BIOL368/F16:Class Journal Week 6

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Matthew K. Oki

  1. In addition to the scientific conclusion for your project, reflect on what 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 definitely gained/improved a different skills while working on this project. I learned a lot more about the HIV virus in general. I learned more about the sequences of HIV specifically, since we were analyzing them so often. I did not even know that there were so many different subtypes of HIV. It was also interesting to see how different the sequences were between each continent. I realized that there would be a good amount of variation, but I did not think it would be so vast. My skills with analyzing sequences vastly improved because we ran so many tests. I also believe that my overall outlining of power points for scientific purposes improved. I think that working with a partner on coming up with an idea for a research project was very helpful. His input definitely helped us come up with an idea for a project in the first place. It gave us an easier starting point than if we were to do it alone. Overall, this was a very rewarding project that improved my skills on many different levels.
  2. What is still not clear to you after having concluded this project?
    • For us, there is still uncertainty on whether or not there is even a correlation between the different subtypes of HIV-1. The sequences we obtained and ran had no sequential correlation between the different subtypes.
  3. If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?
    • I would definitely like to pursue more of a subtype study. We didn't use a large percentage of the sequences available, but there didn't seem to be any correlation. I would like to expand our study more, and analyze these different subtypes on a larger scale. This will give us a better idea if they do or do not actually correlate in a sequential way.

Will Fuchs

  1. In addition to the scientific conclusion for your project, reflect on what 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).
    • Well I've gained a considerable amount of scientific knowledge throughout this project. One of the things that comes to mind is nature of HIV itself as an entity and field of study. The numerous papers I read touch upon the seemingly endless facets of HIV. Our project just covered the env gene and that was already a lot to handle at first. I started to get a real feel for what things are expected in a bioinformatasist and from a scientific level I'm continuing to appreciate the level of professionalism and detail that goes into a project of this nature. From a technical perspective, I've learned to maneuver the Biology Workbench tool much more smoothly and effectively throughout this project. I have also learned different applications of statistics in the form of correlations and the computer tool set associated with that. In my heart I've understood the importance of communication and the absolute necessity for transparency and clear communication is when undertaking a highly technical project. One small error could have serious set backs if one of the members is not on the same page.
  2. What is still not clear to you after having concluded this project?
    • One of the things that is left unanswered for me is the other functions of the Biology Workbench. Will we be utilizing more in the future?
  3. If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?
    • I would expand it beyond the env genes and go across continents to and compare env mutation rates across developed nations vs. undeveloped nations and look for relationships.

William P Fuchs 20:25, 10 October 2016 (EDT)

Colin Wikholm

  1. In addition to the scientific conclusion for your project, reflect on what 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 a substantial amount of information about evolution at a genetic level (focus on genetic sequences). I learned that HIV uses diversity to evade host immunity, and also that this occurs in other microbes. For example, Pseudomonas aeruginosa survives in cystic fibrosis patients in a similar manner. I also learned how to use Biology Workbench and to work with DNA sequences. I found it intriguing to analyze genetic sequences using this mostly intuitive software. Concerning teamwork and collaboration, I learned the importance of face-to-face interaction in working on projects. Although I believe Will Fuchs and I did and effective job, working together in person would have been much more efficient than across the US over Facebook Messenger.
  2. What is still not clear to you after having concluded this project?
    • It is still not clear to me what happened to the patients in the Markham et al. (1998) study. I did not allot time to investigate the data further, but I plan to eventually look into it out of curiosity. I am also not sure how Markham and his team managed to calculate divergence for every patient for each visit. I am curious how long this took and how many people assisted in this process. Finally, still wish to know more about HIV-1. Specifically, I still do not understand the exact dynamics of certain components like reverse transcriptase. Such topics are still not clear to me, and I hope to learn about them soon.
  3. If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?
    • If we had more time, I would simply like to calculate divergence as described by Markham et al. (1998). I feel like we could have gained more from this project if it was a longer term approach. The other direction I wanted to take this project is protein synthesis and folding, although I understand that we may be going in this direction in the near future. Finally, I would also like to investigate the two different models explaining HIV evasion of host immunity. Specifically, if the classic model (mutations causes epitope to escape recognition) or the newer model concerning steric hindrance from glycan conformations.

Colin Wikholm 23:28, 10 October 2016 (EDT)

User: Zachary T. Goldstein

  1. In addition to the scientific conclusion for your project, reflect on what 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 a lot from this project. I came into it now knowing much about HIV but now I feel like I understand the virus on a whole new biological level. I know a lot more about the specifics of how mutations occur, how progression is tracked, and how certain papers, although published in good journals, cannot always be wholly trusted. Technically I learned how to sequence nucleotide strands using software online, create trees, and research articles more efficiently on PubMed and Web of Science. I enhanced my group work ethic by working with Shivum on the project through collaboration in person, research efforts, and article analysis. I feel a lot more comfortable working together on a group project than I did before because I feel like this one went really well.
  2. What is still not clear to you after having concluded this project?
    • If dN/dS ratios are good indicators of progression in HIV-1 patients. Our studies proved our hypotheses wrong, but further research can be done specifically with genetic diversity and divergence looking for a connection between those qualities and the progression of the virus. Another thing that is still not clear to me is exactly what region of the gene we are sequencing in Biology Workbench. I know the env gene is involved and we are looking at a specific region but, out of all regions on all genes, why is this one the center of so much research.
  3. If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?
    • If I decided to work on this project for my Master's thesis, I would stick with working mutation analysis. I might proceed to look into how RNA secondary structure are built up to avoid certain mutations (a subject covered greatly by other research papers), and eventually how researchers might be able to invoke these structures within cells to help slow the progression of the virus, if possible.

Zachary T. Goldstein 20:02, 9 October 2016 (EDT)Zachary T. Goldstein

Courtney L. Merriam

  1. In addition to the scientific conclusion for your project, reflect on what 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).
    • My understanding of the evolutionary aspect of diversification has developed significantly through out my research and readings for this project. I feel that I can now visualize the processes that occur in viral development and why exactly the HIV virus is such a difficult issue to address. I learned how to better utilize the technical aspects of research and now feel more comfortable with using the scientifically oriented programs that enable quicker conducting of experiments and research. I also learned the necessity of cooperation in a scientific setting, and how it’s important to feel comfortable asking questions and giving a helping hand when necessary.
  2. What is still not clear to you after having concluded this project?
    • It is still not clear as to what would have been a better way to group the subjects because the data results seem like viral lode was not significant.
  3. If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?
    • I would like to work with all the subjects, and paying special attention to the CD4 number, determine if tracking this variable could indeed be more informative than simply using viral copy number as the determinate. Then I would try other variables to collect the subjects in to groupings and see eventually what is the most significant way to group the subjects.

Shivum Desai

  1. In addition to the scientific conclusion for your project, reflect on what 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 this research I learned how to conduct different types of sequences analysis and comparisons which is actually very helpful to me because as a Biology major i run into situations that involve DNA sequences and comparisons quite often. So this type of knowledge about how differences are measure using S values and theta values is very helpful. I also learned how to format in openwetware much better because of the need to make make-shift tables for week 6's individual journal assignment. What I learned in terms of teamwork is that it requires a very dedicated group of team members for a scientists to complete a research project. Because many of these project take years to complete and a reliable and trustworthy team must be there for a research to help him or her complete it.
  2. What is still not clear to you after having concluded this project?
    • To me, I am still not completely clear on why a higher number of non synonymous mutations would not lead to more diverse and therefore fast progressing HIV subject. To me the ideology in my mind makes sense and even altering have read a research paper on why dS/dN values are not reliable, I still question why that is.
  3. If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?
    • I would most likely study for more trends in genetic similarities and differences among rapid and nonprogressor subjects to find out why these patients differ so much in the progression of their disease. I would most likely look at frequency of genetic point mutations and what proteins those mutations affect and how that affects the body as a whole.

Shivum A Desai 21:29, 9 October 2016 (EDT):

Anindita Varshneya

  1. In addition to the scientific conclusion for your project, reflect on what 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 HIV and its infection life cycle. In addition, I practiced critically thinking about research and understanding what is known and unknown based on information presented in a research paper. Technical skills I learned include calculating theta values, using ClustalW to analyze data on Biology Workbench, and creating graphs with multiple y-axes. A teamwork quality that I learned is the importance of taking advantage of each teammates strengths, and dividing and conquering whenever possible.
  2. What is still not clear to you after having concluded this project?
    • It is still unclear whether or not genetic diversity of the Env gene in HIV is correlated with the progression of the disease. This is unfortunate since this was the premise of our continued research, but a negative result is still a result!
  3. If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?
    • If I had plenty of time, I would want to collect more data over more time points from more patients of diverse background to truly understand the relationship between genetic diversity and progression of CD4 T cell count. I would want to prepare several types of genetic diversity calculations and correlate that with CD4 T cell count as well as other predictors of the progression of HIV. Furthermore, it would be interesting to observe genetic diversity across other vital genes in the HIV viral genome in addition to the Env gene. This data, though difficult to collect, would be able to confirm the relationship between genetic diversity and the progression of HIV more distinctly than the work we have done thus far.

-- Anindita Varshneya 00:20, 10 October 2016 (EDT)

Mia Huddleston

  1. In addition to the scientific conclusion for your project, reflect on what 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 how difficult it is to create a experiment as conclusive and accurate as you can without spending too many resources on it. With my hands I perfected my powerpoint skills and how to make the most efficient presentation. And with my heart I realized how thankful I am to have a great parter that I can rely on when I do not understand something.
  2. What is still not clear to you after having concluded this project?
    • It is still unclear why our results were so different than what we hypothesized and from the Markham article.
  3. If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?
    • If I had more time I would definitely want to get more conclusive data points with more subjects and find a better way of calculating genetic diversity than with the technology they had when the Markham article was published.

Mia Huddleston 16:04, 10 October 2016 (EDT)

Matthew Allegretti

  1. In addition to the scientific conclusion for your project, reflect on what 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).
    • The conclusion of our project did not yield the results we expected, but within our project, I learned improved methods for narrowing research. I also learned how to analyze sequence data, align it and create trees and base pair comparisons. I learned that communication and ample time are key, but it is also important to be honest with your expectations for each other.
  2. What is still not clear to you after having concluded this project?
    • What determines the rate at which diversity increases within HIV, as well as what other factors affect the progression of HIV within an infected person.
  3. If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?
    • I would like to compare envelope gene sequences within various immunodeficiency diseases or examine how other species are capable of mounting an immune response to an immunodeficiency virus and see how the results compare to humans.

Matthew R Allegretti 22:58, 10 October 2016 (EDT)

Isai Lopez

  1. In addition to the scientific conclusion for your project, reflect on what 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).
    • Aside from the conclusion to our project, I learned with my head a lot about the intricacies of HIV and more about why the virus is so difficult to treat, even with the advent of modern medicine. With my hands, I learned techniques for comparing sequences of DNA as well as calculating distances between sequences in generated trees. With my heart I learned the importance of communication with group mates when developing and analyzing data to efficiently display it.
  2. What is still not clear to you after having concluded this project?
    • I'm still confused about how HIV responds to the body's immune system, as this seems like it varies greatly between individuals without much explanation.
  3. If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?
    • Given more time to conduct an experiment, I would have liked to explore our original hypothesis, which would examine immunodeficiency virus strains for other species such as SIV and FIV, and compare the trends of CD4 decline to those found in the Markham study to see if different immunodeficiency viruses had similar effects on their hosts' immune systems.

Jordan T. Detamore

  • In addition to the scientific conclusion for your project, reflect on what 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).
    • Head: I learned how fast a virus can evolve and how different sequences of the same virus are over generations and in different continents.
    • Hands: I learned how to used sequencing and comparative sequence tools such as ClustalW and ClustalDist.
    • Heart: I learned how easy project can be when you divide up the work efficiently and both partners contribute equally and cooperatively.
  • What is still not clear to you after having concluded this project?
    • It is not clear how the same subtypes of HIV-1 would be shown to be genetically different as seen in the Collison-Streng paper.
  • If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?
    • I would use some of the same techniques as Markham but with current HIV-1 sequences and including subtypes as a method of organization. I would attempt to find out if different subtypes of HIV-1 correlate with different rates of progression
  • Jordan T. Detamore 01:06, 11 October 2016 (EDT):

Avery Vernon-Moore

  1. In addition to the scientific conclusion for your project, reflect on what 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 about the actual mechanics of HIV and how the virus can spread/turn into AIDS (Head). With my hands and heart I learned how to collaborate with a partner and work together to find our results as efficiently as possible.
  2. What is still not clear to you after having concluded this project?
    • This topic is still unclear to me to some degree. I don't fully understand some of the Markham papers findings and how they came to the results they had.
  3. If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?
    • I would probably want to fully research something, possibly more like Matt and Jordans topic, I know for a fact that diversity and viral load numbers are not correlated, so I don't think my research topic would be worth spending extra time on.

Avery Vernon-Moore 12:31, 11 October 2016 (EDT)