BIOL368/F20:Class Journal Week 3

Anna Horvath

What aspect of this assignment came most easily to you?

• • I am a part of Dr. Willette's research lab, where we sometimes hold journal clubs. Additionally, one of my recent research projects involved the analysis of various scientific papers. I have become accustomed to the scientific language and the presentation of information. For this reason, I found that I had a good understanding of many concepts explained within the paper.

What aspect of this assignment was the most challenging to you?

• • Writing about the figures was the most challenging aspect of this for me. I attribute this to the fact that I am more used to describe the texts of articles than analyzing the figures presented. For this reason, I found myself taking a lot of time to carefully understand what each figure meant.

What (yet) do you not understand?

• • I would like to better understand the mechanisms that occurs after the human ACE2 receptor and the RBM regions bind. I now have a good understanding of how these two regions come to attach. However, I am curious about how the virus is able to integrate itself into the host cell fully. I would also like to know more about ways to potentially block these interactions from occurring.

What are you wondering about regarding the journal club article that might become the basis for a research project?

• • I am really interested in the creation of a vaccine for COVID-19. I would like to understand how knowledge of receptor-binding mechanism can aid in the creation of such a vaccine. I am also curious about the way the amino acid residue mutations can impact the way the disease manifests in the body. Is it possible that mutations can cause people to be asymptomatic or is that more dependent on the individual's immune response?

Anna Horvath (talk) 15:49, 22 September 2020 (PDT)

Nida Patel

• What aspect of this assignment came most easily to you?
  • I have always been good at memorizing definitions and excel In comprehensive reading, so reading and understanding the article was the easiest part of this assignment. Many of the definitions for specific or repeated terminology were given within the article which also made understanding its content easier.
• What aspect of this assignment was the most challenging to you?
  • The figures and tables were quite complicated, so when the assignment required providing an explanation for each one I spent a lot of time deciphering the graphs.
• What (yet) do you not understand?
  • Though the article does go over the binding of 2019-nCoV to ACE2 I still have a hard time understanding how specifically the binding occurs. I think my understanding of the way binding sites work is limited to enzyme reactions and thus I didn't understand the differences in a virus. Specifically relating to viruses I would like to know how it goes about entering the cell and begin its own process of self-replication.
• What are you wondering about regarding the journal club article that might become the basis for a research project?
  • I am really interested in drug trials to specifically target the process of 2019-nCoV binding with ACE2. The process of finding a vaccine or treatment to the virus is a big worldwide concern, so furthering studies in drug trials to target specific mechanisms would be the most interesting research going forward.

Nida Patel Nidapatel (talk) 00:17, 24 September 2020 (PDT)

Yaniv Maddahi

1. What aspect of this assignment came most easily to you?
   • What came most easily to me was the mentioning of amino acids and the idea of how the 2019 SARS-CoV compares and contrasts from the different variations of the virus. Understanding that there were different variations of the virus that came at different times was something I was able to follow along with however once the difference came with mutations I began to lose track. It came easy for me to write the description of the different graphs and figures once I was able to discuss them with Dr. Dahlquist.
2. What aspect of this assignment was the most challenging for you?
   • It was challenging for me to keep track of all the mutations and in what ways each mutation affected the virus and its potency. Understanding that there was, for example, a K479N mutation was something I understood, but understanding how exactly this mutation affected the virus’s potency and further the difference between all the mutations and their subsequent effects was a little more difficult for me to grasp. With regard to the actual assignment it was most difficult for me to write my outline while ensuring that I was remaining academically honest. I would never intentionally go against the rules for academic honesty but I think oftentimes when writing an outline one can do it unconsciously and unintentionally.
3. What (yet) do you not understand?
   • I am still a bit confused on the role of angiotensin with regard to the virus.I understand it is the enzyme that works with angiotensin but I am curious as to how this enzyme interacts with the virus. Further, I am still a bit confused/ having trouble with understanding all the different mutations and the differences among the mutation years and between the different organisms.
4. What are you wondering about regarding the journal club article that might become the basis for a research project?
   • I believe truly understanding what gives the 2019-nCoV strain the unique ability to be transmitted human-human. I also believe the researchers mentioned monitoring the virus for an N501T mutation (corresponding to the S487T mutation in SARS-CoV) that may greatly enhance the binding affinity between 2019-nCoV RBD and human ACE2. Both of these, to me, pose as incredible fields to further study. As mentioned in the article, the new strain does have enhanced affinity compared to the 2003 strain yet less compared to the 2002 strain. Monitoring its affinity as well as mutations could be very insightful.

Yaniv Maddahi (talk) 17:52, 22 September 2020 (PDT)

Nathan Beshai

1. What aspect of this assignment came most easily to you?
   • I think interpreting the figures came the most easily to me because they explained them well and also we worked a lot with phylogenetic trees and gene sequencing in biology lab so it was easier to understand this time around.
2. What aspect of this assignment was the most challenging for you?
   • Finding the definitions were the most difficult part of the assignment because some of the more complicated terms were not in any of the glossaries and seemed that not a lot of research was out there since the terms were very specific. Another difficult part for me was tracking the methods and procedures of the article as they were at the end and I did not understand how they came to conclusions until I went back and double-checked them.
3. What (yet) do you not understand?
   • I still don't understand why the amino acid residues affect the transmission rate to the extent that they do. For SARS-CoV the transmission rate was higher in the 2002-2003 period and decreased in the 2003-2004 period. I don't understand what sort of mutation can drastically decrease the transmission rate. I also don't understand how different species can get SARS-CoV and not get 2019-nCoV as the sequences have similarities.
4. What are you wondering about regarding the journal club article that might become the basis for a research project?
   • I was wondering if there was a drug or medicine that can inhibit the binding of the 5 amino acids from the RBD to the ACE2 protein. It seems that if there was a possibility of preventing just a couple of the 5 amino acids from binding it will either prevent the structure from completely binding or reduce the transmission rate significantly. To study this they can test different medications with the model organisms such as the pigs and ensure then attempt to transmit 2019-nCoV to them and see if the transmission is reduced.

Nathan R. Beshai (talk) 20:03, 22 September 2020 (PDT)

Aiden Burnett

1. What aspect of this assignment came most easily to you?
   • 1. Defining the terms that confused me came easily, as this is something I do anytime I am reading and is more of a reflex.
2. What aspect of this assignment was the most challenging for you?
   • Reading the Wan et al. paper was very difficult for me. I understood that it was meant for an audience with prior knowledge on the subject of virus-receptor interactions. This said, I found everything from the language/jargon used, lack of definitions, and sentence structure to be frustratingly dense. I read academic papers fairly regularly when I’m curious about something and with that regular contact with this sort of document this paper stood out as particularly inaccessible.
3. What (yet) do you not understand?
   • I don’t fully understand how spike protein receptor-binding domains interact with host receptor angiotensin-converting enzyme 2. I understand that they interact and this leads to the viral and host cell membranes to fuse, but I don’t actually understand how they interact.
4. What are you wondering about regarding the journal club article that might become the basis for a research project?
   • As someone more interested in ecological than atomic level interactions, I wonder what sort of ecological research can be informed by this paper. The obvious leap for me would be to research how the Wildland Urban Interface (WUI) could be managed differently to prevent reservoir-human transmission. I imagine that having a better understanding of the possible intermediate reservoirs would aid in this research.

Aiden Burnett (talk) 22:44, 23 September 2020 (PDT)

JT Correy

• What aspect of this assignment came most easily to you?
  • I thought that the figures were very well made, and the descriptions were not to challenging to read. So, the question asking us to summarize each of the figures was not too hard. Of course, there was still some vocabulary and specific details that I do not understand, but I think I was able to get a firm understanding pretty easily.
• What aspect of this assignment was the most challenging for you?
  • Definitely just reading the article the couple of times was the most challenging for me. As I read through it more and looked up definitions it became more coherent. The first read through was quite challenging and I felt like I was in pretty far over my head.
• What (yet) do you not understand?
  • I still don’t really understand why all this matters. I get that the spike interacts with the ACE2 protein, but why is that a bad thing? Is the ACE2 protein crucial for human survival? What is the impact on the ACE2 protein after the binding?
• What are you wondering about regarding the journal club article that might become the basis for a research project?
  • I am really curious about the ACE2 protein. I felt like the article was really lacking on information about it, but it is clearly important if it is the main way that COVID is impacting people. I also I’m interested in the previous forms of COVID viruses and why COVID-19 is so much more dangerous and spreadable than the others.

Jcorrey (talk) 17:58, 23 September 2020 (PDT)

Fatimah Alghanem

1. What aspect of this assignment came most easily to you?
   • evaluating the paper since the paper was clear and what's missing was clear to me.
2. What aspect of this assignment was the most challenging for you?
   • Reading the graphs;I found the graphs a little confusing as it had a lot of information in it.
3. What (yet) do you not understand?
   • I do not understand the extent to which this paper could be helpful in the medical feild.
4. What are you wondering about regarding the journal club article that might become the basis for a research project?
   • I am wondering about the other diseases that are similar to COVID-19 and how they are similar and how does that help with understanding the current pendamic.

Falghane (talk) 19:07, 23 September 2020 (PDT)

Owen Dailey

• What aspect of this assignment came most easily to you?
  • Understanding the interactions between the amino acids came easily to me because of my biochem classes and my current subject matter in cell biology.
• What aspect of this assignment was the most challenging for you?
  • The most challenging part of the assignment for me was understanding the phylogenetic trees because the strains of coronaviruses were not made very clear.
• What (yet) do you not understand?
  • Now that we have this information, how can we use it to prevent 2019-nCoV from entering the host cell.
• What are you wondering about regarding the journal club article that might become the basis for a research project?
  • Is there a way to change the conformation of human ACE2 so that 2019-nCOV can not enter the cell?

Owen R. Dailey (talk) 19:45, 23 September 2020 (PDT)

Macie Duran

1. What aspect of this assignment came most easily to you?
   • I felt that interpreting the figures was really interesting. I like to look at figures and tables to further my understanding of the evidence and get a more visual representation. Reading the captions on the figures and the parts of the article that reference to them is very helpful for my understanding of the content, and allows me to picture the processes in my head.
2. What aspect of this assignment was the most challenging for you?
   • The most challenging part was just immersing myself in the study. I read the full article twice for comprehension before starting my outline because I wanted to make sure I had an understanding of the study before starting. Then once I was going through each section to comprehend the information and put it into my own words, I felt like I had a better grasp on the details and findings outlined in the study.
3. What (yet) do you not understand?
   • I would like to know how we use our knowledge of this viral-receptor interaction to approach preventing infection.
4. What are you wondering about regarding the journal club article the might become the basis for a research project?
   • I’m curious about how we can manipulate ACE2 receptors for prevention. I also would like to learn more about how quickly the virus is mutating and how those changes impact the viral-receptor interactions.

(Macie Duran (talk) 22:52, 23 September 2020 (PDT))

Kam Taghizadeh

1. What aspect of this assignment came most easily to you?
   • The part that came easiest to me was evaluating the figures.
2. What aspect of this assignment was the most challenging for you?
   • The most challenging part was comparing the residues between the viral strains
3. What (yet) do you not understand?
   • I still don't understand why it has become so hard to come up with a drug that could affect the ACE2 receptor causing less transmission of the virus.
4. What are you wondering about regarding the journal club article the might become the basis for a research project?
   • I am wondering about the N501T mutation, as it is known to cause much higher binding affinity to ACE2, leading to more infections to occur.

Kam Taghizadeh (talk) 23:05, 23 September 2020 (PDT)

Ian Wright

1. What aspect of this assignment came most easily to you?
   • Annotating and reading the assigned paper. Although a lot of the codes and acronyms were difficult to get used to, I eventually became acclimated and the paper made a lot of sense.
2. What aspect of this assignment was the most challenging for you?
   • Creating an outline and communicating those ideas in my own words was very difficult. I had only just become accustomed to the jargon through reading the paper so reiteration was difficult without using their exact language.
3. What (yet) do you not understand?
   • What is this atomic level analysis they were talking about? Did they use a computer program? Or did they analyze all of the hydrogen bond/ionic interactions by hand? How can you quantify the affinity of one protein to another?
4. What are you wondering about regarding the journal club article that might become the basis for a research project?
   • I have multiple answers to this question
     • Are there sequences of spike proteins from current 2019-nCoV patients?
       • Can these sequences be used to identify mutations at the 501 critical residue?
       • Are there any mutations occurring in 2019-nCoV yet?
     • Do all of our cells have ACE-2 proteins on the membrane? If so, do they differ in connectivity to the spike protein?
     • What are the mechanisms that allow the RBM to be so inclined to mutation?
     • The authors mentioned in the discussion that in the case of SARS-CoV, there were some critical residues that were adapted to human ACE and others that were adapted to civet ACE. This implied a partial adaptation. Is this possible in 2019-nCoV and, if so, what species should we be looking at for partial adaptation?

Ian R. Wright (talk) 23:40, 23 September 2020 (PDT)

Taylor Makela

1. What aspect of this assignment came most easily to you?
   • The aspect of this assignment that came most easily to me was summarizing the figures. I am definitely a visual learner so I think that is what this was the easiest part for me.
2. What aspect of this assignment was the most challenging for you?
   • The most challenging part of this assignment for me was trying to understand the article the first time I read it. Initially, I was very confused and overwhelmed by the article, but after going through and defining word that I did not know, the article was much easier to comprehend.
3. What (yet) do you not understand?
   • I am unsure of why SARS-CoV (2002) is more efficient at using human ACE2 than 2019-nCoV yet SARS-CoV (2003)is less efficient.
4. What are you wondering about regarding the journal club article that might become the basis for a research project?
   • I am interested in further researching intermediate hosts for 2019-CoV since the article rules out mice and rats as intermediate hosts.

Taylor Makela (talk) 00:20, 24 September 2020 (PDT)