BIOL368/F20:Class Journal Week 4

Yaniv Maddahi Reflection

1. Did the in-class discussion of the journal article enhance your understanding of the article? Why or why not?
   • The discussion of the article really helped me understand some areas of the article that were a bit confusing for me and then also helped me to understand the overall structure of the article. Mainly because in talking about it with my peers as well as Dr. Dahlquist I was able to clarify a lot of confusing points for me. I had some trouble interpreting the aspects of the amino acid mutations and so it helped for us to be able to talk through those. Furthermore, I had some trouble understanding the phylogenetic relation of 2019-nCoV with the other forms of the virus.
2. What is your comfort level when working with the bioinformatics database and tool for this assignment? What would increase your comfort level?
   • Initially I am very hesitant to work with the bioinformatics database because I do not really have a lot of experience with it. Thus it is very time consuming for me to work with databases of this nature and for me to navigate them as well. That being said, I do believe the more we work with it the more comfortable I will become and the more fluid my working with such interfaces will be.
3. Do you have any additional critiques of the article now that you've performed a similar analysis yourself?
   • I initially did not critique the materials and methods as much simply because for some reason it did not stand out to me. Although after having needed to present my own steps of how my results were obtained I now would critique the materials and methods of the article even more. I believe reproducibility and allowing others to test out your experiment is incredibly useful for validating labs and if others are not able to figure out how to do such a thing then the validity of one’s own lab comes into question. I do believe that there should be some type of scale or key for what the 0.01 means in the phylogenetic tree as there is also a 0.5 in mine and I do not understand what the units are supposed to be.
4. Go back and look at your answer to question 4 on the Class Journal Week 3 reflection. How would you refine (or entirely change) your question now to make it into a more feasible basis for a research project?
   • I still believe that the researchers could further study what gives the 2019-nCoV strain the unique ability to be transmitted human-human. I also believe the researchers should monitor the amino acid mutation 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. I suppose also further developing the understanding of the origin of 2019-nCoV and it’s relation to other strains could be an interesting field to further study.

Yaniv Maddahi (talk) 08:23, 29 September 2020 (PDT)

Nathan Beshai Journal

1. Did the in-class discussion of the journal article enhance your understanding of the article? Why or why not?
   • The in-class discussion of the journal article did enhance my understanding of the article. I did not realize how many students had the same questions I did and so when they asked them it became more clear. Another thing that it helped with was that the article had a lot of fine details that I missed and other students caught. This helped plug-in pieces of the puzzle and connected things for me. Dr. Dahlquist explain the article with her slides and outlining the article really simplified things and made the article more approachable.
2. What is your comfort level when working with the bioinformatics database and tool for this assignment? What would increase your comfort level?
   • Working with the databases this lab really helped my understanding of them. I feel comfortable enough looking through sequences and finding specific proteins or other locations. After this lab, I figured out how to download the FASTA format and use those sequences inside a word or a text editor.
3. Do you have any additional critiques of the article now that you've performed a similar analysis yourself?
   • The additional critics that I have from the article all involve the sequence alignment and phylogenetic tree. The first critic is that they didn't explain how they found the five critical amino acid sequences and just highlighted them without explanation. This annoyed me because if I wanted to replicate the experiment using a different virus, I would have no clue finding the binding sites and critical amino acid residue points. Another critic is that they did not include their outgroup inside their alignment. This would have helped see how the spike proteins of the SARS viruses were different from sequences on another virus. Lastly, like what was discussed in class, not including their outgroup accession number was not helpful. The purpose of an outgroup is not to only create a separate branch but to see how it is a lot different from the rest of the sequences. Other than what was shown there was no way of comparing the sequences other than just looking at the phylogenetic tree.
4. Go back and look at your answer to question 4 on the Class Journal Week 3 reflection. How would you refine (or entirely change) your question now to make it into a more feasible basis for a research project?
   • I don't think I would change the question. Maybe refine it to look for a mutation in a preventative medication that would cause a mutation in the virus at one of the five residue points causing the spike protein to be unable to bind to human ACE-2.

Nathan R. Beshai (talk) 17:05, 29 September 2020 (PDT)

Aiden Burnett

1. Did the in-class discussion of the journal article enhance your understanding of the article? Why or why not?
   • Absolutely. Hearing others explain their understanding of the concepts presented in the paper was a lot easier to parse than the paper itself. I assume that is is related to the fact that I learn better from lectures/audio than text.
2. What is your comfort level when working with the bioinformatics database and tool for this assignment? What would increase your comfort level?
   • I am not very comfortable yet but mostly from a lack of experience. I am confident that I could become more proficient in these programs given more exposure.
3. Do you have any additional critiques of the article now that you've performed a similar analysis yourself?
   • I think that their procedures are now another part of the article which demonstrates its inaccessibility for non-professionals in their field. Unless the reader is familiar with the programs listed in their "Materials & Methods" section, they would have a very hard time trying to reproduce their results.
4. Go back and look at your answer to question 4 on the Class Journal Week 3 reflection. How would you refine (or entirely change) your question now to make it into a more feasible basis for a research project?
   • My question would more easily lend itself to a research project outside of the scope of this class (concerning ecology). I think that given my very limited experience with these programs I would ask if there is a correlation between a virus' R0 and the length of it's genome, or other features about the genome. I could look at the R0 and genomes of a handful of viruses, as well as other outbreak characteristics such as survivability, rate of recovery, etc.

Macie Duran

1. Did the in-class discussion of the journal article enhance your understanding of the article? Why or why not?
   • The in-class discussion of the journal article was very helpful in my understanding. Talking over everything and having Dr. Dahlquist to answer questions about the more fine details made everything a lot clearer. Additionally, being assigned the task of explaining a section of the results pushed me to make sure I had a clearer understanding of it.
2. What is your comfort level when working with the bioinformatics database and tool for this assignment? What would increase your comfort level?
   • I feel very comfortable with GenBank, as I’ve used it in several different classes before. I had never used Phylogeny.fr before, but with more practice I will be able to gain a better understanding of how this tool can be used in sequence analysis.
3. Do you have any additional critiques of the article now that you’ve performed a similar analysis yourself?
   • Last week I critiqued the replicability of the Wan et al. study, as well as the lack of a detailed materials and methods section. I stand by those critiques, and as I attempted to replicate their results I began to wonder how they were able to determine their five key residues. It’s possible that this process was outlined in previous research they conducted, but it was never explained in this journal. They also failed to provide an outgroup accession number that could be found in GenBank, which made it impossible to truly replicate.
4. Go back and look at your answer to question 4 on the Class Journal Week 3 reflection. How would you refine (or entirely change) your question now to make it into a more feasible basis for a research project?
   • I would still like to understand how quickly natural mutations can occur in SARS-CoV-2, and determine how detrimental the possible mutations could be.

(Macie Duran (talk) 20:21, 30 September 2020 (PDT))

Owen Dailey

• Did the in-class discussion of the journal article enhance your understanding of the article? Why or why not?
  • The in-class discussion of the journal article did indeed enhance my understanding of the article. I believe journal clubs exist because scientific literature is hard to understand for the first time. So, because I was able to re-listen to some topics and hear others communicate the findings of the article, I was able to gain a better understanding.
• What is your comfort level when working with the bioinformatics database and tool for this assignment? What would increase your comfort level?
  • Because of my biochemistry lab experience and my microbiology lab experience, I have a had some practice with GenBank and phylogenetic software’s; however, I would not say that I was completely comfortable with this assignment. GenBank is such a large database, I have found that there are many functions on the database that I am not familiar with.
• Do you have any additional critiques of the article now that you've performed a similar analysis yourself?
  • After going through this assignment, I realize that this would be impossible to replicate with their minimal methods section. A big part of “Open Science” is being able to replicate results and Wan et al. did not allow others to do that.
• Go back and look at your answer to question 4 on the Class Journal Week 3 reflection. How would you refine (or entirely change) your question now to make it into a more feasible basis for a research project?
  • I am still interested in this question: Is there a way to change the conformation of human ACE2 so that 2019-nCOV cannot enter the cell? More related to this assignment: How many of the five critical amino acids have to be un-mutate/conserved to be able to enter human ACE2.

Owen R. Dailey (talk) 20:25, 30 September 2020 (PDT)

JT Correy

• Did the in-class discussion of the journal article enhance your understanding of the article? Why or why not?
  • The journal club definitely enhanced my understanding of the article. I feel like I had a decent understanding of the big picture ideas. Listening to how other people interpreted parts was very helpful with understanding more of the finer details. Also going over the figures in a very in-depth manor was useful since they were somewhat complicated.
• What is your comfort level when working with the bioinformatics database and tool for this assignment? What would increase your comfort level?
  • I felt very comfortable with the tools. This is my second year as a general biology lab TA and we do a very similar unit on phylogenetics so this was not really new to me. We use a different program, but it is still very similar and I feel like I have a good grasp of the techniques and databases.
• Do you have any additional critiques of the article now that you've performed a similar analysis yourself?
  • My major problem with the article is the lack of methods. I understand that I am not an expert in virology, but it seems that there was a severe lack of instruction and that reproducing their study would be near impossible unless you reached out and got more information. I also think that there was quite a bit of unnecessary bragging in their article. I want to know the science behind something, not that this specific group has been doing this research for over a decade and that their results should be held in high regard.
• Go back and look at your answer to question 4 on the Class Journal Week 3 reflection. How would you refine (or entirely change) your question now to make it into a more feasible basis for a research project?
  • I had two questions one about ACE2 and one about the history of COVID-19. I think that given the experience from this past week looking into the origins of SARS type viruses is a feasible option. I think that would be worth exploring as well as identifying why some strains of SARS or COVID are so much more deadly than others.

Jcorrey (talk) 22:09, 30 September 2020 (PDT)

Anna Horvath

1. Did the in-class discussion of the journal article enhance your understanding of the article? Why or why not?
   • The discussion in class about the journal article really helped me to understand the article. There were a few aspects that I was still unsure about after reading it by myself. Dr. Dahlquist helped me to answer any remaining questions I had. She also tied the paper together very nicely, as I was unsure as how some parts of the paper connected to one another.
2. What is your comfort level when working with the bioinformatics database and tool for this assignment? What would increase your comfort level?
   • I have previously worked with this in biochemistry lab. I have therefore had practice with GenBank and analyzing sequences. As a biology TA, I also have used various software to build and analyze phylogenetic trees to infer relationships. For phylogeny.fr, I am still unfamiliar with certain functions, so I think that I still need a bit more practice interpreting what each function does.
3. Do you have any additional critiques of the article now that you've performed a similar analysis yourself?
   • Now that I have performed a similar analysis, I feel even more strongly that they should have expanded their methods section. I do not think that this paper was replicable based off the information they provided. Specifically, the fact that their out-group sequence was incorrect made it very difficult to follow.
4. Go back and look at your answer to question 4 on the Class Journal Week 3 reflection. How would you refine (or entirely change) your question now to make it into a more feasible basis for a research project?
   • I am still interested in the same question: How can mutations affect the entry of COVID into human cells? Can a vaccine be developed in a way that prevents this entry into cells and control for further mutations of the five amino acids the paper mentions?

Anna Horvath (talk) 22:13, 30 September 2020 (PDT)

Ian Wright

1. Did the in-class discussion of the journal article enhance your understanding of the article? Why or why not?
   • Yes. The journal club style of having each group discuss a figure allowed me to understand the figures in further depth. I was focused enough of Figure 3 that I was able to understand it in depth but the other figures did not receive as much attention. Take figure 1B for example. Kam did a fantastic job explaining the mutations and their binding efficiencies. At first, I did not fully understand the < or > signs in this figure but then after hearing the journal club discussion, the meaning of the figure became clear and amplified.
2. What is your comfort level when working with the bioinformatics database and tool for this assignment? What would increase your comfort level?
   • GenBank was really smooth. I like the way it's structured with complete sequences followed by locus sequences. Phylogeny.fy was fun to use as well. The tools provided in the program seem to be very useful and although I only really used one of the editing tools, I can tell the others will be easy to use as well. Downloading and opening sequences in FASTA form was a bit of a hassle but in the end it worked out. Analyzing sequence alignment is really hard for the eyes. I think my comfort would increase with sequence analysis if we learned how to apply residue numbers and highlight points of interest. I wouldve liked to highlight or put certain residues in bold but that would take a very long time because I found that I could really only do them residue by residue.
3. Do you have any additional critiques of the article now that you've performed a similar analysis yourself?
   • My main critique is the lack of methodology. If I were already versed on the subject and comfortable with creating trees and aligning sequences and finding sequences in Databases, I would be able to follow their instructions easily. I only was able to complete this analysis because instructions were provided through the assignment page. I understand that they are writing these findings for a professional community, however, there is a huge educational opportunity to be taken in the methodology section.
4. Go back and look at your answer to question 4 on the Class Journal Week 3 reflection. How would you refine (or entirely change) your question now to make it into a more feasible basis for a research project?
   • I think that analysis of mutations at the 501st residue is feasible utilizing the alignment methods. The question of if ACE-2 is present on every cell can be answered through some good internet research. The next question that I listed, "What are the mechanisms that allow the RBM to be so inclined to mutation?" may be something I'd like to pursue. It will require some further knowledge regarding ORF proteins and the regulatory proteins that we learned about in the video on Week 3. Sequence alignment and phylogeny could be useful in comparing ORF between different coronaviruses. Did something happen to ORF in SARS-CoV-2 that allowed all these rapid mutations in the spike protein? I guess that would require knowing the true predecessor to SARS-CoV-2. Maybe this is the first question.

Ian R. Wright (talk) 22:41, 30 September 2020 (PDT)

Taylor Makela

1. Did the in-class discussion of the journal article enhance your understanding of the article? Why or why not?
   • The discussions that we had in class about the journal article definitely helped me to better understand the article. When I read the article for the first time, I was very confused. However, after looking up the words that I did not know for last weeks assignment and talking about the article in class, I now feel that I better understand it.
2. What is your comfort level when working with the bioinformatics database and tool for this assignment? What would increase your comfort level?
   • I would say that I feel pretty comfortable working with the databases in this course. I found both the GenBank and Phylogeny.fr databases very user friendly and easy to work with. However, I had a difficult time comprehending the various types of results that were produces using Phylogeny.fr and I think spending more time in class working with the data would help increase my comfort level.
3. Do you have any additional critiques of the article now that you've performed a similar analysis yourself?
   • Now that I have performed a similar analysis myself, my main critique of the article would be the lack of detail regarding what exactly was done in the analysis (lacking in the methods and results section of their paper).
4. Go back and look at your answer to question 4 on the Class Journal Week 3 reflection. How would you refine (or entirely change) your question now to make it into a more feasible basis for a research project?
   • After looking at my answer to question 4 from last weeks class journal, I think I would have to entirely change my question into something more feasible for a research project. I would instead look at the differences in sequencing of the SARS-like corona virus spike protein in humans vs bats.

Taylor Makela (talk) 00:06, 1 October 2020 (PDT)

Nida Patel Reflection

1. Did the in-class discussion of the journal article enhance your understanding of the article? Why or why not?
   • Yes, the article contains. a lot of dense information, going over it with the class helped me to prioritize key points and comprehend the figures in a more comprehensive way.
2. What is your comfort level when working with the bioinformatics database and tool for this assignment? What would increase your comfort level?
   • Being technologically unsavvy, I did spend a lot of time trying to decipher how to work the database, but with additional practice I feel like my comfort level will naturally increase. Continuing to practice my skills with the database and tools is the only way I would be more comfortable as the instructions were already detailed and concise.
3. Do you have any additional critiques of the article now that you've performed a similar analysis yourself?
   • The methods section of the article was lacking in its ability to be reproducible based on simply the article. A more detailed explanation of the methods would be the only part of the article I think requires modification.
4. Go back and look at your answer to question 4 on the Class Journal Week 3 reflection. How would you refine (or entirely change) your question now to make it into a more feasible basis for a research project?
   • I think now understanding the immense amount of research and experimentation required to test drugs on a virus, a lot of additional experimentation would need to be done before reaching that step. A replacement or precursor question that would need to be answered is What is the mechanism that Covid-19 enters the body and begins replication? To even begin drug trials, there should be an understanding of what the medication is specifically suppose to accomplish and target within the virus or body.

Nidapatel (talk) 00:17, 1 October 2020 (PDT)

Fatimah Alghanem

1. Did the in-class discussion of the journal article enhance your understanding of the article? Why or why not?
   • Yes it did. explaining the figures in depth helped me in understanding the figures better than when I read it alone. Also, I was confused about the methods and when we discussed it in class it was clear to me that the authors did not do a good job at explaining the methods, it confirmed to me that the methods are not well written.
2. What is your comfort level when working with the bioinformatics database and tool for this assignment? What would increase your comfort level?
   • My comfort level is 8/10, I think I would be more comfortable if there was video guidance instead of written steps because having a lot of text is sometimes confuses me.
3. Do you have any additional critiques of the article now that you've performed a similar analysis yourself?
   • A detailed method was necessary for the article.
4. Go back and look at your answer to question 4 on the Class Journal Week 3 reflection. How would you refine (or entirely change) your question now to make it into a more feasible basis for a research project?
   • How do Covid-19 spikes in the human act when attaching the virus to the human body?

Falghane (talk) 21:13, 1 October 2020 (PDT)

Kam Taghizadeh

• Did the in-class discussion of the journal article enhance your understanding of the article? Why or why not?
  • The in-class discussion of the journal article did enhance my understanding of the article. By analyzing the figures together, I could get a better sense of what was being talked about in the article.
• What is your comfort level when working with the bioinformatics database and tool for this assignment? What would increase your comfort level?
  • I am not that comfortable using the bioinformatics database and tool for this assignment, because I tend to get overwhelmed by anything tech-related. I hope that I can become more comfortable with these things as the class progresses. I think the only thing that could increase my comfort zone is practice.
• Do you have any additional critiques of the article now that you've performed a similar analysis yourself?
  • I would definitely write out a more thorough explanation as to how the figures were generated.
• Go back and look at your answer to question 4 on the Class Journal Week 3 reflection. How would you refine (or entirely change) your question now to make it into a more feasible basis for a research project?
  • I would refine it in that I would only look at human strains.

Kam Taghizadeh (talk) 23:34, 1 October 2020 (PDT)