BIOL368/F16:Class Journal Week 8

Colin Wikholm

1. What was the easiest aspect of reading/understanding the your journal club article?
   • The easiest aspect of reading and understanding my journal club article was understanding the mechanisms described regarding HIV-1 invasion of host cell. This is primarily because I studied this is the last project and presentation, so understanding the primary binding, secondary binding, and membrane fusion was relatively straightforward. It was a detailed review.
2. What was the most difficult aspect of reading/understanding your journal club article?
   • The most difficult aspect of reading and understanding the journal article was following the writing structure. Because the article did not follow sequential ordering of sections (which I am used to in scientific literature), it was very difficult to differentiate background information and results, as well as important and supplemental information. The writing advanced in a way that was extremely difficult to follow and understand conceptually.
3. What new questions do you have about HIV that you would like to answer?
   • I still want to know more about aspects of HIV-1 including reverse transcription and drugs that target this function. In addition, I would like to understand the mechanisms that allow HIV-1 to undergo lysogenic stages as opposed to lytic phases. Lastly, I wish to know more about the overall protein structure of HIV-1. How are the other parts important? So far we seem to have primary studied the surface protein components.

Colin Wikholm 01:36, 25 October 2016 (EDT)

Isai Lopez

1. What was the easiest aspect of reading/understanding the your journal club article?
   • The easiest part of understanding our article was for me the figures depicting the shape of the gp120 protein, as well as those of 17b Fab, and CD4 two domains. The color coding made the domains easier to tell apart, and the inclusion of things like a topography diagram helped my understanding of the overall interaction.
2. What was the most difficult aspect of reading/understanding your journal club article?
   • The format of the paper goes against anything I've read in life science literature. The methodology was last, and the results and discussion sections seemed to be done as one. In addition, background information was included throughout which made it difficult to tell when I was reading new results and when I was getting a recap of previous studies.
3. What new questions do you have about HIV that you would like to answer?
   • After reading our article, I'd like to find out more about the conformational changes that occur and what residues are important for maintaining the structure of the complex.

• Isai Lopez 01:17, 25 October 2016 (EDT):

Anindita Varshneya

1. What was the easiest aspect of reading/understanding the your journal club article?
   • The easiest part of the reading was understanding the overall process for how CD4 binds with gp120 and the corresponding conformational changes.
2. What was the most difficult aspect of reading/understanding your journal club article?
   • The most difficult aspect of the reading was how confusing the article was. The article was structured in a way that combined past research, methods, results, and discussion which made it incredibly difficult to determine the most important findings of the paper in relation to previously discovered concepts. Furthermore, the paper was incredibly dense with jargon which made it difficult to sift through.
3. What new questions do you have about HIV that you would like to answer?
   • After reading the article, I'm curious about the mechanism of the chemokine receptor and how it allows for viral neutralization. I am also curious about the other aspects of the HIV virus and how they play a role in the infectious nature of the disease.

-- Anindita Varshneya 02:59, 25 October 2016 (EDT)

Will Fuchs

1. What was the easiest aspect of reading/understanding the your journal club article?
   • The rhetoric was formal and very scientific which always challenges me, but I need that feeling otherwise I can't grow as a reader, additionally they kept each point rather concise although it was a rather dense and extremely technical article. The organization of the paper was particularly clear and well presented and had no redundancies.
2. What was the most difficult aspect of reading/understanding your journal club article?
   • I felt the most difficult aspect was the degree of specialized knowledge and unfamiliar terms that was implemented throughout the paper. This made the read very slow and tedious given that I felt as if I was continually looking up new terms and processes that were presented frequently. My lack of previous technical knowledge slowed down my ability to digest the paper.
3. What new questions do you have about HIV that you would like to answer?
   • The sub-type covered in this study was one of the less focused on in the U.S. so what makes the strains so different from each other? Is it solely genetic or do phenotypes play a role?

William P Fuchs 00:40, 24 October 2016 (EDT)

Avery Vernon-Moore

1. What was the easiest aspect of reading/understanding your journal club article?
   • I think the easiest aspect is creating an outline based off of the article. I appreciate that scientific articles/study have section headings which makes it much easier for me to follow and to break up and digest sections of the reading. I think it helps in such a difficult assignment that we now have some background knowledge on the subject.
2. What was the most difficult aspect of reading/understanding your journal club article?
   • In general I still have a hard time fully grasping their findings and really understanding what it is that was discovered. Even though we have been working with HIV for a few weeks it still is a lot to comprehend.
3. What new questions do you have about HIV that you would like to answer?
   • I think since my groups article focuses specifically on subtype C and neutralizing antibodies, I want to know if all the subtypes would be affected in the same signature sequences of the env gene, or if they develop significantly different within the body. I think I am just more interested to learn about the different subtypes of HIV-1 in general.

Avery Vernon-Moore 01:18, 19 October 2016 (EDT)

Zach Goldstein

1. What was the easiest aspect of reading/understanding your journal club article?
   • The easiest aspect of reading my article was understanding the conclusions of the research and how it can be applied to anti-AIDS drugs. This was easy because well, firstly the language used was less technical than in other sections, and secondly the conclusions made sense based on things we have already learned about in HIV-1 progression and treatment.
2. What was the most difficult aspect of reading/understanding your journal club article?
   • The most difficult aspect of reading this article was understanding the methods. The majority of this paper centered around making a good model of the V3 region of the gene. A lot of different programs were used in the creation of it, new analytical techniques were used, and I can safely say I still don't fully understand how they did it, although I get the general idea.
3. What new questions do you have about HIV that you would like to answer?
   • As discussed before, I would really like to see how these potential drugs would work to treat HIV/prevent AIDS. This article gets closer to answering that question but how exactly could we manufacture drugs that target the "rigid" secondary structures, and exactly how would they prevent progression of the virus. I would also like to know more about the subtypes and the differences between them. Is it only a genetic difference? Do they progress at different rates? Is one more susceptible to treatment by antibiotics?

Zachary T. Goldstein 02:39, 20 October 2016 (EDT)Zachary T. Goldstein

Matthew K. Oki

1. What was the easiest aspect of reading/understanding the your journal club article?
   • The introduction of the paper was fairly easy to follow and understand why they wanted to look at this area of HIV-1. It gave some nice background on certain terms used in the paper, as well as give us an outline of where they were trying to take the paper.
2. What was the most difficult aspect of reading/understanding your journal club article?
   • The most difficult part of the reading was trying to understand all of the methods they used. They used 5 major steps in this research, but all were done on computer software. So, not knowing what these softwares did was already a disadvantage. They also used a lot of jargon that is not in my regular vocabulary, so I had to read it a few times to get a grasp on what they were trying to do.
3. What new questions do you have about HIV that you would like to answer?
   • I am curious about the difference between the subtypes of HIV-1. We tried answering this question in our first presentation/research with no success. So, I would like to see the actual difference between the different subtypes. I would also like to see if there is a specific difference between the results presented in our paper compared to similar studies of subtype B.

• Matthew K. Oki 23:40, 24 October 2016 (EDT):

Jordan T. Detamore

1. What was the easiest aspect of reading/understanding the your journal club article?
   • While it was tough to grasp any of the contents of this paper, I was able to understand the basic binding principles presented as well as the basics of HIV presented
2. What was the most difficult aspect of reading/understanding your journal club article?
   • The article combined introduction, results and discussion all into the same paragraphs making it nearly impossible to decipher what was new discoveries and what had already been discovered.
3. What new questions do you have about HIV that you would like to answer?
   • I would be interested to know how the information from this study was further used. It is an older study so many scientists may have used these results for further research.

• Jordan T. Detamore 22:17, 24 October 2016 (EDT):

Courtney L. Merriam

1. What was the easiest aspect of reading/understanding your journal club article?
   • The easiest part of the journal reading was the fact that it is compartmentalized into different sections. The article as a whole is very complex, and includes several difficult to understand words that need to be looked up. When the article is broken down, I can work on understanding a sentence, then paragraph, then a section at a time. Then I can comprehend a sort of synopsis of the section, and eventually the article itself. Once I have a general idea, it’s easier to get into the more specific details with a wider context. I’ve found that this is the easiest way to understand complex topics.
2. What was the most difficult aspect of reading/understanding your journal club article?
   • The most difficult and tedious part of the article was having to decipher all the subject specific words and terminologies that experts use so colloquially. The article is so ridden with these words that I’d have to stop every sentence or so to look up words or at least try to consider the context or a term or phrase. Some sections were very dense with things I didn’t understand, especially the methods section, with different programs and techniques being mentioned that I have yet to be acquainted with.
3. What new questions do you have about HIV that you would like to answer?
   • We’ve been focusing a lot of subtype C, and this article is centralizing around subtype C as well. So I would like to learn more about other subtypes, and also if there is a mechanism by which a neutralizing antibody could be synthesized to neutralize every subtype. I don’t yet know enough about the genetic differences between the subtypes to be able to tell if that’s feasible or not.

• Courtney L. Merriam 18:29, 22 October 2016 (EDT):

Mia Huddleston

1. What was the easiest aspect of reading/understanding the your journal club article?
   • The easiest part for me was when the article referenced termeology and concepts that I learned in my immunology class. This article did relate quite well to what we are currently learning in that class such as chemokines which helped me understand the article much better.
2. What was the most difficult aspect of reading/understanding your journal club article?
   • This paper also referenced a lot of terminology and methods that I didn't know anything about. The methods section was extremely difficult to understand because of all of the programs they used.
3. What new questions do you have about HIV that you would like to answer?
   • Since our topic was based on finding a way to help with anti-AIDS drugs, I'm really interested in the most current research and what seems to be working as an anti-AIDS drug.

Mia Huddleston 18:15, 24 October 2016 (EDT)

Shivum Desai

1. What was the easiest aspect of reading/understanding the your journal club article?
   • To be completely honest I did not find any aspect of this reading to be easy at all. But if I had to pick one thing, it would be understanding figure 1, which is a unrooted phylogenetic tree and this was easy to understand because we have used and made these trees previously in class so I had experience with them already.
2. What was the most difficult aspect of reading/understanding your journal club article?
   • The most difficult aspect of reading this paper was understanding the terminology in the paper. I had to look up almost a word every single sentence because the paper did not define almost all of the more complex, scientific, words. Thus, this paper could only be easily understood by a scientist in this field of biology.
3. What new questions do you have about HIV that you would like to answer?
   • I would like to know why there has not been a vaccine made already for the HIV virus if regions like the V4 region have already been identified. What is the next step that is preventing a vaccine?

Shivum A Desai 22:28, 24 October 2016 (EDT):

Matthew Allegretti

1. What was the easiest aspect of reading/understanding the your journal club article?
   • Understanding what the goal of the study was pretty simple to do. The significance and aims of the study were plainly stated.
2. What was the most difficult aspect of reading/understanding your journal club article?
   • Understanding how they went about testing for a broad spectrum neutralizing antibody was quite confusing. Many of the concepts that they addressed seemed beyond my current understanding of biology and the HIV virus. Also, many of their results seemed to not prove or disprove anything, but rather point toward areas of future research where more questions needed to be asked.
3. What new questions do you have about HIV that you would like to answer?
   • Why focus on variable regions within HIV to target with potential vaccines? Are there regions within HIV that are highly conserved, and could these be targeted? If not, why can they not be targeted?

Matthew R Allegretti 22:50, 24 October 2016 (EDT)