BIOL368/S20:Class Journal Week 11

Madeleine King

1. What was the easiest aspect of reading/understanding the your journal club article?
   • The easiest aspect of reading/understanding the journal article was the section where they study the kinetics of the hACE2 receptor binding to the S glycoprotein since I took biochemistry and we learned about basic enzyme kinetics and terms like dissociation constant and other rate constants, which they used in their study.
2. What was the most difficult aspect of reading/understanding your journal club article?
   • The most difficult aspect of reading the journal article was their experiments using cryo-EM since I've never used it before and it was difficult to try to visualize it at first.
3. What new questions do you have about SARS-CoV-2 that you would like to answer in the final project?
   • I'd like to study more about the furin-cleavage site, since that is the main key difference between SARS-2 and other SARS viruses.

Mking44 (talk) 20:57, 15 April 2020 (PDT)

Christina Dominguez

What was the easiest aspect of reading/understanding the your journal club article?

The easiest aspect was the setup of the paper. The paper did a good job of using an importance and introduction section to thoroughly explain how previous studies and work were tying into how they did their analysis for the current study. This made it easy to follow and easy to understand how they were relating it to SARS-CoV.

What was the most difficult aspect of reading/understanding your journal club article?

The most difficult aspect was understanding the science of critical residues changes and how this effected amino acids and thus affinity. The data was presented a little confusing and made it hard to understand. It had a lot of detailed explanation in the text that was difficult to understand initially and required me to read it multiple times.

What new questions do you have about SARS-CoV-2 that you would like to answer in the final project?

Does the affinity binding between ACE2 and RBD have anything to do with the symptomatic response of each individual or infectivity? Cdominguez (talk) 20:59, 13 April 2020 (PDT)

Jenny Chua

What was the easiest aspect of reading/understanding your journal club article?

The easiest aspect of understanding the article was probably the main point of understanding how tight the spike protein binds to the host receptor and how this could be the reason why the symptoms and diagnoses of so many are so fatal.

What was the most difficult aspect of reading/understanding your journal club article?

The most difficult aspect was the methods. I struggled a lot with understanding how they came to the afore mentioned conclusion and the biophysics/math behind RBD and TND. The article also wasn't set up in an outlined format (Methods, Results, Discussion, etc.) so it felt scattered and if I wanted to search the methods for example, it was difficult.

What new questions do you have about SARS-CoV-2 that you would like to answer in the final project?

I would like to know why and how a tight binding to a host receptor could cause such severe symptoms in some, but little to none in others. What happens after the binding takes place that leads to symptom presentation?

Jennymchua (talk) 10:11, 15 April 2020 (PDT)

Maya Paniagua

What was the easiest aspect of reading/understanding the journal club article?

• The easiest thing to understand were the connections the authors made between SARS-CoV and 2019-nCoV and how they made their predictions based on previous knowledge.

What was the most difficult aspect of reading/understanding your journal club article?

• The most difficult aspect was understanding how the specific changes in residues affected the overall structure and binding, the effects of the changes came across confusing

What new questions do you have about SARS-CoV-2 that you would like to answer in the final project?

• I want to know how mutations in ACE2 can affect binding affinity and if certain animals are more susceptible than others

Mpaniag1 (talk) 14:00, 15 April 2020 (PDT)

Nicholas Yeo

1. What was the easiest aspect of reading/understanding the your journal club article?
   • I found it easiest to understand when the authors were comparing the new SARS-CoV-2 to previous coronaviruses. It makes sense that they are similar because they come from the same family of viruses, but it was interesting nonetheless.
2. What was the most difficult aspect of reading/understanding your journal club article?
   • The most difficult aspect of this reading was keeping track of all the abbreviations and names for different proteins and cells within the article and how they all relate with one another.
3. What new questions do you have about SARS-CoV-2 that you would like to answer in the final project?
   • I want to know how these new antibodies inhibit virus entry into target cells.

Nyeo2 (talk) 17:00, 15 April 2020 (PDT)

Carolyn Egekeze

• What was the easiest aspect of reading/understanding the your journal club article?
  • The easiest part of reading the article was reading through the background information about SARS-CoV-2, ACE2, and BAT1. The authors do a good job of explaining why the research is important and how they developed their study based on previous work. They also do a good job of explaining the limitations of their work and how their findings can be used in to learn more about SARS-CoV-2.
• What was the most difficult aspect of reading/understanding your journal club article?
  • The most difficult part of the journal club article was trying to understand how the residues on the structures were interacting. The authors would mention which parts of the proteins belonged to what domain, but it was still difficult for me to understand the binding interactions they were talking about.
• What new questions do you have about SARS-CoV-2 that you would like to answer in the final project?
  • I am interested in how the immune response to SARS-CoV-2 differs among patients. I am also interested in how the structural information that we have about how SARS-CoV-2 interacts with ACE2 can be used to design a drug or antibody that counteracts the binding interaction.

Carolyne (talk) 18:12, 15 April 2020 (PDT)

Drew Cartmel

1. What was the easiest part of reading/understanding the your journal club article?
   • The easiest part of reading/understanding this journal club article was the section comparing the structure of the receptor binding motif of the SARS-CoV virus and the predictive model of the receptor binding motif of 2019-nCoV. The description as well as the figures in this section were very easy to follow and understand.
2. What was the most difficult aspect of reading/understanding your journal club article?
   • The most difficult aspect of reading/understanding this journal article was the section on the mutations in the receptor binding motif of the spike protein that affect its binding to the host ACE2 protein because there were various mutations that can influence how well the RBM of the spike protein binds to the ACE2 protein.
3. What new questions do you have about SARS-COV-2 that you would like to answer in the final project?
   • I would like to investigate if there are any known treatment methods or medications that can be utilized to inhibit the binding between spike proteins and ACE2 proteins in host species.

Dcartmel (talk) 20:55, 15 April 2020 (PDT)

Jack Menzagopian

1. The easiest aspect of reading my assigned article was the conclusions made by the authors and how they relate to addressing the current pandemic. The importance of understanding the structure-function relationship between SARS-CoV-2 and ACE2 was clear and made sense.
2. The most difficult aspect of the article was keeping track of all the parts of the RBD-PD complex. There were so many residues and complexes mentioned in a fairly short paper, which made it hard to keep up and keep track of all the parts mentioned.
3. The authors suggested that, based on comparisons between the RBD-ACE2 complex of SARS-CoV and SARS-CoV-2, the presence of certain polar residues notably impacts the strength of the interaction between the virus and the enzyme, which would be interesting to explore further. I am also interested in how asymptomatic cases develop.

Jmenzago (talk) 21:15, 15 April 2020 (PDT)

Annika Dinulos

1. The easiest aspect of understanding within the article was the importance of visualizing the spike protein and how their findings would help with research to develop a vaccine, and that the 2019-nCoV spike protein binds with a higher affinity to ACE2.
2. The most difficult part to understand was the methods especially since the article wasn't organized in a typical fashion, and how the variations of the novel coronavirus protein sequence change the loops and positions of residues in the RBD.
3. I would like to know if the transmission of 2019-nCoV is more contagious due to the 2019-nCoV S binding to ACE2 with higher affinity, and if that has any relation to who might present symptoms.

Adinulos (talk) 22:16, 15 April 2020 (PDT)

Nathan On

• What was the easiest aspect of reading/understanding the your journal club article?
  • I found it relatively easy understanding the sequence analysis portion of the article as it didn't involve any concepts or experiments that I hadn't seen before.
• What was the most difficult aspect of reading/understanding your journal club article?
  • I found it difficult keeping tracking of all the acronyms, abbreviations and technical terms that were scattered throughout the article.
• What new questions do you have about SARS-CoV-2 that you would like to answer in the final project?
  • Are there possible treatments that could reduce the binding affinity of SARS-CoV-2 to ACE2?

Non (talk) 23:49, 15 April 2020 (PDT)

Karina Vescio

1. What was the easiest aspect of reading/understanding the your journal club article?
   • The easiest aspect of reading/understanding the journal article was the Abstract and the Methods. It was easy to understand what previous studies had been done, and why the team of scientists decided to perform this particular experiment. I also liked the Introduction before the Abstract; it helped give some extra background and context.
2. What was the most difficult aspect of reading/understanding your journal club article?
   • The most difficult aspect of reading the journal article was deciphering the Figures, and how they corresponded to the Results. I found the overall article to be difficult to understand. It took several times of reading it before I had any understanding of the material, but in all, the Figures were the most difficult.
3. What new questions do you have about SARS-CoV-2 that you would like to answer in the final project?
   • I would like to know how the binding of the virus in the human receptor region differs from the binding in SARS-CoV-01.

(Kvescio (talk) 00:00, 16 April 2020 (PDT))

Sahil Patel

• What was the easiest aspect of reading/understanding the your journal club article?
  • I employed a new strategy with reading primary literature that I had stumbled upon on youtube randomly. I started with the abstract/introduction and then read the discussion before I went into the methods and results. This really helped me grasp the importance of the article much better than if I had just read it from start to finish. Often, when I do this I sometimes read the whole thing and barely have any understanding of what I just read. So, this time I though reading and understanding the article was the easiest aspect for me.
• What was the most difficult aspect of reading/understanding your journal club article?
  • The most difficult aspect was that some of the terms they used in this article were new to me, so I was thankful for the definitions portion however some terms were much harder to find.
• What new questions do you have about SARS-CoV-2 that you would like to answer in the final project?
  • Generally, we explore the structure and function relationships when we discuss these viruses; however I would want to look at the antibodies in the blood plasma from people who were previously infected and if this could be researched and developed into some type of treatment.

Sahil Patel (talk) 01:31, 17 April 2020 (PDT)