BIOL368/F16:Class Journal Week 10

Isai Lopez

1. Reflect on your progress with this project. What have you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).
   • During the progress of this project and presentation, I learned much about the available resources for analyzing protein structures both in terms of providing background information, such as the UniProt website, as well as software available to predict 3D structure from amino acid sequence. I also learned a lot about the transmission of HIV, and why the rapid mutation of the virus allows its surface proteins to avoid detection as foreign and malicious by the immune system. Finally, I learned how difficult it could be to communicate with teammates when not talking in person, as scheduling times to communicate with my partner Colin was difficult at times.
2. What is still not clear to you that you would like help with going forward?
   • The vast differences in amino acid sequences, especially in the variable regions of certain HIV sequences and why it doesn't cause the virus to be unable to perform basic functions still puzzles me. I'm not entirely sure why some portions are conserved more often than others, and how mutation is kept from being entirely random.

• Isai Lopez 02:57, 8 November 2016 (EST):

Colin Wikholm

1. Reflect on your progress with this project. What have you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).
   • Like previous projects, progress with this project reaffirmed for me that the best teamwork is often in person. Isai Lopez was a great teammate, but working over Messenger was sometimes frustrating. I also learned that working with multiple sequence alignment tools can be tedious. Although we have used these techniques in the past, more extensive usage this week took much more time and more concentration. Finally, I was reminded of genetic degeneracy. This is a topic I haven't though about since the MCAT exam, and this project showed me the relevance of DNA vs. amino acid sequence changes in the real life topic of HIV-1
2. What is still not clear to you that you would like help with going forward?
   • The only topic left that is not clear to me is certain amino acid multiple sequence analysis tools such as BLOSUM. I would like to know how such tools work, as well as if they are needed for our project. Are they relevant? If so, are they worth utilizing in our analysis?

Colin Wikholm 02:42, 8 November 2016 (EST)

Will Fuchs

1. Reflect on your progress with this project. What have you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).
   • There are many different tools that I've acquired throughout the project thus far. The various programs I've learned has taught me new ways into scientifically addressing a research question and that their are so many viable methods of biology to be utilized through bioinformatics. Additionally I've learned to approach potentially difficult articles with a more meticulous approach so I can maximize my own knowledge of biology to comprehend difficult papers. Some more technical things I've learned is the additional facets of Biology Workbench in analyzing different sequences. I was paired with a friend so I felt very comfortable pursuing our research question and our constant communication yielded good progress to our goals.
2. What is still not clear to you that you would like help with going forward?
   • The further uses of the biology workbench and 3D modeling software for proteins. What is the limitations of these programs and what are the possible inherited risks by using a program vs. in vivo experiments.

William P Fuchs 21:40, 7 November 2016 (EST)

Zach Goldstein

1. Reflect on your progress with this project. What have you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).
   • So far in working on the HIV structure project I have learned how to use specific databases to look up information on proteins such gp160 (in which there is more information than I could have ever imagined), utilize Cn3D software to project and analyze a 3D model of a protein, and how to reinterpret sequence data using amino acid sequences from the Markham paper. I have also realized the significance of seemingly small mutations along regions of genes that are highly influential within a certain function, and realized how important it is that researchers solve crystals structures of proteins so we can actually apply research to a physical model. On a teamwork level I learned that, if at any point during a group project I feel like I don't know what's going on, two things are most likely true: 1) my partner also probably has no idea what is going on, and 2) if we work together to try to understand the material, even if it takes 2 hours, eventually some of it will start to make sense. Jordan and I thought we had a good plan for our hypothesis and question, then realized we were completely confused, however by the end of class we were back on track and we both feel much more comfortable with the material we will be presenting next time.
2. What is still not clear to you that you would like help with going forward?
   • What is still not clear to me is how these amino acid structure changes specifically effect protein function. For example, I think it would be really cool to be able to say, "well if an Alanine was substituted with a Cytasine along the V3 loop of the gp120 protein, we would expect the protein to bind differently here, or alter its function here". Projecting these non-consensus regions on the 3D model is really cool, but I feel like there is another, more practical, level to this that I don't understand yet.

Zachary T. Goldstein 02:19, 3 November 2016 (EDT)Zachary T. Goldstein

Avery Vernon-Moore

1. Reflect on your progress with this project. What have you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).
   • I think this research project is really cool in the sense that we have been following the V3 loop and p120 for so long that I am starting to understand all of the complexities within HIV-1 that I never knew about. I would have never assumed that there was so many components and ways to go about researching HIV. With my head, I have learned all of the basic knowledge I could possibly know about HIV-1, with my hands I have learned how to look at specific parts of the protein and am still learning how to understand the function of these different components. On a teamwork level I am learning how to work through these very complicated systems and understand them with the help of my classmates. This project is definitely a learning experience that I would not have been able to do on my own.
2. What is still not clear to you that you would like help with going forward?
   • I am still pretty confused about the amino acid structures and how they can affect the overall protein. I never learned about the specifics of amino acids in another class, so I have a hard time understanding some of the differences. I don't know how to differentiate between the different mutations that would occur depending on the amino acids present.

Avery Vernon-Moore 23:11, 3 November 2016 (EDT)

Courtney L. Merriam

1. Reflect on your progress with this project. What have you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).
   • I believe this project really helped lay out the work in an easy to manage fashion. By creating a presentation out of the project we performed, the different components became more tangible and understandable. Working with the protein rendering and analysis program provided hands on experience, and laying out the results in an easy to understood fashion made the project more holistic. I also further developed my ability to work in conjunction with other students and share the load of work.
2. What is still not clear to you that you would like help with going forward?
   • I am still struggling to keep every aspect of conducting these studies compartmentalized. It may have to do with the way I process information, but it’s difficult to take each piece of information as it comes, because I tend to try and throw every new individual piece of information into the framework of everything else I know, instead of taking the time to slowly digest it.

Courtney L. Merriam 13:12, 4 November 2016 (EDT):

Matthew Allegretti

1. Reflect on your progress with this project. What have you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).
   • With my head, I learned some things about the three-dimensional structure of proteins, although three-dimensional structures are still far from intuitive for me. With my hands I learned how to compare amino acid sequences to their respective models, as well as becoming familiar with the Cn3d software and a number of other websites that help generate predictions about proteins. With my heart I learned that patience is a virtue when analyzing differences in protein structures and trying to identify the locations at which these differences are occurring. The process is very time consuming and tedious.
2. What is still not clear to you that you would like help with going forward?
   • The relevance of each amino acid as it relates to the overall shape or conformation of the protein is still mostly an unknown to me. While I can imagine how changing the charge or the size of an amino acid would affect how well that individual amino acid would bind to other molecules, how those changes will affect the overall conformation or how the protein will bend is not intuitive at all for me. Also, it is difficult for me to determine what effect this will have on the effectiveness on the protein when I am not aware of what base pair or amino acid positions correspond to which functions of the gp120.

Matthew R Allegretti 01:22, 7 November 2016 (EST)

Anindita Varshneya

1. Reflect on your progress with this project. What have you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).
   • With my head, I learned more about the intricacies of protein structure. I find the balance between the number of nonsynonymous mutations and the functionality of the protein to be incredibly interesting. With my hands, I learned more about the Biology Workbench software as well as the protein modeling softwares we used in class. With my heart, I learned the importance of communication. Because I had to miss last week in class, trying to play catch up purely through the instructions online was incredibly difficult.
2. What is still not clear to you that you would like help with going forward?
   • I would like to further understand the actual impacts that each of the mutations that we found in the protein sequence have with the functionality of the gp120 protein. While we have cool data at the moment about the mutations themselves and the location of those mutations, it would be nice to understand them better in the grander context of the protein.

-- Anindita Varshneya 02:02, 7 November 2016 (EST)

Shivum Desai

1. Reflect on your progress with this project. What have you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).
   • In terms of what I have leaned with my head in this project, is how to use the Biology workbench as a tool to evaluate DNA or Amino acid sequences. I know this is a very particular/specific thing to learn about, but as a biology major it could have major benefits in the future. My technical skills have also grown during this project and the past several as well. I have learned how to quick using operating tools on a computers (i.e. copy and pasting from zip files into other types of files). I have also learned the difference between different file and picture formats. This is something i never knew in the past and it have given me the computer and technical skills to successfully operate in that realm of technology. I can't say I have learned much in terms of personal or teamwork qualities, because I have done so many presentations in the past that I have learned all there is to know about teamwork by now. But I do think this class, with its many presentations and projects, has helped bring the class together personally and that helps when it comes time to ask for assistant from your classmates.
2. What is still not clear to you that you would like help with going forward?
   • I am still not clear on how viral copy number is counted. I understand what the measurement is but I have looked up what it means and it doesn't make sense to me because it all depends on the plasma sample at hand. Also the method of how it is obtained is very vague to me.

Shivum A Desai 14:33, 7 November 2016 (EST):

Matthew K. Oki

1. Reflect on your progress with this project. What have you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).
   • We have made some good progress so far with our project. We obtained interesting data from the s, theta, min, and max numbers for each clone for subject 10. With my head, I learned how certain amino acids can greatly effect the outcome of a protein. This could stem from the charge of the amino acid or the conformational change in the structure of the protein section. With my hands, I learned how to observe this via programs. Since I am taking biochemistry, we discussed the importance of certain amino acids. So, it was very interesting to visualize this in a real world example. With my heart, I learned a group project can feed off of each others ideas. With each question from the group, the advancement of the project increased. Also, each person's knowledge is increased with each question.
2. What is still not clear to you that you would like help with going forward?
   • I am not sure how these changes physically affect a subject. We have taken sequences from a subject and observed the amino acid changes for a subject's worsening conditions. Can these single amino acid changes be seen physically and physiologically?

• Matthew K. Oki 18:37, 7 November 2016 (EST):

Mia Huddleston

1. Reflect on your progress with this project. What have you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).
   • I think we have finally, mostly today made the most progress with our project and finally have been able to feel confident about how to test and answer our hypothesis. I have learned more about how mutations can change the function of a protein and what mutations will create big differences. I have also gotten much more proficient in creating powerpoints and knowing to write in a powerpoint. In my heart I now know that a research field is definitely not something I am interested in as a career.
2. What is still not clear to you that you would like help with going forward?
   • I am not completely confident that we have done everything we can to test and answer our hypothesis. I know we should still create a statistical difference test but I am unsure how we should be doing that and with what numbers would be the best to compare to find a p-value.

Mia Huddleston 18:41, 7 November 2016 (EST)

Jordan Detamore

1. Reflect on your progress with this project. What have you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).
   • I learned how to design a project where discoveries are made without doing actual experiments. I also learned a great deal about HIV as far as how it functions and the specific sequences where it binds. I learned how to use numerous different programs and apply them to the specific research that I am interested in. I also learned how efficient a group can work when all members are working at the same time on different things. Me and Zach have moved this this project with very good pace and I am genuinely understanding the research that is taking place.
2. What is still not clear to you that you would like help with going forward?
   • It is still not clear how the changes in protein structure affect function. We cannot do actual experiments so I do not know if it will be possible to figure out precisely how certain mutations affect function. I also would like to know if there is a statistical test that I can use to decipher if the amount of changes is a significant figure.

• Jordan T. Detamore 21:45, 7 November 2016 (EST):