Writing in Biology - Section 1

A recent story about a man on an airplane that was saved by a celebrity doctor has given rise to the news of a parasite (tick) that can make you allergic to red meats. "The "hygiene" hypothesis, now several decades old, suggests that with no parasites to fight, the immune system doesn't know when to quit and ends up targeting allergens." The symbiosis between parasites and humans is not well understood. Common allergens such as peanuts, bees, pets, and trees can be detected within the immune system while parasites are not. The fact that our bodies do not deal with every parasite suggests that the body purposely does not hurt specific parasites by turning this response off. Another theory could be that parasites have unique methods to alter their host's immune system. The relationship between a parasite-fighting immune system and the cause of an allergen must come down to similarity within the molecule composition and protein structure. "Using blood serum from parasite-infected people in Ghana, experimental studies finally revealed the first known example of a pollen-like protein present in a parasitic worm that gets targeted by IgE." The results reveal that immunotherapy may prove to be useful as long as the allergen-causing protein.

https://www.smithsonianmag.com/science-nature/why-do-humans-have-allergies-parasite-infections-trigger-180957101/?no-ist

Genotyping is a common technique learned in the genetic lab used to figure out the genotype of animals form their DNA. a proper genotyping done in three distinct steps. The first is DNA extraction, the second is PCR, and the third is gel electrophoresis. The first step is DNA extraction this is typically done using silicon columns. In this method, the lysis buffer and proteinase k is added to the tissue and incubated. After this is done the tube is spun so that the supernatant can be removed without contamination. When this is done the supernatant is then put into a spin column. It is then spun. This allows for the DNA to bind to the silicon and the rest of the supernatant to be separated from the DNA. the column is then washed using wash buffer and the column is then put into a new collection tube and eluted. The eluted solution contains DNA. the DNA is then put into another tube, and buffer, forward primer, reverse primer, MgCl2, and taq PCR are added. This is then heated and cooled at the optimal temperature for the gene. The resulting solution is then put into a well of the gel, and the gel is ran. The resulting gel is able to show whether the gene is present or not. However, every gene is different in how it shows in the gel. One of the things that can be done if there is a relatively large amount of soft tissue is to skip on DNA extraction and just boil the tissue at 95 degrees in NaOH, adding tris HCl after. this is a rougher way of extracting DNA however, it is effective in some tissues, such as mouse ear. 

3d Fluorescence imaging is accomplished similar to how flow cytometry works. Both of them rely on tags that have fluorescence attached to them, are used most often in molecular biology in order to determine what enzyme is interacting with which ligand. The two things that are being looked at are both tagged in different colors. The tags are then scanned for with a laser to produce the raw data. The data is then processed so that the information can be processed. This is accomplished by establishing how close the two tags are. It is assumed that if the tag that has the molecules attached are close to each other, then it would make sense that the two are interacting in a chemical way. However, this would depend heavily on the quality of the imaging because the precision of the data is wholly reliant on the quality of the image. In addition, this also has a problem of never actually proving that they are interacting. They can appear to interact but never actually interact. In addition, the coefficient that is obtained from the result is heavily dependent on which one it is based on. For example, if there were a large amount of the ligand, and small of the receptor, the coefficient of ligand to receptor would be much smaller compared to receptor to ligand.  The positive of the technique is that it is relatively cost-efficient, and provide quantitative data from the image. However, this technique is als extremely labor-intensive and can only work well in a few experiments. 

In Junior Year Writing Class at the University of Massachusetts, Amerhst, Professor Brewer assigned a project to capture and replicate signs of phytophagy on the UMass campus. This project allowed students to study what controllable factors and unavoidable discrepancies appear when replicating an individual’s methods. Furthermore, capturing evidence of phytophagy on the UMass campus offered a process to learn about how to create a perfect figure and follow others’ methods. The focus of my figure was a leaf found on a large bush in the rooftop garden of the John W. Olver Design Building. I chose this specimen due to its convenient location and obvious signs of phytophagy. In addition factors were more easily controlled since this is a privately maintained garden therefore the bush would not be destroyed. The time of day, zoom, perspective, and quality of the photos were also considered when this example of phytophagy was captured so that it can be replicated accurately.

I've had the opportunity to work with mice over the summer. It was really interesting to me because I've only ever worked with cell culture before. one of the things that I noticed while working with mice over working with cells is how variable the data was. There were some major differences between the highest number and the lowest number. I asked the postdoc about it and he told me that this is actually quite common. It interested me that there was so much to work with mice, especially working with mice that often didn't live until the reproductive age and as a result, the mut mice could only be produced by two het parents and praying for lots of pups. I've learned what to do and what not to do when making mice lines, and what is possible but still not a good idea.  I've also been quite good at handling the mice and doing oral gavages while the mice are still awake, although I was not quite as good as to do collect the blood without anesthesia. On the other hand, I did manage to collect blood without killing the mice I'm proud. 

I've also learned the reason why mice work was not for everyone. I ended up having my fingers bitten, and because a permanent mice line could not be produced, many of the mice had to be euthanized. This was quite a bit painful to watch and the way of being euthanized was not always framed in a way that looked painful but was not as direct as dislocating the spine. I think I will work with mice again, and it was a really good learning experience, but I think I will be less judgy when people are unwilling to work with mice. 

(Work in progress paragraph from METHODS project)

Between the two pictures, the most evident difference is that these figures are describing two separate trees, located in completely separate areas. The order of the photos is different: all three photos (close, medium, far) are located in different quadrants in both figures. The map, however, is located in the correct quadrant in the replication. Secondly, the aspect ratio of the two figures is quite different. While the second figure was consistent in making a starting template of 1600x1200 pixels in the photo editor, they captured their images-presumably from a cellphone-in a portrait orientation. The result is unused space to both sides of the central figure. Also, a much thinner, longer arrow was used when pointing out information in the replicated figure. In terms of other graphical additions to the figure, the text in the top left of each image is of a different color, order, size, and font than the ones originally used. 

I wanted to write about the most significant word in my life right now. This word is “counteract”. It means “to act against (something) in order to reduce its force or neutralize it.” Now you may ask why it is so significant to me, and why I think it should be significant to anyone going through a hard time right now. In my personal experience, this word has helped me push through my darkest moments, and I hope it can do the same to you. Depression makes us feel worthless and makes us feel like we are in an extremely dark place. However, what I learned recently is that to overcome it, we must do the opposite of what our mind is convincing us. We are being “hijacked” by our brain, convincing us that we cannot do things, and we cannot feel happy at that exact moment. This is where I learned the word “counteract”. When we think negative thoughts, our mind cycles into telling us to keep thinking it. I call it automatic negative thinking, or ANT. 

Phytophagy means “the eating of plants”. This can be done by animals, insects, or even humans. There is plenty of phytophagy around us, in our dining hall, on the ground or you can even spot phytophagy just by staring closely at a plant. In this project, every student will have to find proof of phytophagy, make a multipanel, create their own methods, and have someone else follow their methods. I chose a leaf that was right in front of Tobin Hall, the reason behind why I chose this leaf is because it stood out to me as it was very nicely shaped compared to the other leaves on campus. Also it was not too far from Boyden Gym, where I am most of the day. 

I have always wondered about the psychology behind dreaming. I always wake up the next morning delusional because I wish my dream had been a reality (sometimes). They can be scary, and sometimes people think that dreams can be preminitions to the future. I believe they help with emotional reguation, depending on my mood, I can have a really scary dream or a really happy dream. The ancient Egyptians believed that dreams were communication between Gods. Then Freud made a theory, but many scientists disagree with this theory. I will continue to do research about this topic as I am very curious. 

CHIKV also known s Chinkungunya is an almost fatal illness. This is spread by a mosquito, like Zika and dengue.  The most common symptoms of this virus are joint pain along with fever symptoms. It can become very severe, as it can lead to headaches, swelling of limbs and even can be fatal. There are recent outbreaks in the United States, but this virus is primarily spread in parts of Africa, the Caribbean’s and India. Researchers from the University of Bristol and the French National Centre for Scientific Research (CNRS) in Grenoble, France, have come together and created a vaccine that can withstand very warm temperatures.  They worked with a synthetic protein scaffold with no genetic material inside that is still extremely stable, even without refrigeration. The greatest part about their discovery is that they can insert harmless bits of the Chikungunya to generate a mimic to further use as a vaccine. Although they are still figuring out the logistics of it, computers and technology have helped them create a digital model of the vaccine. Intriguingly, because of this great beginning to fight again CHIKV, they can now rapidly engineer similar vaccines that can combat many other infectious diseases.