BIOL398-01/S10:Class Journal Week 7

Kristoffer Chin

1. The purpose of this week's assignment was to continue with the HIV project by moving to HIV structures. We have already completed HIV evolution by understanding the sequences and how they affect the virus. It was now time to translate these sequences into amino acids and protein structure. From there, we would be bale to understand more about HIV and how it works in humans.
2. From this assignment, I learned that even though there was a great amount of diversity and divergence found in rapid progressors, there is still a possibility of finding similarities in the structures of HIV. Obviously the nucleotide sequence would be different, but the structures may be similar in properties and function. It gave me a better understanding of those that are researching HIV because they are trying to figure out ways to stop it through the DNA/RNA level and the protein level. I would not be surprised if there are other ways to approach this disease. It is also quite interesting that there is much more to learn about a single virus despite its size.
3. I now understand a little more about why HIV vaccines are currently ineffective. I am wondering if thought if there are any big news in HIV research lately and if there is an estimate of time of when a cure can be found and if it is possible that even though if the vaccine is found, will immunogenicity of it be high or low?

BIOL398-01/S10:Week 7

Kristoffer Chin: Week 7

--Kristoffer T. Chin 19:21, 7 March 2010 (EST)

Salomon Garcia

1. The purpose of this assignment was to continue in our study of the HIV virus but this time we are to approach it b looking at its particular structures. And in order to begin in the understanding of the structure we are to begin by looking at our particular paper which in our case was the "Recurring conformation of the human immunodeficiency virus type 1 gp120 V3 loop". And from this begin making a powerpoint presentation for our journal club meeting.
2. One of things that I learned from this article was that it is hard to come up with an effective vaccine because of the many changes that may occur with the virus and that in turn goes to change the structure of a particular protein as was the case that was seen in this study that there were many changes in particular structure.
3. Understanding the paper has been a bit tough because there are many words and procedures that were done that are hard to follow and comprehend at times I've had to stop and reread to fully understand what I was reading

Salomon Garcia Valencia 21:06, 7 March 2010 (EST)

Angela Garibaldi

1. The purpose of this assignment was to practice reading a scientific article in its entirety, summarizing it, understanding it , and then putting it into a powerpoint format for presentation.
2. I learned that even if the assignment is only 10 vocabulary words that you do not understand, sometimes you need to look up more terms than that in order to understand. Furthermore, many times I needed to look up processes and different protocols in order to understand what was being done in the experiment in order to achieve the structure of HIV.
3. At this point I think I understood the assignment and the concepts presented in the paper.However, some of the methods used are unclear to me in that I haven't learned about them yet. Also, the structure is still fairly difficult to visualize. Angela A. Garibaldi 01:17, 8 March 2010 (EST)

• Week 7 Assignment Page

• Week 7 Personal Journal

Alex George

1. This assignment's purpose was to further learn how to present a scientific paper to a community. We are taking notes on vocabulary in addition to the paper in order to fully understand the article. This assignment is the first Journal Club assignment of our own, so we are given the freedom to find what works best.
2. What I learned from the paper was the variability of conformations within the V3 loop could offer explanations for the pathogenicity of HIV. There a certain regions that remain constant throughout different genes that suggest their crucial role in determining relative shape. Also, I realized there a number of ways to approach a disease in terms of trying to find a cure. Distinguishing its function on the protein level is just another approach. Finally, I learned the difficulty of picking apart a biochemical scientific paper.
3. I understand the assignment well enough, but understanding the paper has been a little bit more challenging. It has become difficult to grow accustom to the terms (such as Fab 59.2 and Aib). Also, the results displayed a lot of numbers and angles that I couldn't really grasp. Overall, though, I am slowly getting the gist of the paper.

Alex J. George Week 7

Alex J. George 16:47, 7 March 2010 (EST)

J'aime Moehlman

• Week 7 Assignment Page
• Week 7 Personal Assignment

1. The purpose for this assignment was to learn how to review a scientific research paper and then be able to share it with others in the form of a journal club. We created a powerpoint presentation to assist us in the explaining of the article and we worked in a group to distrubute sections of the article.
2. This week I learned how to try and review a research article based off of the V3 region on the gp120 protein. It helped me learn more about what contributes to the pathogenicity of HIV-1. This week was a bit of a struggle for me and I was a bit frustrated with the amount of vocabulary that I didn't understand.
3. The actual idea of the assignment makes sense to me, however the research article our group was responsible for made very little sense to me. I felt as though I needed much more background information to even begin to understand what they were trying to convey in the article. Most of the tables in the article didn't really make much sense to me and didnt have very good descriptions of them so that I could attempt to learn what they were there for. I still think that I am a bit unsure of what the article was attempting to explain however I do think I understand the key point of the article.

J'aime C. Moehlman 02:21, 8 March 2010 (EST)

KP Ramirez

1. The purpose of this assignment was to continue our Journal clubs as well as undertaking an entire journal club ourselves. This would be the first time that we would be assigned a paper and asked to read through and prepare a presentation based on our findings. There were three papers and our team was assigned the first one. This paper concerned the structure of HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody.
2. This assignment was jumping head first into beginning to understand the structure of HIV. It was very different from earlier papers that looked at how the virus progressed as now we had to understand the conformational changes as well as how things linked together. Our paper focussed on gp120 and several other parts involved in the process. I also learned more about working on a journal club with a team.
3. There were actually several things I did not yet understand about this assignment. There are many aspects of the structure of HIV that are confusing to me, such as the Chemokine receptor sites. Additionally I felt that this was difficult because I had no background in this type of study.

KP Ramirez 1:21 March 7 2010

Individual week 7

Michael Piña

1. The purpose of this assignment was to transition into the biology of the HIV virus. Many of us in class had questions regarding the biology of the virus in regards to the changes in nucleotide sequence when we were observing the evolution of the virus and so this assignment introduced us to more of the structural biology. In addition, this assignment also gave us practice in reading a journal article.
2. I learned much about the structure of the V3 loop in the gp 120 protein and how it plays a vital role to the virus. I also learned about some of the characteristics of antibodies to neutralize the virus. The purpose of the article was basically to add to the existing pool of knowledge of HIV with crystalline structures.
3. Although the article was initially very tough to comprehend, I found that the more and more I spent time with it the more I was able to break it down in ways that I was able to easier understand. The article makes alot of references to amino acids interacting with other amino acids, and while I don't really understand that part, I'm fairly comfortable with the rest of the article.

Week 7 Individual

Janelle N. Ruiz

1. The purpose of this assignment was to read the article and outline the article in order to enhance our understanding of the paper. We also needed to work together as a group to teach the article to the class.
2. I learned a lot about protein structure! I learned more in depth the structure of gp120 and how it interacts with CD4 and the neutralizing Abs and how this mediates viral infection of host cells.
3. I had a tough time reading this article primarily because I don't believe I have the appropriate background in biochemistry and protein structure to be able to fully comprehend many of the article's main points and findings. I certainly don't feel that I am at a level to teach the paper to the class which worries me. I wish we had had a lecture on the article or an introduction to protein structure dynamics before jumping into this journal club

Janelle N. Ruiz 02:58, 8 March 2010 (EST)

Janelle N. Ruiz Assignment 7

Bobak Seddighzadeh

1. What was the purpose of this assignment? The purpose of this assignment was to prepare for our journal club presentation. Our group read an article specific to antibody and HIV-1 V3 loop conformation. We are to develop our analytical skills in the process in order to make a clear presentation of the article.
2. What did you learn from the assignment(head, hands, heart)? I learned a lot just from reading the article. I learned that the conformation of the antibody and peptide have a lot to do with binding. I also learned that the V3 loop of peptides found on the membrane HIV-1 play a large role in viral entry into the cell.
3. Do you have any questions for the project? No I have no confusion or questions as to what my project entails. The paper was relatively clear, but I had to read it several times over in order to gain a strong understanding of what was going on.

• Electronic Journal

1. Bobak Seddighzadeh Week 2
2. Bobak Seddighzadeh Week 3
3. Bobak Seddighzadeh Week 4
4. Bobak Seddighzadeh Week 5
5. Bobak Seddighzadeh Week 6
6. Bobak Seddighzadeh Week 7
7. Bobak Seddighzadeh Week 8
8. Bobak Seddighzadeh Week 9
9. Bobak Seddighzadeh Week 10
10. Bobak Seddighzadeh Week 11
11. Bobak Seddighzadeh Week 12
12. Bobak Seddighzadeh Week 13

• Shared Journal

1. BIOL398-01/S10:Class Journal Week 2
2. BIOL398-01/S10:Class Journal Week 3
3. BIOL398-01/S10:Class Journal Week 4
4. BIOL398-01/S10:Class Journal Week 5
5. BIOL398-01/S10:Class Journal Week 6
6. BIOL398-01/S10:Class Journal Week 7
7. BIOL398-01/S10:Class Journal Week 8
8. BIOL398-01/S10:Class Journal Week 9
9. BIOL398-01/S10:Class Journal Week 10
10. BIOL398-01/S10:Class Journal Week 11
11. BIOL398-01/S10:Class Journal Week 12
12. BIOL398-01/S10:Class Journal Week 13

• Assignments

1. BIOL398-01/S10:Week 2
2. BIOL398-01/S10:Week 3
3. BIOL398-01/S10:Week 4
4. BIOL398-01/S10:Week 5
5. BIOL398-01/S10:Week 6
6. BIOL398-01/S10:Week 7
7. BIOL398-01/S10:Week 8
8. BIOL398-01/S10:Week 9
9. BIOL398-01/S10:Week 10
10. BIOL398-01/S10:Week 11
11. BIOL398-01/S10:Week 12
12. BIOL398-01/S10:Week 13

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Amanda Wavrin

• Amanda N. Wavrin Week 7
• Week 7 Assignment Page

1. What was the purpose of this assignment? The purpose of this assignment was to complete our own journal presentation as a group. Working on the journal club presentation also allowed us to continue our HIV research project by learning more about our topic.
2. What did I learn from this assignment (head, hands, heart)? After this assingment I had a better understanding of and appreciation for scholarly HIV atricles. I learned that the conformation of the V3 loop can have major biological implications.
3. What did I not understand (yet) about this assignment? It was very difficult to understand the HIV article. There were many terms that I did not understand.

Ryan Willhite

1. What was the purpose of this assignment? The purpose of the assignment was to proceed with journal club for week 7. The topic is the structure of Gp120 protein and other aspects of HIV that are being investigated in order to intervene in either the contraction of this virus and/or treatment of the virus. Organizing our thoughts, we were able to devise a powerpoint presentation to best describe the knowledge we have acquired from reading the article.
2. What did I learn from this assignment (head, hands, heart)? I learned that HIV is so complex in finding the one answer to solve the problem. There is so much that goes into tackling viral infections and other diseases. Mainly, a lot of research, even on structure because it truly brings insight as to the characteristics of the virus.
3. What did I not understand (yet) about this assignment? There was nothing I did not understand about the assignment. It was pretty straight forward.

Ryan N. Willhite 20:33, 7 March 2010 (EST)

• Week 7 Assignment Page

• Week 7 Journal