BIOL368/S20:Class Journal Week 3

Madeleine King

1. What aspect of this assignment came most easily to you?
   • The aspect that came easily to me was to read a scientific paper and write an outline of it, as well as defining biological terms that I didn’t already know. I feel like that is a common aspect of reading papers in research and in the field in general.
2. What aspect of this assignment was the most challenging for you?
   • The aspect that was most challenging was to try to understand the background and actual experiments of the article. Once I researched a little about HIV, and some of the terms in the paper such as the different types of progressors and seroconversion,I was able to better understand more about what they were trying to figure out.
3. What (yet) do you not understand?
   • I don’t completely understand some of the methods and statistical tests they performed, but that is just due to the fact that I haven’t taken statistics and I am not in the field at the moment.
4. What are you wondering about regarding the journal club article that might become the basis for a research project?
   • I am wondering more about epitopes and how they can prevent the host immune response to do its job. I am also wondering more about if they studied the subjects for longer periods of time (up to 10 years), and if the results would still be the same. Lastly, I am wondering if different types of antiviral drugs could be injected into the patient, and how it affects the mutation rates of the virus (also in relation to CD4 cell count).

Mking44 (talk) 15:45, 2 February 2020 (PST)

Christina Dominguez

1. The aspect of the assignment that came most easily to me was understanding the discussion and the major findings that they found. When it is talked about in a broader context (like in the discussion), I found it easy to understand what the results meant.
2. The most challenging part of the assignment was understanding the methods. I normally have a hard time with this for every paper and find myself having to reread the methods many times in order to understand it.
3. I do not yet understand the dS/dN ratios and what exactly they did to eliminate bias by doing this. I also do not fully understand everything about the phylogenetic trees that they generated.
4. I am wondering more about Subject 9 and 15 which had different results compared to the other subjects. The authors have a separate methods section pertaining to this however it says "data not shown" which I thought would potentially be interesting to learn more about.

Cdominguez (talk) 13:35, 3 February 2020 (PST)

Jenny Chua

• What aspect of this assignment came most easily to you?
  • My lab last semester had a Writing flag attached to it, so we spent a lot of time writing lab reports and understanding the different parts of a scientific paper. It was easy for me to find answers to the questions the outline asked, and I found myself being able to read the paper, and more importantly understand it, and comprehend the majority of it.
• What aspect of this assignment was the most challenging to you?
  • Understanding the figures fully so I was able to write or talk about them was challenging. I credit this partially to the fact that most of my vocabulary words were the types of statistical tests employed in the study and I had not seen them previously and partially to my skillset as a verbal learner as opposed to a visual learner.
• What (yet) do you not understand?
  • Going back to the vocabulary I discussed in the previous question, I have not taken any sort of biomathematical or statistics class, so many of the techniques employed (Sanger, Tamura-Mei, etc.) I had no idea what the authors of the paper were talking about. However, I'm anticipating learning about them in Journal Club or possibly in office hours with Dr. Dahlquist.
• What are you wondering about regarding the journal club article that might become the basis for a research project?
  • I was really fascinated by the topic of HIV drugs that we discussed in the pre-lab lecture. I find it very fascinating that there are so many different kinds that are targeted for different stages in the virus's life cycle. When I was finished reading the article, I thought to myself, "knowing what we know about the relationship between genetic mutations and CD4 T cells, is there a medicine we can create to target treating a range of mutated viruses?" Perhaps a protease inhibitor, for example, that is able to delay or halt maturation of the virus for more than one or a few strains.

Annika Dinulos

What aspect of this assignment came most easily to you?

• I found that I enjoyed reading the introduction and the discussion. I was able to get a good generalization of what the researchers were trying to say here. I also thought doing background research into the definitions was pretty easy, since you should do that with any research paper you read, just to make sure you have a good understanding of the paper.

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

• The most challenging aspect of this assignment has been the difficulty encoding the results and how the results were obtained. In particular, I noticed that some of the methods, especially with analysis, were harder to follow. The section my partner and I were asked to present was confusing once we tried to dive deeper than the normal 'increased diversity and increased divergence' statements.

What (yet) do you not understand?

• I would like to better understand the nonsynonymous/synonymous mutation information. I have a general understanding of the ratio and what it should favor, but I have a harder time with applying that information to other results values like diversity and divergence. I think it applies to whether those changes are random or not, but I'm not sure.

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

• I'm wondering more about those patient anomaly's that they noticed, like Sub 9 and 15, and whether or not they were able to draw more data from their results, and what made them different. Subject 15 seemed to be most interesting, and since they were a rapid progressor, I wonder if they were able to come up with some hypotheses about the differences.

Karina Vescio

What aspect of this assignment came most easily to you?

• I enjoyed finding the definitions to scientific words I did not know. I also liked reading the Introduction and Discussion, because they were easiest for me to follow.

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

• The most difficult part of the assignment was understanding all the methods. I found that I had to re-read this section of the paper multiple times in order to understand it. I also had a difficult time deciphering the charts and graphs. Even though they had a description below, I had to look over them several times. Lastly, I also had a hard time following the Results. I did not fully understand what they were trying to explain.

What (yet) do you not understand?

• I do not fully understand how to decipher the information provided in Figure 3 and Figure 4. Do not understand how to properly read the phylogenetic tree and be able to relate them to each other.

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

• I am wondering why they particularly chose subjects who were intravenous drug users. It would be interesting to see more research on HIV-1 infected individuals who were born with the virus, verses those who contracted it through intravenous drug use. Wondering how drug use effects the immune response to the CD4-T cells as well.

Kvescio (talk) 21:43, 5 February 2020 (PST)

Sahil Patel

What aspect of this assignment came most easily to you?

• Outlining the article may have taken the most time but since I have read articles like this before and have outlined them in the past, this was not so much of an issue for me.

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

• I did not quite understand all of the terminology or methods that were used, but defining the terms at the start of the assignment helped me overcome this challenge.

What (yet) do you not understand?

• I still do not quite understand how they were able to create accurate phylogenetic trees based on quantitative data.

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

• I enjoyed learning about HIV research because I have always wondered how genetic variation impacts viruses as well as infectious diseases and its ability to spread through masses.

Sahil Patel (talk) 15:54, 5 February 2020 (PST)

Nathan On

What aspect of this assignment came most easily to you?

• The actual outlining aspect came easy to me since I've done countless outlines for a variety of classes.

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

• Some of the materials and methods were hard to decipher since they relied on having technical statistical and/or bioinformatic background.

What (yet) do you not understand?

• I do not really understand how the phylogenetic trees were generated for each of the subjects.

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

• I am wondering what kinds of changes were most helpful in allowing HIV-1 to survive and avoid detection, though I'm not sure how easily answerable that question is.

Non (talk) 22:39, 5 February 2020 (PST)

Drew Cartmel

What aspect of this assignment came most easily to you?

• I would say that the aspect of this assignment that came most easily to me was understanding the figures and tables that were presented because I think that this paper did a very good job of explaining how their data/figures supported their overall findings.

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

• The aspect of this assignment that was most challenging for me was reading the methods section of the paper because it was slightly challenging to understand how exactly they performed some of their methods.

What (yet) do you not understand?

• What I still am having trouble understanding is how exactly they created the phylogenetic trees for the particular individuals that they were studying.

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

• Are there any other viruses besides HIV that show comparable adaptability to human immune system?

Dcartmel (talk) 22:48, 5 February 2020 (PST)

Carolyn Egekeze

What aspect of this assignment came most easily to you?

• Reading and outlining the paper was not terribly difficult because I have read many scientific papers for other upper-division classes and for my research project.

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

• The most challenging part was trying to fully understand what the figures were trying to communicate. I especially found Figure 1 and Figures 3 and 4, which feature the phylogenetic trees, a bit overwhelming and difficult to understand.

What (yet) do you not understand?

• I still don't understand how the researchers used the genetic data to create the phylogenetic trees and how the dS, dN, and dS/dN values were calculated.

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

• One thing that I am wondering about is in the moderate and rapid strains, what amino acids are being selected for? Are there amino acid changes that favor a rapid progressor and are there amino acid changes that favor moderate progressor?

Carolyne (talk) 23:06, 5 February 2020 (PST)

Maya Paniagua

• What aspect of this assignment came most easily to you?

The aspect that came to me the most easily in this assignment is the ability to organize my journal. I enjoyed creating the different sections and I appreciate the questions that were provided so that I could ensure that I was reading the paper thoroughly.

• What aspect of this assignment was the most challenging for you?

The most challenging part of this assignment was learning how to read and extract information from a scientific paper and be able to reiterate it in my own words.

• What (yet) do you not understand?

I do not fully understand, the discussion portion of the paper. When the author went on to discuss the models, especially in regard of the epitopes, I became a little confused.

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

I am wondering if different regions of env demonstrate the same effects that were demonstrated in this paper.

Mpaniag1 (talk) 23:17, 5 February 2020 (PST)

Lizzy Urbina

• What aspect of this assignment came most easily to you?
  • It was easy to understand the layout and the main idea of the paper.
• What aspect of this assignment was the most challenging for you?
  • Personally, it was difficult to understand the statistics' analysis and how the pictures represented it.
• What (yet) do you not understand?
  • I do not understand the divergence portion of the statistics' analysis and the role in their new input of the behavior of the virus.
• What are you wondering about regarding the journal club article that might become the basis for a research project?
  • What makes the nonprogressors be selective against amino acid change and progressor be selective in favor of amino acid change?. How the immune system responds to both virus behavior?

Lurbinah (talk) 23:23, 5 February 2020 (PST)

Jack Menzagopian

1. Reading the paper and having a general understanding of it was not very difficult, especially the discussion section since it ties everything together and puts the results in a bigger picture.
2. It was most challenging to really understand and have a good grasp on some of the smaller details of the paper, especially some of the results and the values they used to analyze and quantify genetic diversity and divergence.
3. I still don't quite understand how they used some of the statistics to reach the conclusions they did.
4. I am curious to see if there are any organisms that have a natural immune response that can keep genetically diverse pathogens at bay since this paper suggests that there is a relationship between genetic diversity and CD4 T cell decline and the researcher hope to develop treatment that is focused on reducing genetic diversity of HIV-1 in hosts.

Jmenzago (talk) 23:25, 5 February 2020 (PST)

Nicholas Yeo

1. What aspect of this assignment came most easily to you?
   • The aspect of the assignment that came most easily to me was finding the definitions of the terms that I did not already know. I think I have a good understanding of how to search and find what I am looking for in a textbook or database. I also think that creating an outline was easy because the flow of the paper was very clear.
2. What aspect of this assignment was the most challenging for you?
   • The aspect that was the most challenging for me was understanding the experiments and statistical tests that were being performed. I did not have any previous knowledge of some of the methods they were using and why they would be using them. I also thought that interpreting some of the figures were difficult.
3. What (yet) do you not understand?
   • I do not understand some of the tests and methods that they used and why they were used. I have never taken statistics, so many of the terms were unfamiliar to me.
4. What are you wondering about regarding the journal club article that might become the basis for a research project?
   • Since I am interested in medicine, I want to know the ways that the virus can be treated and what can be done to prevent it from a gene expression standpoint. I know that some people are born HIV resistant, so maybe there are some clues in these individuals.

Nyeo2 (talk) 23:52, 5 February 2020 (PST)

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)

Aiden Burnett

1. What aspect of this assignment came most easily to you?
   • Defining the terms that confused me came easily, as this is something I do anytime I am reading and is more of a reflex for me.
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 used, lack of definitions, and sentence structure to be frustratingly dense. I read academic papers more often than pop-sci articles when I’m curious about something and with that regular contact with this sort of document this paper stood out as particularly inaccessible to me.
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.

Aiden Burnett (talk) 21:23, 29 September 2020 (PDT)