject of science all have eccentric quirks about them, either they are really humble or there is the occasional pompous one. One characteristic that every scientist shares is passion towards their special interest.

Dr. Mullis was passionate enough to reflect on his techniques at work before he even had the chance to start relaxing at his weekend cabin. It must be exhausting to be that passionate about something where it is all you think about. I liked how when he talked about developing PCR that he had no idea what he was about to discover. He didn’t have a clue about what he was doing weren’t just working out technical kinks, but something much bigger. It makes me feel better that success stories like his can be sort of random and some people aren’t born set up with pre-determined success. It’s encouraging to see that science is attainable to everyone if they work hard at it and don’t get discouraged by failure. Two things I personally struggle with is thinking that I’ll never be as smart as my classmates and that failure is expected. I’m a perfectionist and want everything to turn out my way or get good grades on every project and test. Some of the best scientists emerged from struggle because it meant they learned more from failure, which I need to take into account myself.

In Carly Redelman and her team of researchers at the University of Butler’s article titled “Alcohol treatment enhances Staphylococcus aureus biofilm development” (2012), they determined that exposure to alcohols such as ethanol and isopropanol further enhanced adhesion protein production of established Staphylococcus aureus biofilms. Redelman supports this proposal by providing evidence of stimulated gene expression in vraS, mmpL and, mepA which are genes that control susceptibility to oxacillin and antibiotic efflux pumps. The purpose of this research article is to point out that despite alcohol being a prominent disinfectant method, increased levels of alcohol activate genes that are used by bacteria to promote antibiotic resistance in order to raise awareness that established biofilms may need a better technique for eradication. Redelman appeals to academics and well-versed scientists in fields such as biology or pharmacology to stress the urgency of protecting the public from improper sanitation methods.

One of the greatest responsibilities that a scientist has is writing lab reports and research articles explaining the methods and findings of their experiments. First, an author has to determine which scientific journal they would like to publish in because you can only submit to one journal at a time. Publishing is all about networking. Some scientists know specific editors at a journal, or they were grandfathered in after working under their supervisor or peers. After a research article has been sent to the journal of choice or the journal that they believe they have the best chances at being published in, it is sent off to be reviewed by other scientists within the same general field or that also have high-level scientific knowledge to be peer reviewed. The purpose of peer reviewing is to fill in the gaps that the experiment’s methods might be missing, overall comments about the experiment, advice on how the experiment should be run instead or if it is close to a subject that another scientist is currently writing. Some general guidelines that editors are looking for is a meticulous recount of each step of the experiment so that anyone in the world who reads the paper could recreate the experiment themselves and verify the author’s findings. The paper also has to be in a specific order where each section details a separate concept. The formatting has a special name called IMRAD: intro, methods, results, and discussion.

There are different types of peer review methods: single-blind where the reviewer knows the name of the author but the author doesn’t know the name of the reviewer, double-blind where both the author and the reviewer don’t know who they are, open peer where both the reviewer and author know who each other are, and transparent peer where the reviewers know who the author is and can decide whether or not they want to sign their name on the paper that said they reviewed it. Bias is a huge contender of whether your article gets published or not. As mentioned earlier, publishing is all about networking. An esteemed scientist may know several editors at several journals and have a higher chance of getting their journals peer reviewed and published. The author can also recommend other scientist friends to review their paper to the editor where it has a higher chance of better/more positive advice. A con of bias could be if an editor sends a paper off to a scientist within the same field that hates a particular scientist where it can be ripped to shreds. Both pros and cons affect the credibility of the paper because if your friends review it, its naturally going to have positive advice while your enemies are more than happy to see your downfall. Also, if you’ve known an editor for a very long time and have established a relationship with them, a scientist is more likely to be published.

Manipulating someone’s genetic code may sound like something straight out of a science fiction movie, but scientists today are using technology called CRISPR to do exactly that. Scientists are using the genetic codes from a wide variety of lifeforms like trees, bacteria or even viruses. CRISPR specifically edits the small pieces of DNA that pair up with one another called nucleobases. Nucleobases are the alphabetical code made up of As, Ts, Cs and Gs that when paired up with one another forms the helical shape of DNA. When those pairs of alphabetical code come together, they form a specific sequence that has a specific function called a gene. For example, one short sequence of pairs could encode for the function of an apple to have a red color. Scientists edit these sequences by using a protein called cas9. Scientists could plant the short sequence of the red gene of the apple onto the cas9 protein and the protein would be able to enter an apple cell, locate the same exact short sequence of gene and cut it. The protein cuts both strands of DNA by recognizing a particular pattern of 2-4 pairs of letters and only at these points (Barrangou and Doudna 2016).

Once the DNA is cut, the apple cell has built in mechanisms to try to repair itself but it would make a lot of mistakes. Since the sequence of pairs of the red gene could not be repaired, then the apple won’t be red. Scientists can edit the way the apple cell repairs itself so then the broken red gene could be rearranged and fixed to turn into a purple apple (Redman et al. 2016). Or if scientists wanted to make the apple more sweet, more sour, more tender, more resistant to bugs or the environment they would be able to by using the changed repair method. This could be used to help grow plants in a changing climate, help repair broken genes that cause genetic disorders or make bacteria less resistant to medicines. In our physical lab portion of this class, we test this technology on bacteria by making it resistant to an antibiotic. We had to target the specific gene that binds to the antibiotic to make sure that it can’t bind properly. Since it can’t bind properly to the antibiotic, the bacteria won’t be affected by it. This real life application proves that CRISPR technology is convenient, relatively easy to do and is cost efficient for an entire class. It is the future and essential to our survival as the effects of antibiotic resistance and climate change become more prevalent.

References:

Barrangou R and Doudna J. 2016. Applications of CRISPR technologies in research and beyond. Nature Biotechnology. 34: 933-941. doi: https://doi.org/10.1038/nbt.3659

Redman M, King A, Watson C, King D. 2016. What is CRISPR/cas9?. Archives of Disease in Childhood- Education and Practice. 101:213-215. doi: http://dx.doi.org/10.1136/archdischild-2016-310459.

In parasitology, we learned about vectors that allow different species of parasites to be bred inside of them or pass them along to the next host. A vector is a subject that continues the circle of life even if it is not suitable for the species in that specific moment. If I had to guess what cloning using bacterial vectors means, I would guess that bacteria are the vessels in which cloning takes place. Maybe their internal environment supports the cloning material of interest. Maybe it is DNA that can only survive within a host or need the bacteria’s specific machinery to make a copy of first. Since the first experiment dealt with gel electrophoresis, maybe we will be cloning bacterial DNA. This would be of interest because it isolates the bacteria’s DNA where we could then manipulate it to whatever purpose we need. It would remove the danger of getting infected by our species of interest. When using CRISPR technology, we rearrange the order of nucleobases to encode for a differing function than the original function.

Scientists regularly manipulate the genetic code of their subjects of interest in order to understand them better. Maybe the world doesn’t know a specific mechanism of how their metabolism works or how they can enter in a cell. If you tweak a gene that interferes with a specific step of their metabolism, then you would be able to determine how that gene is linked to that step. In virology we learned that scientists tweak viral DNA by either inserting or removing a gene to gain information on transmissibility or another related function. This helps us create drugs that interfere with the way they transmit to another person and hopefully prevent that from happening.

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