BIOL368/F11:Class Journal Week 9

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Zeb Russo

  1. Looking at the structure to function relationship was much more interesting to me than looking at the evolution. Partially I think it was that due to the nature of HIV and its rapid evolution, there was no clear cut path of evolution at least in my opinion, but looking at structure I can see what each part does and where it is.
  2. Working with a partner allowed us to divide and conquer instead of having to deal with it all on our own. Worst part is still deciding who does what better and piecing the ppt together.
  3. I learned how one needs to almost always redo every test and experiment done to guarantee the results that were obtained.

Zeb Russo 01:16, 1 November 2011 (EDT)

Robert W. Arnold

  1. I think the evolution of the HIV virus was much more interesting. I see the evolution as the bigger picture and I am more concerned with how the virus itself is evolving as opposed to its molecular structure. However, it is important to study both to get a full grasp of the subject.
  2. The best part of working with a partner is getting a different perspective about how to go about solving your question. The worst part is still finding time when you are both free outside of class to meet up and do work for the powerpoint. This is still the same as last time and it will be the same for the next project also.
  3. I have learned that you must be extremely meticulous about your results and double check your data to make sure you are getting good and consistent work.

Robert W Arnold 20:47, 1 November 2011 (EDT)

Alex A. Cardenas

  1. I thought that studying the structure --> function relationship was more interesting. It was more of a hands on lab/experiment and the varying amino acid sequences along with the different V3 loop conformations was interesting to observe. Although our questions answer was not what we thought it would be, we found out that different V3 amino acid sequences allows for more viral infectivity which was a good result.
  2. The best part of working with a partner was coming together and throwing out different ideas about what our experiment question should be. The workload was also cut down and was more manageable. There really wasn't a worst part about working with a partner. This hasn't really changed since the last project, despite the fact that I put down the worst part about working with a partner was that the other person might have known the information he was presenting a little more in depth.
  • I have learned that there is always more research you can do, whether that be looking at more paper or simply just running more experiments with online tools.

Alex A. Cardenas 15:33, 1 November 2011 (EDT)

Nicolette S. Harmon

  1. I thought studying the structure of HIV was more interesting than HIV evolution. It's not that the evolution project wasn't interesting, I'm just more interested in the aspect of how HIV is functioning in a given time period as opposed to how it's changed over the course of a period of time.
  2. The best part about working with a partner is that they have a different perspective on things which comes in handy when you are trying to interpret your results, when you come to a conclusion about your project it's usually well thought out since you have someone to discuss it with. The worst part about working with a partner is trying to get together to meet since you both have different schedules. This hasn't changed since the last project.
  3. I have learned that when you get unexpected results it is oftentimes difficult to explain why this is and you have to figure out what your next step in research is going to be or if you're just going to leave it alone and do something else.

Nicolette S. Harmon 19:29, 1 November 2011 (EDT)

Samantha M. Hurndon

  1. Which project was more interesting to you: studying the evolution of the HIV virus or studying the structure → function relationship? Why? I thought that structure and function was interesting but I really liked looking at the viruses evolution. Seeing how the virus strains on a larger scale was more intriguing to me. Seeing the virus's evolution you can really understand just how much mutation occurs and why the disease is so hard to treat.
  2. What was the best part of working with a partner on this project? What was the worst part? Has this changed since your last project? Why or why not? The best part of working with my partner is that we shared ideas with each other, which really helped out. I worst part was that we have pretty bad schedules so it was hard to meet up.
  3. Besides the scientific conclusion of your project, what have you learned about the process of doing research as a result of this project? I learned that it can be very difficult to try to interpret your results, and that you don't always get what you expected.

Samantha M. Hurndon 23:38, 1 November 2011 (EDT)

Isaiah M. Castaneda

  1. With the tools we had available, I found studying the evolution was more interesting. I feel that the lack of available protein tools hindered the ability to really dive deep into structure studies. I spent alot of time examining secondary structure predictions for the project and it turned out that they were not very useful. Also, the websites provided in our book for looking at other features were either no longer available or required payment. So that was a let-down. Therefore, I felt that more was able to be looked at with the evolution project and was therefore more interesting.
  2. The best part of working with a partner is that work can be divided up and concepts can be tackled as a unit. Also, we could work together to improve the powerpoint itself by combining feedback from all previous presentations. The difficulty in working with a partner is working out meeting times. This is the same as before. Since all students in BIOL 368 are wonderful students, they all make great partners. But since we are all multifaceted, busy scholars, we all have very complex schedules. This is why partner working conditions have not changed since the last project.
  3. I learned that doing research can cost money. I was saddened that certain protein tools required payment, when they sounded so juicy. I was tantalized with promises of intricate predictions and feature details and then slapped with a registration fee when I least expected it. Of course, I did not proceed after the payment requests. Also, I experienced that there is, as the expression goes, "more than one way to skin a cat." I did not actually skin a cat for this project, though. The cat in this, would be the research query. The skinning methods were:
    • Nucleotide sequence studies
    • Amino Acid sequence studies
Different modes of analysis were used to explore the same topic, which was quite neat.

Isaiah M. Castaneda 02:51, 2 November 2011 (EDT)

Chris Rhodes

  1. It was a lot more interesting to study the amino acids versus the nucleotides because the amino acids are much more closely related to function. Differences in the DNA sequences don't necessarily translate to changes in the amino acid sequence so making functional assumptions based on only the DNA sequences is a pretty futile effort. Seeing the potential functional changes in the AA sequences was easier in terms of interpretations of the results.
  2. The best part about working with a partner is how your partner keeps you grounded. Its easy to work on a presentation all by yourself and say that it's clear and understandable but thats more often not the case. Having a partner helps to better articulate your thoughts and decide what is and isn't important to your overall presentation. The worst part about having a partner is in some respects the same has the best part. I haven't really experienced this yet but if your partner and yourself have conflicting ideas about what is and isn't important or what the data means then it could be difficult to formulate a cohesive and focused presentation, not to mention it would severely cut into the efficiency of making the presentation which is already a lengthy process.
  3. From this experiment I learned that sometimes you just don't have all the tools required of you to make concrete and verifiable conclusions. Most of the conclusions we drew about our data are merely best guess hypotheses about potential functional change. We don't have the tools available to do in depth studies into whether or not the changes we see in the amino acid sequence actually translate into a change in functionality. I've learned that you have to work with the tools you have and the sometimes posing future questions is the best you can do until you're capable of using more advanced tools

Chris H. Rhodes 14:46, 2 November 2011 (EDT)